thesis.bib

@article{gilestro_pysolo_2009,
  title = {{{pySolo}}: A Complete Suite for Sleep Analysis in {{Drosophila}}},
  volume = {25},
  issn = {1367-4803, 1460-2059},
  shorttitle = {{{pySolo}}},
  doi = {10.1093/bioinformatics/btp237},
  abstract = {Summary: pySolo is a multiplatform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website.
Availability: Software and documentation are located at http://www.pysolo.net. pySolo is a free software released under the GNU General Public License.
Contact: gilestro@wisc.edu},
  language = {en},
  number = {11},
  journal = {Bioinformatics},
  author = {Gilestro, Giorgio F. and Cirelli, Chiara},
  month = jan,
  year = {2009},
  keywords = {Animals,Sleep,Drosophila melanogaster,Motor Activity,User-Computer Interface,Software,Computational Biology},
  pages = {1466-1467},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VAUC6XFS/Gilestro and Cirelli - 2009 - pySolo a complete suite for sleep analysis in Dro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B77J7H4W/1466.html},
  note = {00017}
}

@article{branson_high-throughput_2009,
  title = {High-Throughput Ethomics in Large Groups of {{Drosophila}}},
  volume = {6},
  copyright = {\textcopyright{} 2009 Nature Publishing Group},
  issn = {1548-7091},
  doi = {10.1038/nmeth.1328},
  abstract = {We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.},
  language = {en},
  number = {6},
  journal = {Nature Methods},
  author = {Branson, Kristin and Robie, Alice A. and Bender, John and Perona, Pietro and Dickinson, Michael H.},
  month = jun,
  year = {2009},
  pages = {451-457},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AX448U84/Branson et al. - 2009 - High-throughput ethomics in large groups of Drosop.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DF4MN2HS/Branson et al. - 2009 - High-throughput ethomics in large groups of iDro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W7NQ7NYY/nmeth.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z4FFQNVA/nmeth.1328.html},
  note = {00136}
}

@article{gilestro_video_2012,
  title = {Video Tracking and Analysis of Sleep in {{Drosophila}} Melanogaster},
  volume = {7},
  copyright = {\textcopyright{} 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  issn = {1754-2189},
  doi = {10.1038/nprot.2012.041},
  language = {en},
  number = {5},
  journal = {Nature Protocols},
  author = {Gilestro, Giorgio F.},
  month = may,
  year = {2012},
  keywords = {neuroscience,Model organisms},
  pages = {995-1007},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HAZVY79Q/Gilestro - 2012 - Video tracking and analysis of sleep in iDrosoph.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WDIMJNAC/Gilestro - 2012 - Video tracking and analysis of sleep in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4UT7WQFT/nprot.2012.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B7QRJ95C/nprot.2012.041.html},
  note = {00005}
}

@article{donelson_high-resolution_2012,
  title = {High-{{Resolution Positional Tracking}} for {{Long}}-{{Term Analysis}} of {{Drosophila Sleep}} and {{Locomotion Using}} the ``{{Tracker}}'' {{Program}}},
  volume = {7},
  doi = {10.1371/journal.pone.0037250},
  abstract = {Drosophila melanogaster has been used for decades in the study of circadian behavior, and more recently has become a popular model for the study of sleep. The classic method for monitoring fly activity involves counting the number of infrared beam crosses in individual small glass tubes. Incident recording methods such as this can measure gross locomotor activity, but they are unable to provide details about where the fly is located in space and do not detect small movements (i.e. anything less than half the enclosure size), which could lead to an overestimation of sleep and an inaccurate report of the behavior of the fly. This is especially problematic if the fly is awake, but is not moving distances that span the enclosure. Similarly, locomotor deficiencies could be incorrectly classified as sleep phenotypes. To address these issues, we have developed a locomotor tracking technique (the ``Tracker'' program) that records the exact location of a fly in real time. This allows for the detection of very small movements at any location within the tube. In addition to circadian locomotor activity, we are able to collect other information, such as distance, speed, food proximity, place preference, and multiple additional parameters that relate to sleep structure. Direct comparisons of incident recording and our motion tracking application using wild type and locomotor-deficient (CASK-$\beta$ null) flies show that the increased temporal resolution in the data from the Tracker program can greatly affect the interpretation of the state of the fly. This is especially evident when a particular condition or genotype has strong effects on the behavior, and can provide a wealth of information previously unavailable to the investigator. The interaction of sleep with other behaviors can also be assessed directly in many cases with this method.},
  number = {5},
  journal = {PLoS ONE},
  author = {Donelson, Nathan and Kim, Eugene Z. and Slawson, Justin B. and Vecsey, Christopher G. and Huber, Robert and Griffith, Leslie C.},
  month = may,
  year = {2012},
  keywords = {Cameras,Computer software,Sleep,Drosophila melanogaster,Animal behavior,Chronobiology,Biological locomotion,Musculoskeletal system},
  pages = {e37250},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JQ6QEGKM/Donelson et al. - 2012 - High-Resolution Positional Tracking for Long-Term .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TTUIHHWX/Donelson et al. - 2012 - High-Resolution Positional Tracking for Long-Term .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NDKNSU9Z/infodoi10.1371journal.pone.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZPG2ZVA6/article.html},
  note = {00006}
}

@article{dankert_automated_2009,
  title = {Automated {{Monitoring}} and {{Analysis}} of {{Social Behavior}} in {{Drosophila}}},
  volume = {6},
  issn = {1548-7091},
  lccn = {0063},
  doi = {10.1038/nmeth.1310},
  abstract = {We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies, and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship ``song'') and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.},
  number = {4},
  journal = {Nature methods},
  author = {Dankert, Heiko and Wang, Liming and Hoopfer, Eric D. and Anderson, David J. and Perona, Pietro},
  month = apr,
  year = {2009},
  pages = {297-303},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FN3AD9EM/Dankert et al. - 2009 - Automated Monitoring and Analysis of Social Behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XCI8JTUF/Dankert et al. - 2009 - Automated Monitoring and Analysis of Social Behavi.pdf},
  note = {Cited by 0074}
}

@article{hurlbert_pseudoreplication_1984,
  title = {Pseudoreplication and the {{Design}} of {{Ecological Field Experiments}}},
  volume = {54},
  issn = {00129615},
  doi = {10.2307/1942661},
  number = {2},
  journal = {Ecological Monographs},
  author = {Hurlbert, Stuart H.},
  month = jun,
  year = {1984},
  pages = {187},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/A4AS9S6F/Hurlbert_1984_EcolMonogr.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K8PXQV8Z/showCitFormats.html}
}

@article{wu_genetic_2008,
  title = {A {{Genetic Screen}} for {{Sleep}} and {{Circadian Mutants Reveals Mechanisms Underlying Regulation}} of {{Sleep}} in {{Drosophila}}},
  volume = {31},
  issn = {0161-8105},
  abstract = {Study Objectives:
In order to characterize the genetic mechanisms underlying sleep, we have carried out a large-scale screen in Drosophila to identify short-sleeping mutants. The objectives of this study were as follows: (1) characterize the phenotypes of the shortest-sleeping mutants; (2) examine whether changes in arousal threshold or sleep homeostasis underlie short-sleeping phenotypes; (3) clone a gene affected in one of the shortest sleepers; and (4) investigate whether circadian mutants can be identified using light:dark (L:D) locomotor data obtained for studying sleep behavior.

Design:
Locomotor activity was measured using the Drosophila Activity Monitoring System in a 12:12 L:D cycle.

Setting:
Drosophila research laboratory.

Participants:
Adult flies from the 2nd chromosome Zuker collection, which contain mutations in most of the nonessential genes on the Drosophila 2nd chromosome.

Measurements and Results:
Our analysis of sleep characteristics suggests that daily activity (but not waking activity) correlates with daily sleep time and that defects in sleep maintenance are more common than defects in sleep initiation. Our shortest sleepers have intact or increased sleep rebound following sleep deprivation but show reduced thresholds for arousal. Molecular analysis of one of the short-sleeping lines indicates that it is a novel allele of a dopamine transporter (DAT). Finally, we describe a novel approach for identifying circadian mutants using L:D data.

Conclusions:
Our data suggest that most short-sleeping mutant phenotypes in Drosophila are characterized by an inability to stay asleep, most likely because of a reduced arousal threshold.

Citation:
Wu MN; Koh K; Yue Z; Joiner WJ; Sehgal A. A genetic screen for sleep and circadian mutants reveals mechanisms underlying regulation of sleep in Drosophila. SLEEP 2008;31(4):465-472.},
  number = {4},
  journal = {Sleep},
  author = {Wu, Mark N. and Koh, Kyunghee and Yue, Zhifeng and Joiner, William J. and Sehgal, Amita},
  month = apr,
  year = {2008},
  keywords = {Sleep,Drosophila,circadian,clock,dat,fumin,screen},
  pages = {465-472},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7F6683KS/Wu et al. - 2008 - A Genetic Screen for Sleep and Circadian Mutants R.pdf},
  note = {00035}
}

@article{shang_light-arousal_2008,
  title = {Light-Arousal and Circadian Photoreception Circuits Intersect at the Large {{PDF}} Cells of the {{Drosophila}} Brain},
  volume = {105},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0809577105},
  abstract = {The neural circuits that regulate sleep and arousal as well as their integration with circadian circuits remain unclear, especially in Drosophila. This issue intersects with that of photoreception, because light is both an arousal signal in diurnal animals and an entraining signal for the circadian clock. To identify neurons and circuits relevant to light-mediated arousal as well as circadian phase-shifting, we developed genetic techniques that link behavior to single cell-type resolution within the Drosophila central brain. We focused on the unknown function of the 10 PDF-containing large ventral lateral neurons (l-LNvs) of the Drosophila circadian brain network and show here that these cells function in light-dependent arousal. They also are important for phase shifting in the late-night (dawn), indicating that the circadian photoresponse is a network property and therefore non-cell-autonomous. The data further indicate that the circuits underlying light-induced arousal and circadian photoentrainment intersect at the l-LNvs and then segregate.},
  language = {en},
  number = {50},
  journal = {Proc. Natl. Acad. Sci.},
  author = {Shang, Yuhua and Griffith, Leslie C. and Rosbash, Michael},
  month = dec,
  year = {2008},
  keywords = {circadian clock,diurnal,phase resetting,photoresponse,sleep/arousal},
  pages = {19587--19594},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NFNPVUCI/Shang et al. - 2008 - Light-arousal and circadian photoreception circuit.pdf},
  pmid = {19060186}
}

@article{hamblen_germ-line_1986,
  title = {Germ-Line Transformation Involving {{DNA}} from the Period Locus in {{Drosophila}} Melanogaster: Overlapping Genomic Fragments That Restore Circadian and Ultradian Rhythmicity to Per0 and per- Mutants.},
  volume = {3},
  issn = {0167-7063},
  doi = {10.3109/01677068609106855},
  abstract = {P-element-mediated transformations involving DNA fragments from the period (per) clock gene of Drosophila melanogaster have shown that several subsegments of the locus restore rhythmicity to per0 or per- mutants. Such fragments overlap in a genomic region complementary to one transcript, a 4.5-kb RNA which is probably the per message, in that it is necessary and (in terms of expression from this X-chromosomal locus) sufficient for the fly's circadian rhythms. It is also at least necessary for the high-frequency oscillations normally produced by courting males as they vibrate their wings. The entirety of the 4.5-kb transcript is not necessary for rather strong rhythmicity; nor does it seem to be sufficient, in transformants, for wild-type behavioral phenotypes. A 0.9-kb RNA, homologous to genomic region immediately adjacent to the source of the 4.5-kb species, oscillates in its abundance over the course of a day; but coverage of this transcript source in several transformants carrying a per0 mutation\textendash{}which eliminates the 0.9-kb RNA's oscillation\textendash{}does not restore rhythmicity. All of the independently isolated arrhythmic mutations tested were covered by the same array of overlapping per+-derived DNA fragments, implying that the only portion of the locus which has mutated to arrhythmicity is complementary to the 4.5-kb transcript.},
  number = {5},
  journal = {J. Neurogenet.},
  author = {Hamblen, M and Zehring, W A and Kyriacou, C P and Reddy, P and Yu, Q and Wheeler, D A and Zwiebel, L J and Konopka, R J and Rosbash, M and Hall, J C},
  month = sep,
  year = {1986},
  keywords = {X chromosome,Female,Male,Animals,Behavior,Animal,Circadian Rhythm,Drosophila melanogaster,Genetic,Chromosome Mapping,Mutation,DNA,DNA: genetics,Drosophila melanogaster: genetics,Genotype,Locomotion,Pedigree,Plasmids,Transformation,courtship song,activity rhythms,clock mutants,P-element transformation,Southern and Northern blot analyses},
  pages = {249--91},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RTWXNYLE/Hamblen et al. - 1986 - Germ-Line Transformation Involving DNA from the pe.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AHDAR6ZX/01677068609106855.html},
  pmid = {3097289}
}

@article{liu_amnesiac_2008,
  title = {Amnesiac Regulates Sleep Onset and Maintenance in {{Drosophila}} Melanogaster},
  volume = {372},
  issn = {0006291X},
  doi = {10.1016/j.bbrc.2008.05.119},
  abstract = {The adenylate cyclase/cAMP signaling pathway and adult mushroom bodies (MBs) have been shown to play an important role in sleep regulation in Drosophila. The amnesiac (amn) gene, encodes a neuropeptide that is homologous with vertebrate pituitary adenylate cyclase-activating peptide (PACAP), is expressed in dorsal paired medial (DPM) neurons and is required for the middle-term memory (MTM) in flies. However, the role of amn on regulation of sleep is as yet unknown. Here we provide evidence that amn plays a major role on sleep maintenance and onset in Drosophila. Flies with the amnesiac allele, loss-of-function amnX8 mutation, showed a fragmented sleep pattern and short sleep latency. Moreover, homeostatic regulation was disrupted in amnX8 mutants after sleep deprivation. Sleep maintenance was also influenced by disruption of neurotransmission in DPM neurons with increased sleep bout number and decreased sleep bout length. Furthermore, age-related sleep fragmentation and initiation were inhibited in amnX8 mutant flies. These data suggest that amn is required in initiation and maintenance of sleep. ?? 2008 Elsevier Inc. All rights reserved.},
  number = {4},
  journal = {Biochem. Biophys. Res. Commun.},
  author = {Liu, Weijie and Guo, Fang and Lu, Beika and Guo, Aike},
  month = aug,
  year = {2008},
  keywords = {Drosophila,aging,Sleep fragmentation,Sleep onset,amnesiac},
  pages = {798--803},
  pmid = {18514063}
}

@article{bushey_sleep_2010,
  title = {Sleep, Aging, and Lifespan in {{Drosophila}}},
  volume = {11},
  issn = {1471-2202},
  doi = {10.1186/1471-2202-11-56},
  abstract = {Epidemiological studies in humans suggest that a decrease in daily sleep duration is associated with reduced lifespan, but this issue remains controversial. Other studies in humans also show that both sleep quantity and sleep quality decrease with age. Drosophila melanogaster is a useful model to study aging and sleep, and inheriting mutations affecting the potassium current Shaker results in flies that sleep less and have a shorter lifespan. However, whether the link between short sleep and reduced longevity exists also in wild-type flies is unknown. Similarly, it is unknown whether such a link depends on sleep amount per se, rather than on other factors such as waking activity. Also, sleep quality has been shown to decrease in old flies, but it remains unclear whether aging-related sleep fragmentation is a generalized phenomenon.},
  number = {1},
  journal = {BMC Neurosci.},
  author = {Bushey, Daniel and Hughes, Kimberly A and Tononi, Giulio and Cirelli, Chiara},
  month = apr,
  year = {2010},
  keywords = {Sleep Duration,Sleep Fragmentation,Sleep Parameter,Sleep Quality,Total Sleep Time},
  pages = {56},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3TYAF3P3/Bushey et al. - 2010 - Sleep, aging, and lifespan in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8PMDXL77/Bushey et al. - 2010 - Sleep, aging, and lifespan in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6TPQ4X87/1471-2202-11-56.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7CP3SEA5/1471-2202-11-56.html},
  pmid = {20429945}
}

@article{allada_molecular_2017,
  title = {Molecular {{Mechanisms}} of {{Sleep Homeostasis}} in {{Flies}} and {{Mammals}}.},
  issn = {1943-0264},
  doi = {10.1101/cshperspect.a027730},
  abstract = {Sleep is homeostatically regulated with sleep pressure accumulating with the increasing duration of prior wakefulness. Yet, a clear understanding of the molecular components of the homeostat, as well as the molecular and cellular processes they sense and control to regulate sleep intensity and duration, remain a mystery. Here, we will discuss the cellular and molecular basis of sleep homeostasis, first focusing on the best homeostatic sleep marker in vertebrates, slow wave activity; second, moving to the molecular genetic analysis of sleep homeostasis in the fruit fly Drosophila; and, finally, discussing more systemic aspects of sleep homeostasis.},
  journal = {Cold Spring Harb. Perspect. Biol.},
  author = {Allada, Ravi and Cirelli, Chiara and Sehgal, Amita},
  month = apr,
  year = {2017},
  pages = {a027730},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/64ABYE7F/Allada et al. - 2017 - Molecular Mechanisms of Sleep Homeostasis in Flies.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SKH8YN6A/a027730.html},
  pmid = {28432135}
}

@article{harbison_quantitative_2008,
  title = {Quantitative Genetic Analysis of Sleep in {{Drosophila}} Melanogaster},
  volume = {178},
  issn = {00166731},
  doi = {10.1534/genetics.107.081232},
  abstract = {Although intensively studied, the biological purpose of sleep is not known. To identify candidate genes affecting sleep, we assayed 136 isogenic P-element insertion lines of Drosophila melanogaster. Since sleep has been negatively correlated with energy reserves across taxa, we measured energy stores (whole-body protein, glycogen, and triglycerides) in these lines as well. Twenty-one insertions with known effects on physiology, development, and behavior affect 24-hr sleep time. Thirty-two candidate insertions significantly impact energy stores. Mutational genetic correlations among sleep parameters revealed that the genetic basis of the transition between sleep and waking states in males and females may be different. Furthermore, sleep bout number can be decoupled from waking activity in males, but not in females. Significant genetic correlations are present between sleep phenotypes and glycogen stores in males, while sleep phenotypes are correlated with triglycerides in females. Differences observed in male and female sleep behavior in flies may therefore be related to sex-specific differences in metabolic needs. Sleep thus emerges as a complex trait that exhibits extensive pleiotropy and sex specificity. The large mutational target that we observed implicates genes functioning in a variety of biological processes, suggesting that sleep may serve a number of different functions rather than a single purpose.},
  number = {4},
  journal = {Genetics},
  author = {Harbison, Susan T and Sehgal, Amita},
  month = apr,
  year = {2008},
  pages = {2341--2360},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/I8JLW9ZW/Harbison and Sehgal - 2008 - Quantitative Genetic Analysis of Sleep in Drosophi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/R3HW9H9X/2341.html},
  pmid = {18430954}
}

@article{crocker_octopamine_2008,
  title = {Octopamine {{Regulates Sleep}} in {{Drosophila}} through {{Protein Kinase A}}-{{Dependent Mechanisms}}},
  volume = {28},
  issn = {0270-6474, 1529-2401},
  doi = {10.1523/JNEUROSCI.3072-08a.2008},
  abstract = {Sleep is a fundamental process, but its regulation and function are still not well understood. The Drosophila model for sleep provides a powerful system to address the genetic and molecular mechanisms underlying sleep and wakefulness. Here we show that a Drosophila biogenic amine, octopamine, is a potent wake-promoting signal. Mutations in the octopamine biosynthesis pathway produced a phenotype of increased sleep, which was restored to wild-type levels by pharmacological treatment with octopamine. Moreover, electrical silencing of octopamine-producing cells decreased wakefulness, whereas excitation of these neurons promoted wakefulness. Because protein kinase A (PKA) is a putative target of octopamine signaling and is also implicated in Drosophila sleep, we investigated its role in the effects of octopamine on sleep. We found that decreased PKA activity in neurons rendered flies insensitive to the wake-promoting effects of octopamine. However, this effect of PKA was not exerted in the mushroom bodies, a site previously associated with PKA action on sleep. These studies identify a novel pathway that regulates sleep in Drosophila.},
  language = {eng},
  number = {38},
  journal = {J. Neurosci.},
  author = {Crocker, Amanda and Sehgal, Amita},
  month = sep,
  year = {2008},
  keywords = {Female,Male,Brain,Arousal,Neurons,Animals,Sleep,Drosophila,Drosophila Proteins,Motor Activity,octopamine,Mutation,Locomotion,Mushroom Bodies,Wakefulness,Administration- Oral,Cyclic AMP-Dependent Protein Kinases,Green Fluorescent Proteins,Norepinephrine,Tyramine,Tyrosine Decarboxylase,biogenic amine},
  pages = {9377--9385},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z5ZNIUBR/Crocker and Sehgal - 2008 - Octopamine Regulates Sleep in Drosophila through P.pdf},
  pmid = {18799671}
}

@article{andretic_essentials_2005,
  series = {Circadian Rhythms},
  title = {Essentials of Sleep Recordings in {{Drosophila}}: {{Moving}} beyond Sleep Time},
  volume = {393},
  issn = {00766879},
  shorttitle = {Essentials of {{Sleep Recordings}} in {{Drosophila}}},
  doi = {10.1016/S0076-6879(05)93040-1},
  abstract = {The power of Drosophila genetics can be used to facilitate the molecular dissection of sleep regulatory mechanisms. While evaluating total sleep time and homeostatic processes provides valuable information, other variables, such as sleep latency, sleep bout duration, sleep cycle length, and the time of day when the longest sleep bout is initiated, should also be used to explore the nature of a genetic lesion on sleep regulatory processes. Each of these variables requires that the recording interval used to identify periods of sleep and waking be determined accurately and empirically. This article describes the procedures for recording sleep in Drosophila and associated methodological constraints. In addition, it provides results from a normative data set of 1037 Canton-S female flies and 639 male flies to illustrate the nature and variability of sleep variables that one can extract from 24 h of data collection in Drosophila. Copyright 2005, Elsevier Inc. All rights reserved.},
  journal = {Methods Enzymol.},
  author = {Andretic, Rozi and Shaw, Paul J.},
  editor = {Young, Michael W.},
  year = {2005},
  pages = {759--772},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3C3NX693/Andretic and Shaw - 2005 - Essentials of sleep recordings in Drosophila Movi.pdf},
  pmid = {15817323}
}

@article{catterson_dietary_2010,
  title = {Dietary {{Modulation}} of {{Drosophila Sleep}}-{{Wake Behaviour}}},
  volume = {5},
  issn = {19326203},
  doi = {10.1371/journal.pone.0012062},
  abstract = {Background A complex relationship exists between diet and sleep but despite its impact on human health, this relationship remains uncharacterized and poorly understood. Drosophila melanogaster is an important model for the study of metabolism and behaviour, however the effect of diet upon Drosophila sleep remains largely unaddressed. Methodology/Principal Findings Using automated behavioural monitoring, a capillary feeding assay and pharmacological treatments, we examined the effect of dietary yeast and sucrose upon Drosophila sleep-wake behaviour for three consecutive days. We found that dietary yeast deconsolidated the sleep-wake behaviour of flies by promoting arousal from sleep in males and shortening periods of locomotor activity in females. We also demonstrate that arousal from nocturnal sleep exhibits a significant ultradian rhythmicity with a periodicity of 85 minutes. Increasing the dietary sucrose concentration from 5\% to 35\% had no effect on total sucrose ingestion per day nor any affect on arousal, however it did lengthen the time that males and females remained active. Higher dietary sucrose led to reduced total sleep by male but not female flies. Locomotor activity was reduced by feeding flies Metformin, a drug that inhibits oxidative phosphorylation, however Metformin did not affect any aspects of sleep. Conclusions We conclude that arousal from sleep is under ultradian control and regulated in a sex-dependent manner by dietary yeast and that dietary sucrose regulates the length of time that flies sustain periods of wakefulness. These findings highlight Drosophila as an important model with which to understand how diet impacts upon sleep and wakefulness in mammals and humans.},
  number = {8},
  journal = {PLoS One},
  author = {Catterson, James H. and {Knowles-Barley}, Seymour and James, Katherine and Heck, Margarete M. S. and Harmar, Anthony J. and Hartley, Paul S.},
  editor = {Crusio, Wim E.},
  month = aug,
  year = {2010},
  keywords = {Sleep,Behavior,Drosophila melanogaster,Mammals,Diet,Sucrose,Biological locomotion,Yeast},
  pages = {e12062},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/REHBXIFZ/Catterson et al. - 2010 - Dietary Modulation of Drosophila Sleep-Wake Behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WLD3PHMC/Catterson et al. - 2010 - Dietary Modulation of Drosophila Sleep-Wake Behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5GQ2US5Q/article.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XWIFIP7H/article.html},
  pmid = {20706579}
}

@article{raizen_lethargus_2008,
  title = {Lethargus Is a {{Caenorhabditis}} Elegans Sleep-like State},
  volume = {451},
  issn = {0028-0836},
  doi = {10.1038/nature06535},
  abstract = {There are fundamental similarities between sleep in mammals and quiescence in the arthropod Drosophila melanogaster, suggesting that sleep-like states are evolutionarily ancient. The nematode Caenorhabditis elegans also has a quiescent behavioural state during a period called lethargus, which occurs before each of the four moults. Like sleep, lethargus maintains a constant temporal relationship with the expression of the C. elegans Period homologue LIN-42 (ref. 5). Here we show that quiescence associated with lethargus has the additional sleep-like properties of reversibility, reduced responsiveness and homeostasis. We identify the cGMP-dependent protein kinase (PKG) gene egl-4 as a regulator of sleep-like behaviour, and show that egl-4 functions in sensory neurons to promote the C. elegans sleep-like state. Conserved effects on sleep-like behaviour of homologous genes in C. elegans and Drosophila suggest a common genetic regulation of sleep-like states in arthropods and nematodes. Our results indicate that C. elegans is a suitable model system for the study of sleep regulation. The association of this C. elegans sleep-like state with developmental changes that occur with larval moults suggests that sleep may have evolved to allow for developmental changes.},
  number = {7178},
  journal = {Nature},
  author = {Raizen, David M. and Zimmerman, John E. and Maycock, Matthew H. and Ta, Uyen D. and You, Young-jai and Sundaram, Meera V. and Pack, Allan I.},
  month = jan,
  year = {2008},
  pages = {569--572},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7ANLP2QW/Raizen et al. - 2008 - Lethargus is a iCaenorhabditis elegansi sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3ZX3NKIM/nature06535.html},
  pmid = {18185515}
}

@article{van_swinderen_uncoupling_2004,
  title = {Uncoupling of {{Brain Activity}} from {{Movement Defines Arousal States}} in {{Drosophila}}},
  volume = {14},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2003.12.057},
  abstract = {Background: An animal's state of arousal is fundamental to all of its behavior. Arousal is generally ascertained by measures of movement complemented by brain activity recordings, which can provide signatures independently of movement activity. Here we examine the relationships among movement, arousal state, and local field potential (LFP) activity in the Drosophila brain. Results: We have measured the correlation between local field potentials (LFPs) in the brain and overt movements of the fruit fly during different states of arousal, such as spontaneous daytime waking movement, visual arousal, spontaneous night-time movement, and stimulus-induced movement. We found that the correlation strength between brain LFP activity and movement was dependent on behavioral state and, to some extent, on LFP frequency range. Brain activity and movement were uncoupled during the presentation of visual stimuli and also in the course of overnight experiments in the dark. Epochs of low correlation or uncoupling were predictive of increased arousal thresholds even in moving flies and thus define a distinct state of arousal intermediate between sleep and waking in the fruit fly. Conclusions: These experiments indicate that the relationship between brain LFPs and movement in the fruit fly is dynamic and that the degree of coupling between these two measures of activity defines distinct states of arousal.},
  language = {eng},
  number = {2},
  journal = {Curr. Biol. CB},
  author = {{van Swinderen}, B. and Nitz, D. A. and Greenspan, R. J.},
  month = jan,
  year = {2004},
  keywords = {Brain,Arousal,Photic Stimulation,Animals,Circadian Rhythm,Drosophila melanogaster,Electroencephalography,movement,Evoked Potentials},
  pages = {81--87},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4A3DHPEH/van Swinderen et al. - 2004 - Uncoupling of Brain Activity from Movement Defines.pdf},
  pmid = {14738728}
}

@article{koh_drosophila_2006,
  title = {A {{Drosophila}} Model for Age-Associated Changes in Sleep:Wake Cycles},
  volume = {103},
  issn = {0027-8424, 1091-6490},
  shorttitle = {A {{Drosophila}} Model for Age-Associated Changes in S},
  doi = {10.1073/pnas.0605903103},
  abstract = {One of the most consistent behavioral changes that occurs with age in humans is the loss of sleep consolidation. This can be quite disruptive and yet little is known about its underlying basis. To better understand the effects of aging on sleep:wake cycles, we sought to study this problem in Drosophila melanogaster, a powerful system for research on aging and behavior. By assaying flies of different ages as well as monitoring individual flies constantly over the course of their lifetime, we found that the strength of sleep:wake cycles decreased and that sleep became more fragmented with age in Drosophila. These changes in sleep:wake cycles became faster or slower with manipulations of ambient temperature that decreased or increased lifespan, respectively, demonstrating that they are a function of physiological rather than chronological age. The effect of temperature on lifespan was not mediated by changes in overall activity level or sleep amount. Flies treated with the oxidative stress-producing reagent paraquat showed a breakdown of sleep:wake cycles similar to that seen with aging, leading us to propose that the accumulation of oxidative damage with age contributes to the changes in rhythm and sleep. Together, these findings establish Drosophila as a valuable model for studying age-associated sleep fragmentation and breakdown of rhythm strength, and indicate that these changes in sleep:wake cycles are an integral part of the physiological aging process.},
  language = {en},
  number = {37},
  journal = {Proc. Natl. Acad. Sci.},
  author = {Koh, Kyunghee and Evans, Joshua M. and Hendricks, Joan C. and Sehgal, Amita},
  month = sep,
  year = {2006},
  keywords = {aging,Sleep fragmentation,Circadian rhythms},
  pages = {13843--13847},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K4HZYG7I/Koh et al. - 2006 - A Drosophila model for age-associated changes in s.pdf}
}

@article{stoleru_coupled_2004,
  title = {Coupled Oscillators Control Morning and Evening Locomotor Behaviour of {{Drosophila}}},
  volume = {431},
  issn = {0028-0836},
  doi = {10.1038/nature02926},
  abstract = {Daily rhythms of physiology and behaviour are precisely timed by an endogenous circadian clock. These include separate bouts of morning and evening activity, characteristic of Drosophila melanogaster and many other taxa, including mammals. Whereas multiple oscillators have long been proposed to orches- trate such complex behavioural programmes, their nature and interplay have remained elusive. By using cell-specific ablation, we show that the timing of morning and evening activity in Drosophila derives from two distinct groups of circadian neurons: morning activity from the ventral lateral neurons that express the neuropeptide PDF, and evening activity from another group of cells, including the dorsal lateral neurons. Although the two oscillators can function autonomously, cell-specific rescue experiments with circadian clock mutants indicate that they are functionally coupled.},
  number = {7010},
  journal = {Nature},
  author = {Stoleru, Dan and Peng, Ying and Agosto, Jos\'e and Rosbash, Michael},
  month = oct,
  year = {2004},
  pages = {862--868},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z3W2H64V/Stoleru et al. - 2004 - Coupled oscillators control morning and evening lo.pdf},
  pmid = {15483615}
}

@article{vorster_sleep_2015,
  title = {Sleep and Memory in Mammals, Birds and Invertebrates},
  volume = {50},
  issn = {01497634},
  doi = {10.1016/j.neubiorev.2014.09.020},
  author = {Vorster, Albrecht P. and Born, Jan},
  year = {2015},
  keywords = {Learning,Memory,learning,Sleep,Invertebrate,Active system consolidation,Bird,Mammal},
  pages = {103--119},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GR6GCVHG/Vorster and Born - 2015 - Sleep and memory in mammals, birds and invertebrat.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K5IVERCR/S0149763414002474.html}
}

@article{swett_effects_1968,
  title = {The Effects of Posterior Hypothalamic Lesions on Behavioral and Electrographic Manifestations of Sleep and Waking in Cats.},
  volume = {106},
  issn = {00039829},
  number = {3},
  journal = {Arch. Ital. Biol.},
  author = {Swett, C P and Hobson, J A},
  month = sep,
  year = {1968},
  pages = {283--293},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XE4D23RZ/106283.html},
  pmid = {5724423}
}

@article{donlea_inducing_2011,
  title = {Inducing {{Sleep}} by {{Remote Control Facilitates Memory Consolidation}} in {{Drosophila}}},
  volume = {332},
  issn = {0036-8075},
  doi = {10.1126/science.1202249},
  abstract = {Sleep is believed to play an important role in memory consolidation. We induced sleep on demand by expressing the temperature-gated nonspecific cation channel Transient receptor potential cation channel (UAS-TrpA1) in neurons, including those with projections to the dorsal fan-shaped body (FB). When the temperature was raised to 31$^\circ$C, flies entered a quiescent state that meets the criteria for identifying sleep. When sleep was induced for 4 hours after a massed-training protocol for courtship conditioning that is not capable of inducing long-term memory (LTM) by itself, flies develop an LTM. Activating the dorsal FB in the absence of sleep did not result in the formation of LTM after massed training.},
  language = {en},
  number = {6037},
  journal = {Science (80-. ).},
  author = {Donlea, Jeffrey M. and Thimgan, Matthew S. and Suzuki, Yasuko and Gottschalk, Laura and Shaw, Paul J.},
  month = jun,
  year = {2011},
  pages = {1571--1576},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H85DT4IT/Donlea et al. - 2011 - Inducing Sleep by Remote Control Facilitates Memor.pdf},
  pmid = {21700877}
}

@article{zimmerman_video_2008,
  title = {A {{Video Method}} to {{Study Drosophila Sleep}}},
  volume = {31},
  issn = {0161-8105},
  doi = {10.1093/sleep/31.11.1587},
  abstract = {Study Objectives: To use video to determine the accuracy of the infrared beam-splitting method for measuring sleep in Drosophila and to determine the effect of time of day, sex, genotype, and age on sleep measurements. Design: A digital image analysis method based on frame subtraction principle was developed to distinguish a quiescent from a moving fly. Data obtained using this method were compared with data obtained using the Drosophila Activity Monitoring System (DAMS). The location of the fly was identified based on its centroid location in the subtracted images. Measurements and Results: The error associated with the identification of total sleep using DAMS ranged from 7\% to 95\% and depended on genotype, sex, age, and time of day. The degree of the total sleep error was dependent on genotype during the daytime (P $\backslash$textless 0.001) and was dependent on age during both the daytime and the nighttime (P $\backslash$textless 0.001 for both). The DAMS method overestimated sleep bout duration during both the day and night, and the degree of these errors was genotype dependent (P $\backslash$textless 0.001). Brief movements that occur during sleep bouts can be accurately identified using video. Both video and DAMS detected a homeostatic response to sleep deprivation. Conclusions: Video digital analysis is more accurate than DAMS in fly sleep measurements. In particular, conclusions drawn from DAMS measurements regarding daytime sleep and sleep architecture should be made with caution. Video analysis also permits the assessment of fly position and brief movements during sleep. Citation: Zimmerman JE; Raizen DM; Maycock MH; Maislin G; Pack AI. A video method to study drosophila sleep. SLEEP 2008;31(11):1587\textendash{}1598.},
  number = {11},
  journal = {Sleep},
  author = {Zimmerman, John E. and Raizen, David M. and Maycock, Matthew H. and Maislin, Greg and Pack, Allan I.},
  month = nov,
  year = {2008},
  pages = {1587--1598},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YATD2YTY/Zimmerman et al. - 2008 - A Video Method to Study Drosophila Sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EZ7PTEEZ/2454133.html},
  pmid = {19014079}
}

@article{murphy_postprandial_2016,
  title = {Postprandial Sleep Mechanics in {{Drosophila}}},
  volume = {5},
  issn = {2050084X},
  doi = {10.7554/eLife.19334},
  abstract = {Food consumption is thought to induce sleepiness. However, little is known about how postprandial sleep is regulated. Here, we simultaneously measured sleep and food intake of individual flies and found a transient rise in sleep following meals. Depending on the amount consumed, the effect ranged from slightly arousing to strongly sleep inducing. Postprandial sleep was positively correlated with ingested volume, protein, and salt\textemdash{}but not sucrose\textemdash{}revealing meal property-specific regulation. Silencing of leucokinin receptor (Lkr) neurons specifically reduced sleep induced by protein consumption. Thermogenetic stimulation of leucokinin (Lk) neurons decreased whereas Lk downregulation by RNAi increased postprandial sleep, suggestive of an inhibitory connection in the Lk-Lkr circuit. We further identified a subset of non-leucokininergic cells proximal to Lkr neurons that rhythmically increased postprandial sleep when silenced, suggesting that these cells are cyclically gated inhibitory inputs to Lkr neurons. Together, these findings reveal the dynamic nature of postprandial sleep.},
  number = {NOVEMBER2016},
  journal = {Elife},
  author = {Murphy, Keith R. and Deshpande, Sonali A. and Yurgel, Maria E. and Quinn, James P. and Weissbach, Jennifer L. and Keene, Alex C. and {Dawson-Scully}, Ken and Huber, Robert and Tomchik, Seth M. and Ja, William W.},
  month = nov,
  year = {2016},
  keywords = {Feeding,Mice,Sleep,Behavior,D. melanogaster,neuroscience,neurogenetics,local sleep,neurokinin-1 receptor,nutrition,slow-wave activity,substance P,tachykinin},
  pages = {260--72},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UZ6BH8UP/Murphy et al. - 2016 - Postprandial sleep mechanics in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6LET6ZBL/19334.html},
  pmid = {27873574}
}

@article{linford_re-patterning_2012,
  title = {Re-Patterning Sleep Architecture in {{Drosophila}} through Gustatory Perception and Nutritional Quality},
  volume = {8},
  issn = {15537390},
  doi = {10.1371/journal.pgen.1002668},
  abstract = {Author Summary Sleep is a fundamental biological process regulated by evolutionarily conserved molecular mechanisms. In this work, we demonstrate a novel link between gustatory perception of sugar and sleep patterning in D. melanogaster . The presence of low dietary sugar reduced the arousal threshold for waking, leading to repartitioning of sleep into a larger number of episodes throughout the day. Gustatory perception was both required and sufficient for this effect. Further addition of sugar to the dietary environment suppressed the effects of gustatory perception through a gustatory-independent mechanism. Although the quantity of dietary sugar also regulated fat accumulation, gustatory perception was not required, indicating that diet-induced changes in obesity and sleep behavior may be mechanistically separable. These findings illustrate a mechanism for the regulation of behavioral state by the availability of dietary nutrients through the interplay between gustatory and non-gustatory factors.},
  number = {5},
  journal = {PLoS Genet.},
  author = {Linford, Nancy J. and Chan, Tammy P. and Pletcher, Scott D.},
  month = may,
  year = {2012},
  keywords = {Sleep,Drosophila melanogaster,Diet,Gustatory system,Nutrients,Sensory perception,Sucrose,food},
  pages = {e1002668},
  pmid = {22570630}
}

@article{garbe_context-specific_2015,
  title = {Context-Specific Comparison of Sleep Acquisition Systems in {{Drosophila}}},
  volume = {4},
  issn = {2046-6390},
  doi = {10.1242/bio.013011},
  abstract = {Sleep is conserved across phyla and can be measured through electrophysiological or behavioral characteristics. The fruit fly, Drosophila melanogaster, provides an excellent model for investigating the genetic and neural mechanisms that regulate sleep. Multiple systems exist for measuring fly activity, including video analysis and single-beam (SB) or multi-beam (MB) infrared (IR)-based monitoring. In this study, we compare multiple sleep parameters of individual flies using a custom-built video-based acquisition system, and commercially available SB- or MB-IR acquisition systems. We report that all three monitoring systems appear sufficiently sensitive to detect changes in sleep duration associated with diet, age, and mating status. Our data also demonstrate that MB-IR detection appeared more sensitive than the SB-IR for detecting baseline nuances in sleep architecture, while architectural changes associated with varying life-history and environment were generally detected across all acquisition types. Finally, video recording of flies in an arena allowed us to measure the effect of ambient environment on sleep. These experiments demonstrate a robust effect of arena shape and size as well as light levels on sleep duration and architecture, and highlighting the versatility of tracking-based sleep acquisition. These findings provide insight into the context-specific basis for choosing between Drosophila sleep acquisition systems, describe a novel cost-effective system for video tracking, and characterize sleep analysis using the MB-IR sleep analysis. Further, we describe a modified dark-place preference sleep assay using video tracking, confirming that flies prefer to sleep in dark locations.},
  language = {en},
  number = {11},
  journal = {Biol. Open},
  author = {Garbe, David S. and Bollinger, Wesley L. and Vigderman, Abigail and Masek, Pavel and Gertowski, Jill and Sehgal, Amita and Keene, Alex C.},
  month = nov,
  year = {2015},
  pages = {1558--1568},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HLA7JTMW/Garbe et al. - 2015 - Context-specific comparison of sleep acquisition s.pdf},
  pmid = {26519516}
}

@article{parisky_pdf_2008,
  title = {{{PDF Cells Are}} a {{GABA}}-{{Responsive Wake}}-{{Promoting Component}} of the {{Drosophila Sleep Circuit}}},
  volume = {60},
  issn = {08966273},
  doi = {10.1016/j.neuron.2008.10.042},
  abstract = {Daily sleep cycles in humans are driven by a complex circuit within which GABAergic sleep-promoting neurons oppose arousal. Drosophila sleep has recently been shown to be controlled by GABA, which acts on unknown cells expressing the Rdl GABAA receptor. We identify here the relevant Rdl-containing cells as PDF-expressing small and large ventral lateral neurons (LNvs) of the circadian clock. LNv activity regulates total sleep as well as the rate of sleep onset; both large and small LNvs are part of the sleep circuit. Flies mutant for pdf or its receptor are hypersomnolent, and PDF acts on the LNvs themselves to control sleep. These features of the Drosophila sleep circuit, GABAergic control of onset and maintenance as well as peptidergic control of arousal, support the idea that features of sleep-circuit architecture as well as the mechanisms governing the behavioral transitions between sleep and wake are conserved between mammals and insects. ?? 2008 Elsevier Inc. All rights reserved.},
  language = {eng},
  number = {4},
  journal = {Neuron},
  author = {Parisky, Katherine M. and Agosto, Jose and Pulver, Stefan R. and Shang, Yuhua and Kuklin, Elena and Hodge, James J. L. and Kang, Keongjin Kyeongjin and Liu, Xu and Garrity, Paul A. and Rosbash, Michael and Griffith, Leslie C. and Kang, Keongjin Kyeongjin and Liu, Xu and Garrity, Paul A. and Rosbash, Michael and Griffith, Leslie C.},
  month = nov,
  year = {2008},
  keywords = {Brain,Arousal,Neurons,Animals,Neural Pathways,Synaptic Transmission,Sleep,Species Specificity,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,MOLNEURO,SYSNEURO,Biological Evolution,Neuropeptides,Mammals,Wakefulness,gamma-Aminobutyric Acid,CELLBIO,TRPC Cation Channels,molecular biology},
  pages = {672--682},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QD7RADTS/Parisky et al. - 2008 - PDF Cells Are a GABA-Responsive Wake-Promoting Com.pdf},
  pmid = {19038223}
}

@article{cirelli_genetic_2009,
  title = {The Genetic and Molecular Regulation of Sleep: From Fruit Flies to Humans},
  volume = {10},
  issn = {1471-003X},
  shorttitle = {The Genetic and Molecular Regulation of Sleep},
  doi = {10.1038/nrn2683},
  abstract = {It has been known for a long time that genetic factors affect sleep quantity and quality. Genetic screens have identified several mutations that affect sleep across species, pointing to an evolutionary conserved regulation of sleep. Moreover, it has also been recognized that sleep affects gene expression. These findings have given valuable insights into the molecular underpinnings of sleep regulation and function that might lead the way to more efficient treatments for sleep disorders.},
  language = {eng},
  number = {8},
  journal = {Nat. Rev. Neurosci.},
  author = {Cirelli, Chiara},
  month = aug,
  year = {2009},
  keywords = {Humans,Animals,Sleep,Drosophila,Signal Transduction,Circadian Rhythm,Drosophila Proteins,Gene Expression Regulation,Mutation,Biological Evolution,Models- Biological},
  pages = {549--560},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3JE6BKYW/Cirelli - 2009 - The genetic and molecular regulation of sleep fro.pdf}
}

@article{buhl_quasimodo_2016-1,
  title = {Quasimodo Mediates Daily and Acute Light Effects on {{Drosophila}} Clock Neuron Excitability},
  volume = {113},
  issn = {0027-8424},
  doi = {10.1073/pnas.1606547113},
  abstract = {We have characterized a light-input pathway regulating Drosophila clock neuron excitability. The molecular clock drives rhythmic electrical excitability of clock neurons, and we show that the recently discovered light-input factor Quasimodo (Qsm) regulates this variation, presumably via an Na+, K+, Cl- cotransporter (NKCC) and the Shaw K+ channel (dKV3.1). Because of light-dependent degradation of the clock protein Timeless (Tim), constant illumination (LL) leads to a breakdown of molecular and behavioral rhythms. Both overexpression (OX) and knockdown (RNAi) of qsm, NKCC, or Shaw led to robust LL rhythmicity. Whole-cell recordings of the large ventral lateral neurons (l-LNv) showed that altering Qsm levels reduced the daily variation in neuronal activity: qsmOX led to a constitutive less active, night-like state, and qsmRNAi led to a more active, day-like state. Qsm also affected daily changes in K+ currents and the GABA reversal potential, suggesting a role in modifying membrane currents and GABA responses in a daily fashion, potentially modulating light arousal and input to the clock. When directly challenged with blue light, wild-type l-LNvs responded with increased firing at night and no net response during the day, whereas altering Qsm, NKKC, or Shaw levels abolished these day/night differences. Finally, coexpression of ShawOX and NKCCRNAi in a qsm mutant background restored LL-induced behavioral arrhythmicity and wild-type neuronal activity patterns, suggesting that the three genes operate in the same pathway. We propose that Qsm affects both daily and acute light effects in l-LNvs probably acting on Shaw and NKCC.},
  number = {47},
  journal = {Proc. Natl. Acad. Sci.},
  author = {Buhl, Edgar and Bradlaugh, Adam and Ogueta, Maite and Chen, Ko-Fan and Stanewsky, Ralf and Hodge, James J L},
  month = nov,
  year = {2016},
  keywords = {circadian rhythms,Circadian rhythms,GABA reversal potential,light input,membrane excitability,potassium currents},
  pages = {13486--13491},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X928KAU9/Buhl et al. - 2016 - Quasimodo mediates daily and acute light effects o.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VI7URT84/13486.html},
  pmid = {27821737}
}

@article{hendricks_gender_2003,
  title = {Gender {{Dimorphism}} in the {{Role}} of Cycle ({{BMAL1}}) in {{Rest}}, {{Rest Regulation}}, and {{Longevity}} in {{Drosophila}} Melanogaster},
  volume = {18},
  issn = {0748-7304},
  doi = {10.1177/0748730402239673},
  abstract = {The central clock is generally thought to provide timing information for rest/activity but not to otherwise participate in regulation of these states. To test the hypothesis that genes that are components of the molecular clock also regulate rest, the authors quantified the duration and intensity of consolidated rest and activity for the four viable Drosophila mutations of the central clock that lead to arrhythmic locomotor behavior and for the pdf mutant that lacks pigment dispersing factor, an output neuropeptide. Only the cycle (cyc0\{superscript 1\}) and Clock (ClkJrk) mutants had abnormalities that mapped to the mutant locus, namely, decreased consolidated rest and grossly extended periods of activity. All mutants with the exception of the cyc0\{superscript 1\} fly exhibited a qualitatively normal compensatory rebound after rest deprivation. This abnormal response in cyc0\{superscript 1\} was sexually dimorphic, being reduced or absent in males and exaggerated in females. Finally, the cyc0\{superscript 1\} mutation shortened the life span of male flies. These data indicate that cycle regulates rest and life span in male Drosophila.},
  number = {1},
  journal = {J. Biol. Rhythms},
  author = {Hendricks, Joan C and Lu, Sumei and Kume, Kazuhiko and Yin, Jerry C.-P. and Yang, Zhaohai and Sehgal, Amita},
  year = {2003},
  pages = {12--25},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QPFCCBHG/Hendricks et al. - 2003 - Gender Dimorphism in the Role of cycle (BMAL1) in .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TWVKKUBY/Hendricks et al. - 2003 - Gender Dimorphism in the Role of cycle (BMAL1) in .pdf},
  pmid = {12568241}
}

@article{harbison_co-regulated_2009,
  title = {Co-Regulated Transcriptional Networks Contribute to Natural Genetic Variation in {{Drosophila}} Sleep},
  volume = {41},
  issn = {1061-4036},
  doi = {10.1038/ng.330},
  abstract = {Sleep disorders are common in humans, and sleep loss increases the risk of obesity and diabetes. Studies in Drosophila have revealed molecular pathways and neural tissues regulating sleep; however, genes that maintain genetic variation for sleep in natural populations are unknown. Here, we characterized sleep in 40 wild-derived Drosophila lines and observed abundant genetic variation in sleep architecture. We associated sleep with genome-wide variation in gene expression to identify candidate genes. We independently confirmed that molecular polymorphisms in Catsup (Catecholamines up) are associated with variation in sleep and that P-element mutations in four candidate genes affect sleep and gene expression. Transcripts associated with sleep grouped into biologically plausible genetically correlated transcriptional modules. We confirmed co-regulated gene expression using P-element mutants. Quantitative genetic analysis of natural phenotypic variation is an efficient method for revealing candidate genes and pathways.},
  language = {en},
  number = {3},
  journal = {Nat. Genet.},
  author = {Harbison, Susan T. and Carbone, Mary Anna and Ayroles, Julien F. and Stone, Eric A. and Lyman, Richard F. and Mackay, Trudy F. C.},
  month = mar,
  year = {2009},
  pages = {371--375},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GUNE42Q8/Harbison et al. - 2009 - Co-regulated transcriptional networks contribute t.pdf},
  pmid = {19234472}
}

@article{guo_circadian_2016,
  title = {Circadian Neuron Feedback Controls the {{Drosophila}} Sleep-Activity Profile.},
  volume = {536},
  issn = {1476-4687},
  doi = {10.1038/nature19097},
  abstract = {Little is known about the ability of Drosophila circadian neurons to promote sleep. Here we show, using optogenetic manipulation and video recording, that a subset of dorsal clock neurons (DN1s) are potent sleep-promoting cells that release glutamate to directly inhibit key pacemaker neurons. The pacemakers promote morning arousal by activating these DN1s, implying that a late-day feedback circuit drives midday siesta and night-time sleep. To investigate more plastic aspects of the sleep program, we used a calcium assay to monitor and compare the real-time activity of DN1 neurons in freely behaving males and females. Our results revealed that DN1 neurons were more active in males than in females, consistent with the finding that male flies sleep more during the day. DN1 activity is also enhanced by elevated temperature, consistent with the ability of higher temperatures to increase sleep. These new approaches indicate that DN1s have a major effect on the fly sleep-wake profile and integrate environmental information with the circadian molecular program.},
  number = {7616},
  journal = {Nature},
  author = {Guo, Fang and Yu, Junwei and Jung, Hyung Jae and Abruzzi, Katharine C. and Luo, Weifei and Griffith, Leslie C. and Rosbash, Michael},
  month = aug,
  year = {2016},
  pages = {292--297},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F5A35A4P/Guo et al. - 2016 - Circadian neuron feedback controls the iDrosophi.pdf},
  pmid = {27479324}
}

@article{everson_sleep_1989,
  title = {Sleep Deprivation in the Rat: {{III}}. {{Total}} Sleep Deprivation.},
  volume = {12},
  issn = {0161-8105},
  shorttitle = {Sleep Deprivation in the Rat},
  abstract = {Ten rats were subjected to total sleep deprivation (TSD) by the disk apparatus. All TSD rats died or were sacrificed when death seemed imminent within 11-32 days. No anatomical cause of death was identified. All TSD rats showed a debilitated appearance, lesions on their tails and paws, and weight loss in spite of increased food intake. Their yoked control (TSC) rats remained healthy. Since dehydration was ruled out and several measures indicated accelerated use rather than failure to absorb nutrients, the food-weight changes in TSD rats were attributed to increased energy expenditure (EE). The measurement of EE, based upon caloric value of food, weight, and wastes, indicated that all TSD rats increased EE, with mean levels reaching more than twice baseline values.},
  number = {1},
  journal = {Sleep},
  author = {Everson, Carol A. and Bergmann, Bernard M. and Rechtschaffen, Allan},
  year = {1989},
  pages = {13--21},
  pmid = {2928622}
}

@article{mallon_immune_2014,
  title = {Immune Stimulation Reduces Sleep and Memory Ability in {{Drosophila}} Melanogaster.},
  volume = {2},
  issn = {2167-8359},
  doi = {10.7717/peerj.434},
  abstract = {Psychoneuroimmunology studies the increasing number of connections between neurobiology, immunology and behaviour. We demonstrate the effects of the immune response on two fundamental behaviours: sleep and memory ability in Drosophila melanogaster. We used the Geneswitch system to upregulate peptidoglycan receptor protein (PGRP) expression, thereby stimulating the immune system in the absence of infection. Geneswitch was activated by feeding the steroid RU486, to the flies. We used an aversive classical conditioning paradigm to quantify memory and measures of activity to infer sleep. Immune stimulated flies exhibited reduced levels of sleep, which could not be explained by a generalised increase in waking activity. Immune stimulated flies also showed a reduction in memory abilities. These results lend support to Drosophila as a model for immune-neural interactions and provide a possible role for sleep in the interplay between the immune response and memory.},
  journal = {PeerJ},
  author = {Mallon, Eamonn B. and Alghamdi, Akram and Holdbrook, Robert T K and Rosato, Ezio},
  month = jun,
  year = {2014},
  keywords = {Fruit fly,Geneswitch,Imd,Immune–neural interactions,PGRP-LCa,Psychoneuroimmunology},
  pages = {e434},
  pmid = {24949247}
}

@article{diekelmann_memory_2010,
  title = {The Memory Function of Sleep.},
  volume = {11},
  issn = {1471-0048},
  doi = {10.1038/nrn2762},
  abstract = {Sleep has been identified as a state that optimizes the consolidation of newly acquired information in memory, depending on the specific conditions of learning and the timing of sleep. Consolidation during sleep promotes both quantitative and qualitative changes of memory representations. Through specific patterns of neuromodulatory activity and electric field potential oscillations, slow-wave sleep (SWS) and rapid eye movement (REM) sleep support system consolidation and synaptic consolidation, respectively. During SWS, slow oscillations, spindles and ripples - at minimum cholinergic activity - coordinate the re-activation and redistribution of hippocampus-dependent memories to neocortical sites, whereas during REM sleep, local increases in plasticity-related immediate-early gene activity - at high cholinergic and theta activity - might favour the subsequent synaptic consolidation of memories in the cortex.},
  number = {2},
  journal = {Nat. Rev. Neurosci.},
  author = {Diekelmann, Susanne and Born, Jan},
  month = feb,
  year = {2010},
  keywords = {Humans,Memory,Hippocampus,learning,Animals,Hippocampus: physiology,Sleep,Sleep: physiology,Memory: physiology,Genes,Synapses,Learning: physiology,Synapses: physiology,Wakefulness,REM,REM: physiology,Wakefulness: physiology,Immediate-Early,Immediate-Early: physiology},
  pages = {114--126},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MT6B6TZW/Diekelmann and Born - 2010 - The memory function of sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FRHLTKQL/nrn2762.html},
  pmid = {20046194}
}

@article{thimgan_perilipin_2010,
  title = {The {{Perilipin}} Homologue, {{Lipid}} Storage Droplet 2, Regulates Sleep Homeostasis and Prevents Learning Impairments Following Sleep Loss},
  volume = {8},
  issn = {15449173},
  doi = {10.1371/journal.pbio.1000466},
  abstract = {Extended periods of waking result in physiological impairments in humans, rats, and flies. Sleep homeostasis, the increase in sleep observed following sleep loss, is believed to counter the negative effects of prolonged waking by restoring vital biological processes that are degraded during sleep deprivation. Sleep homeostasis, as with other behaviors, is influenced by both genes and environment. We report here that during periods of starvation, flies remain spontaneously awake but, in contrast to sleep deprivation, do not accrue any of the negative consequences of prolonged waking. Specifically, the homeostatic response and learning impairments that are a characteristic of sleep loss are not observed following prolonged waking induced by starvation. Recently, two genes, brummer (bmm) and Lipid storage droplet 2 (Lsd2), have been shown to modulate the response to starvation. bmm mutants have excess fat and are resistant to starvation, whereas Lsd2 mutants are lean and sensitive to starvation. Thus, we hypothesized that bmm and Lsd2 may play a role in sleep regulation. Indeed, bmm mutant flies display a large homeostatic response following sleep deprivation. In contrast, Lsd2 mutant flies, which phenocopy aspects of starvation as measured by low triglyceride stores, do not exhibit a homeostatic response following sleep loss. Importantly, Lsd2 mutant flies are not learning impaired after sleep deprivation. These results provide the first genetic evidence, to our knowledge, that lipid metabolism plays an important role in regulating the homeostatic response and can protect against neuronal impairments induced by prolonged waking.},
  number = {8},
  journal = {PLoS Biol.},
  author = {Thimgan, Matthew S. and Suzuki, Yasuko and Seugnet, Laurent and Gottschalk, Laura and Shaw, Paul J.},
  editor = {Hardin, Paul E.},
  month = aug,
  year = {2010},
  keywords = {Sleep,Starvation,Homeostasis,Sleep deprivation,Cognitive impairment,Fats,Human learning,Lipids},
  pages = {29--30},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FYDZV9ZA/Thimgan et al. - 2010 - The Perilipin Homologue, Lipid Storage Droplet 2, .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8UMER4WP/article.html},
  pmid = {20824166}
}

@article{xu_regulation_2008,
  title = {Regulation of {{Feeding}} and {{Metabolism}} by {{Neuronal}} and {{Peripheral Clocks}} in {{Drosophila}}},
  volume = {8},
  issn = {15504131},
  doi = {10.1016/j.cmet.2008.09.006},
  abstract = {Studies in mammals have indicated a connection between circadian clocks and feeding behavior, but the nature of the interaction and its relationship to nutrient metabolism are not understood. In Drosophila, clock proteins are expressed in many metabolically important tissues but have not been linked to metabolic processes. Here we demonstrate that Drosophila feeding behavior displays a 24 hr circadian rhythm that is regulated by clocks in digestive/metabolic tissues. Flies lacking clocks in these tissues, in particular in the fat body, also display increased food consumption but have decreased levels of glycogen and a higher sensitivity to starvation. Interestingly, glycogen levels and starvation sensitivity are also affected by clocks in neuronal cells, but the effects of neuronal clocks generally oppose those of the fat body. We propose that the input of neuronal clocks and clocks in metabolic tissues is coordinated to provide effective energy homeostasis. \textcopyright{} 2008 Elsevier Inc. All rights reserved.},
  number = {4},
  journal = {Cell Metab.},
  author = {Xu, Kanyan and Zheng, Xiangzhong and Sehgal, Amita},
  month = oct,
  year = {2008},
  keywords = {HUMDISEASE,SIGNALING},
  pages = {289--300},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ASPLQNVZ/Xu et al. - 2008 - Regulation of Feeding and Metabolism by Neuronal a.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BGWLYZJF/S1550413108002908.html},
  pmid = {18840359}
}

@article{sallanon_long-lasting_1989,
  title = {Long-Lasting Insomnia Induced by Preoptic Neuron Lesions and Its Transient Reversal by Muscimol Injection into the Posterior Hypothalamus in the Cat},
  volume = {32},
  issn = {03064522},
  doi = {10.1016/0306-4522(89)90289-3},
  abstract = {In order to analyse the role of the anterior hypothalamus in the regulation of the sleep-waking cycle we made bilateral neuronal lesions at different levels of the anterior hypothalamus in cats, by means of microinjections of a cell-specific neurotoxin: ibotenic acid. These lesions resulted in severe insomnia in eight cats. This insomnia was characterized by a large decrease or even disappearance of paradoxical sleep and deep slow wave sleep and, to a lesser extent, by a decrease of light slow wave sleep, for 2-3 weeks. In the other five animals, we observed a large reduction of deep slow wave sleep (0-40\% of control level), but a less intensive decrease of time spent in paradoxical sleep (50-75\% of control level) and no marked effect on light slow wave sleep. During the first 3-6 postoperative days we also noticed hyperthermia in all cats; thereafter, the animals presented only a slight increase in brain temperature which did not appear to trigger the sleep impairment. Histological analysis of the different lesions revealed that the insomnia could be attributed to neuronal cell body destruction in the mediobasal part of the anterior hypothalamus covering: the medial preoptic area and a narrow portion of the lateral preoptic area as well as a restricted part of the anterior hypothalamic nucleus. In order to investigate the putative role of the posterior hypothalamic structures in the mechanism of insomnia after lesion of the mediobasal preoptic area neurons we injected an agonist of GABA into the ventrolateral part of the posterior hypothalamus to locally depress the neuronal activity. The bilateral intracerebral microinjection of muscimol (0.5-5 $\mu$g) induced a transient intensive hypersomnia (slow wave sleep and paradoxical sleep). These findings indicate that neuronal cell loss in the mediobasal preoptic area induced a long lasting insomnia. Thus, it may be hypothesized that the integrity of this structure is necessary for sleep appearance. Finally, our data are in keeping with an intrahypothalamic regulation of the sleep-waking cycle. \textcopyright{} 1989.},
  number = {3},
  journal = {Neuroscience},
  author = {Sallanon, M. and Denoyer, M. and Kitahama, K. and Aubert, C. and Gay, N. and Jouvet, M.},
  month = jan,
  year = {1989},
  pages = {669--683},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4GWYAQQN/0306452289902893.html},
  pmid = {2601839}
}

@article{siegel_sleep_2009,
  title = {Sleep Viewed as a State of Adaptive Inactivity},
  volume = {10},
  issn = {1471-0048},
  doi = {10.1038/nrn2697},
  abstract = {Sleep is often viewed as a vulnerable state that is incompatible with behaviours that nourish and propagate species. This has led to the hypothesis that sleep has survived because it fulfills some universal, but as yet unknown, vital function. I propose that sleep is best understood as a variant of dormant states seen throughout the plant and animal kingdoms and that it is itself highly adaptive because it optimizes the timing and duration of behaviour. Current evidence indicates that ecological variables are the main determinants of sleep duration and intensity across species.},
  language = {en},
  number = {10},
  journal = {Nat. Rev. Neurosci.},
  author = {Siegel, Jerome M.},
  month = oct,
  year = {2009},
  keywords = {Paradoxical sleep,CEREBRAL GLUCOSE-UTILIZATION,CONTINUOUS AUDITORY VIGILANCE,EYE-MOVEMENT SLEEP,GROWTH-HORMONE,LIZARD CTENOSAURA-PECTINATA,MAMMALIAN SLEEP,PHYLOGENETIC ANALYSIS,REM-SLEEP,SLOW-WAVE SLEEP},
  pages = {747--753},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GNJSGMIG/Siegel - 2009 - Sleep viewed as a state of adaptive inactivity.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ITT5PRQ6/nrn2697.html},
  pmid = {19654581}
}

@article{harbison_genome-wide_2013,
  title = {Genome-Wide Association Study of Sleep in {{Drosophila}} Melanogaster},
  volume = {14},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-14-281},
  abstract = {BACKGROUND: Sleep is a highly conserved behavior, yet its duration and pattern vary extensively among species and between individuals within species. The genetic basis of natural variation in sleep remains unknown. RESULTS: We used the Drosophila Genetic Reference Panel (DGRP) to perform a genome-wide association (GWA) study of sleep in D. melanogaster. We identified candidate single nucleotide polymorphisms (SNPs) associated with differences in the mean as well as the environmental sensitivity of sleep traits; these SNPs typically had sex-specific or sex-biased effects, and were generally located in non-coding regions. The majority of SNPs (80.3\%) affecting sleep were at low frequency and had moderately large effects. Additive models incorporating multiple SNPs explained as much as 55\% of the genetic variance for sleep in males and females. Many of these loci are known to interact physically and/or genetically, enabling us to place them in candidate genetic networks. We confirmed the role of seven novel loci on sleep using insertional mutagenesis and RNA interference. CONCLUSIONS: We identified many SNPs in novel loci that are potentially associated with natural variation in sleep, as well as SNPs within genes previously known to affect Drosophila sleep. Several of the candidate genes have human homologues that were identified in studies of human sleep, suggesting that genes affecting variation in sleep are conserved across species. Our discovery of genetic variants that influence environmental sensitivity to sleep may have a wider application to all GWA studies, because individuals with highly plastic genotypes will not have consistent phenotypes.},
  language = {eng},
  number = {1},
  journal = {BMC Genomics},
  author = {Harbison, Susan T. and McCoy, Lenovia J. and Mackay, Trudy FC C.},
  month = apr,
  year = {2013},
  keywords = {Genes; Insect,Mutagenesis; Insertional,Polymorphism; Single Nucleotide,Female,Humans,Male,Animals,Sleep,Sleep Disorders,Drosophila melanogaster,Genotype,RNA Interference,Phenotype,Polymorphism- Single Nucleotide,Genome-Wide Association Study,Genes- Insect,Genetic variance of environmental variation,Genome-wide association,Mutagenesis- Insertional,Sleep Wake Disorders},
  pages = {281},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NPKYFMB9/Harbison et al. - 2013 - Genome-wide association study of sleep in Drosophi}
}

@article{hendricks_non-circadian_2001,
  title = {A Non-Circadian Role for {{cAMP}} Signaling and {{CREB}} Activity in {{Drosophila}} Rest Homeostasis.},
  volume = {4},
  issn = {1097-6256},
  doi = {10.1038/nn743},
  abstract = {In the fruit fly, Drosophila melanogaster, rest shares features with mammalian sleep, including prolonged immobility, decreased sensory responsiveness and a homeostatic rebound after deprivation. To understand the molecular regulation of sleep-like rest, we investigated the involvement of a candidate gene, cAMP response-element binding protein (CREB). The duration of rest was inversely related to cAMP signaling and CREB activity. Acutely blocking CREB activity in transgenic flies did not affect the clock, but increased rest rebound. CREB mutants also had a prolonged and increased homeostatic rebound. In wild types, in vivo CREB activity increased after rest deprivation and remained elevated for a 72-hour recovery period. These data indicate that cAMP signaling has a non-circadian role in waking and rest homeostasis in Drosophila.},
  language = {en},
  number = {11},
  journal = {Nat. Neurosci.},
  author = {Hendricks, Joan C. and Williams, Julie A. and Panckeri, Karen and Kirk, David and Tello, Marcela and Yin, Jerry C.-P. and Sehgal, Amita},
  month = nov,
  year = {2001},
  pages = {1108--1115},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7QQHTIC5/Hendricks et al. - 2001 - A non-circadian role for cAMP signaling and CREB a.pdf},
  pmid = {11687816}
}

@article{zimmerman_genetic_2012,
  title = {Genetic Background Has a Major Impact on Differences in Sleep Resulting from Environmental Influences in {{Drosophila}}.},
  volume = {35},
  issn = {1550-9109},
  doi = {10.5665/sleep.1744},
  abstract = {STUDY OBJECTIVES To determine the effect of different genetic backgrounds on demographic and environmental interventions that affect sleep and evaluate variance of these measures; and to evaluate sleep and variance of sleep behaviors in 6 divergent laboratory strains of common origin. DESIGN Assessment of the effects of age, sex, mating status, food sources, and social experience using video analysis of sleep behavior in 2 different strains of Drosophila, white(1118ex) (w(1118ex)) and white Canton-S (w(CS10)). Sleep was also determined for 6 laboratory strains of Canton-S and 3 inbred lines. The variance of total sleep was determined for all groups and conditions. MEASUREMENTS AND RESULTS The circadian periods and the effects of age upon sleep were the same between w(1118ex) and w(CS10) strains. However, the w(1118ex) and w(CS10) strains demonstrated genotype-dependent differences in the effects upon sleep of sex, mating status, social experience, and being on different foods. Variance of total sleep was found to differ in a genotype dependent manner for interventions between the w(1118ex) and w(CS10) strains. Six different laboratory Canton-S strains were found to have significantly different circadian periods (P $\backslash$textless 0.001) and sleep phenotypes (P $\backslash$textless 0.001). Three inbred lines showed reduced variance for sleep measurements. CONCLUSIONS One must control environmental conditions in a rigorously consistent manner to ensure that sleep data may be compared between experiments. Genetic background has a significant impact upon changes in sleep behavior and variance of behavior due to demographic factors and environmental interventions. This represents an opportunity to discover new genes that modify sleep/wake behavior.},
  number = {4},
  journal = {Sleep},
  author = {Zimmerman, John E and Chan, May T and Jackson, Nicholas and Maislin, Greg and Pack, Allan I},
  month = apr,
  year = {2012},
  keywords = {Drosophila,Genetic background,sleep measurement,variance,video analysis},
  pages = {545--57},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RCPEPWHT/Zimmerman et al. - 2012 - Genetic Background Has a Major Impact on Differenc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3QW8SHTI/2558905.html},
  pmid = {22467993}
}

@article{nitabach_electrical_2006,
  title = {Electrical {{Hyperexcitation}} of {{Lateral Ventral Pacemaker Neurons Desynchronizes Downstream Circadian Oscillators}} in the {{Fly Circadian Circuit}} and {{Induces Multiple Behavioral Periods}}},
  volume = {26},
  issn = {0270-6474, 1529-2401},
  doi = {10.1523/JNEUROSCI.3915-05.2006},
  abstract = {Coupling of autonomous cellular oscillators is an essential aspect of circadian clock function but little is known about its circuit requirements. Functional ablation of the pigment-dispersing factor-expressing lateral ventral subset (LNV) of Drosophila clock neurons abolishes circadian rhythms of locomotor activity. The hypothesis that LNVs synchronize oscillations in downstream clock neurons was tested by rendering the LNVs hyperexcitable via transgenic expression of a low activation threshold voltage-gated sodium channel. When the LNVs are made hyperexcitable, free-running behavioral rhythms decompose into multiple independent superimposed oscillations and the clock protein oscillations in the dorsal neuron 1 and 2 subgroups of clock neurons are phase-shifted. Thus, regulated electrical activity of the LNVs synchronize multiple oscillators in the fly circadian pacemaker circuit.},
  language = {en},
  number = {2},
  journal = {J. Neurosci.},
  author = {Nitabach, Michael N. and Wu, Ying and Sheeba, Vasu and Lemon, William C. and Strumbos, John and Zelensky, Paul K. and White, Benjamin H. and Holmes, Todd C.},
  month = jan,
  year = {2006},
  keywords = {Behavior,Drosophila,Circadian rhythms,arrhythmia,desynchronization,sodium channel},
  pages = {479--489},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FTW9FVBE/Nitabach et al. - 2006 - Electrical Hyperexcitation of Lateral Ventral Pace.pdf}
}

@article{hamada_internal_2008,
  title = {An Internal Thermal Sensor Controlling Temperature Preference in {{Drosophila}}},
  volume = {454},
  issn = {0028-0836},
  doi = {10.1038/nature07001},
  abstract = {Animals from flies to humans are able to distinguish subtle gradations in temperature and show strong temperature preferences. Animals move to environments of optimal temperature and some manipulate the temperature of their surroundings, as humans do using clothing and shelter. Despite the ubiquitous influence of environmental temperature on animal behaviour, the neural circuits and strategies through which animals select a preferred temperature remain largely unknown. Here we identify a small set of warmth-activated anterior cell (AC) neurons located in the Drosophila brain, the function of which is critical for preferred temperature selection. AC neuron activation occurs just above the fly's preferred temperature and depends on dTrpA1, an ion channel that functions as a molecular sensor of warmth. Flies that selectively express dTrpA1 in the AC neurons select normal temperatures, whereas flies in which dTrpA1 function is reduced or eliminated choose warmer temperatures. This internal warmth-sensing pathway promotes avoidance of slightly elevated temperatures and acts together with a distinct pathway for cold avoidance to set the fly's preferred temperature. Thus, flies select a preferred temperature by using a thermal sensing pathway tuned to trigger avoidance of temperatures that deviate even slightly from the preferred temperature. This provides a potentially general strategy for robustly selecting a narrow temperature range optimal for survival.},
  number = {7201},
  journal = {Nature},
  author = {Hamada, Fumika N. and Rosenzweig, Mark and Kang, Kyeongjin and Pulver, Stefan R. and Ghezzi, Alfredo and Jegla, Timothy J. and Garrity, Paul A.},
  month = jul,
  year = {2008},
  pages = {217--220},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YQYDWIT6/Hamada et al. - 2008 - An internal thermal sensor controlling temperature.pdf},
  pmid = {18548007}
}

@article{pimentel_operation_2016,
  title = {Operation of a Homeostatic Sleep Switch},
  volume = {536},
  issn = {0028-0836},
  doi = {10.1038/nature19055},
  abstract = {Sleep disconnects animals from the external world, at considerable risks and costs that must be offset by a vital benefit. Insight into this mysterious benefit will come from understanding sleep homeostasis: to monitor sleep need, an internal bookkeeper must track physiological changes that are linked to the core function of sleep. In Drosophila, a crucial component of the machinery for sleep homeostasis is a cluster of neurons innervating the dorsal fan-shaped body (dFB) of the central complex. Artificial activation of these cells induces sleep, whereas reductions in excitability cause insomnia. dFB neurons in sleep-deprived flies tend to be electrically active, with high input resistances and long membrane time constants, while neurons in rested flies tend to be electrically silent. Correlative evidence thus supports the simple view that homeostatic sleep control works by switching sleep-promoting neurons between active and quiescent states. Here we demonstrate state switching by dFB neurons, identify dopamine as a neuromodulator that operates the switch, and delineate the switching mechanism. Arousing dopamine caused transient hyperpolarization of dFB neurons within tens of milliseconds and lasting excitability suppression within minutes. Both effects were transduced by Dop1R2 receptors and mediated by potassium conductances. The switch to electrical silence involved the downregulation of voltage-gated A-type currents carried by Shaker and Shab, and the upregulation of voltage-independent leak currents through a two-pore-domain potassium channel that we term Sandman. Sandman is encoded by the CG8713 gene and translocates to the plasma membrane in response to dopamine. dFB-restricted interference with the expression of Shaker or Sandman decreased or increased sleep, respectively, by slowing the repetitive discharge of dFB neurons in the ON state or blocking their entry into the OFF state. Biophysical changes in a small population of neurons are thus linked to the control of sleep-wake state.},
  number = {7616},
  journal = {Nature},
  author = {Pimentel, Diogo and Donlea, Jeffrey M and Talbot, Clifford B and Song, Seoho M and Thurston, Alexander J F and Miesenb\"ock, Gero},
  year = {2016},
  pages = {333--337},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S68GRNLT/Pimentel et al. - 2016 - Operation of a homeostatic sleep switch.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PY636PXP/nature19055.html},
  pmid = {27487216}
}

@article{skeldon_mathematical_2014,
  title = {Mathematical Models for Sleep-Wake Dynamics: {{Comparison}} of the Two-Process Model and a Mutual Inhibition Neuronal Model},
  volume = {9},
  issn = {19326203},
  doi = {10.1371/journal.pone.0103877},
  abstract = {Sleep is essential for the maintenance of the brain and the body, yet many features of sleep are poorly understood and mathematical models are an important tool for probing proposed biological mechanisms. The most well-known mathematical model of sleep regulation, the two-process model, models the sleep-wake cycle by two oscillators: a circadian oscillator and a homeostatic oscillator. An alternative, more recent, model considers the mutual inhibition of sleep promoting neurons and the ascending arousal system regulated by homeostatic and circadian processes. Here we show there are fundamental similarities between these two models. The implications are illustrated with two important sleep-wake phenomena. Firstly, we show that in the two-process model, transitions between different numbers of daily sleep episodes occur at grazing bifurcations.This provides the theoretical underpinning for numerical results showing that the sleep patterns of many mammals can be explained by the mutual inhibition model. Secondly, we show that when sleep deprivation disrupts the sleep-wake cycle, ostensibly different measures of sleepiness in the two models are closely related. The demonstration of the mathematical similarities of the two models is valuable because not only does it allow some features of the two-process model to be interpreted physiologically but it also means that knowledge gained from study of the two-process model can be used to inform understanding of the mutual inhibition model. This is important because the mutual inhibition model and its extensions are increasingly being used as a tool to understand a diverse range of sleep-wake phenomena such as the design of optimal shift-patterns, yet the values it uses for parameters associated with the circadian and homeostatic processes are very different from those that have been experimentally measured in the context of the two-process model.},
  number = {8},
  journal = {PLoS One},
  author = {Skeldon, Anne C. and Dijk, Derk Jan and Derks, Gianne},
  editor = {{Csik\'asz-Nagy}, Attila},
  month = aug,
  year = {2014},
  keywords = {Neurons,Sleep,Homeostasis,Sleep deprivation,Chronobiology,Circadian oscillators,Grazing,Neural homeostasis},
  pages = {e103877},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GEFZ42YB/Skeldon et al. - 2014 - Mathematical Models for Sleep-Wake Dynamics Compa.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7KMU6ENP/article.html},
  pmid = {25084361}
}

@article{bernstein_optogenetics_2012,
  title = {Optogenetics and Thermogenetics: Technologies for Controlling the Activity of Targeted Cells within Intact Neural Circuits.},
  volume = {22},
  issn = {1873-6882},
  doi = {10.1016/j.conb.2011.10.023},
  abstract = {In recent years, interest has grown in the ability to manipulate, in a temporally precise fashion, the electrical activity of specific neurons embedded within densely wired brain circuits, in order to reveal how specific neurons subserve behaviors and neural computations, and to open up new horizons on the clinical treatment of brain disorders. Technologies that enable temporally precise control of electrical activity of specific neurons, and not these neurons' neighbors-whose cell bodies or processes might be just tens to hundreds of nanometers away-must involve two components. First, they require as a trigger a transient pulse of energy that supports the temporal precision of the control. Second, they require a molecular sensitizer that can be expressed in specific neurons and which renders those neurons specifically responsive to the triggering energy delivered. Optogenetic tools, such as microbial opsins, can be used to activate or silence neural activity with brief pulses of light. Thermogenetic tools, such as thermosensitive TRP channels, can be used to drive neural activity downstream of increases or decreases in temperature. We here discuss the principles underlying the operation of these two recently developed, but widely used, toolboxes, as well as the directions being taken in the use and improvement of these toolboxes.},
  number = {1},
  journal = {Curr. Opin. Neurobiol.},
  author = {Bernstein, Jacob G and a Garrity, Paul and Boyden, Edward S},
  month = feb,
  year = {2012},
  keywords = {Humans,Brain,Brain: physiology,Neurons,Animals,Light,Neurons: physiology,Neurosciences,Optics and Photonics,Temperature,Genetic Techniques,Genetic Techniques: instrumentation,Neurosciences: instrumentation,Neurosciences: methods,Optics and Photonics: instrumentation,Optics and Photonics: methods},
  pages = {61--71},
  pmid = {22119320}
}

@article{saper_hypothalamic_2005,
  title = {Hypothalamic Regulation of Sleep and Circadian Rhythms},
  volume = {437},
  issn = {0028-0836},
  doi = {10.1038/nature04284},
  abstract = {A series of findings over the past decade has begun to identify the brain circuitry and neurotransmitters that regulate our daily cycles of sleep and wakefulness. The latter depends on a network of cell groups that activate the thalamus and the cerebral cortex. A key switch in the hypothalamus shuts off this arousal system during sleep. Other hypothalamic neurons stabilize the switch, and their absence results in inappropriate switching of behavioural states, such as occurs in narcolepsy. These findings explain how various drugs affect sleep and wakefulness, and provide the basis for a wide range of environmental influences to shape wake-sleep cycles into the optimal pattern for survival.},
  number = {7063},
  journal = {Nature},
  author = {Saper, Clifford B. and Scammell, Thomas E. and Lu, Jun},
  year = {2005},
  pages = {1257--1263},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G4LMFKEM/Saper et al. - 2005 - Hypothalamic regulation of sleep and circadian rhy.pdf},
  pmid = {16251950}
}

@article{seugnet_d1_2008,
  title = {D1 {{Receptor Activation}} in the {{Mushroom Bodies Rescues Sleep}}-{{Loss}}-{{Induced Learning Impairments}} in {{Drosophila}}},
  volume = {18},
  issn = {09609822},
  doi = {10.1016/j.cub.2008.07.028},
  abstract = {Background: Extended wakefulness disrupts acquisition of short-term memories in mammals. However, the underlying molecular mechanisms triggered by extended waking and restored by sleep are unknown. Moreover, the neuronal circuits that depend on sleep for optimal learning remain unidentified. Results: Learning was evaluated with aversive phototaxic suppression. In this task, flies learn to avoid light that is paired with an aversive stimulus (quinine-humidity). We demonstrate extensive homology in sleep-deprivation-induced learning impairment between flies and humans. Both 6 hr and 12 hr of sleep deprivation are sufficient to impair learning in Canton-S (Cs) flies. Moreover, learning is impaired at the end of the normal waking day in direct correlation with time spent awake. Mechanistic studies indicate that this task requires intact mushroom bodies (MBs) and requires the dopamine D1-like receptor (dDA1). Importantly, sleep-deprivation-induced learning impairments could be rescued by targeted gene expression of the dDA1 receptor to the MBs. Conclusions: These data provide direct evidence that extended wakefulness disrupts learning in Drosophila. These results demonstrate that it is possible to prevent the effects of sleep deprivation by targeting a single neuronal structure and identify cellular and molecular targets adversely affected by extended waking in a genetically tractable model organism. ?? 2008 Elsevier Ltd. All rights reserved.},
  number = {15},
  journal = {Curr. Biol.},
  author = {Seugnet, Laurent and Suzuki, Yasuko and Vine, Lucy and Gottschalk, Laura and Shaw, Paul J.},
  month = aug,
  year = {2008},
  keywords = {SYSNEURO},
  pages = {1110--1117},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4IW22WM8/Seugnet et al. - 2008 - D1 Receptor Activation in the Mushroom Bodies Resc.pdf},
  pmid = {18674913}
}

@article{liu_wide_2014,
  title = {{{WIDE AWAKE}} Mediates the Circadian Timing of Sleep Onset},
  volume = {82},
  issn = {10974199},
  doi = {10.1016/j.neuron.2014.01.040},
  abstract = {How the circadian clock regulates the timing of sleep is poorly understood. Here, we identify a Drosophila mutant, wide awake (wake), that exhibits a marked delay in sleep onset at dusk. Loss of WAKE in a set of arousal-promoting clock neurons, the large ventrolateral neurons (l-LNvs), impairs sleep onset. WAKE levels cycle, peaking near dusk, and the expression of WAKE in l-LNvs is Clock dependent. Strikingly, Clock and cycle mutants also exhibit a profound delay in sleep onset, which can be rescued by restoring WAKE expression in LNvs. WAKE interacts with the GABAA receptor Resistant to Dieldrin (RDL), upregulating its levels and promoting its localization to the plasma membrane. In wake mutant l-LNvs, GABA sensitivity is decreased and excitability is increased at dusk. We propose that WAKE acts as a clock output molecule specifically for sleep, inhibiting LNvs at dusk to promote the transition from wake to sleep. \textcopyright{} 2014 Elsevier Inc.},
  language = {ENG},
  number = {1},
  journal = {Neuron},
  author = {Liu, Sha and Lamaze, Angelique and Liu, Qili and Tabuchi, Masashi and Yang, Yong and Fowler, Melissa and Bharadwaj, Rajnish and Zhang, Julia and Bedont, Joseph and Blackshaw, Seth and Lloyd, Thomas E and Montell, Craig and Sehgal, Amita and Koh, Kyunghee and Wu, Mark N},
  month = mar,
  year = {2014},
  pages = {151--166},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YYSSVSSD/Liu et al. - 2014 - WIDE AWAKE mediates the circadian timing of sleep .pdf},
  pmid = {24631345}
}

@article{yapici_receptor_2008,
  title = {A Receptor That Mediates the Post-Mating Switch in {{Drosophila}} Reproductive Behaviour},
  volume = {451},
  issn = {0028-0836},
  doi = {10.1038/nature06483},
  abstract = {Mating in many species induces a dramatic switch in female reproductive behaviour. In most insects, this switch is triggered by factors present in the male's seminal fluid. How these factors exert such profound effects in females is unknown. Here we identify a receptor for the Drosophila melanogaster sex peptide (SP, also known as Acp70A), the primary trigger of post-mating responses in this species. Females that lack the sex peptide receptor (SPR, also known as CG16752), either entirely or only in the nervous system, fail to respond to SP and continue to show virgin behaviours even after mating. SPR is expressed in the female's reproductive tract and central nervous system. The behavioural functions of SPR map to the subset of neurons that also express the fruitless gene, a key determinant of sex-specific reproductive behaviour. SPR is highly conserved across insects, opening up the prospect of new strategies to control the reproductive and host-seeking behaviours of agricultural pests and human disease vectors.},
  number = {7174},
  journal = {Nature},
  author = {Yapici, Nilay and Kim, Young-Joon and Ribeiro, Carlos and Dickson, Barry J},
  year = {2008},
  pages = {33--37},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3PUIU7AA/Yapici et al. - 2008 - A receptor that mediates the post-mating switch in.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ICVWJN6N/nature06483.html},
  pmid = {18066048}
}

@article{donlea_foraging_2012,
  title = {Foraging Alters Resilience/Vulnerability to Sleep Disruption and Starvation in {{Drosophila}}},
  volume = {109},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1112623109},
  abstract = {Recent human studies suggest that genetic polymorphisms allow an individual to maintain optimal cognitive functioning during sleep deprivation. If such polymorphisms were not associated with additional costs, selective pressures would allow these alleles to spread through the population such that an evolutionary alternative to sleep would emerge. To determine whether there are indeed costs associated with resiliency to sleep loss, we challenged natural allelic variants of the foraging gene (for) with either sleep deprivation or starvation. Flies with high levels of Protein Kinase G (PKG) (forR) do not display deficits in short-term memory following 12 h of sleep deprivation. However, short-term memory is significantly disrupted when forR flies are starved overnight. In contrast, flies with low levels of PKG (fors, fors2) show substantial deficits in short-term memory following sleep deprivation but retain their ability to learn after 12 h of starvation. We found that forR phenotypes could be largely recapitulated in fors flies by selectively increasing the level of PKG in the $\alpha$/$\beta$ lobes of the mushroom bodies, a structure known to regulate both sleep and memory. Together, these data indicate that whereas the expression of for may appear to provide resilience in one environmental context, it may confer an unexpected vulnerability in other situations. Understanding how these tradeoffs confer resilience or vulnerability to specific environmental challenges may provide additional clues as to why an evolutionary alternative to sleep has not emerged.},
  language = {en},
  number = {7},
  journal = {Proc. Natl. Acad. Sci.},
  author = {Donlea, Jeffrey and Leahy, Averi and Thimgan, Matthew S. and Suzuki, Yasuko and Hughson, Bryon N. and Sokolowski, Marla B. and Shaw, Paul J.},
  month = feb,
  year = {2012},
  keywords = {Animals,Sleep,Drosophila,Feeding behavior,Starvation,Behavior- Animal},
  pages = {2613--2618},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8QXT28PP/Donlea et al. - 2012 - foraging alters resiliencevulnerability to sleep .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S8ISU4E2/2613.html}
}

@article{crocker_identification_2010,
  title = {Identification of a {{Neural Circuit}} That {{Underlies}} the {{Effects}} of {{Octopamine}} on {{Sleep}}:{{Wake Behavior}}},
  volume = {65},
  issn = {08966273},
  doi = {10.1016/j.neuron.2010.01.032},
  abstract = {An understanding of sleep requires the identification of distinct cellular circuits that mediate the action of specific sleep:wake-regulating molecules, but such analysis has been very limited. We identify here a circuit that underlies the wake-promoting effects of octopamine in Drosophila. Using MARCM, we identified the ASM cells in the medial protocerebrum as the wake-promoting octopaminergic cells. We then blocked octopamine signaling in random areas of the fly brain and mapped the postsynaptic effect to insulin-secreting neurons of the pars intercerebralis (PI). These PI neurons show altered potassium channel function as well as an increase in cAMP in response to octopamine, and genetic manipulation of their electrical excitability alters sleep:wake behavior. Effects of octopamine on sleep:wake are mediated by the cAMP-dependent isoform of the OAMB receptor. These studies define the cellular and molecular basis of octopamine action and suggest that the PI is a sleep:wake-regulating neuroendocrine structure like the mammalian hypothalamus. PaperFlick: \{An electronic component is presented\}. \textcopyright{} 2010 Elsevier Inc. All rights reserved.},
  number = {5},
  journal = {Neuron},
  author = {Crocker, Amanda and Shahidullah, Mohammad and Levitan, Irwin B. and Sehgal, Amita},
  year = {2010},
  pages = {670--681},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FR3DJ632/Crocker et al. - 2010 - Identification of a Neural Circuit that Underlies .pdf},
  pmid = {20223202}
}

@article{foltenyi_activation_2007,
  title = {Activation of {{EGFR}} and {{ERK}} by Rhomboid Signaling Regulates the Consolidation and Maintenance of Sleep in {{Drosophila}}},
  volume = {10},
  issn = {1097-6256},
  doi = {10.1038/nn1957},
  abstract = {Epidermal growth factor receptor (EGFR) signaling in the mammalian hypothalamus is important in the circadian regulation of activity. We have examined the role of this pathway in the regulation of sleep in Drosophila melanogaster. Our results demonstrate that rhomboid (Rho)- and Star-mediated activation of EGFR and ERK signaling increases sleep in a dose-dependent manner, and that blockade of rhomboid (rho) expression in the nervous system decreases sleep. The requirement of rho for sleep localized to the pars intercerebralis, a part of the fly brain that is developmentally and functionally analogous to the hypothalamus in vertebrates. These results suggest that sleep and its regulation by EGFR signaling may be ancestral to insects and mammals.},
  number = {9},
  journal = {Nat. Neurosci.},
  author = {Foltenyi, Krisztina and Greenspan, Ralph J and Newport, John W},
  month = sep,
  year = {2007},
  pages = {1160--1167},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UXEXW72M/Foltenyi et al. - 2007 - Activation of EGFR and ERK by rhomboid signaling r.pdf},
  pmid = {17694052}
}

@article{pitman_dynamic_2006,
  title = {A Dynamic Role for the Mushroom Bodies in Promoting Sleep in {{Drosophila}}},
  volume = {441},
  issn = {0028-0836},
  doi = {10.1038/nature04739},
  abstract = {The fruitfly, Drosophila melanogaster, exhibits many of the cardinal features of sleep, yet little is known about the neural circuits governing its sleep. Here we have performed a screen of GAL4 lines expressing a temperature-sensitive synaptic blocker shibire(ts1) (ref. 2) in a range of discrete neural circuits, and assayed the amount of sleep at different temperatures. We identified three short-sleep lines at the restrictive temperature with shared expression in the mushroom bodies, a neural locus central to learning and memory. Chemical ablation of the mushroom bodies also resulted in reduced sleep. These studies highlight a central role for the mushroom bodies in sleep regulation.},
  language = {en},
  number = {7094},
  journal = {Nature},
  author = {Pitman, Jena L. and McGill, Jermaine J. and Keegan, Kevin P. and Allada, Ravi},
  month = jun,
  year = {2006},
  pages = {753--756},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UWJ8IU4R/Pitman et al. - 2006 - A dynamic role for the mushroom bodies in promotin.pdf},
  pmid = {16760979}
}

@article{campbell_animal_1984,
  title = {Animal Sleep: {{A}} Review of Sleep Duration across Phylogeny},
  volume = {8},
  issn = {01497634},
  shorttitle = {Animal Sleep},
  doi = {10.1016/0149-7634(84)90054-X},
  abstract = {Sleep duration and placement within the twenty-four hour day have been primary indices utilized in the examination of sleep function. It is of value, therefore, to evaluate these variables in a wide range of animal species. The present paper examines the literature concerning sleep duration in over 150 animal species, including invertebrates, fish, amphibians, reptiles, birds, and 14 orders of mammals. We first present annotations of almost 200 studies, including number of animals used, photoperiod employed, sleep duration per twenty-four hours and placement of sleep period within the nychthemeron. Both behavioral and electrographic studies are reviewed, as are laboratory and field studies. These data are subsequently presented in a table with representative literature citations for each species. Following the table, a brief discussion is presented concerning some methodological issues which may affect the measurement of sleep duration and some suggestions are made for future examination of sleep duration. ?? 1984.},
  number = {3},
  journal = {Neurosci. Biobehav. Rev.},
  author = {Campbell, Scott S. and Tobler, Irene},
  year = {1984},
  keywords = {Sleep duration,Animals,Sleep,Behavior,sleep duration,EEG,Phylogeny,Sleep placement},
  pages = {269--300},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8E27FF3U/Campbell and Tobler - 1984 - Animal sleep A review of sleep duration across ph.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9W6VLIJF/014976348490054X.html},
  pmid = {6504414}
}

@article{rechtschaffen_sleep_1995,
  title = {Sleep Deprivation in the Rat by the Disk-over-Water Method},
  volume = {69},
  issn = {01664328},
  doi = {10.1016/0166-4328(95)00020-T},
  abstract = {Chronic sleep deprivation may be required to reveal the most serious physiological consequences of sleep loss, but it usually requires strong stimulation which can obscure the interpretation of effects. The disk-over-water method permits chronic sleep deprivation of rats with gentle physical stimulation that can be equally applied to yoked control rats. A series of studies with this method has revealed little or no pathology in the control rats. The deprived rats show a reliable syndrome that includes temperature changes (which vary with the sleep stages that are lost); heat seeking behavior; increased food intake; weight loss; increased metabolic rate; increased plasma norepinephrine; decreased plasma thyroxine; an increased triiodothyronine-thyroxine ratio; and an increase of an enzyme which mediates thermogenesis by brown adipose tissue. The temperature changes are attributable to excessive heat loss and an elevated thermoregulatory setpoint, both of which increase thermoregulatory load, and the other changes are interpretable as responses to this increased load. This pattern indicates that sleep serves a thermoregulatory function in the rat. The sleep deprived rats also show stereotypic ulcerative and hyperkeratotic lesions localized to the tail and plantar surfaces of the paws, and they die within a matter of weeks; the mediation of these changes is unresolved. ?? 1995.},
  number = {1-2},
  journal = {Behav. Brain Res.},
  author = {Rechtschaffen, Allan and Bergmann, Bernard M},
  year = {1995},
  keywords = {Sleep,Sleep Deprivation,Paradoxical sleep,thermoregulation,Sleep rebound,Sleep function,Sleep deprivation,Paradoxical Sleep; Thermoregulation},
  pages = {55--63},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QE36FZAZ/Rechtschaffen and Bergmann - 1995 - Sleep deprivation in the rat by the disk-over-wate.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QWWEDP57/016643289500020T.html},
  pmid = {7546318}
}

@article{ueno_identification_2012,
  title = {Identification of a Dopamine Pathway That Regulates Sleep and Arousal in {{Drosophila}}},
  volume = {15},
  issn = {1097-6256},
  doi = {10.1038/nn.3238},
  abstract = {Sleep is required to maintain physiological functions, including memory, and is regulated by monoamines across species. Enhancement of dopamine signals by a mutation in the dopamine transporter (DAT) decreases sleep, but the underlying dopamine circuit responsible for this remains unknown. We found that the D1 dopamine receptor (DA1) in the dorsal fan-shaped body (dFSB) mediates the arousal effect of dopamine in Drosophila. The short sleep phenotype of the DAT mutant was completely rescued by an additional mutation in the DA1 (also known as DopR) gene, but expression of wild-type DA1 in the dFSB restored the short sleep phenotype. We found anatomical and physiological connections between dopamine neurons and the dFSB neuron. Finally, we used mosaic analysis with a repressive marker and found that a single dopamine neuron projecting to the FSB activated arousal. These results suggest that a local dopamine pathway regulates sleep.},
  language = {en},
  number = {11},
  journal = {Nat. Neurosci.},
  author = {Ueno, Taro and Tomita, Jun and Tanimoto, Hiromu and Endo, Keita and Ito, Kei and Kume, Shoen and Kume, Kazuhiko},
  month = nov,
  year = {2012},
  pages = {1516--1523},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H9KRQT4U/Ueno et al. - 2012 - Identification of a dopamine pathway that regulate.pdf}
}

@article{klein_sensory_2015,
  title = {Sensory Determinants of Behavioral Dynamics in {{Drosophila}} Thermotaxis},
  volume = {112},
  issn = {0027-8424},
  doi = {10.1073/pnas.1416212112},
  abstract = {Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients toward preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations. In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis.},
  number = {2},
  journal = {Proc. Natl. Acad. Sci.},
  author = {Klein, Mason and Afonso, Bruno and Vonner, Ashley J. and {Hernandez-Nunez}, Luis and Berck, Matthew and Tabone, Christopher J. and Kane, Elizabeth A. and Pieribone, Vincent A. and Nitabach, Michael N. and Cardona, Albert and Zlatic, Marta and Sprecher, Simon G. and Gershow, Marc and Garrity, Paul A. and Samuel, Aravinthan D. T.},
  month = jan,
  year = {2015},
  keywords = {Behavior; Animal,Animals; Genetically Modified,temperature,Animals,Calcium Signaling,Drosophila melanogaster,Larva,Locomotion,Optogenetics,Temperature,Ganglia,calcium imaging,navigation,reverse correlation,voltage imaging,Thermoreceptors,Thermosensing},
  pages = {E220--E229},
  pmid = {25550513}
}

@article{liu_two_2012,
  title = {Two Dopaminergic Neurons Signal to the Dorsal Fan-Shaped Body to Promote Wakefulness in {{Drosophila}}},
  volume = {22},
  issn = {09609822},
  doi = {10.1016/j.cub.2012.09.008},
  abstract = {BACKGROUND: The neuronal circuitry underlying sleep is poorly understood. Although dopamine (DA) is thought to play a key role in sleep/wake regulation, the identities of the individual DA neurons and their downstream targets required for this process are unknown. RESULTS: Here, we identify a DA neuron in each PPL1 cluster that promotes wakefulness in Drosophila. Imaging data suggest that the activity of these neurons is increased during wakefulness, consistent with a role in promoting arousal. Strikingly, these neurons project to the dorsal fan-shaped body, which has previously been shown to promote sleep. The reduced sleep caused by activation of DA neurons can be blocked by loss of DopR, and restoration of DopR expression in the fan-shaped body can rescue the wake-promoting effects of DA in a DopR mutant background. CONCLUSIONS: These experiments define a novel arousal circuit at the single-cell level. Because the dorsal fan-shaped body promotes sleep, these data provide a key link between wake and sleep circuits. Furthermore, these findings suggest that inhibition of sleep centers via monoaminergic signaling is an evolutionarily conserved mechanism to promote arousal.},
  language = {eng},
  number = {22},
  journal = {Curr. Biol.},
  author = {Liu, Qili and Liu, Sha and Kodama, Lay and Driscoll, Maria R. R. and Wu, Mark N. N.},
  month = nov,
  year = {2012},
  keywords = {Animals,Sleep,Drosophila,Signal Transduction,Drosophila Proteins,Gene Expression Regulation,Dopaminergic Neurons,Wakefulness,Central Nervous System},
  pages = {2114--2123},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FYKZVZN3/Liu et al. - 2012 - Two dopaminergic neurons signal to the dorsal fan-.pdf},
  pmid = {23022067}
}

@article{bushey_sleep_2011,
  title = {Sleep and {{Synaptic Homeostasis}}: {{Structural Evidence}} in {{Drosophila}}},
  volume = {332},
  issn = {0036-8075},
  shorttitle = {Sleep and {{Synaptic Homeostasis}}},
  doi = {10.1126/science.1202839},
  abstract = {The functions of sleep remain elusive, but a strong link exists between sleep need and neuronal plasticity. We tested the hypothesis that plastic processes during wake lead to a net increase in synaptic strength and sleep is necessary for synaptic renormalization. We found that, in three Drosophila neuronal circuits, synapse size or number increases after a few hours of wake and decreases only if flies are allowed to sleep. A richer wake experience resulted in both larger synaptic growth and greater sleep need. Finally, we demonstrate that the gene Fmr1 (fragile X mental retardation 1) plays an important role in sleep-dependent synaptic renormalization.},
  language = {en},
  number = {6037},
  journal = {Science (80-. ).},
  author = {Bushey, Daniel and Tononi, Giulio and Cirelli, Chiara},
  month = jun,
  year = {2011},
  pages = {1576--1581},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J9GCQGCL/Bushey et al. - 2011 - Sleep and Synaptic Homeostasis Structural Evidenc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Y26SG2E7/Bushey et al. - 2011 - Sleep and Synaptic Homeostasis Structural Evidenc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H9UCH6DS/1576.html},
  pmid = {21700878}
}

@article{vorster_characterization_2014,
  title = {Characterization of {{Sleep}} in {{Aplysia}} Californica},
  issn = {0161-8105},
  doi = {10.5665/sleep.3992},
  abstract = {STUDY OBJECTIVE: To characterize sleep in the marine mollusk, Aplysia californica.\$$\backslash$backslash\$n\$$\backslash$backslash\$nDESIGN: Animal behavior and activity were assessed using video recordings to measure activity, resting posture, resting place preference, and behavior after rest deprivation. Latencies for behavioral responses were measured for appetitive and aversive stimuli for animals in the wake and rest states.\$$\backslash$backslash\$n\$$\backslash$backslash\$nSETTING: Circadian research laboratory for Aplysia.\$$\backslash$backslash\$n\$$\backslash$backslash\$nPATIENTS OR PARTICIPANTS: A. californica from the Pacific Ocean.\$$\backslash$backslash\$n\$$\backslash$backslash\$nINTERVENTIONS: N/A.\$$\backslash$backslash\$n\$$\backslash$backslash\$nMEASUREMENTS AND RESULTS: Aplysia rest almost exclusively during the night in a semi-contracted body position with preferential resting locations in the upper corners of their tank. Resting animals demonstrate longer latencies in head orientation and biting in response to a seaweed stimulus and less frequent escape response steps following an aversive salt stimulus applied to the tail compared to awake animals at the same time point. Aplysia exhibit rebound rest the day following rest deprivation during the night, but not after similar handling stimulation during the day.\$$\backslash$backslash\$n\$$\backslash$backslash\$nCONCLUSIONS: Resting behavior in Aplysia fulfills all invertebrate characteristics of sleep including: (1) a specific sleep body posture, (2) preferred resting location, (3) reversible behavioral quiescence, (4) elevated arousal thresholds for sensory stimuli during sleep, and (5) compensatory sleep rebound after sleep deprivation.},
  language = {en},
  journal = {Sleep},
  author = {Vorster, Albrecht P.A. and Krishnan, Harini C. and Cirelli, Chiara and Lyons, Lisa C.},
  month = sep,
  year = {2014},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TV55UB74/Vorster et al. - 2014 - Characterization of Sleep in Aplysia californica.pdf},
  pmid = {25142567}
}

@article{ishimoto_factors_2012,
  title = {Factors That Differentially Affect Daytime and Nighttime Sleep in {{Drosophila}} Melanogaster},
  volume = {FEB},
  issn = {16642295},
  doi = {10.3389/fneur.2012.00024},
  abstract = {Rest in the fruit fly Drosophila melanogaster has key characteristics of mammalian sleep and is thus considered as a fly version of sleep. Drosophila sleep has been studied extensively, with the aim of gaining fundamental insights into the evolutionarily conserved functions of sleep as well as the mechanisms that regulate it. An interesting question that has not yet been addressed is whether fly sleep can be classified into distinct sleep types, each having particular biological roles - like rapid eye movement (REM) and non-REM sleep in birds and mammals. Typically, Drosophila sleep displays a bimodal pattern, consisting of distinct daytime and nighttime components. Notably, daytime and nighttime sleep differ with respect to several qualities, such as sleep-bout lengths and arousal thresholds. In this short review, we describe several genetic and environmental factors that differentially affect daytime and nighttime sleep, highlighting the observations suggesting the notion that these temporally distinct components of Drosophila sleep may have unique biological functions and be regulated by different homeostatic regulatory mechanisms.},
  journal = {Front. Neurol.},
  author = {Ishimoto, Hiroshi and Lark, Arianna and Kitamoto, Toshihiro},
  year = {2012},
  keywords = {Drosophila melanogaster,Angiotensin-converting enzyme-related gene,Daytime and nighttime sleep,Ecdysone,Sex peptide,Sleep stage,Acer,DARC,daytime and nighttime sleep,Fabp,sex peptide,sleep stage},
  pages = {1--5},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SKB7GU2Y/Ishimoto et al. - 2012 - Factors that Differentially Affect Daytime and Nig.pdf},
  pmid = {22375135}
}

@article{cirelli_reduced_2005,
  title = {Reduced Sleep in {{Drosophila Shaker}} Mutants},
  volume = {434},
  issn = {0028-0836},
  doi = {10.1038/nature03486},
  abstract = {Most of us sleep 7\textendash{}8 h per night, and if we are deprived of sleep our performance suffers greatly; however, a few do well with just 3\textendash{}4 h of sleep\textemdash{}a trait that seems to run in families. Determining which genes underlie this phenotype could shed light on the mechanisms and functions of sleep. To do so, we performed mutagenesis in Drosophila melanogaster, because flies also sleep for many hours and, when sleep deprived, show sleep rebound and performance impairments. By screening 9,000 mutant lines, we found minisleep (mns), a line that sleeps for one-third of the wild-type amount. We show that mns flies perform normally in a number of tasks, have preserved sleep homeostasis, but are not impaired by sleep deprivation. We then show that mns flies carry a point mutation in a conserved domain of the Shaker gene. Moreover, after crossing out genetic modifiers accumulated over many generations, other Shaker alleles also become short sleepers and fail to complement the mns phenotype. Finally, we show that short-sleeping Shaker flies have a reduced lifespan. Shaker, which encodes a voltage-dependent potassium channel controlling membrane repolarization and transmitter release, may thus regulate sleep need or efficiency.},
  language = {en},
  number = {7037},
  journal = {Nature},
  author = {Cirelli, Chiara and Bushey, Daniel and Hill, Sean and Huber, Reto and Kreber, Robert and Ganetzky, Barry and Tononi, Giulio},
  month = apr,
  year = {2005},
  keywords = {Cancer,Biology,Evolutionary Biology,Science,Science Policy,Signal Transduction,neuroscience,Genetics,RNA,evolution,DNA,computational biology,immunology,Development,Genomics,Cell Cycle,Neurobiology,molecular biology,Ecology,cell signalling,developmental biology,Biochemistry,Nature,astronomy,astrophysics,bioinformatics,biotechnology,climate change,drug discovery,earth science,environmental science,functional genomics,geophysics,interdisciplinary science,life,marine biology,materials science,medical research,medicine,metabolomics,molecular interactions,nanotechnology,palaeobiology,pharmacology,physics,proteomics,quantum physics,science news,structural biology,systems biology,transcriptomics},
  pages = {1087--1092},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G6AEK5G8/Cirelli et al. - 2005 - Reduced sleep in Drosophila Shaker mutants.pdf}
}

@article{donlea_neuronal_2014,
  title = {Neuronal Machinery of Sleep Homeostasis in {{Drosophila}}},
  volume = {81},
  issn = {08966273},
  doi = {10.1016/j.neuron.2013.12.013},
  abstract = {Sleep is under homeostatic control, but the mechanisms that sense sleep need and correct sleep deficits remain unknown. Here, we report that sleep-promoting neurons with projections to the dorsal fan-shaped body (FB) form the output arm of Drosophila's sleep homeostat. Homeostatic sleep control requires the Rho-GTPase-activating protein encoded by the crossveinless-c (cv-c) gene in order to transduce sleep pressure into increased electrical excitability of dorsal FB neurons. cv-c mutants exhibit decreased sleep time, diminished sleep rebound, and memory deficits comparable to those after sleep loss. Targeted ablation and rescue of Cv-c in sleep-control neurons of the dorsal FB impair and restore, respectively, normal sleep patterns. Sleep deprivation increases the excitability of dorsal FB neurons, but this homeostatic adjustment is disrupted in short-sleeping cv-c mutants. Sleep pressure thus shifts the input-output function of sleep-promoting neurons toward heightened activity by modulating ion channel function in a mechanism dependent on Cv-c. ?? 2014 The Authors.},
  number = {4},
  journal = {Neuron},
  author = {Donlea, Jeffrey M and Pimentel, Diogo and Miesenb\"ock, Gero},
  month = feb,
  year = {2014},
  pages = {860--872},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J23FI6TP/Donlea et al. - 2014 - Neuronal machinery of sleep homeostasis in Drosoph.pdf},
  pmid = {24559676}
}

@article{stavropoulos_insomniac_2011,
  title = {Insomniac and Cullin-3 Regulate Sleep and Wakefulness in Drosophila},
  volume = {72},
  issn = {08966273},
  doi = {10.1016/j.neuron.2011.12.003},
  abstract = {In a forward genetic screen in Drosophila, we have isolated insomniac, a mutant that severely reduces the duration and consolidation of sleep. Anatomically restricted genetic manipulations indicate that insomniac functions within neurons to regulate sleep. insomniac expression does not oscillate in a circadian manner, and conversely, the circadian clock is intact in insomniac mutants, suggesting that insomniac regulates sleep by pathways distinct from the circadian clock. The protein encoded by insomniac is a member of the BTB/POZ superfamily, which includes many proteins that function as adaptors for the Cullin-3 (Cul3) ubiquitin ligase complex. We show that Insomniac can physically associate with Cul3, and that reduction of Cul3 activity in neurons recapitulates the insomniac phenotype. The extensive evolutionary conservation of insomniac and Cul3 suggests that protein degradation pathways may have a general role in governing the sleep and wakefulness of animals. ?? 2011 Elsevier Inc.},
  number = {6},
  journal = {Neuron},
  author = {Stavropoulos, Nicholas and Young, Michael W},
  month = dec,
  year = {2011},
  pages = {964--976},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5GC7985Q/Stavropoulos and Young - 2011 - insomniac and Cullin-3 Regulate Sleep and Wakefuln.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TS6JZAF9/Stavropoulos and Young - 2011 - Insomniac and cullin-3 regulate sleep and wakefuln.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PZA7S4VA/S0896627311010452.html},
  pmid = {22196332}
}

@article{cirelli_sleep_2005,
  title = {Sleep and Wakefulness Modulate Gene Expression in {{Drosophila}}},
  volume = {94},
  issn = {00223042},
  doi = {10.1111/j.1471-4159.2005.03291.x},
  abstract = {In the mammalian brain, sleep and wakefulness are associated with widespread changes in gene expression. Sleep in fruit flies shares many features with mammalian sleep, but it is currently unknown to what extent behavioral states affect gene expression in Drosophila. To find out, we performed a comprehensive microarray analysis of gene expression in spontaneously awake, sleep-deprived and sleeping flies. Fly heads were collected at 4 am, after 8 h of spontaneous sleep or sleep deprivation, and at 4 pm, after 8 h of spontaneous wakefulness. As in rats, we found that behavioral state and time of day affect Drosophila gene expression to a comparable extent. As in rats, transcripts with higher expression in wakefulness and in sleep belong to different functional categories, and in several cases these groups overlap with those previously identified in rats. Wakefulness-related genes code for transcription factors and for proteins involved in the stress response, immune response, glutamatergic transmission, and carbohydrate metabolism. Sleep-related transcripts include the glial gene anachronism and several genes involved in lipid metabolism. Finally, the expression of many wakefulness-related and sleep-related Drosophila transcripts is also modulated by the time of day, suggesting an interaction at the molecular level between circadian and homeostatic mechanism of sleep regulation.},
  language = {en},
  number = {5},
  journal = {J. Neurochem.},
  author = {Cirelli, Chiara and LaVaute, Timothy M. and Tononi, Giulio},
  month = sep,
  year = {2005},
  keywords = {Brain,Sleep Deprivation,Fruit fly,microarray},
  pages = {1411--1419},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XFJPJGI2/Cirelli et al. - 2005 - Sleep and wakefulness modulate gene expression in .pdf},
  pmid = {16001966}
}

@article{grima_morning_2004,
  title = {Morning and Evening Peaks of Activity Rely on Different Clock Neurons of the {{Drosophila}} Brain},
  volume = {431},
  issn = {0028-0836},
  doi = {10.1038/nature02935},
  abstract = {In Drosophila, a 'clock' situated in the brain controls circadian rhythms of locomotor activity. This clock relies on several groups of neurons that express the Period (PER) protein, including the ventral lateral neurons (LN(v)s), which express the Pigment-dispersing factor (PDF) neuropeptide, and the PDF-negative dorsal lateral neurons (LN(d)s). In normal cycles of day and night, adult flies exhibit morning and evening peaks of activity; however, the contribution of the different clock neurons to the rest-activity pattern remains unknown. Here, we have used targeted expression of PER to restore the clock function of specific subsets of lateral neurons in arrhythmic per(0) mutant flies. We show that PER expression restricted to the LN(v)s only restores the morning activity, whereas expression of PER in both the LN(v)s and LN(d)s also restores the evening activity. This provides the first neuronal bases for 'morning' and 'evening' oscillators in the Drosophila brain. Furthermore, we show that the LN(v)s alone can generate 24 h activity rhythms in constant darkness, indicating that the morning oscillator is sufficient to drive the circadian system.},
  number = {7010},
  journal = {Nature},
  author = {Grima, Brigitte and Ch\'elot, Elisabeth and Xia, Ruohan and Rouyer, Fran{\c c}ois},
  month = oct,
  year = {2004},
  pages = {869--873},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8NKAB4J8/Grima et al. - 2004 - Morning and evening peaks of activity rely on diff.pdf},
  pmid = {15483616}
}

@article{tobler_is_1995,
  title = {Is Sleep Fundamentally Different between Mammalian Species?},
  volume = {69},
  issn = {01664328},
  doi = {10.1016/0166-4328(95)00025-O},
  abstract = {An avenue to investigate the functions of sleep is the comparison of sleep in different species, particularly in closely related ones and in species with extreme specializations. The features which are usually investigated are the occurrence of both sleep stages non-REM sleep and REM sleep, their amount per 24 h, the duration of the non-REM-REM sleep cycle and the daily distribution of sleep relative to the light-dark cycle of the environment. Recently also sleep homeostasis has been included, because it is now well established that mammalian species can compensate for sleep loss both by an increase in sleep duration as well as by intensifying non-REM sleep. The occurrence of EEG slow-wave activity has served as a measure for sleep intensity. The capacity to sleep more intensely enables animals to react more flexibly to sleep loss. The comparison of mammalian species has revealed striking similarities in the way sleep is regulated which indicates common underlying mechanisms. ?? 1995.},
  language = {eng},
  number = {1-2},
  journal = {Behav. Brain Res.},
  author = {Tobler, Irene},
  month = aug,
  year = {1995},
  keywords = {Humans,Animals,Sleep,Species Specificity,Mammals,Sleep homeostasis,Homeostasis,Sleep Deprivation,Electroencephalogram,Animal sleep,Sleep deprivation},
  pages = {35--41},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B7YUTCWG/Tobler - 1995 - Is sleep fundamentally different between mammalian.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P73K3U96/016643289500025O.html},
  pmid = {7546316}
}

@article{kuo_acute_2014,
  title = {Acute {{Sleep Deprivation Enhances Post}}-{{Infection Sleep}} and {{Promotes Survival}} during {{Bacterial Infection}} in {{Drosophila}}},
  volume = {37},
  issn = {0161-8105},
  doi = {10.5665/sleep.3648},
  abstract = {STUDY OBJECTIVES: Sleep is known to increase as an acute response to infection. However, the function of this behavioral response in host defense is not well understood. To address this problem, we evaluated the effect of acute sleep deprivation on post-infection sleep and immune function in Drosophila.\$$\backslash$backslash\$n\$$\backslash$backslash\$nSETTING: Laboratory.\$$\backslash$backslash\$n\$$\backslash$backslash\$nPARTICIPANTS: Drosophila melanogaster.\$$\backslash$backslash\$n\$$\backslash$backslash\$nMETHODS AND RESULTS: Flies were subjected to sleep deprivation before (early DEP) or after (late DEP) bacterial infection. Relative to a non-deprived control, flies subjected to early DEP had enhanced sleep after infection as well as increased bacterial clearance and survival outcome. Flies subjected to late DEP experienced enhanced sleep following the deprivation period, and showed a modest improvement in survival outcome. Continuous DEP (early and late DEP) throughout infection also enhanced sleep later during infection and improved survival. However, improved survival in flies subjected to late or continuous DEP did not occur until after flies had experienced sleep. During infection, both early and late DEP enhanced NF$\kappa$B transcriptional activity as measured by a luciferase reporter ($\kappa$B-luc) in living flies. Early DEP also increased NF$\kappa$B activity prior to infection. Flies that were deficient in expression of either the Relish or Dif NF$\kappa$B transcription factors showed normal responses to early DEP. However, the effect of early DEP on post-infection sleep and survival was abolished in double mutants, which indicates that Relish and Dif have redundant roles in this process.\$$\backslash$backslash\$n\$$\backslash$backslash\$nCONCLUSIONS: Acute sleep deprivation elevated NF$\kappa$B-dependent activity, increased post-infection sleep, and improved survival during bacterial infection.\$$\backslash$backslash\$n\$$\backslash$backslash\$nCITATION: Kuo TH, Williams JA. Acute sleep deprivation enhances post-infection sleep and promotes survival during bacterial infection in Drosophila. SLEEP 2014;37(5):859-869.},
  number = {5},
  journal = {Sleep},
  author = {Kuo, Tzu-Hsing and Williams, Julie A.},
  month = may,
  year = {2014},
  keywords = {Drosophila,Sleep Deprivation,NFkappaB,bacterial infection,immune response},
  pages = {859--869},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LR8CF6CP/Kuo and Williams - 2014 - Acute Sleep Deprivation Enhances Post-Infection Sl.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J8CIVCBZ/2416811.html},
  pmid = {24790264}
}

@article{schmidt_energy_2014,
  title = {The Energy Allocation Function of Sleep: {{A}} Unifying Theory of Sleep, Torpor, and Continuous Wakefulness},
  volume = {47},
  issn = {18737528},
  doi = {10.1016/j.neubiorev.2014.08.001},
  abstract = {The energy allocation (EA) model defines behavioral strategies that optimize the temporal utilization of energy to maximize reproductive success. This model proposes that all species of the animal kingdom share a universal sleep function that shunts waking energy utilization toward sleep-dependent biological investment. For endotherms, REM sleep evolved to enhance energy appropriation for somatic and CNS-related processes by eliminating thermoregulatory defenses and skeletal muscle tone. Alternating REM with NREM sleep conserves energy by decreasing the need for core body temperature defense. Three EA phenotypes are proposed: sleep-wake cycling, torpor, and continuous (or predominant) wakefulness. Each phenotype carries inherent costs and benefits. Sleep-wake cycling downregulates specific biological processes in waking and upregulates them in sleep, thereby decreasing energy demands imposed by wakefulness, reducing cellular infrastructure requirements, and resulting in overall energy conservation. Torpor achieves the greatest energy savings, but critical biological operations are compromised. Continuous wakefulness maximizes niche exploitation, but endures the greatest energy demands. The EA model advances a new construct for understanding sleep-wake organization in ontogenetic and phylogenetic domains. \textcopyright{} 2014 The Authors.},
  journal = {Neurosci. Biobehav. Rev.},
  author = {Schmidt, Markus H.},
  month = nov,
  year = {2014},
  keywords = {Sleep homeostasis,Sleep Deprivation,Hibernation,torpor,thermoregulation,REM sleep,Sleep function,Energy allocation,Life history theory,NREM sleep,Sleep deprivation,Thermoregulation,Torpor},
  pages = {122--153},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NZPRM48D/Schmidt - 2014 - The energy allocation function of sleep A unifyin.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K7ZWBJ2W/S0149763414001997.html},
  pmid = {25117535}
}

@article{yamazaki_high_2012,
  title = {High Calorie Diet Augments Age-Associats Sleep Impairment in {{Drosophila}}},
  volume = {417},
  issn = {0006291X},
  doi = {10.1016/j.bbrc.2011.12.041},
  number = {2},
  journal = {Biochem. Biophys. Res. Commun.},
  author = {Yamazaki, Masako and Tomita, Jun and Takahama, Kazuhiro and Ueno, Taro and Mitsuyoshi, Madoka and Sakamoto, Erina and Kume, Shoen and Kume, Kazuhiko},
  month = jan,
  year = {2012},
  keywords = {Aging,Sleep,Dopamine,Locomotor activity,Diet},
  pages = {812--816},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FXMIXMCS/Yamazaki et al. - 2012 - High calorie diet augments age-associats sleep imp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DV6WPAL3/S0006291X11022509.html}
}

@article{agosto_modulation_2008,
  title = {Modulation of {{GABAA}} Receptor Desensitization Uncouples Sleep Onset and Maintenance in {{Drosophila}}},
  volume = {11},
  issn = {1097-6256},
  doi = {10.1038/nn2046},
  abstract = {Many lines of evidence indicate that GABA and GABA(A) receptors make important contributions to human sleep regulation. Pharmacological manipulation of these receptors has differential effects on sleep onset and sleep maintenance insomnia. Here we show that sleep is regulated by GABA in Drosophila and that a mutant GABA(A) receptor, Rdl(A302S), specifically decreases sleep latency. The drug carbamazepine (CBZ) has the opposite effect on sleep; it increases sleep latency as well as decreasing sleep. Behavioral and physiological experiments indicated that Rdl(A302S) mutant flies are resistant to the effects of CBZ on sleep latency and that mutant RDL(A302S) channels are resistant to the effects of CBZ on desensitization, respectively. These results suggest that this biophysical property of the channel, specifically channel desensitization, underlies the regulation of sleep latency in flies. These experiments uncouple the regulation of sleep latency from that of sleep duration and suggest that the kinetics of GABA(A) receptor signaling dictate sleep latency.},
  number = {3},
  journal = {Nat. Neurosci.},
  author = {Agosto, Jose and Choi, James C and Parisky, Katherine M and Stilwell, Geoffrey and Rosbash, Michael and Griffith, Leslie C},
  month = mar,
  year = {2008},
  pages = {354--359},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GKWC2YR6/Agosto et al. - 2008 - Modulation of GABAA receptor desensitization uncou.pdf},
  pmid = {18223647}
}

@article{gilestro_widespread_2009,
  title = {Widespread {{Changes}} in {{Synaptic Markers}} as a {{Function}} of {{Sleep}} and {{Wakefulness}} in {{Drosophila}}},
  volume = {324},
  issn = {0036-8075},
  doi = {10.1126/science.1166673},
  abstract = {Sleep is universal, strictly regulated, and necessary for cognition. Why this is so remains a mystery, although recent work suggests that sleep, memory, and plasticity are linked. However, little is known about how wakefulness and sleep affect synapses. Using Western blots and confocal microscopy in Drosophila, we found that protein levels of key components of central synapses were high after waking and low after sleep. These changes were related to behavioral state rather than time of day and occurred in all major areas of the Drosophila brain. The decrease of synaptic markers during sleep was progressive, and sleep was necessary for their decline. Thus, sleep may be involved in maintaining synaptic homeostasis altered by waking activities.},
  language = {en},
  number = {5923},
  journal = {Science (80-. ).},
  author = {Gilestro, Giorgio F. and Tononi, Giulio and Cirelli, Chiara},
  month = apr,
  year = {2009},
  pages = {109--112},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WM68B8DW/Gilestro et al. - 2009 - Widespread Changes in Synaptic Markers as a Functi.pdf},
  pmid = {19342593}
}

@article{andretic_dopaminergic_2005,
  title = {Dopaminergic Modulation of Arousal in {{Drosophila}}},
  volume = {15},
  issn = {09609822},
  doi = {10.1016/j.cub.2005.05.025},
  abstract = {Background: Arousal levels in the brain set thresholds for behavior, from simple to complex. The mechanistic underpinnings of the various phenomena comprising arousal, however, are still poorly understood. Drosophila behaviors have been studied that span different levels of arousal, from sleep to visual perception to psychostimulant responses. Results: We have investigated neurobiological mechanisms of arousal in the Drosophila brain by a combined behavioral, genetic, pharmacological, and electrophysiological approach. Administration of methamphetamine (METH) suppresses sleep and promotes active wakefulness, whereas an inhibitor of dopamine synthesis promotes sleep. METH affects courtship behavior by increasing sexual arousal while decreasing successful sexual performance. Electrophysiological recordings from the medial protocerebrum of wild-type flies showed that METH ingestion has rapid and detrimental effects on a brain response associated with perception of visual stimuli. Recordings in genetically manipulated animals show that dopaminergic transmission is required for these responses and that visual-processing deficits caused by attenuated dopaminergic transmission can be rescued by METH. Conclusions: We show that changes in dopamine levels differentially affect arousal for behaviors of varying complexity. Complex behaviors, such as visual perception, degenerate when dopamine levels are either too high or too low, in accordance with the inverted-U hypothesis of dopamine action in the mammalian brain. Simpler behaviors, such as sleep and locomotion, show graded responses that follow changes in dopamine level. ??2005 Elsevier Ltd All rights reserved.},
  language = {eng},
  number = {13},
  journal = {Curr. Biol.},
  author = {Andretic, Rozi and Van Swinderen, Bruno and Greenspan, Ralph J.},
  month = jul,
  year = {2005},
  keywords = {Brain,Arousal,Visual Perception,Animals,Electrophysiology,Sleep,Drosophila,Animals- Genetically Modified,Drosophila Proteins,Dopamine,Mutation,Sexual Behavior- Animal,Dopa Decarboxylase,Dose-Response Relationship- Drug,Dynamins,Methamphetamine},
  pages = {1165--1175},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QYITBHGS/Andretic et al. - 2005 - Dopaminergic modulation of arousal in Drosophila.pdf},
  pmid = {16005288}
}

@article{kume_dopamine_2005,
  title = {Dopamine {{Is}} a {{Regulator}} of {{Arousal}} in the {{Fruit Fly}}},
  volume = {25},
  issn = {0270-6474},
  doi = {10.1523/JNEUROSCI.2048-05.2005},
  abstract = {Sleep and arousal are known to be regulated by both homeostatic and circadian processes, but the underlying molecular mechanisms are not well understood. It has been reported that the Drosophila rest/activity cycle has features in common with the mammalian sleep/wake cycle, and it is expected that use of the fly genetic model will facilitate a molecular understanding of sleep and arousal. Here, we report the phenotypic characterization of a Drosophila rest/activity mutant known as fumin (fmn). We show that fmn mutants have abnormally high levels of activity and reduced rest (sleep); genetic mapping, molecular analyses, and phenotypic rescue experiments demonstrate that these phenotypes result from mutation of the Drosophila dopamine transporter gene. Consistent with the rest phenotype, fmn mutants show enhanced sensitivity to mechanical stimuli and a prolonged arousal once active, indicating a decreased arousal threshold. Strik-ingly, fmn mutantsdonotshowsignificantreboundinresponsetorestdeprivationasistypicalforwild-typeflies,nordotheyshowdecreasedlife span. These results provide direct evidence that dopaminergic signaling has a critical function in the regulation of insect arousal.},
  language = {en},
  number = {32},
  journal = {J. Neurosci.},
  author = {Kume, K.},
  month = aug,
  year = {2005},
  keywords = {Arousal,Sleep,Drosophila,Dopamine,Rest,dopamine transporter},
  pages = {7377--7384},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7V4HSCLR/Kume - 2005 - Dopamine Is a Regulator of Arousal in the Fruit Fl.pdf},
  pmid = {16093388}
}

@article{kerkhofs_frederic_2000,
  title = {Fr\'ed\'eric {{Bremer}} 1892-1982: A Pioneer in Sleep Research.},
  volume = {4},
  issn = {1087-0792},
  doi = {10.1053/smrv.2000.0112},
  abstract = {Fr\'ed\'eric Bremer was one of the pioneer neurophysiologists who dedicated their career to understanding the neural mechanisms involved in the control of sleep-wake regulation. This paper follows his career and his major achievements. We found that Bremer's interest in sleep resulted from his unexpected observations after transecting the brain at the midcollicular level in the "enc\'ephale isol\'e" preparation. The sleep-like behaviour of the animal, accompanied by slow waves in the cortex, convinced him that sleep resulted from cortical deafferentation. He was further convinced that deafferentation was the cause of sleep when he found that transecting the brain at the medullary level did not much affect the sleep-wake cycle. As we show, Bremer's views that sleep is a passive phenomenon imposed on the brain because of deafferentation was shared by most of his contemporaries. Years later Bremer admitted that he interpreted his experimental findings wrongly. He continued to investigate sleep using his preparations and made important contributions to understanding the relationships between the brainstem reticular formation and the basal forebrain hypnogenic centres, as well as the importance of light on these relationships.},
  number = {5},
  journal = {Sleep Med. Rev.},
  author = {Kerkhofs, M and Lavie, P},
  month = oct,
  year = {2000},
  keywords = {Sleep,Bremer,cerveau isolé,dea,encéphale isolé},
  pages = {505--14},
  pmid = {17210279}
}

@article{dissel_enhanced_2017,
  title = {Enhanced Sleep Reverses Memory Deficits and Underlying Pathology in Drosophila Models of {{Alzheimer}}'s Disease},
  volume = {2},
  issn = {24519944},
  doi = {10.1016/j.nbscr.2016.09.001},
  abstract = {To test the hypothesis that sleep can reverse cognitive impairment during Alzheimer's disease, we enhanced sleep in flies either co-expressing human amyloid precursor protein and Beta-secretase (APP:BACE), or in flies expressing human tau. The ubiquitous expression of APP:BACE or human tau disrupted sleep. The sleep deficits could be reversed and sleep could be enhanced when flies were administered the GABA-A agonist 4,5,6,7-tetrahydroisoxazolo-[5,4-c]pyridine-3-ol (THIP). Expressing APP:BACE disrupted both Short-term memory (STM) and Long-term memory (LTM) as assessed using Aversive Phototaxic Suppression (APS) and courtship conditioning. Flies expressing APP:BACE also showed reduced levels of the synaptic protein discs large (DLG). Enhancing sleep in memory-impaired APP:BACE flies fully restored both STM and LTM and restored DLG levels. Sleep also restored STM to flies expressing human tau. Using live-brain imaging of individual clock neurons expressing both tau and the cAMP sensor Epac1-camps, we found that tau disrupted cAMP signaling. Importantly, enhancing sleep in flies expressing human tau restored proper cAMP signaling. Thus, we demonstrate that sleep can be used as a therapeutic to reverse deficits that accrue during the expression of toxic peptides associated with Alzheimer's disease.},
  journal = {Neurobiol. Sleep Circadian Rhythm.},
  author = {Dissel, Stephane and Klose, Markus and Donlea, Jeff and Cao, Lijuan and English, Denis and {Winsky-Sommerer}, Raphaelle and {van Swinderen}, Bruno and Shaw, Paul J},
  year = {2017},
  pages = {15--26}
}

@article{dietzl_genome-wide_2007,
  title = {A Genome-Wide Transgenic {{RNAi}} Library for Conditional Gene Inactivation in {{Drosophila}}},
  volume = {448},
  issn = {0028-0836},
  doi = {10.1038/nature05954},
  abstract = {Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88\% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.},
  language = {en},
  number = {7150},
  journal = {Nature},
  author = {Dietzl, Georg and Chen, Doris and Schnorrer, Frank and Su, Kuan-Chung and Barinova, Yulia and Fellner, Michaela and Gasser, Beate and Kinsey, Kaolin and Oppel, Silvia and Scheiblauer, Susanne and Couto, Africa and Marra, Vincent and Keleman, Krystyna and Dickson, Barry J.},
  month = jul,
  year = {2007},
  keywords = {Cancer,Biology,Evolutionary Biology,Science,Science Policy,Signal Transduction,neuroscience,Genetics,RNA,evolution,DNA,computational biology,Life Sciences,general,immunology,Microbial Genetics and Genomics,Development,Genomics,Cell Cycle,Neurobiology,molecular biology,Ecology,developmental biology,Biochemistry,Nature,astronomy,astrophysics,bioinformatics,biotechnology,climate change,drug discovery,earth science,environmental science,functional genomics,geophysics,interdisciplinary science,life,marine biology,materials science,medical research,medicine,metabolomics,molecular interactions,nanotechnology,palaeobiology,pharmacology,physics,proteomics,quantum physics,science news,structural biology,systems biology,transcriptomics,Animal Genetics and Genomics,Plant Genetics \& Genomics,Microarrays,cell signalling.},
  pages = {151--156},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/922478XC/Dietzl et al. - 2007 - A genome-wide transgenic RNAi library for conditio.pdf},
  pmid = {17625558}
}

@article{tononi_sleep_2006,
  title = {Sleep Function and Synaptic Homeostasis},
  volume = {10},
  issn = {1087-0792},
  doi = {10.1016/j.smrv.2005.05.002},
  abstract = {Summary This paper reviews a novel hypothesis about the functions of slow wave sleep\textemdash{}the synaptic homeostasis hypothesis. According to the hypothesis, plastic processes occurring during wakefulness result in a net increase in synaptic strength in many brain circuits. The role of sleep is to downscale synaptic strength to a baseline level that is energetically sustainable, makes efficient use of gray matter space, and is beneficial for learning and memory. Thus, sleep is the price we have to pay for plasticity, and its goal is the homeostatic regulation of the total synaptic weight impinging on neurons. The hypothesis accounts for a large number of experimental facts, makes several specific predictions, and has implications for both sleep and mood disorders.},
  number = {1},
  journal = {Sleep Med. Rev.},
  author = {Tononi, Giulio and Cirelli, Chiara},
  month = feb,
  year = {2006},
  keywords = {Learning,Slow waves,learning,slow waves,Consolidation,Delta sleep,Long-term depression,Slow oscillation,Synaptic scaling},
  pages = {49--62},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2BW9GWL2/Tononi and Cirelli - 2006 - Sleep function and synaptic homeostasis.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HYSR599B/abstract.html}
}

@article{martin_temporal_1999,
  title = {Temporal Pattern of Locomotor Activity in {{Drosophila}} Melanogaster},
  volume = {184},
  issn = {03407594},
  doi = {10.1007/s003590050307},
  abstract = {The temporal pattern of locomotor activity of single Drosophila melanogaster flies freely walking in small tubes is described. Locomotor activity monitored by a light gate has a characteristic time-course that depends upon age and the environmental conditions. Several methods are applied to assess the complexity of the temporal pattern. The pattern varies according to sex, genotype, age and environmental conditions (food; light). Activity occurs clustered in bouts. The intrinsic bout structure is quantified by four parameters: number of light gate passages (counts) per bout, duration of a bout, pause between two successive bouts and mean bout period. In addition, the distribution of the periods between light-gate crossings (inter-count intervals) as function of inter-count interval duration reveals a power law, suggesting that the overall distribution of episodes of activity and inactivity has a fractal structure. In the dark without food, the fractal dimension which represents a measure of the complexity of the pattern is sex, genotype and age specific. Fractality is abolished by additional sensory stimulation (food; light). We propose that time-course, bout structure and fractal dimension of the temporal pattern of locomotor activity describe different aspects of the fly's central pattern generator for locomotion and its motivational control.},
  number = {1},
  journal = {J. Comp. Physiol. - A Sensory, Neural, Behav. Physiol.},
  author = {Martin, J. R. and Ernst, R and Heisenberg, M},
  year = {1999},
  keywords = {Locomotor activity,aging,Bout structure,Fractal structure,Time series analysis},
  pages = {73--84},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F4V7A37H/Martin et al. - 1999 - Temporal pattern of locomotor activity in Drosophi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VLUEKZED/10.html},
  pmid = {10077864}
}

@article{stickgold_sleep-dependent_2005,
  title = {Sleep-Dependent Memory Consolidation},
  volume = {437},
  issn = {1476-4687},
  doi = {10.1038/nature04286},
  abstract = {The concept of 'sleeping on a problem' is familiar to most of us. But with myriad stages of sleep, forms of memory and processes of memory encoding and consolidation, sorting out how sleep contributes to memory has been anything but straightforward. Nevertheless, converging evidence, from the molecular to the phenomenological, leaves little doubt that offline memory reprocessing during sleep is an important component of how our memories are formed and ultimately shaped.},
  number = {7063},
  journal = {Nature},
  author = {Stickgold, Robert},
  month = oct,
  year = {2005},
  keywords = {Humans,Memory,Cognition,Hippocampus,Animals,Hippocampus: physiology,Cognition: physiology,Sleep,Sleep: physiology,Memory: physiology,Dreams,Dreams: physiology},
  pages = {1272--1278},
  pmid = {16251952}
}

@article{stephenson_behavioural_2011,
  title = {Behavioural Evidence for a Sleep-like Quiescent State in a Pulmonate Mollusc, {{Lymnaea}} Stagnalis ({{Linnaeus}})},
  volume = {214},
  issn = {0022-0949},
  doi = {10.1242/jeb.050591},
  abstract = {The objective of this study was to determine whether the great pond snail, Lymnaea stagnalis, expresses a sleep-like behavioural state. We found that snails spontaneously enter a relatively brief (22$\pm$1 min) quiescent state characterized by postural relaxation of the foot, mantle and tentacles, and cessation of radula rasping. Quiescence was reversed (`aroused') by appetitive (sucrose solution) and aversive (tactile) stimuli. Responsiveness to both stimuli was significantly lower in quiescent snails than in active snails. However, tactile stimuli evoked a more sustained defensive response in quiescent snails. Quiescence bouts were consolidated into `clusters' over an infradian timescale and were only weakly affected by time of day. Clusters contained 7$\pm$0.5 bouts, lasted 13$\pm$1 h and were separated by long (37$\pm$4 h) intervals of almost continuous activity. Analysis of Kaplan\textendash{}Meier survival curves revealed that the quiescent bout duration was described by an exponential probability distribution (time constant 15$\pm$1 min). Active bout duration was described by a bi-exponential probability distribution (time constants 62$\pm$4 and 592$\pm$48 min). We found no evidence for a `sleep rebound' mechanism and quiescence expression appeared to be regulated through stochastic processes causing state transitions to resemble a Markovian random walk. We conclude that Lymnaea is a potentially valuable model system for studies of cellular function in sleep.},
  language = {en},
  number = {5},
  journal = {J. Exp. Biol.},
  author = {Stephenson, Richard and Lewis, Vern},
  month = mar,
  year = {2011},
  keywords = {Sleep,model organism,Lymnaea stagnalis,mollusc},
  pages = {747--756},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IFF4YD3E/Stephenson and Lewis - 2011 - Behavioural evidence for a sleep-like quiescent st.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6XX42ZCN/747.html},
  pmid = {21307060}
}

@article{hendricks_why_2004,
  title = {Why a Fly? {{Using Drosophila}} to Understand the Genetics of Circadian Rhythms and Sleep.},
  volume = {27},
  issn = {0161-8105},
  abstract = {Among simple model systems, Drosophila has specific advantages for neurobehavioral investigations. It has been particularly useful for understanding the molecular basis of circadian rhythms. In addition, the genetics of fruit-fly sleep are beginning to develop. This review summarizes the current state of understanding of circadian rhythms and sleep in the fruit fly for the readers of Sleep. We note where information is available in mammals, for comparison with findings in fruit flies, to provide an evolutionary perspective, and we focus on recent findings and new questions. We propose that sleep-specific neural activity may alter cellular function and thus accomplish the restorative function or functions of sleep. In conclusion, we sound some cautionary notes about some of the complexities of working with this "simple" organism.},
  number = {2},
  journal = {Sleep},
  author = {Hendricks, Joan C and Sehgal, Amita},
  year = {2004},
  pages = {334--342},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3S23EKTI/Hendricks and Sehgal - 2004 - Why a Fly Using Drosophila to Understand the Gene.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IFWAQG99/2708425.html},
  pmid = {15124732}
}

@article{vyazovskiy_molecular_2008,
  title = {Molecular and Electrophysiological Evidence for Net Synaptic Potentiation in Wake and Depression in Sleep},
  volume = {11},
  issn = {1097-6256},
  doi = {10.1038/nn2035},
  abstract = {Plastic changes occurring during wakefulness aid in the acquisition and consolidation of memories. For some memories, further consolidation requires sleep, but whether plastic processes during wakefulness and sleep differ is unclear. We show that, in rat cortex and hippocampus, GluR1-containing AMPA receptor (AMPAR) levels are high during wakefulness and low during sleep, and changes in the phosphorylation states of AMPARs, CamKII and GSK3beta are consistent with synaptic potentiation during wakefulness and depression during sleep. Furthermore, slope and amplitude of cortical evoked responses increase after wakefulness, decrease after sleep and correlate with changes in slow-wave activity, a marker of sleep pressure. Changes in molecular and electrophysiological indicators of synaptic strength are largely independent of the time of day. Finally, cortical long-term potentiation can be easily induced after sleep, but not after wakefulness. Thus, wakefulness appears to be associated with net synaptic potentiation, whereas sleep may favor global synaptic depression, thereby preserving an overall balance of synaptic strength.},
  number = {2},
  journal = {Nat. Neurosci.},
  author = {Vyazovskiy, Vladyslav V and Cirelli, Chiara and {Pfister-Genskow}, Martha and Faraguna, Ugo and Tononi, Giulio},
  month = feb,
  year = {2008},
  pages = {200--208},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CHGHQNDY/Vyazovskiy et al. - 2008 - Molecular and electrophysiological evidence for ne.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B5SKDIDJ/nn2035.html},
  pmid = {18204445}
}

@article{joiner_sleep_2006,
  title = {Sleep in {{Drosophila}} Is Regulated by Adult Mushroom Bodies},
  volume = {441},
  issn = {0028-0836},
  doi = {10.1038/nature04811},
  abstract = {Sleep is one of the few major whole-organ phenomena for which no function and no underlying mechanism have been conclusively demonstrated. Sleep could result from global changes in the brain during wakefulness or it could be regulated by specific loci that recruit the rest of the brain into the electrical and metabolic states characteristic of sleep. Here we address this issue by exploiting the genetic tractability of the fruitfly, Drosophila melanogaster, which exhibits the hallmarks of vertebrate sleep. We show that large changes in sleep are achieved by spatial and temporal enhancement of cyclic-AMP-dependent protein kinase (PKA) activity specifically in the adult mushroom bodies of Drosophila. Other manipulations of the mushroom bodies, such as electrical silencing, increasing excitation or ablation, also alter sleep. These results link sleep regulation to an anatomical locus known to be involved in learning and memory.},
  language = {en},
  number = {7094},
  journal = {Nature},
  author = {Joiner, William J. and Crocker, Amanda and White, Benjamin H. and Sehgal, Amita},
  month = jun,
  year = {2006},
  pages = {757--760},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5JQJPKLY/Joiner et al. - 2006 - Sleep in Drosophila is regulated by adult mushroom.pdf},
  pmid = {16760980}
}

@article{pfeiffenberger_cul3_2012,
  title = {Cul3 and the {{BTB Adaptor Insomniac Are Key Regulators}} of {{Sleep Homeostasis}} and a {{Dopamine Arousal Pathway}} in {{Drosophila}}},
  volume = {8},
  issn = {15537390},
  doi = {10.1371/journal.pgen.1003003},
  abstract = {Sleep is homeostatically regulated, such that sleep drive reflects the duration of prior wakefulness. However, despite the discovery of genes important for sleep, a coherent molecular model for sleep homeostasis has yet to emerge. To better understand the function and regulation of sleep, we employed a reverse-genetics approach in Drosophila. An insertion in the BTB domain protein CG32810/insomniac (inc) exhibited one of the strongest baseline sleep phenotypes thus far observed, a $\sim$10 h sleep reduction. Importantly, this is coupled to a reduced homeostatic response to sleep deprivation, consistent with a disrupted sleep homeostat. Knockdown of the INC-interacting protein, the E3 ubiquitin ligase Cul3, results in reduced sleep duration, consolidation, and homeostasis, suggesting an important role for protein turnover in mediating INC effects. Interestingly, inc and Cul3 expression in post-mitotic neurons during development contributes to their adult sleep functions. Similar to flies with increased dopaminergic signaling, loss of inc and Cul3 result in hyper-arousability to a mechanical stimulus in adult flies. Furthermore, the inc sleep duration phenotype can be rescued by pharmacological inhibition of tyrosine hydroxylase, the rate-limiting enzyme for dopamine biosynthesis. Taken together, these results establish inc and Cul3 as important new players in setting the sleep homeostat and a dopaminergic arousal pathway in Drosophila.},
  number = {10},
  journal = {PLoS Genet.},
  author = {Pfeiffenberger, Cory and Allada, Ravi},
  month = oct,
  year = {2012},
  pages = {e1003003},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KLTEE33B/Pfeiffenberger and Allada - 2012 - Cul3 and the BTB Adaptor Insomniac Are Key Regulat.PDF},
  pmid = {23055946}
}

@article{bushey_drosophila_2007,
  title = {Drosophila {{Hyperkinetic Mutants Have Reduced Sleep}} and {{Impaired Memory}}},
  volume = {27},
  issn = {0270-6474, 1529-2401},
  doi = {10.1523/JNEUROSCI.0108-07.2007},
  abstract = {In mammals, sleep is thought to be important for health, cognition, and memory. Fruit flies share most features of mammalian sleep, and a recent study found that Drosophila lines carrying loss-of-function mutations in Shaker (Sh) are short sleeping, suggesting that the Sh current plays a major role in regulating daily sleep amount. The Sh current is potentiated by a $\beta$ modulatory subunit coded by Hyperkinetic (Hk). Here, we demonstrate that severe loss-of-function mutations of Hk reduce sleep and do so primarily by affecting the Sh current. Moreover, we prove, using a transgenic approach, that a wild-type copy of Hk is sufficient to restore normal sleep. Furthermore, we show that short-sleeping Hk mutant lines have a memory deficit, whereas flies carrying a weaker hypomorphic Hk allele have normal sleep and normal memory. By comparing six short-sleeping Sh lines with two normal sleeping ones, we also found that only alleles that reduce sleep also impair memory. These data identify a gene, Hk, which is necessary to maintain normal sleep, and provide genetic evidence that short sleep and poor memory are linked.},
  language = {en},
  number = {20},
  journal = {J. Neurosci.},
  author = {Bushey, Daniel and Huber, Reto and Tononi, Giulio and Cirelli, Chiara},
  month = may,
  year = {2007},
  keywords = {Memory,learning,Sleep,Drosophila,shaker,hyperkinetic},
  pages = {5384--5393},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QUE9RZ35/Bushey et al. - 2007 - Drosophila Hyperkinetic Mutants Have Reduced Sleep.pdf},
  pmid = {17507560}
}

@article{swierczek_high-throughput_2011,
  title = {High-Throughput Behavioral Analysis in {{C}}. Elegans},
  volume = {8},
  issn = {1548-7091},
  doi = {10.1038/nmeth.1625},
  abstract = {We designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three traditional behavioral paradigms using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allowed rapid quantification of behavior with minimal human effort. Thus, this system will enable large-scale forward and reverse genetic screens for complex behaviors.},
  language = {en},
  number = {7},
  journal = {Nat. Methods},
  author = {Swierczek, Nicholas A. and Giles, Andrew C. and Rankin, Catharine H. and Kerr, Rex A.},
  month = jul,
  year = {2011},
  pages = {592--598},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4623VGPK/Swierczek et al. - 2011 - High-throughput behavioral analysis in iC. elega.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JY793WZC/nmeth.html},
  pmid = {21642964}
}

@article{tononi_sleep_2003,
  title = {Sleep and Synaptic Homeostasis: A Hypothesis},
  volume = {62},
  issn = {0361-9230},
  shorttitle = {Sleep and Synaptic Homeostasis},
  doi = {10.1016/j.brainresbull.2003.09.004},
  abstract = {During much of sleep, the cerebral cortex is rippled by slow waves, which appear in the electroencephalogram as oscillations between 0.5 and 4.5 Hz. Slow waves are regulated as a function of previous wakefulness, being maximal at the beginning of sleep and then progressively returning to a baseline level. This paper discusses a hypothesis about the significance of slow-wave activity and its homeostatic regulation. The hypothesis is as follows:1. Wakefulness is associated with synaptic potentiation in several cortical circuits; 2. Synaptic potentiation is tied to the homeostatic regulation of slow-wave activity; 3. Slow-wave activity is associated with synaptic downscaling; 4. Synaptic downscaling is tied to the beneficial effects of sleep on performance. The hypothesized link between sleep and synaptic homeostasis is supported by several lines of evidence and leads to testable predictions.},
  number = {2},
  journal = {Brain Res. Bull.},
  author = {Tononi, Giulio and Cirelli, Chiara},
  month = dec,
  year = {2003},
  keywords = {Learning,Slow waves,learning,slow waves,Consolidation,Delta sleep,Long-term depression,Slow oscillation,Synaptic scaling},
  pages = {143--150},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D5TGSANT/Tononi and Cirelli - 2003 - Sleep and synaptic homeostasis a hypothesis.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RAICSJSP/S0361923003002594.html}
}

@article{schmid_new_2011,
  title = {A {{New ImageJ Plug}}-in ``{{ActogramJ}}'' for {{Chronobiological Analyses}}},
  volume = {26},
  issn = {0748-7304},
  doi = {10.1177/0748730411414264},
  abstract = {While the rapid development of personal computers and high-throughput recording systems for circadian rhythms allow chronobiologists to produce huge amounts of data, the software to analyze them often lags behind. Here, we announce newly developed chronobiology software that is easy to use, compatible with many different systems, and freely available. Our system can perform the most frequently used analyses: actogram drawing, periodogram analysis, and waveform analysis. The software is distributed as a pure Java plug-in for ImageJ and so works on the 3 main operating systems: Linux, Macintosh, and Windows. We believe that this free software raises the speed of data analyses and makes studying chronobiology accessible to newcomers.},
  number = {5},
  journal = {J. Biol. Rhythms},
  author = {Schmid, Benjamin and {Helfrich-F\"orster}, Charlotte and Yoshii, Taishi},
  month = oct,
  year = {2011},
  pages = {464--467},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RUI8GTT7/Schmid et al. - 2011 - A New ImageJ Plug-in “ActogramJ” for Chronobiologi.pdf},
  pmid = {21921300}
}

@article{hendricks_modafinil_2003,
  title = {Modafinil Maintains Waking in the Fruit Fly Drosophila Melanogaster.},
  volume = {26},
  issn = {0161-8105},
  abstract = {Fruit flies exhibit a sleep-like rest state that shares behavioral characteristics with mammalian sleep, including a homeostatic increase in rest after deprivation by mechanical methods. We tested the effect of modafinil, a novel wake-promoting agent, to discover whether its effect is conserved. Flies fed various concentrations of modafinil were compared to groups of control flies fed diluent only. Flies were also tested for a homeostatic response to the modafinil-related rest deprivation by examining rest and activity during recovery after 48H modafinil administration, compared to rest deprivation alone and to both treatments combined. The duration and consolidation of rest, and the duration, intensity, and circadian rhythms of activity were measured. Modafinil significantly and dose-dependently decreased rest when fed at concentrations from 2.5 mg/ml to 0.3125 mg/ml. Activity intensity was not increased, and circadian timing was unchanged, although the 2.5 mg/ml dose blunted the amplitude of overt circadian locomotor rhythms. Compared to controls, the duration of rest bouts was decreased in flies fed 2.5 mg/ml, and waking was frequently interrupted by 5-min periods of immobility. A rest rebound (significant increase in rest) followed withdrawal of either 2.5mg/ml or 0.625mg/ml modafinil after 48H. When directly compared to 6H total rest deprivation, the increase after withdrawal was briefer, reminiscent of the attenuated rest rebound seen in mammals, including humans, after modafinil. However, modafinil withdrawal combined with 6H total rest deprivation significantly enhanced the rebound, suggesting that a rest debt is accumulating during modafinil. We conclude that modafinil affects states of arousal in Drosophila in the same direction as it does in mammals. This discovery provides a tool for searching for conserved molecular mechanisms by which modafinil regulates rest and waking.},
  language = {eng},
  number = {2},
  journal = {Sleep},
  author = {Hendricks, Joan C. and Kirk, David and Panckeri, Karen and Miller, Matthew S. and Pack, Allan I.},
  year = {2003},
  keywords = {Arousal,Drosophila,Circadian Rhythm,Drosophila melanogaster,diptera,Rest,Modafinil,Actividad física espontánea,Activité motrice spontanée,Arthropoda,Biological rhythm,CNS stimulant,Comportement fuite,Conducta huída,Descanso,Despertar,Drosophilidae,Escape behavior,Estimulante SNC,Eveil,Geotactismo,Geotaxis,Géotactisme,Insecta,Invertebrata,Modafinilo,Reactividad,Reactivity,Repos,Ritmo biológico,Ritmo circadiano,Rythme biologique,Rythme circadien,Réactivité,Spontaneous physical activity,Stimulant SNC,Vigilance,Vigilancia,state regulation,wake-promoting},
  pages = {139--146},
  pmid = {12683471}
}

@article{rechtschaffen_sleep_2002,
  title = {Sleep Deprivation in the Rat: An Update of the 1989 Paper.},
  volume = {25},
  issn = {0161-8105},
  shorttitle = {Sleep Deprivation in the Rat},
  abstract = {THE REPRINTED REPORT 1 LISTED SEVERAL MAJOR SLEEP DEPRIVATION EFFECTS (SDES) WHICH WERE APPARENT IN ALL RATS subjected to prolonged total sleep deprivation (TSD) or paradoxical sleep deprivation (PSD) by the disk-over-water (DOW) method. The following original effects were confirmed in subsequent studies: 1. Mortality: Unless deprivation was halted, all TSD rats died or showed signs of impending death\textemdash{}usually in about two to three weeks. 2-10 The deaths (after about four to six weeks) of PSD rats were also confirmed. 11,12 2. TSD and PSD rats lost weight in spite of increased food intake. The large rise in energy expenditure (EE), calculated from the caloric values of food intake and weight loss) was confirmed. 2,4-9,13-17 3. The development of scrawny, debilitated appearance was con-firmed. 2,4-7,11 4. The severe ulcerative and hyperkeratotic skin lesions localized to the paws and tails of TSD and PSD rats were confirmed. 2,4-7,9,11 5. As in the original studies, TSD rats showed an initial rise and subsequent decline in waking intraperitoneal temperature (T ip). 2,4,5,10,11,14,16 As before, PSD rats showed only the T ip decline. 11,12 6. As in the earlier report, recovery from extended TSD featured large rebounds of PS. 6,16 Recent studies showed a predominance of PS rebound after only two 18 or four 19 days of TSD. Altogether, the confirmatory studies showed that TSD and PSD produce a reliably elicited syndrome of major biological effects. POSSIBLE CONFOUNDS The introduction to this series of papers 20 emphasized that sleep deprivation studies are essentially correlational. We admin-ister stimuli that produce the responses of sleep reduction and the responses of physiological or behavioral change. These are cor-related responses. We cannot confidently interpret the physio-logical and behavioral changes as effects of the sleep loss until we can discount the plausibility of other putative mediators of the physiological and behavioral change that are produced by the experimental situation. Two alternative mediators have been sug-gested: loss of circadian rhythm and stress. Circadian Rhythm Because sleep deprived rats might have weaker circadian rhythms than control rats, all our experiments had been run in constant light to flatten the circadian rhythms of both sleep deprived and control rats. However, this procedure caused at least one journal reviewer to question whether the effects we reported might have resulted from an interaction of rhythm and sleep loss (i.e., the SDEs might occur only when circadian rhythms were flat). Because we knew of no effects of circadian rhythm loss that resembled the SDEs, and because there was no appealing rationale for the suggested interaction, we doubted its plausibility. Nevertheless, to dispose of such questions, we repeated the basic TSD disk-over-water experiment under 12:12 light-dark conditions. 6 All the major SDEs that we had previ-ously reported were still present, including: increased food intake; decreased weight; increased EE; debilitated appearance; lesions on the paws and tail; an initial increase followed by a large decrease in T ip ; impending death; and recovery which fea-tured large, sustained rebounds of PS and reversal of all TSD-induced changes. Stress},
  language = {eng},
  number = {1},
  journal = {Sleep},
  author = {Rechtschaffen, Allan and Bergmann, Bernard M},
  month = feb,
  year = {2002},
  keywords = {Stress; Physiological,Animals,Rats,Circadian Rhythm,Electroencephalography,Sleep Stages,Sleep Deprivation,Norepinephrine,Body Temperature Regulation,Energy Metabolism,Grooming,Skin Diseases,Stress- Physiological,Thyroxine},
  pages = {18--24},
  pmid = {11833856}
}

@article{keene_clock_2010,
  title = {Clock and Cycle {{Limit Starvation}}-{{Induced Sleep Loss}} in {{Drosophila}}},
  volume = {20},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2010.05.029},
  abstract = {Summary Neural systems controlling the vital functions of sleep and feeding in mammals are tightly interconnected: sleep deprivation promotes feeding, whereas starvation suppresses sleep. Here we show that starvation in Drosophila potently suppresses sleep, suggesting that these two homeostatically regulated behaviors are also integrated in flies. The sleep-suppressing effect of starvation is independent of the mushroom bodies, a previously identified sleep locus in the fly brain, and therefore is regulated by distinct neural circuitry. The circadian clock genes Clock (Clk) and cycle (cyc) are critical for proper sleep suppression during starvation. However, the sleep suppression is independent of light cues and of circadian rhythms as shown by the fact that starved period mutants sleep like wild-type flies. By selectively targeting subpopulations of Clk-expressing neurons, we localize the observed sleep phenotype to the dorsally located circadian neurons. These findings show that Clk and cyc act during starvation to modulate the conflict of whether flies sleep or search for food.},
  language = {English},
  number = {13},
  journal = {Curr. Biol.},
  author = {Keene, Alex C. and Dubou\'e, Erik R. and McDonald, Daniel M. and Dus, Monica and Suh, Greg S. B. and Waddell, Scott and Blau, Justin},
  month = jul,
  year = {2010},
  keywords = {MOLNEURO},
  pages = {1209--1215},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/35AKZTEU/Keene et al. - 2010 - Clock and cycle Limit Starvation-Induced Sleep Los.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L9TEE3TZ/Keene et al. - 2010 - Clock and cycle Limit Starvation-Induced Sleep Los.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5FU4DHR6/S0960982210005968.html}
}

@article{rechtschaffen_physiological_1983,
  title = {Physiological Correlates of Prolonged Sleep Deprivation in Rats},
  volume = {221},
  issn = {0036-8075},
  abstract = {The issue of whether sleep is physiologically necessary has been unresolved because experiments that reported deleterious effects of sleep deprivation did not control for the stimuli used to prevent sleep. In this experiment, however, experimental and control rats received the same relatively mild physical stimuli, but stimulus presentations were timed to reduce sleep severely in experimental rats but not in controls. Experimental rats suffered severe pathology and death; control rats did not.},
  language = {eng},
  number = {4606},
  journal = {Science},
  author = {Rechtschaffen, Allan and Gilliland, Marcia A and Bergmann, Bernard M. and Winter, J B},
  month = jul,
  year = {1983},
  keywords = {Male,Time Factors,Animals,Rats,Electroencephalography,Body Weight,Sleep Deprivation,Organ Size,Adrenal Glands,Rats- Inbred Strains},
  pages = {182--184},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7KXUJRS4/Rechtschaffen et al. - 1983 - Physiological correlates of prolonged sleep depriv.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/696FZ8QW/182.html}
}

@article{regalado_increased_2017,
  title = {Increased Food Intake after Starvation Enhances Sleep in {{Drosophila}} Melanogaster},
  issn = {16738527},
  doi = {10.1016/j.jgg.2017.05.006},
  abstract = {Feeding and sleep are highly conserved, interconnected behaviors essential for survival. Starvation has been shown to potently suppress sleep across species; however, whether satiety promotes sleep is still unclear. Here we use the fruit fly, Drosophila melanogaster, as a model organism to address the interactions between feeding and sleep. We first monitored the sleep of flies that had been starved for 24 h and found that sleep amount increased in the first 4 h after flies were given food. Increased sleep after starvation was due to an increase in sleep bout number and average sleep bout length. Mutants of translin or adipokinetic hormone, which fail to suppress sleep during starvation, still exhibited a sleep increase after starvation, suggesting that sleep increase after starvation is not a consequence of sleep loss during starvation. We also found that feeding activity and food consumption were higher in the first 10\textendash{}30 min after starvation. Restricting food consumption in starved flies to 30 min was sufficient to increase sleep for 1 h. Although flies ingested a comparable amount of food at differing sucrose concentrations, sleep increase after starvation on a lower sucrose concentration was undetectable. Taken together, our results suggest increased food intake after starvation enhances sleep and reveals a novel relationship between feeding and sleep.},
  journal = {J. Genet. Genomics},
  author = {Regalado, Josue M. and Cortez, McKenna B. and Grubbs, Jeremy and Link, Jared A. and {van der Linden}, Alexander and Zhang, Yong},
  year = {2017},
  keywords = {Dose-Response Relationship; Drug,Feeding,Animals,Sleep,Drosophila,Drosophila melanogaster,Starvation,Sucrose,Eating,Satiety}
}

@article{dubowy_circadian_2017,
  title = {Circadian {{Rhythms}} and {{Sleep}} in {{Drosophila}} Melanogaster},
  volume = {205},
  issn = {0016-6731},
  doi = {10.1534/genetics.115.185157},
  abstract = {The advantages of the model organism Drosophila melanogaster, including low genetic redundancy, functional simplicity, and the ability to conduct large-scale genetic screens, have been essential for understanding the molecular nature of circadian ($\sim$24 hr) rhythms, and continue to be valuable in discovering novel regulators of circadian rhythms and sleep. In this review, we discuss the current understanding of these interrelated biological processes in Drosophila and the wider implications of this research. Clock genes period and timeless were first discovered in large-scale Drosophila genetic screens developed in the 1970s. Feedback of period and timeless on their own transcription forms the core of the molecular clock, and accurately timed expression, localization, post-transcriptional modification, and function of these genes is thought to be critical for maintaining the circadian cycle. Regulators, including several phosphatases and kinases, act on different steps of this feedback loop to ensure strong and accurately timed rhythms. Approximately 150 neurons in the fly brain that contain the core components of the molecular clock act together to translate this intracellular cycling into rhythmic behavior. We discuss how different groups of clock neurons serve different functions in allowing clocks to entrain to environmental cues, driving behavioral outputs at different times of day, and allowing flexible behavioral responses in different environmental conditions. The neuropeptide PDF provides an important signal thought to synchronize clock neurons, although the details of how PDF accomplishes this function are still being explored. Secreted signals from clock neurons also influence rhythms in other tissues. SLEEP is, in part, regulated by the circadian clock, which ensures appropriate timing of sleep, but the amount and quality of sleep are also determined by other mechanisms that ensure a homeostatic balance between sleep and wake. Flies have been useful for identifying a large set of genes, molecules, and neuroanatomic loci important for regulating sleep amount. Conserved aspects of sleep regulation in flies and mammals include wake-promoting roles for catecholamine neurotransmitters and involvement of hypothalamus-like regions, although other neuroanatomic regions implicated in sleep in flies have less clear parallels. Sleep is also subject to regulation by factors such as food availability, stress, and social environment. We are beginning to understand how the identified molecules and neurons interact with each other, and with the environment, to regulate sleep. Drosophila researchers can also take advantage of increasing mechanistic understanding of other behaviors, such as learning and memory, courtship, and aggression, to understand how sleep loss impacts these behaviors. Flies thus remain a valuable tool for both discovery of novel molecules and deep mechanistic understanding of sleep and circadian rhythms.},
  number = {4},
  journal = {Genetics},
  author = {Dubowy, Christine and Sehgal, Amita},
  year = {2017},
  keywords = {circadian rhythms,Animals,Sleep,Drosophila,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,neuroscience,Circadian rhythms,FlyBook,molecular neuroscience,FlyBook: Drosophila,sleep,Circadian Rhythm Signaling Peptides and Proteins},
  pages = {1373--1397},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KIR3RACT/Dubowy and Sehgal - 2017 - Circadian Rhythms and Sleep in Drosophila melanoga.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RAUWDLET/Dubowy and Sehgal - 2017 - Circadian Rhythms and Sleep in Drosophila melanoga.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J7ZADPG5/1373.html},
  pmid = {28360128}
}

@article{crocker_genetic_2010,
  title = {Genetic Analysis of Sleep},
  volume = {24},
  issn = {0890-9369, 1549-5477},
  doi = {10.1101/gad.1913110},
  abstract = {Almost 20 years ago, the gene underlying fatal familial insomnia was discovered, and first suggested the concept that a single gene can regulate sleep. In the two decades since, there have been many advances in the field of behavioral genetics, but it is only in the past 10 years that the genetic analysis of sleep has emerged as an important discipline. Major findings include the discovery of a single gene underlying the sleep disorder narcolepsy, and identification of loci that make quantitative contributions to sleep characteristics. The sleep field has also expanded its focus from mammalian model organisms to Drosophila, zebrafish, and worms, which is allowing the application of novel genetic approaches. Researchers have undertaken large-scale screens to identify new genes that regulate sleep, and are also probing questions of sleep circuitry and sleep function on a molecular level. As genetic tools continue to be refined in each model organism, the genes that support a specific function in sleep will become more apparent. Thus, while our understanding of sleep still remains rudimentary, rapid progress is expected from these recently initiated studies.},
  language = {en},
  number = {12},
  journal = {Genes Dev.},
  author = {Crocker, Amanda and Sehgal, Amita},
  month = jun,
  year = {2010},
  keywords = {Arousal,Sleep,Genetics,Circadian rhythms,Behavior in model organisms,Model systems},
  pages = {1220--1235},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SGP4R2X4/Crocker and Sehgal - 2010 - Genetic analysis of sleep.pdf},
  pmid = {20551171}
}

@article{hendricks_rest_2000,
  title = {Rest in {{Drosophila Is}} a {{Sleep}}-like {{State}}},
  volume = {25},
  issn = {08966273},
  doi = {10.1016/S0896-6273(00)80877-6},
  abstract = {To facilitate the genetic study of sleep, we documented that rest behavior in Drosophila melanogaster is a sleep-like state. The animals choose a preferred location, become immobile for periods of up to 157 min at a particular time in the circadian day, and are relatively unresponsive to sensory stimuli. Rest is affected by both homeostatic and circadian influences: when rest is prevented, the flies increasingly tend to rest despite stimulation and then exhibit a rest rebound. Drugs acting on a mammalian adenosine receptor alter rest as they do sleep, suggesting conserved neural mechanisms. Finally, normal homeostatic regulation depends on the timeless but not the period central clock gene. Understanding the molecular features of Drosophila rest should shed new light on the mechanisms and function of sleep.},
  number = {1},
  journal = {Neuron},
  author = {Hendricks, Joan C and Finn, Stefanie M and Panckeri, Karen A and Chavkin, Jessica and Williams, Julie A and Sehgal, Amita and Pack, Allan I},
  month = jan,
  year = {2000},
  pages = {129--138},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CDZN3L9U/Hendricks et al. - 2000 - Rest in Drosophila Is a Sleep-like State.pdf},
  pmid = {10707978}
}

@article{nitz_electrophysiological_2002,
  title = {Electrophysiological Correlates of Rest and Activity in {{Drosophila}} Melanogaster},
  volume = {12},
  issn = {09609822},
  doi = {10.1016/S0960-9822(02)01300-3},
  abstract = {Extended periods of rest in Drosophila melanogaster resemble mammalian sleep states in that they are characterized by heightened arousal thresholds and specific alterations in gene expression [1, 2]. Defined as inactivity periods spanning 5 or more min, amounts of this sleep-like state are, as in mammals, sensitive to prior amounts of waking activity, time of day, and pharmacological intervention [1-3]. Clearly recognizable changes in the pattern and amount of brain electrical activity accompany changes in motor activity and arousal thresholds originally used to identify mammalian sleeping behavior [4-6]. Electroencephalograms (EEGs) and/or local field potentials (LFPs) are now widely used to quantify sleep state amounts and define types of sleep. Thus, slow-wave sleep (SWS) is characterized by EEG spindles and large-amplitude delta-frequency (0-3.5 Hz) waves. Rapid-eye movement (REM) sleep is characterized by irregular gamma-frequency cortical EEG patterns and rhythmic theta-frequency (5-9 Hz) hippocampal EEG activity [7]. It is unknown whether rest and activity in Drosophila are associated with distinct electrophysiological correlates. To address this issue, we monitored motor activity levels and recorded LFPs in the medial brain between the mushroom bodies, structures implicated in the modulation of locomotor activity, of Drosophila [8]. The results indicate that LFPs can be reliably recorded from the brains of awake, moving fruit flies, that targeted genetic manipulations can be used to localize sources of LFP activity, and that brain electrical activity of Drosophila is reliably correlated with activity state.},
  number = {22},
  journal = {Curr. Biol.},
  author = {Nitz, Douglas A and Van Swinderen, Bruno and Tononi, Giulio and Greenspan, Ralph J and DA, Nitz and B, van Swinderen and Tononi, Giulio and RJ, Greenspan},
  month = nov,
  year = {2002},
  pages = {1934--1940},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BY4D3S9G/Nitz et al. - 2002 - Electrophysiological correlates of rest and activi.pdf},
  pmid = {12445387}
}

@article{siegel_all_2008,
  title = {Do All Animals Sleep?},
  volume = {31},
  issn = {0166-2236},
  doi = {10.1016/j.tins.2008.02.001},
  abstract = {Some animals never exhibit a state that meets the behavioral definition of sleep. Others suspend or greatly reduce `sleep' behavior for many weeks during the postpartum period or during seasonal migrations without any consequent `sleep debt.' Rats die from one form of sleep deprivation, but sleep loss has not been shown to cause death in well-controlled studies in other vertebrate species. Some marine mammal species do not show evidence for REM sleep, and convincing evidence for this state in reptiles, fish and insects is lacking. The enormous variation in the nature of rest and sleep states across the animal kingdom and within the mammalian class has important implications for understanding the evolution and functions of sleep.},
  number = {4},
  journal = {Trends Neurosci.},
  author = {Siegel, Jerome M.},
  month = apr,
  year = {2008},
  pages = {208--213},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EKHZWR5M/Siegel - 2008 - Do all animals sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MTNSSBUC/S0166223608000623.html}
}

@article{yuan_sleep-promoting_2006,
  title = {A {{Sleep}}-{{Promoting Role}} for the {{Drosophila Serotonin Receptor 1A}}},
  volume = {16},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2006.04.032},
  abstract = {SummaryBackground Although sleep is an important process essential for life, its regulation is poorly understood. The recently developed Drosophila model for sleep provides a powerful system to genetically and pharmacologically identify molecules that regulate sleep. Serotonin is an important neurotransmitter known to affect many behaviors, but its role in sleep remains controversial. Results We generated or obtained flies with genetically altered expression of each of three Drosophila serotonin receptor subtypes (d5-HT1A, d5-HT1B, and d5-HT2) and assayed them for baseline sleep phenotypes. The data indicated a sleep-regulating role for the d5-HT1A receptor. d5-HT1A mutant flies had short and fragmented sleep, which was rescued by expressing the receptor in adult mushroom bodies, a structure associated with learning and memory in Drosophila. Neither the d5-HT2 receptor nor the d5-HT1B receptor, which was previously implicated in circadian regulation, had any effect on baseline sleep, indicating that serotonin affects sleep and circadian rhythms through distinct receptors. Elevating serotonin levels, either pharmacologically or genetically, enhanced sleep in wild-type flies. In addition, serotonin promoted sleep in some short-sleep mutants, suggesting that it can compensate for some sleep deficits. Conclusions These data show that serotonin promotes baseline sleep in Drosophila. They also link the regulation of sleep behavior by serotonin to a specific receptor in a distinct region of the fly brain.},
  language = {eng},
  number = {11},
  journal = {Curr. Biol.},
  author = {Yuan, Quan and Joiner, William J. and Sehgal, Amita},
  month = jun,
  year = {2006},
  keywords = {Brain,Animals,Sleep,Drosophila,Animals- Genetically Modified,Circadian Rhythm,Drosophila Proteins,SYSNEURO,Chromosome Mapping,Mutation,Phenotype,Receptor- Serotonin- 5-HT1A,Receptor- Serotonin- 5-HT1B,Receptors- Serotonin- 5-HT2},
  pages = {1051--1062},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QUYSNX8S/Yuan et al. - 2006 - A Sleep-Promoting Role for the Drosophila Serotoni.pdf}
}

@article{chung_gabaa_2009,
  title = {The {{GABAA Receptor RDL Acts}} in {{Peptidergic PDF Neurons}} to {{Promote Sleep}} in {{Drosophila}}},
  volume = {19},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2009.01.040},
  abstract = {Summary Sleep is regulated by a circadian clock that times sleep and wake to specific times of day and a homeostat that drives sleep as a function of prior wakefulness [1]. To analyze the role of the circadian clock, we have used the fruit fly Drosophila [2]. Flies display the core behavioral features of sleep, including relative immobility, elevated arousal thresholds, and homeostatic regulation [2, 3]. We assessed sleep-wake modulation by a core set of circadian pacemaker neurons that express the neuropeptide PDF. We find that disruption of PDF function increases sleep during the late night in light:dark and the first subjective day of constant darkness. Flies deploy genetic and neurotransmitter pathways to regulate sleep that are similar to those of their mammalian counterparts, including GABA [4]. We find that RNA interference-mediated knockdown of the GABAA receptor gene, Resistant to dieldrin (Rdl), in PDF neurons reduces sleep, consistent with a role for GABA in inhibiting PDF neuron function. Patch-clamp electrophysiology reveals GABA-activated picrotoxin-sensitive chloride currents on PDF+ neurons. In addition, RDL is detectable most strongly on the large subset of PDF+ pacemaker neurons. These results suggest that GABAergic inhibition of arousal-promoting PDF neurons is an important mode of sleep-wake regulation in vivo.},
  number = {5},
  journal = {Curr. Biol.},
  author = {Chung, Brian Y. and Kilman, Valerie L. and Keath, J. Russel and Pitman, Jena L. and Allada, Ravi and Allada, Ravi and Gasser, B. and Kinsey, K. and Oppel, S. and Scheiblauer, S. and Al, et},
  month = mar,
  year = {2009},
  keywords = {MOLNEURO},
  pages = {386--390},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/25NCRM7K/Chung et al. - 2009 - The GABAA Receptor RDL Acts in Peptidergic PDF Neu.pdf},
  pmid = {19230663}
}

@article{lamaze_regulation_2017,
  title = {Regulation of Sleep Plasticity by a Thermo-Sensitive Circuit in {{Drosophila}}},
  volume = {7},
  issn = {2045-2322},
  doi = {10.1038/srep40304},
  abstract = {Sleep is a highly conserved and essential behaviour in many species, including the fruit fly Drosophila melanogaster. In the wild, sensory signalling encoding environmental information must be integrated with sleep drive to ensure that sleep is not initiated during detrimental conditions. However, the molecular and circuit mechanisms by which sleep timing is modulated by the environment are unclear. Here we introduce a novel behavioural paradigm to study this issue. We show that in male fruit flies, onset of the daytime siesta is delayed by ambient temperatures above 29 $^\circ$C. We term this effect Prolonged Morning Wakefulness (PMW). We show that signalling through the TrpA1 thermo-sensor is required for PMW, and that TrpA1 specifically impacts siesta onset, but not night sleep onset, in response to elevated temperatures. We identify two critical TrpA1-expressing circuits and show that both contact DN1p clock neurons, the output of which is also required for PMW. Finally, we identify the circadian blue-light photoreceptor CRYPTOCHROME as a molecular regulator of PMW, and propose a model in which the Drosophila nervous system integrates information encoding temperature, light, and time to dynamically control when sleep is initiated. Our results provide a platform to investigate how environmental inputs co-ordinately regulate sleep plasticity.},
  journal = {Sci. Rep.},
  author = {Lamaze, Angelique and {\"Ozt\"urk-{\c C}olak}, Arzu and Fischer, Robin and Peschel, Nicolai and Koh, Kyunghee and Jepson, James E. C.},
  month = jan,
  year = {2017},
  pages = {40304},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BTITQAZ8/Lamaze et al. - 2017 - Regulation of sleep plasticity by a thermo-sensiti.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F3IHTYJC/srep40304.html},
  pmid = {28084307}
}

@article{li_sleep_2009,
  title = {Sleep Deprivation Specifically Impairs Short-Term Olfactory Memory in {{Drosophila}}.},
  volume = {32},
  issn = {0161-8105},
  doi = {10.1093/sleep/32.11.1417},
  abstract = {Sleep is crucial to memory consolidation in humans and other animals; however, the effect of insufficient sleep on subsequent learning and memory remains largely elusive.},
  number = {11},
  journal = {Sleep},
  author = {Li, Xinjian and Yu, Feng and Guo, Aike},
  month = nov,
  year = {2009},
  keywords = {Sleep,Drosophila,citation,Learning and memory,mushroom body,camp,Cellular,1,11,1417-1424,2 a large body,32,guo a,li x,mem-,of molecular,ory,role in learning and,short-term olfactory memory in,sleep 2009,sleep deprivation specifically impairs,sleep plays a key,slpd,yu f},
  pages = {1417--1424},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8NRAJSFT/Li et al. - 2009 - Sleep Deprivation Specifically Impairs Short-term .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PLVTEPZZ/2454307.html},
  pmid = {19928381}
}

@article{kunst_calcitonin_2014,
  title = {Calcitonin Gene-Related Peptide Neurons Mediate Sleep-Specific Circadian Output in {{Drosophila}}},
  volume = {24},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2014.09.077},
  abstract = {Background: Imbalances in amount and timing of sleep are harmful to physical and mental health. Therefore, the study of the underlying mechanisms is of great biological importance. Proper timing and amount of sleep are regulated by both the circadian clock and homeostatic sleep drive. However, very little is known about the cellular and molecular mechanisms by which the circadian clock regulates sleep. In this study, we describe a novel role for diuretic hormone 31 (DH31), the fly homolog of the vertebrate neuropeptide calcitonin gene-related peptide, as a circadian wake-promoting signal that awakens the fly in anticipation of dawn. Results: Analysis of loss-of-function and gain-of-function Drosophila mutants demonstrates that DH31 suppresses sleep late at night. DH31 is expressed by a subset of dorsal circadian clock neurons that also express the receptor for the circadian neuropeptide pigment-dispersing factor (PDF). PDF secreted by the ventral pacemaker subset of circadian clock neurons acts on PDF receptors in the DH31-expressing dorsal clock neurons to increase DH31 secretion before dawn. Activation of PDF receptors in DH31-positive DN1 specifically affects sleep and has no effect on circadian rhythms, thus constituting a dedicated locus for circadian regulation of sleep. Conclusions: We identified a novel signaling molecule (DH31) as part of a neuropeptide relay mechanism for circadian control of sleep. Our results indicate that outputs of the clock controlling sleep and locomotor rhythms are mediated via distinct neuronal pathways.},
  number = {22},
  journal = {Curr. Biol.},
  author = {Kunst, Michael and Hughes, Michael E. E and Raccuglia, Davide and Felix, Mario and Li, Michael and Barnett, Gregory and Duah, Janelle and Nitabach, Michael N. N},
  month = nov,
  year = {2014},
  pages = {2652--2664},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NKI7B5TH/Kunst et al. - 2014 - Calcitonin Gene-Related Peptide Neurons Mediate Sl.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GPDIJQTN/S0960982214012731.html},
  pmid = {25455031}
}

@article{huber_sleep_2004,
  title = {Sleep Homeostasis in {{Drosophila}} Melanogaster.},
  volume = {27},
  issn = {0161-8105},
  doi = {10.1093/sleep/27.4.628},
  abstract = {STUDY OBJECTIVES: The fruit fly Drosophila melanogaster is emerging as a promising model system for the genetic dissection of sleep. As in mammals, sleep in the fruit fly is a reversible state of reduced responsiveness to the external world and has been defined using an array of behavioral, pharmacologic, molecular, and electrophysiologic criteria. A central feature of mammalian sleep is its homeostatic regulation by the amount of previous wakefulness. Dissecting the mechanisms of homeostatic regulation is likely to provide key insights into the functions of sleep. Thus, it is important to establish to what extent sleep homeostasis is similar between mammals and flies. This study was designed to determine whether in flies, as in mammals, (1) sleep rebound is dependent on prior time awake; (2) sleep deprivation affects the intensity, in addition to the duration, of sleep rebound; (3) sleep loss impairs vigilance and performance; (4) the sleep homeostatic response is conserved among different wild-type lines, and between female and male flies of the same line. DESIGN: Motor activity of individual flies was recorded at 1-minute intervals using the infrared Drosophila Activity Monitoring System during 2 baseline days; during 6, 12, and 24 hours of sleep deprivation; and during 2 days of recovery. Sleep was defined as any period of uninterrupted behavioral immobility lasting $\backslash$textgreater 5 minutes. Sleep continuity was measured by calculating the number of brief awakenings, the number and duration of sleep episodes, and a sleep continuity score. Vigilance before and after sleep deprivation was assessed by measuring the escape response triggered by 2 different aversive stimuli. SETTING: Fly sleep research laboratory at UW-Madison. PARTICIPANTS AND INTERVENTIONS: Adult flies of the Canton-S (CS) strain and 116 other wild-type lines ($\backslash$textgreater or = 16 female and $\backslash$textgreater or = 16 male flies per line). MEASUREMENTS AND RESULTS: In wild-type CS flies, as in mammals, the amount of sleep recovered after sleep deprivation was dependent on prior time awake. Relative to baseline sleep, recovery sleep in CS flies was less fragmented, with longer sleep episodes, and was associated with a higher arousal threshold. Sleep deprivation in CS flies also reduced performance. Sleep duration and continuity increased after 24 hour of sleep deprivation in all the other wild-type lines tested. CONCLUSION: The sleep homeostatic response in fruit flies is a stable phenotype and shares most of, if not all, the major features of mammalian sleep homeostasis, thus supporting the use of Drosophila as a model system for the genetic dissection of sleep mechanisms and functions.},
  language = {eng},
  number = {4},
  journal = {Sleep},
  author = {Huber, Reto and Hill, Sean L and Holladay, Carie and Biesiadecki, Melissa and Tononi, Giulio and Cirelli, Chiara},
  month = jun,
  year = {2004},
  keywords = {Female,Male,Arousal,Time Factors,Animals,Animal,Drosophila melanogaster,Locomotion,Phenotype,Behavior- Animal,Wakefulness,citation,Escape Reaction,Homeostasis,Sleep Deprivation,Fruit fly,Hot Temperature,Vigilance,info:mesh/Female,27,4,628-39,Immobilization,arousal threshold,brief awakenings,duration of sleep,episodes,hill sl,holladay c et al,huber r,info:mesh/Animals,info:mesh/Arousal,info:mesh/Behavior,info:mesh/Drosophila melanogaster,info:mesh/Escape Reaction,info:mesh/Homeostasis,info:mesh/Hot Temperature,info:mesh/Immobilization,info:mesh/Locomotion,info:mesh/Male,info:mesh/Phenotype,info:mesh/Sleep Deprivation,info:mesh/Time Factors,info:mesh/Wakefulness,sleep 2004,sleep homeostasis in,sleep intensity},
  pages = {628--639},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8UFC2BQE/Huber et al. - 2004 - Sleep homeostasis in Drosophila melanogaster..pdf},
  pmid = {15282997}
}

@article{dubowy_genetic_2016,
  title = {Genetic {{Dissociation}} of {{Daily Sleep}} and {{Sleep Following Thermogenetic Sleep Deprivation}} in {{Drosophila}}.},
  volume = {39},
  issn = {0161-8105},
  doi = {10.5665/sleep.5760},
  abstract = {Abstract: Sleep rebound - the increase in sleep that follows sleep deprivation (SD) - is a hallmark of homeostatic sleep regulation that is conserved...},
  language = {eng},
  number = {5},
  journal = {Sleep},
  author = {Dubowy, Christine and Moravcevic, Katarina and Yue, Zhifeng and Wan, Joy Y. JY and Van Dongen, HP Hans P.A. and Sehgal, Amita and C, Dubowy and K, Moravcevic and Z, Yue and Jy, Wan and Hp, Van Dongen and A, Sehgal},
  month = feb,
  year = {2016},
  pages = {1083--1095},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/M4D2VTBX/Dubowy et al. - 2016 - Genetic Dissociation of Daily Sleep and Sleep Foll.pdf}
}

@article{isaac_drosophila_2010,
  title = {Drosophila Male Sex Peptide Inhibits Siesta Sleep and Promotes Locomotor Activity in the Post-Mated Female},
  volume = {277},
  issn = {0962-8452},
  doi = {10.1098/rspb.2009.1236},
  abstract = {Quiescence, or a sleep-like state, is a common and important feature of the daily lives of animals from both invertebrate and vertebrate taxa, suggesting that sleep appeared early in animal evolution. Recently, Drosophila melanogaster has been shown to be a relevant and powerful model for the genetic analysis of sleep behaviour. The sleep architecture of D. melanogaster is sexually dimorphic, with females sleeping much less than males during day-time, presumably because reproductive success requires greater foraging activity by the female as well as the search for egg-laying sites. However, this loss of sleep and increase in locomotor activity will heighten the risk for the female from environmental and predator hazards. In this study, we show that virgin females can minimize this risk by behaving like males, with an extended afternoon 'siesta'. Copulation results in the female losing 70 per cent of day-time sleep and becoming more active. This behaviour lasts for at least 8 days after copulation and is abolished if the mating males lack sex peptide (SP), normally present in the seminal fluid. Our results suggest that SP is the molecular switch that promotes wakefulness in the post-mated female, a change of behaviour compatible with increased foraging and egg-laying activity. The stress resulting from SP-dependent sleep deprivation might be an important contribution to the toxic side-effects of male accessory gland products that are known to reduce lifespan in post-mated females.},
  language = {en},
  number = {1678},
  journal = {Proc. R. Soc. B Biol. Sci.},
  author = {Isaac, R. Elwyn and Li, Chenxi and Leedale, Amy E. and Shirras, Alan D.},
  month = sep,
  year = {2010},
  pages = {65--70},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D9UXSIF9/Isaac et al. - 2010 - Drosophila male sex peptide inhibits siesta sleep .pdf},
  pmid = {19793753}
}

@article{maret_sleep_2011,
  title = {Sleep and Waking Modulate Spine Turnover in the Adolescent Mouse Cortex},
  volume = {14},
  issn = {1097-6256},
  doi = {10.1038/nn.2934},
  abstract = {Cortical development involves synaptic formation and elimination. Although synaptogenesis predominates in the early stages and pruning in the later stages, the two processes are thought to happen concurrently. In adults, synaptic strength is modulated by behavioral state, and we asked whether synaptic remodeling may be affected by sleep and waking states. Using two-photon microscopy in adolescent mice, we found that waking results in a net increase in cortical spines, whereas sleep is associated with net spine loss.},
  number = {11},
  journal = {Nat. Neurosci.},
  author = {Maret, Stephanie and Faraguna, Ugo and Nelson, Aaron B and Cirelli, Chiara and Tononi, Giulio},
  month = oct,
  year = {2011},
  pages = {1418--1420},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DQLKK59K/Maret et al. - 2011 - Sleep and wake modulate spine turnover in the adol.pdf},
  pmid = {21983682}
}

@article{tobler_effect_1983,
  title = {Effect of Forced Locomotion on the Rest-Activity Cycle of the Cockroach},
  volume = {8},
  issn = {01664328},
  doi = {10.1016/0166-4328(83)90180-8},
  abstract = {Many insects are known to exhibit clear circadian rest-activity rhythms. Attention has focussed more on active behaviors such as locomotion than on rest. I investigated the consequences of disturbances of the rest period on activity states of the cockroach Leucophea maderae. The 24-h rest-activity rhythm of individual animals maintained under a 12 h light-12 h dark schedule was continuously recorded by timelapse video recording. Three activity states were scored: locomotion, immobility, and limb or antenna movements without locomotion. The effect of (i) 3 h forced activity; and of (ii) handling and a new environment was studied. Forced activity during the last 3 h of the light period caused a significant reduction of locomotion, and of limb or antenna movements; and an enhancement of immobility in the first hours of the dark period. However, over the entire 12 h dark period, these parameters did not differ from control. Brief handling in conjunction with a change in environment during the last 3 h of the dark period, was followed by similar, though smaller changes in locomotion as seen after forced locomotion. The results indicate that the time spent in immobility corresponds to a resting state which is regulated as a function of prior activity. Thus immobility in an invertebrate may exhibit similar regulating mechanisms as rest or sleep in vertebrates. ?? 1983.},
  number = {3},
  journal = {Behav. Brain Res.},
  author = {Tobler, Irene},
  year = {1983},
  keywords = {cockroach,forced locomotion,rest-activity cycle},
  pages = {351--360},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CXEYPVXB/Tobler - 1983 - Effect of forced locomotion on the rest-activity c.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T5TIQWGN/Tobler - 1983 - Effect of forced locomotion on the rest-activity c.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/99UIAZPX/0166432883901808.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J4T65TDK/0166432883901808.html},
  pmid = {6871020}
}

@article{adams_genome_2000,
  title = {The Genome Sequence of {{Drosophila}} Melanogaster},
  volume = {287},
  number = {5461},
  journal = {Science (80-. ).},
  author = {Adams, Mark D. and Celniker, Susan E. and Holt, Robert A. and Evans, Cheryl A. and Gocayne, Jeannine D. and Amanatides, Peter G. and Scherer, Steven E. and Li, Peter W and Hoskins, Roger A. and Galle, Richard F. and George, Reed A. and Lewis, Suzanna E. and Richards, Stephen and Ashburner, Michael and Henderson, Scott N. and Sutton, Granger G. and Wortman, Jennifer R. and Yandell, Mark D. and Zhang, Qing and Chen, Lin X. and Brandon, Rhonda C. and Rogers, Yu-Hui Hui and Blazej, Robert G. and Champe, Mark and Pfeiffer, Barret D. and Wan, Kenneth H. and Doyle, Clare and Baxter, Evan G. and Helt, Gregg and Nelson, Catherine R and Gabor Miklos, George L and Abril, Josep F. and Agbayani, Anna and An, Hui Jin and {Andrews-Pfannkoch}, Cynthia and Baldwin, Danita and Ballew, Richard M. and Basu, Anand and Baxendale, James and Bayraktaroglu, Leyla and Beasley, Ellen M. and Beeson, Karen Y. and Benos, P. V. and Berman, Benjamin P. and Bhandari, Deepali and Bolshakov, Slava and Borkova, Dana and Botchan, Michael R. and Bouck, John and Brokstein, Peter and Brottier, Phillipe and Burtis, Kenneth C. and Busam, Dana A. and Butler, Heather and Cadieu, Edouard and Center, Angela and Chandra, Ishwar and Cherry, J.Michael and Cawley, Simon and Dahlke, Carl and Davenport, Lionel B. and Davies, Peter and {de Pablos}, Beatriz and Delcher, Arthur and Deng, Zuoming and Mays, Anne Deslattes and Dew, Ian and Dietz, Suzanne M. and Dodson, Kristina and Doup, Lisa E. and Downes, Michael and {Dugan-Rocha}, Shannon and Dunkov, Boris C. and Dunn, Patrick and Durbin, Kenneth J. and Evangelista, Carlos C. and Ferraz, Concepcion and Ferriera, Steven and Fleischmann, Wolfgang and Fosler, Carl and Gabrielian, Andrei E. and Garg, Neha S. and Gelbart, William M. and Glasser, Ken and Glodek, Anna and Gong, Fangcheng and Gorrell, J.Harley and Gu, Zhiping and Guan, Ping and Harris, Michael and Harris, Nomi L. and Harvey, Damon and Heiman, Thomas J. and Hernandez, Judith R. and Houck, Jarrett and Hostin, Damon and Houston, Kathryn A. and Howland, Timothy J. and Wei, Ming Hui and Ibegwam, Chinyere and Jalali, Mena and Kalush, Francis and Karpen, Gary H. and Ke, Zhaoxi and Kennison, James A. and Ketchum, Karen A. and Kimmel, Bruce E. and Kodira, Chinnappa D. and Kraft, Cheryl and Kravitz, Saul and Kulp, David and Lai, Zhongwu and Lasko, Paul and Lei, Yiding and Levitsky, Alexander A. and Li, Jiayin and Li, Zhenya and Liang, Yong and Lin, Xiaoying and Liu, Xiangjun and Mattei, Bettina and McIntosh, Tina C. and McLeod, Michael P. and McPherson, Duncan and Merkulov, Gennady and Milshina, Natalia V. and Mobarry, Clark and Morris, Joe and Moshrefi, Ali and Mount, Stephen M. and Moy, Mee and Murphy, Brian and Murphy, Lee and Muzny, Donna M. and Nelson, David L and Nelson, David R and Nelson, Keith A. and Nixon, Katherine and Nusskern, Deborah R. and Pacleb, Joanne M. and Palazzolo, Michael and Pittman, Gjange S. and Pan, Sue and Pollard, John and Puri, Vinita and Reese, Martin G. and Reinert, Knut and Remington, Karin and Saunders, Robert D and Scheeler, Frederick and Shen, Hua and Shue, Bixiang Christopher and Kiamos, Inga and Simpson, Michael and Skupski, Marian P. and Smith, Tom and Spier, Eugene and Spradling, Allan C. and Stapleton, Mark and Strong, Renee and Sun, Eric and Svirskas, Robert and Tector, Cyndee and Turner, Russell and Venter, Eli and Wang, Aihui H and Wang, Xin and Wang, Zhen Yuan and Wassarman, David A. and Weinstock, George M. and Weissenbach, Jean and Williams, Sherita M. and Woodage, Trevor and Worley, Kim C. and Wu, David and Yang, Song and Yao, Q.Alison and Ye, Jane and Yeh, Ru Fang and Zaveri, Jayshree S. and Zhan, Ming and Zhang, Guangren and Zhao, Qi and Zheng, Liansheng and Zheng, Xiangqun H. and Zhong, Fei N and Zhong, Wenyan and Zhou, Xiaojun and Zhu, Shiaoping and Zhu, Xiaohong and Smith, Hamilton O. and Gibbs, Richard A. and Myers, Eugene W. and Rubin, Gerald M. and Venter, J.Craig},
  year = {2000},
  pages = {2185--2195},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QMBA9P2E/Adams et al. - 2000 - The Genome Sequence of Drosophila melanogaster.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CXAUR4EK/2185.html}
}

@article{dissel_sleep_2015,
  title = {Sleep Restores Behavioral Plasticity to Drosophila Mutants},
  volume = {25},
  issn = {09609822},
  doi = {10.1016/j.cub.2015.03.027},
  abstract = {Given the role that sleep plays in modulating plasticity, we hypothesized that increasing sleep would restore memory to canonical memory mutants without specifically rescuing the causal molecular lesion. Sleep was increased using three independent strategies: activating the dorsal fan-shaped body, increasing the expression of Fatty acid binding protein (dFabp), or by administering the GABA-A agonist 4,5,6,7-tetrahydroisoxazolo-[5,4-c]pyridine-3-ol (THIP). Short-term memory (STM) or long-term memory (LTM) was evaluated in rutabaga (rut) and dunce (dnc) mutants using aversive phototaxic suppression and courtship conditioning. Each of the three independent strategies increased sleep and restored memory to rut and dnc mutants. Importantly, inducing sleep also reverses memory defects in a Drosophila model of Alzheimer's disease. Together, these data demonstrate that sleep plays a more fundamental role in modulating behavioral plasticity than previously appreciated and suggest that increasing sleep may benefit patients with certain neurological disorders.},
  number = {10},
  journal = {Curr. Biol.},
  author = {Dissel, Stephane and Angadi, Veena and Kirszenblat, Leonie and Suzuki, Yasuko and Donlea, Jeff and Klose, Markus and Koch, Zachary and English, Denis and {Winsky-Sommerer}, Raphaelle and Van Swinderen, Bruno and Shaw, Paul J},
  month = may,
  year = {2015},
  pages = {1270--1281},
  pmid = {25913403}
}

@article{demir_fruitless_2005,
  title = {Fruitless Splicing Specifies Male Courtship Behavior in {{Drosophila}}},
  volume = {121},
  issn = {00928674},
  doi = {10.1016/j.cell.2005.04.027},
  abstract = {All animals exhibit innate behaviors that are specified during their development. Drosophila melanogaster males (but not females) perform an elaborate and innate courtship ritual directed toward females (but not males). Male courtship requires products of the fruitless (fru) gene, which is spliced differently in males and females. We have generated alleles of fru that are constitutively spliced in either the male or the female mode. We show that male splicing is essential for male courtship behavior and sexual orientation. More importantly, male splicing is also sufficient to generate male behavior in otherwise normal females. These females direct their courtship toward other females (or males engineered to produce female pheromones). The splicing of a single neuronal gene thus specifies essentially all aspects of a complex innate behavior. Copyright \textcopyright{}2005 by Elsevier Inc.},
  number = {5},
  journal = {Cell},
  author = {Demir, Ebru and Dickson, Barry J.},
  month = jun,
  year = {2005},
  pages = {785--794},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GJ8ZBNXF/Demir and Dickson - 2005 - fruitless Splicing Specifies Male Courtship Behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IZLITA8G/Demir and Dickson - 2005 - fruitless Splicing Specifies Male Courtship Behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/C65MMG9U/S0092867405004071.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T2KI834S/S0092867405004071.html},
  pmid = {15935764}
}

@article{itskov_automated_2014,
  title = {Automated Monitoring and Quantitative Analysis of Feeding Behaviour in {{Drosophila}}},
  volume = {5},
  issn = {2041-1723},
  doi = {10.1038/ncomms5560},
  abstract = {Food ingestion is one of the defining behaviours of all animals, but its quantification and analysis remain challenging. This is especially the case for feeding behaviour in small, genetically tractable animals such as Drosophila melanogaster. Here, we present a method based on capacitive measurements, which allows the detailed, automated and high-throughput quantification of feeding behaviour. Using this method, we were able to measure the volume ingested in single sips of an individual, and monitor the absorption of food with high temporal resolution. We demonstrate that flies ingest food by rhythmically extending their proboscis with a frequency that is not modulated by the internal state of the animal. Instead, hunger and satiety homeostatically modulate the microstructure of feeding. These results highlight similarities of food intake regulation between insects, rodents, and humans, pointing to a common strategy in how the nervous systems of different animals control food intake.},
  language = {en},
  journal = {Nat. Commun.},
  author = {Itskov, Pavel M. and Moreira, Jos\'e-Maria and Vinnik, Ekaterina and Lopes, Gon{\c c}alo and Safarik, Steve and Dickinson, Michael H. and Ribeiro, Carlos},
  month = aug,
  year = {2014},
  keywords = {neuroscience,bioinformatics,Biological sciences},
  pages = {4560},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XMU49H48/Itskov et al. - 2014 - Automated monitoring and quantitative analysis of .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PN253HEB/ncomms5560.html},
  pmid = {25087594}
}

@article{donlea_use-dependent_2009,
  title = {Use-Dependent Plasticity in Clock Neurons Regulates Sleep Need in {{Drosophila}}.},
  volume = {324},
  issn = {1095-9203},
  doi = {10.1126/science.1166657},
  abstract = {Sleep is important for memory consolidation and is responsive to waking experience. Clock circuitry is uniquely positioned to coordinate interactions between processes underlying memory and sleep need. Flies increase sleep both after exposure to an enriched social environment and after protocols that induce long-term memory. We found that flies mutant for rutabaga, period, and blistered were deficient for experience-dependent increases in sleep. Rescue of each of these genes within the ventral lateral neurons (LNVs) restores increased sleep after social enrichment. Social experiences that induce increased sleep were associated with an increase in the number of synaptic terminals in the LNV projections into the medulla. The number of synaptic terminals was reduced during sleep and this decline was prevented by sleep deprivation.},
  number = {5923},
  journal = {Science},
  author = {Donlea, Jeffrey M and Ramanan, Narendrakumar and Shaw, Paul J},
  month = apr,
  year = {2009},
  keywords = {Female,Male,Memory,Brain,Brain: physiology,Models,Neurons,Social Behavior,Animals,Sleep,Sleep: physiology,Animal,Biological Clocks,Receptor,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,Nuclear Proteins,Period Circadian Proteins,Neuronal Plasticity,Neurons: physiology,Genes,Mutation,Drosophila Proteins: genetics,Drosophila Proteins: metabolism,Drosophila melanogaster: physiology,Receptors,Drosophila melanogaster: genetics,Synapses,Insect,Synapses: physiology,Neurons: ultrastructure,Sleep Deprivation,Biological Clocks: genetics,Circadian Rhythm: genetics,Nuclear Proteins: genetics,Nuclear Proteins: physiology,Drosophila Proteins: physiology,Adenylate Cyclase,Adenylate Cyclase: genetics,epidermal growth factor,Adenylate Cyclase: physiology,Drosophila melanogaster: cytology,Presynaptic Terminals,Presynaptic Terminals: physiology,Presynaptic Terminals: ultrastructure,Epidermal Growth Factor: genetics,Epidermal Growth Factor: metabolism,Invertebrate Peptide,Invertebrate Peptide: genetics,Invertebrate Peptide: metabolism,Serum Response Factor,Serum Response Factor: genetics,Serum Response Factor: physiology},
  pages = {105--8},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2FS54Q5M/Donlea et al. - 2009 - Use-dependent plasticity in clock neurons regulate.pdf},
  pmid = {19342592}
}

@article{imeri_how_2009,
  title = {How (and Why) the Immune System Makes Us Sleep},
  volume = {10},
  issn = {1471-003X},
  doi = {10.1038/nrn2576},
  abstract = {Good sleep is necessary for physical and mental health. For example, sleep loss impairs immune function, and sleep is altered during infection. Immune signalling molecules are present in the healthy brain, where they interact with neurochemical systems to contribute to the regulation of normal sleep. Animal studies have shown that interactions between immune signalling molecules (such as the cytokine interleukin 1) and brain neurochemical systems (such as the serotonin system) are amplified during infection, indicating that these interactions might underlie the changes in sleep that occur during infection. Why should the immune system cause us to sleep differently when we are sick? We propose that the alterations in sleep architecture during infection are exquisitely tailored to support the generation of fever, which in turn imparts survival value.},
  language = {en},
  number = {3},
  journal = {Nat. Rev. Neurosci.},
  author = {Imeri, Luca and Opp, Mark R.},
  month = mar,
  year = {2009},
  pages = {199--210},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JBGYCEX6/Imeri and Opp - 2009 - How (and why) the immune system makes us sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/85FGUQ83/nrn2576.html},
  pmid = {19209176}
}

@article{van_alphen_dynamic_2013,
  title = {A Dynamic Deep Sleep Stage in {{Drosophila}}},
  volume = {33},
  issn = {0270-6474},
  doi = {10.1523/JNEUROSCI.0061-13.2013},
  abstract = {How might one determine whether simple animals such as flies sleep in stages? Sleep in mammals is a dynamic process involving different stages of sleep intensity, and these are typically associated with measurable changes in brain activity (Blake and Gerard, 1937; Rechtschaffen and Kales, 1968; Webb and Agnew, 1971). Evidence for different sleep stages in invertebrates remains elusive, even though it has been well established that many invertebrate species require sleep (Campbell and Tobler, 1984; Hendricks et al., 2000; Shaw et al., 2000; Sauer et al., 2003). Here we used electrophysiology and arousal-testing paradigms to show that the fruit fly, Drosophila melanogaster, transitions between deeper and lighter sleep within extended bouts of inactivity, with deeper sleep intensities after $\sim$15 and $\sim$30 min of inactivity. As in mammals, the timing and intensity of these dynamic sleep processes in flies is homeostatically regulated and modulated by behavioral experience. Two molecules linked to synaptic plasticity regulate the intensity of the first deep sleep stage. Optogenetic upregulation of cyclic adenosine monophosphate during the day increases sleep intensity at night, whereas loss of function of a molecule involved in synaptic pruning, the fragile-X mental retardation protein, increases sleep intensity during the day. Our results show that sleep is not homogenous in insects, and suggest that waking behavior and the associated synaptic plasticity mechanisms determine the timing and intensity of deep sleep stages in Drosophila.},
  language = {eng},
  number = {16},
  journal = {J. Neurosci.},
  author = {{van Alphen}, Bart and Yap, Melvyn H.W. W. and Kirszenblat, Leonie and Kottler, Benjamin and {van Swinderen}, Bruno},
  month = apr,
  year = {2013},
  keywords = {Female,Male,Brain,Time Factors,Social Behavior,Animals,Drosophila,Animals- Genetically Modified,Drosophila Proteins,Gene Expression Regulation,Mutation,Locomotion,Sleep Stages,Synapses,Wakefulness,Optogenetics,Sleep Deprivation,Evoked Potentials,Nonlinear Dynamics,CREB-Binding Protein,Physical Stimulation,Adenylate Cyclase,Sensory Thresholds,Fragile X Mental Retardation Protein,Automatic Data Processing,Hu Paraneoplastic Encephalomyelitis Antigens,Statistics- Nonparametric,Tropomyosin},
  pages = {6917--6927},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VSYP3HEZ/Alphen et al. - 2013 - A Dynamic Deep Sleep Stage in Drosophila.pdf},
  pmid = {23595750}
}

@article{borbely_sleep_1981,
  title = {Sleep Deprivation: {{Effect}} on Sleep Stages and {{EEG}} Power Density in Man},
  volume = {51},
  issn = {00134694},
  doi = {10.1016/0013-4694(81)90225-X},
  abstract = {Sleep was analysed in 8 young adults subjects during two baseline nights and two recovery nights following 40.5 h sleep deprivation. Sleep stages were scored from the polygraph records according to conventional criteria. In addition, the EEG records of the entire nights were subjected to spectral analysis to compute the frequency distribution of the power density in the 0.25-25 Hz range for 0.5 Hz or 1.0 Hz bins. In the first recovery night, the power density in the delta band was significantly higher than baseline for total sleep time as well as for sleep stages 2, 3 and 4, 4 and REM. These changes were not restricted to the delta band, but extended to higher frequency bands. Minor, but significant, effects of sleep deprivation were seen in the power density distribution of the second recovery night. In the baseline nights, a progressive reduction of power density in the delta/theta range was present for successive non-REM-REM sleep cycles for total sleep time and stages 2, 3 and 4, and 4. The results show that effects of sleep deprivation as well as trends within the sleep periods are readily apparent from spectral analysis, but are inadequately reflected by conventional sleep scoring. When the power density values were integrated over the entire frequency range (0.75-25 Hz) for each non-REM-REM sleep cycle, an exponential decline from cycle 1 to cycle 3 was suggested. The present findings support the hypothesis that the EEG power density in the low frequency range is an indicator of a progressively declining process during sleep whose initial value is determined by the duration of prior waking.},
  number = {5},
  journal = {Electroencephalogr. Clin. Neurophysiol.},
  author = {Borbely, Alexander and Baumann, Fritz and Brandeis, Daniel and Strauch, Inge and Lehmann, Dietrich and Borb\'ely, A A and Baumann, Fritz and Brandeis, Daniel and Strauch, Inge and Lehmann, Dietrich},
  month = may,
  year = {1981},
  pages = {483--493},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9976PV49/001346948190225X.html},
  pmid = {6165548}
}

@article{sheeba_large_2008,
  title = {Large {{Ventral Lateral Neurons Modulate Arousal}} and {{Sleep}} in {{Drosophila}}},
  volume = {18},
  issn = {09609822},
  doi = {10.1016/j.cub.2008.08.033},
  abstract = {Background: Large ventral lateral clock neurons (lLNvs) exhibit higher daytime-light-driven spontaneous action-potential firing rates in Drosophila, coinciding with wakefulness and locomotor-activity behavior. To determine whether the lLNvs are involved in arousal and sleep/wake behavior, we examined the effects of altered electrical excitation of the LNvs. Results: LNv-hyperexcited flies reverse the normal day-night firing pattern, showing higher lLNv firing rates at night and pigment-dispersing-factor-mediated enhancement of nocturnal locomotor-activity behavior and reduced quantity and quality of sleep. lLNv hyperexcitation impairs sensory arousal, as shown by physiological and behavioral assays. lLNv-hyperexcited flies lacking sLNvs exhibit robust hyperexcitation-induced increases in nocturnal behavior, suggesting that the sLNvs are not essential for mediation of arousal. Conclusions: Light-activated lLNvs modulate behavioral arousal and sleep in Drosophila. \textcopyright{} 2008 Elsevier Ltd. All rights reserved.},
  number = {20},
  journal = {Curr. Biol.},
  author = {Sheeba, Vasu and Fogle, Keri J and Kaneko, Maki and Rashid, Saima and Chou, Yu Ting and Sharma, Vijay K and Holmes, Todd C},
  month = oct,
  year = {2008},
  keywords = {MOLNEURO},
  pages = {1537--1545},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VUCNGZKR/Sheeba et al. - 2008 - Large Ventral Lateral Neurons Modulate Arousal and.pdf},
  pmid = {18771923}
}

@article{liu_sleep_2015,
  title = {Sleep in {{Populations}} of {{Drosophila Melanogaster}}},
  volume = {2},
  issn = {2373-2822},
  doi = {10.1523/ENEURO.0071-15.2015},
  abstract = {The fruit fly Drosophila melanogaster is a diurnal insect active during the day with consolidated sleep at night. Social interactions between pairs of flies have been shown to affect locomotor activity patterns, but effects on locomotion and sleep patterns have not been assessed for larger populations. Here, we use a commercially available locomotor activity monitor (LAM25H) system to record and analyze sleep behavior. Surprisingly, we find that same-sex populations of flies synchronize their sleep/wake activity, resulting in a population sleep pattern, which is similar but not identical to that of isolated individuals. Like individual flies, groups of flies show circadian and homeostatic regulation of sleep, as well as sexual dimorphism in sleep pattern and sensitivity to starvation and a known sleep-disrupting mutation ( amnesiac ). Populations of flies, however, exhibit distinct sleep characteristics from individuals. Differences in sleep appear to be due to olfaction-dependent social interactions and change with population size and sex ratio. These data support the idea that it is possible to investigate neural mechanisms underlying the effects of population behaviors on sleep by directly looking at a large number of animals in laboratory conditions.},
  number = {4},
  journal = {eNeuro},
  author = {Liu, Chang and Haynes, Paula R and Donelson, Nathan C and Aharon, Shani and Griffith, Leslie C},
  year = {2015},
  keywords = {Sleep,Drosophila,Cues,Population,affected by social,although flies have been,an interactive environment in,and sleep can be,in recent years,most species live in,significance statement,the mechanisms of sleep,their natural habitats,widely used to understand,sleep,population},
  pages = {ENEURO.0071--15.2015},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MU9MMJTI/Liu et al. - 2015 - Sleep in Populations of Drosophila Melanogaster.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MKD4IIB3/eneuro.0071-15.html},
  pmid = {26465005}
}

@article{stahl_sleep-dependent_2017,
  title = {Sleep-{{Dependent Modulation Of Metabolic Rate In Drosophila}}},
  issn = {0161-8105},
  doi = {10.1093/sleep/zsx084},
  abstract = {Dysregulation of sleep is associated with metabolic diseases, and metabolic rate is acutely regulated by sleep-wake behavior. In humans and rodent models, sleep loss is associated with obesity, reduced metabolic rate, and negative energy balance, yet little is known about the neural mechanisms governing interactions between sleep and metabolism. We have developed a system to simultaneously measure sleep and metabolic rate in individual Drosophila, allowing for interrogation of neural systems governing interactions between sleep and metabolic rate. Like mammals, metabolic rate in flies is reduced during sleep and increased during sleep deprivation suggesting sleep-dependent regulation of metabolic rate is conserved across phyla. The reduction of metabolic rate during sleep is not simply a consequence of inactivity because metabolic rate is reduced $\sim$30 minutes following the onset of sleep, raising the possibility that CO2 production provides a metric to distinguish different sleep states in the fruit fly. To examine the relationship between sleep and metabolism, we determined basal and sleep-dependent changes in metabolic rate is reduced in starved flies, suggesting that starvation inhibits normal sleep-associated effects on metabolic rate. Further, translin mutant flies that fail to suppress sleep during starvation demonstrate a lower basal metabolic rate, but this rate was further reduced in response to starvation, revealing that regulation of starvation-induced changes in metabolic rate and sleep duration are genetically distinct. Therefore, this system provides the unique ability to simultaneously measure sleep and oxidative metabolism, providing novel insight into the physiological changes associated with sleep and wakefulness in the fruit fly.},
  journal = {bioRxiv},
  author = {Stahl, Bethany A. and Slocumb, Melissa and Chaitin, Hersh and DiAngelo, Justin and Keene, Alex C.},
  month = may,
  year = {2017},
  keywords = {Sleep,Drosophila,metabolism,calorimetry,respirometry},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YX2AVB6J/Stahl et al. - 2017 - Sleep-Dependent Modulation of Metabolic Rate in Dr.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XVFS4GC9/3852476.html},
  pmid = {28541527}
}

@article{chi_larval_2014,
  title = {Larval {{Population Density Alters Adult Sleep}} in {{Wild}}-{{Type Drosophila}} Melanogaster but {{Not}} in {{Amnesiac Mutant Flies}}},
  volume = {4},
  issn = {2076-3425},
  doi = {10.3390/brainsci4030453},
  abstract = {Sleep has many important biological functions, but how sleep is regulated remains poorly understood. In humans, social isolation and other stressors early in life can disrupt adult sleep. In fruit flies housed at different population densities during early adulthood, social enrichment was shown to increase subsequent sleep, but it is unknown if population density during early development can also influence adult sleep. To answer this question, we maintained Drosophila larvae at a range of population densities throughout larval development, kept them isolated during early adulthood, and then tested their sleep patterns. Our findings reveal that flies that had been isolated as larvae had more fragmented sleep than those that had been raised at higher population densities. This effect was more prominent in females than in males. Larval population density did not affect sleep in female flies that were mutant for amnesiac, which has been shown to be required for normal memory consolidation, adult sleep regulation, and brain development. In contrast, larval population density effects on sleep persisted in female flies lacking the olfactory receptor or83b, suggesting that olfactory signals are not required for the effects of larval population density on adult sleep. These findings show that population density during early development can alter sleep behavior in adulthood, suggesting that genetic and/or structural changes are induced by this developmental manipulation that persist through metamorphosis.},
  number = {3},
  journal = {Brain Sci},
  author = {Chi, Michael W and Griffith, Leslie C and Vecsey, Christopher G},
  month = aug,
  year = {2014},
  keywords = {development,sleep,<i>amnesiac</i>,<i>Drosophila</i>,<i>or83b</i>,population density,social isolation and enrichment},
  pages = {453--470},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7DTNWIX3/Chi et al. - 2014 - Larval Population Density Alters Adult Sleep in Wi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RG7B2ZLX/htm.html},
  pmid = {25116571}
}

@article{kuo_increased_2014,
  title = {Increased {{Sleep Promotes Survival}} during a {{Bacterial Infection}} in {{Drosophila}}},
  volume = {37},
  issn = {0161-8105},
  doi = {10.5665/sleep.3764},
  abstract = {STUDY OBJECTIVES: The relationship between sleep and immune function is not well understood at a functional or molecular level. We therefore used a genetic approach in Drosophila to manipulate sleep and evaluated effects on the ability of flies to fight bacterial infection.\$$\backslash$backslash\$n\$$\backslash$backslash\$nSETTING: Laboratory.\$$\backslash$backslash\$n\$$\backslash$backslash\$nPARTICIPANTS: Drosophila melanogaster.\$$\backslash$backslash\$n\$$\backslash$backslash\$nMETHODS AND RESULTS: We used a genetic approach to transiently alter neuronal excitability in the mushroom body, a region in the central brain that is known to regulate sleep. Flies with increased sleep for up to two days prior to a bacterial infection showed increased resistance to the infection and improved survival. These flies also had increased expression levels of a subset of anti-microbial peptide mRNA prior to infection, as well as increased NF$\kappa$B activity during infection as indicated by in vivo luciferase reporter activity. In contrast, flies that experienced reduced sleep for up to two days prior to infection had no effect on survival or on NF$\kappa$B activity during infection. However, flies with reduced sleep showed an altered defense mechanism, such that resistance to infection was increased, but at the expense of reduced tolerance. This effect was dependent on environmental condition.\$$\backslash$backslash\$n\$$\backslash$backslash\$nCONCLUSIONS: Increasing sleep enhanced activity of an NF$\kappa$B transcription factor, increased resistance to infection, and strongly promoted survival. Together, these findings support the hypothesis that sleep is beneficial to the host by maintaining a robust immune system.},
  number = {6},
  journal = {Sleep},
  author = {Kuo, Tzu-Hsing and Williams, Julie A},
  month = jun,
  year = {2014},
  keywords = {Drosophila,Ion Channels,bacterial infection,Innate immunity,NFκB},
  pages = {1077--86, 1086A--1086D},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YX5HEXLF/Kuo and Williams - 2014 - Increased Sleep Promotes Survival during a Bacteri.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5UUSYS2G/2416831.html},
  pmid = {24882902}
}

@article{ganguly-fitzgerald_waking_2006,
  title = {Waking {{Experience Affects Sleep Need}} in {{Drosophila}}},
  volume = {313},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1130408},
  abstract = {Sleep is a vital, evolutionarily conserved phenomenon, whose function is unclear. Although mounting evidence supports a role for sleep in the consolidation of memories, until now, a molecular connection between sleep, plasticity, and memory formation has been difficult to demonstrate. We establish Drosophila as a model to investigate this relation and demonstrate that the intensity and/or complexity of prior social experience stably modifies sleep need and architecture. Furthermore, this experience-dependent plasticity in sleep need is subserved by the dopaminergic and adenosine 3${'}$,5${'}$-monophosphate signaling pathways and a particular subset of 17 long-term memory genes.},
  language = {en},
  number = {5794},
  journal = {Science (80-. ).},
  author = {{Ganguly-Fitzgerald}, Indrani and Donlea, Jeff and Shaw, Paul J.},
  month = sep,
  year = {2006},
  pages = {1775--1781},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5CKMNDW7/Ganguly-Fitzgerald et al. - 2006 - Waking Experience Affects Sleep Need in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/M3ZFV8FL/Ganguly-Fitzgerald et al. - 2006 - Waking Experience Affects Sleep Need in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IL3L7BNR/1775.html}
}

@article{yokogawa_characterization_2007,
  title = {Characterization of Sleep in Zebrafish and Insomnia in Hypocretin Receptor Mutants},
  volume = {5},
  issn = {15449173},
  doi = {10.1371/journal.pbio.0050277},
  abstract = {Zebrafish sleep, and have the receptor for the wake-inducing molecule hypocretin. While mutation in this receptor causes narcolepsy in mammals, in fish, sleep is fragmented, demonstrating differences in sleep control in vertebrates.},
  number = {10},
  journal = {PLoS Biol.},
  author = {Yokogawa, Tohei and Marin, Wilfredo and Faraco, Juliette and P\'ezeron, Guillaume and Appelbaum, Lior and Zhang, Jian and Rosa, Fr\'ed\'eric and Mourrain, Philippe and Mignot, Emmanuel},
  month = oct,
  year = {2007},
  keywords = {Hypothalamus,Sleep,Narcolepsy,Mammals,Zebrafish,Sleep deprivation,Functional electrical stimulation,Sleep disorders},
  pages = {2379--2397},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BPUHXZYD/Yokogawa et al. - 2007 - Characterization of Sleep in Zebrafish and Insomni.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BRES3S9H/article.html},
  pmid = {17941721}
}

@article{klein_mapping_2014,
  title = {Mapping Sleeping Bees within Their Nest: {{Spatial}} and Temporal Analysis of Worker Honey Bee Sleep},
  volume = {9},
  issn = {19326203},
  doi = {10.1371/journal.pone.0102316},
  abstract = {Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns.},
  number = {7},
  journal = {PLoS One},
  author = {Klein, Barrett Anthony and Stiegler, Martin and Klein, Arno and Tautz, J\"urgen},
  editor = {Gronenberg, Wulfila},
  month = jul,
  year = {2014},
  keywords = {Honey bees,Cameras,Sleep,Abdomen,Bees,Social systems,Surface temperature,Thorax},
  pages = {e102316},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U26GXU7M/Klein et al. - 2014 - Mapping Sleeping Bees within Their Nest Spatial a.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/56WMDRHQ/article.html},
  pmid = {25029445}
}

@article{shaw_stress_2002,
  title = {Stress Response Genes Protect against Lethal Effects of Sleep Deprivation in {{Drosophila}}},
  volume = {417},
  issn = {0028-0836},
  doi = {10.1038/417287a},
  abstract = {Sleep is controlled by two processes: a homeostatic drive that increases during waking and dissipates during sleep, and a circadian pacemaker that controls its timing. Although these two systems can operate independently, recent studies indicate a more intimate relationship. To study the interaction between homeostatic and circadian processes in Drosophila, we examined homeostasis in the canonical loss-of-function clock mutants period (per01), timeless (tim01), clock (Clkjrk) and cycle (cyc01). cyc01 mutants showed a disproportionately large sleep rebound and died after 10 hours of sleep deprivation, although they were more resistant than other clock mutants to various stressors. Unlike other clock mutants, cyc01 flies showed a reduced expression of heat-shock genes after sleep loss. However, activating heat-shock genes before sleep deprivation rescued cyc01 flies from its lethal effects. Consistent with the protective effect of heat-shock genes, was the observation that flies carrying a mutation for the heat-shock protein Hsp83 (Hsp8308445) showed exaggerated homeostatic response and died after sleep deprivation. These data represent the first step in identifying the molecular mechanisms that constitute the sleep homeostat.},
  language = {en},
  number = {6886},
  journal = {Nature},
  author = {Shaw, Paul J. and Tononi, Giulio and Greenspan, Ralph J. and Robinson, Donald F.},
  month = may,
  year = {2002},
  keywords = {Cancer,Female,Biology,Evolutionary Biology,Science,Science Policy,Animals,Sleep,Darkness,Signal Transduction,CLOCK Proteins,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,Insect Proteins,Light,Nuclear Proteins,Period Circadian Proteins,Gene Expression Regulation,neuroscience,Mutation,Genetics,RNA,evolution,DNA,computational biology,Oxidative Stress,Wakefulness,immunology,Development,Genomics,Cell Cycle,Neurobiology,Homeostasis,Sleep Deprivation,Trans-Activators,molecular biology,Genes- Lethal,Stress- Physiological,Ecology,Food deprivation,Genes- Insect,cell signalling,developmental biology,Biochemistry,Nature,astronomy,astrophysics,bioinformatics,biotechnology,climate change,drug discovery,earth science,environmental science,functional genomics,geophysics,interdisciplinary science,life,marine biology,materials science,medical research,medicine,metabolomics,molecular interactions,nanotechnology,palaeobiology,pharmacology,physics,proteomics,quantum physics,science news,structural biology,systems biology,transcriptomics,ARNTL Transcription Factors,Basic Helix-Loop-Helix Transcription Factors,Survival Rate,Dehydration,Heat-Shock Proteins,Heat-Shock Response},
  pages = {287--291},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5MAZ8CQD/Shaw et al. - 2002 - Stress response genes protect against lethal effec.pdf}
}

@article{gopalakrishnan_sleep_2004,
  title = {Sleep Deprivation and Cellular Responses to Oxidative Stress.},
  volume = {27},
  issn = {0161-8105},
  abstract = {STUDY OBJECTIVES: It has been hypothesized that sleep deprivation represents an oxidative challenge for the brain and that sleep may have a protective role against oxidative damage. This study was designed to test this hypothesis by measuring in rats the effects of sleep loss on markers of oxidative stress (oxidant production and antioxidant enzyme activities) as well as on markers of cellular oxidative damage (lipid peroxidation and protein oxidation). DESIGN: The analyses were performed in the brain and in peripheral tissues (liver and skeletal muscle), after short-term sleep deprivation (8 hours), after long-term sleep deprivation (3-14 days), and during recovery sleep after 1 week of sleep loss. Short-term sleep deprivation was performed by gentle handling; long-term sleep deprivation was performed using the disk-over-water method. SETTING: Sleep research laboratory at University of Wisconsin-Madison. PARTICIPANTS AND INTERVENTIONS: Adult male Wistar Kyoto rats (n = 69) implanted for polygraphic (electroencephalogram, electromyogram) recording. MEASUREMENTS AND RESULTS: Aliquots of brain, liver, or skeletal muscle homogenate were used to assess oxidant production, superoxide dismutase activity, lipid peroxidation, and protein oxidation. No evidence of oxidative damage was observed at the lipid and/or at the protein level in long-term sleep-deprived animals relative to their yoked controls, nor in the cerebral cortex or in peripheral tissues. Also, no consistent change in antioxidant enzymatic activities was found after prolonged sleep deprivation, nor was any evidence of increased oxidant production in the brain or in peripheral tissues. CONCLUSION: The available data do not support the assumption that prolonged wakefulness may cause oxidative damage, nor that it can represent an oxidative stress for the brain or for peripheral tissue such as liver and skeletal muscle.},
  number = {1},
  journal = {Sleep},
  author = {Gopalakrishnan, Anupama and Ji, Li Li and Cirelli, Chiara},
  month = feb,
  year = {2004},
  keywords = {rat,Cerebral Cortex,Stress,Oxidative Stress,citation,Sleep Deprivation,Norepinephrine,1,27,sleep 2004,27-35,cirelli c,disk-over-water method,gopalakrishnan a,ji ll,lar responses to oxidative,sleep deprivation and cellu-},
  pages = {27--35},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DWXFGZKS/Gopalakrishnan et al. - 2004 - Sleep Deprivation and Cellular Responses to Oxidat.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/73JPLE3V/2707929.html},
  pmid = {14998234}
}

@article{faville_how_2015,
  title = {How Deeply Does Your Mutant Sleep? {{Probing}} Arousal to Better Understand Sleep Defects in {{Drosophila}}},
  volume = {5},
  issn = {2045-2322},
  shorttitle = {How Deeply Does Your Mutant Sleep?},
  doi = {10.1038/srep08454},
  abstract = {The fruitfly, Drosophila melanogaster, has become a critical model system for investigating sleep functions. Most studies use duration of inactivity to measure sleep. However, a defining criterion for sleep is decreased behavioral responsiveness to stimuli. Here we introduce the Drosophila ARousal Tracking system (DART), an integrated platform for efficiently tracking and probing arousal levels in animals. This video-based platform delivers positional and locomotion data, behavioral responsiveness to stimuli, sleep intensity measures, and homeostatic regulation effects - all in one combined system. We show how insight into dynamically changing arousal thresholds is crucial for any sleep study in flies. We first find that arousal probing uncovers different sleep intensity profiles among related genetic background strains previously assumed to have equivalent sleep patterns. We then show how sleep duration and sleep intensity can be uncoupled, with distinct manipulations of dopamine function producing opposite effects on sleep duration but similar sleep intensity defects. We conclude by providing a multi-dimensional assessment of combined arousal and locomotion metrics in the mutant and background strains. Our approach opens the door for deeper insights into mechanisms of sleep regulation and provides a new method for investigating the role of different genetic manipulations in controlling sleep and arousal.},
  journal = {Sci. Rep.},
  author = {Faville, R. and Kottler, B. and Goodhill, G. J. and Shaw, P. J. and {van Swinderen}, B. and Swinderen, B Van and {van Swinderen}, B.},
  month = feb,
  year = {2015},
  pages = {8454},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9V8EC9HF/Faville et al. - 2015 - How deeply does your mutant sleep Probing arousal.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QEDTVVVC/srep08454.html},
  pmid = {25677943}
}

@article{zehring_p-element_1984,
  title = {P-Element Transformation with Period Locus {{DNA}} Restores Rhythmicity to Mutant, Arrhythmic Drosophila Melanogaster},
  volume = {39},
  issn = {00928674},
  doi = {10.1016/0092-8674(84)90015-1},
  abstract = {Mutations at the period (per) locus of Drosophila melanogaster disrupt several biological rhythms. Molecular cloning of DNA sequences encompassing the per+ locus has allowed germ-line transformation experiments to be carried out. Certain subsegments of the per region, transduced into the genome of arrhythmic pero flies, restore rhythmicity in circadian locomotor behavior and the male's courtship song. ?? 1984.},
  number = {2 PART 1},
  journal = {Cell},
  author = {Zehring, William A. and Wheeler, David A. and Reddy, Pranhitha and Konopka, Ronald J. and Kyriacou, Charalambos P. and Rosbash, Michael and Hall, Jeffrey C.},
  month = dec,
  year = {1984},
  keywords = {Sexual Behavior; Animal,Female,Male,Animals,Circadian Rhythm,Drosophila melanogaster,Genes,Mutation,Phenotype,DNA Restriction Enzymes,Cloning; Molecular,Transformation; Genetic,Vocalization; Animal},
  pages = {369--376},
  pmid = {6094014}
}

@article{kaiser_neuronal_1983,
  title = {Neuronal Correlates of Sleep, Wakefulness and Arousal in a Diurnal Insect},
  volume = {301},
  issn = {0028-0836},
  doi = {10.1038/301707a0},
  number = {5902},
  journal = {Nature},
  author = {Kaiser, Walter and {Steiner-Kaiser}, Jana},
  month = feb,
  year = {1983},
  pages = {707--709},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D7CU2PEQ/Kaiser and Steiner-Kaiser - 1983 - Neuronal correlates of sleep, wakefulness and arou.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F7WZ3S43/301707a0.html}
}

@article{parisky_reorganization_2016,
  title = {Reorganization of {{Sleep}} by {{Temperature}} in {{Drosophila Requires Light}}, the {{Homeostat}}, and the {{Circadian Clock}}},
  volume = {26},
  issn = {09609822},
  doi = {10.1016/j.cub.2016.02.011},
  abstract = {Increasing ambient temperature reorganizes the Drosophila sleep pattern in a way similar to the human response to heat, increasing daytime sleep while decreasing nighttime sleep. Mutation of core circadian genes blocks the immediate increase in daytime sleep, but not the heat-stimulated decrease in nighttime sleep, when animals are in a light:dark cycle. The ability of per01 flies to increase daytime sleep in light:dark can be rescued by expression of PER in either LNv or DN1p clock cells and does not require rescue of locomotor rhythms. Prolonged heat exposure engages the homeostat to maintain daytime sleep in the face of nighttime sleep loss. In constant darkness, all genotypes show an immediate decrease in sleep in response to temperature shift during the subjective day, implying that the absence of light input uncovers a clock-independent pro-arousal effect of increased temperature. Interestingly, the effects of temperature on nighttime sleep are blunted in constant darkness and in cryOUT mutants in light:dark, suggesting that they are dependent on the presence of light the previous day. In contrast, flies of all genotypes kept in constant light sleep more at all times of day in response to high temperature, indicating that the presence of light can invert the normal nighttime response to increased temperature. The effect of temperature on sleep thus reflects coordinated regulation by light, the homeostat, and components of the clock, allowing animals to reorganize sleep patterns in response to high temperature with rough preservation of the total amount of sleep.},
  number = {7},
  journal = {Curr. Biol.},
  author = {Parisky, Katherine M. and Agosto Rivera, Jos\'e L. and Donelson, Nathan C. and Kotecha, Sejal and Griffith, Leslie C.},
  year = {2016},
  pages = {882--892},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3WRNC3PN/Parisky et al. - 2016 - Reorganization of Sleep by Temperature in Drosophi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VGYCN83S/S096098221630063X.html},
  pmid = {26972320}
}

@article{xie_sleep_2013,
  title = {Sleep Drives Metabolite Clearance from the Adult Brain.},
  volume = {342},
  issn = {1095-9203},
  doi = {10.1126/science.1241224},
  abstract = {The conservation of sleep across all animal species suggests that sleep serves a vital function. We here report that sleep has a critical function in ensuring metabolic homeostasis. Using real-time assessments of tetramethylammonium diffusion and two-photon imaging in live mice, we show that natural sleep or anesthesia are associated with a 60\% increase in the interstitial space, resulting in a striking increase in convective exchange of cerebrospinal fluid with interstitial fluid. In turn, convective fluxes of interstitial fluid increased the rate of $\beta$-amyloid clearance during sleep. Thus, the restorative function of sleep may be a consequence of the enhanced removal of potentially neurotoxic waste products that accumulate in the awake central nervous system.},
  language = {en},
  number = {6156},
  journal = {Science},
  author = {Xie, Lulu and Kang, Hongyi and Xu, Qiwu and Chen, Michael J. and Liao, Yonghong and Thiyagarajan, Meenakshisundaram and O'Donnell, John and Christensen, Daniel J. and Nicholson, Charles and Iliff, Jeffrey J. and Takano, Takahiro and Deane, Rashid and Nedergaard, Maiken},
  month = oct,
  year = {2013},
  pages = {373--7},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8M7PRZ87/Xie et al. - 2013 - Sleep drives metabolite clearance from the adult b.pdf},
  pmid = {24136970}
}

@article{konopka_clock_1971,
  title = {Clock Mutants of {{Drosophila}} Melanogaster.},
  volume = {68},
  issn = {0027-8424},
  doi = {10.1073/pnas.68.9.2112},
  abstract = {Three mutants have been isolated in which the normal 24-hour rhythm is drastically changed. One mutant is arrhythmic; another has a period of 19 hr; a third has a period of 28 hr. Both the eclosion rhythm of a population and the locomotor activity of individual flies are affected. All these mutations appear to involve the same functional gene on the X chromosome.},
  number = {9},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  author = {Konopka, R J and Benzer, S},
  month = sep,
  year = {1971},
  keywords = {Sex chromosomes,Female,Male,Animals,Circadian Rhythm,Drosophila melanogaster,Genetic,Genes,Chromosome Mapping,Mutation,Genotype,Locomotion,Phenotype,Recombination,Temperature,Genetic Linkage,Recombination; Genetic,Sex Chromosomes},
  pages = {2112--6},
  pmid = {5002428}
}

@article{garbe_changes_2016,
  title = {Changes in {{Female Drosophila Sleep}} Following {{Mating Are Mediated}} by {{SPSN}}-{{SAG Neurons}}},
  volume = {XX},
  issn = {0748-7304},
  doi = {10.1177/0748730416668048},
  abstract = {Female Drosophila melanogaster, like many other organisms, exhibit different behavioral repertoires after mating with a male. These postmating responses (PMRs) include increased egg production and laying, increased rejection behavior (avoiding further male advances), decreased longevity, altered gustation and decreased sleep. Sex Peptide (SP), a protein transferred from the male during copulation, is largely responsible for many of these behavioral responses, and acts through a specific circuit to induce rejection behavior and alter dietary preference. However, less is known about the mechanisms and neurons that influence sleep in mated females. In this study, we investigated postmating changes in female sleep across strains and ages and on different media, and report that these changes are robust and relatively consistent under a variety of conditions. We find that female sleep is reduced by male-derived SP acting through the canonical sex peptide receptor (SPR) within the same neurons responsible for altering other PMRs. This circuit includes the SPSN-SAG neurons, whose silencing by DREADD induces postmating behaviors including sleep. Our data are consistent with the idea that mating status is communicated to the central brain through a common circuit that diverges in higher brain centers to modify a collection of postmating sensorimotor processes.},
  number = {X},
  journal = {J. Biol. Rhythms},
  author = {Garbe, D. S. and Vigderman, A. S. and Moscato, E. and Dove, A. E. and Vecsey, C. G. and Kayser, M. S. and Sehgal, A.},
  month = dec,
  year = {2016},
  keywords = {Sleep,Drosophila,Sex peptide,sex peptide receptor,DREADD,Gender,across many insect species,for example,in,influence an organism,mating alters a variety,of behaviors and physiological,responses that can,s fitness},
  pages = {551--567},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8M7DX5UB/Garbe et al. - 2016 - Changes in Female Drosophila Sleep following Matin.pdf},
  pmid = {27658900}
}

@article{cirelli_extensive_2004,
  title = {Extensive and Divergent Effects of Sleep and Wakefulness on Brain Gene Expression.},
  volume = {41},
  issn = {0896-6273},
  doi = {10.1016/s0896-6273(03)00814-6},
  abstract = {Sleep is present in all species where it has been studied, but its functions remain unknown. To investigate what benefits sleep may bring at the cellular level, we profiled gene expression in awake and sleeping rats by using high-density microarrays. We find that approximately 10\% of the transcripts in the cerebral cortex change their expression between day and night and demonstrate that half of them are modulated by sleep and wakefulness independent of time of day. We also show that molecular correlates of sleep are found in the cerebellum, a structure not known for generating sleep rhythms. Finally, we show that different functional categories of genes are selectively associated with sleep and wakefulness. The approximately 100 known genes whose expression increases during sleep provide molecular support for the proposed involvement of sleep in protein synthesis and neural plasticity and point to a novel role for sleep in membrane trafficking and maintenance.},
  number = {1},
  journal = {Neuron},
  author = {Cirelli, Chiara and Gutierrez, Christina M. and Tononi, Giulio and Ahn, S. and Ginty, D.D. and Linden, D.J. and Akhtar, R.A. and Reddy, A.B. and Maywood, E.S. and Clayton, J.D. and King, V.M. and Smith, A.G. and Gant, T.W. and Hastings, M.H. and Kyriacou, C.P. and {Aston-Jones}, G. and Bloom, F.E. and Bolstad, B.M. and Irizarry, R.A. and Astrand, M. and Speed, T.P. and Borb\'ely, A.A. and Achermann, P. and Cameron, A.M. and Steiner, J.P. and Roskams, A.J. and Ali, S.M. and Ronnett, G.V. and Snyder, S.H. and Ceriani, M.F. and Hogenesch, J.B. and Yanovsky, M. and Panda, S. and Straume, M. and Kay, S.A. and Cirelli, Chiara and Cirelli, Chiara and Tononi, Giulio and Cirelli, Chiara and Tononi, Giulio and Cirelli, Chiara and Pompeiano, M. and Tononi, Giulio and {Claridge-Chang}, A. and Wijnen, H. and Naef, F. and Boothroyd, C. and Rajewsky, N. and Young, M.W. and Cooper, J.R. and Bloom, F.E. and Roth, R.H. and Ereci\~nska, M. and Silver, I.A. and Frank, M.G. and Issa, N.P. and Stryker, M.P. and Goldstein, S.A. and Bockenhauer, D. and O'Kelly, I. and Zilberberg, N. and Gruenberg, J. and Hobson, J.A. and Hobson, J.A. and McCarley, R.W. and Horne, J.A. and Jurevics, H. and Hostettler, J. and Barrett, C. and Morell, P. and Toews, A.D. and Kang, H. and Sun, L.D. and Atkins, C.M. and Soderling, T.R. and Wilson, M.A. and Tonegawa, S. and Kaufman, R.J. and Scheuner, D. and Schroder, M. and Shen, X. and Lee, K. and Liu, C.Y. and Arnold, S.M. and Kramer, E.M. and Schardt, A. and Nave, K.A. and Krueger, J.M. and Obal, F. and Kapas, L. and Fang, J. and Li, W.W. and Alexandre, S. and Cao, X. and Lee, A.S. and Lin, Y. and Han, M. and Shimada, B. and Wang, L. and Gibler, T.M. and Amarakone, A. and Awad, T.A. and Stormo, G.D. and Gelder, R.N. Van and Taghert, P.H. and Maquet, P. and Maquet, P. and Masubuchi, S. and Honma, S. and Abe, H. and Ishizaki, K. and Namihira, M. and Ikeda, M. and Honma, K. and Mauch, D.H. and Nagler, K. and Schumacher, S. and Goritz, C. and Muller, E.C. and Otto, A. and Pfieger, F.W. and McCormick, D.A. and Bal, T. and McDonald, M.J. and Rosbash, M. and Meuthw, S.G. and Budde, T. and Kanyshkova, T. and Broicher, T. and Munsch, T. and Pape, H.C. and Moruzzi, G. and Nakanishi, H. and Sun, Y. and Nakamura, R.K. and Mori, K. and Ito, M. and Suda, S. and Namba, H. and Storch, F.I. and Dang, T.P. and Mendelson, W. and Al., Et and Ogawa, A. and Yano, M. and Tsujinaka, T. and Morimoto, T. and Morita, S. and Taniguchi, M. and Shiozaki, H. and Okamoto, K. and Sato, S. and Monden, M. and Panda, S. and Antoch, M.P. and Miller, B.H. and Su, A.I. and Schook, A.B. and Straume, M. and Schultz, P.G. and Kay, S.A. and Takahashi, J.S. and Hogenesch, J.B. and Petit, J.M. and Tobler, I. and Allaman, I. and Borbely, A.A. and Magistretti, P.J. and Ramm, P. and Smith, C.T. and Rechtschaffen, A. and Rhyner, T.A. and Borbely, A.A. and Mallet, J. and Shaffery, J.P. and Sinton, C.M. and Bissette, G. and Roffwarg, H.P. and Marks, G.A. and Shaw, P.J. and Cirelli, Chiara and Greenspan, R.J. and Tononi, Giulio and Shaw, P.J. and Tononi, Giulio and Greenspan, R.J. and Robinson, D.F. and Steriade, M. and Hobson, J.A. and Steriade, M. and Timofeev, I. and Stickgold, R. and Hobson, J.A. and Fosse, R. and Fosse, M. and Storch, K.F. and Lipan, O. and Leykin, I. and Viswanathan, N. and Davis, F.C. and Wong, W.H. and Weitz, C.J. and Terao, A. and Steininger, T.L. and Hyder, K. and {Apte-Deshpande}, A. and Ding, J. and Rishipathak, D. and Davis, R.W. and Heller, H.C. and Kilduff, T.S. and Tobler, I. and Tononi, Giulio and Cirelli, Chiara and Tononi, Giulio and Cirelli, Chiara and Ueda, H.R. and Chen, W. and Adachi, A. and Wakamatsu, H. and Hayashi, S. and Takasugi, T. and Nagano, M. and Nakahama, K. and Suzuki, Y. and Sugano, S. and Al., Et and Ueda, H.R. and Matsumoto, A. and Kawamura, M. and Iino, M. and Tanimura, T. and Hashimoto, S. and Dongen, H.P.A. Van and Maislin, G. and Mullington, J.M. and Dinges, D.F. and Walker, M.P. and Brakefield, T. and Morgan, A. and Hobson, J.A. and Stickgold, R. and Wisor, J.P. and O'Hara, B.F. and Terao, A. and Selby, C.P. and Kilduff, T.S. and Sancar, A. and Edgar, D.M. and Franken, P. and Wuarin, J. and Schibler, U. and Yamada, M. and Nagatomo, J. and Setoguchi, Y. and Kuroki, N. and Higashi, S. and Setoguchi, T.},
  month = jan,
  year = {2004},
  pages = {35--43},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CPA7IZSN/Cirelli et al. - 2004 - Extensive and divergent effects of sleep and wakef.pdf},
  pmid = {14715133}
}

@article{kuo_sleep_2010,
  title = {Sleep Triggered by an Immune Response in {{Drosophila}} Is Regulated by the Circadian Clock and Requires the {{NFkappaB Relish}}},
  volume = {11},
  issn = {1471-2202},
  doi = {10.1186/1471-2202-11-17},
  abstract = {BACKGROUND: Immune challenge impacts behavior in many species. In mammals, this adaptive behavior is often manifested as an increase in sleep. Sleep has therefore been proposed to benefit the host by enhancing immune function and thereby overcome the challenge. To facilitate genetic studies on the relationship between sleep and immune function, we characterized the effect of the immune response on sleep in Drosophila melanogaster. Behavioral features of sleep as well as the innate immune response signaling pathways are well characterized in flies and are highly conserved in mammals. RESULTS: An immune response induced by infection with Gram-negative bacteria or by aseptic injury increased sleep in flies. The increase in sleep occurred during the morning hours after treatment and the magnitude of the effect was dependent on the time-of-day of inoculation or injury such that night-time treatment had a stronger effect than that during the daytime. This pattern persisted in constant darkness, indicating a role of the circadian clock. Mutants of the circadian clock gene, period, eliminated the increase in sleep observed in the morning, but instead showed enhanced sleep immediately after injury or infection.Null mutants of the Nuclear Factor kappaB (NFkappaB) Relish, which is central to the innate immune response, do not increase sleep in response to injury or infection at any time of day. Instead, they maintain a normal sleep pattern until they die. Expression of a full-length Relish transgene in the fat bodies of Relish mutants restored the morning increase in sleep during an immune response. Fat bodies are a major site of immune signalling in flies and have a key role in host defense. CONCLUSIONS: These data demonstrate that an immune response increases sleep in flies in a manner that is gated by the circadian clock and that requires the NFkappaB Relish. These findings support a role of sleep in a recovery process and demonstrate a conserved feature of the Drosophila model of sleep.},
  language = {en},
  number = {1},
  journal = {BMC Neurosci.},
  author = {Kuo, Tzu-Hsing and Pike, Douglas H. and Beizaeipour, Zahra and Williams, Julie A.},
  month = feb,
  year = {2010},
  keywords = {Baseline Sleep,Circadian Clock,Immune Challenge,Injured Group,Locomotor Activity Rhythm},
  pages = {17},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W64P69PN/Kuo et al. - 2010 - Sleep triggered by an immune response in Drosophil.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7KBQKTYL/1471-2202-11-17.html},
  pmid = {20144235}
}

@article{tobler_rest_1988,
  title = {Rest in the Scorpion\textemdash{}a Sleep-like State?},
  volume = {163},
  issn = {0340-7594},
  doi = {10.1007/BF00612431},
  abstract = {Forest-dwelling scorpions (Heterometrus, Pandinus) were continuously observed by time- lapse video recording and their behavior and body position were analyzed. Activity recorded on the tapes was scored into three states:(1) activity,(2) alert immobility, and (3) relaxed ...},
  number = {2},
  journal = {J. Comp. Physiol. A Neuroethol.},
  author = {Tobler, Irene and Stalder, Jaqueline},
  year = {1988},
  pages = {227--235},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HS7LLCQE/Tobler and Stalder - 1988 - Rest in the scorpion — a sleep-like state.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3MJRNW83/BF00612431.html}
}

@article{bellen_100_2010,
  title = {100 Years of {{Drosophila}} Research and Its Impact on Vertebrate Neuroscience: A History Lesson for the Future},
  volume = {11},
  issn = {1471-003X},
  shorttitle = {100 Years of {{Drosophila}} Research and Its Impact On},
  doi = {10.1038/nrn2839},
  abstract = {Discoveries in fruit flies have greatly contributed to our understanding of neuroscience. The use of an unparalleled wealth of tools, many of which originated between 1910\textendash{}1960, has enabled milestone discoveries in nervous system development and function. Such findings have triggered and guided many research efforts in vertebrate neuroscience. After 100 years, fruit flies continue to be the choice model system for many neuroscientists. The combinational use of powerful research tools will ensure that this model organism will continue to lead to key discoveries that will impact vertebrate neuroscience.},
  language = {en},
  number = {7},
  journal = {Nat. Rev. Neurosci.},
  author = {Bellen, Hugo J. and Tong, Chao and Tsuda, Hiroshi},
  month = jul,
  year = {2010},
  pages = {514--522},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3526WHSD/Bellen et al. - 2010 - 100 years of Drosophila research and its impact on.pdf}
}

@article{glou_circadian_2012,
  title = {Circadian Modulation of Consolidated Memory Retrieval Following Sleep Deprivation in {{Drosophila}}},
  volume = {35},
  issn = {1550-9109},
  doi = {10.5665/sleep.2118},
  abstract = {OBJECTIVES: Several lines of evidence indicate that sleep plays a critical role in learning and memory. The aim of this study was to evaluate anesthesia resistant memory following sleep deprivation in Drosophila. DESIGN: Four to 16 h after aversive olfactory training, flies were sleep deprived for 4 h. Memory was assessed 24 h after training. Training, sleep deprivation, and memory tests were performed at different times during the day to evaluate the importance of the time of day for memory formation. The role of circadian rhythms was further evaluated using circadian clock mutants. RESULTS: Memory was disrupted when flies were exposed to 4 h of sleep deprivation during the consolidation phase. Interestingly, normal memory was observed following sleep deprivation when the memory test was performed during the 2 h preceding lights-off, a period characterized by maximum wake in flies. We also show that anesthesia resistant memory was less sensitive to sleep deprivation in flies with disrupted circadian rhythms. CONCLUSIONS: Our results indicate that anesthesia resistant memory, a consolidated memory less costly than long-term memory, is sensitive to sleep deprivation. In addition, we provide evidence that circadian factors influence memory vulnerability to sleep deprivation and memory retrieval. Taken together, the data show that memories weakened by sleep deprivation can be retrieved if the animals are tested at the optimal circadian time.},
  language = {eng},
  number = {10},
  journal = {Sleep},
  author = {Glou, Eric Le and Seugnet, Laurent and Shaw, Paul J and Preat, Thomas and Goguel, Val\'erie and Le Glou, Eric and Seugnet, Laurent and Shaw, Paul J and Preat, Thomas and Goguel, Val\'erie and Glou, Eric Le and Seugnet, Laurent and Shaw, Paul J and Preat, Thomas and Goguel, Val\'erie},
  month = oct,
  year = {2012},
  keywords = {Female,Memory,Animals,Drosophila,Circadian Rhythm,Drosophila melanogaster,Mutation,Circadian rhythms,10,citation,Sleep Deprivation,memory retrieval,seugnet l,shaw pj,memory consolidation,Conditioning- Classical,1377-1384,35,activity peak,circadian modulation of consolidated,clock mutant,deprivation in,goguel v,le glou e,memory retrieval following sleep,preat t,recall,sleep 2012},
  pages = {1377--1384B}
}

@article{borbely_two-process_2016,
  title = {The Two-Process Model of Sleep Regulation: {{A}} Reappraisal},
  volume = {25},
  issn = {13652869},
  doi = {10.1111/jsr.12371},
  abstract = {In the last three decades the two-process model of sleep regulation has served as a major conceptual framework in sleep research. It has been applied widely in studies on fatigue and performance and to dissect individual differences in sleep regulation. The model posits that a homeostatic process (Process S) interacts with a process controlled by the circadian pacemaker (Process C), with time-courses derived from physiological and behavioural variables. The model simulates successfully the timing and intensity of sleep in diverse experimental protocols. Electrophysiological recordings from the suprachiasmatic nuclei (SCN) suggest that S and C interact continuously. Oscillators outside the SCN that are linked to energy metabolism are evident in SCN-lesioned arrhythmic animals subjected to restricted feeding or methamphetamine administration, as well as in human subjects during internal desynchronization. In intact animals these peripheral oscillators may dissociate from the central pacemaker rhythm. A sleep/fast and wake/feed phase segregate antagonistic anabolic and catabolic metabolic processes in peripheral tissues. A deficiency of Process S was proposed to account for both depressive sleep disturbances and the antidepressant effect of sleep deprivation. The model supported the development of novel non-pharmacological treatment paradigms in psychiatry, based on manipulating circadian phase, sleep and light exposure. In conclusion, the model remains conceptually useful for promoting the integration of sleep and circadian rhythm research. Sleep appears to have not only a short-term, use-dependent function; it also serves to enforce rest and fasting, thereby supporting the optimization of metabolic processes at the appropriate phase of the 24-h cycle.},
  number = {2},
  journal = {J. Sleep Res.},
  author = {Borb\'ely, Alexander A. and Daan, Serge and {Wirz-Justice}, Anna and Deboer, Tom},
  month = apr,
  year = {2016},
  keywords = {rest-activity cycle,Circadian phase,Forced desynchrony,Napping,Neuronal light response,Seasonal affective disorder,circadian phase,forced desynchrony,napping,neuronal light response,seasonal affective disorder},
  pages = {131--143},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Y4T3FEAC/Borbély et al. - The two-process model of sleep regulation a reapp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BX84DDWF/00061050.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SHW79757/jsr.html},
  pmid = {26762182}
}

@article{koh_identification_2008,
  title = {Identification of {{SLEEPLESS}}, a Novel Sleep-Promoting Factor},
  volume = {321},
  issn = {0036-8075},
  doi = {10.1126/science.1155942},
  abstract = {Sleep is an essential process conserved from flies to humans. The importance of sleep is underscored by its tight homeostatic control. Here, through a forward-genetic screen, we identify a novel gene, sleepless, required for sleep in Drosophila. sleepless encodes a brain-enriched, glycosyl-phosphatidylinositol-anchored protein. Loss of SLEEPLESS protein causes an extreme ($\backslash$textgreater80\%) reduction in sleep. Furthermore, a moderate reduction in SLEEPLESS protein has minimal effects on baseline sleep, but markedly reduces recovery sleep following sleep deprivation. Genetic and molecular analyses reveal that quiver, a mutation that impairs Shaker-dependent K+ current, is an allele of sleepless. Consistent with this finding, Shaker protein level is reduced in sleepless mutants. We propose that SLEEPLESS is a signaling molecule that connects sleep drive to lowered membrane excitability.},
  number = {5887},
  journal = {Science},
  author = {Koh, Kyunghee and Joiner, William J. and Wu, Mark N. and Yue, Zhifeng and Smith, Corinne J. and Sehgal, Amita},
  month = jul,
  year = {2008},
  pages = {372--376},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GYSJWNXQ/Koh et al. - 2008 - Identification of SLEEPLESS, a novel sleep-promoti.pdf}
}

@article{tononi_sleep_2014,
  title = {Sleep and the Price of Plasticity: From Synaptic and Cellular Homeostasis to Memory Consolidation and Integration.},
  volume = {81},
  issn = {1097-4199},
  doi = {10.1016/j.neuron.2013.12.025},
  abstract = {Sleep is universal, tightly regulated, and its loss impairs cognition. But why does the brain need to disconnect from the environment for hours every day? The synaptic homeostasis hypothesis (SHY) proposes that sleep is the price the brain pays for plasticity. During a waking episode, learning statistical regularities about the current environment requires strengthening connections throughout the brain. This increases cellular needs for energy and supplies, decreases signal-to-noise ratios, and saturates learning. During sleep, spontaneous activity renormalizes net synaptic strength and restores cellular homeostasis. Activity-dependent down-selection of synapses can also explain the benefits of sleep on memory acquisition, consolidation, and integration. This happens through the offline, comprehensive sampling of statistical regularities incorporated in neuronal circuits over a lifetime. This Perspective considers the rationale and evidence for SHY and points to open issues related to sleep and plasticity.},
  number = {1},
  journal = {Neuron},
  author = {Tononi, Giulio and Cirelli, Chiara},
  month = jan,
  year = {2014},
  keywords = {Learning,Humans,Brain,Animals,Sleep,Neuronal Plasticity,Synapses,Homeostasis},
  pages = {12--34},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W3GY7WQJ/Tononi and Cirelli - 2014 - Sleep and the price of plasticity from synaptic a.pdf},
  pmid = {24411729}
}

@article{rasch_odor_2007,
  title = {Odor Cues during Slow-Wave Sleep Prompt Declarative Memory Consolidation.},
  volume = {315},
  abstract = {Sleep facilitates memory consolidation. A widely held model assumes that this is because newly encoded memories undergo covert reactivation during sleep. We cued new memories in humans during sleep by presenting an odor that had been presented as context during prior learning, and so showed that reactivation indeed causes memory consolidation during sleep. Re-exposure to the odor during slow-wave sleep (SWS) improved the retention of hippocampus-dependent declarative memories but not of hippocampus-independent procedural memories. Odor re-exposure was ineffective during rapid eye movement sleep or wakefulness or when the odor had been omitted during prior learning. Concurring with these findings, functional magnetic resonance imaging revealed significant hippocampal activation in response to odor re-exposure during SWS.},
  number = {5817},
  journal = {Science (80-. ).},
  author = {Rasch, Bj\"orn and B\"uchel, Christian and Gais, Steffen and Born, Jan},
  year = {2007},
  pages = {1426--1429},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DM8F7EPK/Rasch et al. - 2007 - Odor Cues During Slow-Wave Sleep Prompt Declarativ.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U8R3RD6U/Rasch et al. - 2007 - Odor Cues During Slow-Wave Sleep Prompt Declarativ.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9DKYBCCW/1426.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QRJA7KD4/1426.html},
  pmid = {17347444}
}

@article{rasch_maintaining_2007,
  title = {Maintaining Memories by Reactivation.},
  volume = {17},
  abstract = {According to a widely held concept, the formation of long-term memories relies on a reactivation and redistribution of newly acquired memory representations from temporary storage to neuronal networks supporting long-term storage. Here, we review evidence showing that this process of system consolidation takes place preferentially during sleep as an 'off-line' period during which memories are spontaneously reactivated and redistributed in the absence of interfering external inputs. Moreover, postlearning sleep leads to a reorganization of neuronal representations and qualitative changes of memory content. We propose that memory reactivations during sleep are accompanied by a transient destabilization of memory traces. Unlike wake reactivations that form part of an updating of memories with respect to current perceptual input, reactivations during sleep allow for gradually adapting newly acquired memories to pre-existing long-term memories whereby invariants and certain other features of these memories become extracted.},
  number = {6},
  journal = {Curr. Opin. Neurobiol.},
  author = {Rasch, Bj\"orn and Born, Jan},
  year = {2007},
  pages = {698--703},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5AFY5EPA/Rasch and Born - 2007 - Maintaining memories by reactivation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9UVP5VIX/S0959438807001249.html},
  pmid = {18222688}
}

@article{elbaz_circadian_2013,
  title = {Circadian Clocks, Rhythmic Synaptic Plasticity and the Sleep-Wake Cycle in Zebrafish.},
  volume = {7},
  issn = {1662-5110},
  doi = {10.3389/fncir.2013.00009},
  abstract = {The circadian clock and homeostatic processes are fundamental mechanisms that regulate sleep. Surprisingly, despite decades of research, we still do not know why we sleep. Intriguing hypotheses suggest that sleep regulates synaptic plasticity and consequently has a beneficial role in learning and memory. However, direct evidence is still limited and the molecular regulatory mechanisms remain unclear. The zebrafish provides a powerful vertebrate model system that enables simple genetic manipulation, imaging of neuronal circuits and synapses in living animals, and the monitoring of behavioral performance during day and night. Thus, the zebrafish has become an attractive model to study circadian and homeostatic processes that regulate sleep. Zebrafish clock- and sleep-related genes have been cloned, neuronal circuits that exhibit circadian rhythms of activity and synaptic plasticity have been studied, and rhythmic behavioral outputs have been characterized. Integration of this data could lead to a better understanding of sleep regulation. Here, we review the progress of circadian clock and sleep studies in zebrafish with special emphasis on the genetic and neuroendocrine mechanisms that regulate rhythms of melatonin secretion, structural synaptic plasticity, locomotor activity and sleep.},
  number = {February},
  journal = {Front. Neural Circuits},
  author = {Elbaz, Idan and Foulkes, Nicholas S and Gothilf, Yoav and Appelbaum, Lior},
  month = jan,
  year = {2013},
  keywords = {Sleep,circadian clock,Circadian Rhythm,synaptic plasticity,Hypocretin,Orexin,Circadian rhythms,Melatonin,Zebrafish,hypocretin,Circadian clock,orexin},
  pages = {9},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/I4WVR5FL/Elbaz et al. - 2013 - Circadian clocks, rhythmic synaptic plasticity and.pdf},
  pmid = {23378829}
}

@article{beckwith_regulation_2017,
  title = {Regulation of Sleep Homeostasis by Sexual Arousal},
  volume = {6},
  copyright = {All rights reserved},
  issn = {2050-084X},
  doi = {10.7554/eLife.27445},
  abstract = {In all animals, sleep pressure is under continuous tight regulation. It is universally accepted that this regulation arises from a two-process model, integrating both a circadian and a homeostatic controller. Here we explore the role of environmental social signals as a third, parallel controller of sleep homeostasis and sleep pressure. We show that, in Drosophila melanogaster males, sleep pressure after sleep deprivation can be counteracted by raising their sexual arousal, either by engaging the flies with prolonged courtship activity or merely by exposing them to female pheromones., Humans spend one-third of their lifetime sleeping, but why we (and other animals) need to sleep remains an unresolved mystery of biology. Our desire to sleep changes depending on how much sleep we've already had. If we've had a long nap during the day, we may find it harder to fall asleep at night; conversely, if we stay up all night partying, we'll have a difficult time staying alert the next day. This change in the pressure to sleep is known as ``sleep homeostasis''., Can sleep homeostasis be suppressed? We know that some migratory birds are able to resist sleep while flying over the ocean. In addition, males of an Arctic bird species forgo sleep for courtship during the three-week window every year when females of its species are fertile. These examples suggest that some behavioral or environmental factors may influence sleep homeostasis., Beckwith et al. now show that sexual arousal can disrupt sleep homeostasis in fruit flies. In ``blind date'' experiments, young male fruit flies were kept in a small tube with female fruit flies, prompting a 24-hour period of courtship and mating. The males went without sleep during that period, and they did not make up for the lost sleep afterward., In other experiments, male fruit flies were kept awake by a robot that disturbed them every time they tried to sleep. After such treatment, the flies normally attempted to nap. But if the sleep-deprived flies were exposed to a chemical emitted by female flies that increased their sexual arousal, they no longer needed to sleep., Overall, the results presented by Beckwith et al. show that sleep is a biological drive that can be overcome under certain conditions. This will be important for sleep researchers to remember, because it means that it's possible to affect sleep regulation (perhaps by making the animal stressed or aroused) without activating the brain circuits directly involved in regulating sleep.},
  journal = {eLife},
  author = {Beckwith, E. J. and Geissmann, Q. and French, A. S. and Gilestro, G. F.},
  year = {2017},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XJ8CRF7B/Beckwith et al. - Regulation of sleep homeostasis by sexual arousal.pdf},
  pmid = {28893376},
  pmcid = {PMC5630259}
}

@article{geissmann_opencfu_2013,
  title = {{{OpenCFU}}, a {{New Free}} and {{Open}}-{{Source Software}} to {{Count Cell Colonies}} and {{Other Circular Objects}}},
  volume = {8},
  copyright = {All rights reserved},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0054072},
  abstract = {Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.},
  number = {2},
  journal = {PLOS ONE},
  author = {Geissmann, Q.},
  month = feb,
  year = {2013},
  keywords = {Image processing,Computer software,Imaging techniques,Open source software,Biologists,User interfaces,Pollen,Algorithms},
  pages = {e54072},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SFD3KKPD/Geissmann - 2013 - OpenCFU, a New Free and Open-Source Software to Co.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EPUTNSA5/article.html}
}

@article{lebestky_two_2009,
  title = {Two {{Different Forms}} of {{Arousal}} in {{Drosophila Are Oppositely Regulated}} by the {{Dopamine D1 Receptor Ortholog DopR}} via {{Distinct Neural Circuits}}},
  volume = {64},
  issn = {0896-6273},
  doi = {10.1016/j.neuron.2009.09.031},
  abstract = {Summary
Arousal is fundamental to many behaviors, but whether it is unitary or whether there are different types of behavior-specific arousal has not been clear. In Drosophila, dopamine promotes sleep-wake arousal. However, there is conflicting evidence regarding its influence on environmentally stimulated arousal. Here we show that loss-of-function mutations in the D1 dopamine receptor DopR enhance repetitive startle-induced arousal while decreasing sleep-wake arousal (i.e., increasing sleep). These two types of arousal are also inversely influenced by cocaine, whose effects in each case are opposite to, and abrogated by, the DopR mutation. Selective restoration of DopR function in the central complex rescues the enhanced stimulated arousal but not the increased sleep phenotype of DopR mutants. These data provide evidence for at least two different forms of arousal, which are independently regulated by dopamine in opposite directions, via distinct neural circuits.},
  number = {4},
  journal = {Neuron},
  author = {Lebestky, Tim and Chang, Jung-Sook C. and Dankert, Heiko and Zelnik, Lihi and Kim, Young-Cho and Han, Kyung-An and Wolf, Fred W. and Perona, Pietro and Anderson, David J.},
  month = nov,
  year = {2009},
  keywords = {cellbio,molneuro,sysbio},
  pages = {522-536},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6QZ5PLSM/Lebestky et al. - 2009 - Two Different Forms of Arousal in Drosophila Are O.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VMZ4ZYIY/S0896627309007429.html}
}

@article{nitabach_electrical_2002,
  title = {Electrical {{Silencing}} of {{Drosophila Pacemaker Neurons Stops}} the {{Free}}-{{Running Circadian Clock}}},
  volume = {109},
  issn = {0092-8674},
  doi = {10.1016/S0092-8674(02)00737-7},
  abstract = {Electrical silencing of Drosophila circadian pacemaker neurons through targeted expression of K+ channels causes severe deficits in free-running circadian locomotor rhythmicity in complete darkness. Pacemaker electrical silencing also stops the free-running oscillation of PERIOD (PER) and TIMELESS (TIM) proteins that constitutes the core of the cell-autonomous molecular clock. In contrast, electrical silencing fails to abolish PER and TIM oscillation in light-dark cycles, although it does impair rhythmic behavior. On the basis of these findings, we propose that electrical activity is an essential element of the free-running molecular clock of pacemaker neurons along with the transcription factors and regulatory enzymes that have been previously identified as required for clock function.},
  number = {4},
  journal = {Cell},
  author = {Nitabach, Michael N and Blau, Justin and Holmes, Todd C},
  month = may,
  year = {2002},
  pages = {485-495},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5CZB3W6M/Nitabach et al. - 2002 - Electrical Silencing of Drosophila Pacemaker Neuro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AZC4E9AZ/S0092867402007377.html}
}

@article{shang_imaging_2011,
  title = {Imaging Analysis of Clock Neurons Reveals Light Buffers the Wake-Promoting Effect of Dopamine},
  volume = {14},
  copyright = {2011 Nature Publishing Group},
  issn = {1546-1726},
  doi = {10.1038/nn.2860},
  abstract = {How animals maintain proper amounts of sleep yet remain flexible to changes in environmental conditions remains unknown. We found that environmental light suppressed the wake-promoting effects of dopamine in fly brains. The ten large lateral-ventral neurons (l-LNvs), a subset of clock neurons, are wake-promoting and respond to dopamine, octopamine and light. Behavioral and imaging analyses suggested that dopamine is a stronger arousal signal than octopamine. Notably, light exposure not only suppressed l-LNv responses, but also synchronized responses of neighboring l-LNvs. This regulation occurred by distinct mechanisms: light-mediated suppression of octopamine responses was regulated by the circadian clock, whereas light regulation of dopamine responses occurred by upregulation of inhibitory dopamine receptors. Plasticity therefore alters the relative importance of diverse cues on the basis of the environmental mix of stimuli. The regulatory mechanisms described here may contribute to the control of sleep stability while still allowing behavioral flexibility.},
  language = {en},
  number = {7},
  journal = {Nature Neuroscience},
  author = {Shang, Yuhua and Haynes, Paula and P\'irez, Nicol\'as and Harrington, Kyle I. and Guo, Fang and Pollack, Jordan and Hong, Pengyu and Griffith, Leslie C. and Rosbash, Michael},
  month = jul,
  year = {2011},
  pages = {889-895},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z4YZY5NE/Shang et al. - 2011 - Imaging analysis of clock neurons reveals light bu.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HYKUL4TS/nn.html}
}

@article{allada_unearthing_2008,
  title = {Unearthing the {{Phylogenetic Roots}} of {{Sleep}}},
  volume = {18},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2008.06.033},
  abstract = {Summary
Why we sleep remains one of the enduring unanswered questions in biology. At its core, sleep can be defined behaviorally as a homeostatically regulated state of reduced movement and sensory responsiveness. The cornerstone of sleep studies in terrestrial mammals, including humans, has been the measurement of coordinated changes in brain activity during sleep measured using the electroencephalogram (EEG). Yet among a diverse set of animals, these EEG sleep traits can vary widely and, in some cases, are absent, raising questions as to whether they define~a universal, or even essential, feature of sleep. Over the~past decade, behaviorally defined sleep-like states have been identified in a series of genetic model organisms, including fish, flies and worms. Genetic analyses in these systems are revealing a remarkable conservation in the underlying mechanisms controlling sleep behavior. Taken together, these studies suggest an ancient origin for sleep and raise the possibility that model organism genetics may reveal the molecular mechanisms that guide sleep and wake.},
  number = {15},
  journal = {Current Biology},
  author = {Allada, Ravi and Siegel, Jerome M.},
  month = aug,
  year = {2008},
  pages = {R670-R679},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UT7QH952/Allada and Siegel - 2008 - Unearthing the Phylogenetic Roots of Sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XIQNJWZ8/S0960982208007550.html}
}

@article{sehgal_genetics_2011,
  title = {Genetics of {{Sleep}} and {{Sleep Disorders}}},
  volume = {146},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2011.07.004},
  abstract = {Sleep remains one of the least understood phenomena in biology\textemdash{}even its role in synaptic plasticity remains debatable. Since sleep was recognized to be regulated genetically, intense research has launched on two fronts: the development of model organisms for deciphering the molecular mechanisms of sleep and attempts to identify genetic underpinnings of human sleep disorders. In this Review, we describe how unbiased, high-throughput screens in model organisms are uncovering sleep regulatory mechanisms and how pathways, such as the circadian clock network and specific neurotransmitter signals, have conserved effects on sleep from Drosophila to humans. At the same time, genome-wide association studies (GWAS) have uncovered $\sim$14 loci increasing susceptibility to sleep disorders, such as narcolepsy and restless leg syndrome. To conclude, we discuss how these different strategies will be critical to unambiguously defining the function of sleep.},
  number = {2},
  journal = {Cell},
  author = {Sehgal, Amita and Mignot, Emmanuel},
  month = jul,
  year = {2011},
  pages = {194-207},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FQ54SZK8/Sehgal and Mignot - 2011 - Genetics of Sleep and Sleep Disorders.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZQI8BM78/S0092867411007598.html}
}

@article{shaw_correlates_2000,
  title = {Correlates of {{Sleep}} and {{Waking}} in {{Drosophila}} Melanogaster},
  volume = {287},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.287.5459.1834},
  abstract = {Drosophila exhibits a circadian rest-activity cycle, but it is not known whether fly rest constitutes sleep or is mere inactivity. It is shown here that, like mammalian sleep, rest inDrosophila is characterized by an increased arousal threshold and is homeostatically regulated independently of the circadian clock. As in mammals, rest is abundant in young flies, is reduced in older flies, and is modulated by stimulants and hypnotics. Several molecular markers modulated by sleep and waking in mammals are modulated by rest and activity in Drosophila, including cytochrome oxidase C, the endoplasmic reticulum chaperone protein BiP, and enzymes implicated in the catabolism of monoamines. Flies lacking one such enzyme, arylalkylamine N-acetyltransferase, show increased rest after rest deprivation. These results implicate the catabolism of monoamines in the regulation of sleep and waking in the fly and suggest that Drosophila may serve as a model system for the genetic dissection of sleep.},
  language = {en},
  number = {5459},
  journal = {Science},
  author = {Shaw, Paul J. and Cirelli, Chiara and Greenspan, Ralph J. and Tononi, Giulio},
  month = mar,
  year = {2000},
  pages = {1834-1837},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z29JIHCG/Shaw et al. - 2000 - Correlates of Sleep and Waking in Drosophila melan.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TCRZUA2L/Shaw et al. - 2000 - Correlates of Sleep and Waking in Drosophila melan.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XMF2SQ62/1834.html},
  pmid = {10710313}
}

@book{layard_discoveries_1853,
  title = {Discoveries in the Ruins of {{Nineveh}} and {{Babylon}} : With Travels in {{Armenia}}, {{Kurdistan}} and the Desert : Being the Result of a Second Expedition},
  copyright = {http://creativecommons.org/publicdomain/mark/1.0/},
  shorttitle = {Discoveries in the Ruins of {{Nineveh}} and {{Babylon}}},
  abstract = {M\'as detallesPUBLICACI\'ONNew York G. P. Putnam and Co., 1853DESCR. F\'ISICAXXIII, 686 p. : il. ; 23 cm
SubjectIrak -- Antig\"uedadesN\'inive (Ciudad antigua)Babilonia (Ciudad antigua)CLASIF. ABREV.904
SIGNATURAH H\textordfeminine{} Antigua 904(35) LAY/Dis

Cat\'alogo Fama},
  language = {eng},
  publisher = {{New York : G. P. Putnam and Co.}},
  author = {Layard, Austen Henry},
  collaborator = {{Biblioteca de la Universidad de Sevilla}},
  year = {1853},
  keywords = {Fondo de Humanidades}
}

@book{george_epic_2002,
  title = {The Epic of {{Gilgamesh}}: The {{Babylonian}} Epic Poem and Other Texts in {{Akkadian}} and {{Sumerian}}},
  shorttitle = {The Epic of {{Gilgamesh}}},
  publisher = {{Penguin}},
  author = {George, Andrew},
  year = {2002},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/279WIY9Q/George - 2002 - The epic of Gilgamesh the Babylonian epic poem an.pdf}
}

@article{qiao_automated_2018,
  title = {Automated Analysis of Long-Term Grooming Behavior in {{Drosophila}} Using a k-Nearest Neighbors Classifier},
  volume = {7},
  copyright = {\textcopyright{} 2018 Qiao et al.. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  doi = {10.7554/eLife.34497},
  language = {en},
  journal = {eLife},
  author = {Qiao, Bing and Li, Chiyuan and Allen, Victoria W. and {Shirasu-Hiza}, Mimi M. and Syed, Sheyum},
  month = feb,
  year = {2018},
  pages = {e34497},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KG2D7UYQ/Qiao et al. - 2018 - Automated analysis of long-term grooming behavior .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/27C4IKIF/figures.html}
}

@book{plato_cratylus_1998,
  title = {Cratylus},
  isbn = {978-0-87220-416-4},
  abstract = {The Cratylus, Plato's sole dialogue devoted to the relation between language and reality, is acknowledged to be one of his masterpieces. But owing to its often enigmatic content no more than a handful of passages from it have played a part in the global evaluation of Plato's philosophy. This new English translation by C D C Reeve is the first since 1926, and incomparably the most helpful and accessible now available. It opens up the Cratylus to all philosophically interested readers, as well as to cultural historians and to those whose primary concern is the history of linguistics. The full and lucid introduction does much to illuminate the internal dynamic of this important text and to explain its place within Plato's oeuvre.},
  language = {en},
  publisher = {{Hackett Publishing}},
  author = {Plato},
  year = {1998},
  keywords = {Philosophy / History \& Surveys / Ancient \& Classical}
}

@book{sedley_platos_2003,
  title = {Plato's {{Cratylus}}},
  isbn = {978-1-139-43919-0},
  abstract = {Plato's Cratylus is a brilliant but enigmatic dialogue. It bears on a topic, the relation of language to knowledge, which has never ceased to be of central philosophical importance, but tackles it in ways which at times look alien to us. In this reappraisal of the dialogue, Professor Sedley argues that the etymologies which take up well over half of it are not an embarrassing lapse or semi-private joke on Plato's part. On the contrary, if taken seriously as they should be, they are the key to understanding both the dialogue itself and Plato's linguistic philosophy more broadly. The book's main argument is so formulated as to be intelligible to readers with no knowledge of Greek, and will have a significant impact both on the study of Plato and on the history of linguistic thought.},
  language = {en},
  publisher = {{Cambridge University Press}},
  author = {Sedley, David},
  month = nov,
  year = {2003},
  keywords = {Philosophy / History \& Surveys / Ancient \& Classical,Language Arts \& Disciplines / Linguistics / General},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H5FCUFKY/Sedley - 2003 - Plato's Cratylus.pdf}
}

@phdthesis{petzold_identification_2017,
  type = {Ph.{{D}}.},
  title = {Identification and Characterisation of a Novel Aldo-Keto Reductase Regulating Sleep in {{Drosophila}} Melanogaster},
  abstract = {Sleep is an important behaviour that has been observed in all animals studied so far, including Drosophila melanogaster. While a range of studies demonstrates that sleep is crucial to preserve an animal's cognitive and physical health, relatively little is known about its regulation. Specifically, the molecular mechanisms that regulate sleep are still unclear, although a strong heritable component prevails. While the gene network governing sleep timing \textendash{} the circadian system \textendash{} is comparatively well described, the network calibrating the sleep homeostat is still vague. The study of sleep-regulatory mechanisms was greatly advanced by the adoption of the relatively simple model organism Drosophila melanogaster. Following seminal studies that demonstrated the suitability of Drosophila for the study of sleep, several sleep mutants were identified. Among those, hyperkinetic \textendash{} a member of the aldo-keto reductase (AKR) family of enzymes \textendash{} was one of the first Drosophila sleep mutants ever described. The abundance and importance of AKRs for human health and disease in combination with their conservation in Drosophila provides an excellent basis to examine whether AKRs systematically act as molecular regulators of sleep behaviour. Thus, we produced the first in silico study of potential Drosophila AKRs. We experimentally tested potential AKRs for neural sleep-regulatory roles through a nervous system-wide and Mushroom body-specific screen. We identified and further characterised the neural populations expressing particular candidates and the role these candidate AKRs fulfil to modulate sleep behaviour. We identified a novel AKR, CG10638, which specifically acts through a pair of wake-promoting peptidergic projection neurons termed ``inferior contralateral interneurons'' (ICLI) whose inhibition is necessary to relieve sleep pressure built up during the day, or specifically induced through dedicated sleep deprivation. We also demonstrate that ICLI neurons receive inputs from the major `clock' neurons of the fly brain, and show that CG10638 negatively regulates ICLI neurons to acutely gauge the sleep homeostat and to integrate sleep pressure with the circadian network. We also identified a Mushroom body-specific sleep-regulatory AKR, CG3397, that may be close to Hyperkinetic in structure and function.},
  language = {eng},
  school = {Imperial College London},
  author = {Petzold, Anne},
  year = {2017},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WVLTMBHV/Petzold-A-2017-PhD-Thesis-embedded.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LYGKL3ZD/OrderDetails.html}
}

@article{geissmann_ethoscopes_2017,
  title = {Ethoscopes: {{An}} Open Platform for High-Throughput Ethomics},
  volume = {15},
  issn = {1545-7885},
  shorttitle = {Ethoscopes},
  doi = {10.1371/journal.pbio.2003026},
  abstract = {Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.},
  language = {en},
  number = {10},
  journal = {PLOS Biology},
  author = {Geissmann, Quentin and Rodriguez, Luis Garcia and Beckwith, Esteban J. and French, Alice S. and Jamasb, Arian R. and Gilestro, Giorgio F.},
  month = oct,
  year = {2017},
  keywords = {Computer networks,Cameras,Sleep,Drosophila melanogaster,Animal behavior,3D printing,Light-emitting diodes,Sleep deprivation},
  pages = {e2003026},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7V3L4VAL/Geissmann et al. - 2017 - Ethoscopes An open platform for high-throughput e.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G9J863M7/Geissmann et al. - 2017 - Ethoscopes An open platform for high-throughput e.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WUN2JWMB/Geissmann et al. - 2017 - Ethoscopes An open platform for high-throughput e.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DCQP5V5G/article.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IL42JIYC/article.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YVN4B8WL/article.html}
}

@incollection{pieron1913probleme,
  title = {Le Probl\`eme Physiologique Du Sommeil},
  booktitle = {Le Probl\'eme Physiologique Du Sommeil},
  author = {Pi\'eron, Henri},
  year = {1913}
}

@article{borbely_two_1982,
  title = {A Two Process Model of Sleep Regulation.},
  volume = {1},
  issn = {0721-9075},
  abstract = {Author: Borb\'ely AA, Journal: Human neurobiology[1982]},
  language = {eng},
  number = {3},
  journal = {Human neurobiology},
  author = {Borb\'ely, A. A.},
  year = {1982},
  pages = {195-204},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U8R5R7ER/Borbely - A Two Process Model of Sleep Regulation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UZNVFPKD/7185792.html},
  pmid = {7185792}
}

@article{cirelli_is_2008,
  title = {Is {{Sleep Essential}}?},
  volume = {6},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.0060216},
  abstract = {No current hypothesis can explain why animals need to sleep. Yet, sleep is universal, tightly regulated, and cannot be deprived without deleterious consequences. This suggests that searching for a core function of sleep, particularly at the cellular level, is still a worthwhile exercise.},
  language = {en},
  number = {8},
  journal = {PLOS Biology},
  author = {Cirelli, Chiara and Tononi, Giulio},
  month = aug,
  year = {2008},
  keywords = {Sleep,Swimming,Electroencephalography,Synapses,Homeostasis,Sleep deprivation,Cognitive impairment,Dolphins},
  pages = {e216},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XVR8NJTM/Cirelli and Tononi - 2008 - Is Sleep Essential.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/93UDWJLR/article.html}
}

@article{zimmerman_conservation_2008,
  title = {Conservation of {{Sleep}}: {{Insights}} from {{Non}}-{{Mammalian Model Systems}}},
  volume = {31},
  issn = {0166-2236},
  shorttitle = {Conservation of {{Sleep}}},
  doi = {10.1016/j.tins.2008.05.001},
  abstract = {The past ten years have seen new approaches to elucidating genetic pathways regulating sleep. The emerging theme is that sleep-like states are conserved in evolution, with similar signaling pathways playing a role in animals as distantly related as flies and humans. We review the evidence for the presence of sleep states in non-mammalian species including zebrafish (Danio rerio), fruit flies (Drosophila melanogaster), and round worms (Caenorhabditis elegans). We describe conserved sleep-regulatory molecular pathways with a focus on cAMP and Epidermal Growth Factor (EGF) signaling; neurotransmitters with conserved effects on sleep and wake regulation, including dopamine and GABA; and a conserved molecular response to sleep deprivation involving the chaperone protein BiP/GRP78.},
  number = {7},
  journal = {Trends in neurosciences},
  author = {Zimmerman, John E. and Naidoo, Nirinjini and Raizen, David M. and Pack, Allan I.},
  month = jul,
  year = {2008},
  pages = {371-376},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SJXY8CPQ/Zimmerman et al. - 2008 - Conservation of Sleep Insights from Non-Mammalian.pdf},
  pmid = {18538867},
  pmcid = {PMC2930986}
}

@article{flanigan_sleep_1973,
  title = {Sleep and Wakefulness in Iguanid Lizards, {{Ctenosaura}} Pectinata and {{Iguana}} Iguana},
  volume = {8},
  abstract = {Black (Ctenosaura pectinata) and green (Iguana iguana) iguanid lizards were implanted with chronic electrodes in forebrain, orbital cavities and nuchal muscles; electrodes were also attached to abdominal cavity skin. Electrographic recordings were obtained for 7-11 consecutive days. Behavioral response latencies during behavioral wakefulness and behavioral sleep were evaluated. Four characteristic postures described the behavior of lizards: limbs flexed and supporting body, head and neck elevated, eyes open (active waking); posture similar to above, but with the body resting on floor (quiet waking); limbs slightly flexed or one to three limbs extended backward and positioned against body/tail, head rested on floor, eyes usually closed; all limbs extended backward and positioned against body/tail, head on floor, eyes usually closed. Frequency and latency of response to stimulation, respectively, changed from 94.1-100\% and 0.62-0.69 sec for behavioral waking to 50-51.3\% and 1.32-2.01 sec for Postures 3 and 4 (eyes closed). Postures 3 and 4 (eyes closed) denote behavioral sleep, i.e. stereotypic posture, immobility, increased response threshold, and rapid state reversibility. EEGs were dominated by small amplitude monophasic sharp and sawtooth waves during behavioral waking, but EEGs became polymorphic and irregular in form during behavioral sleep (EEG frequencies slightly declined and amplitudes substantially diminished with sleep). Neither epochs of slow waves nor paradoxical sleep were recorded. Arhythmic (up to 385 $\mu$V) spikes (25-80 msec duration) and sharp waves (80-190 msec duration) characterized lizard EEGs. Spike and sharp wave activity reached peak levels only during behavioral sleep and vanished or dramatically declined with waking. Spikes and sharp waves substantially increased during recovery from 48 hr of enforced waking.},
  number = {6},
  journal = {Brain, Behavior and Evolution},
  author = {Flanigan, Jr},
  year = {1973},
  pages = {401-436},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RNJXW5V3/display.html}
}

@incollection{durie1981sleep,
  title = {Sleep in Animals},
  booktitle = {Psychopharmacology of Sleep},
  publisher = {{Raven Press New York}},
  author = {Durie, DJ Bruce},
  year = {1981},
  pages = {1-18}
}

@book{waal_ape_2001,
  title = {Ape and the Sushi Master},
  isbn = {978-0-465-04175-6},
  language = {English},
  publisher = {{Basic Books}},
  author = {Waal, F. B. M. de (Frans B. M. ) and {1948-}},
  year = {2001},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NPLRAHIV/search.html}
}

@article{slama_new_1988,
  title = {A {{New Look}} at {{Insect Respiration}}},
  volume = {175},
  issn = {0006-3185, 1939-8697},
  doi = {10.2307/1541570},
  language = {en},
  number = {2},
  journal = {The Biological Bulletin},
  author = {Sl\'aMa, Karel},
  month = oct,
  year = {1988},
  pages = {289-300},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FXLMJHV4/SláMa - 1988 - A New Look at Insect Respiration.pdf}
}

@article{hoffmann_innate_1995,
  title = {Innate Immunity of Insects},
  volume = {7},
  issn = {0952-7915},
  doi = {10.1016/0952-7915(95)80022-0},
  abstract = {Insects are particularly resistant to microorganisms. Their host-defense system relies on several innate reactions: upon injury, the immediate onset of two proteolytic cascades leading to localized blood clotting and to melanization, the latter process involving production of cytotoxic molecules (namely reactive oxygen intermediates); the phagocytosis of bacteria and the encapsulation of larger parasites by blood cells; the induced synthesis by the fat body of a battery of potent antimicrobial peptides/polypeptides which are secreted into the hemolymph where they act synergistically to kill the invading microorganisms. The insect host defence system shares many of the basic characteristics of the mammalian acute phase response, especially at the level of the coordinate control of gene expression, where similar cis-regulatory and inducible transactivators appear to play key functions. The powerful techniques developed to study the genetics of Drosophila provide a unique opportunity to dissect the development and differentiation of this primordial immune system and may contribute to our understanding of the innate immune response in higher organisms.},
  number = {1},
  journal = {Current Opinion in Immunology},
  author = {Hoffmann, Jules A},
  month = feb,
  year = {1995},
  pages = {4-10},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F3EV5XZR/Hoffmann - 1995 - Innate immunity of insects.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VXVNHIY2/0952791595800220.html}
}

@article{hendricks_need_2000,
  title = {The Need for a Simple Animal Model to Understand Sleep},
  volume = {61},
  issn = {0301-0082},
  abstract = {Simple animal models have allowed biologists to apply the tools of modern molecular genetics to such complex behaviors as circadian rhythms and long-term memory consolidation. The mechanisms and molecules discovered in these simple animals are evolutionarily conserved in other species, including mammals. Sleep research lacks a simple animal model because criteria based on the electroencephalogram have been met only in birds and mammals. We argue that straightforward behavioral criteria could allow the identification of a sleep-like rest state that might be useful for molecular investigations to understand the regulation and function of sleep. Candidate model systems are discussed, leading to the conclusion that several species have complementary strengths. Specifically, techniques developed for larval zebrafish can be used to visualize neural firing patterns in the living animal, and the fruit fly Drosophila melanogaster has been used successfully for molecular and genetic dissection of complex behaviors. We conclude with a hypothesis that one putative function of sleep, the optimization of neural plasticity, would also have adaptive value in simple organisms and might therefore be evolutionarily conserved.},
  language = {eng},
  number = {4},
  journal = {Progress in Neurobiology},
  author = {Hendricks, J. C. and Sehgal, A. and Pack, A. I.},
  month = jul,
  year = {2000},
  keywords = {Behavior; Animal,Learning,Memory,Animals,Sleep,Circadian Rhythm,Drosophila melanogaster,Xenopus laevis,Zebrafish,Central Nervous System,Sensory Thresholds,Research Design,Aplysia},
  pages = {339-351},
  pmid = {10727779}
}

@article{moruzzi_brain_1949,
  title = {Brain Stem Reticular Formation and Activation of the {{EEG}}},
  volume = {1},
  issn = {0013-4694},
  doi = {10.1016/0013-4694(49)90219-9},
  number = {1},
  journal = {Electroencephalography and Clinical Neurophysiology},
  author = {Moruzzi, G. and Magoun, H. W.},
  month = jan,
  year = {1949},
  pages = {455-473},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XU75B36H/0013469449902199.html}
}

@article{lesku_phylogenetic_2006,
  title = {A {{Phylogenetic Analysis}} of {{Sleep Architecture}} in {{Mammals}}: {{The Integration}} of {{Anatomy}}, {{Physiology}}, and {{Ecology}}},
  issn = {0003-0147/2006/16804-41496\$15.00},
  shorttitle = {A {{Phylogenetic Analysis}} of {{Sleep Architecture}} in {{Mammals}}},
  doi = {10.1086/506973},
  abstract = {Abstract: Among mammalian species, the time spent in the two main ``architectural'' states of sleep\textemdash{}slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep\textemdash{}varies greatly. Previous comparative studies of sleep architecture found that larger mammals, those with bigger brains, and those with higher absolute basal metabolic rates (BMR) tended to engage in less SWS and REM sleep. Species experiencing a greater risk of predation also exhibited less SWS and REM sleep. In all cases, however, these studies lacked a formal phylogenetic and theoretical framework and used mainly correlational analyses. Using independent contrasts and an updated data set, we extended existing approaches with path analysis to examine the integrated influence of anatomy, physiology, and ecology on sleep architecture. Path model structure was determined by nonmutually exclusive hypotheses for the function of sleep. We found that species with higher relative BMRs engage in less SWS, whereas species with larger relative brain masses engage...},
  language = {en},
  journal = {The American Naturalist},
  author = {Lesku, John and II, Timothy C. Roth and J. Amlaner, Charles and L. Lima, Steven},
  year = {2006},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FL6ZN7TC/A. Lesku et al. - 2015 - A Phylogenetic Analysis of Sleep Architecture in M.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HMKXCP5Z/506973.html}
}

@book{bremer1937activite,
  title = {L'activit\'e C\'er\'ebrale Au Cours Du Sommeil et de La Narcose: Contribution \`a l'\'etude Du M\'ecanisme Du Sommeil},
  author = {Bremer, Fr\'ed\'eric},
  year = {1937}
}

@book{laland_question_2009,
  title = {The {{Question}} of {{Animal Culture}}},
  isbn = {978-0-674-03126-5},
  abstract = {Fifty years ago, a troop of Japanese macaques was observed washing sandy sweet potatoes in a stream, sending ripples through the fields of ethology, comparative psychology, and cultural anthropology. The issue of animal culture has been hotly debated ever since. Now Kevin Laland and Bennett Galef have gathered key voices in the often rancorous debate to summarize the views along the continuum from ``Culture? Of course!'' to ``Culture? Of course not!'' The result is essential reading for anyone interested in the validity of animal culture, and what it might say about our own.},
  language = {en},
  publisher = {{Harvard University Press}},
  author = {Laland, Kevin N. and Galef, Bennett G.},
  year = {2009},
  keywords = {Science / Life Sciences / Zoology / General,Social Science / Anthropology / Cultural \& Social}
}

@article{whiten_scope_2011,
  title = {The Scope of Culture in Chimpanzees, Humans and Ancestral Apes},
  volume = {366},
  copyright = {This journal is \textcopyright{} 2011 The Royal Society},
  issn = {0962-8436, 1471-2970},
  doi = {10.1098/rstb.2010.0334},
  abstract = {More studies have focused on aspects of chimpanzee behaviour and cognition relevant to the evolution of culture than on any other species except our own. Accordingly, analysis of the features shared by chimpanzees and humans is here used to infer the scope of cultural phenomena in our last common ancestor, at the same time clarifying the nature of the special characteristics that advanced further in the hominin line. To do this, culture is broken down into three major aspects: the large scale, population-level patterning of traditions; social learning mechanisms; and the behavioural and cognitive contents of culture. Each of these is further dissected into subcomponents. Shared features, as well as differences, are identified in as many as a dozen of these, offering a case study for the comparative analysis of culture across animal taxa and a deeper understanding of the roots of our own cultural capacities.},
  language = {en},
  number = {1567},
  journal = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
  author = {Whiten, Andrew},
  month = apr,
  year = {2011},
  pages = {997-1007},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CKBXYM44/Whiten - 2011 - The scope of culture in chimpanzees, humans and an.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5U398BD9/997.html},
  pmid = {21357222}
}

@article{land_evolution_1992,
  title = {The Evolution of Eyes},
  volume = {15},
  issn = {0147-006X},
  doi = {10.1146/annurev.ne.15.030192.000245},
  language = {eng},
  journal = {Annual Review of Neuroscience},
  author = {Land, M. F. and Fernald, R. D.},
  year = {1992},
  keywords = {Humans,Animals,Biological Evolution,Ocular Physiological Phenomena},
  pages = {1-29},
  pmid = {1575438}
}

@article{stern_genetic_2013,
  title = {The Genetic Causes of Convergent Evolution},
  volume = {14},
  copyright = {2013 Nature Publishing Group},
  issn = {1471-0064},
  doi = {10.1038/nrg3483},
  abstract = {This Review distinguishes between three distinct routes by which similar genetic changes contribute to convergent evolution and discusses examples from diverse taxa. Convergent genetic evolution might result from the fact that some mutations both minimize pleiotropic effects and maximize adaptation.},
  language = {en},
  number = {11},
  journal = {Nature Reviews Genetics},
  author = {Stern, David L.},
  month = nov,
  year = {2013},
  pages = {751},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WIV2XQGP/Stern - 2013 - The genetic causes of convergent evolution.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HPZ35W8K/nrg3483.html}
}

@book{nation_insect_2008,
  title = {Insect Physiology and Biochemistry},
  isbn = {978-1-4200-6177-2},
  language = {English},
  publisher = {{CRC Press/Taylor \& Francis}},
  author = {Nation, James L.},
  year = {2008},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QA4R4CXM/search.html}
}

@article{flajnik_origin_2010,
  title = {Origin and Evolution of the Adaptive Immune System: Genetic Events and Selective Pressures},
  volume = {11},
  issn = {1471-0056},
  shorttitle = {Origin and Evolution of the Adaptive Immune System},
  doi = {10.1038/nrg2703},
  abstract = {The adaptive immune system (AIS) in mammals, which is centred on lymphocytes bearing antigen receptors that are generated by somatic recombination, arose approximately 500 million years ago in jawed fish. This intricate defence system consists of many molecules, mechanisms and tissues that are not present in jawless vertebrates. Two macroevolutionary events are believed to have contributed to the genesis of the AIS: the emergence of the recombination-activating gene (RAG) transposon, and two rounds of whole-genome duplication. It has recently been discovered that a non-RAG-based AIS with similarities to the jawed vertebrate AIS \textemdash{} including two lymphoid cell lineages \textemdash{} arose in jawless fish by convergent evolution. We offer insights into the latest advances in this field and speculate on the selective pressures that led to the emergence and maintenance of the AIS.},
  number = {1},
  journal = {Nature reviews. Genetics},
  author = {Flajnik, Martin F. and Kasahara, Masanori},
  month = jan,
  year = {2010},
  pages = {47-59},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T9DIHDNR/Flajnik and Kasahara - 2010 - Origin and evolution of the adaptive immune system.pdf},
  pmid = {19997068},
  pmcid = {PMC3805090}
}

@article{rose_evolution_2008,
  title = {Evolution of Ageing since {{Darwin}}},
  volume = {87},
  issn = {0022-1333, 0973-7731},
  doi = {10.1007/s12041-008-0059-6},
  abstract = {In the late 19th century, the evolutionary approach to the problem of ageing was initiated by August Weismann, who argued that natural selection was more important for ageing than any physiological mechanism. In the mid-twentieth century, J. B. S. Haldane, P. B. Medawar and G. C. Williams informally argued that the force of natural selection falls with adult age. In 1966, W. D. Hamilton published formal equations that showed mathematically that two' forces of natural selection' do indeed decline with age, though his analysis was not genetically explicit. Brian Charlesworth then developed the required mathematical population genetics for the evolution of ageing in the 1970's. In the 1980's, experiments using Drosophila showed that the rate of ageing evolves as predicted by Hamilton's' forces of natural selection'. The discovery of the cessation of ageing late in life in the 1990's was followed by its explanation in terms of evolutionary theory based on Hamilton's forces. Recently, it has been shown that the cessation of ageing can also be manipulated experimentally using Hamilton's' forces of natural selection'. Despite the success of evolutionary research on ageing, mainstream gerontological research has largely ignored both this work and the opportunity that it provides for effective intervention in ageing.},
  language = {en},
  number = {4},
  journal = {Journal of Genetics},
  author = {Rose, Michael R. and Burke, Molly K. and Shahrestani, Parvin and Mueller, Laurence D.},
  month = dec,
  year = {2008},
  pages = {363},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/THJ2BMN4/Rose et al. - 2008 - Evolution of ageing since Darwin.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QG8ZR2TV/s12041-008-0059-6.html}
}

@article{partridge_optimally_1993,
  title = {Optimally, Mutation and the Evolution of Ageing},
  volume = {362},
  issn = {0028-0836},
  doi = {10.1038/362305a0},
  abstract = {Evolutionary explanations of ageing fall into two classes. Organisms might have evolved the optimal life history, in which survival and fertility late in life are sacrificed for the sake of early reproduction and survival. Alternatively, the life history might be depressed below this optimal compromise by deleterious mutations: because selection against late-acting mutations is weaker, these will impose a greater load on late life. Evidence for the importance of both is emerging, and unravelling their relative importance presents experimentalists with a major challenge.},
  journal = {Nature},
  author = {Partridge, L. and Barton, N. H.},
  month = mar,
  year = {1993},
  pages = {305-311}
}

@article{johnson_molecular_1999,
  title = {Molecular {{Biology}} of {{Aging}}},
  volume = {96},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/S0092-8674(00)80567-X},
  language = {English},
  number = {2},
  journal = {Cell},
  author = {Johnson, F. Brad and Sinclair, David A. and Guarente, Leonard},
  month = jan,
  year = {1999},
  pages = {291-302},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G52WWI87/Johnson et al. - 1999 - Molecular Biology of Aging.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZQHDNFDA/S0092-8674(00)80567-X.html},
  pmid = {9988222}
}

@article{sun_mitochondrial_2016,
  title = {The {{Mitochondrial Basis}} of {{Aging}}},
  volume = {61},
  issn = {1097-2765},
  doi = {10.1016/j.molcel.2016.01.028},
  abstract = {A decline in mitochondrial quality and activity has been associated with normal aging and correlated with the development of a wide range of age-related diseases. Here, we review the evidence that a decline in mitochondria function contributes to aging. In particular, we discuss how mitochondria contribute to specific aspects of the aging process, including cellular senescence, chronic inflammation, and the age-dependent decline in stem cell activity. Signaling pathways regulating the mitochondrial unfolded protein response and mitophagy are also reviewed, with particular emphasis placed on how these pathways might, in turn, regulate longevity. Taken together, these observations suggest that mitochondria influence or regulate a number of key aspects of aging and suggest that strategies directed at improving mitochondrial quality and function might have far-reaching beneficial effects.},
  language = {English},
  number = {5},
  journal = {Molecular Cell},
  author = {Sun, Nuo and Youle, Richard J. and Finkel, Toren},
  month = mar,
  year = {2016},
  pages = {654-666},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3ZMF73DT/Sun et al. - 2016 - The Mitochondrial Basis of Aging.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/78ICLUPQ/S1097-2765(16)00081-2.html},
  pmid = {26942670}
}

@article{nath_jellyfish_2017,
  title = {The {{Jellyfish Cassiopea Exhibits}} a {{Sleep}}-like {{State}}},
  volume = {27},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2017.08.014},
  abstract = {Summary
Do all animals sleep? Sleep has been observed in many vertebrates, and there is a growing body of evidence for sleep-like states in arthropods and nematodes [1, 2, 3, 4, 5]. Here we show that sleep is also present in Cnidaria [6, 7, 8], an earlier-branching metazoan lineage. Cnidaria and Ctenophora are the first metazoan phyla to evolve tissue-level organization and differentiated cell types, such as neurons and muscle [9, 10, 11, 12, 13, 14, 15]. In Cnidaria, neurons are organized into a~non-centralized radially symmetric nerve net [11, 13, 15, 16, 17] that nevertheless shares fundamental properties with the vertebrate nervous system: action potentials, synaptic transmission, neuropeptides, and neurotransmitters [15, 16, 17, 18, 19, 20]. It was reported that cnidarian soft corals [21] and box jellyfish [22, 23] exhibit periods of quiescence, a pre-requisite for sleep-like states, prompting us to ask whether sleep is present in Cnidaria. Within Cnidaria, the upside-down jellyfish Cassiopea spp. displays a quantifiable pulsing behavior, allowing us to perform long-term behavioral tracking. Monitoring of Cassiopea pulsing activity for consecutive days and nights revealed behavioral quiescence at night that is rapidly reversible, as well as a delayed response to stimulation in the quiescent state. When deprived of nighttime quiescence, Cassiopea exhibited decreased activity and reduced responsiveness to a sensory stimulus during the subsequent day, consistent with homeostatic regulation of the quiescent state. Together, these results indicate that Cassiopea has a sleep-like state, supporting the hypothesis that sleep arose early in the metazoan lineage, prior to the emergence of a centralized nervous system.},
  number = {19},
  journal = {Current Biology},
  author = {Nath, Ravi D. and Bedbrook, Claire N. and Abrams, Michael J. and Basinger, Ty and Bois, Justin S. and Prober, David A. and Sternberg, Paul W. and Gradinaru, Viviana and Goentoro, Lea},
  month = oct,
  year = {2017},
  keywords = {Cnidaria,jellyfish,sleep,evolution of sleep},
  pages = {2984-2990.e3},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K9ILVQVV/Nath et al. - 2017 - The Jellyfish Cassiopea Exhibits a Sleep-like Stat.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SFGRG3ZB/S0960982217310230.html}
}

@article{joiner_unraveling_2016,
  title = {Unraveling the {{Evolutionary Determinants}} of {{Sleep}}},
  volume = {26},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2016.08.068},
  abstract = {Despite decades of intense study, the functions of sleep are still shrouded in mystery. The difficulty in understanding these functions can be at least partly attributed to the varied manifestations of sleep in different animals. Daily sleep duration can range from 4\textendash{}20~hrs among mammals, and sleep can manifest throughout the brain, or it can alternate over time between cerebral hemispheres, depending on the species. Ecological factors are likely to have shaped these and other sleep behaviors during evolution by altering the properties of conserved arousal circuits in the brain. Nonetheless, core functions of sleep are likely to have arisen early and to have persisted to the present day in diverse organisms. This review will discuss the evolutionary forces that may be responsible for phylogenetic differences in sleep and the potential core functions that sleep fulfills.},
  number = {20},
  journal = {Current Biology},
  author = {Joiner, William J.},
  month = oct,
  year = {2016},
  pages = {R1073-R1087},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/R7FNYKD2/Joiner - 2016 - Unraveling the Evolutionary Determinants of Sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/68WAWR5D/S0960982216310132.html}
}

@article{dunn_animal_2014,
  title = {Animal {{Phylogeny}} and {{Its Evolutionary Implications}}},
  volume = {45},
  issn = {1543-592X},
  doi = {10.1146/annurev-ecolsys-120213-091627},
  abstract = {In recent years, scientists have made remarkable progress reconstructing the animal phylogeny. There is broad agreement regarding many deep animal relationships, including the monophyly of animals, Bilateria, Protostomia, Ecdysozoa, and Spiralia. This stability now allows researchers to articulate the diminishing number of remaining questions in terms of well-defined alternative hypotheses. These remaining questions include relationships at the base of the animal tree, the position of Xenacoelomorpha, and the internal relationships of Spiralia. Recent progress in the field of animal phylogeny has important implications for our understanding of the evolution of development, morphology, genomes, and other characters. A remarkable pattern emerges\textemdash{}there is far more homoplasy for all these characters than had previously been anticipated, even among many complex characters such as segmentation and nervous systems. The fossil record dates most deep branches of the animal tree to an evolutionary radiation in the early Cambrian with roots in the Late Neoproterozoic.},
  number = {1},
  journal = {Annual Review of Ecology, Evolution, and Systematics},
  author = {Dunn, Casey W. and Giribet, Gonzalo and Edgecombe, Gregory D. and Hejnol, Andreas},
  month = nov,
  year = {2014},
  pages = {371-395},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6XGPGEMN/Dunn et al. - 2014 - Animal Phylogeny and Its Evolutionary Implications.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BMBA2XDB/annurev-ecolsys-120213-091627.html}
}

@article{katsuki_jellyfish_2013,
  title = {Jellyfish Nervous Systems},
  volume = {23},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2013.03.057},
  number = {14},
  journal = {Current Biology},
  author = {Katsuki, Takeo and Greenspan, Ralph J.},
  month = jul,
  year = {2013},
  pages = {R592-R594},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/76NM4DJA/Katsuki and Greenspan - 2013 - Jellyfish nervous systems.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/69QS3DHY/S096098221300359X.html}
}

@article{arendt_nerve_2016,
  title = {From Nerve Net to Nerve Ring, Nerve Cord and Brain--Evolution of the Nervous System},
  volume = {17},
  issn = {1471-0048},
  doi = {10.1038/nrn.2015.15},
  abstract = {The puzzle of how complex nervous systems emerged remains unsolved. Comparative studies of neurodevelopment in cnidarians and bilaterians suggest that this process began with distinct integration centres that evolved on opposite ends of an initial nerve net. The 'apical nervous system' controlled general body physiology, and the 'blastoporal nervous system' coordinated feeding movements and locomotion. We propose that expansion, integration and fusion of these centres gave rise to the bilaterian nerve cord and brain.},
  language = {eng},
  number = {1},
  journal = {Nature Reviews. Neuroscience},
  author = {Arendt, Detlev and Tosches, Maria Antonietta and Marlow, Heather},
  month = jan,
  year = {2016},
  keywords = {Humans,Brain,Neurons,Animals,Nerve Net,Nervous System,Biological Evolution,Nervous System Physiological Phenomena},
  pages = {61-72},
  pmid = {26675821}
}

@article{trojanowski_call_2016,
  title = {Call It {{Worm Sleep}}},
  volume = {39},
  issn = {0166-2236},
  doi = {10.1016/j.tins.2015.12.005},
  abstract = {The nematode Caenorhabditis elegans stops feeding and moving during a larval transition stage called lethargus and following exposure to cellular stressors. These behaviors have been termed `sleep-like states'. We argue that these behaviors should instead be called sleep. Sleep during lethargus is similar to sleep regulated by circadian timers in insects and mammals, and sleep in response to cellular stress is similar to sleep induced by sickness in other animals. Sleep in mammals and Drosophila shows molecular and functional conservation with C. elegans sleep. The simple neuroanatomy and powerful genetic tools of C. elegans have yielded insights into sleep regulation and hold great promise for future research into sleep regulation and function.},
  number = {2},
  journal = {Trends in Neurosciences},
  author = {Trojanowski, Nicholas F. and Raizen, David M.},
  month = feb,
  year = {2016},
  keywords = {development,evolution,quiescence,cellular stress,sleep},
  pages = {54-62},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SFEHZVME/Trojanowski and Raizen - 2016 - Call it Worm Sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YQ6J4TAU/S0166223615002684.html}
}

@article{hill_cellular_2014,
  title = {Cellular {{Stress Induces}} a {{Protective Sleep}}-like {{State}} in {{C}}.~Elegans},
  volume = {24},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2014.08.040},
  abstract = {Summary
Sleep is recognized to be ancient in origin, with vertebrates and invertebrates experiencing behaviorally quiescent states that are regulated by conserved genetic mechanisms [1, 2]. Despite its conservation throughout phylogeny, the function of sleep remains debated. Hypotheses for the purpose of sleep include nervous-system-specific functions such as modulation of synaptic strength and clearance of metabolites from the brain [3, 4], as well as more generalized cellular functions such as energy conservation and macromolecule biosynthesis [5]. These models are supported by the identification of synaptic and metabolic processes that are perturbed during prolonged wakefulness. It remains to be seen whether perturbations of cellular homeostasis in turn drive sleep. Here we show that under conditions of cellular stress, including noxious heat, cold, hypertonicity, and tissue damage, the nematode Caenorhabditis elegans engages a behavioral quiescence program. The stress-induced quiescent state displays properties of sleep and is~dependent on the ALA neuron, which mediates the conserved soporific effect of epidermal growth factor (EGF) ligand overexpression. We characterize heat-induced quiescence in detail and show that it is indeed dependent on components of EGF signaling, providing physiological relevance to the behavioral effects of EGF family ligands. We find that after noxious heat exposure, quiescence-defective animals show elevated expression of cellular stress reporter genes and are impaired for survival, demonstrating the benefit of stress-induced behavioral quiescence. These data provide evidence that cellular stress can induce a protective sleep-like state in C.~elegans and suggest that a deeply conserved function of sleep is to mitigate disruptions of cellular homeostasis.},
  number = {20},
  journal = {Current Biology},
  author = {Hill, Andrew J. and Mansfield, Richard and Lopez, Jessie M. N. G. and Raizen, David M. and Van Buskirk, Cheryl},
  month = oct,
  year = {2014},
  pages = {2399-2405},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GXIA4J2B/Hill et al. - 2014 - Cellular Stress Induces a Protective Sleep-like St.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8EVFPTKG/S0960982214010537.html}
}

@article{cassada_dauerlarva_1975,
  title = {The Dauerlarva, a Post-Embryonic Developmental Variant of the Nematode {{Caenorhabditis}} Elegans},
  volume = {46},
  issn = {0012-1606},
  language = {eng},
  number = {2},
  journal = {Developmental Biology},
  author = {Cassada, R. C. and Russell, R. L.},
  month = oct,
  year = {1975},
  keywords = {Animals,Mutation,Glucose,Larva,Temperature,Environment,Sodium Chloride,Feeding Behavior,Nematoda,Sodium Dodecyl Sulfate},
  pages = {326-342},
  pmid = {1183723}
}

@article{driver_daf-16/foxo_2013,
  title = {{{DAF}}-16/{{FOXO}} Regulates Homeostasis of Essential Sleep-like Behavior during Larval Transitions in {{C}}. Elegans},
  volume = {23},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2013.02.009},
  abstract = {Sleep homeostasis, which refers to the maintenance of sleep amount or depth following sleep deprivation, indicates that sleep and sleep-like states serve fundamental functions that cannot be bypassed []. Homeostasis of sleep-like behavior is observed during C. elegans lethargus, a 2-3 hour behavioral quiescent period that occurs during larval state transitions []. Here, we report a role for DAF-16/FOXO, a transcription factor that is active under conditions of stress [], in the response to deprivation of lethargus quiescence. Forced locomotion during lethargus results in nuclear translocation of DAF-16. The formation of dauer larvae, a developmental state promoted by daf-16, is increased in response to quiescence deprivation. daf-16 mutants show an impaired homeostatic response to deprivation of lethargus quiescence, and are hypersensitive to the lethal effects of forced locomotion during lethargus. DAF-16 expression in muscle cells but not in neurons is sufficient to restore a homeostatic response to deprivation of quiescence, pointing to a role for muscle in sleep homeostasis. These findings are relevant to clinical observations of altered metabolic signaling in response to sleep deprivation and suggest that these signaling pathways may act in non-neuronal tissue to regulate sleep behaviors.},
  number = {6},
  journal = {Current biology : CB},
  author = {Driver, Robert J. and Lamb, Annesia L. and Wyner, Abraham J. and Raizen, David M.},
  month = mar,
  year = {2013},
  pages = {501-506},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V6FRKQUI/Driver et al. - 2013 - DAF-16FOXO regulates homeostasis of essential sle.pdf},
  pmid = {23477722},
  pmcid = {PMC3924873}
}

@article{iwanir_microarchitecture_2013,
  title = {The Microarchitecture of {{C}}. Elegans Behavior during Lethargus: Homeostatic Bout Dynamics, a Typical Body Posture, and Regulation by a Central Neuron},
  volume = {36},
  issn = {1550-9109},
  shorttitle = {The Microarchitecture of {{C}}. Elegans Behavior during Lethargus},
  doi = {10.5665/sleep.2456},
  abstract = {STUDY OBJECTIVES: The nematode C. elegans develops through four larval stages before it reaches adulthood. At the transition between stages and before it sheds its cuticle, it exhibits a sleep-like behavior during a stage termed lethargus. The objectives of this study were to characterize in detail behavioral patterns and physiological activity of a command interneuron during lethargus.
MEASUREMENTS AND RESULTS: We found that lethargus behavior was composed of bouts of quiescence and motion. The duration of individual bouts ranged from 2 to 100 seconds, and their dynamics exhibited local homeostasis: the duration of bouts of quiescence positively correlated with the duration of bouts of motion that immediately preceded them in a cAMP-dependent manner. In addition, we identified a characteristic body posture during lethargus: the average curvature along the body of L4 lethargus larvae was lower than that of L4 larvae prior to lethargus, and the positions of body bends were distributed non-uniformly along the bodies of quiescent animals. Finally, we found that the AVA interneurons, a pair of backward command neurons, mediated locomotion patterns during L4 lethargus in similar fashion to their function in L4 larvae prior to lethargus. Interestingly, in both developmental stages backward locomotion was initiated and terminated asymmetrically with respect to AVA intraneuronal calcium concentration.
CONCLUSIONS: The complex behavioral patterns during lethargus can be dissected to quantifiable elements, which exhibit rich temporal dynamics and are actively regulated by the nervous system. Our findings support the identification of lethargus as a sleep-like state.
CITATION: Iwanir S; Tramm N; Nagy S; Wright C; Ish D; Biron D. The microarchitecture of C. elegans behavior during lethargus: homeostatic bout dynamics, a typical body posture, and regulation by a central neuron. SLEEP 2013;36(3):385-395.},
  language = {eng},
  number = {3},
  journal = {Sleep},
  author = {Iwanir, Shachar and Tramm, Nora and Nagy, Stanislav and Wright, Charles and Ish, Daniel and Biron, David},
  month = mar,
  year = {2013},
  keywords = {Behavior; Animal,Neurons,Animals,Interneurons,Sleep,Behavior,Signal Transduction,Larva,Locomotion,Homeostasis,Caenorhabditis elegans,lethargus,C. elegans,homeostasis,Posture},
  pages = {385-395},
  pmid = {23449971},
  pmcid = {PMC3571756}
}

@article{white_structure_1986,
  title = {The Structure of the Nervous System of the Nematode {{Caenorhabditis}} Elegans},
  volume = {314},
  copyright = {Scanned images copyright \textcopyright{} 2017, Royal Society},
  issn = {0080-4622, 2054-0280},
  doi = {10.1098/rstb.1986.0056},
  abstract = {The structure and connectivity of the nervous system of the nematode Caenorhabditis elegans has been deduced from reconstructions of electron micrographs of serial sections. The hermaphrodite nervous system has a total complement of 302 neurons, which are arranged in an essentially invariant structure. Neurons with similar morphologies and connectivities have been grouped together into classes; there are 118 such classes. Neurons have simple morphologies with few, if any, branches. Processes from neurons run in defined positions within bundles of parallel processes, synaptic connections being made en passant. Process bundles are arranged longitudinally and circumferentially and are often adjacent to ridges of hypodermis. Neurons are generally highly locally connected, making synaptic connections with many of their neighbours. Muscle cells have arms that run out to process bundles containing motoneuron axons. Here they receive their synaptic input in defined regions along the surface of the bundles, where motoneuron axons reside. Most of the m orphologically identifiable synaptic connections in a typical animal are described. These consist of about 5000 chemical synapses, 2000 neuromuscular junctions and 600 gap junctions.},
  language = {en},
  number = {1165},
  journal = {Phil. Trans. R. Soc. Lond. B},
  author = {White, John Graham and Southgate, Eileen and Thomson, J. N. and Brenner, Sydney},
  month = nov,
  year = {1986},
  pages = {1-340},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6P67IUQX/White et al. - 1986 - The structure of the nervous system of the nematod.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NDHRWFCN/1.html},
  pmid = {22462104}
}

@article{bargmann_beyond_2012,
  title = {Beyond the Connectome: {{How}} Neuromodulators Shape Neural Circuits},
  volume = {34},
  copyright = {Copyright \textcopyright{} 2012 WILEY Periodicals, Inc.},
  issn = {1521-1878},
  shorttitle = {Beyond the Connectome},
  doi = {10.1002/bies.201100185},
  abstract = {Powerful ultrastructural tools are providing new insights into neuronal circuits, revealing a wealth of anatomically-defined synaptic connections. These wiring diagrams are incomplete, however, because functional connectivity is actively shaped by neuromodulators that modify neuronal dynamics, excitability, and synaptic function. Studies of defined neural circuits in crustaceans, C. elegans, Drosophila, and the vertebrate retina have revealed the ability of modulators and sensory context to reconfigure information processing by changing the composition and activity of functional circuits. Each ultrastructural connectivity map encodes multiple circuits, some of which are active and some of which are latent at any given time.},
  language = {en},
  number = {6},
  journal = {BioEssays},
  author = {Bargmann, Cornelia I.},
  year = {2012},
  keywords = {neuropeptides,Drosophila,neural circuits,C. elegans,retina},
  pages = {458-465},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NCMDU34Y/Bargmann - Beyond the connectome How neuromodulators shape n.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QHRLWKUX/bies.html}
}

@article{stephenson_prolonged_2007,
  title = {Prolonged Deprivation of Sleep-like Rest Raises Metabolic Rate in the {{Pacific}} Beetle Cockroach, {{Diploptera}} Punctata ({{Eschscholtz}})},
  volume = {210},
  copyright = {\textcopyright{} The Company of Biologists Limited 2007},
  issn = {0022-0949, 1477-9145},
  doi = {10.1242/jeb.005322},
  abstract = {Skip to Next Section
Rats respond to sustained sleep deprivation with increased mortality preceded by a rise in resting metabolic rate that may or may not be attributed to dysfunction of the thermoregulatory system. The present study was designed to test the hypothesis that deprivation of sleep-like rest will lead to increased metabolic rate in an ectothermic insect, the Pacific beetle cockroach. A mild alerting stimulus consisting of a brief $<$1\% pulse of CO2 and simultaneous 2 s rotation (1 cm motion) of the animal chamber consistently prevented the adoption of a sleep-like resting posture in cockroaches. Two groups of 15 male adult cockroaches were studied; a group targeted for deprivation of sleep-like rest (SD) was presented with one stimulus per minute continuously, and a group of stimulus controls (SC) was given the same number of stimuli per day but scheduled such that the animals received a 3 h interval without stimuli four times per day. This protocol led to significantly increased mortality in the SD group beginning on day 17 (averaging 0.57 deaths per day thereafter), but not in the SC group (averaging 0.17 deaths per day throughout). Oxygen consumption (V\.O2) increased significantly after 4 weeks in the SD group but not the SC group. V\.O2 was 82\% above pre-deprivation baseline after 35 days in the SD group (P=0.009). Body mass was unchanged throughout. We conclude that sleep-like rest is essential for long-term viability in insects and that prolonged vigilance leads to an increase in whole-animal metabolic rate in this ectothermic species.},
  language = {en},
  number = {14},
  journal = {Journal of Experimental Biology},
  author = {Stephenson, Richard and Chu, Karen M. and Lee, James},
  month = jul,
  year = {2007},
  keywords = {cockroach,sleep,mortality,oxygen consumption},
  pages = {2540-2547},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZNSICBSY/Stephenson et al. - 2007 - Prolonged deprivation of sleep-like rest raises me.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZMZQ8SL2/2540.html},
  pmid = {17601958}
}

@article{hussaini_sleep_2009,
  title = {Sleep Deprivation Affects Extinction but Not Acquisition Memory in Honeybees},
  volume = {16},
  issn = {1072-0502, 1549-5485},
  doi = {10.1101/lm.1578409},
  abstract = {Sleep-like behavior has been studied in honeybees before, but the relationship between sleep and memory formation has not been explored. Here we describe a new approach to address the question if sleep in bees, like in other animals, improves memory consolidation. Restrained bees were observed by a web camera, and their antennal activities were used as indicators of sleep. We found that the bees sleep more during the dark phase of the day compared with the light phase. Sleep phases were characterized by two distinct patterns of antennal activities: symmetrical activity, more prominent during the dark phase; and asymmetrical activity, more common during the light phase. Sleep-deprived bees showed rebound the following day, confirming effective deprivation of sleep. After appetitive conditioning of the bees to various olfactory stimuli, we observed their sleep. Bees conditioned to odor with sugar reward showed lesser sleep compared with bees that were exposed to either reward alone or air alone. Next, we asked whether sleep deprivation affects memory consolidation. While sleep deprivation had no effect on retention scores after odor acquisition, retention for extinction learning was significantly reduced, indicating that consolidation of extinction memory but not acquisition memory was affected by sleep deprivation.},
  language = {en},
  number = {11},
  journal = {Learning \& Memory},
  author = {Hussaini, Syed Abid and Bogusch, Lisa and Landgraf, Tim and Menzel, Randolf},
  month = jan,
  year = {2009},
  pages = {698-705},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/62BZQBYR/Hussaini et al. - 2009 - Sleep deprivation affects extinction but not acqui.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E6RCQQNK/Hussaini et al. - 2009 - Sleep deprivation affects extinction but not acqui.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FZ2ZJTKQ/698.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JCDWWDBM/698.html},
  pmid = {19864296}
}

@article{klein_sleep_2010,
  title = {Sleep Deprivation Impairs Precision of Waggle Dance Signaling in Honey Bees},
  volume = {107},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1009439108},
  abstract = {Sleep is essential for basic survival, and insufficient sleep leads to a variety of dysfunctions. In humans, one of the most profound consequences of sleep deprivation is imprecise or irrational communication, demonstrated by degradation in signaling as well as in receiving information. Communication in nonhuman animals may suffer analogous degradation of precision, perhaps with especially damaging consequences for social animals. However, society-specific consequences of sleep loss have rarely been explored, and no function of sleep has been ascribed to a truly social (eusocial) organism in the context of its society. Here we show that sleep-deprived honey bees (Apis mellifera) exhibit reduced precision when signaling direction information to food sources in their waggle dances. The deterioration of the honey bee's ability to communicate is expected to reduce the foraging efficiency of nestmates. This study demonstrates the impact of sleep deprivation on signaling in a eusocial animal. If the deterioration of signals made by sleep-deprived honey bees and humans is generalizable, then imprecise communication may be one detrimental effect of sleep loss shared by social organisms.},
  language = {en},
  number = {52},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Klein, Barrett A. and Klein, Arno and Wray, Margaret K. and Mueller, Ulrich G. and Seeley, Thomas D.},
  month = dec,
  year = {2010},
  keywords = {recovery sleep,dance language,signal precision,sleep rebound},
  pages = {22705-22709},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S6E2PCDA/Klein et al. - 2010 - Sleep deprivation impairs precision of waggle danc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WJJ9UQBJ/Klein et al. - 2010 - Sleep deprivation impairs precision of waggle danc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/A9IV3JYU/22705.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RV97VZS5/22705.html},
  pmid = {21156830}
}

@article{tobler_24-h_1992,
  title = {24-h Variation of Vigilance in the Cockroach {{Blaberus}} Giganteus},
  volume = {1},
  issn = {1365-2869},
  abstract = {Our objective was to investigate whether sleep-like states occur in the cockroach, Blaberus giganteus by applying the methods formerly used for another cockroach species, Leucophaea maderae and the scorpions, Heterometrus and Pandinus. The behaviour of isolated animals (n = 10) kept under LD 12:12 h was recorded by time-lapse video for three consecutive 24-h periods. Nine behavioural states were scored for 1-min real-time epochs. Rest was subdivided into 4 sub-states on the basis of body posture and the position of the antennae. The cockroaches showed a nocturnal behaviour exhibiting a bout of locomotion at dark onset which lasted several hours, and a preference for rest in the light period. Immobility with both the body and the antennae touching the substrate (state 1) was the predominating state in the light period. In order to establish whether the sub-states of rest represented different levels of vigilance the arousal threshold was measured by determining the latency of a behavioural response to a vibration stimulus. The levels of arousal differed significantly in four behavioural states in the light period but not in the dark period. In state 1 the animals exhibited the lowest arousal whereas in the activity states arousal was the highest. The state with the highest arousal threshold occurred in the beginning of the light period. Thereafter, arousal progressively increased and remained relatively high during the dark period. The effect of 6-h deprivation of rest by the gentle shaking of the cages whenever the animals were immobile, resulted in a reduced latency to state 1, a small increase of state 1 and a more prominent initial increase of activity during recovery. In conclusion, this study provides evidence for the existence of a 24-h variation of vigilance in the cockroach. It further indicates that a 'rest deficit' gives rise to a compensatory response. The data support the notion that sleep-like states are present in these insects.},
  language = {eng},
  number = {4},
  journal = {Journal of Sleep Research},
  author = {Tobler, null and {Neuner-Jehle}, null},
  month = dec,
  year = {1992},
  pages = {231-239},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/URAXNJ7I/Tobler and Neuner-Jehle - 1992 - 24-h variation of vigilance in the cockroach Blabe.pdf},
  pmid = {10607056}
}

@article{sauer_sleep_2004,
  title = {Sleep Deprivation in Honey Bees.},
  volume = {13},
  issn = {0962-1105},
  doi = {10.1111/j.1365-2869.2004.00393.x},
  abstract = {Abstract: Rest at night in forager honey bees (Apis mellifera) meets essential criteria of sleep. This paper reports the effect of a 12-h total sleep...},
  language = {eng},
  number = {2},
  journal = {Journal of sleep research},
  author = {Sauer, S. and Herrmann, E. and Kaiser, W.},
  month = jun,
  year = {2004},
  keywords = {antennal immobility,behavioural sleep,honey bee,Sleep Deprivation,Honey bee,Antennal immobility,Behavioural sleep,sleep deprivation},
  pages = {145-152},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5RZCW6PZ/Sauer et al. - Sleep deprivation in honey bees1.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QBDJCPU5/Sauer et al. - Sleep deprivation in honey bees1.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LFV9MVSQ/j.1365-2869.2004.00393.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V59HPYVY/15175094.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WMRYDCQZ/j.1365-2869.2004.00393.html},
  pmid = {15175094}
}

@article{andersen1968sleep,
  title = {Sleep in Moths and Its Dependence on the Frequency of Stimulation in {{Anagasta}} Kuehniella},
  volume = {33},
  journal = {Opusc. ent},
  author = {Andersen, F Sogaard},
  year = {1968},
  pages = {15-24}
}

@article{kaiser1985comparative,
  title = {Comparative Neurobiology of Sleep-the Honey Bee Model},
  volume = {84},
  journal = {Sleep},
  author = {Kaiser, W},
  year = {1985},
  pages = {225-227}
}

@article{kaiser1988electromyographic,
  title = {Electromyographic Indicators of Sleep and Wakefulness in Honey Bees},
  volume = {8},
  journal = {Sleep},
  author = {Kaiser, W and Jander, JP},
  year = {1988},
  pages = {249-251}
}

@article{frank_preliminary_2012,
  title = {A {{Preliminary Analysis}} of {{Sleep}}-{{Like States}} in the {{Cuttlefish Sepia}} Officinalis},
  volume = {7},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0038125},
  abstract = {Sleep has been observed in several invertebrate species, but its presence in marine invertebrates is relatively unexplored. Rapid-eye-movement (REM) sleep has only been observed in vertebrates. We investigated whether the cuttlefish Sepia officinalis displays sleep-like states. We find that cuttlefish exhibit frequent quiescent periods that are homeostatically regulated, satisfying two criteria for sleep. In addition, cuttlefish transiently display a quiescent state with rapid eye movements, changes in body coloration and twitching of the arms, that is possibly analogous to REM sleep. Our findings thus suggest that at least two different sleep-like states may exist in Sepia officinalis.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Frank, Marcos G. and Waldrop, Robert H. and Dumoulin, Michelle and Aton, Sara and Boal, Jean G.},
  month = jun,
  year = {2012},
  keywords = {Sleep,Mammals,Eyes,Invertebrates,Body plan organization,Cephalopods,Chromatophores,Eye movements},
  pages = {e38125},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/28528V88/Frank et al. - 2012 - A Preliminary Analysis of Sleep-Like States in the.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T448GBKM/article.html}
}

@article{brown_brain_2006,
  title = {Brain and Behavioural Evidence for Rest-Activity Cycles in {{Octopus}} Vulgaris},
  volume = {172},
  issn = {0166-4328},
  doi = {10.1016/j.bbr.2006.05.009},
  abstract = {Octopus vulgaris maintained under a 12/12h light/dark cycle exhibit a pronounced nocturnal activity pattern. Animals deprived of rest during the light period show a marked `rebound' in activity in the following 24h. `Active' octopuses attack faster than `quiet' animals and brain activity recorded electrically intensifies during `quiet' behaviour. Thus, in Octopus as in vertebrates, brain areas involved in memory or `higher' processes exhibit `off-line' activity during rest periods.},
  number = {2},
  journal = {Behavioural Brain Research},
  author = {Brown, Euan R. and Piscopo, Stefania and De Stefano, Rosanna and Giuditta, Antonio},
  month = sep,
  year = {2006},
  keywords = {Vertical lobe,Octopus brain,Electrical recordings,Sleep,Invertebrates,Circadian rhythm},
  pages = {355-359},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7IQFNDY8/Brown et al. - 2006 - Brain and behavioural evidence for rest-activity c.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4YK9ZBS3/S0166432806002816.html}
}

@article{odegaard_how_2000,
  title = {How Many Species of Arthropods? {{Erwin}}'s Estimate Revised},
  volume = {71},
  issn = {0024-4066},
  shorttitle = {How Many Species of Arthropods?},
  doi = {10.1111/j.1095-8312.2000.tb01279.x},
  abstract = {Abstract.  Erwin's much debated estimate of 30 million species of arthropods is revised. The original estimate is based on the evaluation of host specificity of},
  language = {en},
  number = {4},
  journal = {Biological Journal of the Linnean Society},
  author = {\O{}degaard, Frode},
  month = dec,
  year = {2000},
  pages = {583-597},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D7DM67A3/Ødegaard - 2000 - How many species of arthropods Erwin's estimate r.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YXHHZSW9/2638652.html}
}

@article{ganihar_biomass_1997,
  title = {Biomass Estimates of Terrestrial Arthropods Based on Body Length},
  volume = {22},
  issn = {0250-5991, 0973-7138},
  doi = {10.1007/BF02704734},
  abstract = {The relationship between body length and biomass (dry weight) was investigated for nineteen taxa of terrestrail arthropods and for the combined sample that included all insect taxa. The specimens were collected from forests of Bicholim taluk of Goa. Four models were evaluated, a linear function, a logarithmic function, a power function and an exponential function. The linear function best describes dry weights in the order Isopoda of class Crustacea and dictyopteran, coleopteran larvae of class Insecta. The logarithmic function fits well for only one group namely Opiliones of class Arachnida. The power functions fits best for Scutigeromorpha and Scolopendromorpha of class Chilopoda, Araneae of class Arachnida, Collembola, Thysanura, Orthoptera, Hemiptera, Homoptera, coleopteran adults, Diptera, lepidopteran adults and Hymenoptera of class Insecta and the combined data on adult insects. An exponential function fits well for the dermapteran and lepidopteran larvae of class Insecta. The usefulness of these estimates of Arthropod biomass in community ecology is discussed.},
  language = {en},
  number = {2},
  journal = {Journal of Biosciences},
  author = {Ganihar, S. R.},
  month = mar,
  year = {1997},
  pages = {219-224},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WDY2WZR2/Ganihar - 1997 - Biomass estimates of terrestrial arthropods based .pdf}
}

@article{stork_abundance_1993,
  title = {Abundance, {{Body Size}} and {{Biomass}} of {{Arthropods}} in {{Tropical Forest}}},
  volume = {67},
  issn = {0030-1299},
  doi = {10.2307/3545360},
  abstract = {Samples representing 32624 arthropods were collected using standard sampling methods from five habitats in lowland rain forest (canopy, tree trunks, low herb layer, leaf litter and soil) in Seram, Indonesia. The relationships between arthropod abundance (number of individuals), body size, and biomass are described for these five habitats, for the predicted arthropod fauna of a hectare of forest, and for different trophic groups. The results are similar for all five habitats; abundance decreases and biomass increases with body size. Broadly similar principles apply for herbivores, decomposers and predators but not for "tourists". Thus the "equal biomass hypothesis", which predicts roughly constant biomass across logarithmic size classes, is rejected. Previous studies have suggested that the fractal nature of surfaces is important in determining abundance-body size relationships in animal communities. These predict slopes of approximately -3.25 for log abundance against log body size. In this study the steepest slope was only -2.43. This suggests that the fractal nature of surfaces are less important in determining arthropod assemblages than has been considered. Two factors may account for the difference in predicted and observed slopes. First, the assumed metabolic rate component in fractal arguments (i.e. that metabolic rate scales with body size to the 0.75 power) is wrong, and second, smaller organisms are under-sampled from all habitats. Under-sampling of smaller organisms may also account, at least in part, for the observed slopes which result in our rejection of the "equal biomass hypothesis".},
  number = {3},
  journal = {Oikos},
  author = {Stork, Nigel E. and Blackburn, Tim M.},
  year = {1993},
  pages = {483-489}
}

@article{klein_work_2011,
  title = {Work or Sleep? {{Honeybee}} Foragers Opportunistically Nap during the Day When Forage Is Not Available},
  volume = {82},
  issn = {0003-3472},
  shorttitle = {Work or Sleep?},
  doi = {10.1016/j.anbehav.2011.03.026},
  abstract = {Shifts in work schedules test humans' capacity to be flexible in the timing of both work and sleep. Honeybee, Apis mellifera, foragers also shift their work schedules, but how flexible they are in the timing of sleep as they shift the timing of work is unknown, despite the importance of colony-level plasticity in the face of a changing environment. We hypothesized that sleep schedules of foragers are not fixed and instead vary depending on the time when food is available. We trained bees to visit a food source made available for several hours in the early morning (AM) or several hours in the late afternoon (PM), then monitored their sleep behaviour for 24h after training, specifically comparing their sleep during the AM and PM periods previously designated as training periods. Following AM training, honeybee foragers slept more during the afternoon than during the morning, but following PM training, the same bees `slept in' the next morning, and so slept more in the morning than in the afternoon. Although foragers did not change the total amount of time devoted to each of their behaviours (including sleep), the timing of their sleep did change. Thus, plasticity in timing of foraging was matched by plasticity in timing of sleep. The apparent correlation between the timing patterns of foraging and sleeping demonstrates temporal plasticity of sleep under ecologically realistic conditions in an invertebrate. Testing how shift work affects the health and performance of honeybees may shed light on the role of sleep in a nonhuman social animal.},
  number = {1},
  journal = {Animal Behaviour},
  author = {Klein, Barrett A. and Seeley, Thomas D.},
  month = jul,
  year = {2011},
  keywords = {nap,plasticity,sleep,foraging,honeybee,shift work},
  pages = {77-83},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FXSPYXJV/Klein and Seeley - 2011 - Work or sleep Honeybee foragers opportunistically.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LCEECAPD/S0003347211001424.html}
}

@article{bloch_chronobiology_2001,
  title = {Chronobiology: {{Reversal}} of Honeybee Behavioural Rhythms},
  volume = {410},
  copyright = {2001 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {Chronobiology},
  doi = {10.1038/35074183},
  abstract = {Adult honeybees have sleep-like states1,2 and, like human infants3, bees develop their own endogenous circadian rhythms as they mature4,5. But whereas disruption of our sleep cycles and synchronized internal rhythms may adversely affect our physiology and performance3, we show here that honeybees can revert to certain arrhythmic behaviours when necessary. To our knowledge, this chronobiological plasticity is the first example in any animal of a socially mediated reversal in activity rhythms.},
  language = {en},
  number = {6832},
  journal = {Nature},
  author = {Bloch, Guy and Robinson, Gene E.},
  month = apr,
  year = {2001},
  pages = {1048},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/N9ILXME8/Bloch and Robinson - 2001 - Chronobiology Reversal of honeybee behavioural rh.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E2DEG2F4/35074183.html}
}

@article{zwaka_context_2015,
  title = {Context {{Odor Presentation}} during {{Sleep Enhances Memory}} in {{Honeybees}}},
  volume = {25},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2015.09.069},
  abstract = {Summary
Sleep plays an important role in stabilizing new memory traces after learning [1\textendash{}3]. Here we investigate whether sleep's role in memory processing is similar in evolutionarily distant species and demonstrate that a context trigger during deep-sleep phases improves memory in invertebrates, as it does in humans. We show that in honeybees (Apis mellifera), exposure to an odor during deep sleep that has been present during learning improves memory performance the following day. Presentation of the context odor during wake phases or novel odors during sleep does not enhance memory. In humans, memory consolidation can be triggered by presentation of a context odor during slow-wave sleep that had been present during learning [3\textendash{}5]. Our results reveal that deep-sleep phases in honeybees have the potential to prompt memory consolidation, just~as they do in humans. This study provides strong evidence for a conserved role of sleep\textemdash{}and how it~affects memory processes\textemdash{}from insects to mammals.},
  number = {21},
  journal = {Current Biology},
  author = {Zwaka, Hanna and Bartels, Ruth and Gora, Jacob and Franck, Vivien and Culo, Ana and G\"otsch, Moritz and Menzel, Randolf},
  month = nov,
  year = {2015},
  pages = {2869-2874},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LKIM7P5L/Zwaka et al. - 2015 - Context Odor Presentation during Sleep Enhances Me.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IKUMJJVZ/S0960982215012233.html}
}

@article{eban-rothschild_differences_2008,
  title = {Differences in the Sleep Architecture of Forager and Young Honeybees ({{Apis}} Mellifera)},
  volume = {211},
  copyright = {\textcopyright{} The Company of Biologists Limited 2008},
  issn = {0022-0949, 1477-9145},
  doi = {10.1242/jeb.016915},
  abstract = {Skip to Next Section
Honeybee (Apis mellifera) foragers are among the first invertebrates for which sleep behavior has been described. Foragers (typically older than 21 days) have strong circadian rhythms; they are active during the day, and sleep during the night. We explored whether young bees ($\sim$3 days of age), which are typically active around-the-clock with no circadian rhythms, also exhibit sleep behavior. We combined 24-hour video recordings, detailed behavioral observations, and analyses of response thresholds to a light pulse for individually housed bees in various arousal states. We characterized three sleep stages in foragers on the basis of differences in body posture, bout duration, antennae movements and response threshold. Young bees exhibited sleep behavior consisting of the same three stages as observed in foragers. Sleep was interrupted by brief awakenings, which were as frequent in young bees as in foragers. Beyond these similarities, we found differences in the sleep architecture of young bees and foragers. Young bees passed more frequently between the three sleep stages, and stayed longer in the lightest sleep stage than foragers. These differences in sleep architecture may represent developmental and/or environmentally induced variations in the neuronal network underlying sleep in honeybees. To the best of our knowledge, this is the first evidence for plasticity in sleep behavior in insects.},
  language = {en},
  number = {15},
  journal = {Journal of Experimental Biology},
  author = {{Eban-Rothschild}, Ada D. and Bloch, Guy},
  month = aug,
  year = {2008},
  keywords = {Apis mellifera,sleep,behavioral development,insect,response threshold},
  pages = {2408-2416},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BVP44PU5/Eban-Rothschild and Bloch - 2008 - Differences in the sleep architecture of forager a.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TCP7JKH8/2408.html},
  pmid = {18626074}
}

@article{menzel_honeybee_2012,
  title = {The Honeybee as a Model for Understanding the Basis of Cognition},
  volume = {13},
  copyright = {2012 Nature Publishing Group},
  issn = {1471-0048},
  doi = {10.1038/nrn3357},
  abstract = {Honeybees contradict the notion that insect behaviour tends to be relatively inflexible and stereotypical. Indeed, they live in colonies and exhibit complex social, navigational and communication behaviours, as well as a relatively rich cognitive repertoire. Because these relatively complex behaviours are controlled by a brain consisting of only 1 million or so neurons, honeybees offer an opportunity to study the relationship between behaviour and cognition in neural networks that are limited in size and complexity. Most recently, the honeybee has been used to model learning and memory formation, highlighting its utility for neuroscience research, in particular for understanding the basis of cognition.},
  language = {en},
  number = {11},
  journal = {Nature Reviews Neuroscience},
  author = {Menzel, Randolf},
  month = nov,
  year = {2012},
  pages = {758-768},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RQIN2KV6/Menzel - 2012 - The honeybee as a model for understanding the basi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JIBVKMLX/nrn3357.html}
}

@article{srinivasan_honey_2010,
  title = {Honey {{Bees}} as a {{Model}} for {{Vision}}, {{Perception}}, and {{Cognition}}},
  volume = {55},
  doi = {10.1146/annurev.ento.010908.164537},
  abstract = {Among the so-called simpler organisms, the honey bee is one of the few examples of an animal with a highly evolved social structure, a rich behavioral repertoire, an exquisite navigational system, an elaborate communication system, and an extraordinary ability to learn colors, shapes, fragrances, and navigational routes quickly and accurately. This review examines vision and complex visually mediated behavior in the honey bee, outlining the structure and function of the compound eyes, the perception and discrimination of colors and shapes, the learning of complex tasks, the ability to establish and exploit complex associations, and the capacity to abstract general principles from a task and apply them to tackle novel situations. All this is accomplished by a brain that weighs less than a milligram and carries fewer than a million neurons, thus making the bee a promising subject in which to study a variety of fundamental questions about behavior and brain function.},
  number = {1},
  journal = {Annual Review of Entomology},
  author = {Srinivasan, Mandyam V.},
  year = {2010},
  pages = {267-284},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2IU49M7L/Srinivasan - 2010 - Honey Bees as a Model for Vision, Perception, and .pdf},
  pmid = {19728835}
}

@book{frisch_dance_1967,
  title = {The Dance Language and Orientation of Bees},
  language = {en},
  publisher = {{Belknap Press of Harvard University Press}},
  author = {von Frisch, Karl},
  year = {1967},
  keywords = {Bees,Animal orientation,Bees/ Behavior,Bees/ Orientation,Honeybee,Insects,Nature / Animals / Insects \& Spiders,Nature / Insects \& Spiders,Pets / General,Science / Life Sciences / Biology,Science / Life Sciences / Zoology / Entomology}
}

@article{homberg_search_2004,
  title = {In Search of the Sky Compass in the Insect Brain},
  volume = {91},
  issn = {0028-1042, 1432-1904},
  doi = {10.1007/s00114-004-0525-9},
  abstract = {Like many vertebrate species, insects rely on a sun compass for spatial orientation and long- range navigation. In addition to the sun, however, insects can also use the polarization pattern of the sky as a reference for estimating navigational directions. Recent analysis of polarization vision pathways in the brain of orthopteroid insects sheds some light onto brain areas that might act as internal navigation centers. Here I review the significance, peripheral mechanisms, and central processing stages for polarization vision in insects with special reference to the locust Schistocerca gregaria. As in other insect species, polarization vision in locusts relies on specialized photoreceptor cells in a small dorsal rim area of the compound eye. Stages in the brain involved in polarized light signaling include specific areas in the lamina, medulla and lobula of the optic lobe and, in the midbrain, the anterior optic tubercle, the lateral accessory lobe, and the central complex. Integration of polarized-light signals with information on solar position appears to start in the optic lobe. In the central complex, polarization-opponent interneurons form a network of interconnected neurons. The organization of the central complex, its connections to thoracic motor centers, and its involvement in the spatial control of locomotion strongly suggest that it serves as a spatial organizer within the insect brain, including the functions of compass orientation and path integration. Time compensation in compass orientation is possibly achieved through a neural pathway from the internal circadian clock in the accessory medulla to the protocerebral bridge of the central complex.},
  language = {en},
  number = {5},
  journal = {Naturwissenschaften},
  author = {Homberg, Uwe},
  month = may,
  year = {2004},
  pages = {199-208},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q9KDJHNZ/Homberg - 2004 - In search of the sky compass in the insect brain.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3XDIIQVY/s00114-004-0525-9.html}
}

@article{milner_cognitive_1998,
  title = {Cognitive {{Neuroscience}} and the {{Study}} of {{Memory}}},
  volume = {20},
  issn = {0896-6273},
  doi = {10.1016/S0896-6273(00)80987-3},
  language = {English},
  number = {3},
  journal = {Neuron},
  author = {Milner, Brenda and Squire, Larry R. and Kandel, Eric R.},
  month = mar,
  year = {1998},
  pages = {445-468},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BHHZJRIX/Milner et al. - 1998 - Cognitive Neuroscience and the Study of Memory.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HTD8JVMG/S0896-6273(00)80987-3.html},
  pmid = {9539121}
}

@article{rosenberg_new_2014,
  title = {A {{New Critical Estimate}} of {{Named Species}}-{{Level Diversity}} of the {{Recent Mollusca}}},
  volume = {32},
  issn = {0740-2783},
  doi = {10.4003/006.032.0204},
  abstract = {:   Modern estimates of species-level diversity in the recent Mollusca range from 34,000 to 120,000 described species, with total diversity including undescribed species often cited as 200,000. Most estimates are unverifiable, not being based on reproducible methods. Ultimately the best way to gauge diversity is explicit enumeration: actual listing of known species. Comprehensive lists of species are valued as a basis for systematic revisions and for comparing diversity across taxa, but it is less appreciated that they also provide a means for statistical sampling of biodiversity databases. I assessed the completeness of molluscan species listings in the World Register of Marine Species (WoRMS) by comparing it to a standardized inventory of the species represented in the Malacology collection of the Academy of Natural Sciences of Philadelphia (ANSP). Random samples of names were scored for presence or absence in WoRMS, with standard errors calculated from the binomial distribution. The WoRMS database has about 1,200 duplicate or extraneous listings for mollusk species and is missing about 1,300 (3\%). Overall marine molluscan diversity is estimated at 43,600 $\pm$ 900 species, where 900 is a 95\% confidence interval. The validity of this confidence interval depends on the WoRMS database and the ANSP collection not having correlated weaknesses. Lack of relatively complete species databases prevents similar assessments for terrestrial and freshwater mollusks, but, using less rigorous methods, I estimate that there are 70,000 to 76,000 described species of recent Mollusca. The low end of this estimate, 70,000 species, is similar to the number of recent chordate species, 69,000, so it is possible that the Mollusca are not the second most diverse phylum of animals in terms of recognized recent species. Naming rates for chordate are currently higher than for mollusk, 750 versus 600 species per year, although the Mollusca are regarded as having higher undescribed diversity. The Mollusca have long been considered the most species-rich marine phylum, but the estimate of 43,600 is substantially below the 56,000 species of Arthropoda listed in WoRMS. Globally, the ratio of marine gastropod to marine bivalve species in WoRMS is 4:1, which is higher than in any regional fauna, suggesting that gastropods have smaller geographic ranges on average than bivalves. The main remaining gaps in WoRMS are among opisthobranchs (8\% missing) and Indo-Pacific marine mollusks (6\%). The most diverse molluscan genus in WoRMS is Turbonilla, with more than 1,000 species listed as accepted.},
  number = {2},
  journal = {American Malacological Bulletin},
  author = {Rosenberg, Gary},
  month = sep,
  year = {2014},
  pages = {308-322},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T55PLQEK/Rosenberg - 2014 - A New Critical Estimate of Named Species-Level Div.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G9BJUI2E/006.032.html}
}

@article{kandel_mechanism_1964,
  title = {Mechanism of {{Prolonged Heterosynaptic Facilitation}}},
  volume = {202},
  copyright = {1964 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/202145a0},
  abstract = {Mechanism of Prolonged Heterosynaptic Facilitation},
  language = {en},
  number = {4928},
  journal = {Nature},
  author = {Kandel, E. R. and Tauc, L.},
  month = apr,
  year = {1964},
  pages = {145-147},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W3BUQ4A2/Kandel and Tauc - 1964 - Mechanism of Prolonged Heterosynaptic Facilitation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UD22NMIJ/202145a0.html}
}

@article{mendoza-angeles_slow_2007,
  title = {Slow Waves during Sleep in Crayfish: {{A}} Time\textendash{}frequency Analysis},
  volume = {162},
  issn = {0165-0270},
  shorttitle = {Slow Waves during Sleep in Crayfish},
  doi = {10.1016/j.jneumeth.2007.01.025},
  abstract = {NREM phases of sleep in vertebrates are characterized by slow waves. Crayfish also sleeps while lying on one side on the surface of the water. At this time the numerous spikes on an almost flat base line generated by the brain when alert are replaced by slow waves of 15\textendash{}20Hz. In this work, we conducted experiments to determine the temporal relationship between the lying on one side position and the brain slow waves. We videotaped chronically implanted animals to detect their body position and simultaneously recorded their brain electrical activity. To analyze brain electrical activity, we developed a wavelet based method and correlated the results with body position. Among results are: (a) during sleep signals in the frequency range 30\textendash{}45Hz show a large decrease in power; (b) sleep slow waves are generated 1\textendash{}2min after the animal lies on one side and are maintained throughout the whole period in such position. We conclude that the strong correlation between brain slow waves and lying on one side position further indicates periods of true sleep in these animals.},
  number = {1},
  journal = {Journal of Neuroscience Methods},
  author = {{Mendoza-Angeles}, Karina and Cabrera, Agust\'in and {Hern\'andez-Falc\'on}, Jes\'us and Ram\'on, Fidel},
  month = may,
  year = {2007},
  keywords = {Slow waves,Brain,Electrophysiology,Sleep,Invertebrate,Crayfish,Wavelet analysis},
  pages = {264-271},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2U92SV6I/Mendoza-Angeles et al. - 2007 - Slow waves during sleep in crayfish A time–freque.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/USGYUDJW/S0165027007000659.html}
}

@article{mendoza-angeles_slow_2010,
  title = {Slow Waves during Sleep in Crayfish. {{Origin}} and Spread},
  volume = {213},
  issn = {1477-9145},
  doi = {10.1242/jeb.038240},
  abstract = {Previous results show that when unrestrained crayfish sleep, the electrical activity of the brain changes from multiple spikes (frequencies above 300 Hz) on a flat baseline to continuous slow waves at a frequency of 15-20 Hz. To study the temporal organization of such activity, we developed a tethered crayfish preparation that allows us to place electrodes on visually identified regions of the brain. Recording the electrical activity of different brain areas shows that when the animal is active (awake), slow waves are present only in the central complex. However, simultaneously with the animal becoming limp (sleeping), slow waves spread first to deuto- and then to protocerebrum, suggesting that the central complex of the crayfish brain acts as the sleep generator.},
  language = {eng},
  number = {Pt 12},
  journal = {The Journal of Experimental Biology},
  author = {{Mendoza-Angeles}, Karina and {Hern\'andez-Falc\'on}, Jes\'us and Ram\'on, Fidel},
  month = jun,
  year = {2010},
  keywords = {Male,Brain,Brain Mapping,Animals,Sleep,Cluster Analysis,Wakefulness,Electrophysiological Phenomena,Astacoidea,Evoked Potentials; Visual},
  pages = {2154-2164},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NI4UYYNW/Mendoza-Angeles et al. - 2010 - Slow waves during sleep in crayfish. Origin and sp.pdf},
  pmid = {20511530}
}

@article{ramon_slow_2004,
  title = {Slow Wave Sleep in Crayfish},
  volume = {101},
  copyright = {Copyright \textcopyright{} 2004, The National Academy of Sciences},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0402015101},
  abstract = {Clear evidence of sleep in invertebrates is still meager. Defined as a distinct state of reduced activity, arousability, attention, and initiative, it is well established in mammals, birds, reptiles, and teleosts. It is commonly defined by additional electroencephalographic criteria that are only well established in mammals and to some extent in birds. Sleep states similar to those in mammals, except for electrical criteria, seem to occur in some invertebrates, based on behavior and some physiological observations. Currently the most compelling evidence for sleep in invertebrates (evidence that meets most standard criteria for sleep) has been obtained in the fruit fly Drosophila melanogaster. However, in mammals, sleep is also characterized by a brain state different from that at rest but awake. The electrophysiological slow wave criterion for this state is not seen in Drosophila or in honey bees. Here, we show that, in crayfish, a behavioral state with elevated threshold for vibratory stimulation is accompanied by a distinctive form of slow wave electrical activity of the brain, quite different from that during waking rest. Therefore, crayfish can attain a sleep state comparable to that of mammals.},
  language = {en},
  number = {32},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Ram\'on, Fidel and {Hern\'andez-Falc\'on}, Jes\'us and Nguyen, Bao and Bullock, Theodore H.},
  month = aug,
  year = {2004},
  pages = {11857-11861},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WNIKXQD6/Ramón et al. - 2004 - Slow wave sleep in crayfish.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FF67VD7U/11857.html},
  pmid = {15286285}
}

@article{edwards_fifty_1999,
  title = {Fifty Years of a Command Neuron: The Neurobiology of Escape Behavior in the Crayfish},
  volume = {22},
  issn = {0166-2236},
  shorttitle = {Fifty Years of a Command Neuron},
  doi = {10.1016/S0166-2236(98)01340-X},
  abstract = {Fifty years ago C.A.G. Wiersma established that the giant axons of the crayfish nerve cord drive tail-flip escape responses. The circuitry that includes these giant neurons has now become one of the best-understood neural circuits in the animal kingdom. Although it controls a specialized behavior of a relatively simple animal, this circuitry has provided insights that are of general neurobiological interest concerning matters as diverse as the identity of the neural substrates involved in making behavioral decisions, the cellular bases of learning, subcellular neuronal computation, voltage-gated electrical synaptic transmission and modification of neuromodulator actions that result from social experience. This work illustrates the value of studying a circuit of moderate, but tractable, complexity and known behavioral function.},
  number = {4},
  journal = {Trends in Neurosciences},
  author = {Edwards, Donald H. and Heitler, William J. and Krasne, Franklin B.},
  month = apr,
  year = {1999},
  keywords = {Invertebrate,Crayfish,Command neuron,Escape,Giant axon,Neural circuitry},
  pages = {153-161},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z2BCGSPK/Edwards et al. - 1999 - Fifty years of a command neuron the neurobiology .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XHTJWFTX/S016622369801340X.html}
}

@article{zhdanova_sleep_2011,
  title = {Sleep and Its Regulation in Zebrafish},
  volume = {22},
  issn = {2191-0200},
  doi = {10.1515/rns.2011.005},
  abstract = {The function of sleep remains a central enigma of modern biology, in spite of the obvious importance of sleep for normal physiology and cognition. The zebrafish has emerged as a promising new model for studying sleep, its changes with age, and the impact of sleep alterations on cognitive function. Recent studies of this diurnal vertebrate have provided new insights into the dual role of the pineal hormone melatonin and its receptors, regulating sleep in diurnal vertebrates through both homeostatic and circadian mechanisms. Research in zebrafish has also revealed interactions between melatonin and the hypocretin/orexin system, another important sleep-wake modulator. Future investigations should benefit from the conservation in zebrafish of mechanisms that regulate normal sleep, our extensive knowledge of their molecular biology, the availability of multiple transgenic and mutant phenotypes, and the feasibility of applying sensitive in vivo imaging techniques to record sleep-related neuronal activity in these optically transparent subjects. The established sensitivity of zebrafish to many pharmacological hypnotics should also contribute to the development of new, safe and effective sleep medications.},
  number = {1},
  journal = {Reviews in the Neurosciences},
  author = {Zhdanova, Irina V.},
  year = {2011},
  keywords = {zebrafish,circadian,sleep,homeostatic,hypocretin,melatonin},
  pages = {27--36},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2E56SPHP/Zhdanova - 2011 - Sleep and its regulation in zebrafish.pdf}
}

@article{zhdanova_melatonin_2001,
  title = {Melatonin Promotes Sleep-like State in Zebrafish},
  volume = {903},
  issn = {0006-8993},
  abstract = {The sleep-promoting effect of the pineal hormone melatonin in humans is known for decades. However, the mechanisms of this phenomenon remain obscure, mainly due to lack of a simple, genetically tractable, animal model. We now report that melatonin promotes sleep-like state in a diurnal lower vertebrate, zebrafish (Danio rerio), and this effect is mediated through activation of specific melatonin membrane receptors. Furthermore, our data show that the sleep-like state in zebrafish has fundamental similarities with sleep in mammals, including characteristic postures, elevated arousal threshold to sensory stimulation and a compensatory rest rebound following rest deprivation, and can be induced by conventional hypnotics, diazepam and sodium pentobarbital. Collectively, these data indicate that melatonin is evolutionary conserved sleep-promoting agent in diurnal species and suggest that zebrafish provide an efficient animal model for studying the molecular mechanisms of sleep regulation and for screening new types of hypnotic medications.},
  language = {eng},
  number = {1-2},
  journal = {Brain Research},
  author = {Zhdanova, I. V. and Wang, S. Y. and Leclair, O. U. and Danilova, N. P.},
  month = jun,
  year = {2001},
  keywords = {Animals,Sleep,Species Specificity,Motor Activity,Melatonin,Zebrafish,Hypnotics and Sedatives,Anticonvulsants,Diazepam,Pentobarbital},
  pages = {263-268},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5TUYXHH4/Zhdanova et al. - 2001 - Melatonin promotes sleep-like state in zebrafish.pdf},
  pmid = {11382414}
}

@article{tobler_effect_1985,
  title = {Effect of Rest Deprivation on Motor Activity of Fish},
  volume = {157},
  issn = {0340-7594, 1432-1351},
  doi = {10.1007/BF01350078},
  abstract = {SummaryThe rest-activity behavior of two fish species,Cichlosoma nigrofasciatum andCarassius auratus kept under 12-h light-12-h dim condition was investigated. Rest and activity were determined from continuous time-lapse video recordings. Three states were discriminated based on the degree of motor activity. Both species exhibited a clear rest-activity rhythm with activity predominating during the light period (Figs. 1, 2). `Rest deprivation' was carried out in perch during the habitual dim period by exposing the animals to either 12 h continuous light or to 6 h intermittent light (1 h light \textemdash{} 1 h dim for 12 h). Both light schedules enhanced activity and reduced rest (Fig. 3). Light-induced activation was followed by an increase in low activity and rest behavior which prevailed for 12 h following continuous light, and for 6 h following intermittent light (Figs. 3, 4). The results indicate that homeostatic mechanisms are involved in the regulation of rest and activity in fish. These mechanisms may be similar to those underlying sleep regulation in mammals.},
  language = {en},
  number = {6},
  journal = {Journal of Comparative Physiology A},
  author = {Tobler, Irene and Borb\'ely, Alexander A.},
  month = nov,
  year = {1985},
  pages = {817-822},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FEQA5MJA/Tobler and Borbély - 1985 - Effect of rest deprivation on motor activity of fi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DS386J7G/BF01350078.html}
}

@article{zhdanova_sleep_2006,
  title = {Sleep in {{Zebrafish}}},
  volume = {3},
  issn = {1545-8547},
  doi = {10.1089/zeb.2006.3.215},
  abstract = {Zebrafish (Danio rerio), a small prolific rapidly-developing diurnal vertebrate, shows behavioral, physiological, and pharmacological characteristics of mammalian sleep. Zebrafish brain has well-developed neuronal structures and neurochemical systems that are known to be necessary and sufficient for sleep regulation in other vertebrate species. Rich behavioral repertoire in zebrafish permits investigation of the effects of sleep and sleep deprivation on cognitive functions and performance. Sensitivity of this fish to hypnotic agents helps in designing high throughput screens for new hypnotic medications, evaluation of their efficacy, and potential side effects. The optical transparency of larval zebrafish and intracellular fluorescent markers of calcium responses available make it possible to visualize neuronal activity with single cell resolution in a behaving fish. Given the accumulated experience in conducting large-scale genetic screens in zebrafish, multiple available mutant phenotypes, and advanced genetic and physical maps of this vertebrate, zebrafish is an excellent model for studying the enigmatic basic sleep function and mechanisms of sleep regulation.},
  number = {2},
  journal = {Zebrafish},
  author = {Zhdanova, Irina V.},
  month = jun,
  year = {2006},
  pages = {215-226},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JCI34UYX/Zhdanova - 2006 - Sleep in Zebrafish.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YIDZW59S/zeb.2006.3.html}
}

@article{hoegg_phylogenetic_2004,
  title = {Phylogenetic {{Timing}} of the {{Fish}}-{{Specific Genome Duplication Correlates}} with the {{Diversification}} of {{Teleost Fish}}},
  volume = {59},
  issn = {0022-2844, 1432-1432},
  doi = {10.1007/s00239-004-2613-z},
  abstract = {For many genes, ray-finned fish (Actinopterygii) have two paralogous copies, where only one ortholog is present in tetrapods. The discovery of an additional, almost-complete set of Hox clusters in teleosts (zebrafish, pufferfish, medaka, and cichlid) but not in basal actinopterygian lineages (Polypterus) led to the formulation of the fish-specific genome duplication hypothesis. The phylogenetic timing of this genome duplication during the evolution of ray-finned fish is unknown, since only a few species of basal fish lineages have been investigated so far. In this study, three nuclear genes (fzd8, sox11, tyrosinase) were sequenced from sturgeons (Acipenseriformes), gars (Semionotiformes), bony tongues (Osteoglossomorpha), and a tenpounder (Elopomorpha). For these three genes, two copies have been described previously teleosts (e.g., zebrafish, pufferfish), but only one orthologous copy is found in tetrapods. Individual gene trees for these three genes and a concatenated dataset support the hypothesis that the fish-specific genome duplication event took place after the split of the Acipenseriformes and the Semionotiformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. If these three genes were duplicated during the proposed fish-specific genome duplication event, then this event separates the species-poor early-branching lineages from the species-rich teleost lineage. The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish.},
  language = {en},
  number = {2},
  journal = {Journal of Molecular Evolution},
  author = {Hoegg, Simone and Brinkmann, Henner and Taylor, John S. and Meyer, Axel},
  month = aug,
  year = {2004},
  pages = {190-203},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JQC629M7/Hoegg et al. - 2004 - Phylogenetic Timing of the Fish-Specific Genome Du.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9HC6KTR5/s00239-004-2613-z.html}
}

@article{lieschke_animal_2007,
  title = {Animal Models of Human Disease: Zebrafish Swim into View},
  volume = {8},
  copyright = {2007 Nature Publishing Group},
  issn = {1471-0064},
  shorttitle = {Animal Models of Human Disease},
  doi = {10.1038/nrg2091},
  abstract = {Despite the pre-eminence of the mouse in modelling human disease, several aspects of murine biology limit its routine use in large-scale genetic and therapeutic screening. Many researchers who are interested in an embryologically and genetically tractable disease model have now turned to zebrafish. Zebrafish biology allows ready access to all developmental stages, and the optical clarity of embryos and larvae allow real-time imaging of developing pathologies. Sophisticated mutagenesis and screening strategies on a large scale, and with an economy that is not possible in other vertebrate systems, have generated zebrafish models of a wide variety of human diseases. This Review surveys the achievements and potential of zebrafish for modelling human diseases and for drug discovery and development.},
  language = {en},
  number = {5},
  journal = {Nature Reviews Genetics},
  author = {Lieschke, Graham J. and Currie, Peter D.},
  month = may,
  year = {2007},
  pages = {353-367},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BRA3JVPA/Lieschke and Currie - 2007 - Animal models of human disease zebrafish swim int.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2B9WW49E/nrg2091.html}
}

@article{hill_zebrafish_2005,
  title = {Zebrafish as a {{Model Vertebrate}} for {{Investigating Chemical Toxicity}}},
  volume = {86},
  issn = {1096-6080},
  doi = {10.1093/toxsci/kfi110},
  abstract = {Abstract.  Zebrafish (Danio rerio) has been a prominent model vertebrate in a variety of biological disciplines. Substantial information gathered from developme},
  language = {en},
  number = {1},
  journal = {Toxicological Sciences},
  author = {Hill, Adrian J. and Teraoka, Hiroki and Heideman, Warren and Peterson, Richard E.},
  month = jul,
  year = {2005},
  pages = {6-19},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q3TADYBJ/Hill et al. - 2005 - Zebrafish as a Model Vertebrate for Investigating .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XSHAQ82I/1654090.html}
}

@article{norton_adult_2010,
  title = {Adult Zebrafish as a Model Organism for Behavioural Genetics},
  volume = {11},
  issn = {1471-2202},
  doi = {10.1186/1471-2202-11-90},
  abstract = {Recent research has demonstrated the suitability of adult zebrafish to model some aspects of complex behaviour. Studies of reward behaviour, learning and memory, aggression, anxiety and sleep strongly suggest that conserved regulatory processes underlie behaviour in zebrafish and mammals. The isolation and molecular analysis of zebrafish behavioural mutants is now starting, allowing the identification of novel behavioural control genes. As a result of this, studies of adult zebrafish are now helping to uncover the genetic pathways and neural circuits that control vertebrate behaviour.},
  journal = {BMC Neuroscience},
  author = {Norton, William and {Bally-Cuif}, Laure},
  month = aug,
  year = {2010},
  keywords = {Cocaine,Adult Zebrafish,Agonistic Behaviour,Conditioned Place Preference,Nicotine},
  pages = {90},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RUJ27ECG/Norton and Bally-Cuif - 2010 - Adult zebrafish as a model organism for behavioura.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LDPNHR2L/1471-2202-11-90.html}
}

@book{tigay_evolution_2002,
  title = {The {{Evolution}} of the {{Gilgamesh Epic}}},
  isbn = {978-0-86516-546-5},
  abstract = {"The Epic of Gilgamesh is one of the world's oldest known epics-itpredates Homer by several centuries and is recognized as seminal to the cultural history of the Ancient Near East. Interpretation and decipherment of the story of Gilgamesh--fragmentary and contradictory as its several variants are--has been a monumental scholarly task, spanning more than a century...until Jeffrey Tigay teased out the epic's evolution. In this volume, Tigay traces the development of the composition of "The Gilgamesh Epic over nearly two millennia and through the several languages in which it has been transmitted. The result is a study both comprehensive in breadth and impressive in methodology. The author breaks from his scholarly predecessors in relying on documented textual evidence rather than on critical analysis and hypotheses. The immense contribution represented by this study has been acknowledged since its first publication in 1982. This reprint edition once again makes Tigay's groundbreaking work readily available to humanists, historians of literature and religion, biblical and classical scholars, anthropologists, and folklorists.},
  language = {en},
  publisher = {{Bolchazy-Carducci Publishers}},
  author = {Tigay, Jeffrey H.},
  year = {2002},
  keywords = {Literary Criticism / Reference}
}

@article{gingerich_new_1994,
  title = {New Whale from the {{Eocene}} of {{Pakistan}} and the Origin of Cetacean Swimming},
  volume = {368},
  copyright = {1994 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/368844a0},
  abstract = {MODERN whales (order Cetacea) are marine mammals that evolved from a land-mammal ancestor, probably a cursorial Palaeocene\textendash{}Eocene mesonychid1\textendash{}3. Living whales are streamlined, lack external hind limbs, and all swim by dorsoventral oscillation of a heavily muscled tail4,5. A steamlined rigid body minimizes resistance, while thrust is provided by a lunate horizontal fluke attached to the tail at a narrow base or pedicle6. We describe here a new 46\textendash{}47-million-year-old archaeocete intermediate between land mammals and later whales. It has short cervical vertebrae, a reduced femur, and the flexible sacrum, robust tail and high neural spines on lumbars and caudals required for dorsoventral oscillation of a heavily muscled tail. This is the oldest fossil whale described from deep-neritic shelf deposits, and it shows that tail swimming evolved early in the history of cetaceans.},
  language = {en},
  number = {6474},
  journal = {Nature},
  author = {Gingerich, Philip D. and Raza, S. Mahmood and Arif, Muhammad and Anwar, Mohammad and Zhou, Xiaoyuan},
  month = apr,
  year = {1994},
  pages = {844-847},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YF3PQH8E/Gingerich et al. - 1994 - New whale from the Eocene of Pakistan and the orig.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZR7AP8XA/368844a0.html}
}

@book{berta_marine_2005,
  title = {Marine {{Mammals}}: {{Evolutionary Biology}}},
  isbn = {978-0-08-048934-6},
  shorttitle = {Marine {{Mammals}}},
  abstract = {Berta and Sumich have succeeded yet again in creating superior marine reading! This book is a succinct yet comprehensive text devoted to the systematics, evolution, morphology, ecology, physiology, and behavior of marine mammals. The first edition, considered the leading text in the field, is required reading for all marine biologists concerned with marine mammals. Revisions include updates of citations, expansion of nearly every chapter and full color photographs. This title continues the tradition by fully expanding and updating nearly all chapters.* Comprehensive, up-to-date coverage of the biology of all marine mammals * Provides a phylogenetic framework that integrates phylogeny with behavior and ecology * Features chapter summaries, further readings, an appendix, glossary and an extensive bibliography* Exciting new color photographs and additional distribution maps},
  language = {en},
  publisher = {{Elsevier}},
  author = {Berta, Annalisa and Sumich, James L. and Kovacs, Kit M.},
  month = dec,
  year = {2005},
  keywords = {Science / Life Sciences / Zoology / General,Nature / Environmental Conservation \& Protection,Science / Life Sciences / Marine Biology}
}

@article{hammond_phocid_2012,
  title = {Phocid {{Seal Leptin}}: {{Tertiary Structure}} and {{Hydrophobic Receptor Binding Site Preservation}} during {{Distinct Leptin Gene Evolution}}},
  volume = {7},
  issn = {1932-6203},
  shorttitle = {Phocid {{Seal Leptin}}},
  doi = {10.1371/journal.pone.0035395},
  abstract = {The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.},
  language = {en},
  number = {4},
  journal = {PLOS ONE},
  author = {Hammond, John A. and Hauton, Chris and Bennett, Kimberley A. and Hall, Ailsa J.},
  month = apr,
  year = {2012},
  keywords = {Leptin,Mammals,Marine mammals,Phylogenetic analysis,Sea lions,Seals,Sequence alignment,Surfactants},
  pages = {e35395},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q8A87T2T/Hammond et al. - 2012 - Phocid Seal Leptin Tertiary Structure and Hydroph.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FGHRRHJ8/article.html}
}

@article{rattenborg_evidence_2016,
  title = {Evidence That Birds Sleep in Mid-Flight},
  volume = {7},
  copyright = {2016 Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/ncomms12468},
  abstract = {Many birds fly non-stop for days or longer, but do they sleep in flight and if so, how? It is commonly assumed that flying birds maintain environmental awareness and aerodynamic control by sleeping with only one eye closed and one cerebral hemisphere at a time. However, sleep has never been demonstrated in flying birds. Here, using electroencephalogram recordings of great frigatebirds (Fregata minor) flying over the ocean for up to 10 days, we show that they can sleep with either one hemisphere at a time or both hemispheres simultaneously. Also unexpectedly, frigatebirds sleep for only 0.69 h d-1 (7.4\% of the time spent sleeping on land), indicating that ecological demands for attention usually exceed the attention afforded by sleeping unihemispherically. In addition to establishing that birds can sleep in flight, our results challenge the view that they sustain prolonged flights by obtaining normal amounts of sleep on the wing.},
  language = {en},
  journal = {Nature Communications},
  author = {Rattenborg, Niels C. and Voirin, Bryson and Cruz, Sebastian M. and Tisdale, Ryan and Dell'Omo, Giacomo and Lipp, Hans-Peter and Wikelski, Martin and Vyssotski, Alexei L.},
  month = aug,
  year = {2016},
  pages = {12468},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MV9XPWIZ/Rattenborg et al. - 2016 - Evidence that birds sleep in mid-flight.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WZJFFBS5/ncomms12468.html}
}

@article{basner_sleep_2013,
  title = {Sleep Deprivation and Neurobehavioral Dynamics},
  volume = {23},
  issn = {1873-6882},
  doi = {10.1016/j.conb.2013.02.008},
  abstract = {Lifestyles involving sleep deprivation are common, despite mounting evidence that both acute total sleep deprivation and chronically restricted sleep degrade neurobehavioral functions associated with arousal, attention, memory and state stability. Current research suggests dynamic differences in the way the central nervous system responds to acute versus chronic sleep restriction, which is reflected in new models of sleep-wake regulation. Chronic sleep restriction likely induces long-term neuromodulatory changes in brain physiology that could explain why recovery from it may require more time than from acute sleep loss. High intraclass correlations in neurobehavioral responses to sleep loss suggest that these trait-like differences are phenotypic and may include genetic components. Sleep deprivation induces changes in brain metabolism and neural activation that involve distributed networks and connectivity.},
  language = {eng},
  number = {5},
  journal = {Current Opinion in Neurobiology},
  author = {Basner, Mathias and Rao, Hengyi and Goel, Namni and Dinges, David F.},
  month = oct,
  year = {2013},
  keywords = {Humans,Brain,Animals,Sleep Initiation and Maintenance Disorders,Sleep Deprivation,Cognition Disorders},
  pages = {854-863},
  pmid = {23523374},
  pmcid = {PMC3700596}
}

@article{rattenborg_avian_2009,
  title = {Avian Sleep Homeostasis: {{Convergent}} Evolution of Complex Brains, Cognition and Sleep Functions in Mammals and Birds},
  volume = {33},
  issn = {0149-7634},
  shorttitle = {Avian Sleep Homeostasis},
  doi = {10.1016/j.neubiorev.2008.08.010},
  abstract = {Birds are the only taxonomic group other than mammals that exhibit high-amplitude slow-waves in the electroencephalogram (EEG) during sleep. This defining feature of slow-wave sleep (SWS) apparently evolved independently in mammals and birds, as reptiles do not exhibit similar EEG activity during sleep. In mammals, the level of slow-wave activity (SWA) (low-frequency spectral power density) during SWS increases and decreases as a function of prior time spent awake and asleep, respectively, and therefore reflects homeostatically regulated sleep processes potentially tied to the function of SWS. Although birds also exhibit SWS, previous sleep deprivation studies in birds did not detect a compensatory increase in SWS-related SWA during recovery, as observed in similarly sleep-deprived mammals. This suggested that, unlike mammalian SWS, avian SWS is not homeostatically regulated, and therefore might serve a different function. However, we recently demonstrated that SWA during SWS increases in pigeons following short-term sleep deprivation. Herein we summarize research on avian sleep homeostasis, and cast our evidence for this phenomenon within the context of theories for the function of SWS in mammals. We propose that the convergent evolution of homeostatically regulated SWS in mammals and birds was directly linked to the convergent evolution of large, heavily interconnected brains capable of performing complex cognitive processes in each group. Specifically, as has been proposed for mammals, the interconnectivity that forms the basis of complex cognition in birds may also instantiate slow, synchronous network oscillations during SWS that in turn maintain interconnectivity and cognition at an optimal level.},
  number = {3},
  journal = {Neuroscience \& Biobehavioral Reviews},
  author = {Rattenborg, Niels C. and {Martinez-Gonzalez}, Dolores and Lesku, John A.},
  month = mar,
  year = {2009},
  keywords = {Cognition,Homeostasis,REM sleep,Slow oscillation,Connectivity,Dorsal cortex,Dorsal ventricular ridge,Hyperpallium,Mesopallium,Nidopallium,Pallium,Slow-wave sleep},
  pages = {253-270},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q2BEJSVR/Rattenborg et al. - 2009 - Avian sleep homeostasis Convergent evolution of c.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HBRQH5VN/S0149763408001425.html}
}

@article{lendrem_sleeping_1984,
  title = {Sleeping and Vigilance in Birds, {{II}}. {{An}} Experimental Study of the {{Barbary}} Dove ({{Streptopelia}} Risoria)},
  volume = {32},
  issn = {0003-3472},
  doi = {10.1016/S0003-3472(84)80343-7},
  abstract = {Sleep in birds involves a period of eye closure interrupted by short `peeks' of eye-opening. These peeks allow a bird to scan the sleeping site for predators. Peeking and eye closure were recorded for eight focal birds in flocks of 1, 2, 3 and 6 doves. Half these doves were high risk (predator presented before the sleeping bout) and half low risk (no predator). Individual vigilance fell with increasing flock size, and was higher in high-risk birds. However, corporate vigilance increased with flock size. High-risk flocks were more vigilant than low-risk flocks. These results are discussed with reference to the costs and benefits of eye closure and peeking.},
  number = {1},
  journal = {Animal Behaviour},
  author = {Lendrem, D. W.},
  month = feb,
  year = {1984},
  pages = {243-248},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VH95S4KS/S0003347284803437.html}
}

@article{rattenborg_behavioral_2000,
  title = {Behavioral, Neurophysiological and Evolutionary Perspectives on Unihemispheric Sleep},
  volume = {24},
  issn = {0149-7634},
  doi = {10.1016/S0149-7634(00)00039-7},
  abstract = {Several animals mitigate the fundamental conflict between sleep and wakefulness by engaging in unihemispheric sleep, a unique state during which one cerebral hemisphere sleeps while the other remains awake. Among mammals, unihemispheric sleep is restricted to aquatic species (Cetaceans, eared seals and manatees). In contrast to mammals, unihemispheric sleep is widespread in birds, and may even occur in reptiles. Unihemispheric sleep allows surfacing to breathe in aquatic mammals and predator detection in birds. Despite the apparent utility in being able to sleep unihemispherically, very few mammals sleep in this manner. This is particularly interesting since the reptilian ancestors to mammals may have slept unihemispherically. The relative absence of unihemispheric sleep in mammals suggests that a trade off exists between unihemispheric sleep and other adaptive brain functions occurring during sleep or wakefulness. Presumably, the benefits of sleeping unihemispherically only outweigh the costs under extreme circumstances such as sleeping at sea. Ultimately, a greater understanding of the reasons for little unihemispheric sleep in mammals promises to provide insight into the functions of sleep, in general.},
  number = {8},
  journal = {Neuroscience \& Biobehavioral Reviews},
  author = {Rattenborg, N. C and Amlaner, C. J and Lima, S. L},
  month = dec,
  year = {2000},
  keywords = {Birds,Sleep regulation,Reptiles,Sleep function,Slow-wave sleep,Aquatic mammals,Functional lateralization,Predator detection,Sleep mechanisms,Unihemispheric},
  pages = {817-842},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3HSL6QFQ/Rattenborg et al. - 2000 - Behavioral, neurophysiological and evolutionary pe.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FJ53Z7BS/Rattenborg et al. - 2000 - Behavioral, neurophysiological and evolutionary pe.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5GF84I3V/S0149763400000397.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AEGH9VYN/S0149763400000397.html}
}

@article{szymczak_study_1996,
  title = {A Study of Sleep in the {{European}} Blackbird},
  volume = {60},
  issn = {0031-9384},
  doi = {10.1016/0031-9384(96)00231-4},
  abstract = {Sleep states in the blackbird, Turdus merula, were determined by recording the electroencephalogram (EEG), electrooculogram (EOG), electromyogram (EMG), and heart rate (HR), and from behavioral observations and responses to auditory stimulation by natural calls. The presence of changes in slow wave activity was determined from the power spectra of the EEG. Spectral power density in the 0.5\textendash{}4.0 Hz band during slow wave sleep (SWS) attained highest values in the first part of the night, then declined. This trend in EEG spectra, which occurred across the night, probably reflects a homeostatic process strikingly similar to that observed in mammals. The reactivity to natural calls during SWS episodes also decreased across the night. Episodes of interhemispheric EEG asymmetry, which typically lasted from 2 to 4 s, occurred when birds displayed the front sleep posture and they constituted 140\textendash{}200 s of each night. Unihemispheric sleep episodes probably result from unilateral activation of the visual system, and they could be considered as an evolutionary adaptation. HR was highest in wakefulness and lower in sleep but, due to large variability, reliable discrimination between sleep and wakefulness could not be made. Comparison of the blackbird's behavior during 4 different nights revealed a strong effect of the first night on sleeping behavior. A significant reduction in back sleep posture occurred during the baseline night, when lead wires were connected.},
  number = {4},
  journal = {Physiology \& Behavior},
  author = {Szymczak, J. T. and Kaiser, W. and Helb, H. W. and Beszczy\'nska, B.},
  month = oct,
  year = {1996},
  keywords = {Slow wave activity,Auditory stimulation,Blackbird,Effect of adaptation,Heart rate,Unihemispheric sleep},
  pages = {1115-1120},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/C6GGAJBH/Szymczak et al. - 1996 - A study of sleep in the European blackbird.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X4NKWKF9/0031938496002314.html}
}

@article{rattenborg_half-awake_1999,
  title = {Half-Awake to the Risk of Predation},
  volume = {397},
  copyright = {1999 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/17037},
  abstract = {Birds have overcome the problem of sleeping in risky situations by developing the ability to sleep with one eye open and one hemisphere of the brain awake1. Such unihemispheric slow-wave sleep is in direct contrast to the typical situation in which sleep and wakefulness are mutually exclusive states of the whole brain. We have found that birds can detect approaching predators during unihemispheric slow-wave sleep, and that they can increase their use of unihemispheric sleep as the risk of predation increases. We believe this is the first evidence for an animal behaviourally controlling sleep and wakefulness simultaneously in different regions of the brain.},
  language = {en},
  number = {6718},
  journal = {Nature},
  author = {Rattenborg, Niels C. and Lima, Steven L. and Amlaner, Charles J.},
  month = feb,
  year = {1999},
  pages = {397-398},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/99TGVZAF/Rattenborg et al. - 1999 - Half-awake to the risk of predation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VXFAYXR9/17037.html}
}

@article{lesku_adaptive_2012,
  title = {Adaptive {{Sleep Loss}} in {{Polygynous Pectoral Sandpipers}}},
  volume = {337},
  copyright = {Copyright \textcopyright{} 2012, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1220939},
  abstract = {The functions of sleep remain elusive. Extensive evidence suggests that sleep performs restorative processes that sustain waking brain performance. An alternative view proposes that sleep simply enforces adaptive inactivity to conserve energy when activity is unproductive. Under this hypothesis, animals may evolve the ability to dispense with sleep when ecological demands favor wakefulness. Here, we show that male pectoral sandpipers (Calidris melanotos), a polygynous Arctic breeding shorebird, are able to maintain high neurobehavioral performance despite greatly reducing their time spent sleeping during a 3-week period of intense male-male competition for access to fertile females. Males that slept the least sired the most offspring. Our results challenge the view that decreased performance is an inescapable outcome of sleep loss.
Male pectoral sandpipers go without sleep for days in order to mate as often as possible in the high Arctic.
Male pectoral sandpipers go without sleep for days in order to mate as often as possible in the high Arctic.},
  language = {en},
  number = {6102},
  journal = {Science},
  author = {Lesku, John A. and Rattenborg, Niels C. and Valcu, Mihai and Vyssotski, Alexei L. and Kuhn, Sylvia and Kuemmeth, Franz and Heidrich, Wolfgang and Kempenaers, Bart},
  month = sep,
  year = {2012},
  pages = {1654-1658},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CC596JF4/Lesku et al. - 2012 - Adaptive Sleep Loss in Polygynous Pectoral Sandpip.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K8S363BZ/1654.html},
  pmid = {22878501}
}

@article{tully_discovery_1996,
  title = {Discovery of Genes Involved with Learning and Memory: {{An}}  Experimental Synthesis of {{Hirschian}} and {{Benzerian}}\,Perspectives},
  volume = {93},
  issn = {0027-8424},
  shorttitle = {Discovery of Genes Involved with Learning and Memory},
  abstract = {The biological bases of learning and memory are being revealed
 today with a wide array of molecular approaches, most of which entail
 the analysis of dysfunction produced by gene disruptions. This
 perspective derives both from early ``genetic dissections'' of
 learning in mutant Drosophila by Seymour Benzer and
 colleagues and from earlier behavior-genetic analyses of learning and
 in Diptera by Jerry Hirsch and coworkers. Three quantitative-genetic
 insights derived from these latter studies serve as guiding principles
 for the former. First, interacting polygenes underlie complex traits.
 Consequently, learning/memory defects associated with single-gene
 mutants can be quantified accurately only in equilibrated,
 heterogeneous genetic backgrounds. Second, complex behavioral responses
 will be composed of genetically distinct functional components. Thus,
 genetic dissection of complex traits into specific biobehavioral
 properties is likely. Finally, disruptions of genes involved with
 learning/memory are likely to have pleiotropic effects. As a result,
 task-relevant sensorimotor responses required for normal learning must
 be assessed carefully to interpret performance in learning/memory
 experiments. In addition, more specific conclusions will be obtained
 from reverse-genetic experiments, in which gene disruptions are
 restricted in time and/or space.},
  number = {24},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Tully, Tim},
  month = nov,
  year = {1996},
  pages = {13460-13467},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4E4FVKNT/Tully - 1996 - Discovery of genes involved with learning and memo.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VWR97GTZ/Tully - 1996 - Discovery of genes involved with learning and memo.pdf},
  pmid = {8942957},
  pmcid = {PMC33631}
}

@article{rosato_analysis_2006,
  title = {Analysis of Locomotor Activity Rhythms in {{{\emph{Drosophila}}}}},
  volume = {1},
  copyright = {2006 Nature Publishing Group},
  issn = {1750-2799},
  doi = {10.1038/nprot.2006.79},
  abstract = {The genetic, molecular and anatomical dissection of the circadian clock in Drosophila and other higher organisms relies on the quantification of rhythmic phenotypes. Here, we introduce the methods currently in use in our laboratories for the analysis of fly locomotor activity rhythms. This phenotype provides a relatively simple, automated, efficient, reliable and robust output for the circadian clock. Thus it is not surprising that it is the preferred readout for measuring rhythmicity under a variety of conditions for most fly clock laboratories. The procedure requires at least 10 days of data collection and several days for analysis. In this protocol we advise on fly maintenance and on experimental design when studying the genetics of behavioral traits. We describe the setup for studying locomotor activity rhythms in the fruit fly and we introduce the statistical methods in use in our laboratories for the analysis of periodic data.},
  language = {en},
  number = {2},
  journal = {Nature Protocols},
  author = {Rosato, Ezio and Kyriacou, Charalambos P.},
  month = aug,
  year = {2006},
  pages = {559-568},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VN4KLMAD/Rosato and Kyriacou - 2006 - Analysis of locomotor activity rhythms in iDroso.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/I85P7H95/nprot.2006.html}
}

@article{mayhew_why_2007,
  title = {Why Are There so Many Insect Species? {{Perspectives}} from Fossils and Phylogenies},
  volume = {82},
  copyright = {2007 Cambridge Philosophical Society},
  issn = {1469-185X},
  shorttitle = {Why Are There so Many Insect Species?},
  doi = {10.1111/j.1469-185X.2007.00018.x},
  abstract = {Over half of all described species are insects, but until recently our understanding of the reasons for this diversity was based on very little macroevolutionary evidence. Here I summarize the hypotheses that have been posed, tests of these hypotheses and their results, and hence identify gaps in knowledge for future researchers to pursue. I focus on inferences from the following sources: (i) the fossil record, normally at family level, and (ii) insect phylogenies, sometimes combined with: (iii) the species richness of insect higher taxa, and (iv) current extinction risks. There is evidence that the species richness of insects has been enhanced by: (i) their relative age, giving time for diversification to take place; (ii) low extinction rates. There is little evidence that rates of origination have generally been high or that there are limits on numbers of species. However, the evidence on macroevolutionary rates is not yet so extensive or coherent as to present unequivocal messages. As regards morphological, ecological, or behavioural hypotheses, there is evidence that diversity has been enhanced by (iii) flight or properties resulting from it like enhanced dispersal, (iv) wing folding, and (v) complete metamorphosis. However, in all these cases the evidence is somewhat equivocal, either because of statistical issues or because evidence from different sources is conflicting. There is extensive evidence that diversity is affected by (vi) the ecological niche. Comparative studies indicate that phytophagy generally increases net diversification rates, and reduces extinction risk. However, niche specialization is also associated with an increase in extinction risk. Small body size (vii) is often associated with low extinction risk in comparative studies, but as yet there is no solid evidence that it consistently enhances net rates of diversification. Mouthpart diversity (viii) has generally increased over time in the insects, but cannot explain the apparent great increase in diversity seen in the Cretaceous and Tertiary. Sexual selection and sexual conflict (ix) are two processes that are widespread in insects, and there is comparative evidence linking both to increased diversification. Although some comparative evidence links tropical distributions (x) to increased rates of diversification, the extent to which latitudinal richness gradients are unusual in insects is equivocal. There is little to no direct evidence from fossils and phylogenies that insect diversity has generally been affected by (i) sensory- or neuro-sophistication, (ii) population size or density, (iii) generation time or fecundity, (iv) the presence of an exoskeleton or cuticle, (v) segmentation or appendage diversity, (vi) adaptability or genetic versatility, though all of these remain plausible hypotheses awaiting further tests. The data suggest that the insect body ground plan itself had no direct effect on insect diversity. Thus, whilst studies to date have given substantial understanding, substantial gaps still remain. Future challenges include: (i) interpreting conflicting messages from different sources of data; (ii) rating the importance of different hypotheses that are statistically supported; (iii) linking specific proximate to specific ultimate explanations and vice versa; and (iv) understanding how different ultimate hypotheses might be dependent on each other.},
  language = {en},
  number = {3},
  journal = {Biological Reviews},
  author = {Mayhew, Peter J.},
  year = {2007},
  keywords = {flight,speciation,co-evolution,dispersal evolution,diversity,extinction,herbivory,macroevolution,phytophagy,species richness},
  pages = {425-454},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4KC3Z2B5/Mayhew - 2007 - Why are there so many insect species Perspectives.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TT8SSPYM/j.1469-185X.2007.00018.html}
}

@article{beltrami_emphasis_2010,
  title = {Drosophila Pupation Behavior in the Wild},
  volume = {24},
  issn = {0269-7653, 1573-8477},
  doi = {10.1007/s10682-009-9310-8},
  abstract = {We investigated pupa distributions of D. simulans, D. buzzatii, D. melanogaster, D. immigrans and D. hydei on a number of natural breeding sites. Pupae of all five species showed aggregated distributions, which prompted us to examine these aggregations in a more detail for two species that commonly co-occur in breeding sites, D. simulans and D. buzzatii. We found that pupae of both species tend to be aggregated in conspecific clusters. Subsequent experiments revealed that both species are attracted to the odors of other larvae, though only D. buzzatii differentiated between conspecifics and heterospecifics (they preferred conspecific). Furthermore, third instar larvae of both species preferred more alkaline substrates. Altogether, our results demonstrate that Drosophila species form conspecific pupa aggregations in natural breeding sites, and that pupation site selection depends on interactions among conspecific and heterospecific larvae and on chemical characteristics of the breeding sites.},
  language = {en},
  number = {2},
  journal = {Evolutionary Ecology},
  author = {Beltram\'i, Marcial and {Medina-Mu\~noz}, Mar\'ia Cristina and Arce, David and {Godoy-Herrera}, Ra\'ul},
  month = mar,
  year = {2010},
  pages = {347-358},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AF2KIMGS/Beltramí et al. - 2010 - Emphasis Type=ItalicDrosophilaEmphasis pupa.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6HC2U6LJ/s10682-009-9310-8.html}
}

@article{markow_natural_2015,
  title = {The {{Natural History}} of {{Model Organisms}}: {{The}} Secret Lives of {{Drosophila}} Flies},
  volume = {4},
  copyright = {\textcopyright{} 2015 Markow. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  shorttitle = {The {{Natural History}} of {{Model Organisms}}},
  doi = {10.7554/eLife.06793},
  abstract = {After decades of intensive research, D. melanogaster and its relatives could provide important tools for investigating future biological questions about human health and environmental change, but only if we better understand their natural history.},
  language = {en},
  journal = {eLife},
  author = {Markow, Therese Ann},
  month = jun,
  year = {2015},
  pages = {e06793},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5GDX7JLJ/Markow - 2015 - The Natural History of Model Organisms The secret.pdf}
}

@article{carlson_how_2013,
  title = {How Fruit Flies Came to Launch the Chromosome Theory of Heredity},
  volume = {753},
  issn = {1383-5742},
  doi = {10.1016/j.mrrev.2013.03.001},
  abstract = {Fruit flies were used by several laboratories between 1901 and 1910 for studies of experimental evolution at Harvard, Indiana University, and Cold Spring Harbor before Thomas Hunt Morgan found his white-eyed mutation that we associate with the beginnings of the fly lab at Columbia University. The major players prior to Morgan were William Castle and his students at Harvard University, Frank Lutz at Cold Spring Harbor, and Fernandus Payne whose ideas for working with fruit flies were shaped by his studies of blind cave fauna at Indiana University. Payne's interests were stimulated by the work of Carl Eigenmann, an authority on blind cave fauna, and William Moenkhaus, who introduced Payne to fruit flies at Indiana University before Payne moved to Columbia to pursue graduate work with Morgan and Edmund Wilson. The motivations of the laboratories differed in the theories used for their work. Castle spread the word about the utility of fruit flies for research, but Payne gave Morgan his first fruit flies for research leading to the discovery of the white-eye mutation.},
  number = {1},
  journal = {Mutation Research/Reviews in Mutation Research},
  author = {Carlson, Elof Axel},
  month = jul,
  year = {2013},
  keywords = {Experimental evolution,Blind cave fish,Fernandus Payne,Fly lab,Origin of classical genetics,T.H. Morgan},
  pages = {1-6},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VQPCA3SE/Carlson - 2013 - How fruit flies came to launch the chromosome theo.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EE26EZTR/S1383574213000264.html}
}

@article{sokolowski_drosophila_2001,
  title = {{\emph{Drosophila}}: {{Genetics}} Meets Behaviour},
  volume = {2},
  copyright = {2001 Nature Publishing Group},
  issn = {1471-0064},
  shorttitle = {{\emph{Drosophila}}},
  doi = {10.1038/35098592},
  abstract = {Genes are understandably crucial to physiology, morphology and biochemistry, but the idea of genes contributing to individual differences in behaviour once seemed outrageous. Nevertheless, some scientists have aspired to understand the relationship between genes and behaviour, and their research has become increasingly informative and productive over the past several decades. At the forefront of behavioural genetics research is the fruitfly Drosophila melanogaster, which has provided us with important insights into the molecular, cellular and evolutionary bases of behaviour.},
  language = {en},
  number = {11},
  journal = {Nature Reviews Genetics},
  author = {Sokolowski, Marla B.},
  month = nov,
  year = {2001},
  pages = {879-890},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5AJCXB5B/Sokolowski - 2001 - iDrosophilai Genetics meets behaviour.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BYVIQTES/Sokolowski - 2001 - iDrosophilai Genetics meets behaviour.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5H3B9RDF/35098592.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SHAECDQR/35098592.html}
}

@article{benzer_genetic_1973,
  title = {Genetic {{Dissection}} of {{Behavior}}},
  volume = {229},
  issn = {0036-8733},
  doi = {10.1038/scientificamerican1273-24},
  language = {en},
  number = {6},
  journal = {Scientific American},
  author = {Benzer, Seymour},
  month = dec,
  year = {1973},
  pages = {24-37},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HM7NQF4S/Benzer - 1973 - Genetic Dissection of Behavior.pdf}
}

@article{nusslein-volhard_determination_1987,
  title = {Determination of Anteroposterior Polarity in {{Drosophila}}},
  volume = {238},
  copyright = {\textcopyright{} 1987},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.3686007},
  abstract = {The principles of pattern formation in embryogenesis can be studied in Drosophila by means of a powerful combination of genetic and transplantation experiments. The segmented pattern of the Drosophila embryo is organized by two activities localized at the anterior and posterior egg poles. Both activities exert inducing and polarizing effects on the pattern when transplanted to other egg regions. A small set of maternal genes have been identified that are required for these activities. Mutants in these genes lack either the anterior or posterior part of the segmented pattern. The unsegmented terminal embryonic regions require a third class of genes and form independently of the anterior and posterior centers.},
  language = {en},
  number = {4834},
  journal = {Science},
  author = {{Nusslein-Volhard}, C. and Frohnhofer, H. G. and Lehmann, R.},
  month = dec,
  year = {1987},
  pages = {1675-1681},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XSIDCMRB/Nusslein-Volhard et al. - 1987 - Determination of anteroposterior polarity in Droso.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JKD5S6IH/1675.html},
  pmid = {3686007}
}

@article{benzer_behavioral_1967,
  volume = {58},
  issn = {0027-8424},
  language = {eng},
  number = {3},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Benzer, S.},
  month = sep,
  year = {1967},
  pages = {1112-1119},
  pmid = {16578662},
  pmcid = {PMC335755}
}

@article{bargiello_molecular_1984,
  title = {Molecular Genetics of a Biological Clock in {{Drosophila}}},
  volume = {81},
  issn = {0027-8424},
  abstract = {Ninety kilobase pairs (kb) of DNA have been isolated from the 3B region of the X chromosome of Drosophila melanogaster. Previous cytogenetic analyses have placed a gene required for rhythmic behavior (per) in this chromosomal interval. Physical characterization of a series of chromosomal rearrangements altering per locus activity indicates that DNA affecting behavioral rhythms is found in a 7.1-kb HindIII fragment. A single 4.5-kb poly(A)(+) RNA is transcribed from this DNA in wild-type pupae and adult flies. The transcript is eliminated by a per mutant that retains some rhythmic activity, but this mutant substitutes two novel transcripts, 11.5 kb and 0.9 kb. It is suggested that the new poly(A)(+) transcripts provide residual per locus activity.},
  language = {eng},
  number = {7},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Bargiello, T. A. and Young, M. W.},
  month = apr,
  year = {1984},
  pages = {2142-2146},
  pmid = {16593450},
  pmcid = {PMC345453}
}

@article{bargiello_restoration_1984,
  title = {Restoration of Circadian Behavioural Rhythms by Gene Transfer in {{Drosophila}}},
  volume = {312},
  issn = {0028-0836},
  abstract = {The per locus of Drosophila melanogaster has a fundamental role in the construction or maintenance of a biological clock. Three classes of per mutations have been identified: per mutants have circadian behavioural rhythms with a 29-h rather than a 24-h period, pers mutants have short-period rhythms of 19 h, and per mutants have no detectable circadian rhythms. Each of these mutations has a corresponding influence on the 55-s periodicity of male courtship song. Long- and short-period circadian rhythm phenotypes can also be obtained by altering the dosage of the wild-type gene: for example, females carrying only one dose of this X-linked gene have circadian rhythms with periodicities about 1 h longer than those carrying two doses. In a previous report, cloned DNA was used to localize several chromosomal rearrangement breakpoints that alter per locus function. The rearrangements all affected a 7-kilobase (kb) interval that encodes a 4.5-kb poly(A)+ RNA. We report here that when a 7.1-kb fragment from a per+ fly, including the sequences encoding the 4.5-kb transcript, is introduced into the genome of a per (arrhythmic) fly by P element-mediated transformation, circadian rhythmicity of behaviour such as eclosion and locomotor activity is restored. The transforming DNA complements per locus deletions and is transcribed, forming a single 4.5-kb poly(A)+ RNA comparable to that produced by wild-type flies.},
  language = {eng},
  number = {5996},
  journal = {Nature},
  author = {Bargiello, T. A. and Jackson, F. R. and Young, M. W.},
  month = dec,
  year = {1984},
  keywords = {Behavior; Animal,Animals,Circadian Rhythm,Drosophila melanogaster,Light,Motor Activity,Genes; Regulator,RNA; Messenger},
  pages = {752-754},
  pmid = {6440029}
}

@article{reddy_molecular_1984,
  title = {Molecular Analysis of the Period Locus in {{Drosophila}} Melanogaster and Identification of a Transcript Involved in Biological Rhythms},
  volume = {38},
  issn = {0092-8674},
  abstract = {We have isolated and analyzed DNA sequences encompassing the period (per) locus of Drosophila melanogaster. The location of this clock gene was delimited by the molecular mapping of chromosome aberrations at or very near the per locus. At least five RNAs are transcribed from this region. One of these transcripts, a 0.9 kb species, is strongly implicated in per's control of biological rhythms. Two independently isolated arrhythmic mutations at the per locus dramatically reduce the level of this transcript. Furthermore, the level of the 0.9 kb transcript is strongly modulated during a light/dark cycle. We discuss evidence, from previously reported genetic and phenotypic analysis of per's function, suggesting that this region may be complex and that several gene products from the per region, including this 0.9 kb transcript, may be involved in the different aspects of normal rhythmicity influenced by this clock gene.},
  language = {eng},
  number = {3},
  journal = {Cell},
  author = {Reddy, P. and Zehring, W. A. and Wheeler, D. A. and Pirrotta, V. and Hadfield, C. and Hall, J. C. and Rosbash, M.},
  month = oct,
  year = {1984},
  keywords = {Animals,Drosophila melanogaster,Chromosome Mapping,Mutation,Larva,Plasmids,Periodicity,Cloning; Molecular,Nucleic Acid Hybridization,Pupa,Transcription; Genetic,Translocation; Genetic},
  pages = {701-710},
  pmid = {6435882}
}

@article{oneill_history_2013,
  title = {The History of {{Toll}}-like Receptors \textemdash{} Redefining Innate Immunity},
  volume = {13},
  copyright = {2013 Nature Publishing Group},
  issn = {1474-1741},
  doi = {10.1038/nri3446},
  abstract = {The discovery of Toll-like receptors (TLRs) was an important event for immunology research and was recognized as such with the awarding of the 2011 Nobel Prize in Physiology or Medicine to Jules Hoffmann and Bruce Beutler, who, together with Ralph Steinman, the third winner of the 2011 Nobel Prize and the person who discovered the dendritic cell, were pioneers in the field of innate immunity. TLRs have a central role in immunity \textemdash{} in this Timeline article, we describe the landmark findings that gave rise to this important field of research.},
  language = {en},
  number = {6},
  journal = {Nature Reviews Immunology},
  author = {O'Neill, Luke A. J. and Golenbock, Douglas and Bowie, Andrew G.},
  month = jun,
  year = {2013},
  pages = {453-460},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J2JTYF7Y/O'Neill et al. - 2013 - The history of Toll-like receptors — redefining in.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G2QKEIMI/nri3446.html}
}

@article{lemaitre_dorsoventral_1996,
  title = {The {{Dorsoventral Regulatory Gene Cassette}} Sp\"atzle/{{Toll}}/Cactus {{Controls}} the {{Potent Antifungal Response}} in {{Drosophila Adults}}},
  volume = {86},
  issn = {0092-8674},
  doi = {10.1016/S0092-8674(00)80172-5},
  abstract = {The cytokine-induced activation cascade of NF-$\kappa$B in mammals and the activation of the morphogen dorsal in Drosophila embryos show striking structural and functional similarities (Toll/IL-1, Cactus/I-$\kappa$B, and dorsal/NF-$\kappa$B). Here we demonstrate that these parallels extend to the immune response of Drosophila. In particular, the intracellular components of the dorsoventral signaling pathway (except for dorsal) and the extracellular Toll ligand, sp\"atzle, control expression of the antifungal peptide gene drosomycin in adults. We also show that mutations in the Toll signaling pathway dramatically reduce survival after fungal infection. Antibacterial genes are induced either by a distinct pathway involving the immune deficiency gene (imd) or by combined activation of both imd and dorsoventral pathways.},
  number = {6},
  journal = {Cell},
  author = {Lemaitre, Bruno and Nicolas, Emmanuelle and Michaut, Lydia and Reichhart, Jean-Marc and Hoffmann, Jules A},
  month = sep,
  year = {1996},
  pages = {973-983},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L3EH27T2/Lemaitre et al. - 1996 - The Dorsoventral Regulatory Gene Cassette spätzle.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T5IVC2AT/S0092867400801725.html}
}

@article{pelandakis_molecular_1993,
  title = {Molecular Phylogeny of {{Drosophila}} Based on Ribosomal {{RNA}} Sequences},
  volume = {37},
  issn = {0022-2844, 1432-1432},
  doi = {10.1007/BF00160433},
  abstract = {Nucleotide sequences of 72 species of Drosophilidae were determined for divergent D1 and D2 domains (representing 200 and 341 nucleotides respectively in D. melanogaster) of large ribosomal RNA, using the rRNA direct sequencing method. Molecular phylogenetic trees were reconstructed using both distance and parsimony methods and the robustness of the nodes was evaluated by the bootstrap procedure. The trees obtained by these methods revealed four main lineages or clades which do not correspond to the taxonomical hierarchy. In our results, the genus Chymomyza is associated with the subgenus Scaptodrosophila of the genus Drosophila and their cluster constitutes the most ancient clade. The two other clades are constituted of groups belonging to the subgenus Sophophora of the genus Drosophila: the so-called Neotropical clade including the willistoni and saltans groups and the obscura-melanogaster clade itself split into three lineages: (1) obscura group + ananassae subgroup, (2) montium subgroup, and (3) melanogaster + Oriental subgroups. The fourth clade, the Drosophila one, contains three lineages. D. polychaeta, D. iri, and D. fraburu are branched together and constitute the most ancient lineage; the second lineage includes the annulimana, bromeliae, dreyfusi, melanica, mesophragmatica, repleta, robusta, and virilis groups. The third lineage is composed of the immigrans and the cardini, funebris, guaramunu, guarani, histrio, pallidipennis, quinaria, and tripunctata groups. The genera Samoaia, Scaptomyza, and Zaprionus are branched within the Drosophila clade. Although these four clades appear regularly in almost all tree calculations, additional sequencing will be necessary to determine their precise relationships.},
  language = {en},
  number = {5},
  journal = {Journal of Molecular Evolution},
  author = {P\'elandakis, Michel and Solignac, Michel},
  month = nov,
  year = {1993},
  pages = {525-543},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LQF74RJE/BF00160433.html}
}

@article{brown_ethology_2018,
  title = {Ethology as a Physical Science},
  copyright = {2018 The Publisher},
  issn = {1745-2481},
  doi = {10.1038/s41567-018-0093-0},
  abstract = {The study of animal behaviour, ethology, is becoming more quantitative. New theory is emerging, driven by better imaging and novel representations of animal posture dynamics that span the vast range of relevant behavioural timescales.},
  language = {en},
  journal = {Nature Physics},
  author = {Brown, Andr\'e E. X. and de Bivort, Benjamin},
  month = apr,
  year = {2018},
  pages = {1},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CCFCXWQA/Brown and Bivort - 2018 - Ethology as a physical science.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JJBBQS98/Brown and Bivort - 2018 - Ethology as a physical science.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7UJJEDQ7/s41567-018-0093-0.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G4CMXCR9/s41567-018-0093-0.html}
}

@article{reiser_ethomics_2009,
  title = {The Ethomics Era?},
  volume = {6},
  copyright = {2009 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth0609-413},
  abstract = {Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.},
  language = {en},
  number = {6},
  journal = {Nature Methods},
  author = {Reiser, Michael},
  month = jun,
  year = {2009},
  pages = {413-414},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/32CJWUSR/Reiser - 2009 - The ethomics era.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UQSILY6A/Reiser - 2009 - The ethomics era.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5AGWMZK4/nmeth0609-413.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EA47BY5U/nmeth0609-413.html}
}

@article{anderson_toward_2014,
  title = {Toward a {{Science}} of {{Computational Ethology}}},
  volume = {84},
  issn = {0896-6273},
  doi = {10.1016/j.neuron.2014.09.005},
  abstract = {The new field of ``Computational Ethology'' is made possible by advances in technology, mathematics, and engineering that allow scientists to automate the measurement and the analysis of animal behavior. We explore the opportunities and long-term directions of research in this area.},
  number = {1},
  journal = {Neuron},
  author = {Anderson, David J. and Perona, Pietro},
  month = oct,
  year = {2014},
  pages = {18-31},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CWN8Q256/Anderson and Perona - 2014 - Toward a Science of Computational Ethology.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TE7Y4MMZ/Anderson and Perona - 2014 - Toward a Science of Computational Ethology.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HX7QXXX5/S0896627314007934.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QNX4MPYM/S0896627314007934.html}
}

@article{lasbleiz_courtship_2006,
  title = {Courtship Behaviour of {{Drosophila}} Melanogaster Revisited},
  volume = {72},
  issn = {0003-3472},
  doi = {10.1016/j.anbehav.2006.01.027},
  abstract = {Nearly all studies of Drosophila melanogaster courtship have focused exclusively on male behaviour. Female precopulatory behaviour is often relegated to `accept' or `reject' mating, and how female behaviour interacts with that of males remains largely unknown. Using a video-computing approach, we measured 10 behavioural states and 22 elementary behaviours that occur during the precopulatory phase of Canton-S (Cs) flies. Male and female behaviours were studied under a variety of social conditions. This allowed us to identify which one(s) is relevant to courtship or to general activity. Our analysis showed that the courtship repertoire was not constant over time, as female and male behaviours varied during courtship, and that virgin Cs females showed several behavioural sequences whose frequency, latency and total duration could predict their mating success. The most striking index of females' willingness to copulate was the way they extruded the ovipositor: a partial extrusion stimulated male courtship, whereas total extrusion inhibited it. Furthermore, females that mated preened their abdomen more frequently than did females that did not mate. We also observed that male sexual activity was strongly increased when the female emitted a tiny volatile droplet at the tip of the ovipositor. We hypothesized that partial ovipositor extrusion, droplet emission and abdominal preening are related behaviours that result in the active dispersion of compounds spread on the female's abdomen. Such a detailed picture of the precopulatory behaviours should allow better characterization of the sensory stimuli exchanged during courtship in Drosophila.},
  number = {5},
  journal = {Animal Behaviour},
  author = {Lasbleiz, Christelle and Ferveur, Jean-Fran{\c c}ois and Everaerts, Claude},
  month = nov,
  year = {2006},
  pages = {1001-1012},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DJI2TD4V/Lasbleiz et al. - 2006 - Courtship behaviour of Drosophila melanogaster rev.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T6Y8YG57/S0003347206002703.html}
}

@article{arthur_multi-channel_2013,
  title = {Multi-Channel Acoustic Recording and Automated Analysis of {{Drosophila}} Courtship Songs},
  volume = {11},
  issn = {1741-7007},
  doi = {10.1186/1741-7007-11-11},
  abstract = {Drosophila melanogaster has served as a powerful model system for genetic studies of courtship songs. To accelerate research on the genetic and neural mechanisms underlying courtship song, we have developed a sensitive recording system to simultaneously capture the acoustic signals from 32 separate pairs of courting flies as well as software for automated segmentation of songs.},
  journal = {BMC Biology},
  author = {Arthur, Benjamin J. and {Sunayama-Morita}, Tomoko and Coen, Philip and Murthy, Mala and Stern, David L.},
  month = jan,
  year = {2013},
  keywords = {neurobiology,genetics,Drosophila,evolution,courtship song,multi-channel recording,song segmentation software},
  pages = {11},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FAIFW8UK/Arthur et al. - 2013 - Multi-channel acoustic recording and automated ana.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5B34GWXX/1741-7007-11-11.html}
}

@article{berman_measuring_2018,
  title = {Measuring Behavior across Scales},
  volume = {16},
  issn = {1741-7007},
  doi = {10.1186/s12915-018-0494-7},
  abstract = {The need for high-throughput, precise, and meaningful methods for measuring behavior has been amplified by our recent successes in measuring and manipulating neural circuitry. The largest challenges associated with moving in this direction, however, are not technical but are instead conceptual: what numbers should one put on the movements an animal is performing (or not performing)? In this review, I will describe how theoretical and data analytical ideas are interfacing with recently-developed computational and experimental methodologies to answer these questions across a variety of contexts, length scales, and time scales. I will attempt to highlight commonalities between approaches and areas where further advances are necessary to place behavior on the same quantitative footing as other scientific fields.},
  journal = {BMC Biology},
  author = {Berman, Gordon J.},
  month = feb,
  year = {2018},
  pages = {23},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CLSN4IDQ/Berman - 2018 - Measuring behavior across scales.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IT4V6FFA/Berman - 2018 - Measuring behavior across scales.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EILQFTMU/s12915-018-0494-7.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J4E7GFM6/s12915-018-0494-7.html}
}

@article{richard_hierachical_1976,
  title = {Hierachical Organization and Postural Facilitation: {{Rules}} for Grooming in Flies},
  volume = {24},
  issn = {0003-3472},
  shorttitle = {Hierachical Organization and Postural Facilitation},
  doi = {10.1016/S0003-3472(76)80003-6},
  abstract = {This paper is about rules governing grooming sequences in blowflies. Time was divided exhaustively into eight grooming and two non-grooming states. Using a keyboard connected to a computer, the times of all transitions between states during 1 hr were recorded for each of six flies. There is a strong tendency for certain acts to alternate with others. A model of alternating choice `slots' and determined slots is presented. Grooming acts fall into discrete bouts, each involving either the prothoracic legs or the metathoracic legs, but not both. A great majority of bouts contain an odd number of acts. The beginning and ending of a bout constitute a characteristic structure regardless of the length of the intervening middle period. Unconvincing evidence for hierarchical organization of grooming decisions is presented. Convincing evidence is presented that postural facilitation is involved in the control of grooming.},
  number = {4},
  journal = {Animal Behaviour},
  author = {{Richard} and Dawkins, Marian},
  month = nov,
  year = {1976},
  pages = {739-755},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HRWTJARF/S0003347276800036.html}
}

@article{gomez-marin_hierarchical_2016,
  title = {Hierarchical Compression of {{Caenorhabditis}} Elegans Locomotion Reveals Phenotypic Differences in the Organization of Behaviour},
  volume = {13},
  copyright = {\textcopyright{} 2016 The Authors.. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.},
  issn = {1742-5689, 1742-5662},
  doi = {10.1098/rsif.2016.0466},
  abstract = {Regularities in animal behaviour offer insights into the underlying organizational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here, we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression algorithm to behavioural sequences from the nematode worm Caenorhabditis elegans freely crawling on an agar plate both with and without food and during chemotaxis. We find that the motifs identified by the compression algorithm are rare but relevant for comparisons between worms in different environments, suggesting that hierarchical compression can be a useful step in behaviour analysis. We also use compressibility as a new quantitative phenotype and find that the behaviour of wild-isolated strains of C. elegans is more compressible than that of the laboratory strain N2 as well as the majority of mutant strains examined. Importantly, in distinction to more conventional phenotypes such as overall motor activity or aggregation behaviour, the increased compressibility of wild isolates is not explained by the loss of function of the gene npr-1, which suggests that erratic locomotion is a laboratory-derived trait with a novel genetic basis. Because hierarchical compression can be applied to any sequence, we anticipate that compressibility can offer insights into the organization of behaviour in other animals including humans.},
  language = {en},
  number = {121},
  journal = {Journal of The Royal Society Interface},
  author = {{Gomez-Marin}, Alex and Stephens, Greg J. and Brown, Andr\'e E. X.},
  month = aug,
  year = {2016},
  pages = {20160466},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V24VMPIY/Gomez-Marin et al. - 2016 - Hierarchical compression of Caenorhabditis elegans.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5J2DSFJW/20160466.html},
  pmid = {27581484}
}

@article{berman_predictability_2016,
  title = {Predictability and Hierarchy in {{Drosophila}} Behavior},
  volume = {113},
  copyright = {\textcopyright{}  . http://www.pnas.org/site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1607601113},
  abstract = {Even the simplest of animals exhibit behavioral sequences with complex temporal dynamics. Prominent among the proposed organizing principles for these dynamics has been the idea of a hierarchy, wherein the movements an animal makes can be understood as a set of nested subclusters. Although this type of organization holds potential advantages in terms of motion control and neural circuitry, measurements demonstrating this for an animal's entire behavioral repertoire have been limited in scope and temporal complexity. Here, we use a recently developed unsupervised technique to discover and track the occurrence of all stereotyped behaviors performed by fruit flies moving in a shallow arena. Calculating the optimally predictive representation of the fly's future behaviors, we show that fly behavior exhibits multiple time scales and is organized into a hierarchical structure that is indicative of its underlying behavioral programs and its changing internal states.},
  language = {en},
  number = {42},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Berman, Gordon J. and Bialek, William and Shaevitz, Joshua W.},
  month = oct,
  year = {2016},
  keywords = {behavior,Drosophila,hierarchy,information bottleneck},
  pages = {11943-11948},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VE3KNXYT/Berman et al. - 2016 - Predictability and hierarchy in Drosophila behavio.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QCCIR73X/11943.html},
  pmid = {27702892}
}

@article{dawkins1976hierarchical,
  title = {Hierarchical Organisation: A Candidate Principle for Ethology.},
  author = {Dawkins, Richard},
  year = {1976},
  publisher = {{Cambridge U Press}}
}

@article{ruf_lomb-scargle_1999,
  title = {The {{Lomb}}-{{Scargle Periodogram}} in {{Biological Rhythm Research}}: {{Analysis}} of {{Incomplete}} and {{Unequally Spaced Time}}-{{Series}}},
  volume = {30},
  issn = {0929-1016},
  shorttitle = {The {{Lomb}}-{{Scargle Periodogram}} in {{Biological Rhythm Research}}},
  doi = {10.1076/brhm.30.2.178.1422},
  abstract = {This paper investigates the utility of the Lomb\textendash{}Scargle periodogram for the analysis of biological rhythms. This method is particularly suited to detect periodic components in unequally sampled time-series and data sets with missing values, but restricts all calculations to actually measured values. The Lomb-Scargle method was tested on both real and simulated time-series with even and uneven sampling, and compared to a standard method in biomedical rhythm research, the Chi-square periodogram. Results indicate that the Lomb\textendash{}Scargle algorithm shows a clearly better detection efficiency and accuracy in the presence of noise, and avoids possible bias or erroneous results that may arise from replacement of missing data by interpolation techniques. Hence, the Lomb\textendash{}Scargle periodogram may serve as a useful method for the study of biological rhythms, especially when applied to telemetrical or observational time-series obtained from free-living animals, i.e., data sets that notoriously lack points.},
  number = {2},
  journal = {Biological Rhythm Research},
  author = {Ruf, T.},
  month = apr,
  year = {1999},
  pages = {178-201},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J8WC5AIV/Ruf - 1999 - The Lomb-Scargle Periodogram in Biological Rhythm .pdf}
}

@article{sokolove_chi_1978,
  title = {The Chi Square Periodogram: {{Its}} Utility for Analysis of Circadian Rhythms},
  volume = {72},
  issn = {0022-5193},
  shorttitle = {The Chi Square Periodogram},
  doi = {10.1016/0022-5193(78)90022-X},
  abstract = {It is proposed that chi-square statistic be employed in constructing periodograms for the analysis of hourly time series data obtained in studies of circadian rhythmicity. We show that even for relatively short (10 day) time series, the integral-valued chi-square periodogram can distinguish circadian-periodic from random series at a level of significance of about 0$\cdot$01. In addition, we describe the effects of serial correlation and examine the resolving power of the method for two periodic components in the circadian range. We suggest how the method can be most profitably employed in the analysis of event-recorder data for detection of rhythmicity in the range 14 to 34 h., and for the estimation of period to $\pm$0$\cdot$2 h.},
  number = {1},
  journal = {Journal of Theoretical Biology},
  author = {Sokolove, Phillip G. and Bushell, Wayne N.},
  month = may,
  year = {1978},
  pages = {131-160}
}

@article{nitabach_organization_2008,
  title = {Organization of the {{Drosophila}} Circadian Control Circuit},
  volume = {18},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2007.11.061},
  abstract = {Molecular genetics has revealed the identities of several components of the fundamental circadian molecular oscillator - an evolutionarily conserved molecular mechanism of transcription and translation that can operate in a cell-autonomous manner. Therefore, it was surprising when studies of circadian rhythmic behavior in the fruit fly Drosophila suggested that the normal operations of circadian clock cells, which house the molecular oscillator, in fact depend on non-cell-autonomous effects - interactions between the clock cells themselves. Here we review several genetic analyses that broadly extend that viewpoint. They support a model whereby the approximately 150 circadian clock cells in the brain of the fly are sub-divided into functionally discrete rhythmic centers. These centers alternatively cooperate or compete to control the different episodes of rhythmic behavior that define the fly's daily activity profile.},
  language = {eng},
  number = {2},
  journal = {Current biology: CB},
  author = {Nitabach, Michael N. and Taghert, Paul H.},
  month = jan,
  year = {2008},
  keywords = {Brain,Animals,Glutamic Acid,Biological Clocks,Circadian Rhythm,Drosophila Proteins,Drosophila melanogaster,Light,Neuropeptides,Locomotion,Temperature,Environment},
  pages = {R84-93},
  pmid = {18211849}
}

@article{perez-escudero_idtracker_2014,
  title = {{{idTracker}}: Tracking Individuals in a Group by Automatic Identification of Unmarked Animals},
  volume = {11},
  copyright = {2014 Nature Publishing Group},
  issn = {1548-7105},
  shorttitle = {{{idTracker}}},
  doi = {10.1038/nmeth.2994},
  abstract = {Animals in groups touch each other, move in paths that cross, and interact in complex ways. Current video tracking methods sometimes switch identities of unmarked individuals during these interactions. These errors propagate and result in random assignments after a few minutes unless manually corrected. We present idTracker, a multitracking algorithm that extracts a characteristic fingerprint from each animal in a video recording of a group. It then uses these fingerprints to identify every individual throughout the video. Tracking by identification prevents propagation of errors, and the correct identities can be maintained indefinitely. idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. We tested it on fish (Danio rerio and Oryzias latipes), flies (Drosophila melanogaster), ants (Messor structor) and mice (Mus musculus).},
  language = {en},
  number = {7},
  journal = {Nature Methods},
  author = {{P\'erez-Escudero}, Alfonso and {Vicente-Page}, Juli\'an and Hinz, Robert C. and Arganda, Sara and {de Polavieja}, Gonzalo G.},
  month = jul,
  year = {2014},
  pages = {743-748},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9Q9XQEMC/Pérez-Escudero et al. - 2014 - idTracker tracking individuals in a group by auto.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PD4V9LSR/nmeth.html}
}

@book{dowle_data.table_2017,
  title = {Data.Table: {{Extension}} of ‘data.Frame‘},
  author = {Dowle, Matt and Srinivasan, Arun},
  year = {2017}
}

@book{r_core_team_r_2017,
  address = {Vienna, Austria},
  title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
  publisher = {{R Foundation for Statistical Computing}},
  author = {{R Core Team}},
  year = {2017}
}

@article{pelkowski_novel_2011,
  title = {A Novel High-Throughput Imaging System for Automated Analyses of Avoidance Behavior in Zebrafish Larvae},
  volume = {223},
  issn = {0166-4328},
  doi = {10.1016/j.bbr.2011.04.033},
  abstract = {Early brain development can be influenced by numerous genetic and environmental factors, with long-lasting effects on brain function and behavior. The identification of these factors is facilitated by recent innovations in high-throughput screening. However, large-scale screening in whole organisms remains challenging, in particular when studying changes in brain function or behavior in vertebrate model systems. In this study, we present a novel imaging system for high-throughput analyses of behavior in zebrafish larvae. The three-camera system can image 12 multiwell plates simultaneously and is unique in its ability to provide local visual stimuli in the wells of a multiwell plate. The acquired images are converted into a series of coordinates, which characterize the location and orientation of the larvae. The developed imaging techniques were tested by measuring avoidance behaviors in seven-day-old zebrafish larvae. The system effectively quantified larval avoidance and revealed an increased edge preference in response to a blue or red `bouncing ball' stimulus. Larvae also avoid a bouncing ball stimulus when it is counter-balanced with a stationary ball, but do not avoid blinking balls counter-balanced with a stationary ball. These results indicate that the seven-day-old larvae respond specifically to movement, rather than color, size, or local changes in light intensity. The imaging system and assays for measuring avoidance behavior may be used to screen for genetic and environmental factors that cause developmental brain disorders and for novel drugs that could prevent or treat these disorders.},
  number = {1},
  journal = {Behavioural Brain Research},
  author = {Pelkowski, Sean D. and Kapoor, Mrinal and Richendrfer, Holly A. and Wang, Xingyue and Colwill, Ruth M. and Creton, Robbert},
  month = sep,
  year = {2011},
  keywords = {Behavior,Zebrafish,Automated image analysis,Avoidance,High-throughput imaging,Thigmotaxis,Visual stimuli},
  pages = {135-144}
}

@article{ro_flic_2014,
  title = {{{FLIC}}: {{High}}-{{Throughput}}, {{Continuous Analysis}} of {{Feeding Behaviors}} in {{Drosophila}}},
  volume = {9},
  issn = {1932-6203},
  shorttitle = {{{FLIC}}},
  doi = {10.1371/journal.pone.0101107},
  abstract = {We present a complete hardware and software system for collecting and quantifying continuous measures of feeding behaviors in the fruit fly, Drosophila melanogaster. The FLIC (Fly Liquid-Food Interaction Counter) detects analog electronic signals as brief as 50 $\mathrm{\mu}$s that occur when a fly makes physical contact with liquid food. Signal characteristics effectively distinguish between different types of behaviors, such as feeding and tasting events. The FLIC system performs as well or better than popular methods for simple assays, and it provides an unprecedented opportunity to study novel components of feeding behavior, such as time-dependent changes in food preference and individual levels of motivation and hunger. Furthermore, FLIC experiments can persist indefinitely without disturbance, and we highlight this ability by establishing a detailed picture of circadian feeding behaviors in the fly. We believe that the FLIC system will work hand-in-hand with modern molecular techniques to facilitate mechanistic studies of feeding behaviors in Drosophila using modern, high-throughput technologies.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Ro, Jennifer and Harvanek, Zachary M. and Pletcher, Scott D.},
  month = jun,
  year = {2014},
  keywords = {Behavior,Drosophila melanogaster,Circadian rhythms,Sucrose,Capillary tubes,Chronobiology,Decision making,Food consumption},
  pages = {e101107},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/736JNFY7/Ro et al. - 2014 - FLIC High-Throughput, Continuous Analysis of Feed.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AUTGYWT5/article.html}
}

@article{cazelles_wavelet_2008,
  title = {Wavelet Analysis of Ecological Time Series},
  volume = {156},
  issn = {0029-8549, 1432-1939},
  doi = {10.1007/s00442-008-0993-2},
  abstract = {Wavelet analysis is a powerful tool that is already in use throughout science and engineering. The versatility and attractiveness of the wavelet approach lie in its decomposition properties, principally its time-scale localization. It is especially relevant to the analysis of non-stationary systems, i.e., systems with short-lived transient components, like those observed in ecological systems. Here, we review the basic properties of the wavelet approach for time-series analysis from an ecological perspective. Wavelet decomposition offers several advantages that are discussed in this paper and illustrated by appropriate synthetic and ecological examples. Wavelet analysis is notably free from the assumption of stationarity that makes most methods unsuitable for many ecological time series. Wavelet analysis also permits analysis of the relationships between two signals, and it is especially appropriate for following gradual change in forcing by exogenous variables.},
  language = {en},
  number = {2},
  journal = {Oecologia},
  author = {Cazelles, Bernard and Chavez, Mario and Berteaux, Dominique and M\'enard, Fr\'ed\'eric and Vik, Jon Olav and Jenouvrier, St\'ephanie and Stenseth, Nils C.},
  month = may,
  year = {2008},
  pages = {287-304},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UDHDI3DC/Cazelles et al. - 2008 - Wavelet analysis of ecological time series.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GZWZ73T2/s00442-008-0993-2.html}
}

@article{aguiar-conraria_business_2011,
  title = {Business Cycle Synchronization and the {{Euro}}: {{A}} Wavelet Analysis},
  volume = {33},
  issn = {0164-0704},
  shorttitle = {Business Cycle Synchronization and the {{Euro}}},
  doi = {10.1016/j.jmacro.2011.02.005},
  abstract = {We use wavelet analysis to study business cycle synchronization across the EU-15 and the Euro-12 countries. Based on the wavelet transform, we propose a metric to measure and test for business cycles synchronization. Several conclusions emerge. France and Germany form the core of the Euro land, being the most synchronized countries with the rest of Europe. Portugal, Greece, Ireland and Finland do not show statistically relevant degrees of synchronization with Europe. We also show that some countries (like Spain) have a French accent, while others have a German accent (e.g., Austria). Perhaps surprisingly, we find that the French business cycle has been leading the German business cycle as well as the rest of Europe. Among the countries that may, in the future, join the Euro, the Czech Republic seems the most promising candidate.},
  number = {3},
  journal = {Journal of Macroeconomics},
  author = {{Aguiar-Conraria}, Lu\i\textasciiacute{}s and Joana Soares, Maria},
  month = sep,
  year = {2011},
  keywords = {Business cycle synchronization,Continuous wavelet transform,European Union integration,Multidimensional scaling,Wavelet distance matrix},
  pages = {477-489},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7L9HVUNM/Aguiar-Conraria and Joana Soares - 2011 - Business cycle synchronization and the Euro A wav.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7ADMHH4R/S016407041100019X.html}
}

@article{lau_climate_1995,
  title = {Climate {{Signal Detection Using Wavelet Transform}}: {{How}} to {{Make}} a {{Time Series Sing}}},
  volume = {76},
  issn = {0003-0007},
  shorttitle = {Climate {{Signal Detection Using Wavelet Transform}}},
  doi = {10.1175/1520-0477(1995)076<2391:CSDUWT>2.0.CO;2},
  abstract = {In this paper, the application of the wavelet transform (WT) to climate time series analyses is introduced. A tutorial description of the basic concept of WT, compared with similar concepts used in music, is also provided. Using an analogy between WT representation of a time series and a music score, the authors illustrate the importance of local versus global information in the time\textendash{}frequency localization of climate signals. Examples of WT applied to climate data analysis are demonstrated using analytic signals as well as real climate time series. Results of WT applied to two climate time series\textemdash{}that is, a proxy paleoclimate time series with a 2.5-Myr deep-sea sediment record of $\delta$18 O and a 140-yr monthly record of Northern Hemisphere surface temperature\textemdash{}are presented. The former shows the presence of a 40-kyr and a 100-kyr oscillation and an abrupt transition in the oscillation regime at 0.7 Myr before the present, consistent with previous studies. The latter possesses a myriad of oscillatory modes from interannual (2\textendash{}5 yr), interdecadal (10\textendash{}12 yr, 20\textendash{}25 yr, and 40\textendash{}60 yr), and century (\textasciitilde{}180 yr) scales at different periods of the data record. In spite of the large difference in timescales, common features in time\textendash{}frequency characteristics of these two time series have been identified. These features suggest that the variations of the earth's climate are consistent with those exhibited by a nonlinear dynamical system under external forcings.},
  number = {12},
  journal = {Bulletin of the American Meteorological Society},
  author = {Lau, K.-M. and Weng, Hengyi},
  month = dec,
  year = {1995},
  pages = {2391-2402},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MK6AILA4/Lau and Weng - 1995 - Climate Signal Detection Using Wavelet Transform .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GIWEXK9B/1520-0477(1995)0762391CSDUWT2.0.html}
}

@article{grossmann_decomposition_1984,
  title = {Decomposition of {{Hardy Functions}} into {{Square Integrable Wavelets}} of {{Constant Shape}}},
  volume = {15},
  issn = {0036-1410},
  doi = {10.1137/0515056},
  abstract = {An arbitrary square integrable real-valued function (or, equivalently, the associated Hardy function) can be conveniently analyzed into a suitable family of square integrable wavelets of constant shape, (i.e. obtained by shifts and dilations from any one of them.) The resulting integral transform is isometric and self-reciprocal if the wavelets satisfy an ``admissibility condition'' given here. Explicit expressions are obtained in the case of a particular analyzing family that plays a role analogous to that of coherent states (Gabor wavelets) in the usual \$L\_2 \$ -theory. They are written in terms of a modified \$$\backslash$Gamma \$-function that is introduced and studied. From the point of view of group theory, this paper is concerned with square integrable coefficients of an irreducible representation of the nonunimodular \$ax + b\$-group.},
  number = {4},
  journal = {SIAM Journal on Mathematical Analysis},
  author = {Grossmann, A. and Morlet, J.},
  month = jul,
  year = {1984},
  pages = {723-736},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S3ZYN2D4/Grossmann and Morlet - 1984 - Decomposition of Hardy Functions into Square Integ.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IESHKVZ9/0515056.html}
}

@article{brown_study_2017,
  title = {The Study of Animal Behaviour as a Physical Science},
  copyright = {\textcopyright{} 2017, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  doi = {10.1101/220855},
  abstract = {Behaviour is the ultimate output of an animal's nervous system and choosing the right action at the right time can be critical for survival. A quantitative understanding of behaviour would therefore advance research in neuroscience as well as ecology and evolution. However, animal posture typically has many degrees of freedom and behavioural dynamics vary on timescales ranging from milliseconds to years, presenting both technical and conceptual challenges. Here we review 1) advances in imaging and computer vision that are making it possible to capture increasingly complete records of animal motion and 2) new approaches to understanding the resulting behavioural data sets. With the right analytical approaches, these data are allowing researchers to revisit longstanding questions about the structure and organisation of animal behaviour and to put unifying principles on a quantitative footing. Contributions from both experimentalists and theorists are leading to the emergence of a physics of behaviour and the prospect of discovering laws and developing theories with broad applicability. We believe that there now exists an opportunity to develop theories of behaviour which can be tested using these data sets leading to a deeper understanding of how and why animals behave.},
  language = {en},
  journal = {bioRxiv},
  author = {Brown, Andre EX and de Bivort, Benjamin},
  month = nov,
  year = {2017},
  pages = {220855},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WI3Y6FRM/220855.html}
}

@book{wickham_ggplot2_2016,
  title = {Ggplot2: {{Elegant Graphics}} for {{Data Analysis}}},
  isbn = {978-3-319-24277-4},
  shorttitle = {Ggplot2},
  abstract = {This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to: produce handsome, publication-quality plots with automatic legends created from the plot specificationsuperimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scalesadd customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regressionsave any ggplot2 plot (or part thereof) for later modification or reusecreate custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plotsapproach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page.},
  language = {en},
  publisher = {{Springer}},
  author = {Wickham, Hadley},
  month = jun,
  year = {2016},
  keywords = {Computers / Computer Graphics,Computers / Mathematical \& Statistical Software,Mathematics / Combinatorics,Mathematics / Graphic Methods,Mathematics / Probability \& Statistics / Stochastic Processes}
}

@book{wickham_tidyverse_2017,
  title = {Tidyverse: {{Easily Install}} and {{Load}} the '{{Tidyverse}}'},
  author = {Wickham, Hadley},
  year = {2017}
}

@article{lopes_bonsai_2015,
  title = {Bonsai: An Event-Based Framework for Processing and Controlling Data Streams},
  volume = {9},
  issn = {1662-5196},
  shorttitle = {Bonsai},
  doi = {10.3389/fninf.2015.00007},
  abstract = {The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation.},
  language = {English},
  journal = {Frontiers in Neuroinformatics},
  author = {Lopes, Gon{\c c}alo and Bonacchi, Niccol\`o and Fraz\~ao, Jo\~ao and Neto, Joana P. and Atallah, Bassam V. and Soares, Sofia and Moreira, Lu\'is and Matias, Sara and Itskov, Pavel M. and Correia, Patr\'icia A. and Medina, Roberto E. and Calcaterra, Lorenza and Dreosti, Elena and Paton, Joseph J. and Kampff, Adam R.},
  year = {2015},
  keywords = {Electrophysiology,Behavior Control,closed-loop system,data acquisition system,data stream processing,open-source,parallel processing,Rapid prototyping,video tracking},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G2FJX862/Lopes et al. - 2015 - Bonsai an event-based framework for processing an.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V2YY3UKH/Lopes et al. - 2015 - Bonsai an event-based framework for processing an.pdf}
}

@article{scargle_studies_1982,
  title = {Studies in Astronomical Time Series Analysis. {{II}} - {{Statistical}} Aspects of Spectral Analysis of Unevenly Spaced Data},
  volume = {263},
  issn = {0004-637X},
  doi = {10.1086/160554},
  abstract = {Detection of a periodic signal hidden in noise is frequently a goal in 
astronomical data analysis. This paper does not introduce a new
detection technique, but instead studies the reliability and efficiency
of detection with the most commonly used technique, the periodogram, in
the case where the observation times are unevenly spaced. This choice
was made because, of the methods in current use, it appears to have the
simplest statistical behavior. A modification of the classical
definition of the periodogram is necessary in order to retain the simple
statistical behavior of the evenly spaced case. With this modification,
periodogram analysis and least-squares fitting of sine waves to the data
are exactly equivalent. Certain difficulties with the use of the
periodogram are less important than commonly believed in the case of
detection of strictly periodic signals. In addition, the standard method
for mitigating these difficulties (tapering) can be used just as well if
the sampling is uneven. An analysis of the statistical significance of
signal detections is presented, with examples},
  journal = {The Astrophysical Journal},
  author = {Scargle, J. D.},
  month = dec,
  year = {1982},
  keywords = {Spectrum Analysis,Astronomy,Fourier Transformation,Frequency Response,Power Spectra,Signal Detection,Signal To Noise Ratios,Statistical Distributions,Time Series Analysis},
  pages = {835-853},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9NHFTCBK/Scargle - 1982 - Studies in astronomical time series analysis. II -.pdf}
}

@article{ogueta_maite_2018_1172980,
  title = {{{LL Behaviour}} of {{TIM Gal4}} $>$ {{NKCC OX}} and {{NKCC OX}} / + Flies},
  doi = {10.5281/zenodo.1172980},
  journal = {Zenodo},
  author = {Ogueta, Maite and Stanewsky, Ralf},
  month = feb,
  year = {2018}
}

@article{leise_wavelet_2013,
  title = {Wavelet Analysis of Circadian and Ultradian Behavioral Rhythms},
  volume = {11},
  issn = {1740-3391},
  doi = {10.1186/1740-3391-11-5},
  abstract = {We review time-frequency methods that can be useful in quantifying circadian and ultradian patterns in behavioral records. These records typically exhibit details that may not be captured through commonly used measures such as activity onset and so may require alternative approaches. For instance, activity may involve multiple bouts that vary in duration and magnitude within a day, or may exhibit day-to-day changes in period and in ultradian activity patterns. The discrete Fourier transform and other types of periodograms can estimate the period of a circadian rhythm, but we show that they can fail to correctly assess ultradian periods. In addition, such methods cannot detect changes in the period over time. Time-frequency methods that can localize frequency estimates in time are more appropriate for analysis of ultradian periods and of fluctuations in the period. The continuous wavelet transform offers a method for determining instantaneous frequency with good resolution in both time and frequency, capable of detecting changes in circadian period over the course of several days and in ultradian period within a given day. The discrete wavelet transform decomposes a time series into components associated with distinct frequency bands, thereby facilitating the removal of noise and trend or the isolation of a particular frequency band of interest. To demonstrate the wavelet-based analysis, we apply the transforms to a numerically-generated example and also to a variety of hamster behavioral records. When used appropriately, wavelet transforms can reveal patterns that are not easily extracted using other methods of analysis in common use, but they must be applied and interpreted with care.},
  journal = {Journal of Circadian Rhythms},
  author = {Leise, Tanya L.},
  month = jul,
  year = {2013},
  keywords = {Wavelet transform,Circadian rhythms,Time series analysis,Ultradian rhythms,Estrous cycle,Fourier transform,Rodent locomotor activity},
  pages = {5},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7BMMSUZT/Leise - 2013 - Wavelet analysis of circadian and ultradian behavi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9QZWR67G/1740-3391-11-5.html}
}

@article{tsai_image_2012,
  title = {Image {{Tracking Study}} on {{Courtship Behavior}} of {{Drosophila}}},
  volume = {7},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0034784},
  abstract = {Background In recent years, there have been extensive studies aimed at decoding the DNA. Identifying the genetic cause of specific changes in a simple organism like Drosophila may help scientists recognize how multiple gene interactions may make some people more susceptible to heart disease or cancer. Investigators have devised experiments to observe changes in the gene networks in mutant Drosophila that responds differently to light, or have lower or higher locomotor activity. However, these studies focused on the behavior of the individual fly or on pair-wise interactions in the study of aggression or courtship. The behavior of these activities has been captured on film and inspected by a well-trained researcher after repeatedly watching the recorded film. Some studies also focused on ways to reduce the inspection time and increase the accuracy of the behavior experiment. Methodology In this study, the behavior of drosophila during courtship was analyzed automatically by machine vision. We investigated the position and behavior discrimination during courtship using the captured images. Identification of the characteristics of drosophila, including sex, size, heading direction, and wing angles, can be computed using image analysis techniques that employ the Gaussian mixture model. The behavior of multiple drosophilae can also be analyzed simultaneously using the motion-prediction model and the variation constraint of heading direction. Conclusions The overlapped fruit flies can be identified based on the relationship between body centers. Moreover, the behaviors and profiles can be correctly recognized by image processing based on the constraints of the wing angle and the size of the body. Therefore, the behavior of the male fruit flies can be discriminated when two or three fruit flies form a close cluster. In this study, the courtship behavior, including wing songs and attempts, can currently be distinguished with accuracies of 95.8\% and 90\%, respectively.},
  language = {en},
  number = {4},
  journal = {PLOS ONE},
  author = {Tsai, Hung-Yin and Huang, Yen-Wen},
  month = apr,
  year = {2012},
  keywords = {Behavior,Drosophila,Drosophila melanogaster,Wings,Abdomen,Biological locomotion,Ellipses,Probability density},
  pages = {e34784},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AMWLDYPP/Tsai and Huang - 2012 - Image Tracking Study on Courtship Behavior of Dros.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SMXKP5WH/article.html}
}

@article{sejnowski_putting_2014,
  title = {{Putting big data to good use in neuroscience}},
  volume = {17},
  issn = {1097-6256},
  doi = {10.1038/nn.3839},
  language = {English (US)},
  number = {11},
  journal = {Nature Neuroscience},
  author = {Sejnowski, Terrence J. and Churchland, Patricia S. and Movshon, J. Anthony},
  month = oct,
  year = {2014},
  pages = {1440-1441},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LPZK7B9V/putting-big-data-to-good-use-in-neuroscience.html},
  pmid = {25349909}
}

@article{morin_shining_2012,
  title = {Shining {{Light}} into {{Black Boxes}}},
  volume = {336},
  copyright = {Copyright \textcopyright{} 2012, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1218263},
  abstract = {The publication and open exchange of knowledge and material form the backbone of scientific progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs ``black boxes'' in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences. Eliminating this disparity will require concerted policy action by funding agencies and journal publishers, as well as changes in the way research institutions receiving public funds manage their intellectual property (IP).
Funders, publishers, and research institutions must act to ensure that research computer code is made widely available.
Funders, publishers, and research institutions must act to ensure that research computer code is made widely available.},
  language = {en},
  number = {6078},
  journal = {Science},
  author = {Morin, A. and Urban, J. and Adams, P. D. and Foster, I. and Sali, A. and Baker, D. and Sliz, P.},
  month = apr,
  year = {2012},
  pages = {159-160},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZJZ6J68N/Morin et al. - 2012 - Shining Light into Black Boxes.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VI36ASLP/159.html},
  pmid = {22499926}
}

@article{leipzig_review_2017,
  title = {A Review of Bioinformatic Pipeline Frameworks},
  volume = {18},
  issn = {1467-5463},
  doi = {10.1093/bib/bbw020},
  abstract = {High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.},
  language = {en},
  number = {3},
  journal = {Briefings in Bioinformatics},
  author = {Leipzig, Jeremy},
  month = may,
  year = {2017},
  pages = {530-536},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CNYJHSNT/Leipzig - 2017 - A review of bioinformatic pipeline frameworks.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VFK9TDAW/2562749.html}
}

@article{roumpeka_review_2017,
  title = {A {{Review}} of {{Bioinformatics Tools}} for {{Bio}}-{{Prospecting}} from {{Metagenomic Sequence Data}}},
  volume = {8},
  issn = {1664-8021},
  doi = {10.3389/fgene.2017.00023},
  abstract = {The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.},
  language = {English},
  journal = {Frontiers in Genetics},
  author = {Roumpeka, Despoina D. and Wallace, R. John and Escalettes, Frank and Fotheringham, Ian and Watson, Mick},
  year = {2017},
  keywords = {bioinformatics,Assembly,Bioprospecting,gene prediction,Metagenomics,next generation sequencing},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MQ4QE88R/Roumpeka et al. - 2017 - A Review of Bioinformatics Tools for Bio-Prospecti.pdf}
}

@article{huber_orchestrating_2015,
  title = {Orchestrating High-Throughput Genomic Analysis with {{Bioconductor}}},
  volume = {12},
  copyright = {2015 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth.3252},
  abstract = {Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.},
  language = {en},
  number = {2},
  journal = {Nature Methods},
  author = {Huber, Wolfgang and Carey, Vincent J. and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S. and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D. and Irizarry, Rafael A. and Lawrence, Michael and Love, Michael I. and MacDonald, James and Obenchain, Valerie and Ole\'s, Andrzej K. and Pag\`es, Herv\'e and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K. and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin},
  month = feb,
  year = {2015},
  pages = {115-121},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JT5VACEF/Huber et al. - 2015 - Orchestrating high-throughput genomic analysis wit.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CCIRSVDT/nmeth.html}
}

@article{hashem_rise_2015,
  title = {The Rise of ``Big Data'' on Cloud Computing: {{Review}} and Open Research Issues},
  volume = {47},
  issn = {0306-4379},
  shorttitle = {The Rise of ``Big Data'' on Cloud Computing},
  doi = {10.1016/j.is.2014.07.006},
  abstract = {Cloud computing is a powerful technology to perform massive-scale and complex computing. It eliminates the need to maintain expensive computing hardware, dedicated space, and software. Massive growth in the scale of data or big data generated through cloud computing has been observed. Addressing big data is a challenging and time-demanding task that requires a large computational infrastructure to ensure successful data processing and analysis. The rise of big data in cloud computing is reviewed in this study. The definition, characteristics, and classification of big data along with some discussions on cloud computing are introduced. The relationship between big data and cloud computing, big data storage systems, and Hadoop technology are also discussed. Furthermore, research challenges are investigated, with focus on scalability, availability, data integrity, data transformation, data quality, data heterogeneity, privacy, legal and regulatory issues, and governance. Lastly, open research issues that require substantial research efforts are summarized.},
  journal = {Information Systems},
  author = {Hashem, Ibrahim Abaker Targio and Yaqoob, Ibrar and Anuar, Nor Badrul and Mokhtar, Salimah and Gani, Abdullah and Ullah Khan, Samee},
  month = jan,
  year = {2015},
  keywords = {Big data,Cloud computing,Hadoop},
  pages = {98-115},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6XMWU7E5/Hashem et al. - 2015 - The rise of “big data” on cloud computing Review .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VDVMR3XR/S0306437914001288.html}
}

@misc{schmidbauer_waveletcomp_2018,
  title = {{{WaveletComp}}: {{Computational Wavelet Analysis}}},
  copyright = {GPL-2},
  shorttitle = {{{WaveletComp}}},
  abstract = {Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.},
  author = {Schmidbauer, Angi Roesch {and} Harald},
  month = mar,
  year = {2018},
  keywords = {TimeSeries}
}

@article{lomb_least-squares_1976,
  title = {Least-Squares Frequency Analysis of Unequally Spaced Data},
  volume = {39},
  issn = {0004-640X},
  doi = {10.1007/BF00648343},
  abstract = {The statistical properties of least-squares frequency analysis of unequally spaced data are examined. It is shown that, in the
least-squares spectrum of gaussian noise, the reduction in the sum of squares at a particular frequency is a chi2-squared variable. The reductions at different frequencies are not independent, as there is a correlation between the height of the spectrum at any two frequencies, f1 and f2, which is equal to the mean height of the spectrum due to a sinusoidal signal of frequency f1, at the frequency f2. These correlations reduce the distortion in the spectrum of a signal affected by noise. Some numerical illustrations of the properties of least-squares frequency spectra are given.},
  journal = {Astrophysics and Space Science},
  author = {Lomb, N. R.},
  month = feb,
  year = {1976},
  keywords = {Spectrum Analysis,Astronomy,Power Spectra,Background Noise,Data Reduction,Least Squares Method,Sine Waves,Statistical Analysis,Variable Stars},
  pages = {447-462},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3DJAPQS9/Lomb - 1976 - Least-squares frequency analysis of unequally spac.pdf}
}

@article{robie_mapping_2017,
  title = {Mapping the {{Neural Substrates}} of {{Behavior}}},
  volume = {170},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/j.cell.2017.06.032},
  abstract = {$<$h2$>$Summary$<$/h2$><$p$>$Assigning behavioral functions to neural structures has long been a central goal in neuroscience and is a necessary first step toward a circuit-level understanding of how the brain generates behavior. Here, we map the neural substrates of locomotion and social behaviors for \emph{Drosophila melanogaster} using automated machine-vision and machine-learning techniques. From videos of 400,000 flies, we quantified the behavioral effects of activating 2,204 genetically targeted populations of neurons. We combined a novel quantification of anatomy with our behavioral analysis to create brain-behavior correlation maps, which are shared as browsable web pages and interactive software. Based on these maps, we generated hypotheses of regions of the brain causally related to sensory processing, locomotor control, courtship, aggression, and sleep. Our maps directly specify genetic tools to target these regions, which we used to identify a small population of neurons with a role in the control of walking.$<$/p$>$},
  language = {English},
  number = {2},
  journal = {Cell},
  author = {Robie, Alice A. and Hirokawa, Jonathan and Edwards, Austin W. and Umayam, Lowell A. and Lee, Allen and Phillips, Mary L. and Card, Gwyneth M. and Korff, Wyatt and Rubin, Gerald M. and Simpson, Julie H. and Reiser, Michael B. and Branson, Kristin},
  month = jul,
  year = {2017},
  pages = {393-406.e28},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DIQRWGY7/Robie et al. - 2017 - Mapping the Neural Substrates of Behavior.pdf},
  pmid = {28709004, 28709004}
}

@article{kabra_jaaba_2013,
  title = {{{JAABA}}: Interactive Machine Learning for Automatic Annotation of Animal Behavior},
  volume = {10},
  copyright = {2012 Nature Publishing Group},
  issn = {1548-7105},
  shorttitle = {{{JAABA}}},
  doi = {10.1038/nmeth.2281},
  abstract = {We present a machine learning\textendash{}based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, including mice and adult and larval Drosophila.},
  language = {en},
  number = {1},
  journal = {Nature Methods},
  author = {Kabra, Mayank and Robie, Alice A. and {Rivera-Alba}, Marta and Branson, Steven and Branson, Kristin},
  month = jan,
  year = {2013},
  pages = {64-67},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9RPSWFD3/Kabra et al. - 2013 - JAABA interactive machine learning for automatic .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z587JJGS/nmeth.html}
}

@article{schatz_biological_2015,
  title = {Biological Data Sciences in Genome Research},
  volume = {25},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.191684.115},
  abstract = {The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.},
  language = {en},
  number = {10},
  journal = {Genome Research},
  author = {Schatz, Michael C.},
  month = jan,
  year = {2015},
  pages = {1417-1422},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RAAUZ2FG/Schatz - 2015 - Biological data sciences in genome research.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TWJCVVBM/1417.html},
  pmid = {26430150}
}

@article{stodden_toward_2013,
  title = {Toward {{Reproducible Computational Research}}: {{An Empirical Analysis}} of {{Data}} and {{Code Policy Adoption}} by {{Journals}}},
  volume = {8},
  issn = {1932-6203},
  shorttitle = {Toward {{Reproducible Computational Research}}},
  doi = {10.1371/journal.pone.0067111},
  abstract = {Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38\% had a data policy, 22\% had a code policy, and 66\% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16\% in the number of data policies, a 30\% increase in code policies, and a 7\% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Stodden, Victoria and Guo, Peixuan and Ma, Zhaokun},
  month = jun,
  year = {2013},
  keywords = {Bibliometrics,Computational biology,Data management,Open access publishing,Open data,Reproducibility,Science policy,Scientific publishing},
  pages = {e67111},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HPN3KFDU/Stodden et al. - 2013 - Toward Reproducible Computational Research An Emp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NAEXD22K/article.html}
}

@article{peng_reproducible_2011,
  title = {Reproducible {{Research}} in {{Computational Science}}},
  volume = {334},
  copyright = {Copyright \textcopyright{} 2011, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1213847},
  abstract = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.},
  language = {en},
  number = {6060},
  journal = {Science},
  author = {Peng, Roger D.},
  month = dec,
  year = {2011},
  pages = {1226-1227},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BDB2MGJR/Peng - 2011 - Reproducible Research in Computational Science.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z8PXWS87/tab-pdf.html},
  pmid = {22144613}
}

@article{stephens_big_2015,
  title = {Big {{Data}}: {{Astronomical}} or {{Genomical}}?},
  volume = {13},
  issn = {1545-7885},
  shorttitle = {Big {{Data}}},
  doi = {10.1371/journal.pbio.1002195},
  abstract = {Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a ``four-headed beast''\textemdash{}it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the ``genomical'' challenges of the next decade.},
  language = {en},
  number = {7},
  journal = {PLOS Biology},
  author = {Stephens, Zachary D. and Lee, Skylar Y. and Faghri, Faraz and Campbell, Roy H. and Zhai, Chengxiang and Efron, Miles J. and Iyer, Ravishankar and Schatz, Michael C. and Sinha, Saurabh and Robinson, Gene E.},
  month = jul,
  year = {2015},
  keywords = {Animal genomics,Cancer genomics,Data acquisition,Genome complexity,Genome sequencing,Genomic medicine,Human genomics,Mammalian genomics},
  pages = {e1002195},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/APIIIQVP/Stephens et al. - 2015 - Big Data Astronomical or Genomical.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HD4ZBMKA/article.html}
}

@incollection{liu_wavelet_1994,
  series = {Wavelets in Geophysics},
  title = {Wavelet {{Spectrum Analysis}} and {{Ocean Wind Waves}}},
  volume = {4},
  abstract = {Wavelet spectrum analysis is applied to a set of measured ocean wind waves data collected during the 1990 SWADE (Surface Wave Dynamics Experiment) program. The results reveal significantly new and previously unexplored insights on wave grouping parameterizations, phase relations during wind wave growth, and detecting wave breaking characteristics. These insights are due to the nature of the wavelet transform that would not be immediately evident using a traditional Fourier transform approach.},
  booktitle = {Wavelet {{Analysis}} and {{Its Applications}}},
  publisher = {{Academic Press}},
  author = {Liu, Paul C.},
  editor = {{Foufoula-Georgiou}, Efi and Kumar, Praveen},
  month = jan,
  year = {1994},
  pages = {151-166},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DZTMJGT8/B9780080520872500128.html},
  doi = {10.1016/B978-0-08-052087-2.50012-8}
}

@article{pereira_fast_2018,
  title = {Fast Animal Pose Estimation Using Deep Neural Networks},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  doi = {10.1101/331181},
  abstract = {Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neural network with as little as 10 frames of labeled data for training. This framework consists of a graphical interface for interactive labeling of body parts and software for training the network and fast prediction on new data (1 hr to train, 185 Hz predictions). We validate LEAP using videos of freely behaving fruit flies (Drosophila melanogaster) and track 32 distinct points on the body to fully describe the pose of the head, body, wings, and legs with an error rate of $<$3\% of the animal's body length. We recapitulate a number of reported findings on insect gait dynamics and show LEAP's applicability as the first step in unsupervised behavioral classification. Finally, we extend the method to more challenging imaging situations (pairs of flies moving on a mesh-like background) and movies from freely moving mice (Mus musculus) where we track the full conformation of the head, body, and limbs.},
  language = {en},
  journal = {bioRxiv},
  author = {Pereira, Talmo and Aldarondo, Diego and Willmore, Lindsay and Kislin, Mikhail and Wang, Samuel S. and Murthy, Mala and Shaevitz, Joshua W.},
  month = may,
  year = {2018},
  pages = {331181},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VW455H26/Pereira et al. - 2018 - Fast animal pose estimation using deep neural netw.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DY4ZHVDI/331181.html}
}

@book{ameisen_quest-ce_2017,
  title = {{Qu'est-ce que mourir ?}},
  isbn = {978-2-7465-1232-0},
  abstract = {Cet ouvrage explore, \`a la lumi\`ere de la biologie, de la philosophie, de la science des religions, de l'histoire et de la psychanalyse, quelques-unes des innombrables interrogations que fait surgir la question du \guillemotleft{}mourir\guillemotright.},
  language = {fr},
  publisher = {{Humensis}},
  author = {Ameisen, Jean Claude and {Hevieu-L\'eger}, Dani\`ele and Hirsch, Emmanuel},
  month = mar,
  year = {2017},
  keywords = {Medical / General,Science / Life Sciences / Biology,Medical / Immunology,Philosophy / Ethics \& Moral Philosophy,Philosophy / General,Political Science / Public Policy / Social Policy,Religion / History,Social Science / Death \& Dying,Social Science / Disease \& Health Issues,Social Science / General,Social Science / Sociology of Religion}
}

@article{pascual_computational_2005,
  title = {Computational {{Ecology}}: {{From}} the {{Complex}} to the {{Simple}} and {{Back}}},
  volume = {1},
  issn = {1553-7358},
  shorttitle = {Computational {{Ecology}}},
  doi = {10.1371/journal.pcbi.0010018},
  language = {en},
  number = {2},
  journal = {PLOS Computational Biology},
  author = {Pascual, Mercedes},
  year = {29 juil. 2005},
  keywords = {Community structure,Disease dynamics,Ecosystem modeling,Ecosystems,Food web structure,Population dynamics,Species interactions,Theoretical ecology},
  pages = {e18},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5SP3E45Y/Pascual - 2005 - Computational Ecology From the Complex to the Sim.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WUPDDG5P/article.html}
}

@article{levitt_birth_2001-3,
  title = {The Birth of Computational Structural Biology},
  language = {en},
  author = {Levitt, Michael},
  year = {2001},
  pages = {2},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LMMRP2GG/Levitt - The birth of computational structural biology.pdf}
}

@article{bonini_tribute_2008,
  title = {A {{Tribute}} to {{Seymour Benzer}}, 1921\textendash{}2007},
  volume = {180},
  copyright = {Copyright \textcopyright{} 2008 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.104.97782},
  abstract = {Anecdotal, Historical and Critical Commentaries on Genetics

Edited by James F. Crow and William F. Dove

NOVEMBER 2007 was marked by the loss of Seymour Benzer, long considered the father of the field of neurogenetics. Benzer's scientific contributions are broad and span from physics (his Ph.D.},
  language = {en},
  number = {3},
  journal = {Genetics},
  author = {Bonini, Nancy M.},
  month = nov,
  year = {2008},
  pages = {1265-1273},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YUB3QSMD/Bonini - 2008 - A Tribute to Seymour Benzer, 1921–2007.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8KHUKJZF/1265.html},
  pmid = {19001297}
}

@article{fry_trackfly_2008,
  title = {{{TrackFly}}: {{Virtual}} Reality for a Behavioral System Analysis in Free-Flying Fruit Flies},
  volume = {171},
  issn = {0165-0270},
  shorttitle = {{{TrackFly}}},
  doi = {10.1016/j.jneumeth.2008.02.016},
  abstract = {Modern neuroscience and the interest in biomimetic control design demand increasingly sophisticated experimental techniques that can be applied in freely moving animals under realistic behavioral conditions. To explore sensorimotor flight control mechanisms in free-flying fruit flies (Drosophila melanogaster), we equipped a wind tunnel with a Virtual Reality (VR) display system based on standard digital hardware and a 3D path tracking system. We demonstrate the experimental power of this approach by example of a `one-parameter open loop' testing paradigm. It provided (1) a straightforward measure of transient responses in presence of open loop visual stimulation; (2) high data throughput and standardized measurement conditions from process automation; and (3) simplified data analysis due to well-defined testing conditions. Being based on standard hardware and software techniques, our methods provide an affordable, easy to replicate and general solution for a broad range of behavioral applications in freely moving animals. Particular relevance for advanced behavioral research tools originates from the need to perform detailed behavioral analyses in genetically modified organisms and animal models for disease research.},
  number = {1},
  journal = {Journal of Neuroscience Methods},
  author = {Fry, Steven N. and Rohrseitz, Nicola and Straw, Andrew D. and Dickinson, Michael H.},
  month = jun,
  year = {2008},
  keywords = {Behavior,Vision,Flight,Insects,Control,Tracking,Virtual reality},
  pages = {110-117},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YBFMYX72/Fry et al. - 2008 - TrackFly Virtual reality for a behavioral system .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4QUPETI7/S0165027008001210.html}
}

@article{kain_leg-tracking_2013,
  title = {Leg-Tracking and Automated Behavioural Classification in {{{\emph{Drosophila}}}}},
  volume = {4},
  copyright = {2013 Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/ncomms2908},
  abstract = {Much remains unknown about how the nervous system of an animal generates behaviour, and even less is known about the evolution of behaviour. How does evolution alter existing behaviours or invent novel ones? Progress in computational techniques and equipment will allow these broad, complex questions to be explored in great detail. Here we present a method for tracking each leg of a fruit fly behaving spontaneously upon a trackball, in real time. Legs were tracked with infrared-fluorescent dyes invisible to the fly, and compatible with two-photon microscopy and controlled visual stimuli. We developed machine-learning classifiers to identify instances of numerous behavioural features (for example, walking, turning and grooming), thus producing the highest-resolution ethological profiles for individual flies.},
  language = {en},
  journal = {Nature Communications},
  author = {Kain, Jamey and Stokes, Chris and Gaudry, Quentin and Song, Xiangzhi and Foley, James and Wilson, Rachel and de Bivort, Benjamin},
  month = may,
  year = {2013},
  pages = {1910},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RZ6UPAI6/Kain et al. - 2013 - Leg-tracking and automated behavioural classificat.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AN9RJ9E2/ncomms2908.html}
}

@article{sherman_comparison_2003,
  title = {A Comparison of Visual and Haltere-Mediated Equilibrium Reflexes in the Fruit Fly {{Drosophila}} Melanogaster},
  volume = {206},
  copyright = {\textcopyright{} The Company of Biologists Limited 2003},
  issn = {0022-0949, 1477-9145},
  doi = {10.1242/jeb.00075},
  abstract = {Skip to Next Section
Flies exhibit extraordinary maneuverability, relying on feedback from multiple sensory organs to control flight. Both the compound eyes and the mechanosensory halteres encode angular motion as the fly rotates about the three body axes during flight. Since these two sensory modalities differ in their mechanisms of transduction, they are likely to differ in their temporal responses. We recorded changes in stroke kinematics in response to mechanical and visual rotations delivered within a flight simulator. Our results show that the visual system is tuned to relatively slow rotation whereas the haltere-mediated response to mechanical rotation increases with rising angular velocity. The integration of feedback from these two modalities may enhance aerodynamic performance by enabling the fly to sense a wide range of angular velocities during flight.},
  language = {en},
  number = {2},
  journal = {Journal of Experimental Biology},
  author = {Sherman, Alana and Dickinson, Michael H.},
  month = jan,
  year = {2003},
  keywords = {flight,fruit fly,Drosophila melanogaster,control system,haltere,mechanosensory},
  pages = {295-302},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/63W6U555/Sherman and Dickinson - 2003 - A comparison of visual and haltere-mediated equili.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RFEPLM9J/295.html},
  pmid = {12477899}
}

@article{maimon_simple_2008,
  title = {A {{Simple Vision}}-{{Based Algorithm}} for {{Decision Making}} in {{Flying Drosophila}}},
  volume = {18},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2008.02.054},
  abstract = {Summary
Animals must quickly recognize objects in their environment and act accordingly. Previous studies indicate that looming visual objects trigger avoidance reflexes in many species [1\textendash{}5]; however, such reflexes operate over a close range and might not detect a threatening stimulus at a safe distance. We analyzed how fruit flies (Drosophila melanogaster) respond to simple visual stimuli both in free flight and in a tethered-flight simulator. Whereas Drosophila, like many other insects, are attracted toward long vertical objects [6\textendash{}10], we found that smaller visual stimuli elicit not weak attraction but rather strong repulsion. Because aversion to small spots depends on the vertical size of a moving object, and not on looming, it can function at a much greater distance than expansion-dependent reflexes. The opposing responses to long stripes and small spots reflect a simple but effective object classification system. Attraction toward long stripes would lead flies toward vegetative perches or feeding sites, whereas repulsion from small spots would help them avoid aerial predators or collisions with other insects. The motion of flying Drosophila depends on a balance of these two systems, providing a foundation for studying the neural basis of behavioral choice in a genetic model organism.},
  number = {6},
  journal = {Current Biology},
  author = {Maimon, Gaby and Straw, Andrew D. and Dickinson, Michael H.},
  month = mar,
  year = {2008},
  keywords = {SYSNEURO},
  pages = {464-470},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7U7C8H4F/Maimon et al. - 2008 - A Simple Vision-Based Algorithm for Decision Makin.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WQWHIAQC/S0960982208002418.html}
}

@article{gotz_course-control_1987,
  title = {Course-{{Control}}, {{Metabolism}} and {{Wing Interference During Ultralong Tethered Flight}} in {{Drosophila Melanogaster}}},
  volume = {128},
  copyright = {\textcopyright{} 1987 by Company of Biologists},
  issn = {0022-0949, 1477-9145},
  abstract = {Skip to Next Section
Tethered flight in a 3-day-old female Drosophila was sustained for 32.2 h with only short interruptions during uptake of sucrose solution. The course-control reactions derived from the difference of the wingbeat amplitudes on either side have been used to simulate the rotatory displacement of the surrounding landmarks during a comparable turn in free flight. Stabilization of a target in the preferred area of the visual field requires continuous visual attention. A rate of about 5 course-correcting manoeuvres per second was maintained throughout the experiment. Drosophila seems to be able to cover long distances in search of a favourable habitat.
Flight-specific carbohydrate consumption is equivalent to a metabolic power input per body weight of about 18 W N-1. The tethered fly produces about 40 \% of the lift required to sustain hovering flight. The resulting mechanochemical efficiency of about 0.04-0.07 is within the expected order of magnitude for flying insects. Expenditure of reserve substances may account for the difference between the comparatively low power input of about 7 WN-1 derived from carbohydrate uptake in the first hours of flight (Wigglesworth, 1949), and the actual metabolic turnover of about 21WN-1 derived from oxygen consumption during this period (Laurie-Ahlberg et al. 1985).
Weis-Fogh's `clap and fling', a widespread lift-generating process exploiting the aerodynamic wing interference at the dorsal end of the wingbeat, was in action throughout the flight. However, there were two significant modifications (as first conceived by Ellington, 1980): (1) during `clap', there is a progress of wing contact from the leading to the trailing edge, which is likely to `squeeze' a thrust-generating jet of air to the rear; (2) during `fling', there is a progress of wing separation in the same direction, which is described as a `peel' resembling the progressive separation of two plastic foils pulled apart against forces of mutual attraction. The wings of the test fly survived about 23 million such peels without damage. Increasing airspeed decreases the intensity of `clap and fling' in Drosophila: results obtained in the wind tunnel show the transition to a `near clap and fling', lacking mutual wing contact.},
  language = {en},
  number = {1},
  journal = {Journal of Experimental Biology},
  author = {G\"otz, Karl G.},
  month = mar,
  year = {1987},
  pages = {35-46},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7YHZC8PP/Götz - 1987 - Course-Control, Metabolism and Wing Interference D.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NVQ5Q8D3/35.html}
}

@article{tammero_influence_2002,
  title = {The Influence of Visual Landscape on the Free Flight Behavior of the Fruit Fly {{Drosophila}} Melanogaster},
  volume = {205},
  copyright = {\textcopyright{} The Company of Biologists Limited 2002},
  issn = {0022-0949, 1477-9145},
  abstract = {$<$h3$>$SUMMARY$<$/h3$>$ $<$p$>$\textbf{To study the visual cues that control steering behavior in the fruit fly \emph{Drosophila melanogaster}, we reconstructed three-dimensional trajectories from images taken by stereo infrared video cameras during free flight within structured visual landscapes. Flies move through their environment using a series of straight flight segments separated by rapid turns, termed saccades, during which the fly alters course by approximately 90$^\circ$ in less than 100\&nbsp;ms. Altering the amount of background visual contrast caused significant changes in the fly's translational velocity and saccade frequency. Between saccades, asymmetries in the estimates of optic flow induce gradual turns away from the side experiencing a greater motion stimulus, a behavior opposite to that predicted by a flight control model based upon optomotor equilibrium. To determine which features of visual motion trigger saccades, we reconstructed the visual environment from the fly's perspective for each position in the flight trajectory. From these reconstructions, we modeled the fly's estimation of optic flow on the basis of a two-dimensional array of Hassenstein\textendash{}Reichardt elementary motion detectors and, through spatial summation, the large-field motion stimuli experienced by the fly during the course of its flight. Event-triggered averages of the large-field motion preceding each saccade suggest that image expansion is the signal that triggers each saccade. The asymmetry in output of the local motion detector array prior to each saccade influences the direction (left \emph{versus} right) but not the magnitude of the rapid turn. Once initiated, visual feedback does not appear to influence saccade kinematics further. The total expansion experienced before a saccade was similar for flight within both uniform and visually textured backgrounds. In summary, our data suggest that complex behavioral patterns seen during free flight emerge from interactions between the flight control system and the visual environment.}$<$/p$>$},
  language = {en},
  number = {3},
  journal = {Journal of Experimental Biology},
  author = {Tammero, Lance F. and Dickinson, Michael H.},
  month = feb,
  year = {2002},
  keywords = {flight,Drosophila melanogaster,behaviour,motion detection.,optic flow,saccade,visual control},
  pages = {327-343},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CKEGCCZD/Tammero and Dickinson - 2002 - The influence of visual landscape on the free flig.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SJ3YMU4C/327.html},
  pmid = {11854370}
}

@article{martin_portrait_2004,
  title = {A Portrait of Locomotor Behaviour in {{Drosophila}} Determined by a Video-Tracking Paradigm},
  volume = {67},
  issn = {0376-6357},
  doi = {10.1016/j.beproc.2004.04.003},
  abstract = {This paper presents a detailed characterisation of locomotor behaviour of a single Drosophila fly freely walking in a small square arena. Locomotor activity is monitored by a video-tracking paradigm. Multiple parameters are extracted to construct the portrait of locomotor activity: the total distance moved, the number of episodes of activity and inactivity, the duration of activity, and the mean walking speed. To initiate a quantification of the fly's spatial walking movements, the number of passages in a virtual centre zone has also been determined. Moreover, to reveal the trajectory, as an index of fly's navigation ability, the turning angle, the angular velocity and the meander have been measured. Finally, we show that the number of episodes of inactivity as function of their duration follows a power law, while its counterpart, the episodes of activity does not, suggesting that the overall pattern of locomotor activity adheres to a fractal-like structure. Remarkably, the majority of these parameters are sexually dimorphic. This fine description of locomotor activity represents a new tool which will facilitate the study of the role of the different brain structures in the organisation of locomotor activity and the localisation of the fly's central pattern generator for locomotion and its motivational control.},
  number = {2},
  journal = {Behavioural Processes},
  author = {Martin, Jean-Ren\'e},
  month = sep,
  year = {2004},
  keywords = {Video-tracking,Centrophobism,Behaviour,Locomotor activity,Fractal structure},
  pages = {207-219},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W536TGVJ/Martin - 2004 - A portrait of locomotor behaviour in Drosophila de.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZQBUYK8E/S0376635704000944.html}
}

@article{cole_fractal_1995,
  title = {Fractal Time in Animal Behaviour: The Movement Activity of {{Drosophila}}},
  volume = {50},
  issn = {0003-3472},
  shorttitle = {Fractal Time in Animal Behaviour},
  doi = {10.1016/0003-3472(95)80047-6},
  abstract = {The organization of episodes of activity and inactivity of Drosophila melanogaster has a complex structure. Episodes of apparently continuous activity have shorter episodes of inactivity embedded within them. This pattern of activity has a self-similar structure; the activity record appears the same regardless of the time scale used. There is a power law dependence of the rate `constants' that describes how the activity of flies turns on and off. As a consequence no natural time scale for the measurement of the activity level exists, and the amount of activity depends on the time scale of measurement. The observation of fractal time variability in animal behaviour may illuminate the processes that produce activity. Fractal time variation in movement activity can lead to L\'evy flight patterns of movement, which produce efficient searches.},
  number = {5},
  journal = {Animal Behaviour},
  author = {Cole, Blaine J.},
  month = jan,
  year = {1995},
  pages = {1317-1324},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BU993AVX/Cole - 1995 - Fractal time in animal behaviour the movement act.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IIDLN9EJ/0003347295800476.html}
}

@article{risse_quantifying_2015,
  title = {Quantifying Subtle Locomotion Phenotypes of {{Drosophila}} Larvae Using Internal Structures Based on {{FIM}} Images},
  volume = {63},
  issn = {0010-4825},
  doi = {10.1016/j.compbiomed.2014.08.026},
  abstract = {Quantitative analysis of behavioral traits requires precise image acquisition and sophisticated image analysis to detect subtle locomotion phenotypes. In the past, we have established Frustrated Total Internal Reflection (FTIR) to improve the measurability of small animals like insects. This FTIR-based Imaging Method (FIM) results in an excellent foreground/background contrast and even internal organs and other structures are visible without any complicated imaging or labeling techniques. For example, the trachea and muscle organizations are detectable in FIM images. Here these morphological details are incorporated into phenotyping by performing cluster analysis using histogram-based statistics for the first time. We demonstrate that FIM enables the precise quantification of locomotion features namely rolling behavior or muscle contractions. Both were impossible to quantify automatically before. This approach extends the range of FIM applications by enabling advanced automatic phenotyping for particular locomotion patterns.},
  journal = {Computers in Biology and Medicine},
  author = {Risse, Benjamin and Berh, Dimitri and Otto, Nils and Jiang, Xiaoyi and Kl\"ambt, Christian},
  month = aug,
  year = {2015},
  keywords = {Neuroscience,Clustering,Frustrated Total Internal Reflection (FTIR),FTIR-based Imaging Method (FIM),Histogram analysis,Internal organs,larva,Peristalsis,Rolling behavior,Trachea},
  pages = {269-276},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BGBNPD75/Risse et al. - 2015 - Quantifying subtle locomotion phenotypes of Drosop.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YV7ENXTQ/S0010482514002285.html}
}

@article{risse_fim_2013,
  title = {{{FIM}}, a {{Novel FTIR}}-{{Based Imaging Method}} for {{High Throughput Locomotion Analysis}}},
  volume = {8},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0053963},
  abstract = {We designed a novel imaging technique based on frustrated total internal reflection (FTIR) to obtain high resolution and high contrast movies. This FTIR-based Imaging Method (FIM) is suitable for a wide range of biological applications and a wide range of organisms. It operates at all wavelengths permitting the in vivo detection of fluorescent proteins. To demonstrate the benefits of FIM, we analyzed large groups of crawling Drosophila larvae. The number of analyzable locomotion tracks was increased by implementing a new software module capable of preserving larval identity during most collision events. This module is integrated in our new tracking program named FIMTrack which subsequently extracts a number of features required for the analysis of complex locomotion phenotypes. FIM enables high throughput screening for even subtle behavioral phenotypes. We tested this newly developed setup by analyzing locomotion deficits caused by the glial knockdown of several genes. Suppression of kinesin heavy chain (khc) or rab30 function led to contraction pattern or head sweeping defects, which escaped in previous analysis. Thus, FIM permits forward genetic screens aimed to unravel the neural basis of behavior.},
  language = {en},
  number = {1},
  journal = {PLOS ONE},
  author = {Risse, Benjamin and Thomas, Silke and Otto, Nils and L\"opmeier, Tim and Valkov, Dimitar and Jiang, Xiaoyi and Kl\"ambt, Christian},
  month = jan,
  year = {2013},
  keywords = {Cameras,Crawling,Computer software,Imaging techniques,Drosophila melanogaster,Biological locomotion,Larvae,Luminance},
  pages = {e53963},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B6NKH9LF/Risse et al. - 2013 - FIM, a Novel FTIR-Based Imaging Method for High Th.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MKDENQ3A/article.html}
}

@article{sinadinos_increased_2012,
  title = {Increased Throughput Assays of Locomotor Dysfunction in {{Drosophila}} Larvae},
  volume = {203},
  issn = {0165-0270},
  doi = {10.1016/j.jneumeth.2011.08.037},
  abstract = {Larval locomotion is a sensitive readout of a range of nervous system deficits in Drosophila, and has been utilised to quantify modulation of the disease phenotype in models of human disease. Single larvae are typically analysed in series using manual quantification of parameters such as contraction rate, or grouped together and studied en-masse. Here, we describe the development of tests for the analysis of several spatially isolated third instar larvae in parallel. We rapidly quantify larval turning rate and velocity during wandering behaviour in a 4 plate assay. In a second test, larvae are recorded as they race along five parallel lanes towards a yeast stimulus. This allows increased throughput analysis of comparative genotypes simultaneously, video archiving, and detection of exacerbation or rescue of defective locomotion in a Drosophila model of tauopathy, as we demonstrate genetically and through delivery of candidate therapeutic chemicals in fly food. The tests are well-suited for rapid comparison of locomotion capability in Drosophila mutants or candidate modulation screens in Drosophila models of human disease.},
  number = {2},
  journal = {Journal of Neuroscience Methods},
  author = {Sinadinos, C. and Cowan, C. M. and Wyttenbach, A. and Mudher, A.},
  month = jan,
  year = {2012},
  keywords = {Video tracking,Behaviour,Larva,Locomotion,Increased throughput},
  pages = {325-334},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2NNP33VL/Sinadinos et al. - 2012 - Increased throughput assays of locomotor dysfuncti.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ILJQUYM2/S0165027011004961.html}
}

@article{straw_multi-camera_2010,
  title = {Multi-Camera Real-Time Three-Dimensional Tracking of Multiple Flying Animals},
  copyright = {\textcopyright{} 2010 The Royal Society. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.},
  issn = {1742-5689, 1742-5662},
  doi = {10.1098/rsif.2010.0230},
  abstract = {Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time\textemdash{}with minimal latency\textemdash{}opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as `virtual reality'-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.},
  language = {en},
  journal = {Journal of The Royal Society Interface},
  author = {Straw, Andrew D. and Branson, Kristin and Neumann, Titus R. and Dickinson, Michael H.},
  month = jul,
  year = {2010},
  pages = {rsif20100230},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/52BVLILI/Straw et al. - 2010 - Multi-camera real-time three-dimensional tracking .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8D4KHPIA/rsif.2010.0230.html},
  pmid = {20630879}
}

@article{pistori_mice_2010,
  series = {20th SIBGRAPI: Advances in Image Processing and Computer Vision},
  title = {Mice and Larvae Tracking Using a Particle Filter with an Auto-Adjustable Observation Model},
  volume = {31},
  issn = {0167-8655},
  doi = {10.1016/j.patrec.2009.05.015},
  abstract = {This paper proposes a novel way to combine different observation models in a particle filter framework. This, so called, auto-adjustable observation model, enhance the particle filter accuracy when the tracked objects overlap without infringing a great runtime penalty to the whole tracking system. The approach has been tested under two important real world situations related to animal behavior: mice and larvae tracking. The proposal was compared to some state-of-art approaches and the results show, under the datasets tested, that a good trade-off between accuracy and runtime can be achieved using an auto-adjustable observation model.},
  number = {4},
  journal = {Pattern Recognition Letters},
  author = {Pistori, Hemerson and Viana Aguiar Odakura, Valguima Victoria and Oliveira Monteiro, Jo\~ao Bosco and Gon{\c c}alves, Wesley Nunes and Roel, Antonia Railda and {de Andrade Silva}, Jonathan and Machado, Bruno Brandoli},
  month = mar,
  year = {2010},
  keywords = {Animal tracking,Dengue,Particle filters},
  pages = {337-346},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DAT6HLID/Pistori et al. - 2010 - Mice and larvae tracking using a particle filter w.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NZGZNNUR/S0167865509001330.html}
}

@article{romero-ferrero_idtracker.ai_2018,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1803.04351},
  primaryClass = {cs},
  title = {Idtracker.Ai: {{Tracking}} All Individuals in Large Collectives of Unmarked Animals},
  shorttitle = {Idtracker.Ai},
  abstract = {Our understanding of collective animal behavior is limited by our ability to track each of the individuals. We describe an algorithm and software, idtracker.ai, that extracts from video all trajectories with correct identities at a high accuracy for collectives of up to 100 individuals. It uses two deep networks, one detecting when animals touch or cross and another one for animal identification, trained adaptively to conditions and difficulty of the video.},
  journal = {arXiv:1803.04351 [cs]},
  author = {{Romero-Ferrero}, Francisco and Bergomi, Mattia G. and Hinz, Robert and Heras, Francisco J. H. and {de Polavieja}, Gonzalo G.},
  month = mar,
  year = {2018},
  keywords = {Computer Science - Computer Vision and Pattern Recognition},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NHAI3GWX/Romero-Ferrero et al. - 2018 - idtracker.ai Tracking all individuals in large co.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/34HFT4LR/1803.html}
}

@article{vogelstein_discovery_2014,
  title = {Discovery of {{Brainwide Neural}}-{{Behavioral Maps}} via {{Multiscale Unsupervised Structure Learning}}},
  volume = {344},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1250298},
  abstract = {Optogenetic Insights
Mapping functional neural circuits for many behaviors has been almost impossible, so Vogelstein et al. (p. 386, published online 27 March; see the Perspective by O'Leary and Marder) developed a broadly applicable optogenetic method for neuron-behavior mapping and used it to phenotype larval Drosophila and thus developed a reference atlas. As optogenetic experiments become routine in certain fields of neuroscience research, creating even more specialized tools is imperative (see the Perspective by Hayashi). By engineering channelrhodopsin, Wietek et al. (p. 409, published online 27 March) and Berndt et al. (p. 420) created two different light-gated anion channels to block action potential generation during synaptic stimulation or depolarizing current injections. These new tools not only improve understanding of channelrhodopsins but also provide a way to silence cells.
A single nervous system can generate many distinct motor patterns. Identifying which neurons and circuits control which behaviors has been a laborious piecemeal process, usually for one observer-defined behavior at a time. We present a fundamentally different approach to neuron-behavior mapping. We optogenetically activated 1054 identified neuron lines in Drosophila larvae and tracked the behavioral responses from 37,780 animals. Application of multiscale unsupervised structure learning methods to the behavioral data enabled us to identify 29 discrete, statistically distinguishable, observer-unbiased behavioral phenotypes. Mapping the neural lines to the behavior(s) they evoke provides a behavioral reference atlas for neuron subsets covering a large fraction of larval neurons. This atlas is a starting point for connectivity- and activity-mapping studies to further investigate the mechanisms by which neurons mediate diverse behaviors.
An atlas is generated to reveal activation of which specific neurons in a Drosophila larva produce specific behaviors. [Also see Perspective by O'Leary and Marder]
An atlas is generated to reveal activation of which specific neurons in a Drosophila larva produce specific behaviors. [Also see Perspective by O'Leary and Marder]},
  language = {en},
  number = {6182},
  journal = {Science},
  author = {Vogelstein, Joshua T. and Park, Youngser and Ohyama, Tomoko and Kerr, Rex A. and Truman, James W. and Priebe, Carey E. and Zlatic, Marta},
  month = apr,
  year = {2014},
  pages = {386-392},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XIEWBMUY/Vogelstein et al. - 2014 - Discovery of Brainwide Neural-Behavioral Maps via .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H9WTTNE2/386.html},
  pmid = {24674869}
}

@article{gomez-marin_big_2014,
  title = {Big Behavioral Data: Psychology, Ethology and the Foundations of Neuroscience},
  volume = {17},
  copyright = {2014 Nature Publishing Group},
  issn = {1546-1726},
  shorttitle = {Big Behavioral Data},
  doi = {10.1038/nn.3812},
  abstract = {Behavior is a unifying organismal process where genes, neural function, anatomy and environment converge and interrelate. Here we review the current state and discuss the future effect of accelerating advances in technology for behavioral studies, focusing on rodents as an example. We frame our perspective in three dimensions: the degree of experimental constraint, dimensionality of data and level of description. We argue that 'big behavioral data' presents challenges proportionate to its promise and describe how these challenges might be met through opportunities afforded by the two rival conceptual legacies of twentieth century behavioral science, ethology and psychology. We conclude that, although 'more is not necessarily better', copious, quantitative and open behavioral data has the potential to transform and unify these two disciplines and to solidify the foundations of others, including neuroscience, but only if the development of new theoretical frameworks and improved experimental designs matches the technological progress.},
  language = {en},
  number = {11},
  journal = {Nature Neuroscience},
  author = {{Gomez-Marin}, Alex and Paton, Joseph J. and Kampff, Adam R. and Costa, Rui M. and Mainen, Zachary F.},
  month = nov,
  year = {2014},
  pages = {1455-1462},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GDHSF92C/Gomez-Marin et al. - 2014 - Big behavioral data psychology, ethology and the .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/I827N86T/nn.html}
}

@article{egnor_computational_2016,
  title = {Computational {{Analysis}} of {{Behavior}}},
  volume = {39},
  doi = {10.1146/annurev-neuro-070815-013845},
  abstract = {In this review, we discuss the emerging field of computational behavioral analysis\textemdash{}the use of modern methods from computer science and engineering to quantitatively measure animal behavior. We discuss aspects of experiment design important to both obtaining biologically relevant behavioral data and enabling the use of machine vision and learning techniques for automation. These two goals are often in conflict. Restraining or restricting the environment of the animal can simplify automatic behavior quantification, but it can also degrade the quality or alter important aspects of behavior. To enable biologists to design experiments to obtain better behavioral measurements, and computer scientists to pinpoint fruitful directions for algorithm improvement, we review known effects of artificial manipulation of the animal on behavior. We also review machine vision and learning techniques for tracking, feature extraction, automated behavior classification, and automated behavior discovery, the assumptions they make, and the types of data they work best with.},
  number = {1},
  journal = {Annual Review of Neuroscience},
  author = {Egnor, S. E. Roian and Branson, Kristin},
  year = {2016},
  pages = {217-236},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AMX9LKVI/Egnor and Branson - 2016 - Computational Analysis of Behavior.pdf},
  pmid = {27090952}
}

@book{rockmore_modern_2004,
  title = {Modern {{Signal Processing}}},
  isbn = {978-0-521-82706-5},
  abstract = {Signal processing is everywhere in modern technology. Its mathematical basis and many areas of application are the subject of this book, based on a series of graduate-level lectures held at the Mathematical Sciences Research Institute. Emphasis is on challenges in the subject, particular techniques adapted to particular technologies, and certain advances in algorithms and theory. The book covers two main areas: computational harmonic analysis, envisioned as a technology for efficiently analysing real data using inherent symmetries; and the challenges inherent in the acquisition, processing and analysis of images and sensing data in general [EMDASH] ranging from sonar on a submarine to a neuroscientist's fMRI study.},
  language = {en},
  publisher = {{Cambridge University Press}},
  author = {Rockmore, Daniel N. and Jr, Dennis M. Healy},
  month = apr,
  year = {2004},
  keywords = {Computers / Natural Language Processing,Mathematics / Applied,Mathematics / Probability \& Statistics / General,Technology \& Engineering / Electronics / General,Technology \& Engineering / Telecommunications}
}

@article{berman_mapping_2014,
  title = {Mapping the Stereotyped Behaviour of Freely Moving Fruit Flies},
  volume = {11},
  copyright = {. \textcopyright{} 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.},
  issn = {1742-5689, 1742-5662},
  doi = {10.1098/rsif.2014.0672},
  abstract = {A frequent assumption in behavioural science is that most of an animal's activities can be described in terms of a small set of stereotyped motifs. Here, we introduce a method for mapping an animal's actions, relying only upon the underlying structure of postural movement data to organize and classify behaviours. Applying this method to the ground-based behaviour of the fruit fly, Drosophila melanogaster, we find that flies perform stereotyped actions roughly 50\% of the time, discovering over 100 distinguishable, stereotyped behavioural states. These include multiple modes of locomotion and grooming. We use the resulting measurements as the basis for identifying subtle sex-specific behavioural differences and revealing the low-dimensional nature of animal motions.},
  language = {en},
  number = {99},
  journal = {Journal of The Royal Society Interface},
  author = {Berman, Gordon J. and Choi, Daniel M. and Bialek, William and Shaevitz, Joshua W.},
  month = oct,
  year = {2014},
  pages = {20140672},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8GT77CN4/Berman et al. - 2014 - Mapping the stereotyped behaviour of freely moving.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PX8MUPZT/20140672.html},
  pmid = {25142523}
}

@article{maaten_visualizing_2008,
  title = {Visualizing {{Data}} Using T-{{SNE}}},
  volume = {9},
  issn = {ISSN 1533-7928},
  number = {Nov},
  journal = {Journal of Machine Learning Research},
  author = {van der Maaten, Laurens and Hinton, Geoffrey},
  year = {2008},
  pages = {2579-2605},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H9P7NW87/Maaten and Hinton - 2008 - Visualizing Data using t-SNE.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2EU5JRMJ/vandermaaten08a.html}
}

@article{belle_heredity_1987,
  title = {Heredity of Rover/Sitter: {{Alternative}} Foraging Strategies of {{{\emph{Drosophila}}}}{\emph{ Melanogaster}} Larvae},
  volume = {59},
  copyright = {1987 Nature Publishing Group},
  issn = {1365-2540},
  shorttitle = {Heredity of Rover/Sitter},
  doi = {10.1038/hdy.1987.98},
  abstract = {The heredity of rover/sitter, a naturally occurring polymorphism in the locomotory component of Drosophila melanogaster third instar larval foraging behaviour was analysed by comparing 16 reciprocal crosses made using isogenic rover and sitter parental strains. Results from both male and female data sets indicated that rover/sitter differences have an autosomal basis, with rover showing complete dominance over sitter. The Y-chromosome, permanent cytoplasmic factors, transient maternal factors and interactions between them made no significant contributions to rover/sitter inheritance. A minor X-chromosome effect was observed in the female data. Rover/sitter ratios in both males and females of the 16 reciprocal crosses were not significantly different from those expected assuming a one gene, complete dominance model of autosomal inheritance.},
  language = {en},
  number = {1},
  journal = {Heredity},
  author = {de Belle, J. Steven and Sokolowski, Marla B.},
  month = aug,
  year = {1987},
  pages = {73-83},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NZ438LLP/Belle and Sokolowski - 1987 - Heredity of roversitter Alternative foraging str.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XQ4P7M6G/hdy198798.html}
}

@article{sokolowski_foraging_1980,
  title = {Foraging Strategies Of{{Drosophila}} Melanogaster: {{A}} Chromosomal Analysis},
  volume = {10},
  issn = {0001-8244, 1573-3297},
  shorttitle = {Foraging Strategies Of{{Drosophila}} Melanogaster},
  doi = {10.1007/BF01067774},
  abstract = {Two larval foraging strategies inDrosophila melanogaster were identified, ``rover'' and ``sitter.'' ``Rovers'' traverse a large area while feeding whereas ``sitters'' cover a small area. The difference between ``rovers'' and ``sitters'' was analyzed genetically by chromosomal substitutions between isogenic stocks. Differences in larval locomotor behavior (``crawling behavior'') can be attributed to the second chromosome, the ``rover'' strategy being dominant over the ``sitter'' strategy. Differences in feeding rate (``shoveling behavior'') are affected additively by both the second and third chromosomes. Natural populations ofDrosophila larvae were sampled three times over a 2-month period; ``rovers'' and ``sitters'' were at constant frequencies in these populations. The two foraging strategies are discussed in the light of resource utilization in environments where food is distributed continuously or discontinuously.},
  language = {en},
  number = {3},
  journal = {Behavior Genetics},
  author = {Sokolowski, Marla B.},
  month = may,
  year = {1980},
  pages = {291-302},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RXB5E4II/Sokolowski - 1980 - Foraging strategies ofEmphasis Type=ItalicDros.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XGZZKG6X/BF01067774.html}
}

@article{osborne_natural_1997,
  title = {Natural {{Behavior Polymorphism Due}} to a {{cGMP}}-{{Dependent Protein Kinase}} of {{Drosophila}}},
  volume = {277},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.277.5327.834},
  abstract = {Naturally occuring polymorphisms in behavior are difficult to map genetically and thus are refractory to molecular characterization. An exception is the foraging gene (for), a gene that has two naturally occurring variants in Drosophila melanogaster food-search behavior: rover and sitter. Molecular mapping placed for mutations in the dg2 gene, which encodes a cyclic guanosine monophosphate (cGMP)\textendash{}dependent protein kinase (PKG). Rovers had higher PKG activity than sitters, and transgenic sitters expressing a dg2 complementary DNA from rover showed transformation of behavior to rover. Thus, PKG levels affected food-search behavior, and natural variation in PKG activity accounted for a behavioral polymorphism.},
  language = {en},
  number = {5327},
  journal = {Science},
  author = {Osborne, K. A. and Robichon, A. and Burgess, E. and Butland, S. and Shaw, R. A. and Coulthard, A. and Pereira, H. S. and Greenspan, R. J. and Sokolowski, M. B.},
  month = aug,
  year = {1997},
  pages = {834-836},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5A6N2XM5/Osborne et al. - 1997 - Natural Behavior Polymorphism Due to a cGMP-Depend.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P9M7RCV5/834.html},
  pmid = {9242616}
}

@article{greenspan_courtship_2000,
  title = {Courtship in {{Drosophila}}},
  volume = {34},
  doi = {10.1146/annurev.genet.34.1.205},
  abstract = {Courtship is a complex behavior in Drosophila that recruits a wide range of genes for its realization, including those concerning sex determination, ion channels, and circadian rhythms. Results from different experimental approaches\textemdash{}behavioral and genetic comparisons between species, analysis of mutants and mosaics, and identification of specific sensory stimuli\textemdash{}sketch the outlines of a set of pleiotropic genes acting on a distributed system in the brain to produce the species-specific sequence of responses and actions.},
  number = {1},
  journal = {Annual Review of Genetics},
  author = {Greenspan, Ralph J. and Ferveur, Jean-Fran{\c c}ois},
  year = {2000},
  pages = {205-232},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JZVZIQDF/Greenspan and Ferveur - 2000 - Courtship in Drosophila.pdf},
  pmid = {11092827}
}

@article{greenspan_understanding_1995,
  title = {Understanding the {{Genetic Construction}} of {{Behavior}}},
  volume = {272},
  issn = {0036-8733},
  number = {4},
  journal = {Scientific American},
  author = {Greenspan, Ralph J.},
  year = {1995},
  pages = {72-78},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JLVJED9G/Greenspan - 1995 - Understanding the Genetic Construction of Behavior.pdf}
}

@article{ferveur_genetic_1995,
  title = {Genetic Feminization of Brain Structures and Changed Sexual Orientation in Male {{Drosophila}}},
  volume = {267},
  copyright = {\textcopyright{} 1995},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.7846534},
  abstract = {The neural basis of sexual orientation in Drosophila was studied by the production of males with regionally feminized brains. Such flies express the female form of the sex determination gene transformer in a limited number of neurons under the control of GAL4 enhancer trap inserts. This method facilitated the creation of lines with a stable pattern of feminization. In tests of sexual preferences, flies that were feminized in a portion of the antennal lobes or in a subset of the corpora pedunculata (mushroom bodies) courted both males and females. These two brain structures, both of which are involved in olfactory processing, may function in the recognition of sex-specific pheromones, in the control of sex-specific behaviors, or both.},
  language = {en},
  number = {5199},
  journal = {Science},
  author = {Ferveur, J. F. and Stortkuhl, K. F. and Stocker, R. F. and Greenspan, R. J.},
  month = feb,
  year = {1995},
  pages = {902-905},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DXZZ7476/Ferveur et al. - 1995 - Genetic feminization of brain structures and chang.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/M86D8G6E/902.html},
  pmid = {7846534}
}

@article{villella_extended_1997,
  title = {Extended {{Reproductive Roles}} of the Fruitless {{Gene}} in {{Drosophila}} Melanogaster {{Revealed}} by {{Behavioral Analysis}} of {{New}} Fru {{Mutants}}},
  volume = {147},
  copyright = {Copyright \textcopyright{} 1997 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  abstract = {The fruitless mutants fru3 and fru4 were assessed for sex-specific reproductive-behavioral phenotypes and compared to the previously reported fru mutants. Among the several behavioral anomalies exhibited by males expressing these relatively new mutations, some are unique. fru3 and fru4 males are less stimulated to court females than and fru1 and fru2 . No courtship pulse song is generated by either fru3 or fru4 males, even though they perform brief wing extensions. fru3 and fru4 males display significantly less chaining behavior than do fru1 males. The hierarchy of courtship responses by fru males directed toward females vs. males, when presented with both sexes simultaneously, is that fru1 males perform vigorous and indiscriminant courtship directed at either sex; fru4 males are similarly indiscriminant, but courtship levels were lower than fru1 ; fru2 males prefer females; fru3 males show a courtship bias toward males. fru3 and fru4 males essentially lack the Muscle of Lawrence (MOL). On several reproductive criteria, there was no difference between fru-variant females and fru +. The increases in phenotypic severity measured for the new mutants are discussed in the context of the emerging molecular genetics of fru and with regard to the gene's position within the sex-determination pathway.},
  language = {en},
  number = {3},
  journal = {Genetics},
  author = {Villella, Adriana and Gailey, Donald A. and Berwald, Barbra and Ohshima, Saiyou and Barnes, Phillip T. and Hall, Jeffrey C.},
  month = nov,
  year = {1997},
  pages = {1107-1130},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/646SJ2RS/Villella et al. - 1997 - Extended Reproductive Roles of the fruitless Gene .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/N2VGB4DT/1107.html},
  pmid = {9383056}
}

@article{aigaki_ectopic_1991,
  title = {Ectopic Expression of Sex Peptide Alters Reproductive Behavior of Female {{D}}. Melanogaster},
  volume = {7},
  issn = {0896-6273},
  doi = {10.1016/0896-6273(91)90368-A},
  abstract = {Sex peptide, a secreted component of the male accessory glands, has been shown to induce behavioral and physiological changes in mated Drosophila. We transformed flies with a hybrid gene containing an hsp70 promoter fused to a cDNA encoding sex peptide. Heat-induced ectopic expression of the peptide in transgenic virgin females altered their reproductive behavior, in the presence of courting males, to that observed in mated females. This demonstrates that the peptide is functional as expected. Time course studies revealed that the behavioral change appeared earlier than the stimulated ovulation. We have also introduced a modified sex peptide gene that is driven by the yp1 enhancer, conferring expression in adult females, and shown that these flies refuse mating constitutively in the presence of courting males and lay unfertilized eggs at the rate of mated females.},
  number = {4},
  journal = {Neuron},
  author = {Aigaki, Toshiro and Fleischmann, Ir\'ene and Chen, Pei-Shen and Kubli, Eric},
  month = oct,
  year = {1991},
  pages = {557-563},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7945F79H/Aigaki et al. - 1991 - Ectopic expression of sex peptide alters reproduct.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E7HK6CQU/089662739190368A.html}
}

@article{gill_mutation_1963,
  title = {A Mutation Causing Abnormal Courtship and Mating Behavior in Males of {{Drosophila}} Melanogaster.},
  volume = {3},
  journal = {Am. Zool.},
  author = {GILL, K. S.},
  year = {1963},
  pages = {507},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/33EBIY5D/10005823296.html}
}

@article{hall_courtship_1978,
  title = {Courtship among Males Due to a Male-Sterile Mutation In{{Drosophila}} Melanogaster},
  volume = {8},
  issn = {0001-8244, 1573-3297},
  doi = {10.1007/BF01066870},
  abstract = {Drosophila melanogaster males carrying the fruitless mutation have been studied in their interactions with males and females. Mutant males\textemdash{}expressing a single recessive factor on the third chromosome\textemdash{}court mutant or wild-type males about 7 times more frequently than wild-type males court each other. Courtship by a fruitless male of a wild-type male is sustained and takes up an amount of time almost 100 times greater than the courtship interactions recorded between two normal males. While the mutant males do court females in a sustained manner, they attempt to copulate in less than 1\% of the trials, never do copulate, and are thus behaviorally sterile. Fruitless males, when interacting with other males, are deficient in their degree of rejection responses, but this defect is not sufficient to explain the abnormal male-male interactions. The mutants stimulate wild-type males to court them with a frequency which is about 5 times higher than that observed between normal males. Fruitless males can stimulate other males to court them even when the former have been etherized or cut into pieces.},
  language = {en},
  number = {2},
  journal = {Behavior Genetics},
  author = {Hall, Jeffrey C.},
  month = mar,
  year = {1978},
  pages = {125-141},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GT4AZ8PH/Hall - 1978 - Courtship among males due to a male-sterile mutati.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XAELSZ95/BF01066870.html}
}

@article{newman_sleep_2008,
  title = {Sleep Deprivation in the Pigeon Using the {{Disk}}-{{Over}}-{{Water}} Method},
  volume = {93},
  issn = {0031-9384},
  doi = {10.1016/j.physbeh.2007.07.012},
  abstract = {A well-defined sleep deprivation (SD) syndrome has been observed in studies with rats under conditions of severe sleep loss on the Disk-Over-Water (DOW) apparatus. Observation of the sleep deprivation syndrome across taxa would assist in the elucidation of the function of sleep. In the present study, the effects of total sleep deprivation were assessed in pigeons, a biologically relevant choice given that birds are the only non-mammalian taxon known to exhibit unequivocal rapid-eye-movement (REM) sleep and non-REM (NREM) sleep. Pigeons were deprived of sleep for 24\textendash{}29~days on the DOW by rotating the disk and requiring them to walk whenever sleep was initiated. Control (C) birds were also housed on the DOW and required to walk only when the deprived (D) birds were required to walk due to sleep initiation. NREM and REM sleep amounts were reduced from baseline during the deprivation for both D and C birds, although D birds obtained less NREM sleep than controls. Across the deprivation, D birds had their total sleep reduced by 54\% of baseline (scored in 4~s epochs), whereas previous studies in rats on the DOW reported total sleep reduction of as much as 91\% (scored in 30~s epochs). Pigeons proved to be more resistant to sleep deprivation by the DOW method and were much more difficult to deprive over the course of the experiment. Overall, the pigeons showed recovery sleep patterns similar to those seen in rats; i.e., rebound sleep during recovery was disproportionately composed of REM sleep. They did not, however, show the obvious external physical signs of the SD syndrome nor the large metabolic and thermoregulatory changes associated with the syndrome. The DOW method was thus effective in producing sleep loss in the pigeon, but was not as effective as it is in rats. The absence of the full SD syndrome is discussed in the context of limitations of the DOW apparatus and the possibility of species-specific adaptations that birds may possess to withstand or adapt to conditions of limited sleep opportunity.},
  number = {1},
  journal = {Physiology \& Behavior},
  author = {Newman, Sarah M. and Paletz, Elliott M. and Rattenborg, Niels C. and Obermeyer, William H. and Benca, Ruth M.},
  month = jan,
  year = {2008},
  keywords = {Recovery sleep,Sleep deprivation,Disk-Over-Water,Pigeons},
  pages = {50-58},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VNTVP7J4/Newman et al. - 2008 - Sleep deprivation in the pigeon using the Disk-Ove.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DF7TW3BY/S0031938407002934.html}
}

@article{bentivoglio_pioneering_1997,
  title = {The {{Pioneering Experimental Studies}} on {{Sleep Deprivation}}},
  volume = {20},
  issn = {0161-8105},
  doi = {10.1093/sleep/20.7.570},
  abstract = {Summary:.  The experimental studies on sleep deprivation were initiated by the Russian physician and scientist, Marie de Manac\'eine, who studied sleep-deprived p},
  language = {en},
  number = {7},
  journal = {Sleep},
  author = {Bentivoglio, Marina and {Grassi-Zucconi}, Gigliola},
  month = jul,
  year = {1997},
  pages = {570-576},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RI99KBY2/Bentivoglio and Grassi-Zucconi - 1997 - The Pioneering Experimental Studies on Sleep Depri.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PY8UNNZS/2732145.html}
}

@article{cook_neurophysiological_1974,
  title = {Neurophysiological Changes Associated with Paralysis Arising from Body Stress in the Cockroach, {{Periplaneta}} Americana},
  volume = {20},
  issn = {0022-1910},
  doi = {10.1016/0022-1910(74)90120-6},
  abstract = {Two hours after physical stress, Periplaneta americana could be separated into three behavioural categories: normal to hyperactive; torpid with ataxia; and paralysed. At 2 hr, 68 per cent were either torpid or paralysed, at 20 hr, 83 per cent were paralysed. Weight loss was a distinct physiological symptom of stress paralysis: The calculated mean loss was 9$\cdot$5 mg/hr for torpid insects and 12$\cdot$4 mg/hr for paralysed cockroaches, losses were four to six times larger than those occurring in starved cockroaches. However, the haemolymph osrnolarities of the three categories showed no appreciable differences. Only starved and paralysed cockroaches showed a noticeable reduction in muscle fibre membrane potentials of the flexor tibia\textemdash{}a mean value below 40 mV for starved insects and a mean value below 50 mV for paralysed insects. Both of these categories consistently showed a lower amplitude for junctional potentials, but paralysed cockroaches showed a much higher incidence of complete failure to neural stimulation. Most muscle fibres of completely paralysed insects lost their sensitivity to direct extracellular stimulation while the loss in sensitivity was less evident in starved cockroaches. Axonal conduction on the crural nerve was not changed by stress, and the spontaneous efferent activity of completely paralysed insects was similar to the pattern of activity for normal cockroaches. Stress seemed to alter the volume and content of the intermyofibral spaces of muscles.},
  number = {1},
  journal = {Journal of Insect Physiology},
  author = {Cook, Benjamin J. and Holt, Gerald G.},
  month = jan,
  year = {1974},
  pages = {21-40},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PG8I9Z6T/0022191074901206.html}
}

@article{karamanou_antoine-laurent_2013,
  title = {Antoine-{{Laurent}} de {{Lavoisier}} (1743-1794) and the Birth of Respiratory Physiology},
  volume = {68},
  issn = {1468-3296},
  doi = {10.1136/thoraxjnl-2013-203840},
  abstract = {BACKGROUND: For more than 1500 years, the status of knowledge concerning the physiology of human respiration has remained almost unchanged. In the 18th century, the French chemist Antoine-Laurent de Lavoisier conducted breathing experiments on human and animal respiration.
METHODS: The main bibliographic sources concerning Lavoisier's life and work on respiration have been investigated and analysed.
RESULTS: Using an ice-calorimeter, Lavoisier proved that combustion and respiration were one and the same. He also measured the oxygen consumed during respiration and concluded that the amount changes depending on human activities: exercise, eating, fasting, and sitting in a warm or cold room. Moreover, he found variations in pulse and breathing rate.
CONCLUSIONS: Lavoisier's work on respiration is of great historical significance as it represents the first effort to measure human respiratory gas metabolism contributing significantly to the development of respiratory physiology.},
  language = {eng},
  number = {10},
  journal = {Thorax},
  author = {Karamanou, Marianna and Androutsos, George},
  month = oct,
  year = {2013},
  keywords = {Physiology,Humans,Male,Middle Aged,Respiration,Oxygen Consumption,France,History; 18th Century,Lung Physiology,Not Applicable},
  pages = {978-979},
  pmid = {23723342}
}

@book{campbell_milton_2007,
  title = {Milton and the {{Manuscript}} of {{De Doctrina Christiana}}},
  isbn = {978-0-19-929649-1},
  abstract = {Debate about the authorship of the manuscript known to us as De Doctrina Christiana has bedevilled Milton studies over recent years. In this book four leading scholars give an account of the research project that demonstrated its Miltonic provenance beyond reasonable doubt. But the authors do much more besides, locating Milton's systematic theology in its broader European context, picking open the stages and processes of its composition, and analysing itsLatinity.},
  language = {en},
  publisher = {{OUP Oxford}},
  author = {Campbell, Gordon and Corns, Thomas N. and Hale, John K. and Tweedie, Fiona J.},
  month = nov,
  year = {2007},
  keywords = {Literary Criticism / European / English; Irish; Scottish; Welsh,Literary Criticism / Renaissance,Poetry / European / English; Irish; Scottish; Welsh,Religion / Christian Theology / General,Religion / Christian Theology / History}
}

@incollection{asaad_sleep_2015,
  title = {Sleep in {{Ancient Egypt}}},
  isbn = {978-1-4939-2088-4 978-1-4939-2089-1},
  abstract = {The ancient Egyptian civilization is one of the oldest and most fascinating in history. The contribution of ancient Egypt to the field of sleep medicine is quite evident. The concept of sleep had been linked to death, and the Egyptians were the first to describe similarity between dreams and awakenings. Dream interpretation and analysis had been extensively practiced for thousands of years before the modern psychoanalytic theories. Sleep was also used as a method of healing in special sleep temples, designed for dream incubation. Early mentioning of sleep disorders and their treatment could be found in the few survived papyri dealing with the ancient Egyptian medicine. The first hypnotic medication in history was prescribed by the Egyptians, who used poppy seeds (opium) to treat insomnia, headache, and as an anesthetic.},
  language = {en},
  booktitle = {Sleep {{Medicine}}},
  publisher = {{Springer, New York, NY}},
  author = {Asaad, Tarek},
  year = {2015},
  pages = {13-19},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HFI9P5CK/Asaad - 2015 - Sleep in Ancient Egypt.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LLBMKZGE/978-1-4939-2089-1_2.html},
  doi = {10.1007/978-1-4939-2089-1_2}
}

@book{milton_treatise_1825,
  title = {A {{Treatise}} on {{Christian Doctrine}}: {{Compiled}} from the {{Holy Scriptures Alone}}},
  shorttitle = {A {{Treatise}} on {{Christian Doctrine}}},
  language = {en},
  publisher = {{Cummings, Hilliard}},
  author = {Milton, John},
  year = {1825},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/H5EFVUFH/Milton - 1825 - A Treatise on Christian Doctrine Compiled from th.pdf}
}

@book{ragon_espace_2012,
  title = {{L'Espace de la mort: Essai sur l'architecture, la d\'ecoration et l'urbanisme fun\'eraires}},
  isbn = {978-2-226-22871-0},
  shorttitle = {{L'Espace de la mort}},
  abstract = {Si les derni\`eres ann\'ees ont vu para\^itre de nombreux livres sur l'histoire et la sociologie de la mort, il n'existait aucun ouvrage r\'ecent sur l'architecture, la d\'ecoration et l'urbanisme fun\'eraires. Michel Ragon s'est collet\'e avec ce th\`eme immense durant une dizaine d'ann\'ees.Dans L'Espace de la mort, il nous montre le tombeau comme une seconde maison et le cimeti\`ere comme un double id\'ealis\'e de la ville. Du cimeti\`ere antique bordant les grandes routes au cimeti\`ere m\'edi\'eval entourant l'\'eglise, Michel Ragon nous conduit aux cimeti\`eres naturistes du XVIIIe si\`ecle, aux cimeti\`eresmus\'ees du XIXe si\`ecle puis aux cimeti\`eres modernes s'identifiant de plus en plus aux \guillemotleft{} grands ensembles \guillemotright.Les chapitres les plus \'etonnants sont sans doute ceux qui ont trait au fonctionnalisme et \`a la mort : du bouleversement des cultes fun\'eraires pendant la R\'evolution fran{\c c}aise aux projets de d\'eportation des morts parisiens d'Haussmann, \`a l'\'economie radicale du terrain par l'incin\'eration, aux gares fun\'eraires et aux actuels h\^opitaux-mouroirs climatis\'es.Mais L'Espace de la mort est aussi, fatalement, une histoire des coutumes fun\'eraires de tous les temps et de tous les pays. Avec les implications sociologiques, politiques, m\'etaphysiques que cela entra\^ine. D\'ecors fun\`ebres, architectures de l'Au-del\`a (chez Dante, Swedenborg, etc.), supplices-spectacles sur la place du Martroi, po\'etique des tombeaux au XVIIIe si\`ecle; culte du coeur, des os et des reliques; embaumements et momifications; revenants (l \^ame errante, sans maison); mobilier fun\'eraire, monuments aux morts...Michel Ragon nous donne un livre surprenant, foisonnant mais rigoureux, qui est une v\'eritable encyclop\'edie de \guillemotleft{} l'espace de la mort \guillemotright.},
  language = {fr},
  publisher = {{Albin Michel}},
  author = {Ragon, Michel},
  month = nov,
  year = {2012},
  keywords = {Architecture / General,Art / General}
}

@book{shakespeare_hamlet_1905,
  title = {Hamlet},
  language = {en},
  publisher = {{Lippincott}},
  author = {Shakespeare, William},
  year = {1905},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/96DMMJU4/hamlet.pdf}
}

@book{gaiger_enigma_1996,
  title = {The {{Enigma}} of {{Health}}},
  author = {Gaiger, Jason and Walker, Nicholas},
  year = {1996}
}

@book{williams_sleep_2013,
  title = {Sleep and {{Society}}: {{Sociological Ventures}} into the {{Un}}(Known)},
  isbn = {978-1-134-25848-2},
  shorttitle = {Sleep and {{Society}}},
  abstract = {Exploring the sociological aspects of sleep and their links to current health debates, this unique text discusses why sleep has been so neglected in sociological literature and examines significant modern issues such as:  the 24-hour society  sleep and work  homelessness  dream analysis  the medicalization and commodification of sleep.  Written by a key international figure in medical sociology, this is the first sociological examination of sleep, making it important reading for academics and advanced students of medical sociology, health studies, and sociology, as well as for professionals and policy makers involved in the area.},
  language = {en},
  publisher = {{Routledge}},
  author = {Williams, Simon J.},
  month = apr,
  year = {2013},
  keywords = {Health \& Fitness / Sleep \& Sleep Disorders,Health \& Fitness / General,Social Science / Sociology / General}
}

@article{buchner_elementary_1976,
  title = {Elementary Movement Detectors in an Insect Visual System},
  volume = {24},
  issn = {0340-1200, 1432-0770},
  doi = {10.1007/BF00360648},
  abstract = {In the theoretical part of the present work the input-output relation for a multi-input system is developed into a functional power series. This is formally equivalent to a decomposition of the system into a sum of all possible combinations of 1-, 2-, 3-... input subsystems. The average response of the system to a uniformly moving patern is known to be a Fourier series with respect to spatial frequency. The coefficients of the series are linear combinations of the ``weights'' by which different subsystems contribute to the total reaction. If a system can be shown to have essential nonlinearities of no higher than second order it is possible to calculate, from a Fourier analysis of the average movement response, the ``weight'' by which the nonlinear interaction between any two input elements contributes to the total reaction. This interaction is termed ``elementary movement detector''. By the analysis presented here the arrangement of the elementary movement detectors may be determined for a two-dimensional array of input elements and the strength of their contributions to the total movement reaction may be calculated. Special experimental methods have been developed which allow one to apply this analysis to the visual system of the fruitfly Drosophila. The preliminary data presented show that the direction sensitive optomotor response of Drosophila can be attributed predominantly to the contributions from two ``elementary movement detectors'' which interconnect neighbouring visual elements. The detectors are oriented in the hexagonal array of the compound eye at +30$^\circ$ and at-30$^\circ$ with respect to the horizontal line of symmetry. A weak contribution from a detector between neighbouring elements along the horizontal line of symmetry is suggested by the present data. In the course of the analysis the contrast transfer properties of the compound eye are characterized.},
  language = {en},
  number = {2},
  journal = {Biological Cybernetics},
  author = {Buchner, E.},
  month = jun,
  year = {1976},
  pages = {85-101},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LJWNF7GK/Buchner - 1976 - Elementary movement detectors in an insect visual .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F2I4A8VL/BF00360648.html}
}

@article{akerstedt_sleep_2017,
  title = {Sleep Duration, Mortality and the Influence of Age},
  volume = {32},
  issn = {0393-2990, 1573-7284},
  doi = {10.1007/s10654-017-0297-0},
  abstract = {Prior work has shown that both short and long sleep predict mortality. However, sleep duration decreases with age and this may affect the relationship of sleep duration with mortality. The purpose of the present study was to assess whether the association between sleep duration and mortality varies with age. Prospective cohort study. 43,863 individuals (64\% women), recruited in September 1997 during the Swedish National March and followed through record-linkages for 13 years. Sleep duration was self-reported and measured using the Karolinska Sleep Questionnaire, and grouped into 4 categories: $\leq$5, 6, 7 (reference) and $\geq$8 h. Up to 2010 3548 deaths occurred. Multivariable Cox proportional hazards regression models with attained age as time scale were fitted to estimate mortality rate ratios. Among individuals $<$65 years, short ($\leq$5 h) and long ($\geq$8 h) sleep duration showed a significant relationship with mortality (HR 1.37, 95\% CI 1.09\textendash{}1.71, and HR 1.27, 95\% CI 1.08\textendash{}1.48). Among individuals 65 years or older, no relationships between sleep duration and mortality were observed. The effect of short and long sleep duration on mortality was highest among young individuals and decreased with increasing age. The results suggest that age plays an important role in the relationship between sleep duration and mortality.},
  language = {en},
  number = {10},
  journal = {European Journal of Epidemiology},
  author = {\AA{}kerstedt, Torbj\"orn and Ghilotti, Francesca and Grotta, Alessandra and Bellavia, Andrea and Lagerros, Ylva Trolle and Bellocco, Rino},
  month = oct,
  year = {2017},
  pages = {881-891},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MNS8HC92/Åkerstedt et al. - 2017 - Sleep duration, mortality and the influence of age.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5G24E77C/28856478.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/N6BSFUCH/s10654-017-0297-0.html}
}

@article{kurina_sleep_2013,
  title = {Sleep Duration and All-Cause Mortality: A Critical Review of Measurement and Associations},
  volume = {23},
  issn = {1047-2797, 1873-2585},
  shorttitle = {Sleep Duration and All-Cause Mortality},
  doi = {10.1016/j.annepidem.2013.03.015},
  language = {English},
  number = {6},
  journal = {Annals of Epidemiology},
  author = {Kurina, Lianne M. and McClintock, Martha K. and Chen, Jen-Hao and Waite, Linda J. and Thisted, Ronald A. and Lauderdale, Diane S.},
  month = jun,
  year = {2013},
  keywords = {Adult,Sleep,Polysomnography,Review,Mortality,Epidemiology,Actigraphy},
  pages = {361-370},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U92A3XAC/Kurina et al. - 2013 - Sleep duration and all-cause mortality a critical.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HB4MQVP3/fulltext.html}
}

@article{akerstedt_sleep_2018,
  title = {Sleep Duration and Mortality - {{Does}} Weekend Sleep Matter?},
  issn = {0962-1105},
  doi = {10.1111/jsr.12712},
  abstract = {Abstract: Previous studies have found a U-shaped relationship between mortality and (weekday) sleep duration. We here address the association of both...},
  language = {eng},
  journal = {Journal of sleep research},
  author = {\AA{}kerstedt, T. and Ghilotti, F. and Grotta, A. and Zhao, H. and Adami, H. O. and {Trolle-Lagerros}, Y. and Bellocco, R.},
  month = may,
  year = {2018},
  pages = {e12712-e12712},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6HPT8LKG/Åkerstedt et al. - Sleep duration and mortality – Does weekend sleep .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/89FPEL8H/29790200.html},
  pmid = {29790200}
}

@article{harbison_selection_2017,
  title = {Selection for Long and Short Sleep Duration in {{Drosophila}} Melanogaster Reveals the Complex Genetic Network Underlying Natural Variation in Sleep},
  volume = {13},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1007098},
  abstract = {Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways-EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.},
  language = {eng},
  number = {12},
  journal = {PLoS genetics},
  author = {Harbison, Susan T. and Serrano Negron, Yazmin L. and Hansen, Nancy F. and Lobell, Amanda S.},
  month = dec,
  year = {2017},
  keywords = {Female,Male,Time Factors,Animals,Sleep,Signal Transduction,Drosophila Proteins,Drosophila melanogaster,Mutation,Intracellular Signaling Peptides and Proteins,Mitogen-Activated Protein Kinases,Phenotype,Mutagenesis,Gene Frequency,Gene Regulatory Networks,Polymorphism; Genetic,Protein-Serine-Threonine Kinases,Receptor; Epidermal Growth Factor,Receptors; Invertebrate Peptide,Selection; Genetic,Whole Genome Sequencing,Wnt1 Protein},
  pages = {e1007098},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZV3PA8SV/Harbison et al. - 2017 - Selection for long and short sleep duration in Dro.pdf},
  pmid = {29240764},
  pmcid = {PMC5730107}
}

@article{schenkein_self_2006,
  title = {Self {{Management}} of {{Fatal Familial Insomnia}}. {{Part}} 1: {{What Is FFI}}?},
  volume = {8},
  issn = {1531-0132},
  shorttitle = {Self {{Management}} of {{Fatal Familial Insomnia}}. {{Part}} 1},
  abstract = {Context
Fatal familial insomnia (FFI) is a genetically transmitted neurodegenerative prion disease that incurs great suffering and has neither a treatment nor a cure. The clinical literature is devoid of management plans (other than palliative). Part 1 of this article reviews the sparse literature about FFI, including case descriptions. Part 2 of this paper describes the efforts of 1 patient (with the rapid-course Met-Met subtype) to contend with his devastating symptoms and improve the quality of his life.

Design
Interventions were based on the premise that some symptoms may be secondary to insomnia and not a direct result of the disease itself. Strategies (derived by trial and error) were devised to induce sleep and increase alertness. Interventions included vitamin supplementation, narcoleptics, anesthesia, stimulants, sensory deprivation, exercise, light entrainment, growth hormone, and electroconvulsive therapy.

Results
The patient exceeded the average survival time by nearly 1 year, and during this time (when most patients are totally incapacitated), he was able to write a book and to successfully drive hundreds of miles.

Conclusion
Methods to induce sleep may extend and enhance life during the disease, although they do not prevent death. It is hoped that some of his methods might inspire further clinical studies.},
  number = {3},
  journal = {Medscape General Medicine},
  author = {Schenkein, Joyce and Montagna, Pasquale},
  month = sep,
  year = {2006},
  pages = {65},
  pmid = {17406188},
  pmcid = {PMC1781306}
}

@article{libourel_sleep_,
  title = {Sleep in Amphibians and Reptiles: A Review and a Preliminary Analysis of Evolutionary Patterns},
  volume = {91},
  issn = {1469-185X},
  shorttitle = {Sleep in Amphibians and Reptiles},
  doi = {10.1111/brv.12197},
  abstract = {Despite the ubiquitous nature of sleep, its functions remain a mystery. In an attempt to address this, many researchers have studied behavioural and electrophysiological phenomena associated with sleep in a diversity of animals. The great majority of vertebrates and invertebrates display a phase of immobility that could be considered as a sort of sleep. Terrestrial mammals and birds, both homeotherms, show two sleep states with distinct behavioural and electrophysiological features. However, whether these features have evolved independently in each clade or were inherited from a common ancestor remains unknown. Unfortunately, amphibians and reptiles, key taxa in understanding the evolution of sleep given their position at the base of the tetrapod and amniote tree, respectively, remain poorly studied in the context of sleep. This review presents an overview of what is known about sleep in amphibians and reptiles and uses the existing data to provide a preliminary analysis of the evolution of behavioural and electrophysiological features of sleep in amphibians and reptiles. We also discuss the problems associated with analysing existing data, as well as the difficulty in inferring homologies of sleep stages based on limited data in the context of an essentially mammalian-centric definition of sleep. Finally, we highlight the importance of developing comparative approaches to sleep research that may benefit from the great diversity of species with different ecologies and morphologies in order to understand the evolution and functions of sleep.},
  language = {en},
  number = {3},
  journal = {Biological Reviews},
  author = {Libourel, Paul-Antoine and Herrel, Anthony},
  keywords = {evolution,REM sleep,sleep,active sleep,amphibian,paradoxical sleep,quiet sleep,reptile,slow-wave sleep},
  pages = {833-866},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GWIG7WCV/Libourel and Herrel - Sleep in amphibians and reptiles a review and a p.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9PLRZDEP/brv.html}
}

@article{mignot_why_2008,
  title = {Why {{We Sleep}}: {{The Temporal Organization}} of {{Recovery}}},
  volume = {6},
  issn = {1545-7885},
  shorttitle = {Why {{We Sleep}}},
  doi = {10.1371/journal.pbio.0060106},
  abstract = {Why we sleep seems like a simple question, yet it has baffled scientists for generations. Based on recent data, Emmanuel Mignot argues that the function of sleep is essentially a resilient form of cellular recovery, organized anatomically and temporally by natural evolution, that has taken on additional functions over time.},
  language = {en},
  number = {4},
  journal = {PLOS Biology},
  author = {Mignot, Emmanuel},
  month = apr,
  year = {2008},
  keywords = {Neurons,Sleep,Electroencephalography,Mammals,Homeostasis,Sleep deprivation,Chronobiology,Cholinergics},
  pages = {e106},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HGEFJ4GQ/Mignot - 2008 - Why We Sleep The Temporal Organization of Recover.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/P6DW7WGZ/article.html}
}

@article{mcmahon_respiratory_1988,
  title = {Respiratory {{Response}} to {{Periodic Emergence}} in {{Intertidal Molluscs}}},
  volume = {28},
  issn = {1540-7063},
  doi = {10.1093/icb/28.1.97},
  abstract = {Abstract.  SYNOPSIS: The ratio of aerial: aquatic V\textperiodcentered{}O2 (V\textperiodcentered{}o2(a): V\textperiodcentered{}o2(W))
 was computed for species of intertidal molluscs. This ratio was \&lt;1 for sub- and lo},
  language = {en},
  number = {1},
  journal = {Integrative and Comparative Biology},
  author = {Mcmahon, Robert F.},
  month = feb,
  year = {1988},
  pages = {97-114},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HRC5IU68/Mcmahon - 1988 - Respiratory Response to Periodic Emergence in Inte.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VIKFHPB6/169959.html}
}

@article{dahlhoff_physiological_2002,
  title = {Physiological {{Community Ecology}}: {{Variation}} in {{Metabolic Activity}} of {{Ecologically Important Rocky Intertidal Invertebrates Along Environmental Gradients}}},
  volume = {42},
  issn = {1540-7063},
  shorttitle = {Physiological {{Community Ecology}}},
  doi = {10.1093/icb/42.4.862},
  abstract = {Abstract.  Rocky intertidal invertebrates live in heterogeneous habitats characterized by steep gradients in wave activity, tidal flux, temperature, food qualit},
  language = {en},
  number = {4},
  journal = {Integrative and Comparative Biology},
  author = {Dahlhoff, Elizabeth P. and Stillman, Jonathon H. and Menge, Bruce A.},
  month = aug,
  year = {2002},
  pages = {862-871},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JFL9JR5P/Dahlhoff et al. - 2002 - Physiological Community Ecology Variation in Meta.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PKDHIFAJ/659148.html}
}

@article{connor_high-resolution_2011,
  title = {High-Resolution Analysis of Metabolic Cycles in the Intertidal Mussel {{Mytilus}} Californianus},
  volume = {302},
  issn = {0363-6119},
  doi = {10.1152/ajpregu.00453.2011},
  abstract = {Inhabitants of the marine rocky intertidal live in an environment that alternates between aquatic and terrestrial due to the rise and fall of the tide. The tide creates a cyclical availability of oxygen with animals having access to oxygenated water during episodes of submergence, while access to oxygen is restricted during aerial emergence. Here we performed liquid chromatography and gas chromatography-mass spectrometry enabled metabolomic profiling of gill samples isolated from the California ribbed mussel, Mytilus californianus, to investigate how metabolism is orchestrated in this variable environment. We created a simulated intertidal environment in which mussels were acclimated to alternating high and low tides of 6 h duration, and samples were taken every 2 h for 72 h to capture reproducible changes in metabolite levels over six high and six low tides. We quantified 169 named metabolites of which 24 metabolites cycled significantly with a 12-h period that was linked to the tidal cycle. These data confirmed the presence of alternating phases of fermentation and aerobic metabolism and highlight a role for carnitine-conjugated metabolites during the anaerobic phase of this cycle. Mussels at low tide accumulated eight carnitine-conjugated metabolites, arising from the degradation of fatty acids, branched-chain amino acids, and mitochondrial $\beta$-oxidation end products. The data also implicate sphingosine as a potential signaling molecule during aerial emergence. These findings identify new levels of metabolic control whose role in intertidal adaptation remains to be elucidated.},
  number = {1},
  journal = {American Journal of Physiology-Regulatory, Integrative and Comparative Physiology},
  author = {Connor, Kwasi M. and Gracey, Andrew Y.},
  month = oct,
  year = {2011},
  pages = {R103-R111},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V8YWYSWN/Connor and Gracey - 2011 - High-resolution analysis of metabolic cycles in th.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X2VJQ8F4/ajpregu.00453.html}
}

@article{herreid_metabolism_1977,
  title = {Metabolism of Land Snails ({{Otala}} Lactea) during Dormancy, Arousal, and Activity},
  volume = {56},
  issn = {0300-9629},
  language = {eng},
  number = {2},
  journal = {Comparative Biochemistry and Physiology. A, Comparative Physiology},
  author = {Herreid, C. F.},
  year = {1977},
  keywords = {Snails,Arousal,Animals,Species Specificity,Body Weight,Hibernation,Oxygen Consumption,Humidity},
  pages = {211-215},
  pmid = {11936}
}

@article{rahman_consequences_2012,
  title = {Consequences of {{Aestivation}} in the {{Giant African Land Snail Achatina}} Fulica {{Bowdich}} ({{Gastropoda}}: {{Achatinidae}})},
  volume = {65},
  issn = {0373-5893, 0974-6919},
  shorttitle = {Consequences of {{Aestivation}} in the {{Giant African Land Snail Achatina}} Fulica {{Bowdich}} ({{Gastropoda}}},
  doi = {10.1007/s12595-012-0041-4},
  abstract = {The consequences of aestivation in the giant African land snails Achatina fulica Bowdich occurring in Calcutta, India have been studied. It was noted that these snails under laboratory conditions, during aestivation had to face the hazards when the body weight was reduced by 50.33 \%, the heart rate was reduced by 85 \%, the oxygen consumption rate was reduced by 83 \%, the blood sugar level was reduced by 50 \%, the concentration on Ca++ and Mg++ ions was increased by 50 and 34 \%, respectively, and the amount of haemolypmh protein was increased by 33 \%, for survival. The effects were not much rigorous in aestivated snails in the field due to interruption of aestivation because of occasional shower. Though the snails, irrespective of size-groups had to face the consequences of aestivation, the extent of effect is very much influenced by the water content of the snail's body concerned.},
  language = {en},
  number = {2},
  journal = {Proceedings of the Zoological Society},
  author = {Rahman, M. S. and Raut, S. K.},
  month = dec,
  year = {2012},
  keywords = {Achatina fulica,Aestivation,Animal Anatomy / Morphology / Histology,Consequences,Conservation Biology/Ecology,India (Calcutta),Land snail,Life Sciences; general,Zoology,Animal Genetics and Genomics,Biodiversity},
  pages = {95-104},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L3UHD4YX/Rahman and Raut - 2012 - Consequences of Aestivation in the Giant African L.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7INESEP2/s12595-012-0041-4.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EDEP7Q4S/s12595-012-0041-4.html},
  note = {00001}
}

@article{romero_role_1992,
  title = {Role of the Visceral Nerve in Heart Rate Variations during Different Behavioral Patterns in {{Megalobulimus}} Sanctipauli (Mollusca, Gastropoda, Pulmonata)},
  volume = {103},
  issn = {0300-9629},
  doi = {10.1016/0300-9629(92)90246-M},
  abstract = {1.
1. The role of the visceral nerve in mediating the changes in heart rate associated with different behavioral patterns was investigated in Megalobulimus sanctipauli.
2.
2. The results of acute and chronic denervation experiments indicate that the visceral nerve has no excitatory or inhibitory tonic action on the heart of snails retracted into the shell, nor does it account for the increase in heart rate associated with the locomotion and feeding behaviors.
3.
3. These changes in heart rate are, probably, indirect effects of increased activity such as an increase in venous return.
4.
4. The visceral nerve is responsible for approximately 3/4 of the increase in heart rate associated with the first minute of extrusion.
5.
5. The small increase in heart rate observed in denervated animals is probably caused by an increase in venous return generated by muscle activity that forces the head and food out of the shell.},
  number = {1},
  journal = {Comparative Biochemistry and Physiology Part A: Physiology},
  author = {Romero, Sonia Maria Brazil and Hoffmann, Anette},
  month = sep,
  year = {1992},
  pages = {93-98},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NUE6VJ72/030096299290246M.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YJJKKIJ6/030096299290246M.html},
  note = {00004}
}

@article{wunnenberg_diurnal_1991,
  title = {Diurnal Rhythms of Heart Rate in the Snail {{Helix}} Pomatia {{L}}.},
  volume = {99},
  issn = {0300-9629},
  doi = {10.1016/0300-9629(91)90026-9},
  abstract = {1.
1. Under constant temperature and humidity conditions and a 12:12 light-dark cycle heart rates of Helix pomatia show a diurnal rhythm with minimum values at 12.00 hr and maximum values at 24.00 hr.
2.
2. Diurnal rhythm persists during estivation.
3.
3. In hibernating snails periodic fluctuations of heart rate occur which are not synchronized by the prevailing photoperiod.},
  number = {3},
  journal = {Comparative Biochemistry and Physiology Part A: Physiology},
  author = {W\"unnenberg, W.},
  year = {1991},
  pages = {415-417},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JYGPQXBQ/Wünnenberg - 1991 - Diurnal rhythms of heart rate in the snail Helix p.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6RHP4CFA/0300962991900269.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TP2ZLEY4/0300962991900269.html},
  note = {00006}
}

@article{milberg_does_1998,
  title = {Does Cold Stratification Level out Differences in Seed Germinability between Populations?},
  volume = {134},
  issn = {1385-0237, 1573-5052},
  doi = {10.1023/A:1009793119466},
  abstract = {Populations of seeds can vary greatly in their dormancy-breaking and germination characteristics. The purpose of this study was to determine if such dormancy differences are levelled out by cold stratification. Seeds of 33 annual weed species, each represented by three populations, were tested in light and darkness 7 weeks after harvest and after two stratification treatments: 18 weeks at 3 $^\circ$C in the laboratory and 19 weeks outdoors in soil during winter. Cold stratification removed population differences in some species, but in several species such differences became apparent only after stratification. This happened either because dormancy became stronger in weakly dormant seeds (winter annuals) or weaker in strongly dormant seeds (summer annuals). In several species, the light requirement for germination increased after stratification. These results clearly indicate that germination tests performed on fresh seeds from a single population may not adequately predict germination percentages in the field.},
  language = {en},
  number = {2},
  journal = {Plant Ecology},
  author = {Milberg, Per and Andersson, Lars},
  month = feb,
  year = {1998},
  pages = {225-234},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VV3C5KIL/Milberg and Andersson - 1998 - Does cold stratification level out differences in .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8WRTAX8F/A1009793119466.html}
}

@article{bentsink_seed_2008,
  title = {Seed {{Dormancy}} and {{Germination}}},
  volume = {6},
  issn = {1543-8120},
  doi = {10.1199/tab.0119},
  abstract = {Seed dormancy allows seeds to overcome periods that are unfavourable for seedling established and is therefore important for plant ecology and agriculture. Several processes are known to be involved in the induction of dormancy and in the switch from the dormant to the germinating state. The role of plant hormones, the different tissues and genes involved, including newly identified genes in dormancy and germination are described in this chapter, as well as the use transcriptome, proteome and metabolome analyses to study these mechanistically not well understood processes.},
  journal = {The Arabidopsis Book / American Society of Plant Biologists},
  author = {Bentsink, Le\'onie and Koornneef, Maarten},
  month = dec,
  year = {2008},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AFR4JU5F/Bentsink and Koornneef - 2008 - Seed Dormancy and Germination.pdf},
  pmid = {22303244},
  pmcid = {PMC3243337}
}

@article{heller_sleep_2004,
  title = {Sleep and {{Circadian Rhythms}} in {{Mammalian Torpor}}},
  volume = {66},
  doi = {10.1146/annurev.physiol.66.032102.115313},
  abstract = {Sleep and circadian rhythms are the primary determinants of arousal state, and torpor is the most extreme state change that occurs in mammals. The view that torpor is an evolutionary extension of sleep is supported by electrophysiological studies. However, comparisons of factors that influence the expression of sleep and torpor uncover significant differences. Deep sleep immediately following torpor suggests that torpor is functionally a period of sleep deprivation. Recent studies that employ post-torpor sleep deprivation, however, show that the post-torpor intense sleep is not homeostatically regulated, but might be a reflection of synaptic loss and replacement. The circadian system regulates sleep expression in euthermic mammals in such a way that would appear to preclude multiday bouts of torpor. Indeed, the circadian system is robust in animals that show shallow torpor, but its activity in hibernators is at least damped if not absent. There is good evidence from some species, however, that the circadian system plays important roles in the timing of bouts of torpor.},
  number = {1},
  journal = {Annual Review of Physiology},
  author = {Heller, H. Craig and Ruby, Norman F.},
  year = {2004},
  pages = {275-289},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7UX3WF74/Heller and Ruby - 2004 - Sleep and Circadian Rhythms in Mammalian Torpor.pdf},
  pmid = {14977404}
}

@incollection{adam_sleep_1980,
  title = {Sleep as a {{Restorative Process}} and a {{Theory}} to {{Explain Why}}},
  volume = {53},
  abstract = {Restoration or repair must, like growth, depend on protein synthesis. This chapter presents evidence to support this proposition from nearly 60 reports showing that rates of protein synthesis or of mitotic division are higher at the time of rest and sleep. In addition, the chapter presents a theory, based on fundamental principles, to explain why this should be so. Oscillations about a mean are inherent in any system subject to feedback control, and this is true of all living systems. In the simplest organisms there are oscillations between food-engulfing activity on the one hand and inactivity with assimilation on the other. There will also be oscillations between a state in which degradative chemical processes are accelerated and one in which synthetic processes are enhanced. It is proposed in this chapter that it is the differing energy demands of the activity/inactivity rhythm that chiefly determine the degradative/synthetic rhythm, such that the synthetic period inevitably coincides with the inactive or rest period, and that this is equally true in higher organisms in which a central nervous system ensures rest's integrity through positive unresponsiveness during sleep, and that such relationships, present throughout the animal kingdom, rely upon a fundamental metabolic co-coordinator, the ``cellular energy charge''. The energy charge is a measure of the available free energy in the form of adenosine triphosphate (ATP).},
  booktitle = {Progress in {{Brain Research}}},
  publisher = {{Elsevier}},
  author = {Adam, Kirstine},
  editor = {McConnell, P. S. and Boer, G. J. and Romijn, H. J. and Van De Poll, N. E. and Corner, M. A.},
  month = jan,
  year = {1980},
  pages = {289-305},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z8W8ASD3/S0079612308600709.html},
  doi = {10.1016/S0079-6123(08)60070-9}
}

@article{ramanathan_sleep_2002,
  title = {Sleep Deprivation Decreases Superoxide Dismutase Activity in Rat Hippocampus and Brainstem},
  volume = {13},
  issn = {0959-4965},
  abstract = {Sleep deprivation by the disk-over-water technique results in a predictable syndrome of physiological changes in rats. It has been proposed that reactive oxygen species (ROS) may be responsible for some of these effects. A variety of antioxidative enzymes such as superoxide dismutase (SOD) and glutathione peroxidase (GPx) help to regulate the level of ROS. In this study we investigated the effects of prolonged (5\textendash{}11 days) sleep deprivation on the activities of SOD and GPx as well as the metabolic activity of the mitochondria (using alamar blue) in several brain regions (cortex, hippocampus, hypothalamus, brainstem and cerebellum). We show that prolonged sleep deprivation significantly decreased Cu/Zn-SOD activity in the hippocampus and brainstem, suggesting an alteration in the metabolism of ROS resulting in oxidative stress.},
  language = {en-US},
  number = {11},
  journal = {NeuroReport},
  author = {Ramanathan, Lalini and Gulyani, Seema and Nienhuis, Robert and Siegel, Jerome M.},
  month = aug,
  year = {2002},
  pages = {1387},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CK24BP6A/Sleep_deprivation_decreases_superoxide_dismutase.7.html}
}

@incollection{marshall_brain-immune_2002,
  series = {Neurobiology of the Immune System},
  title = {Brain-{{Immune}} Interactions in Sleep},
  volume = {52},
  abstract = {This chapter discusses various levels of interactions between the brain and the immune system in sleep. Sleep-wake behavior and the architecture of sleep are influenced by microbial products and cytokines. On the other hand, sleep processes, and perhaps also specific sleep states, appear to promote the production and/or release of certain cytokines. The effects of immune factors such as endotoxin and cytokines on sleep reveal species specificity and usually strong dependence on parameters such as substance concentration, time relative to administration or infection with microbial products, and phase relation to sleep and/or the light-dark cycle. For instance, endotoxin increased SWS and EEG SWA in humans only at very low concentrations, whereas higher concentrations increased sleep stage 2 only, but not SWS. In animals, increases in NREM sleep and SWA were more consistent over a wide range of endotoxin doses. Also, administration of proinflammatory cytokines such as IL-6 and IFN-$\alpha$ in humans acutely disturbed sleep while in rats such cytokines enhanced SWS and sleep. Overall, the findings in humans indicate that strong nonspecific immune responses are acutely linked to an arousing effect. Although subjects feel subjectively tired, their sleep flattens. However, some observations indicate a delayed enhancing effect on sleep which could be related to the induction of secondary, perhaps T -cell-related factors. This would also fit with results in animals in which the Tcell-derived cytokine IL-2 enhanced sleep while cytokines with immunosuppressive functions like IL-4 and L-10 suppressed sleep. The most straightforward similarity in the cascade of events inducing sleep in both animals and humans is the enhancing effect of GHRH on SWS, and possibly the involvement of the pro-inflammatory cytokine systems of IL-1$\beta$ and TNF-$\alpha$. The precise mechanisms through which administered cytokines influence the central nervous system sleep processes are still unclear, although extensive research has identified the involvement of various molecular intermediates, neuropeptides, and neurotransmitters (cp. Fig. 5, Section III.B). Cytokines are not only released and found in peripheral blood mononuclear cells, but also in peripheral nerves and the brain (e.g., Hansen and Krueger, 1997; M\"arz et al., 1998). Cytokines are thereby able to influence the central nervous system sleep processes through different routes. In addition, neuronal and filial sources have been reported for various cytokines as well as for their soluble receptors (e.g., Kubota et al., 2001a). Links between the immune and endocrine systems represent a further important route through which cytokines influence sleep and, vice versa, sleep-associated processes, including variations in neurotransmitter and neuronal activity may influence cytokine levels. The ability of sleep to enhance the release and/or production of certain cytokines was also discussed. Most consistent results were found for IL-2, which may indicate a sleep-associated increase in activity of the specific immune system. Furthermore, in humans the primary response to antigens following viral challenge is enhanced by sleep. In animals results are less consistent and have focused on the secondary response. The sleep-associated modulation in cytokine levels may be mediated by endocrine parameters. Patterns of endocrine activity during sleep are probably essential for the enhancement of IL-2 and T-cell diurnal functions seen in humans: Whereas prolactin and GH release stimulate Thl-derived cytokines such as IL-2, cortisol which is decreased during the beginning of nocturnal sleep inhibits Th1-derived cytokines. The immunological function of neurotrophins, in particular NGF and BDNF, has received great interest. Effects of sleep and sleep deprivation on this cytokine family are particularly relevant in view of the effects these endogenous neurotrophins can have not only on specific immune functions and the development of immunological memories, but also on synaptic reorganization and neuronal memory formation (e.g., Rachal el al., 2001).},
  booktitle = {International {{Review}} of {{Neurobiology}}},
  publisher = {{Academic Press}},
  author = {Marshall, Lisa and Born, Jan},
  month = jan,
  year = {2002},
  pages = {93-131},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K6JYY8T6/S0074774202520079.html},
  doi = {10.1016/S0074-7742(02)52007-9}
}

@article{bryant_sick_2004,
  title = {Sick and Tired: Does Sleep Have a Vital Role in the Immune System?},
  volume = {4},
  copyright = {2004 Nature Publishing Group},
  issn = {1474-1741},
  shorttitle = {Sick and Tired},
  doi = {10.1038/nri1369},
  abstract = {It is a common belief that we are more susceptible to infections when deprived of sleep. Consistent with this, there is increasing evidence that sleep deprivation has detrimental effects on the immune response, indicating that sleep should be considered a vital part of the immune system and that there is a reciprocal relationship between sleep and immunity. This relationship is important because, over recent decades, there has been a documented decrease in the mean duration and quality of sleep in the population. The concept that lack of sleep might be compromising immunity in the population has far-reaching public-health implications for both individuals and society.},
  language = {en},
  number = {6},
  journal = {Nature Reviews Immunology},
  author = {Bryant, Penelope A. and Trinder, John and Curtis, Nigel},
  month = jun,
  year = {2004},
  pages = {457-467},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/456LQ87I/Bryant et al. - 2004 - Sick and tired does sleep have a vital role in th.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DFG67WN8/nri1369.html}
}

@article{toth_alteration_1988,
  title = {Alteration of Sleep in Rabbits by {{Staphylococcus}} Aureus Infection.},
  volume = {56},
  issn = {0019-9567, 1098-5522},
  abstract = {Abundant evidence suggests that sleep might be altered during infectious disease, although the relationship between sleep and infectious disease has never been examined systematically. To address this issue, we determined the effects of Staphylococcus aureus infection on rabbit sleep. Rabbits inoculated intravenously with S. aureus demonstrated the expected physiological changes consistent with a state of infectious disease (e.g., lymphopenia, neutrophilia, and fever), as well as time-dependent changes in sleep patterns. The sleep changes were characterized initially by increases in (i) the time spent in slow-wave sleep, (ii) the electroencephalographic slow-wave amplitudes during slow-wave sleep, and (iii) the duration of individual bouts of slow-wave sleep. At 20 to 36 h after inoculation, sleep responses fell to levels below corresponding control values for 6 to 12 h. At 6 to 10 h after inoculation, rapid-eye-movement sleep was suppressed and remained at low levels throughout the remainder of the 48-h recording period. These effects of bacterial infection on sleep were attenuated by antibiotic (cephalothin) therapy. Inoculation with killed bacteria produced similar changes in sleep and other physiological parameters, although significantly higher numbers of organisms were required to produce equivalent responses. We postulate that changes in sleep may represent an adaptive response of the host to infectious disease.},
  language = {en},
  number = {7},
  journal = {Infection and Immunity},
  author = {Toth, L. A. and Krueger, J. M.},
  month = jan,
  year = {1988},
  pages = {1785-1791},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BGVDJ8YK/Toth and Krueger - 1988 - Alteration of sleep in rabbits by Staphylococcus a.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2Y56IK57/1785.html},
  pmid = {3384477}
}

@article{lancel_lipopolysaccharide_1995,
  title = {Lipopolysaccharide Increases {{EEG}} Delta Activity within Non-{{REM}} Sleep and Disrupts Sleep Continuity in Rats},
  volume = {268},
  issn = {0363-6119},
  doi = {10.1152/ajpregu.1995.268.5.R1310},
  abstract = {Activation of the immune system by microorganisms or specific microbial constituents promotes non-rapid-eye-movement (REM) sleep (non-REMS). In this study, we assessed the effects of lipopolysaccharide (LPS) on sleep duration, electroencephalogram (EEG) power spectra, and brain temperature (Tbr) in rats. Twenty-four hour recordings were made before and after intraperitoneal injection of vehicle or 30 or 100 micrograms/kg LPS at lights on. During the first 12 h after administration of both doses of LPS, Tbr was elevated, REMS duration was reduced, and non-REMS duration was unchanged, whereas the non-REMS episodes were shortened. EEG activity within non-REMS from 0.5 to 7 Hz was enhanced during hours 3-12. During the second 12-h period, the number of non-REMS and REMS episodes and the total time in both states were increased. EEG activity within non-REMS was mainly reduced in the entire frequency range (0.5-25.5 Hz). The effects of LPS did not differ between the doses. The effects of LPS on EEG power spectra are similar to those observed after sleep deprivation, i.e., a physiological intensification of non-REMS, indicating that both manipulations may activate common sleep EEG regulatory mechanisms. However, the disruption of non-REMS continuity following LPS administration at light onset contrasts the changes induced by sleep deprivation and may reflect an effect of a systemic inflammatory response on sleep maintenance.},
  number = {5},
  journal = {American Journal of Physiology-Regulatory, Integrative and Comparative Physiology},
  author = {Lancel, M. and Cronlein, J. and {Muller-Preuss}, P. and Holsboer, F.},
  month = may,
  year = {1995},
  pages = {R1310-R1318},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6E7GJYIC/Lancel et al. - 1995 - Lipopolysaccharide increases EEG delta activity wi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T3JK8SHX/ajpregu.1995.268.5.html}
}

@article{spiegel_effect_2002,
  title = {Effect of {{Sleep Deprivation}} on {{Response}} to {{Immunizaton}}},
  volume = {288},
  issn = {0098-7484},
  doi = {10.1001/jama.288.12.1469},
  abstract = {To the Editor: Popular wisdom holds that not
getting enough sleep increases the propensity of catching a cold or other
ailments. In America, sleep duration has steadily declined from nearly 9 hours
in 1960 to less than 7 hours currently.1,2 Although
adverse effects of sleep deprivation on immune...},
  language = {en},
  number = {12},
  journal = {JAMA},
  author = {Spiegel, Karine and Sheridan, John F. and Cauter, Eve Van},
  month = sep,
  year = {2002},
  pages = {1471-1472},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VUWURJUT/Spiegel et al. - 2002 - Effect of Sleep Deprivation on Response to Immuniz.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GFAIICT4/1032061.html}
}

@article{renegar_progression_2000,
  title = {Progression of Influenza Viral Infection through the Murine Respiratory Tract: The Protective Role of Sleep Deprivation.},
  volume = {23},
  issn = {0161-8105},
  shorttitle = {Progression of Influenza Viral Infection through the Murine Respiratory Tract},
  abstract = {Abstract: Sleep deprivation is reported to have both beneficial and harmful effects upon host defenses. In the work reported herein, we address the effects...},
  language = {eng},
  number = {7},
  journal = {Sleep},
  author = {Renegar, K. B. and Crouse, D. and Floyd, R. A. and Krueger, J.},
  month = nov,
  year = {2000},
  pages = {859-863},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9YJJL5ED/11083594.html},
  pmid = {11083594}
}

@article{ehlen_bmal1_2017,
  title = {Bmal1 Function in Skeletal Muscle Regulates Sleep},
  volume = {6},
  copyright = {This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.},
  issn = {2050-084X},
  doi = {10.7554/eLife.26557},
  abstract = {Expression of transcription factor BMAL1 in skeletal muscle reduces the recovery response to sleep loss and is both necessary and sufficient to regulate total sleep amount.},
  language = {en},
  journal = {eLife},
  author = {Ehlen, J. Christopher and Brager, Allison J. and Baggs, Julie and Pinckney, Lennisha and Gray, Cloe L. and DeBruyne, Jason P. and Esser, Karyn A. and Takahashi, Joseph S. and Paul, Ketema N.},
  month = jul,
  year = {2017},
  pages = {e26557},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B8HKX7Z5/Ehlen et al. - 2017 - Bmal1 function in skeletal muscle regulates sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/75U592AU/26557.html}
}

@book{hesiod_theogony_2006,
  title = {Theogony: {{And}}, {{Works}} and {{Days}}},
  isbn = {978-0-472-06932-3},
  shorttitle = {Theogony},
  abstract = {Written in the late eighth century BC by Hesiod, one of the oldest known of Greek poets, Theogony and Works and Days represent the earliest account of the origin of the Greek gods, and an invaluable compendium of advice for leading a moral life, both offering unique insights into archaic Greek society. There are a number of modern translations of Hesiod available, rendered in serviceable English, but until now no one has created a work of literature equal to the original. This translation is the result of a unique collaboration between a classicist and a poet, capturing in English fourteeners the works' true poetic flavor while remaining faithful to the Greek text and the archaic world in which it was composed.This translation contains a general introduction, a translator's introduction, notes, and a glossary.~ It will be of interest to general readers, students of and specialists in classical literature, and lovers of poetry.~"This Schlegel-Weinfield translation of Hesiod is superbly crafted: compelling, unforgettable poetry to be read aloud with delight and gratitude."\textemdash{}Allen Mandelbaum, Endowed Kenan Professor of Humanities, Wake Forest University~"This exciting and unique collaboration between a classical philologist and a poet will not just provide insight into archaic Greek society, but also offer something new: the opportunity to experience the richness of Hesiod's style, language, and modes of thought with remarkable fidelity to the ancient Greek.~ Weinfield and Schlegel make Hesiod sing."\textemdash{}Carole Newlands, Classics Department, University of Wisconsin~"Schlegel and Weinfield have produced one of the most remarkable of a current resurgence of translations from the classics, allowing the modern world to hear a poet who may have known Homer. Hesiod's song makes us understand why the Greeks thought a poet could draw dolphins through the seas or raise the walls of Thebes. Weinfield translates by ear and transfers what he hears to the page, resonant fourteeners, a worthy echo of the past."\textemdash{}Charles Stanley Ross, Professor, Department of English, and Director, Comparative Literature, PurdueUniversity~Catherine Schlegel is Associate Professor of Classics, University of Notre Dame.~ Henry Weinfield is Professor and Chair of Liberal Studies, University of Notre Dame, and translator of The Collected Poems of Stephane Mallarme.},
  language = {en},
  publisher = {{University of Michigan Press}},
  author = {Hesiod},
  year = {2006},
  keywords = {Poetry / Ancient \& Classical}
}

@article{dilley_behavioral_2018,
  title = {Behavioral and {{Genetic Features}} of {{Sleep Ontogeny}} in {{Drosophila}}.},
  issn = {0161-8105},
  doi = {10.1093/sleep/zsy086},
  abstract = {Abstract: The fruit fly Drosophila melanogaster, like most organisms, exhibits increased sleep amount and depth in young compared to mature animals. While...},
  language = {eng},
  journal = {Sleep},
  author = {Dilley, L. C. and Vigderman, A. and Williams, C. E. and Kayser, M. S.},
  month = may,
  year = {2018},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WLZMW2LG/Dilley et al. - 2018 - Behavioral and genetic features of sleep ontogeny .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZX6THKAU/29746663.html},
  pmid = {29746663}
}

@article{cavanaugh_drosophila_2016,
  title = {The {{Drosophila Circadian Clock Gates Sleep}} through {{Time}}-of-{{Day Dependent Modulation}} of {{Sleep}}-{{Promoting Neurons}}},
  volume = {39},
  issn = {0161-8105},
  doi = {10.5665/sleep.5442},
  abstract = {AbstractStudy Objectives:.  Sleep is under the control of homeostatic and circadian processes, which interact to determine sleep timing and duration, but the me},
  language = {en},
  number = {2},
  journal = {Sleep},
  author = {Cavanaugh, Daniel J. and Vigderman, Abigail S. and Dean, Terry and Garbe, David S. and Sehgal, Amita},
  month = feb,
  year = {2016},
  pages = {345-356},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X9J55ANN/Cavanaugh et al. - 2016 - The Drosophila Circadian Clock Gates Sleep through.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8PSY5ZY6/2418002.html}
}

@article{ly_neurobiological_2018,
  title = {The Neurobiological Basis of Sleep: {{Insights}} from {{Drosophila}}},
  volume = {87},
  issn = {0149-7634},
  shorttitle = {The Neurobiological Basis of Sleep},
  doi = {10.1016/j.neubiorev.2018.01.015},
  abstract = {Sleep is a biological enigma that has raised numerous questions about the inner workings of the brain. The fundamental question of why our nervous systems have evolved to require sleep remains a topic of ongoing scientific deliberation. This question is largely being addressed by research using animal models of sleep. Drosophila melanogaster, also known as the common fruit fly, exhibits a sleep state that shares common features with many other species. Drosophila sleep studies have unearthed an immense wealth of knowledge about the neuroscience of sleep. Given the breadth of findings published on Drosophila sleep, it is important to consider how all of this information might come together to generate a more holistic understanding of sleep. This review provides a comprehensive summary of the neurobiology of Drosophila sleep and explores the broader insights and implications of how sleep is regulated across species and why it is necessary for the brain.},
  journal = {Neuroscience \& Biobehavioral Reviews},
  author = {Ly, Sarah and Pack, Allan I. and Naidoo, Nirinjini},
  month = apr,
  year = {2018},
  keywords = {Sleep,Drosophila melanogaster,Neurobiology,Sleep regulation},
  pages = {67-86},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L6763F26/Ly et al. - 2018 - The neurobiological basis of sleep Insights from .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XN6RSW74/Ly et al. - 2018 - The neurobiological basis of sleep Insights from .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3ZXF3WP7/S0149763417308898.html;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/948GU8RJ/S0149763417308898.html}
}

@article{rodrigues_short-term_2018,
  title = {Short-Term Sleep Deprivation with Exposure to Nocturnal Light Alters Mitochondrial Bioenergetics in {{Drosophila}}},
  volume = {120},
  issn = {0891-5849},
  doi = {10.1016/j.freeradbiomed.2018.04.549},
  abstract = {Many studies have shown the effects of sleep deprivation in several aspects of health and disease. However, little is known about how mitochondrial bioenergetics function is affected under this condition. To clarify this, we developed a simple model of short-term sleep deprivation, in which fruit-flies were submitted to a nocturnal light condition and then mitochondrial parameters were assessed by high resolution respirometry (HRR). Exposure of flies to constant light was able to alter sleep patterns, causing locomotor deficits, increasing ROS production and lipid peroxidation, affecting mitochondrial activity, antioxidant defense enzymes and caspase activity. HRR analysis showed that sleep deprivation affected mitochondrial bioenergetics capacity, decreasing respiration at oxidative phosphorylation (OXPHOS) and electron transport system (ETS). In addition, the expression of genes involved in the response to oxidative stress and apoptosis were increased. Thus, our results suggest a connection between sleep deprivation and oxidative stress, pointing to mitochondria as a possible target of this relationship.},
  journal = {Free Radical Biology and Medicine},
  author = {Rodrigues, Nathane Rosa and Macedo, Giulianna Echeverria and Martins, Illana Kemmerich and Gomes, Karen Kich and {de Carvalho}, N\'elson Rodrigues and Posser, Tha\'is and Franco, Jeferson Luis},
  month = may,
  year = {2018},
  keywords = {Nrf2,Sleep disorders,Akt1,Antioxidant enzymes,Hsp83,Oxidative stress,p38β,Pale,Pp2a},
  pages = {395-406},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DU3XM8VF/Rodrigues et al. - 2018 - Short-term sleep deprivation with exposure to noct.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HH9SL2K2/S0891584918307263.html}
}

@article{kayser_sleep_2015,
  title = {Sleep Deprivation Suppresses Aggression in {{Drosophila}}},
  volume = {4},
  copyright = {\textcopyright{} 2015 Kayser et al.. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  doi = {10.7554/eLife.07643},
  abstract = {A single night of sleep deprivation suppresses fighting behaviors in male fruit flies, with consequent impairments in reproductive fitness.},
  language = {en},
  journal = {eLife},
  author = {Kayser, Matthew S. and Mainwaring, Benjamin and Yue, Zhifeng and Sehgal, Amita},
  month = jul,
  year = {2015},
  pages = {e07643},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KD54MMKH/Kayser et al. - 2015 - Sleep deprivation suppresses aggression in Drosoph.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GE27TMAT/07643.html}
}

@article{bi_wolbachia_2018,
  title = {Wolbachia Affects Sleep Behavior in {{Drosophila}} Melanogaster},
  volume = {107},
  issn = {0022-1910},
  doi = {10.1016/j.jinsphys.2018.02.011},
  abstract = {Wolbachia are endosymbiotic bacteria present in a wide range of insects. Although their dramatic effects on host reproductive biology have been well studied, the effects of Wolbachia on sleep behavior of insect hosts are not well documented. In this study, we report that Wolbachia infection caused an increase of total sleep time in both male and female Drosophila melanogaster. The increase in sleep was associated with an increase in the number of nighttime sleep bouts or episodes, but not in sleep bout duration. Correspondingly, Wolbachia infection also reduced the arousal threshold of their fly hosts. However, neither circadian rhythm nor sleep rebound following deprivation was influenced by Wolbachia infection. Transcriptional analysis of the dopamine biosynthesis pathway revealed that two essential genes, Pale and Ddc, were significantly upregulated in Wolbachia-infected flies. Together, these results indicate that Wolbachia mediates the expression of dopamine related genes, and decreases the sleep quality of their insect hosts. Our findings help better understand the host-endosymbiont interactions and in particular the Wolbachia's impact on behaviors, and thus on ecology and evolution in insect hosts.},
  journal = {Journal of Insect Physiology},
  author = {Bi, Jie and Sehgal, Amita and Williams, Julie A. and Wang, Yu-Feng},
  month = may,
  year = {2018},
  keywords = {Arousal,Sleep,Dopamine},
  pages = {81-88},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KXAWYYW2/Bi et al. - 2018 - Wolbachia affects sleep behavior in Drosophila mel.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MVGT9NL5/S0022191017303918.html}
}

@article{selkrig_drosophila_2018,
  title = {The {{Drosophila}} Microbiome Has a Limited Influence on Sleep, Activity, and Courtship Behaviors},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
  doi = {10.1101/287045},
  abstract = {In animals, commensal microbes modulate various physiological functions, including behavior. While microbiota exposure is required for normal behavior in mammals, it is not known how widely this dependency is present in other animal species. We proposed the hypothesis that the microbiome has a major influence on the behavior of the vinegar fly (Drosophila melanogaster), a major invertebrate model organism. Several assays were used to test the contribution of the microbiome on some well-characterized behaviors: defensive behavior, sleep, locomotion, and courtship in microbe-bearing, control flies and two generations of germ-free animals. None of the behaviors were largely influenced by the absence of a microbiome, and the small or moderate effects were not generalizable between replicates and/or generations. These results refute the hypothesis, indicating that the Drosophila microbiome does not have a major influence over several behaviors fundamental to the animal's survival and reproduction. The impact of commensal microbes on animal behaviour may not be broadly conserved.},
  language = {en},
  journal = {bioRxiv},
  author = {Selkrig, Joel and Mohammad, Farhan and Ng, Soon Hwee and Chua, Jia Yi and Tumkaya, Tayfun and Ho, Joses and Chiang, Yin Ning and Rieger, Dirk and Pettersson, Sven and {Helfrich-Foerster}, Charlotte and Yew, Joanne and {Claridge-Chang}, Adam},
  month = mar,
  year = {2018},
  pages = {287045},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BIA85JUV/Selkrig et al. - 2018 - The Drosophila microbiome has a limited influence .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V2CMR8YE/287045.html}
}

@article{hughes_evolutionary_2004,
  title = {Evolutionary and Mechanistic Theories of Aging},
  volume = {50},
  issn = {0066-4170},
  doi = {10.1146/annurev.ento.50.071803.130409},
  abstract = {Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?},
  number = {1},
  journal = {Annual Review of Entomology},
  author = {Hughes, Kimberly A. and Reynolds, Rose M.},
  month = sep,
  year = {2004},
  pages = {421-445},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LDJJA2IW/Hughes and Reynolds - 2004 - Evolutionary and mechanistic theories of aging.pdf}
}

@article{austad_comparative_2009,
  title = {Comparative {{Biology}} of {{Aging}}},
  volume = {64A},
  issn = {1079-5006},
  doi = {10.1093/gerona/gln060},
  abstract = {Abstract.  Virtually, all research on basic mechanisms of aging has used species that are short lived and thus demonstrably unsuccessful at combating basic agin},
  language = {en},
  number = {2},
  journal = {The Journals of Gerontology: Series A},
  author = {Austad, Steven N.},
  month = feb,
  year = {2009},
  pages = {199-201},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PIF4PP42/Austad - 2009 - Comparative Biology of Aging.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DPQN3KTL/664850.html}
}

@article{machado_identification_nodate,
  title = {Identification of Octopaminergic Neurons That Modulate Sleep Suppression by Male Sex Drive},
  volume = {6},
  issn = {2050-084X},
  doi = {10.7554/eLife.23130},
  abstract = {Molecular and circuit mechanisms for balancing competing drives are not well understood. While circadian and homeostatic mechanisms generally ensure sufficient sleep at night, other pressing needs can overcome sleep drive. Here, we demonstrate that the balance between sleep and sex drives determines whether male flies sleep or court, and identify a subset of octopaminergic neurons (MS1) that regulate sleep specifically in males. When MS1 neurons are activated, isolated males sleep less, and when MS1 neurons are silenced, the normal male sleep suppression in female presence is attenuated and mating behavior is impaired. MS1 neurons do not express the sexually dimorphic FRUITLESS (FRU) transcription factor, but form male-specific contacts with FRU-expressing neurons; calcium imaging experiments reveal bidirectional functional connectivity between MS1 and FRU neurons. We propose octopaminergic MS1 neurons interact with the FRU network to mediate sleep suppression by male sex drive., DOI:
http://dx.doi.org/10.7554/eLife.23130.001, Most people sleep for around seven or eight hours at night, but if there is something important or interesting to do \textendash{} for example, taking care of a baby, finishing a task before a deadline, or watching an entertaining movie \textendash{} we may stay up late. In other words, sleep is regulated by motivational states. The drive to sleep accumulates during wakefulness and decreases during sleep. Thus sleep and other motivational drives compete to decide whether we sleep or engage in other important or interesting activities., The idea that sleep and sex drives might compete with each other is intuitive, but had not been studied experimentally. Machado, Afonso et al. have now studied how this competition determines the behavior of male fruit flies. The presence of a female fly usually keeps a male fly awake at night. However, a male that has recently mated several times (and has low sex drive) or one that was sleep deprived (and has high sleep drive) ignores the female and goes to sleep., Further investigation revealed a small number of previously unknown neurons (termed MS1) are required for sexual arousal to overcome the male's desire to sleep. These neurons do not belong to a circuit that is known to be important for male sexual behavior, but they do communicate with that circuit using a neurotransmitter called octopamine. This communication suppresses sleep and promotes courtship., The next steps will be to identify the specific neurons that communicate directly with the MS1 neurons and to determine whether MS1 neurons have a direct role in regulating sex drive. Investigating these details will help us to understand more generally how competing drives influence behavioral choices., DOI:
http://dx.doi.org/10.7554/eLife.23130.002},
  journal = {eLife},
  author = {Machado, Daniel R and Afonso, Dinis JS and Kenny, Alexandra R and {\"Ozt\"urk-{\c C}olak}, Arzu and Moscato, Emilia H and Mainwaring, Benjamin and Kayser, Matthew and Koh, Kyunghee},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/A5FX7JBV/Machado et al. - Identification of octopaminergic neurons that modu.pdf},
  pmid = {28510528},
  pmcid = {PMC5433852}
}

@article{gillott_male_2003,
  title = {Male {{Accessory Gland Secretions}}: {{Modulators}} of {{Female Reproductive Physiology}} and {{Behavior}}},
  volume = {48},
  issn = {0066-4170},
  shorttitle = {Male {{Accessory Gland Secretions}}},
  doi = {10.1146/annurev.ento.48.091801.112657},
  abstract = {Secretions of male accessory glands contain a variety of bioactive molecules. When transferred during mating, these molecules exert wide-ranging effects on female reproductive activity and they improve the male's chances of siring a significant proportion of the female's offspring. The accessory gland secretions may affect virtually all aspects of the female's reproductive activity. The secretions may render her unwilling or unable to remate for some time, facilitating sperm storage and ensuring that any eggs laid will be fertilized by that male's sperm. They may stimulate an increase in the number and rate of development of eggs and modulate ovulation and/or oviposition. Antimicrobial agents in the secretions ensure that the female reproductive tract is a hospitable environment during sperm transfer. In a few species the secretions include noxious chemicals. These are sequestered by developing eggs that are thereby protected from predators and pathogens when laid.},
  number = {1},
  journal = {Annual Review of Entomology},
  author = {Gillott, Cedric},
  month = jan,
  year = {2003},
  pages = {163-184},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NF8UAGCB/Gillott - 2003 - Male Accessory Gland Secretions Modulators of Fem.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EWS8HY8T/annurev.ento.48.091801.html}
}

@article{kapelnikov_mating_2008,
  title = {Mating Induces an Immune Response and Developmental Switch in the {{Drosophila}} Oviduct},
  volume = {105},
  copyright = {\textcopyright{} 2008 by The National Academy of Sciences of the USA},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0710997105},
  abstract = {Mating triggers physiological and behavioral changes in females. To understand how females effect these changes, we used microarray, proteomic, and comparative analyses to characterize gene expression in oviducts of mated and unmated Drosophila females. The transition from non-egg laying to egg laying elicits a distinct molecular profile in the oviduct. Immune-related transcripts and proteins involved in muscle and polarized epithelial function increase, whereas cell growth and differentiation-related genes are down-regulated. Our combined results indicate that mating triggers molecular and biochemical changes that mediate progression from a ``poised'' state to a mature, functional stage.},
  language = {en},
  number = {37},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Kapelnikov, Anat and Zelinger, Einat and Gottlieb, Yuval and Rhrissorrakrai, Kahn and Gunsalus, Kristin C. and Heifetz, Yael},
  month = sep,
  year = {2008},
  keywords = {network,antimicrobial peptides,reproduction},
  pages = {13912-13917},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U3Q5BJ2F/Kapelnikov et al. - 2008 - Mating induces an immune response and developmenta.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/89HVRHB5/13912.html},
  pmid = {18725632}
}

@article{mcgraw_genes_2004,
  title = {Genes {{Regulated}} by {{Mating}}, {{Sperm}}, or {{Seminal Proteins}} in {{Mated Female Drosophila}} Melanogaster},
  volume = {14},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2004.08.028},
  abstract = {In Drosophila melanogaster, sperm and accessory gland proteins (``Acps,'' a major component of seminal fluid) transferred by males during mating trigger many physiological and behavioral changes in females (reviewed in [1\textendash{}5]). Determining the genetic changes triggered in females by male-derived molecules and cells is a crucial first step in understanding female responses to mating and the female's role in postcopulatory processes such as sperm competition, cryptic female choice, and sexually antagonistic coevolution. We used oligonucleotide microarrays to compare gene expression in D. melanogaster females that were either virgin, mated to normal males, mated to males lacking sperm, or mated to males lacking both sperm and Acps. Expression of up to 1783 genes changed as a result of mating, most less than 2-fold. Of these, 549 genes were regulated by the receipt of sperm and 160 as a result of Acps that females received from their mates. The remaining genes whose expression levels changed were modulated by nonsperm/non-Acp aspects of mating. The mating-dependent genes that we have identified contribute to many biological processes including metabolism, immune defense, and protein modification.},
  number = {16},
  journal = {Current Biology},
  author = {McGraw, Lisa A. and Gibson, Greg and Clark, Andrew G. and Wolfner, Mariana F.},
  month = aug,
  year = {2004},
  pages = {1509-1514},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LLXEWYWW/McGraw et al. - 2004 - Genes Regulated by Mating, Sperm, or Seminal Prote.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/47AA6MZ8/S0960982204006098.html}
}

@article{innocenti_immunogenic_nodate,
  title = {Immunogenic Males: A Genome-Wide Analysis of Reproduction and the Cost of Mating in {{Drosophila}} Melanogaster Females},
  volume = {22},
  issn = {1420-9101},
  shorttitle = {Immunogenic Males},
  doi = {10.1111/j.1420-9101.2009.01708.x},
  abstract = {In Drosophila melanogaster, mating radically transforms female physiology and behaviour. Post-mating responses include an increase in the oviposition rate, a reduction in female receptivity and an activation of the immune system. The fitness consequences of mating are similarly dramatic \textendash{} females must mate once in order to produce fertile eggs, but additional matings have a clear negative effect. Previously, microarrays have been used to examine gene expression of females differing in their reproductive status with the aim of identifying genes influenced by mating. However, as only virgin and single mated females were compared, transcriptional changes associated with reproduction (under natural selection) and male-induced effects (possibly under sexually antagonistic selection) cannot be disentangled. We partitioned these fundamentally different effects by instead examining the expression profiles of virgin, single mated and double mated females. We found substantial effects relating to reproduction and further effects that are only attributable to mating itself. Immune response genes dominate this male-induced effect indicating that the cost of mating may be due partly to this system's activation. We propose that both sexually antagonistic and natural selection have been important in the evolution of the innate immunity genes, thereby contributing to the sexual dimorphism and rapid evolution at these loci.},
  language = {en},
  number = {5},
  journal = {Journal of Evolutionary Biology},
  author = {Innocenti, P. and Morrow, E. H.},
  keywords = {Drosophila melanogaster,BioConductor,cost of mating,innate immunity,microarrays,post-mating female response,sexual conflict,sperm competition},
  pages = {964-973},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7LHHEUBL/Innocenti and Morrow - Immunogenic males a genome-wide analysis of repro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PJ3WVP3L/j.1420-9101.2009.01708.html}
}

@article{ribeiro_sex_2010,
  title = {Sex {{Peptide Receptor}} and {{Neuronal TOR}}/{{S6K Signaling Modulate Nutrient Balancing}} in {{Drosophila}}},
  volume = {20},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2010.03.061},
  abstract = {Summary
Animals often decide between alternative actions according to their current needs, and hence the value they assign to each of the competing options [1\textendash{}4]. This process is of special relevance during nutrient balancing, in which animals choose between different food sources according to their current nutritional state [5\textendash{}7]. How such value-based decision making is implemented at the molecular and neuronal level in the brain is not well understood. Here we describe Drosophila melanogaster food choice as a genetically tractable model to study value-based decision making in the context of nutrient balancing. When faced with a choice between yeast and an alternative food source, flies deprived of protein prefer the yeast. We show here that mating status is a critical modulator of this decision-making process in females and that it relies on the action of the sex peptide receptor in internal ppk+ sensory neurons. Neuronal TOR/S6K function is another critical input to this decision, possibly signaling the fly's current nutritional status. We propose that the brain uses these internal states to assign value to external sensory information from potential food sources, thereby guiding food choice and ensuring nutrient homeostasis.},
  number = {11},
  journal = {Current Biology},
  author = {Ribeiro, Carlos and Dickson, Barry J.},
  month = jun,
  year = {2010},
  keywords = {MOLNEURO},
  pages = {1000-1005},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ITQLYPSL/Ribeiro and Dickson - 2010 - Sex Peptide Receptor and Neuronal TORS6K Signalin.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5QQSHAIZ/S0960982210003878.html}
}

@article{walker_postmating_2015,
  title = {Postmating {{Circuitry Modulates Salt Taste Processing}} to {{Increase Reproductive Output}} in {{Drosophila}}},
  volume = {25},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2015.08.043},
  abstract = {Summary
To optimize survival and reproduction, animals must match their nutrient intake to their current needs. Reproduction profoundly changes nutritional requirements, with many species showing an appetite for sodium during reproductive periods. How this internal state modifies neuronal information processing to ensure homeostasis is not understood. Here, we show that dietary sodium levels positively affect reproductive output in Drosophila melanogaster; to satisfy this requirement, females develop a strong, specific appetite for sodium following mating. We show that mating modulates gustatory processing to increase the probability of initiating feeding on salt. This postmating effect is not due to salt depletion by egg production, since abolishing egg production leaves the sodium appetite intact. Rather, the salt appetite is induced need-independently by male-derived Sex Peptide acting on the Sex Peptide Receptor in female reproductive tract neurons. We~further demonstrate that postmating appetites for both salt and yeast are driven by the resultant silencing of downstream SAG neurons. Surprisingly, unlike the postmating yeast appetite, the salt appetite does not require octopamine, suggesting a divergence in the postmating circuitry. These findings demonstrate that the postmating circuit supports reproduction by increasing the palatability of specific nutrients. Such a feedforward regulation of sensory processing may represent a common mechanism through which reproductive state-sensitive circuits modify complex behaviors across species.},
  number = {20},
  journal = {Current Biology},
  author = {Walker, Samuel James and {Corrales-Carvajal}, Ver\'onica Mar\'ia and Ribeiro, Carlos},
  month = oct,
  year = {2015},
  pages = {2621-2630},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JQ3N3LQ4/Walker et al. - 2015 - Postmating Circuitry Modulates Salt Taste Processi.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MNPIEW5P/S0960982215010143.html}
}

@article{wu_genotype_2018,
  title = {Genotype {{Influences Day}}-to-{{Day Variability}} in {{Sleep}} in {{Drosophila}} Melanogaster},
  volume = {41},
  issn = {0161-8105},
  doi = {10.1093/sleep/zsx205},
  abstract = {Abstract.  Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One po},
  language = {en},
  number = {2},
  journal = {Sleep},
  author = {Wu, Katherine J. and Kumar, Shailesh and Negron, Serrano and L, Yazmin and Harbison, Susan T.},
  month = feb,
  year = {2018},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3VM2XKEA/Wu et al. - 2018 - Genotype Influences Day-to-Day Variability in Slee.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DECDFUXE/4710951.html}
}

@article{tougeron_ecological_2017,
  title = {An {{Ecological Perspective}} on {{Sleep Disruption}}},
  volume = {190},
  issn = {0003-0147},
  doi = {10.1086/692604},
  abstract = {Despite its evolutionary importance and apparent ubiquity among animals, the ecological significance of sleep is largely unresolved. The ecology of sleep has been particularly neglected in invertebrates. In insects, recent neurobehavioral research convincingly demonstrates that resting behavior shares several common characteristics with sleep in vertebrates. Laboratory studies have produced compelling evidence that sleep disruption can cause changes in insect daily activity patterns (via ``sleep rebound'') and have consequences for behavioral performance during active periods. However, factors that could cause insect sleep disruption in nature have not been considered nor have the ecological consequences. Drawing on evidence from laboratory studies, we argue that sleep disruption may be an overlooked component of insect ecology and could be caused by a variety of anthropogenic and nonanthropogenic factors in nature. We identify several candidate sleep-disrupting factors and provide new insights on the potential consequences of sleep disruption on individual fitness, species interactions, and ecosystem services. We propose an experimental framework to bridge the current gap in knowledge between laboratory and field studies. We conclude that sleep disruption is a potential mechanism underpinning variation in behavioral, population, and community-level processes associated with several aspects of global change.},
  number = {3},
  journal = {The American Naturalist},
  author = {Tougeron, K\'evin and Abram, Paul K.},
  month = jun,
  year = {2017},
  pages = {E55-E66},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LQQ2CBGI/Tougeron and Abram - 2017 - An Ecological Perspective on Sleep Disruption.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VKN9YSF2/692604.html}
}

@article{shih_statistical_2011,
  series = {Computer Physics Communications Special Edition for Conference on Computational Physics Kaohsiung, Taiwan, Dec 15-19, 2009},
  title = {Statistical Analysis and Modeling of the Temperature-Dependent Sleep Behavior of Drosophila},
  volume = {182},
  issn = {0010-4655},
  doi = {10.1016/j.cpc.2010.07.021},
  abstract = {The sleep behavior of drosophila is analyzed under different temperatures. The activity per minute of the flies is recorded automatically. Sleep for a fruit fly is defined as the periods without any activity and longer than 5 minutes. Several parameters such as total sleep time, circadian sleep profile, quality of sleep are analyzed. The sleep behaviors are significantly different for flies at different temperature. Interestingly, the durations of daytime sleep periods show a common scale-free power law distribution. We propose a stochastic model to simulate the activities of the population of neurons which regulate the dynamics of sleep\textendash{}wake process to explain the distribution of daytime sleep.},
  number = {1},
  journal = {Computer Physics Communications},
  author = {Shih, Chi-Tin and Lin, Hsuan-Wen and Chiang, Ann-Shyn},
  month = jan,
  year = {2011},
  keywords = {Drosophila,Computational neuroscience,Sleep behavior},
  pages = {195-197},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FHLPHMKE/Shih et al. - 2011 - Statistical analysis and modeling of the temperatu.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AJ9SFUGX/S0010465510002547.html}
}

@article{lima_sleeping_2005,
  title = {Sleeping under the Risk of Predation},
  volume = {70},
  issn = {0003-3472},
  doi = {10.1016/j.anbehav.2005.01.008},
  abstract = {Every studied animal engages in sleep, and many animals spend much of their lives in this vulnerable behavioural state. We believe that an explicit description of this vulnerability will provide many insights into both the function and architecture (or organization) of sleep. Early studies of sleep recognized this idea, but it has been largely overlooked during the last 20 years. We critically evaluate early models that suggested that the function of sleep is antipredator in nature, and outline a new model in which we argue that whole-brain or `blackout' sleep may be the safest way to sleep given a functionally interconnected brain. Early comparative work also suggested that the predatory environment is an important determinant of sleep architecture. For example, species that sleep in risky environments spend less time in the relatively vulnerable states of sleep. Recent experimental work suggests that mammals and birds shift to relatively vigilant (lighter) states of sleep in response to an increase in perceived risk; these results mirror the influence of stress on sleep in humans and rats. We also outline a conceptual model of sleep architecture in which dynamic changes in sleep states reflect a trade-off between the benefits of reducing a sleep debt and the cost of predation. Overall, many aspects of plasticity in sleep related to predation risk require further study, as do the ways in which sleeping animals monitor predatory threats. More work outside of the dominant mammalian paradigm in sleep is also needed. An ecologically based view of sleeping under the risk of predation will provide an important complement to the traditional physiological and neurological approaches to studying sleep and its functions.},
  number = {4},
  journal = {Animal Behaviour},
  author = {Lima, Steven L. and Rattenborg, Niels C. and Lesku, John A. and Amlaner, Charles J.},
  month = oct,
  year = {2005},
  pages = {723-736},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8D8RPK75/Lima et al. - 2005 - Sleeping under the risk of predation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WJSJG6EH/S0003347205002009.html}
}

@article{zug_still_2012,
  title = {Still a {{Host}} of {{Hosts}} for {{Wolbachia}}: {{Analysis}} of {{Recent Data Suggests That}} 40\% of {{Terrestrial Arthropod Species Are Infected}}},
  volume = {7},
  issn = {1932-6203},
  shorttitle = {Still a {{Host}} of {{Hosts}} for {{Wolbachia}}},
  doi = {10.1371/journal.pone.0038544},
  abstract = {Wolbachia are intracellular bacteria that manipulate the reproduction of their arthropod hosts in remarkable ways. They are predominantly transmitted vertically from mother to offspring but also occasionally horizontally between species. In doing so, they infect a huge range of arthropod species worldwide. Recently, a statistical analysis estimated the infection frequency of Wolbachia among arthropod hosts to be 66\%. At the same time, the authors of this analysis highlighted some weaknesses of the underlying data and concluded that in order to improve the estimate, a larger number of individuals per species should be assayed and species be chosen more randomly. Here we apply the statistical approach to a more appropriate data set from a recent survey that tested both a broad range of species and a sufficient number of individuals per species. Indeed, we find a substantially different infection frequency: We now estimate the proportion of Wolbachia-infected species to be around 40\% which is lower than the previous estimate but still points to a surprisingly high number of arthropods harboring the bacteria. Notwithstanding this difference, we confirm the previous result that, within a given species, typically most or only a few individuals are infected. Moreover, we extend our analysis to include several reproductive parasites other than Wolbachia that were also screened for in the aforementioned empirical survey. For these symbionts we find a large variation in estimated infection frequencies and corroborate the finding that Wolbachia are the most abundant endosymbionts among arthropod species.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Zug, Roman and Hammerstein, Peter},
  year = {07-Jun-2012},
  keywords = {Arthropoda,Meta-analysis,Parasitic diseases,Polymerase chain reaction,Rickettsia,Species diversity,Spiroplasma,Wolbachia},
  pages = {e38544},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/C625NVT5/Zug and Hammerstein - 2012 - Still a Host of Hosts for Wolbachia Analysis of R.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GK3286JF/article.html}
}

@article{zug_wolbachia_2015,
  title = {Wolbachia and the Insect Immune System: What Reactive Oxygen Species Can Tell Us about the Mechanisms of {{Wolbachia}}\textendash{}host Interactions},
  volume = {6},
  issn = {1664-302X},
  shorttitle = {Wolbachia and the Insect Immune System},
  doi = {10.3389/fmicb.2015.01201},
  abstract = {Wolbachia are intracellular bacteria that infect a vast range of arthropod species, making them one of the most prevalent endosymbionts in the world. Wolbachia's stunning evolutionary success is mostly due to their reproductive parasitism but also to mutualistic effects such as increased host fecundity or protection against pathogens. However, the mechanisms underlying Wolbachia phenotypes, both parasitic and mutualistic, are only poorly understood. Moreover, it is unclear how the insect immune system is involved in these phenotypes and why it is not more successful in eliminating the bacteria. Here we argue that reactive oxygen species (ROS) are likely to be key in elucidating these issues. ROS are essential players in the insect immune system, and Wolbachia infection can affect ROS levels in the host. Based on recent findings, we elaborate a hypothesis that considers the different effects of Wolbachia on the oxidative environment in novel vs. native hosts. We propose that newly introduced Wolbachia trigger an immune response and cause oxidative stress, whereas in coevolved symbioses, infection is not associated with oxidative stress, but rather with restored redox homeostasis. Redox homeostasis can be restored in different ways, depending on whether Wolbachia or the host is in charge. This hypothesis offers a mechanistic explanation for several of the observed Wolbachia phenotypes.},
  language = {English},
  journal = {Frontiers in Microbiology},
  author = {Zug, Roman and Hammerstein, Peter},
  year = {2015},
  keywords = {Reactive Oxygen Species,Insects,Wolbachia,Immune System,symbiont-host interactions},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L6LIFV5W/Zug and Hammerstein - 2015 - Wolbachia and the insect immune system what react.pdf}
}

@article{werren_wolbachia_2008,
  title = {{\emph{Wolbachia:}} Master Manipulators of Invertebrate Biology},
  volume = {6},
  copyright = {2008 Nature Publishing Group},
  issn = {1740-1534},
  shorttitle = {{\emph{Wolbachia}}},
  doi = {10.1038/nrmicro1969},
  abstract = {Wolbachia are common intracellular bacteria that are found in arthropods and nematodes. These alphaproteobacteria endosymbionts are transmitted vertically through host eggs and alter host biology in diverse ways, including the induction of reproductive manipulations, such as feminization, parthenogenesis, male killing and sperm\textendash{}egg incompatibility. They can also move horizontally across species boundaries, resulting in a widespread and global distribution in diverse invertebrate hosts. Here, we review the basic biology of Wolbachia, with emphasis on recent advances in our understanding of these fascinating endosymbionts.},
  language = {en},
  number = {10},
  journal = {Nature Reviews Microbiology},
  author = {Werren, John H. and Baldo, Laura and Clark, Michael E.},
  month = oct,
  year = {2008},
  pages = {741-751},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BDGR3WKZ/Werren et al. - 2008 - iWolbachiai master manipulators of invertebr.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BR4F8SR3/nrmicro1969.html}
}

@article{rohrscheib_wolbachia_2015,
  title = {Wolbachia {{Influences}} the {{Production}} of {{Octopamine}} and {{Affects Drosophila Male Aggression}}},
  volume = {81},
  issn = {0099-2240, 1098-5336},
  doi = {10.1128/AEM.00573-15},
  abstract = {Wolbachia bacteria are endosymbionts that infect approximately 40\% of all insect species and are best known for their ability to manipulate host reproductive systems. Though the effect Wolbachia infection has on somatic tissues is less well understood, when present in cells of the adult Drosophila melanogaster brain, Wolbachia exerts an influence over behaviors related to olfaction. Here, we show that a strain of Wolbachia influences male aggression in flies, which is critically important in mate competition. A specific strain of Wolbachia was observed to reduce the initiation of aggressive encounters in Drosophila males compared to the behavior of their uninfected controls. To determine how Wolbachia was able to alter aggressive behavior, we investigated the role of octopamine, a neurotransmitter known to influence male aggressive behavior in many insect species. Transcriptional analysis of the octopamine biosynthesis pathway revealed that two essential genes, the tyrosine decarboxylase and tyramine $\beta$-hydroxylase genes, were significantly downregulated in Wolbachia-infected flies. Quantitative chemical analysis also showed that total octopamine levels were significantly reduced in the adult heads.},
  language = {en},
  number = {14},
  journal = {Applied and Environmental Microbiology},
  author = {Rohrscheib, Chelsie E. and Bondy, Elizabeth and Josh, Peter and Riegler, Markus and Eyles, Darryl and van Swinderen, Bruno and Weible, Michael W. and Brownlie, Jeremy C.},
  month = jul,
  year = {2015},
  pages = {4573-4580},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FQIVLCT6/Rohrscheib et al. - 2015 - Wolbachia Influences the Production of Octopamine .pdf},
  pmid = {25934616}
}

@article{vale_sex-specific_2015,
  title = {Sex-Specific Behavioural Symptoms of Viral Gut Infection and {{Wolbachia}} in {{Drosophila}} Melanogaster},
  volume = {Complete},
  issn = {0022-1910},
  doi = {10.1016/j.jinsphys.2015.08.005},
  abstract = {All organisms are infected with a range of symbionts spanning the spectrum of beneficial mutualists to detrimental parasites. The fruit fly Drosophila melanogaster is a good example, as both endosymbiotic Wolbachia, and pathogenic Drosophila C Virus (DCV) commonly infect it. While the pathophysiology and immune responses against both symbionts are the focus of intense study, the behavioural effects of these infections have received less attention. Here we report sex-specific behavioural responses to these infections in D. melanogaster. DCV infection caused increased sleep in female flies, but had no detectable effect in male flies. The presence of Wolbachia did not reduce this behavioural response to viral infection. We also found evidence for a sex-specific cost of Wolbachia, as male flies infected with the endosymbiont became more lethargic when awake. We discuss these behavioural symptoms as potentially adaptive sickness behaviours.},
  language = {English},
  number = {82},
  journal = {Journal of Insect Physiology},
  author = {Vale, Pedro F. and Jardine, Michael D.},
  year = {2015},
  pages = {28-32},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5WKDBAP5/bwmeta1.element.html}
}

@article{stahlschmidt_context_2013,
  title = {Context Dependency and Generality of Fever in Insects},
  volume = {100},
  issn = {0028-1042, 1432-1904},
  doi = {10.1007/s00114-013-1057-y},
  abstract = {Fever can reduce mortality in infected animals. Yet, despite its fitness-enhancing qualities, fever often varies among animals. We used several approaches to examine this variation in insects. Texas field crickets (Gryllus texensis) exhibited a modest fever (1 $^\circ$C increase in preferred body temperature, T pref) after injection of prostaglandin, which putatively mediates fever in both vertebrates and invertebrates, but they did not exhibit fever during chronic exposure to heat-killed bacteria. Further, chronic food limitation and mating status did not affect T pref or the expression of behavioural fever, suggesting limited context dependency of fever in G. texensis. Our meta-analysis of behavioural fever studies indicated that behavioural fever occurs in many insects, but it is not ubiquitous. Thus, both empirical and meta-analytical results suggest that the fever response in insects `is widespread, although certainly not inevitable' (Moore 2002). We highlight the need for future work focusing on standardizing an experimental protocol to measure behavioural fever, understanding the specific mechanism(s) underlying fever in insects, and examining whether ecological or physiological costs often outweigh the benefits of fever and can explain the sporadic nature of fever in insects.},
  language = {en},
  number = {7},
  journal = {Naturwissenschaften},
  author = {Stahlschmidt, Z. R. and Adamo, S. A.},
  month = jul,
  year = {2013},
  pages = {691-696},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D99WHHKZ/Stahlschmidt and Adamo - 2013 - Context dependency and generality of fever in inse.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4BZV4Z9S/s00114-013-1057-y.html}
}

@article{ayres_role_2009,
  title = {The {{Role}} of {{Anorexia}} in {{Resistance}} and {{Tolerance}} to {{Infections}} in {{Drosophila}}},
  volume = {7},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.1000150},
  abstract = {Infections initiate a signaling loop in which sick animals become anorexic, and the resulting change in diet alters the body's ability to fight infections in good and bad ways.},
  language = {en},
  number = {7},
  journal = {PLOS Biology},
  author = {Ayres, Janelle S. and Schneider, David S.},
  year = {14-Jul-2009},
  keywords = {Drosophila melanogaster,Diet,Anorexia nervosa,Enterococcus faecalis,Immune response,Listeria monocytogenes,Salmonella typhimurium,Trophic interactions},
  pages = {e1000150},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PIIMJ2QH/Ayres and Schneider - 2009 - The Role of Anorexia in Resistance and Tolerance t.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ET785UEN/article.html}
}

@article{van_houte_walking_2013,
  title = {Walking with Insects: Molecular Mechanisms behind Parasitic Manipulation of Host Behaviour},
  volume = {22},
  issn = {1365-294X},
  shorttitle = {Walking with Insects},
  doi = {10.1111/mec.12307},
  abstract = {Parasitic infections are often followed by changes in host behaviour. Numerous and exquisite examples of such behavioural alterations are known, covering a broad spectrum of parasites and hosts. Most descriptions of such parasite-induced changes in host behaviour are observational reports, while experimentally confirmed examples of parasite genes inducing these changes are limited. In this study, we review changes in invertebrate host behaviour observed upon infection by parasites and discuss such changes in an evolutionary context. We then explore possible mechanisms involved in parasite-induced changes in host behaviour. Genes and pathways known to play a role in invertebrate behaviour are reviewed, and we hypothesize how parasites (may) affect these pathways. This review provides the state of the art in this exciting, interdisciplinary field by exploring possible pathways triggered in hosts, suggesting methodologies to unravel the molecular mechanisms that lead to changes in host behaviour.},
  language = {en},
  number = {13},
  journal = {Molecular Ecology},
  author = {van {van Houte}, Stineke and Ros, Vera I. D. and van Oers, Monique M.},
  year = {2013},
  keywords = {Behavior; Animal,Animals,Molecular Sequence Data,Biological Evolution,Phylogeny,Phenotype,Insecta,behavioural manipulation,extended phenotype,host–parasite interactions,invertebrate,parasite,Host-Parasite Interactions,Parasites,Parasitic Diseases},
  pages = {3458-3475},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/V5F45KB8/Houte et al. - Walking with insects molecular mechanisms behind .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZEZ427KL/mec.html}
}

@article{shirasu-hiza_interactions_2007,
  title = {Interactions between Circadian Rhythm and Immunity in {{Drosophila}} Melanogaster},
  volume = {17},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2007.03.049},
  language = {English},
  number = {10},
  journal = {Current Biology},
  author = {{Shirasu-Hiza}, Mimi M. and Dionne, Marc S. and Pham, Linh N. and Ayres, Janelle S. and Schneider, David S.},
  month = may,
  year = {2007},
  pages = {R353-R355},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7AYLQ4IE/Shirasu-Hiza et al. - 2007 - Interactions between circadian rhythm and immunity.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ID6XGSXA/S0960-9822(07)01187-6.html},
  pmid = {17502084}
}

@article{williams_interaction_2007,
  title = {Interaction {{Between Sleep}} and the {{Immune Response}} in {{Drosophila}}: {{A Role}} for the {{NF$\kappa$B Relish}}},
  volume = {30},
  issn = {0161-8105},
  shorttitle = {Interaction {{Between Sleep}} and the {{Immune Response}} in {{Drosophila}}},
  doi = {10.1093/sleep/30.4.389},
  abstract = {AbstractStudy Objectives:.  The regulation of sleep is poorly understood. While some molecules, including those involved in inflammatory/immune responses, have},
  language = {en},
  number = {4},
  journal = {Sleep},
  author = {Williams, Julie A. and Sathyanarayanan, Sriram and Hendricks, Joan C. and Sehgal, Amita},
  month = apr,
  year = {2007},
  pages = {389-400},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IACHTU5K/Williams et al. - 2007 - Interaction Between Sleep and the Immune Response .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T2F2V9LH/2708189.html}
}

@article{piper_holidic_2014,
  title = {A Holidic Medium for {{{\emph{Drosophila}}}}{\emph{ Melanogaster}}},
  volume = {11},
  copyright = {2013 Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/nmeth.2731},
  abstract = {A critical requirement for research using model organisms is a well-defined and consistent diet. There is currently no complete chemically defined (holidic) diet available for Drosophila melanogaster. We describe a holidic medium that is equal in performance to an oligidic diet optimized for adult fecundity and lifespan. This holidic diet supports development over multiple generations but at a reduced rate. Over 7 years of experiments, the holidic diet yielded more consistent experimental outcomes than did oligidic food for egg laying by females. Nutrients and drugs were more available to flies in holidic medium and, similar to dietary restriction on oligidic food, amino acid dilution increased fly lifespan. We used this holidic medium to investigate amino acid\textendash{}specific effects on food-choice behavior and report that folic acid from the microbiota is sufficient for Drosophila development.},
  language = {en},
  number = {1},
  journal = {Nature Methods},
  author = {Piper, Matthew D. W. and Blanc, Eric and {Leit\~ao-Gon{\c c}alves}, Ricardo and Yang, Mingyao and He, Xiaoli and Linford, Nancy J. and Hoddinott, Matthew P. and Hopfen, Corinna and Soultoukis, George A. and Niemeyer, Christine and Kerr, Fiona and Pletcher, Scott D. and Ribeiro, Carlos and Partridge, Linda},
  month = jan,
  year = {2014},
  pages = {100-105},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U7RMN9Y9/Piper et al. - 2014 - A holidic medium for iDrosophila melanogasteri.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PTDD5NGG/nmeth.html}
}

@incollection{humphreys_behavioural_1987,
  title = {Behavioural {{Temperature Regulation}}},
  isbn = {978-3-642-71554-9 978-3-642-71552-5},
  abstract = {Most of the information on temperature regulation in spiders has been deduced from their behaviour; this contrasts with other ectothermic animals, especially reptiles and insects, on which many direct measurements of temperature have been made. This chapter shows that spiders exhibit a broad spectrum of thermal behaviours and suggests behaviours which might be expected with further study; less than 0.1\% of spider species have been examined in this context. The general background to thermoregulation has been covered well in a number of recent reviews (Bligh et al. 1976; Gans and Pough 1982) as well as in works concerned specifically with invertebrates (Cloudsley-Thompson 1970; Heinrich 1979, 1981; Crawford 1981).},
  language = {en},
  booktitle = {Ecophysiology of {{Spiders}}},
  publisher = {{Springer, Berlin, Heidelberg}},
  author = {Humphreys, William F.},
  year = {1987},
  pages = {56-65},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S7Y2YHRE/978-3-642-71552-5_4.html},
  doi = {10.1007/978-3-642-71552-5_4}
}

@article{heinrich_insect_1995,
  title = {Insect Thermoregulation},
  volume = {19},
  issn = {0160-9327},
  doi = {10.1016/0160-9327(95)98891-I},
  abstract = {Except in special circumstances, such as hibernation, mammals commonly keep their body temperatures within quite narrow limits. With insects, however, the situation is different. Rapid and considerable temperature changes occur in response to changing needs: for example, the transition from a resting state to extremely rapid wing movement in flight. This article reviews the regulatory mechanisms involved and how they come into effect.},
  number = {1},
  journal = {Endeavour},
  author = {Heinrich, B.},
  month = jan,
  year = {1995},
  pages = {28-33},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U5ISYERF/Heinrich - 1995 - Insect thermoregulation.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FCQRP4BK/016093279598891I.html}
}

@article{prince_adaptive_1977,
  title = {Adaptive Behaviour of {{Drosophila}} Adults in Relation to Temperature and Humidity},
  volume = {25},
  issn = {1446-5698},
  doi = {10.1071/zo9770285},
  abstract = {The reactions of three Drosophila species (D. melanogaster, D. simulans and D. immigrans) were studied in a temperature gradient at different humidities. In a saturation-deficit gradient all three species showed adaptive behaviour which could be related to their physiological resistance to desiccation. This is taken as experimental evidence for similar avoidance of stressful conditions in the field.},
  language = {en},
  number = {2},
  journal = {Australian Journal of Zoology},
  author = {Prince, G. J. and Parsons, P. A.},
  year = {1977},
  pages = {285-290},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JRNU2LCZ/ZO9770285.html}
}

@article{stoleru_drosophila_2007,
  title = {The {{Drosophila Circadian Network Is}} a {{Seasonal Timer}}},
  volume = {129},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2007.02.038},
  abstract = {Summary
Previous work in Drosophila has defined two populations of circadian brain neurons, morning cells (M-cells) and evening cells (E-cells), both of which keep circadian time and regulate morning and evening activity, respectively. It has long been speculated that a multiple oscillator circadian network in animals underlies the behavioral and physiological pattern variability caused by seasonal fluctuations of photoperiod. We have manipulated separately the circadian photoentrainment pathway within E- and M-cells and show that E-cells process light information and function as master clocks in the~presence of light. M-cells in contrast need darkness to cycle autonomously and dominate the network. The results indicate that the network switches control between these two centers as a function of photoperiod. Together with the different entraining properties of the two clock centers, the results suggest that the~functional organization of the network underlies the behavioral adjustment to variations in daylength and season.},
  number = {1},
  journal = {Cell},
  author = {Stoleru, Dan and Nawathean, Pipat and Fern\'andez, Mar\'ia de la Paz and Menet, Jerome S. and Ceriani, M. Fernanda and Rosbash, Michael},
  month = apr,
  year = {2007},
  keywords = {MOLNEURO,SYSNEURO},
  pages = {207-219},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HK37XGIG/Stoleru et al. - 2007 - The Drosophila Circadian Network Is a Seasonal Tim.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IXKZTEVL/S0092867407003145.html}
}

@article{costa_latitudinal_1992,
  title = {A Latitudinal Cline in a {{Drosophila}} Clock Gene},
  volume = {250},
  copyright = {Scanned images copyright \textcopyright{} 2017, Royal Society},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.1992.0128},
  abstract = {The clock gene period determines biological rhythmicity in Drosophila melanogaster and encodes a protein characterized by an alternating series of threonine-glycine pairs. The minisatellite region encoding the threonine-glycine repeat is polymorphic in length in natural Drosophila melanogaster populations. In this paper we report the geographical analysis of this polymorphism within Europe and North Africa. A robust clinal pattern is observed along a north-south axis. We suggest the possibility that the length polymorphism could be maintained by thermal selection because the threonine-glycine region has been shown to provide thermostability to the circadian phenotype.},
  language = {en},
  number = {1327},
  journal = {Proc. R. Soc. Lond. B},
  author = {Costa, Rodolfo and Peixoto, Alexandre A. and Barbujani, Guido and Kyriacou, Charalambos P.},
  month = oct,
  year = {1992},
  pages = {43-49},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8NULB3XI/Costa et al. - 1992 - A latitudinal cline in a Drosophila clock gene.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WVQZ8S8E/43.html},
  pmid = {1361061}
}

@article{sokolowski_social_2010,
  title = {Social Interactions in "Simple" Model Systems},
  volume = {65},
  issn = {1097-4199},
  doi = {10.1016/j.neuron.2010.03.007},
  abstract = {Deciphering the genetic and neurobiological underpinnings of social behavior is a difficult task. Simple model organisms such as C. elegans, Drosophila, and social insects display a wealth of social behaviors similar to those in more complex animals, including social dominance, group decision making, learning from experienced individuals, and foraging in groups. Although the study of social interactions is still in its infancy, the ability to assess the contributions of gene expression, neural circuitry, and the environment in response to social context in these simple model organisms is unsurpassed. Here, I take a comparative approach, discussing selected examples of social behavior across species and highlighting the common themes that emerge.},
  language = {eng},
  number = {6},
  journal = {Neuron},
  author = {Sokolowski, Marla B.},
  month = mar,
  year = {2010},
  keywords = {Models; Biological,Humans,Social Behavior,Animals,Social Environment,Interpersonal Relations},
  pages = {780-794},
  pmid = {20346755}
}

@article{navarro_pattern_1975,
  title = {Pattern of Spatial Distribution in {{Drosophila}} Melanogaster},
  volume = {5},
  issn = {0001-8244},
  abstract = {The effect of temperature and sex on spatial distribution of Drosophila melanogaster adults was studied in a specially designed apparatus. It was observed that individuals tend to aggregate in sections of the sphere independently of sex and temperature. Nevertheless, decrease in temperature increase aggregation. The mobility of both males and females indicates a negative geotactic tendency.},
  language = {eng},
  number = {1},
  journal = {Behavior Genetics},
  author = {Navarro, J. and {del Solar}, E.},
  month = jan,
  year = {1975},
  keywords = {Sexual Behavior; Animal,Female,Male,Time Factors,Social Behavior,Animals,Drosophila melanogaster,Motor Activity,Spatial Behavior,Sex Factors,Temperature,Gravitation,Movement},
  pages = {9-16},
  pmid = {803834}
}

@article{simon_simple_2012,
  title = {A Simple Assay to Study Social Behavior in {{Drosophila}}: Measurement of Social Space within a Group},
  volume = {11},
  issn = {1601-1848},
  shorttitle = {A Simple Assay to Study Social Behavior in {{Drosophila}}},
  doi = {10.1111/j.1601-183X.2011.00740.x},
  abstract = {We have established a new simple behavioral paradigm in Drosophila melanogaster to determine how genes and the environment influence the behavior of flies within a social group. Specifically, we measure social space as the distance between two flies. The majority of Canton-s flies, regardless of their gender, are within two-body lengths from each other. Their social experience affects this behavior, with social isolation reducing and mating enhancing social space respectively, in both males and females. Unlike several other social behaviors in the fly, including the formation of social groups themselves (a well described behavior - Bartelt et al., 1985, De Gee et al., 2008, Lof et al., 2008, Lof et al., 2009), social space does not require the perception of the previously identified aggregation pheromone cis-Vaccenyl Acetate (Bartelt et al., 1985). Conversely, performance of the assay in darkness or mutations in the eye pigmentation gene white increased social space. Our results establish a new assay for the genetic dissection of a fundamental mode of social interaction.},
  number = {2},
  journal = {Genes, Brain, and Behavior},
  author = {Simon, Anne F. and Chou, Man-Ting and Salazar, Evelyn D. and Nicholson, Terriann and Saini, Navdeep and Metchev, Stanimir and Krantz, David E.},
  month = mar,
  year = {2012},
  pages = {243-252},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GMPYPTU2/Simon et al. - 2012 - A simple assay to study social behavior in Drosoph.pdf},
  pmid = {22010812},
  pmcid = {PMC3268943}
}

@article{lefranc_non-independence_2001,
  title = {Non-Independence of Individuals in a Population of {{Drosophila}} Melanogaster: Effects on Spatial Distribution and Dispersal},
  volume = {324},
  issn = {0764-4469},
  shorttitle = {Non-Independence of Individuals in a Population of {{Drosophila}} Melanogaster},
  abstract = {We used a simple quadrat analysis to globally categorise the spatial distribution of Drosophila melanogaster individuals. Individuals were spatially aggregated and this was not only due to sexual attraction. This aggregation seemed to be maintained during dispersal, hence explaining the great variability of this behaviour observed in our work and by other authors. Thus, individuals are expected to arrive as small groups into a new patch. This may induce costs through competition and benefits by ensuring the presence of reproductive mates and/or if there is a phenomenon of local resource enhancement by the presence of conspecifics, hence influencing the evolution of dispersal.},
  language = {eng},
  number = {3},
  journal = {Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie},
  author = {Lefranc, A. and Jeune, B. and {Thomas-Orillard}, M. and Danchin, E.},
  month = mar,
  year = {2001},
  keywords = {Sexual Behavior; Animal,Female,Male,Social Behavior,Animals,Darkness,Circadian Rhythm,Drosophila melanogaster,Light,Ecosystem},
  pages = {219-227},
  pmid = {11291308}
}

@article{tinette_cooperation_2004,
  title = {Cooperation between {{Drosophila}} Flies in Searching Behavior},
  volume = {3},
  issn = {1601-1848},
  abstract = {In Drosophila melanogaster food search behaviour, groups of flies swarm around and aggregate on patches of food. We wondered whether flies explore their environment in a cooperative way as interactions between individual flies within a population might influence the flies' ability to locate food sources. We have shown that the food search behavior in the fruit fly Drosophila is a two-step process. Firstly, 'primer' flies search the environment and randomly land on different food patches. Secondly, the remaining group of flies move to the most favorable food source and aggregate there. We call this a 'search-aggregation' cycle. Our data demonstrate that flies do not individually assess all available food resources. Rather, social interactions between flies appear to affect their choice of a specific food patch. A genetic analysis of this 'search-aggregation' behavior shows that flies carrying mutations in specific genes (for example, the dunce (dnc) gene which codes for a phosphodiesterase) were defective in this search-aggregation behavior when compared to normal flies. Future investigations of the neuronal signaling involved in this behavior will help us to understand the complexities of this aspect of Drosophila social behaviour.},
  language = {eng},
  number = {1},
  journal = {Genes, Brain, and Behavior},
  author = {Tinette, S. and Zhang, L. and Robichon, A.},
  month = feb,
  year = {2004},
  keywords = {Female,Male,Social Behavior,Animals,Drosophila,Mutation,Avoidance Learning,Cues,Exploratory Behavior,Conditioning (Psychology),Appetitive Behavior,Cooperative Behavior,Food,Odorants},
  pages = {39-50},
  pmid = {14960014}
}

@article{szuperak_sleep_2018,
  title = {A Sleep State in {{Drosophila}} Larvae Required for Neural Stem Cell Proliferation},
  volume = {7},
  copyright = {\textcopyright{} 2018 Szuperak et al.. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  doi = {10.7554/eLife.33220},
  abstract = {A role for sleep in developmental neurogenesis is revealed using a new system for studying sleep during nascent periods.},
  language = {en},
  journal = {eLife},
  author = {Szuperak, Milan and Churgin, Matthew A. and Borja, Austin J. and Raizen, David M. and {Fang-Yen}, Christopher and Kayser, Matthew S.},
  month = feb,
  year = {2018},
  pages = {e33220},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GTNH5DVI/Szuperak et al. - 2018 - A sleep state in Drosophila larvae required for ne.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L8VAPF42/33220.html}
}

@article{rillich_losing_2017,
  title = {Losing without {{Fighting}} - {{Simple Aversive Stimulation Induces Submissiveness Typical}} for {{Social Defeat}} via the {{Action}} of {{Nitric Oxide}}, but {{Only When Preceded}} by an {{Aggression Priming Stimulus}}},
  volume = {11},
  issn = {1662-5153},
  doi = {10.3389/fnbeh.2017.00050},
  abstract = {Losing a fight (social defeat) induces submissiveness and behavioral depression in many animals, but the mechanisms are unclear. Here we investigate how the social defeat syndrome can be established as a result of experiencing aversive stimuli and the roles of neuromodulators in the process. While biogenic amines and nitric oxide (NO) are associated with reduced aggression in mammals and insects, their specific actions during conflict are unknown. Although the social defeat syndrome normally results from complex interactions, we could induce it in male crickets simply by applying aversive stimuli (AS) in an aggressive context. Aggressive crickets became immediately submissive and behaved like losers after experiencing two brief AS (light wind puffs to the cerci), but only when preceded by a priming stimulus (PS, stroking the antenna with another male antenna). Notably, submissiveness was not induced when the PS preceded the AS by more than 1 min, or when the PS followed the AS, or using a female antenna as the preceding stimulus. These findings suggest that any potentially detrimental stimulus can acquire the attribute of an aversive agonistic signal when experienced in an aggressive context. Crickets, it seems, need only to evaluate their net sensory impact rather than the qualities of a variety of complex agonistic signals. Selective drug treatments revealed that NO, but not serotonin, dopamine or octopamine, is necessary to establish the submissive status following pairing of the priming and aversive stimuli. Moreover, treatment with an NO donor also induced the social defeat syndrome, but only when combined with the PS. This confirms our hypothesis that aversive agonistic experiences accumulated by crickets during fighting invoke social defeat via the action of NO and illustrates that a relatively simple mechanism underlies the seemingly complex social decision to flee. The simple stimulus regime for inducing social defeat opens new avenues for investigating the cellular control of subordinate behavior and post-conflict depression.},
  language = {English},
  journal = {Frontiers in Behavioral Neuroscience},
  author = {Rillich, Jan and Stevenson, Paul A.},
  year = {2017},
  keywords = {decision-making,Insects,Association,Biogenic Amines,experience-dependent-plasticity,Neuromodulation,priming,Submissive behavior},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UH7JEB83/Rillich and Stevenson - 2017 - Losing without Fighting - Simple Aversive Stimulat.pdf}
}

@article{kravitz_aggression_2015,
  title = {Aggression in {\emph{Drosophila}}},
  volume = {129},
  issn = {0735-7044},
  doi = {10.1037/bne0000089},
  abstract = {Aggression is used by essentially all species of animals to gain access to desired resources, including territory, food, and potential mates: Fruit flies are no exception. In Drosophila, both males and females compete in same sex fights for resources, but only males establish hierarchical relationships. Many investigators now study aggression using the fruit fly model, mainly because (a) aggression in fruit flies is a quantifiable well-defined and easily evoked behavior; (b) powerful genetic methods allow investigators to manipulate genes of interest at any place or time during embryonic, larval, pupal or adult life, and while flies are behaving; (c) the growth of the relatively new field of optogenetics makes physiological studies possible at single neuron levels despite the small sizes of neurons and other types of cells in fly brains; and (d) the rearing of fly stocks with their short generation times and limited growth space requirements can easily be performed at relatively low cost in most laboratories. This review begins with an examination of the behavior, both from a historical perspective and then from the birth of the ``modern'' era of studies of aggression in fruit flies including its quantitative analysis. The review continues with examinations of the roles of genes, neurotransmitters and neurohormones, peptides, nutritional and metabolic status, and surface cuticular hydrocarbons in the initiation and maintenance of aggression. It concludes with suggestions for future studies with this important model system.},
  language = {ENGLISH},
  number = {5},
  journal = {Behavioral Neuroscience},
  author = {Kravitz, Edward A. and Fernandez, Maria de la Paz},
  month = oct,
  year = {2015},
  pages = {549-563},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/72BM36EQ/Kravitz and Fernandez - 2015 - Aggression in idrosophilai.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TPNRXSQD/00001975.html},
  pmid = {00001975-201510000-00001}
}

@article{baldal_effects_2005,
  title = {The Effects of Larval Density on Adult Life-History Traits in Three Species of {{Drosophila}}},
  volume = {126},
  issn = {0047-6374},
  doi = {10.1016/j.mad.2004.09.035},
  abstract = {There is evidence that longevity and starvation resistance are determined by a common genetic mechanism. Starvation resistance in Drosophila strongly correlates with both fat content and longevity, and is affected by density during rearing. In this study, we examine how three species, Drosophila melanogaster, Drosophila ananassae and Drosophila willistoni, respond to three larval density treatments. Starvation resistance after adult eclosion, and after 2 days of feeding, and longevity were examined in each sex. D. willistoni reacted differently to larval density than the other two species. This species showed an effect of density on longevity whilst D. ananassae and D. melanogaster showed no such effects. The results also indicate that starvation resistance is not solely determined by fat content. Resistance to starvation at two time points after eclosion differed among species. This may reflect differences in resource acquisition and allocation, and we discuss our findings in relation to how selection may operate in the different species.},
  number = {3},
  journal = {Mechanisms of Ageing and Development},
  author = {Baldal, E. A. and {van der Linde}, K. and {van Alphen}, J. J. M. and Brakefield, P. M. and Zwaan, B. J.},
  month = mar,
  year = {2005},
  keywords = {Feeding,Longevity,Starvation resistance,Fat,Life history},
  pages = {407-416},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LWSMB9QQ/Baldal et al. - 2005 - The effects of larval density on adult life-histor.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AGEMHWQW/S0047637404002374.html}
}

@article{stahl_sleep_2017,
  title = {Sleep: {{To}} Rebound or Not to Rebound},
  volume = {6},
  copyright = {\textcopyright{} 2017 Stahl et al.. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  shorttitle = {Sleep},
  doi = {10.7554/eLife.31646},
  abstract = {Sexual arousal in flies counteracts the effects of sleep deprivation.},
  language = {en},
  journal = {eLife},
  author = {Stahl, Bethany A. and Keene, Alex C.},
  month = oct,
  year = {2017},
  pages = {e31646},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FLCHMDIX/Stahl and Keene - 2017 - Sleep To rebound or not to rebound.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9QZN5DLK/31646.html}
}

@book{tsomo_into_2012,
  title = {Into the {{Jaws}} of {{Yama}}, {{Lord}} of {{Death}}: {{Buddhism}}, {{Bioethics}}, and {{Death}}},
  isbn = {978-0-7914-8145-5},
  shorttitle = {Into the {{Jaws}} of {{Yama}}, {{Lord}} of {{Death}}},
  abstract = {This book explores the Buddhist view of death and its implications for contemporary bioethics. Writing primarily from within the Tibetan tradition, author Karma Lekshe Tsomo discusses Buddhist notions of human consciousness and personal identity and how these figure in the Buddhist view of death. Beliefs about death and enlightenment and states between life and death are also discussed. Tsomo goes on to examine such hot-button topics as cloning, abortion, assisted suicide, euthanasia, organ donation, genetic engineering, and stem-cell research within a Buddhist context, introducing new ways of thinking about these highly controversial issues.},
  language = {en},
  publisher = {{SUNY Press}},
  author = {Tsomo, Karma Lekshe},
  month = feb,
  year = {2012},
  keywords = {Medical / Ethics,Religion / Buddhism / General,Religion / Buddhism / Tibetan}
}

@incollection{osuna_aztec_2015,
  title = {The {{Aztec}}, {{Maya}}, and {{Inca Civilizations}}},
  isbn = {978-1-4939-2088-4 978-1-4939-2089-1},
  abstract = {Three major civilizations in South America\textemdash{}the Aztecs, the Mayas, and the Incas\textemdash{}mentioned briefly about the practice of medicine but rarely about sleep and sleep medicine. In the Aztec society (the earliest Mexican civilization around 955 BC), explicit cultural codes governed interpersonal relations and daily activities. For example, the first rule prohibited one from sleeping excessively, otherwise the individual would be called a heavy sleeper or dreamer. Contrary to modern sleep hygiene recommendations, the Mayas used tobacco to ease sleep, and the effects of daily activities. In accordance with the fundamental structure of Inca cosmology, sleep is essential to wakefulness and vice versa, which is similar to modern concepts of sleep\textendash{}wake homeostasis. During the Inca civilization, treatment by herbal medicine was, by far, the most popular remedy. For example, an infusion of Datura calmed the nerves and induced sleep. Belladonna (Datura ferox) was widely used as a ``twilight sleep'' for childbirth.},
  language = {en},
  booktitle = {Sleep {{Medicine}}},
  publisher = {{Springer, New York, NY}},
  author = {Osuna, Edgar S.},
  year = {2015},
  pages = {55-59},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DFJIPFSV/978-1-4939-2089-1_9.html},
  doi = {10.1007/978-1-4939-2089-1_9}
}

@article{achermann_two-process_2004,
  title = {The Two-Process Model of Sleep Regulation Revisited.},
  volume = {75},
  issn = {0095-6562},
  abstract = {Abstract: The two-process model of sleep regulation posits that the interaction of its two constituent processes, a sleep/wake dependent homeostatic...},
  language = {eng},
  number = {3 Suppl},
  journal = {Aviation, space, and environmental medicine},
  author = {Achermann, P.},
  month = mar,
  year = {2004},
  pages = {A37-43},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J35W55FP/15018264.html},
  pmid = {15018264}
}

@article{jenkins_obliviscence_1924,
  title = {Obliviscence during {{Sleep}} and {{Waking}}},
  volume = {35},
  issn = {0002-9556},
  doi = {10.2307/1414040},
  number = {4},
  journal = {The American Journal of Psychology},
  author = {Jenkins, John G. and Dallenbach, Karl M.},
  year = {1924},
  pages = {605-612}
}

@article{crick_function_1982,
  title = {The Function of Dream Sleep},
  volume = {304},
  abstract = {We propose that the function of dream sleep (more properly rapid-eye movement or REM sleep) is to remove certain undesirable modes of interaction in networks of cells in the cerebral cortex. We postulate that this is done in REM sleep by a reverse learning mechanism, so that the trace in the brain of the unconscious dream is weakened, rather than strengthened, by the dream.},
  journal = {Nature},
  author = {Crick, Francis and Mitchison, Graeme},
  month = jul,
  year = {1982},
  keywords = {sleep,computational-modeling,dreams,rem,unlearning},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HJTMR753/crick304.pdf}
}

@article{mcclelland_why_1995,
  title = {Why There Are Complementary Learning Systems in the Hippocampus and Neocortex: Insights from the Successes and Failures of Connectionist Models of Learning and Memory},
  volume = {102},
  issn = {0033-295X},
  shorttitle = {Why There Are Complementary Learning Systems in the Hippocampus and Neocortex},
  abstract = {Damage to the hippocampal system disrupts recent memory but leaves remote memory intact. The account presented here suggests that memories are first stored via synaptic changes in the hippocampal system, that these changes support reinstatement of recent memories in the neocortex, that neocortical synapses change a little on each reinstatement, and that remote memory is based on accumulated neocortical changes. Models that learn via changes to connections help explain this organization. These models discover the structure in ensembles of items if learning of each item is gradual and interleaved with learning about other items. This suggests that the neocortex learns slowly to discover the structure in ensembles of experiences. The hippocampal system permits rapid learning of new items without disrupting this structure, and reinstatement of new memories interleaves them with others to integrate them into structured neocortical memory systems.},
  language = {eng},
  number = {3},
  journal = {Psychological Review},
  author = {McClelland, J. L. and McNaughton, B. L. and O'Reilly, R. C.},
  month = jul,
  year = {1995},
  keywords = {Learning,Humans,Memory,Hippocampus,Cerebral Cortex,Neural Networks (Computer),Amnesia; Retrograde},
  pages = {419-457},
  pmid = {7624455}
}

@article{marshall_contribution_2007,
  title = {The Contribution of Sleep to Hippocampus-Dependent Memory Consolidation},
  volume = {11},
  issn = {1364-6613},
  doi = {10.1016/j.tics.2007.09.001},
  abstract = {There is now compelling evidence that sleep promotes the long-term consolidation of declarative and procedural memories. Behavioral studies suggest that sleep preferentially consolidates explicit aspects of these memories, which during encoding are possibly associated with activation in prefrontal\textendash{}hippocampal circuitry. Hippocampus-dependent declarative memory benefits particularly from slow-wave sleep (SWS), whereas rapid-eye-movement (REM) sleep seems to benefit procedural aspects of memory. Consolidation of hippocampus-dependent memories relies on a dialog between the neocortex and hippocampus. Crucial features of this dialog are the neuronal reactivation of new memories in the hippocampus during SWS, which stimulates the redistribution of memory representations to neocortical networks; and the neocortical slow ($<$1Hz) oscillation that synchronizes hippocampal-to-neocortical information transfer to activity in other brain structures.},
  number = {10},
  journal = {Trends in Cognitive Sciences},
  author = {Marshall, Lisa and Born, Jan},
  month = oct,
  year = {2007},
  pages = {442-450},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E3UZMQW4/Marshall and Born - 2007 - The contribution of sleep to hippocampus-dependent.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GCJ4YMBA/S1364661307002124.html}
}

@article{girardeau_selective_2009,
  title = {Selective Suppression of Hippocampal Ripples Impairs Spatial Memory},
  volume = {12},
  copyright = {2009 Nature Publishing Group},
  issn = {1546-1726},
  doi = {10.1038/nn.2384},
  abstract = {Sharp wave\textendash{}ripple (SPW-R) complexes in the hippocampus-entorhinal cortex are believed to be important for transferring labile memories from the hippocampus to the neocortex for long-term storage. We found that selective elimination of SPW-Rs during post-training consolidation periods resulted in performance impairment in rats trained on a hippocampus-dependent spatial memory task. Our results provide evidence for a prominent role of hippocampal SPW-Rs in memory consolidation.},
  language = {en},
  number = {10},
  journal = {Nature Neuroscience},
  author = {Girardeau, Gabrielle and Benchenane, Karim and Wiener, Sidney I. and Buzs\'aki, Gy\"orgy and Zugaro, Micha\"el B.},
  month = oct,
  year = {2009},
  pages = {1222-1223},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UTBVRB29/Girardeau et al. - 2009 - Selective suppression of hippocampal ripples impai.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WVJ49YXR/nn.html}
}

@article{ellenbogen_human_2007,
  title = {Human Relational Memory Requires Time and Sleep},
  volume = {104},
  copyright = {\textcopyright{} 2007 by The National Academy of Sciences of the USA},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0700094104},
  abstract = {Relational memory, the flexible ability to generalize across existing stores of information, is a fundamental property of human cognition. Little is known, however, about how and when this inferential knowledge emerges. Here, we test the hypothesis that human relational memory develops during offline time periods. Fifty-six participants initially learned five ``premise pairs'' (A$>$B, B$>$C, C$>$D, D$>$E, and E$>$F). Unknown to subjects, the pairs contained an embedded hierarchy (A$>$B$>$C$>$D$>$E$>$F). Following an offline delay of either 20 min, 12 hr (wake or sleep), or 24 hr, knowledge of the hierarchy was tested by examining inferential judgments for novel ``inference pairs'' (B$>$D, C$>$E, and B$>$E). Despite all groups achieving near-identical premise pair retention after the offline delay (all groups, $>$85\%; the building blocks of the hierarchy), a striking dissociation was evident in the ability to make relational inference judgments: the 20-min group showed no evidence of inferential ability (52\%), whereas the 12- and 24-hr groups displayed highly significant relational memory developments (inference ability of both groups, $>$75\%; P $<$ 0.001). Moreover, if the 12-hr period contained sleep, an additional boost to relational memory was seen for the most distant inferential judgment (the B$>$E pair; sleep = 93\%, wake = 69\%, P = 0.03). Interestingly, despite this increase in performance, the sleep benefit was not associated with an increase in subjective confidence for these judgments. Together, these findings demonstrate that human relational memory develops during offline time delays. Furthermore, sleep appears to preferentially facilitate this process by enhancing hierarchical memory binding, thereby allowing superior performance for the more distant inferential judgments, a benefit that may operate below the level of conscious awareness.},
  language = {en},
  number = {18},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Ellenbogen, Jeffrey M. and Hu, Peter T. and Payne, Jessica D. and Titone, Debra and Walker, Matthew P.},
  month = may,
  year = {2007},
  keywords = {learning,association,inference,offline},
  pages = {7723-7728},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B5XSHJTP/Ellenbogen et al. - 2007 - Human relational memory requires time and sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZXBSFK58/7723.html},
  pmid = {17449637}
}

@article{wagner_sleep_2004,
  title = {Sleep Inspires Insight},
  volume = {427},
  copyright = {2004 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature02223},
  abstract = {Insight denotes a mental restructuring that leads to a sudden gain of explicit knowledge allowing qualitatively changed behaviour1,2. Anecdotal reports on scientific discovery suggest that pivotal insights can be gained through sleep3. Sleep consolidates recent memories4,5,6 and, concomitantly, could allow insight by changing their representational structure. Here we show a facilitating role of sleep in a process of insight. Subjects performed a cognitive task requiring the learning of stimulus\textendash{}response sequences, in which they improved gradually by increasing response speed across task blocks. However, they could also improve abruptly after gaining insight into a hidden abstract rule underlying all sequences. Initial training establishing a task representation was followed by 8 h of nocturnal sleep, nocturnal wakefulness, or daytime wakefulness. At subsequent retesting, more than twice as many subjects gained insight into the hidden rule after sleep as after wakefulness, regardless of time of day. Sleep did not enhance insight in the absence of initial training. A characteristic antecedent of sleep-related insight was revealed in a slowing of reaction times across sleep. We conclude that sleep, by restructuring new memory representations, facilitates extraction of explicit knowledge and insightful behaviour.},
  language = {en},
  number = {6972},
  journal = {Nature},
  author = {Wagner, Ullrich and Gais, Steffen and Haider, Hilde and Verleger, Rolf and Born, Jan},
  month = jan,
  year = {2004},
  pages = {352-355},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RK6EZX6G/Wagner et al. - 2004 - Sleep inspires insight.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JW4KSQJ5/nature02223.html}
}

@article{vyazovskiy_cortical_2009,
  title = {Cortical {{Firing}} and {{Sleep Homeostasis}}},
  volume = {63},
  issn = {0896-6273},
  doi = {10.1016/j.neuron.2009.08.024},
  abstract = {Summary
The need to sleep grows with the duration of wakefulness and dissipates with time spent asleep,~a process called sleep homeostasis. What are the consequences of staying awake on brain cells, and why is sleep needed? Surprisingly, we do not know whether the firing of cortical neurons is affected by how long an animal has been awake or asleep. Here, we found that after sustained wakefulness cortical neurons fire at higher frequencies in all behavioral states. During early NREM sleep after sustained wakefulness, periods of population activity (ON) are short, frequent, and associated with synchronous firing, while periods of neuronal silence are long and frequent. After sustained sleep, firing rates and synchrony decrease, while the duration of ON periods increases. Changes in firing patterns in NREM sleep correlate with changes in slow-wave activity, a marker of sleep homeostasis. Thus, the systematic increase of firing during wakefulness is counterbalanced by staying asleep.},
  number = {6},
  journal = {Neuron},
  author = {Vyazovskiy, Vladyslav V. and Olcese, Umberto and Lazimy, Yaniv M. and Faraguna, Ugo and Esser, Steve K. and Williams, Justin C. and Cirelli, Chiara and Tononi, Giulio},
  month = sep,
  year = {2009},
  keywords = {SYSNEURO,SIGNALING,SYSBIO},
  pages = {865-878},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K23243KU/Vyazovskiy et al. - 2009 - Cortical Firing and Sleep Homeostasis.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4NG355I2/S0896627309006370.html}
}

@article{liu_direct_2010,
  title = {Direct {{Evidence}} for {{Wake}}-{{Related Increases}} and {{Sleep}}-{{Related Decreases}} in {{Synaptic Strength}} in {{Rodent Cortex}}},
  volume = {30},
  copyright = {Copyright \textcopyright{} 2010 the authors 0270-6474/10/308671-05\$15.00/0},
  issn = {0270-6474, 1529-2401},
  doi = {10.1523/JNEUROSCI.1409-10.2010},
  abstract = {Despite evidence that waking is associated with net synaptic potentiation and sleep with depression, direct proof for changes in synaptic currents is lacking in large brain areas such as the cerebral cortex. By recording miniature EPSCs (mEPSCs) from frontal cortex slices of mice and rats that had been awake or asleep, we found that the frequency and amplitude of mEPSCs increased after waking and decreased after sleep, independent of time of day. Recovery sleep after deprivation also decreased mEPSCs, suggesting that sleep favors synaptic homeostasis. Since stronger synapses require more energy, space, and supplies, a generalized renormalization of synapses may be an important function of sleep.},
  language = {en},
  number = {25},
  journal = {Journal of Neuroscience},
  author = {Liu, Zhong-Wu and Faraguna, Ugo and Cirelli, Chiara and Tononi, Giulio and Gao, Xiao-Bing},
  month = jun,
  year = {2010},
  pages = {8671-8675},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IAXIBHJQ/Liu et al. - 2010 - Direct Evidence for Wake-Related Increases and Sle.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VSQD3CW2/8671.html},
  pmid = {20573912}
}

@article{lante_removal_2011,
  title = {Removal of Synaptic {{Ca}}$^2$+-Permeable {{AMPA}} Receptors during Sleep},
  volume = {31},
  issn = {1529-2401},
  doi = {10.1523/JNEUROSCI.3210-10.2011},
  abstract = {There is accumulating evidence that sleep contributes to memory formation and learning, but the underlying cellular mechanisms are incompletely understood. To investigate the impact of sleep on excitatory synaptic transmission, we obtained whole-cell patch-clamp recordings from layer V pyramidal neurons in acute slices of somatosensory cortex of juvenile rats (postnatal days 21-25). In animals after the dark period, philanthotoxin 74 (PhTx)-sensitive calcium-permeable AMPA receptors (CP-AMPARs) accounted for $\sim$25\% of total EPSP size, and current-voltage (I-V) relationships of the underlying EPSCs showed inward rectification. In contrast, in similar experiments after the light period, EPSPs were PhTx insensitive with linear I-V characteristics, indicating that CP-AMPARs were less abundant. Combined EEG and EMG recordings confirmed that slow-wave sleep-associated delta wave power peaked at the onset of the more quiescent, lights-on phase of the cycle. Subsequently, we show that burst firing, a characteristic action potential discharge mode of layer V pyramidal neurons during slow-wave sleep has a dual impact on synaptic AMPA receptor composition: repetitive burst firing without synaptic stimulation eliminated CP-AMPARs by activating serine/threonine phosphatases. Additionally, repetitive burst-firing paired with EPSPs led to input-specific long-term depression (LTD), affecting Ca(2+) impermeable AMPARs via protein kinase C signaling. In agreement with two parallel mechanisms, simple bursts were ineffective after the light period but paired bursts induced robust LTD. In contrast, incremental LTD was generated by both conditioning protocols after the dark cycle. Together, our results demonstrate qualitative changes at neocortical glutamatergic synapses that can be induced by discharge patterns characteristic of non-rapid eye movement sleep.},
  language = {eng},
  number = {11},
  journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
  author = {Lant\'e, Fabien and {Toledo-Salas}, Juan-Carlos and Ondrejcak, Tomas and Rowan, Michael J. and Ulrich, Daniel},
  month = mar,
  year = {2011},
  keywords = {Electromyography,Neurons,Animals,Electrophysiology,Excitatory Postsynaptic Potentials,Sleep,Rats,Calcium,Action Potentials,Analysis of Variance,Electroencephalography,Synapses,Somatosensory Cortex,Polyamines,Phenols,Rats; Wistar,Receptors; AMPA},
  pages = {3953-3961},
  pmid = {21411638}
}

@article{karni_dependence_1994,
  title = {Dependence on {{REM}} Sleep of Overnight Improvement of a Perceptual Skill},
  volume = {265},
  copyright = {\textcopyright{} 1994},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.8036518},
  abstract = {Several paradigms of perceptual learning suggest that practice can trigger long-term, experience-dependent changes in the adult visual system of humans. As shown here, performance of a basic visual discrimination task improved after a normal night's sleep. Selective disruption of rapid eye movement (REM) sleep resulted in no performance gain during a comparable sleep interval, although non-REM slow-wave sleep disruption did not affect improvement. On the other hand, deprivation of REM sleep had no detrimental effects on the performance of a similar, but previously learned, task. These results indicate that a process of human memory consolidation, active during sleep, is strongly dependent on REM sleep.},
  language = {en},
  number = {5172},
  journal = {Science},
  author = {Karni, A. and Tanne, D. and Rubenstein, B. S. and Askenasy, J. J. and Sagi, D.},
  month = jul,
  year = {1994},
  pages = {679-682},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7LHP4YCW/Karni et al. - 1994 - Dependence on REM sleep of overnight improvement o.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VWY9B4F4/679.html},
  pmid = {8036518}
}

@article{plihal_effects_1997,
  title = {Effects of {{Early}} and {{Late Nocturnal Sleep}} on {{Declarative}} and {{Procedural Memory}}},
  volume = {9},
  issn = {0898-929X},
  doi = {10.1162/jocn.1997.9.4.534},
  abstract = {Recall of paired-associate lists (declarative memory) and mirror-tracing skills (procedural memory) was assessed after retention intervals defined over early and late nocturnal sleep. In addition, effects of sleep on recall were compared with those of early and late retention intervals filled with wakefulness. Twenty healthy men served as subjects. Saliva cortisol concentrations were determined before and after the retention intervals to determine pituitary-adrenal secretory activity. Sleep was determined somnopolygraphically. Sleep generally enhanced recall when compared with the effects of corresponding retention intervals of wakefulness. The benefit from sleep on recall depended on the phase of sleep and on the type of memory: Recall of paired-associate lists improved more during early sleep, and recall of mirror-tracing skills improved more during late sleep. The effects may reflect different influences of slow wave sleep (SWS) and rapid eye movement (REM) sleep since time in SWS was 5 times longer during the early than late sleep retention interval, and time in REM sleep was twice as long during late than early sleep (p $<$ 0.005). Changes in cortisol concentrations, which independently of sleep and wakefulness were lower during early retention intervals than late ones, cannot account for the effects of sleep on memory. The experiments for the first time dissociate specific effects of early and late sleep on two principal types of memory, declarative and procedural, in humans.},
  number = {4},
  journal = {Journal of Cognitive Neuroscience},
  author = {Plihal, Werner and Born, Jan},
  month = jul,
  year = {1997},
  pages = {534-547},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X6M5E8UV/jocn.1997.9.4.html}
}

@article{smith_evidence_1996,
  title = {Evidence for a Paradoxical Sleep Window for Place Learning in the {{Morris}} Water Maze},
  volume = {59},
  issn = {0031-9384},
  doi = {10.1016/0031-9384(95)02054-3},
  abstract = {Sprague-Dawley rats were given 4 consecutive days of training in the hidden platform version of the Morris water maze. They were then given paradoxical sleep deprivation (PSD) for 12 h either immediately after each training session or after a 12-h delay. The former group showed impaired learning on the second day of training compared to the 12-h-delayed PSD group or a nondeprived control group. In a second experiment, three groups of rats were trained as before and then given PSD for a 4-h interval beginning either immediately after, 4 h after, or 8 h after the end of each training session. Only rats exposed to PSD during the period beginning 4 h after the end of training each day showed an acquisition deficit. In a third experiment, rats were trained in a visible platform version of the water maze and exposed to PSD for a 12-h period either beginning immediately after the last training trial each day or after a 12-h rest delay. Neither of these groups was impaired on the task compared to a non-PSD control group. These results suggest that there is a PS window for place, but not cue, learning in the Morris water maze.},
  number = {1},
  journal = {Physiology \& Behavior},
  author = {Smith, Carlyle and Rose, Gregory M.},
  month = jan,
  year = {1996},
  keywords = {Learning,Memory,Paradoxical sleep,Paradoxical sleep deprivation,Place learning Water maze,Sprague-Dawley rat},
  pages = {93-97},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/E9D2D9K9/Smith and Rose - 1996 - Evidence for a paradoxical sleep window for place .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NWVUVXFV/0031938495020543.html}
}

@article{stickgold_visual_2000,
  title = {Visual Discrimination Learning Requires Sleep after Training},
  volume = {3},
  copyright = {2000 Nature Publishing Group},
  issn = {1546-1726},
  doi = {10.1038/81756},
  abstract = {Performance on a visual discrimination task showed maximal improvement 48\textendash{}96 hours after initial training, even without intervening practice. When subjects were deprived of sleep for 30 hours after training and then tested after two full nights of recovery sleep, they showed no significant improvement, despite normal levels of alertness. Together with previous findings11 that subjects show no improvement when retested the same day as training, this demonstrates that sleep within 30 hours of training is absolutely required for improved performance.},
  language = {en},
  number = {12},
  journal = {Nature Neuroscience},
  author = {Stickgold, Robert and James, LaTanya and Hobson, J. Allan},
  month = dec,
  year = {2000},
  pages = {1237-1238},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DLX5ZIDI/Stickgold et al. - 2000 - Visual discrimination learning requires sleep afte.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8Y2M3YL9/nn1200_1237.html}
}

@article{walker_sleep_2003,
  title = {Sleep and the {{Time Course}} of {{Motor Skill Learning}}},
  volume = {10},
  issn = {1072-0502, 1549-5485},
  doi = {10.1101/lm.58503},
  abstract = {Growing evidence suggests that sleep plays an important role in the process of procedural learning. Most recently, sleep has been implicated in the continued development of motor-skill learning following initial acquisition. However, the temporal evolution of motor learning before and after sleep, the effects of different training regimens, and the long-term development of motor learning across multiple nights of sleep remain unknown. Here, we report data for subjects trained and retested on a sequential finger-tapping task across multiple days. The findings demonstrate firstly that following initial training, small practice-dependent improvements are possible before, but not following the large practice-independent gains that develop across a night of sleep. Secondly, doubling the quantity of initial training does not alter the amount of subsequent sleep-dependent learning that develops overnight. Thirdly, the amount of sleep-dependent learning does not correlate with the amount of practice-dependent learning achieved during training, suggesting the existence of two discrete motor-learning processes. Finally, whereas the majority of sleep-dependent motor-skill learning develops during the first night of sleep following training, additional nights of sleep still offer continued improvements.},
  language = {en},
  number = {4},
  journal = {Learning \& Memory},
  author = {Walker, Matthew P. and Brakefield, Tiffany and Seidman, Joshua and Morgan, Alexandra and Hobson, J. Allan and Stickgold, Robert},
  month = jan,
  year = {2003},
  pages = {275-284},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XQN8YZVQ/Walker et al. - 2003 - Sleep and the Time Course of Motor Skill Learning.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JR39QY6X/275.html},
  pmid = {12888546}
}

@article{walker_practice_2002,
  title = {Practice with {{Sleep Makes Perfect}}: {{Sleep}}-{{Dependent Motor Skill Learning}}},
  volume = {35},
  issn = {0896-6273},
  shorttitle = {Practice with {{Sleep Makes Perfect}}},
  doi = {10.1016/S0896-6273(02)00746-8},
  abstract = {Improvement in motor skill performance is known to continue for at least 24 hr following training, yet the relative contributions of time spent awake and asleep are unknown. Here we provide evidence that a night of sleep results in a 20\% increase in motor speed without loss of accuracy, while an equivalent period of time during wake provides no significant benefit. Furthermore, a significant correlation exists between the improved performance overnight and the amount of stage 2 NREM sleep, particularly late in the night. This finding of sleep-dependent motor skill improvement may have important implications for the efficient learning of all skilled actions in humans.},
  number = {1},
  journal = {Neuron},
  author = {Walker, Matthew P. and Brakefield, Tiffany and Morgan, Alexandra and Hobson, J. Allan and Stickgold, Robert},
  month = jul,
  year = {2002},
  pages = {205-211},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7UA5JNQ3/Walker et al. - 2002 - Practice with Sleep Makes Perfect Sleep-Dependent.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BFCRRL4W/S0896627302007468.html}
}

@book{schloerke_ggally_2018,
  title = {{{GGally}}: {{Extension}} to 'Ggplot2'},
  author = {Schloerke, Barret and Crowley, Jason and Cook, Di and Briatte, Francois and Marbach, Moritz and Thoen, Edwin and Elberg, Amos and Larmarange, Joseph},
  year = {2018},
  note = {R package version 1.4.0}
}

@article{fenzl_fully_2007,
  series = {Special Section on Neurobiology of Attention-Deficit Hyperactivity Disorder (ADHD): From Gene to Therapy},
  title = {Fully Automated Sleep Deprivation in Mice as a Tool in Sleep Research},
  volume = {166},
  issn = {0165-0270},
  doi = {10.1016/j.jneumeth.2007.07.007},
  abstract = {Although total sleep deprivation is frequently used in sleep research, the techniques used such as gentle handling are labor consuming and not standardized (and boring). In order to minimize these limitations, we developed a fully automated setup, which can be used for total sleep deprivation. A shortfall of individually adjustable thresholds of electromyogram (EMG) signals from sleep deprived animals was used online to switch running wheels incorporated into the home cages. Randomized direction of rotations, adaptable rotational speed and automatic deactivation of the running wheels during quiet waking of the animals provided robust and standardized sleep deprivation without increased stress, when compared to gentle handling. The setup can easily be introduced to a variety of home cages and is individually adaptable to each animal to be sleep deprived.},
  number = {2},
  journal = {Journal of Neuroscience Methods},
  author = {Fenzl, Thomas and Romanowski, Christoph P. N. and Flachskamm, Cornelia and Honsberg, Karlheinz and Boll, Erwin and Hoehne, Arnold and Kimura, Mayumi},
  month = nov,
  year = {2007},
  keywords = {Mice,Sleep deprivation,Automated,Gentle handling},
  pages = {229-235},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RFV9PL2T/S0165027007003718.html}
}

@article{underwood_lavoisier_1944,
  title = {Lavoisier and the {{History}} of {{Respiration}}},
  volume = {37},
  issn = {0035-9157},
  abstract = {Images
null},
  number = {6},
  journal = {Proceedings of the Royal Society of Medicine},
  author = {Underwood, E. Ashworth},
  month = apr,
  year = {1944},
  pages = {247-262},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z7H29YZJ/Underwood - 1944 - Lavoisier and the History of Respiration.pdf},
  pmid = {19992823},
  pmcid = {PMC2180993}
}

@book{pliny_the_elder_natural_1855,
  title = {The Natural History of {{Pliny}}},
  abstract = {Book digitized by Google and uploaded to the Internet Archive by user tpb.},
  language = {eng},
  publisher = {{London, H. G. Bohn}},
  author = {{Pliny the Elder}},
  translator = {Bostock, John and Riley, Henry Thomas},
  year = {1855},
  keywords = {Natural history},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LAH4Z33I/Pliny - 1855 - The natural history of Pliny.pdf}
}

@book{hamilton_ggtern_2017,
  title = {Ggtern: {{An Extension}} to 'Ggplot2', for the {{Creation}} of {{Ternary Diagrams}}},
  author = {Hamilton, Nicholas},
  year = {2017},
  note = {R package version 2.2.1}
}

@article{geissmann_rethomics_2018,
  title = {Rethomics: An {{R}} Framework to Analyse High-Throughput Behavioural Data},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  shorttitle = {Rethomics},
  doi = {10.1101/305664},
  abstract = {The recent development of automatised methods to score various behaviours on a large number of animals provides biologists with an unprecedented set of tools to decipher these complex phenotypes. Analysing such data comes with several challenges that are largely shared across acquisition platform and paradigms. Here, we present rethomics, a set of R packages that unifies the analysis of behavioural datasets in an efficient and flexible manner. rethomics offers a computational solution to storing, manipulating and visualising large amounts of behavioural data. We propose it as a tool to bridge the gap between behavioural biology and data sciences, thus connecting computational and behavioural scientists. rethomics comes with a extensive documentation as well as a set of both practical and theoretical tutorials (available at https://rethomics.github.io).},
  language = {en},
  journal = {bioRxiv},
  author = {Geissmann, Quentin and Rodriguez, Luis Garcia and Beckwith, Esteban J. and Gilestro, Giorgio F.},
  month = apr,
  year = {2018},
  pages = {305664},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F9DIXQWJ/Geissmann et al. - 2018 - Rethomics an R framework to analyse high-throughp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6XV5RMCA/305664.html}
}

@book{r_core_team_r_2014,
  address = {Vienna, Austria},
  title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
  publisher = {{R Foundation for Statistical Computing}},
  author = {{R Core Team}},
  year = {2014},
  note = {00003}
}

@incollection{efron_bootstrap_1992,
  series = {Springer Series in Statistics},
  title = {Bootstrap {{Methods}}: {{Another Look}} at the {{Jackknife}}},
  isbn = {978-0-387-94039-7 978-1-4612-4380-9},
  shorttitle = {Bootstrap {{Methods}}},
  abstract = {We discuss the following problem given a random sample X = (X 1, X 2,\ldots, X n) from an unknown probability distribution F, estimate the sampling distribution of some prespecified random variable R(X, F), on the basis of the observed data x. (Standard jackknife theory gives an approximate mean and variance in the case R(X, F) = \texttheta{}(F\^)-\texttheta{}(F)\texttheta{}(F\^)-\texttheta{}(F)$\backslash$theta $\backslash$left( \{$\backslash$hat F\} $\backslash$right) - $\backslash$theta $\backslash$left( F $\backslash$right), \texttheta{} some parameter of interest.) A general method, called the ``bootstrap'', is introduced, and shown to work satisfactorily on a variety of estimation problems. The jackknife is shown to be a linear approximation method for the bootstrap. The exposition proceeds by a series of examples: variance of the sample median, error rates in a linear discriminant analysis, ratio estimation, estimating regression parameters, etc.},
  language = {en},
  booktitle = {Breakthroughs in {{Statistics}}},
  publisher = {{Springer, New York, NY}},
  author = {Efron, Bradley},
  year = {1992},
  pages = {569-593},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/82L5X9LJ/978-1-4612-4380-9_41.html},
  doi = {10.1007/978-1-4612-4380-9_41}
}

@article{fowlkes_method_1983,
  title = {A {{Method}} for {{Comparing Two Hierarchical Clusterings}}},
  volume = {78},
  issn = {0162-1459},
  doi = {10.1080/01621459.1983.10478008},
  abstract = {This article concerns the derivation and use of a measure of similarity between two hierarchical clusterings. The measure, Bk , is derived from the matching matrix, [mij ], formed by cutting the two hierarchical trees and counting the number of matching entries in the k clusters in each tree. The mean and variance of Bk  are determined under the assumption that the margins of [mij ] are fixed. Thus, Bk  represents a collection of measures for k = 2, \ldots, n \textendash{} 1. (k, Bk ) plots are found to be useful in portraying the similarity of two clusterings. Bk  is compared to other measures of similarity proposed respectively by Baker (1974) and Rand (1971). The use of (k, Bk ) plots for studying clustering methods is explored by a series of Monte Carlo sampling experiments. An example of the use of (k, Bk ) on real data is given.},
  number = {383},
  journal = {Journal of the American Statistical Association},
  author = {Fowlkes, E. B. and Mallows, C. L.},
  month = sep,
  year = {1983},
  pages = {553-569},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JPMY2WT3/01621459.1983.html}
}

@article{sokal_statistical_1958,
  title = {A Statistical Method for Evaluating Systematic Relationship},
  volume = {28},
  journal = {University of Kansas Science Bulletin},
  author = {Sokal, R. R.},
  year = {1958},
  pages = {1409-1438},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BYBUB2QF/10011406054.html}
}

@article{bhattacharyya_measure_1943,
  title = {On a Measure of Divergence between Two Statistical Populations Defined by Their Probability Distributions},
  volume = {35},
  journal = {Bulletin of Calcutta Maths Society},
  author = {Bhattacharyya, A.},
  year = {1943},
  pages = {99-110},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/B9BGKYQQ/10016436164.html}
}

@book{menant_bibliotheque_1880,
  title = {La Biblioth\`eque Du Palais de {{Ninive}} : D\'ecouvertes Assyriennes},
  copyright = {domaine public},
  shorttitle = {La Biblioth\`eque Du Palais de {{Ninive}}},
  abstract = {La biblioth\`eque du palais de Ninive : d\'ecouvertes assyriennes / par M. Joachim Menant -- 1880 -- livre},
  language = {EN},
  author = {Menant, Joachim},
  year = {1880},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/K3JUBZKC/f41.html}
}

@article{breiman_random_2001,
  title = {Random {{Forests}}},
  volume = {45},
  issn = {0885-6125, 1573-0565},
  doi = {10.1023/A:1010933404324},
  abstract = {Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges a.s. to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the correlation between them. Using a random selection of features to split each node yields error rates that compare favorably to Adaboost (Y. Freund \& R. Schapire, Machine Learning: Proceedings of the Thirteenth International conference, ***, 148\textendash{}156), but are more robust with respect to noise. Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the splitting. Internal estimates are also used to measure variable importance. These ideas are also applicable to regression.},
  language = {en},
  number = {1},
  journal = {Machine Learning},
  author = {Breiman, Leo},
  month = oct,
  year = {2001},
  keywords = {Computing Methodologies,Artificial Intelligence (incl. Robotics),Simulation and Modeling,Language Translation and Linguistics,Automation and Robotics,regression,Classification,Ensemble},
  pages = {5-32},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JD9SLIWC/Breiman - 2001 - Random Forests.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/USH4NK8U/A1010933404324.html}
}

@book{jones_scipy_2001,
  title = {{{SciPy}}: {{Open}} Source Scientific Tools for {{Python}}},
  author = {Jones, Eric and Oliphant, Travis and Peterson, Pearu and {others}},
  year = {2001},
  note = {00816 
[Online; accessed 2015-06-29]}
}

@article{walt_numpy_2011,
  title = {The {{NumPy Array}}: {{A Structure}} for {{Efficient Numerical Computation}}},
  volume = {13},
  issn = {1521-9615},
  shorttitle = {The {{NumPy Array}}},
  doi = {10.1109/MCSE.2011.37},
  abstract = {In the Python world, NumPy arrays are the standard representation for numerical data and enable efficient implementation of numerical computations in a high-level language. As this effort shows, NumPy performance can be improved through three techniques: vectorizing calculations, avoiding copying data in memory, and minimizing operation counts.},
  number = {2},
  journal = {Computing in Science \& Engineering},
  author = {van der Walt, St\'efan and Colbert, S. Chris and Varoquaux, Ga\"el},
  month = mar,
  year = {2011},
  pages = {22-30},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RUCDVEQD/MCSE.2011.html},
  note = {00066}
}

@article{bradski_opencv_2000,
  title = {The {{OpenCV Library}}},
  journal = {Dr. Dobb's Journal of Software Tools},
  author = {Bradski, G},
  year = {2000},
  keywords = {bibtex-import},
  note = {03691}
}

@inproceedings{piccardi_background_2004,
  title = {Background Subtraction Techniques: A Review},
  volume = {4},
  shorttitle = {Background Subtraction Techniques},
  doi = {10.1109/ICSMC.2004.1400815},
  abstract = {Background subtraction is a widely used approach for detecting moving objects from static cameras. Many different methods have been proposed over the recent years and both the novice and the expert can be confused about their benefits and limitations. In order to overcome this problem, this paper provides a review of the main methods and an original categorisation based on speed, memory requirements and accuracy. Such a review can effectively guide the designer to select the most suitable method for a given application in a principled way. Methods reviewed include parametric and non-parametric background density estimates and spatial correlation approaches.},
  booktitle = {2004 {{IEEE International Conference}} on {{Systems}}, {{Man}} and {{Cybernetics}}},
  author = {Piccardi, M.},
  month = oct,
  year = {2004},
  keywords = {Information technology,Layout,image motion analysis,object detection,background density estimation,background subtraction technique,spatial correlation,static cameras,Australia,Cameras,Computer vision,Filters,Geometry,Subtraction techniques,Videos,feature extraction},
  pages = {3099-3104 vol.4},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NZ9RNMWI/Piccardi - 2004 - Background subtraction techniques a review.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7GSC42MT/abs_all.html},
  note = {01533}
}

@inproceedings{koller_towards_1994,
  title = {Towards Robust Automatic Traffic Scene Analysis in Real-Time},
  volume = {1},
  doi = {10.1109/ICPR.1994.576243},
  abstract = {Automatic symbolic traffic scene analysis is essential to many areas of IVHS (Intelligent Vehicle Highway Systems). Traffic scene information can be used to optimize traffic flow during busy periods, identify stalled vehicles and accidents, and aid the decision-making of an autonomous vehicle controller. Improvements in technologies for machine vision-based surveillance and high-level symbolic reasoning have enabled the authors to develop a system for detailed, reliable traffic scene analysis. The machine vision component of the system employs a contour tracker and an affine motion model based on Kalman filters to extract vehicle trajectories over a sequence of traffic scene images. The symbolic reasoning component uses a dynamic belief network to make inferences about traffic events such as vehicle lane changes and stalls. In this paper, the authors discuss the key tasks of the vision and reasoning components as well as their integration into a working prototype. Preliminary results of an implementation on special purpose hardware using C-40 Digital Signal Processors show that near real-time performance can be achieved without further improvements},
  booktitle = {, {{Proceedings}} of the 12th {{IAPR International Conference}} on {{Pattern Recognition}}, 1994. {{Vol}}. 1 - {{Conference A}}: {{Computer Vision}} Amp; {{Image Processing}}},
  author = {Koller, D. and Weber, J. and Huang, T. and Malik, J. and Ogasawara, G. and Rao, B. and Russell, S.},
  month = oct,
  year = {1994},
  keywords = {Kalman filters,IVHS,affine motion model,autonomous vehicle controller,contour tracker,decision-making,dynamic belief network,high-level symbolic reasoning,intelligent vehicle highway systems,machine vision-based surveillance,near real-time performance,robust automatic traffic scene analysis,stalled vehicles,traffic flow optimisation,vehicle lane changes,Automated highways,Image analysis,Intelligent vehicles,Layout,Mobile robots,Remotely operated vehicles,Road accidents,Telecommunication traffic,Traffic control,Robustness},
  pages = {126-131 vol.1},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TN64XYGS/Koller et al. - 1994 - Towards robust automatic traffic scene analysis in.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ABK9D7BA/abs_all.html},
  note = {00518}
}

@article{halasz_nature_nodate,
  title = {The Nature of Arousal in Sleep},
  volume = {13},
  issn = {1365-2869},
  doi = {10.1111/j.1365-2869.2004.00388.x},
  abstract = {The role of arousals in sleep is gaining interest among both basic researchers and clinicians. In the last 20 years increasing evidence shows that arousals are deeply involved in the pathophysiology of sleep disorders. The nature of arousals in sleep is still a matter of debate. According to the conceptual framework of the American Sleep Disorders Association criteria, arousals are a marker of sleep disruption representing a detrimental and harmful feature for sleep. In contrast, our view indicates arousals as elements weaved into the texture of sleep taking part in the regulation of the sleep process. In addition, the concept of micro-arousal (MA) has been extended, incorporating, besides the classical low-voltage fast-rhythm electroencephalographic (EEG) arousals, high-amplitude EEG bursts, be they like delta-like or K-complexes, which reflects a special kind of arousal process, mobilizing parallely antiarousal swings. In physiologic conditions, the slow and fast MA are not randomly scattered but appear structurally distributed within sleep representing state-specific arousal responses. MA preceded by slow waves occurs more frequently across the descending part of sleep cycles and in the first cycles, while the traditional fast type of arousals across the ascending slope of cycles prevails during the last third of sleep. The uniform arousal characteristics of these two types of MAs is supported by the finding that different MAs are associated with an increasing magnitude of vegetative activation ranging hierarchically from the weaker slow EEG types (coupled with mild autonomic activation) to the stronger rapid EEG types (coupled with a vigorous autonomic activation). Finally, it has been ascertained that MA are not isolated events but are basically endowed with a periodic nature expressed in non-rapid eye movement (NREM) sleep by the cyclic alternating pattern (CAP). Understanding the role of arousals and CAP and the relationship between physiologic and pathologic MA can shed light on the adaptive properties of the sleeping brain and provide insight into the pathomechanisms of sleep disturbances. Functional significance of arousal in sleep, and particularly in NREM sleep, is to ensure the reversibility of sleep, without which it would be identical to coma. Arousals may connect the sleeper with the surrounding world maintaining the selection of relevant incoming information and adapting the organism to the dangers and demands of the outer world. In this dynamic perspective, ongoing phasic events carry on the one hand arousal influences and on the other elements of information processing. The other function of arousals is tailoring the more or less stereotyped endogenously determined sleep process driven by chemical influences according to internal and external demands. In this perspective, arousals shape the individual course of night sleep as a variation of the sleep program.},
  language = {en},
  number = {1},
  journal = {Journal of Sleep Research},
  author = {Hal\'asz, P\'eter and Terzano, Mario and Parrino, Liborio and B\'odizs, R\'obert},
  keywords = {NREM sleep,cyclic alternating pattern (CAP),K-complex,micro-arousal},
  pages = {1-23},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/D3KWVBFS/Halász et al. - The nature of arousal in sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U74Q83FV/j.1365-2869.2004.00388.html}
}

@article{dattilo_sleep_2011,
  title = {Sleep and Muscle Recovery: {{Endocrinological}} and Molecular Basis for a New and Promising Hypothesis},
  volume = {77},
  issn = {0306-9877},
  shorttitle = {Sleep and Muscle Recovery},
  doi = {10.1016/j.mehy.2011.04.017},
  language = {English},
  number = {2},
  journal = {Medical Hypotheses},
  author = {Dattilo, M. and Antunes, H. K. M. and Medeiros, A. and Neto, M. M\^onico and Souza, H. S. and Tufik, S. and de Mello, M. T.},
  month = aug,
  year = {2011},
  pages = {220-222},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XTD7SKVY/abstract.html},
  pmid = {21550729}
}

@article{orzel-gryglewska_consequences_2010,
  title = {Consequences of Sleep Deprivation},
  volume = {23},
  issn = {1896-494X(Electronic),1232-1087(Print)},
  doi = {10.2478/v10001-010-0004-9},
  abstract = {This paper presents the history of research and the results of recent studies on the effects of sleep deprivation in animals and humans. Humans can bear several days of continuous sleeplessness, experiencing deterioration in wellbeing and effectiveness; however, also a shorter reduction in the sleep time may lead to deteriorated functioning. Sleeplessness accounts for impaired perception, difficulties in keeping concentration, vision disturbances, slower reactions, as well as the appearance of microepisodes of sleep during wakefulness which lead to lower capabilities and efficiency of task performance and to increased number of errors. Sleep deprivation results in poor memorizing, schematic thinking, which yields wrong decisions, and emotional disturbances such as deteriorated interpersonal responses and increased aggressiveness. The symptoms are accompanied by brain tissue hypometabolism, particularly in the thalamus, prefrontal, frontal and occipital cortex and motor speech centres. Sleep deficiency intensifies muscle tonus and coexisting tremor, speech performance becomes monotonous and unclear, and sensitivity to pain is higher. Sleeplessness also relates to the changes in the immune response and the pattern of hormonal secretion, of the growth hormone in particular. The risk of obesity, diabetes and cardiovascular disease increases. The impairment of performance which is caused by 20-25 hours of sleeplessness is comparable to that after ethanol intoxication at the level of 0.10\% blood alcohol concentration. The consequences of chronic sleep reduction or a shallow sleep repeated for several days tend to accumulate and resemble the effects of acute sleep deprivation lasting several dozen hours. At work, such effects hinder proper performance of many essential tasks and in extreme situations (machine operation or vehicle driving), sleep loss may be hazardous to the worker and his/her environment. (PsycINFO Database Record (c) 2016 APA, all rights reserved)},
  number = {1},
  journal = {International Journal of Occupational Medicine and Environmental Health},
  author = {{Orze\l{}-Gryglewska}, Jolanta},
  year = {2010},
  keywords = {Insomnia,Sleep Deprivation,Performance,Animal Development,Consequence,Experimentation,Human Development,Psychophysiology,Species Differences},
  pages = {95-114},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZDJYEW4I/2010-13439-002.html}
}

@article{lyamin_animal_2005,
  title = {Animal Behaviour: {{Continuous}} Activity in Cetaceans after Birth},
  volume = {435},
  copyright = {2005 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {Animal Behaviour},
  doi = {10.1038/4351177a},
  abstract = {All mammals previously studied take maximal rest or sleep after birth, with the amount gradually decreasing as they grow to adulthood1,2, and adult fruitflies and rats die if they are forcibly deprived of sleep3,4. It has therefore been assumed that sleep is necessary for development and serves a vital function in adults. But we show here that, unlike terrestrial mammals, killer-whale and bottlenose-dolphin neonates and their mothers show little or no typical sleep behaviour for the first postpartum month, avoiding obstacles and remaining mobile for 24 hours a day. We find that neonates and their mothers gradually increase the amount of time they spend resting to normal adult levels over a period of several months, but never exceed these levels. Our findings indicate either that sleep behaviour may not have the developmental and life-sustaining functions attributed to it, or that alternative mechanisms may have evolved in cetaceans.},
  language = {en},
  number = {7046},
  journal = {Nature},
  author = {Lyamin, Oleg and Pryaslova, Julia and Lance, Valentine and Siegel, Jerome},
  month = jun,
  year = {2005},
  pages = {1177}
}

@article{tobler_behavioural_1996,
  title = {Behavioural Sleep in the Giraffe ({{Giraffa}} Camelopardalis) in a Zoological Garden},
  volume = {5},
  issn = {0962-1105},
  abstract = {Behavioural sleep was assessed for 152 nights in 5 adult, 2 immature and 1 juvenile giraffes at a zoological garden, using continuous time-lapse video recording. Sleep occurred while the giraffes were standing (SS) and in recumbency (RS). Paradoxical sleep (PS) was recognized by the peculiar positioning of the head on the croup and by phasic events. The 24-h sleep profile had a main bimodal nocturnal sleep period between 20.00 and 07.00 hours, with a trough between 02.00 and 04.00 hours, and several short naps between 12.00 and 16.00 hours. Total sleep time (TST), excluding the juvenile, was 4.6 h, whereby PS comprised only 4.7\%. TST was not age dependent, but the lowest amount of RS and the highest amount of SS occurred in the oldest and the two oldest animals, respectively. Sleep was fragmented, as indicated by the predominance of RS episodes lasting less than 11 min. Sleep cycle duration was very variable with most values between 1 and 35 min (when no waking or RS was allowed within PS episodes), or 6-35 min (when the criteria for ending a PS episode allowed 1-2 min interruptions by RS). There were several indications for sleep regulation: (i) RS and SS complemented each other to yield a relatively stable daily value of TST; (ii) sleep was redistributed on nights following a day when the giraffes spent a few hours in an outside enclosure. The first peak of the bimodal sleep profile was absent and RS was more prominent in the second half of the night compared with nights following days spent in the barn; and (iii) napping was followed by a minor reduction of RS and an increase in SS in the subsequent night compared with nights following days without naps.},
  language = {eng},
  number = {1},
  journal = {Journal of Sleep Research},
  author = {Tobler, I. and Schwierin, B.},
  month = mar,
  year = {1996},
  keywords = {Behavior; Animal,Female,Male,Animals,Circadian Rhythm,Age Factors,Wakefulness,Animals; Zoo,Sleep; REM},
  pages = {21-32},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HXC7XMJK/Tobler and Schwierin - Behavioural sleep in the giraffe (Giraffa camelopa.pdf},
  pmid = {8795798}
}

@article{zepelin_mammalian_1974,
  title = {Mammalian {{Sleep}}, {{Longevity}}, and {{Energy Metabolism}}; Pp. 447\textendash{}470},
  volume = {10},
  issn = {0006-8977, 1421-9743},
  doi = {10.1159/000124331},
  abstract = {Based on data for 53 mammalian species reported in the literature, statistical analyses revealed that daily sleep quotas correlate positively with metabolic rate and negatively with maximum life span and brain weight. Sleep cycle length correlates positively with life span and brain weight and negatively with metabolic rate. Paradoxical sleep figures in these intercorrelations only by virtue of its positive correlation with slow wave sleep. The correlation between sleep time and metabolic rate suggests that sleep has the function of enforcing rest and limiting metabolic requirements, although some inconsistent findings are noted. Strong correlations of cycle length with brain weight and metabolic rate suggest that the significance of cycle length has not been sufficiently explored.},
  language = {english},
  number = {6},
  journal = {Brain, Behavior and Evolution},
  author = {Zepelin, Harold and Rechtschaffen, Allan},
  year = {1974},
  pages = {447-470},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6VMP28CU/124331.html}
}

@article{giorgi_energetic_2001,
  title = {The Energetic Grooming Costs Imposed by a Parasitic Mite ({{Spinturnix}} Myoti) upon Its Bat Host ({{Myotis}} Myotis)},
  volume = {268},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2001.1686},
  abstract = {Parasites often exert severe negative effects upon their host's fitness. Natural selection has therefore prompted the evolution of anti\textendash{}parasite mechanisms such as grooming. Grooming is efficient at reducing parasitic loads in both birds and mammals, but the energetic costs it entails have not been properly quantified. We measured both the energetic metabolism and behaviour of greater mouse\textendash{}eared bats submitted to three different parasite loads (no, 20 and 40 mites) during whole daily cycles. Mites greatly affected their time and energy budgets. They caused increased grooming activity, reduced the overall time devoted to resting and provoked a dramatic shortening of resting bout duration. Correspondingly, the bats' overall metabolism (oxygen consumption) increased drastically with parasite intensity and, during the course of experiments, the bats lost more weight when infested with 40 rather than 20 or no parasites. The short\textendash{}term energetic constraints induced by anti\textendash{}parasite grooming are probably associated with long-term detrimental effects such as a decrease in survival and overall reproductive value.},
  language = {en},
  number = {1480},
  journal = {Proceedings of the Royal Society of London B: Biological Sciences},
  author = {Giorgi, Maud S. and Arlettaz, Rapha\"e and Christe, Philippe and Vogel, Peter},
  month = oct,
  year = {2001},
  pages = {2071-2075},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CUJWFFK5/2071.html},
  pmid = {11571055}
}

@article{tobler_behavioral_1992,
  title = {Behavioral Sleep in the {{Asian}} Elephant in Captivity},
  volume = {15},
  issn = {0161-8105},
  abstract = {Sleeping behavior was investigated during 294 nights for female Asian elephants (circus: n = 7; zoo: n = 5; including an infant). The animals were recorded continuously on time-lapse video tapes for 7-16 days consecutively. Seasonal changes in sleep behavior were studied by comparing summer (16-day) and winter (13-15-day) recordings; and sleep development was assessed by recording a mother and her infant for three consecutive nights per month for 15 months (age 5-19 months). Sleep occurred in a recumbent (RS) and in a standing position (standing sleep: SS). Although signs of paradoxical sleep (PS) were often evident, the exact onset and end of a PS episode could not be determined. Sleep onset occurred after 2100 hours, and sleep increased progressively reaching a maximum between 0100 and 0400 hours. Total sleep time (TST) in the adults comprised 4.0-6.5 hours per night (including 13.8-130.9 minutes of SS) and did not differ between the two groups. Seasonal differences were present in TST and in the distribution of sleep within the night; more sleep occurred in the winter. The duration of RS episodes in the adults was 72.0 minutes, a value far below the sleep-cycle length of 124 minutes that others have reported for elephants. TST in the infant decreased during the course of the 15-month recording period from 8.1 hours to 5.1 hours. SS occurred for the first time at the age of 9 months.},
  language = {eng},
  number = {1},
  journal = {Sleep},
  author = {Tobler, I.},
  month = feb,
  year = {1992},
  keywords = {Female,Animals,Circadian Rhythm,Age Factors,Sleep Stages,Social Environment,Seasons,Posture,Animals; Zoo,Elephants},
  pages = {1-12},
  pmid = {1557589}
}

@article{zepelin_mammalian_nodate,
  title = {Mammalian Sleep},
  author = {Zepelin, Harold and Siegel, Jerome M and Tobler, Irene},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TD72V65T/e349b63e71421fd5b41fb439f96c1482cd3d.pdf}
}

@article{martino_microbial_2017,
  series = {Mobile genetic elements and HGT in prokaryotes * Microbiota},
  title = {Microbial Influence on {{Drosophila}} Biology},
  volume = {38},
  issn = {1369-5274},
  doi = {10.1016/j.mib.2017.06.004},
  abstract = {Commensal bacteria profoundly affect the biology of their animal partners. Drosophila melanogaster has been broadly used to study microbiota effects on invertebrates, whose findings are frequently applicable to translational studies. The beneficial role of commensal microbes on Drosophila biology is extensively described, ranging from growth to metabolism, immunity and even behaviour. However, the mechanisms underlying these effects are not well understood. Studies continue to discover new layers of complexity in the host\textendash{}bacteria partnership that constantly changes depending on a plethora of different variables. This review discusses the latest advances in understanding the molecular bases of microbiota impact on Drosophila physiology and behaviour, emphasizing its broad influence and the intricate interdependence of the two partners in shaping their biology.},
  journal = {Current Opinion in Microbiology},
  author = {Martino, ME and Ma, D and Leulier, F},
  month = aug,
  year = {2017},
  pages = {165-170},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2XL6VGW6/S1369527417300413.html}
}

@article{sonn_serine_2018,
  title = {Serine Metabolism in the Brain Regulates Starvation-Induced Sleep Suppression in {{Drosophila}} Melanogaster},
  copyright = {Copyright \textcopyright{} 2018 the Author(s). Published by PNAS.. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1719033115},
  abstract = {Sleep and metabolism are physiologically and behaviorally intertwined; however, the molecular basis for their interaction remains poorly understood. Here, we identified a serine metabolic pathway as a key mediator for starvation-induced sleep suppression. Transcriptome analyses revealed that enzymes involved in serine biosynthesis were induced upon starvation in Drosophila melanogaster brains. Genetic mutants of astray (aay), a fly homolog of the rate-limiting phosphoserine phosphatase in serine biosynthesis, displayed reduced starvation-induced sleep suppression. In contrast, a hypomorphic mutation in a serine/threonine-metabolizing enzyme, serine/threonine dehydratase (stdh), exaggerated starvation-induced sleep suppression. Analyses of double mutants indicated that aay and stdh act on the same genetic pathway to titrate serine levels in the head as well as to adjust starvation-induced sleep behaviors. RNA interference-mediated depletion of aay expression in neurons, using cholinergic Gal4 drivers, phenocopied aay mutants, while a nicotinic acetylcholine receptor antagonist selectively rescued the exaggerated starvation-induced sleep suppression in stdh mutants. Taken together, these data demonstrate that neural serine metabolism controls sleep during starvation, possibly via cholinergic signaling. We propose that animals have evolved a sleep-regulatory mechanism that reprograms amino acid metabolism for adaptive sleep behaviors in response to metabolic needs.},
  language = {en},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Sonn, Jun Young and Lee, Jongbin and Sung, Min Kyung and Ri, Hwajung and Choi, Jung Kyoon and Lim, Chunghun and Choe, Joonho},
  month = jun,
  year = {2018},
  keywords = {starvation,serine,sleep regulation},
  pages = {201719033},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HULDRCEK/Sonn et al. - 2018 - Serine metabolism in the brain regulates starvatio.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JB7LKXLX/1719033115.html},
  pmid = {29915051}
}

@article{beale_circadian_2013,
  title = {Circadian Rhythms in {{Mexican}} Blind Cavefish {{{\emph{Astyanax}}}}{\emph{ Mexicanus}} in the Lab and in the Field},
  volume = {4},
  copyright = {2013 Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/ncomms3769},
  abstract = {Biological clocks have evolved as an adaptation to life on a rhythmic planet, synchronising physiological processes to the environmental light\textendash{}dark cycle. Here we examine circadian clock function in Mexican blind cavefish Astyanax mexicanus and its surface counterpart. In the lab, adult surface fish show robust circadian rhythms in per1, which are retained in cave populations, but with substantial alterations. These changes may be due to increased levels of light-inducible genes in cavefish, including clock repressor per2. From a molecular standpoint, cavefish appear as if they experience `constant light' rather than perpetual darkness. Micos River samples show similar per1 oscillations to those in the lab. However, data from Chica Cave shows complete repression of clock function, while expression of several light-responsive genes is raised, including DNA repair genes. We propose that altered expression of light-inducible genes provides a selective advantage to cavefish at the expense of a damped circadian oscillator.},
  language = {en},
  journal = {Nature Communications},
  author = {Beale, Andrew and Guibal, Christophe and Tamai, T. Katherine and Klotz, Linda and Cowen, Sophie and Peyric, Elodie and Reynoso, V\'ictor H. and Yamamoto, Yoshiyuki and Whitmore, David},
  month = nov,
  year = {2013},
  pages = {2769},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2M9NCEG8/Beale et al. - 2013 - Circadian rhythms in Mexican blind cavefish iAst.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KLX68XUF/ncomms3769.html}
}

@article{duboue_evolutionary_2011,
  title = {Evolutionary {{Convergence}} on {{Sleep Loss}} in {{Cavefish Populations}}},
  volume = {21},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2011.03.020},
  abstract = {Summary
Patterns of sleep vary widely among species [1, 2, 3, 4], but the functional and evolutionary principles responsible for this diversity remain unknown. The characin fish, Astyanax mexicanus, has eyed surface and numerous blind cave populations [5]. The cave populations are largely independent in their origins, and the species is ideal for studying the genetic bases of convergent evolution [5, 6, 7]. Here we show that this system is also uniquely valuable for the investigation of variability in patterns of sleep. We find that a clearly defined change in ecological conditions, from surface to cave, is correlated with a dramatic reduction in sleep in three independently derived cave populations of A.~mexicanus. Analyses of surface \texttimes{} cave hybrids show that the alleles for reduced sleep in the Pach\'on and Tinaja cave populations are dominant in effect to the surface alleles. Genetic analysis of hybrids between surface and Pach\'on cavefish suggests that only a small number of loci with dominant effects are involved. Our results demonstrate that sleep is an evolutionarily labile phenotype, highly responsive to changes in ecological conditions. To our knowledge, this is the first example of a single species with a convergence on sleep loss exhibited by several independently evolved populations correlated with population-specific ecologies.},
  number = {8},
  journal = {Current Biology},
  author = {Dubou\'e, Erik R. and Keene, Alex C. and Borowsky, Richard L.},
  month = apr,
  year = {2011},
  pages = {671-676},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FXNSRYQ3/Duboué et al. - 2011 - Evolutionary Convergence on Sleep Loss in Cavefish.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VGGPTUZN/S0960982211002922.html}
}

@article{jaggard_hypocretin_2018,
  title = {Hypocretin Underlies the Evolution of Sleep Loss in the {{Mexican}} Cavefish},
  volume = {7},
  copyright = {\textcopyright{} 2018 Jaggard et al.. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  doi = {10.7554/eLife.32637},
  abstract = {The identification of evolutionarily-derived changes in Hypocretin function within the brains of short-sleeping Mexican cavefish provides a system for investigating the mechanistic basis of sleep differences throughout the animal kingdom.},
  language = {en},
  journal = {eLife},
  author = {Jaggard, James B. and Stahl, Bethany A. and Lloyd, Evan and Prober, David A. and Duboue, Erik R. and Keene, Alex C.},
  month = feb,
  year = {2018},
  pages = {e32637},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/APHF52RC/Jaggard et al. - 2018 - Hypocretin underlies the evolution of sleep loss i.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/22HIK4ZZ/32637.html}
}

@book{polastron_books_2007,
  title = {Books on {{Fire}}: {{The Tumultuous Story}} of the {{World}}'s {{Great Libraries}}},
  isbn = {978-0-500-51384-2},
  shorttitle = {Books on {{Fire}}},
  abstract = {Here is a magisterial history of the destruction of knowledge over the millennia. Hugely impressive in scope, Polastron's book takes the reader on a journey from ancient Mesopotamia to modern times, showing how the urge to write, read and collect books has always gone hand in hand with the impulse to destroy them. This investigation also reveals a new danger facing libraries today with the digitalization of books threatening both the existence of the physical book and the very idea of reading for free.},
  language = {en},
  publisher = {{Thames \& Hudson}},
  author = {Polastron, Lucien X.},
  year = {2007}
}

@misc{aristotle_history_1965,
  title = {History of {{Animals}}},
  language = {en},
  publisher = {{Harvard University Press}},
  author = {{Aristotle}},
  translator = {Peck, A. L.},
  year = {1965},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PLY2Z8KG/Aristotle - 1965 - History of Animals.pdf},
  doi = {10.4159/DLCL.aristotle-history_animals.1965}
}

@article{keene_origins_2018,
  title = {The Origins and Evolution of Sleep},
  volume = {221},
  copyright = {\textcopyright{} 2018. Published by The Company of Biologists Ltd},
  issn = {0022-0949, 1477-9145},
  doi = {10.1242/jeb.159533},
  abstract = {Skip to Next Section
Sleep is nearly ubiquitous throughout the animal kingdom, yet little is known about how ecological factors or perturbations to the environment shape the duration and timing of sleep. In diverse animal taxa, poor sleep negatively impacts development, cognitive abilities and longevity. In addition to mammals, sleep has been characterized in genetic model organisms, ranging from the nematode worm to zebrafish, and, more recently, in emergent models with simplified nervous systems such as Aplysia and jellyfish. In addition, evolutionary models ranging from fruit flies to cavefish have leveraged natural genetic variation to investigate the relationship between ecology and sleep. Here, we describe the contributions of classical and emergent genetic model systems to investigate mechanisms underlying sleep regulation. These studies highlight fundamental interactions between sleep and sensory processing, as well as a remarkable plasticity of sleep in response to environmental changes. Understanding how sleep varies throughout the animal kingdom will provide critical insight into fundamental functions and conserved genetic mechanisms underlying sleep regulation. Furthermore, identification of naturally occurring genetic variation regulating sleep may provide novel drug targets and approaches to treat sleep-related diseases.},
  language = {en},
  number = {11},
  journal = {Journal of Experimental Biology},
  author = {Keene, Alex C. and Duboue, Erik R.},
  month = jun,
  year = {2018},
  pages = {jeb159533},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ENMM8UU2/jeb159533.html},
  pmid = {29895581}
}

@article{howard_numerical_2018,
  title = {Numerical Ordering of Zero in Honey Bees},
  volume = {360},
  copyright = {Copyright \textcopyright{} 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.aar4975},
  abstract = {Understanding zero
It has been said that the development of an understanding of zero by society initiated a major intellectual advance in humans, and we have been thought to be unique in this understanding. Although recent research has shown that some other vertebrates understand the concept of the ``empty set,'' Howard et al. now show that an understanding of this concept is present in untrained honey bees (see the Perspective by Nieder). This finding suggests that such an understanding has evolved independently in distantly related species that deal with complexity in their environments, and that it may be more widespread than previously appreciated.
Science, this issue p. 1124; see also p. 1069
Some vertebrates demonstrate complex numerosity concepts\textemdash{}including addition, sequential ordering of numbers, or even the concept of zero\textemdash{}but whether an insect can develop an understanding for such concepts remains unknown. We trained individual honey bees to the numerical concepts of ``greater than'' or ``less than'' using stimuli containing one to six elemental features. Bees could subsequently extrapolate the concept of less than to order zero numerosity at the lower end of the numerical continuum. Bees demonstrated an understanding that parallels animals such as the African grey parrot, nonhuman primates, and even preschool children.
Honey bees display an understanding that zero is an empty set at the base of the number line.
Honey bees display an understanding that zero is an empty set at the base of the number line.},
  language = {en},
  number = {6393},
  journal = {Science},
  author = {Howard, Scarlett R. and {Avargu\`es-Weber}, Aurore and Garcia, Jair E. and Greentree, Andrew D. and Dyer, Adrian G.},
  month = jun,
  year = {2018},
  pages = {1124-1126},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LPA2IAFA/1124.html},
  pmid = {29880690}
}

@article{staunton_mammalian_2005,
  title = {Mammalian Sleep},
  volume = {92},
  issn = {0028-1042, 1432-1904},
  doi = {10.1007/s00114-005-0618-0},
  abstract = {This review examines the biological background to the development of ideas on rapid eye movement sleep (REM sleep), so-called paradoxical sleep (PS), and its relation to dreaming. Aspects of the phenomenon which are discussed include physiological changes and their anatomical location, the effects of total and selective sleep deprivation in the human and animal, and REM sleep behavior disorder, the latter with its clinical manifestations in the human. Although dreaming also occurs in other sleep phases (non-REM or NREM sleep), in the human, there is a contingent relation between REM sleep and dreaming. Thus, REM is taken as a marker for dreaming and as REM is distributed ubiquitously throughout the mammalian class, it is suggested that other mammals also dream. It is suggested that the overall function of REM sleep/dreaming is more important than the content of the individual dream; its function is to place the dreamer protagonist/observer on the topographical world. This has importance for the developing infant who needs to develop a sense of self and separateness from the world which it requires to navigate and from which it is separated for long periods in sleep. Dreaming may also serve to maintain a sense of `I'ness or ``self'' in the adult, in whom a fragility of this faculty is revealed in neurological disorders.},
  language = {en},
  number = {5},
  journal = {Naturwissenschaften},
  author = {Staunton, Hugh},
  month = may,
  year = {2005},
  pages = {203-220},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UAXH47V6/Staunton - 2005 - Mammalian sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KIF844M7/10.html}
}

@article{elgar_sleep_1988,
  title = {Sleep in Mammals},
  volume = {36},
  issn = {0003-3472},
  doi = {10.1016/S0003-3472(88)80211-2},
  abstract = {Quiet sleep (QS) was correlated with a different set of constitutional variables from those associated with active sleep (AS), in a sample of 69 species of mammals. The time spent in quiet sleep was negatively correlated with body size and basal metabolic rate. The latter relationship remained even after controlling for the effects of body weight. Neither the total time spent in active sleep, nor active sleep as a percentage of total sleep time was significantly correlated with body weight or metabolic rate. Altricial species spend more time in active sleep than do precocial species. The time between the onset of successive episodes of active sleep, the AS-QS cycle length, was positively correlated with body weight. For their body sizes, species that live in temperate regions have shorter AS-QS cycles than those living in tropical or sub-tropical regions. Correlations between patterns of sleep and adult brain weight probably result from the confounding effects of body weight. These findings were used to evaluate several explanations for interspecific differences in patterns of sleep among mammals.},
  number = {5},
  journal = {Animal Behaviour},
  author = {Elgar, Mark A. and Pagel, Mark D. and Harvey, Paul H.},
  month = sep,
  year = {1988},
  pages = {1407-1419},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SVARI7L8/S0003347288802112.html}
}

@article{nicolau_why_2000,
  title = {Why We Sleep: The Evolutionary Pathway to the Mammalian Sleep},
  volume = {62},
  issn = {0301-0082},
  shorttitle = {Why We Sleep},
  doi = {10.1016/S0301-0082(00)00013-7},
  abstract = {The cause of sleep is a complex question, which needs first, a clear distinction amongst the different meanings of a causal relationship in the study of a given behavior, second, the requisites to be met by a suggested cause, and third, a precise definition of sleep to distinguish behavioral from polygraphic sleep. This review aims at clarifying the meaning of the question and at showing the phylogenetic origin of the mammalian and avian sleep. The phylogenetic appearance of sleep can be approached through a study of the evolution of the vertebrate brain. This began as an undifferentiated dorsal nerve, which was followed by the development of an anterior simplified brain and ended with the formation of the multilayered mammalian neocortex or the avian neostriate. The successive stages in the differentiation of the vertebrate brain produced, at least, two different waking types. The oldest one is the diurnal activity, bound to the light phase of the circadian cycle. Poikilotherms control the waking from the whole brainstem, where their main sensorymotor areas lie. Mammals developed the thalamocortical lines, which displaced the waking up to the cortex after acquiring homeothermy and nocturnal lifestyle. In order to avoid competence between duplicate systems, the early waking type, controlled from the brainstem, was suppressed, and by necessity was turned into inactivity, probably slow wave sleep. On the other hand, the nocturnal rest of poikilotherms most probably resulted in rapid eye movement sleep. The complex structure of the mammalian sleep should thus be considered an evolutionary remnant; the true acquisition of mammals is the cortical waking and not the sleep.},
  number = {4},
  journal = {Progress in Neurobiology},
  author = {Nicolau, M. C. and Aka\^arir, M. and Gamund\i\', A. and Gonz\'alez, J. and Rial, R. V.},
  month = nov,
  year = {2000},
  keywords = {Sleep function,Cortical waking,Mammalian evolution,Sleep evolution},
  pages = {379-406},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W7CA3AYD/Nicolau et al. - 2000 - Why we sleep the evolutionary pathway to the mamm.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JCS45UPJ/S0301008200000137.html}
}

@article{lyamin_cetacean_2008,
  series = {Special section: The European Workshop in Imagery and Cognition: Neurocognition and Visual Imagery},
  title = {Cetacean Sleep: {{An}} Unusual Form of Mammalian Sleep},
  volume = {32},
  issn = {0149-7634},
  shorttitle = {Cetacean Sleep},
  doi = {10.1016/j.neubiorev.2008.05.023},
  abstract = {Our knowledge of the form of lateralized sleep behavior, known as unihemispheric slow wave sleep (USWS), seen in all members of the order Cetacea examined to date, is described. We trace the discovery of this phenotypically unusual form of mammalian sleep and highlight specific aspects that are different from sleep in terrestrial mammals. We find that for cetaceans sleep is characterized by USWS, a negligible amount or complete absence of rapid eye movement (REM) sleep, and a varying degree of movement during sleep associated with body size, and an asymmetrical eye state. We then compare the anatomy of the mammalian somnogenic system with what is known in cetaceans, highlighting areas where additional knowledge is needed to understand cetacean sleep. Three suggested functions of USWS (facilitation of movement, more efficient sensory processing and control of breathing) are discussed. Lastly, the possible selection pressures leading to this form of sleep are examined, leading us to the suggestion that the selection pressure necessitating the evolution of cetacean sleep was most likely the need to offset heat loss to the water from birth and throughout life. Aspects such as sentinel functions and breathing are likely to be proximate evolutionary phenomenon of this form of sleep.},
  number = {8},
  journal = {Neuroscience \& Biobehavioral Reviews},
  author = {Lyamin, Oleg I. and Manger, Paul R. and Ridgway, Sam H. and Mukhametov, Lev M. and Siegel, Jerome M.},
  month = oct,
  year = {2008},
  keywords = {Rapid eye movement sleep,Slow wave sleep,Vigilance,Unihemispheric sleep,Thermoregulation,Evolution,Laterality},
  pages = {1451-1484},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HNR6FFT7/Lyamin et al. - 2008 - Cetacean sleep An unusual form of mammalian sleep.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DCZFEA69/S0149763408000912.html}
}

@article{van_twyver_sleep_1969,
  title = {Sleep Patterns of Five Rodent Species},
  volume = {4},
  issn = {0031-9384},
  doi = {10.1016/0031-9384(69)90038-9},
  abstract = {Electrographic and behavioral observations were made on five rodent species under controlled conditions. These were:Mus musculus, Rattus norvegicus, Mesocricetus auratus, Citellus tridecemlineatus and Chinchilla laniger. Normative values for sleep characteristics of the five species were derived from 48 hr recording periods. Analysis of sleep pattern characteristics showed: (1) well defined stages of slow wave sleep and paradoxical sleep in all animals; (2) sleep occupied from 52\textendash{}60 per cent of each day for the different species; (3) different species differed in percentage of paradoxical sleep ranging from 10 per cent for the mouse to 24 per cent for hamsters and ground squirrels; (4) hibernators slept in significantly longer periods, had higher percentages of paradoxical sleep and slightly higher percentages of total sleep time. Hibernators also seemed to sleep more deeply than non-hibernators.},
  number = {6},
  journal = {Physiology \& Behavior},
  author = {Van Twyver, Henry},
  month = nov,
  year = {1969},
  keywords = {Sleep,Paradoxical sleep,Circadian rhythm,Hibernators,Rodents},
  pages = {901-905},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4UNC7THB/Van Twyver - 1969 - Sleep patterns of five rodent species.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CRMCX62S/0031938469900389.html}
}

@article{davis_study_1972,
  title = {A Study of Paradoxical Sleep Depth in the Rat},
  volume = {26},
  issn = {0033-3131},
  doi = {10.3758/BF03335472},
  abstract = {Arousal tests were conducted on five rats implanted with EEG electrodes to monitor sleep stages. The arousing stimulus was mild vibration of the cage floor, which by several criteria can be considered a biologically relevant stimulus. Behavioral and EEG reactions to this stimulus were compared for wakefulness, paradoxical sleep, and slow-wave sleep. Probability of arousal was high during wakefulness and slow-wave sleep, but much lower during paradoxical sleep. This finding has relevance for one interpretation of the ``sentinel'' hypothesis of paradoxical sleep. It indicates paradoxical sleep to be a deeper phase than slow-wave sleep.},
  language = {en},
  number = {3},
  journal = {Psychonomic Science},
  author = {Davis, Kenneth and Heins, Elizabeth and Twyver, Henry Van},
  month = mar,
  year = {1972},
  pages = {173-174},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LBFBC7J5/Davis et al. - 1972 - A study of paradoxical sleep depth in the rat.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/S95MQDUR/BF03335472.html}
}

@article{neckelmann_sleep_1993,
  title = {Sleep Stages and {{EEG}} Power Spectrum in Relation to Acoustical Stimulus Arousal Threshold in the Rat},
  volume = {16},
  issn = {0161-8105},
  abstract = {This study was designed to functionally validate earlier described criteria for visual sleep scoring with respect to acoustical stimulus threshold for arousal. A further objective was to explore the relation between electroencephalographic (EEG) power spectrum and acoustical stimulus threshold for arousal. After habituation to an acoustical stimulus (a 1,000-Hz sine tone, increasing 1.5 dB per second for 45 seconds), values for latency to arousal after acoustical stimulus onset were analyzed. Arousal was determined based on EEG and electromyographic (EMG) criteria. There was a significant effect of sleep stage, with slow wave sleep 2 (SWS-2) having higher arousal threshold than slow wave sleep 1 (SWS-1), rapid eye movement (REM) sleep and transition type sleep. This indicates that the subdivision of nonrapid eye movement (NREM) sleep in the rat into SWS-1 and SWS-2 had functional validity in this paradigm. Time of day also had a significant effect, with lower arousal threshold in the last 2 hours (ninth and tenth hour of the light period) of the 8-hour registration period. Furthermore, there was a significant effect of EEG delta power density. Epochs with high delta power had increased arousal threshold relative to epochs with low arousal threshold. The results were consistent with the notion that delta activity is an indicator of depth within NREM sleep.},
  language = {eng},
  number = {5},
  journal = {Sleep},
  author = {Neckelmann, D. and Ursin, R.},
  month = aug,
  year = {1993},
  keywords = {Male,Arousal,Electromyography,Animals,Rats,Circadian Rhythm,Electroencephalography,Sleep Stages,Wakefulness,Acoustic Stimulation,Rats; Wistar,Sleep; REM},
  pages = {467-477},
  pmid = {8378687}
}

@article{mouret_paradoxical_1969,
  title = {Paradoxical Sleep Rebound in the Rat. {{Effects}} of Physical Procedures Involved in Intracisternal Injection},
  volume = {15},
  issn = {0006-8993},
  language = {eng},
  number = {2},
  journal = {Brain Research},
  author = {Mouret, J. and Pujol, J. F. and Kiyono, S.},
  month = oct,
  year = {1969},
  keywords = {Parietal Lobe,Animals,Rats,Cerebral Cortex,Sleep Stages,Sleep Deprivation,Norepinephrine,Occipital Lobe,Sleep; REM,Injections; Spinal},
  pages = {501-506},
  pmid = {4310121}
}

@article{ohayon_meta-analysis_2004,
  title = {Meta-{{Analysis}} of {{Quantitative Sleep Parameters From Childhood}} to {{Old Age}} in {{Healthy Individuals}}: {{Developing Normative Sleep Values Across}} the {{Human Lifespan}}},
  volume = {27},
  issn = {0161-8105},
  shorttitle = {Meta-{{Analysis}} of {{Quantitative Sleep Parameters From Childhood}} to {{Old Age}} in {{Healthy Individuals}}},
  doi = {10.1093/sleep/27.7.1255},
  abstract = {AbstractObjectives:.  The purposes of this study were to identify age-related changes in objectively recorded sleep patterns across the human life span in healt},
  language = {en},
  number = {7},
  journal = {Sleep},
  author = {Ohayon, Maurice M. and Carskadon, Mary A. and Guilleminault, Christian and Vitiello, Michael V.},
  month = oct,
  year = {2004},
  pages = {1255-1273},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZAI5TK7N/Ohayon et al. - 2004 - Meta-Analysis of Quantitative Sleep Parameters Fro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YXFUUE2F/2696819.html}
}

@article{watson_genetic_2006,
  title = {Genetic and {{Environmental Influences}} on {{Insomnia}}, {{Daytime Sleepiness}}, and {{Obesity}} in {{Twins}}},
  volume = {29},
  issn = {0161-8105},
  doi = {10.1093/sleep/29.5.645},
  abstract = {AbstractStudy Objectives:.  To better understand the relationships of insomnia, sleepiness, and obesity.Design:.  Classic twin study.Setting:.  A community-base},
  language = {en},
  number = {5},
  journal = {Sleep},
  author = {Watson, Nathaniel F. and Goldberg, Jack and Arguelles, Lester and Buchwald, Dedra},
  month = may,
  year = {2006},
  pages = {645-649},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BYIBQ4CB/Watson et al. - 2006 - Genetic and Environmental Influences on Insomnia, .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CW3RBHDJ/2708163.html}
}

@article{thomas_neural_2000,
  title = {Neural Basis of Alertness and Cognitive Performance Impairments during Sleepiness. {{I}}. {{Effects}} of 24 h of Sleep Deprivation on Waking Human Regional Brain Activity},
  volume = {9},
  issn = {1365-2869},
  doi = {10.1046/j.1365-2869.2000.00225.x},
  abstract = {The negative effects of sleep deprivation on alertness and cognitive performance suggest decreases in brain activity and function, primarily in the thalamus, a subcortical structure involved in alertness and attention, and in the prefrontal cortex, a region subserving alertness, attention, and higher-order cognitive processes. To test this hypothesis, 17 normal subjects were scanned for quantifiable brain activity changes during 85 h of sleep deprivation using positron emission tomography (PET) and 18Fluorine-2-deoxyglucose (18FDG), a marker for regional cerebral metabolic rate for glucose (CMRglu) and neuronal synaptic activity. Subjects were scanned prior to and at 24-h intervals during the sleep deprivation period, for a total of four scans per subject. During each 30 min 18FDG uptake, subjects performed a sleep deprivation-sensitive Serial Addition/Subtraction task. Polysomnographic monitoring confirmed that subjects were awake. Twenty-four hours of sleep deprivation, reported here, resulted in a significant decrease in global CMRglu, and significant decreases in absolute regional CMRglu in several cortical and subcortical structures. No areas of the brain evidenced a significant increase in absolute regional CMRglu. Significant decreases in relative regional CMRglu, reflecting regional brain reductions greater than the global decrease, occurred predominantly in the thalamus and prefrontal and posterior parietal cortices. Alertness and cognitive performance declined in association with these brain deactivations. This study provides evidence that short-term sleep deprivation produces global decreases in brain activity, with larger reductions in activity in the distributed cortico-thalamic network mediating attention and higher-order cognitive processes, and is complementary to studies demonstrating deactivation of these cortical regions during NREM and REM sleep.},
  language = {en},
  number = {4},
  journal = {Journal of Sleep Research},
  author = {Thomas, Maria and Sing, Helen and Belenky, Gregory and Holcomb, Henry and Mayberg, Helen and Dannals, Robert and Jr, Henry Wagner and Thorne, David and Popp, Kathryn and Rowland, Laura and Welsh, Amy and Balwinski, Sharon and Redmond, Daniel},
  year = {2000},
  keywords = {sleep deprivation,alertness,cognitive performance,prefrontal cortex,regional brain activity,thalamus},
  pages = {335-352},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LECWTBW3/Thomas et al. - Neural basis of alertness and cognitive performanc.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IBPCQ32J/j.1365-2869.2000.00225.html}
}

@article{yoo_human_2007,
  title = {The Human Emotional Brain without Sleep \textemdash{} a Prefrontal Amygdala Disconnect},
  volume = {17},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2007.08.007},
  abstract = {Summary
Sleep deprivation is known to impair a range of functions, including immune regulation and metabolic control, as well as neurocognitive processes, such as learning and memory [1]. But evidence for the role of sleep in regulating our emotional brain-state is surprisingly scarce, and while the dysregulation of affective stability following sleep loss has received subjective documentation 2, 3, any neural examination remains absent. Clinical evidence suggests that sleep and emotion interact; nearly all psychiatric and neurological disorders expressing sleep disruption display corresponding symptoms of affective imbalance [4]. Independent of sleep, knowledge of the basic neural and cognitive mechanisms regulating emotion is remarkably advanced. The amygdala has a well-documented role in the processing of emotionally salient information, particularly aversive stimuli 5, 6. The extent of amygdala engagement can also be influenced by a variety of connected systems, particularly the medial-prefrontal cortex (MPFC); the MPFC is proposed to exert an inhibitory, top-down control of amygdala function, resulting in contextually appropriate emotional responses 5, 6. We have focused on this network and using functional magnetic resonance image (fMRI) have obtained evidence, reported here, that a lack of sleep inappropriately modulates the human emotional brain response to negative aversive stimuli (see Supplemental data available on-line with this issue).},
  number = {20},
  journal = {Current Biology},
  author = {Yoo, Seung-Schik and Gujar, Ninad and Hu, Peter and Jolesz, Ferenc A. and Walker, Matthew P.},
  month = oct,
  year = {2007},
  pages = {R877-R878},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BPCIHVDP/Yoo et al. - 2007 - The human emotional brain without sleep — a prefro.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PN5L4EBY/S0960982207017836.html}
}

@article{aulsebrook_sleep_2016,
  title = {Sleep {{Ecophysiology}}: {{Integrating Neuroscience}} and {{Ecology}}},
  volume = {31},
  issn = {0169-5347},
  shorttitle = {Sleep {{Ecophysiology}}},
  doi = {10.1016/j.tree.2016.05.004},
  abstract = {Here, we propose an original approach to explain one of the great unresolved questions in animal biology: what is the function of sleep? Existing ecological and neurological approaches to this question have become roadblocks to an answer. Ecologists typically treat sleep as a simple behavior, instead of a heterogeneous neurophysiological state, while neuroscientists generally fail to appreciate the critical insights offered by the consideration of ecology and evolutionary history. Redressing these shortfalls requires cross-disciplinary integration. By bringing together aspects of behavioral ecology, evolution, and conservation with neurophysiology, we can achieve a more comprehensive understanding of sleep, including its implications for adaptive waking behavior and fitness.},
  number = {8},
  journal = {Trends in Ecology \& Evolution},
  author = {Aulsebrook, Anne E. and Jones, Ther\'esa M. and Rattenborg, Niels C. and Roth, Timothy C. and Lesku, John A.},
  month = aug,
  year = {2016},
  keywords = {electroencephalogram,animal behavior,predation risk,rapid eye movement sleep,sleep function,slow wave sleep},
  pages = {590-599},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T6D69N9S/Aulsebrook et al. - 2016 - Sleep Ecophysiology Integrating Neuroscience and .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4VYPCATK/S0169534716300489.html}
}

@article{partinen_genetic_1983,
  title = {Genetic and Environmental Determination of Human Sleep},
  volume = {6},
  issn = {0161-8105},
  abstract = {Self-reported sleep data from 2238 monozygotic and 4545 dizygotic adult twin pairs indicated a significant hereditary effect on sleep length [overall heritability estimate (h2 = 0.44)] and on sleep quality (h2 = 0.44). When the data were examined in subgroups defined by sex, age (18-24 years and 25 or more years of age), and cohabitation status of the twin pair, the highest heritability estimates for sleep length were for twins living together aged 25 or older. For twins living apart the heritability estimates were statistically significant in all women and men aged 25 or older. For sleep quality significant heritability estimates were found for all groups except women living together.},
  language = {eng},
  number = {3},
  journal = {Sleep},
  author = {Partinen, M. and Kaprio, J. and Koskenvuo, M. and Putkonen, P. and Langinvainio, H.},
  year = {1983},
  keywords = {Adolescent,Adult,Female,Humans,Male,Time Factors,Sleep,Genetics,Pregnancy,Environment,Twins,Twins; Dizygotic,Twins; Monozygotic},
  pages = {179-185},
  pmid = {6684786}
}

@article{bakwin_sleep-walking_1970,
  series = {Originally published as Volume 2, Issue 7670},
  title = {{{SLEEP}}-{{WALKING IN TWINS}}},
  volume = {296},
  issn = {0140-6736},
  doi = {10.1016/S0140-6736(70)90058-9},
  abstract = {To investigate the possibility of a hereditary predisposition to sleep-walking, the degree of concordance in monozygotic and dizygotic twins was compared. Monozygotic twins were concordant for the symptom six times as often as dizygotic twins (p=0$\cdot$04)\textemdash{}a finding consistent with a genetic basis. The increased incidence of sleep-walking in the children when a parent had been a somnambulist also favours this view. Enuresis and persistent finger-sucking were commoner in the somnambulists than in the non-sleep-walkers; the prevalence of nail-biting was the same in these two groups.},
  number = {7670},
  journal = {The Lancet},
  author = {Bakwin, Harry},
  month = aug,
  year = {1970},
  pages = {446-447},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GPBE39HW/S0140673670900589.html}
}

@article{petit_childhood_2015,
  title = {Childhood {{Sleepwalking}} and {{Sleep Terrors}}: {{A Longitudinal Study}} of {{Prevalence}} and {{Familial Aggregation}}},
  volume = {169},
  issn = {2168-6203},
  shorttitle = {Childhood {{Sleepwalking}} and {{Sleep Terrors}}},
  doi = {10.1001/jamapediatrics.2015.127},
  abstract = {$<$h3$>$Importance$<$/h3$><$p$>$Childhood sleepwalking and sleep terrors are 2 parasomnias with a risk of serious injury for which familial aggregation has been shown.$<$/p$><$h3$>$Objectives$<$/h3$><$p$>$To assess the prevalence of sleepwalking and sleep terrors during childhood; to investigate the link between early sleep terrors and sleepwalking later in childhood; and to evaluate the degree of association between parental history of sleepwalking and presence of somnambulism and sleep terrors in children.$<$/p$><$h3$>$Design, Setting, and Participants$<$/h3$><$p$>$Sleep data from a large prospective longitudinal cohort (the Quebec Longitudinal Study of Child Development) of 1940 children born in 1997 and 1998 in the province were studied from March 1999 to March 2011.$<$/p$><$h3$>$Main Outcomes and Measures$<$/h3$><$p$>$Prevalence of sleep terrors and sleepwalking was assessed yearly from ages 1\textsuperscript{1}/\textsubscript{2}and 2\textsuperscript{1}/\textsubscript{2}years, respectively, to age 13 years through a questionnaire completed by the mother. Parental history of sleepwalking was also queried.$<$/p$><$h3$>$Results$<$/h3$><$p$>$The peak of prevalence was observed at 1\textsuperscript{1}/\textsubscript{2}years for sleep terrors (34.4\% of children; 95\% CI, 32.3\%-36.5\%) and at age 10 years for sleepwalking (13.4\%; 95\% CI, 11.3\%-15.5\%). As many as one-third of the children who had early childhood sleep terrors developed sleepwalking later in childhood. The prevalence of childhood sleepwalking increases with the degree of parental history of sleepwalking: 22.5\% (95\% CI, 19.2\%-25.8\%) for children without a parental history of sleepwalking, 47.4\% (95\% CI, 38.9\%-55.9\%) for children who had 1 parent with a history of sleepwalking, and 61.5\% (95\% CI, 42.8\%-80.2\%) for children whose mother and father had a history of sleepwalking. Moreover, parental history of sleepwalking predicted the incidence of sleep terrors in children as well as the persistent nature of sleep terrors.$<$/p$><$h3$>$Conclusions and Relevance$<$/h3$><$p$>$These findings substantiate the strong familial aggregation for the 2 parasomnias and lend support to the notion that sleepwalking and sleep terrors represent 2 manifestations of the same underlying pathophysiological entity.$<$/p$>$},
  language = {en},
  number = {7},
  journal = {JAMA Pediatrics},
  author = {Petit, Dominique and Pennestri, Marie-H\'el\`ene and Paquet, Jean and Desautels, Alex and Zadra, Antonio and Vitaro, Frank and Tremblay, Richard E. and Boivin, Michel and Montplaisir, Jacques},
  month = jul,
  year = {2015},
  pages = {653-658},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VLY5JMQ3/Petit et al. - 2015 - Childhood Sleepwalking and Sleep Terrors A Longit.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9K2DPAY6/2281574.html}
}

@article{siclari_neural_2017,
  title = {The Neural Correlates of Dreaming},
  volume = {20},
  copyright = {2017 Nature Publishing Group},
  issn = {1546-1726},
  doi = {10.1038/nn.4545},
  abstract = {Consciousness never fades during waking. However, when awakened from sleep, we sometimes recall dreams and sometimes recall no experiences. Traditionally, dreaming has been identified with rapid eye-movement (REM) sleep, characterized by wake-like, globally 'activated', high-frequency electroencephalographic activity. However, dreaming also occurs in non-REM (NREM) sleep, characterized by prominent low-frequency activity. This challenges our understanding of the neural correlates of conscious experiences in sleep. Using high-density electroencephalography, we contrasted the presence and absence of dreaming in NREM and REM sleep. In both NREM and REM sleep, reports of dream experience were associated with local decreases in low-frequency activity in posterior cortical regions. High-frequency activity in these regions correlated with specific dream contents. Monitoring this posterior 'hot zone' in real time predicted whether an individual reported dreaming or the absence of dream experiences during NREM sleep, suggesting that it may constitute a core correlate of conscious experiences in sleep.},
  language = {en},
  number = {6},
  journal = {Nature Neuroscience},
  author = {Siclari, Francesca and Baird, Benjamin and Perogamvros, Lampros and Bernardi, Giulio and LaRocque, Joshua J. and Riedner, Brady and Boly, Melanie and Postle, Bradley R. and Tononi, Giulio},
  month = jun,
  year = {2017},
  pages = {872-878},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3C6SVJLP/Siclari et al. - 2017 - The neural correlates of dreaming.pdf}
}

@article{begemann_daylight_1997,
  title = {Daylight, Artificial Light and People in an Office Environment, Overview of Visual and Biological Responses},
  volume = {20},
  issn = {0169-8141},
  doi = {10.1016/S0169-8141(96)00053-4},
  abstract = {Long-term behaviour /response of people has been studied in standard window zone offices during daytime working hours. Regular cell-offices were equipped with experimental lighting systems delivering lighting conditions that are known to influence human physiology. The results show that most people prefer to follow a daylight cycle instead of a constant level. Preferred lighting levels are significantly higher than today's indoor lighting standards and correspond to levels where biological stimulation can occur. The results strongly suggest that meeting biological lighting needs is very different from meeting visual needs. Results of two permanent occupants show striking differences in lighting settings, which correspond to individual circadian cycles and performance. This strengthens that present indoor lighting levels (and standards) are too low for biological stimulation. Medical research has shown that a prolonged lack of `light vitamin' can cause health problems ranging from minor sleep and performance difficulties to major depressions. This inevitably suggests that `poor' indoor lighting is the underlying cause of many of the health and performance problems. By naming this the `ill-lighting syndrome' we may well have identified the fundamental mechanism that can result in many different negative health/performance effects. Creating healthy indoor lighting can be a simple form of preventive medicine and providing a new challenge for the lighting community.},
  number = {3},
  journal = {International Journal of Industrial Ergonomics},
  author = {Begemann, S. H. A. and {van den Beld}, G. J. and Tenner, A. D.},
  month = sep,
  year = {1997},
  keywords = {Biological clock,Performance,Alertness,Daylight,Health,Office lighting},
  pages = {231-239},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/RVQ8QW52/Begemann et al. - 1997 - Daylight, artificial light and people in an office.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/WNR9HKLC/S0169814196000534.html}
}

@article{yetish_natural_2015,
  title = {Natural {{Sleep}} and {{Its Seasonal Variations}} in {{Three Pre}}-Industrial {{Societies}}},
  volume = {25},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2015.09.046},
  abstract = {Summary
How did humans sleep before the modern era? Because the tools to measure sleep under natural conditions were developed long after the invention of the electric devices suspected of delaying and reducing sleep, we investigated sleep in three preindustrial societies [1, 2, 3]. We find that all three show similar sleep organization, suggesting that they express core human sleep patterns, most likely characteristic of pre-modern era Homo sapiens. Sleep periods, the times from onset to offset, averaged 6.9\textendash{}8.5~hr, with sleep durations of 5.7\textendash{}7.1~hr, amounts near the low end of those industrial societies [4, 5, 6, 7]. There was a difference of nearly 1~hr between summer and winter sleep. Daily variation in sleep duration was strongly linked to time of onset, rather than offset. None of these groups began sleep near sunset, onset occurring, on average, 3.3~hr after sunset. Awakening was usually before sunrise. The sleep period consistently occurred during the nighttime period of falling environmental temperature, was not interrupted by extended periods of waking, and terminated, with vasoconstriction, near the nadir of daily ambient temperature. The daily cycle of temperature change, largely eliminated from modern sleep environments, may be a potent natural regulator of sleep. Light exposure was maximal in the morning and greatly decreased at noon, indicating that all three groups seek shade at midday and that light activation of the suprachiasmatic nucleus is~maximal in the morning. Napping occurred on~$<$7\% of days in winter and $<$22\% of days in summer. Mimicking aspects of the natural environment might be effective in treating certain modern sleep disorders.},
  number = {21},
  journal = {Current Biology},
  author = {Yetish, Gandhi and Kaplan, Hillard and Gurven, Michael and Wood, Brian and Pontzer, Herman and Manger, Paul R. and Wilson, Charles and McGregor, Ronald and Siegel, Jerome M.},
  month = nov,
  year = {2015},
  pages = {2862-2868},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QMXMS8QT/Yetish et al. - 2015 - Natural Sleep and Its Seasonal Variations in Three.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SHJUFFN5/S0960982215011574.html}
}

@article{de_la_iglesia_access_2015,
  title = {Access to {{Electric Light Is Associated}} with {{Shorter Sleep Duration}} in a {{Traditionally Hunter}}-{{Gatherer Community}}                                                    ,                                                             {{Access}} to {{Electric Light Is Associated}} with {{Shorter Sleep Duration}} in a {{Traditionally Hunter}}-{{Gatherer Community}}},
  volume = {30},
  issn = {0748-7304},
  doi = {10.1177/0748730415590702},
  abstract = {Access to electric light might have shifted the ancestral timing and duration of human sleep. To test this hypothesis, we studied two communities of the historically hunter-gatherer indigenous Toba/Qom in the Argentinean Chaco. These communities share the same ethnic and sociocultural background, but one has free access to electricity while the other relies exclusively on natural light. We fitted participants in each community with wrist activity data loggers to assess their sleep-wake cycles during one week in the summer and one week in the winter. During the summer, participants with access to electricity had a tendency to a shorter daily sleep bout (43 $\pm$ 21 min) than those living under natural light conditions. This difference was due to a later daily bedtime and sleep onset in the community with electricity, but a similar sleep offset and rise time in both communities. In the winter, participants without access to electricity slept longer (56 $\pm$ 17 min) than those with access to electricity, and this was also related to earlier bedtimes and sleep onsets than participants in the community with electricity. In both communities, daily sleep duration was longer during the winter than during the summer. Our field study supports the notion that access to inexpensive sources of artificial light and the ability to create artificially lit environments must have been key factors in reducing sleep in industrialized human societies., Access to electric light might have shifted the ancestral timing and duration of human sleep. To test this hypothesis, we studied two communities of the historically hunter-gatherer indigenous Toba/Qom in the Argentinean Chaco. These communities share the same ethnic and sociocultural background, but one has free access to electricity while the other relies exclusively on natural light. We fitted participants in each community with wrist activity data loggers to assess their sleep-wake cycles during one week in the summer and one week in the winter. During the summer, participants with access to electricity had a tendency to a shorter daily sleep bout (43 $\pm$ 21 min) than those living under natural light conditions. This difference was due to a later daily bedtime and sleep onset in the community with electricity, but a similar sleep offset and rise time in both communities. In the winter, participants without access to electricity slept longer (56 $\pm$ 17 min) than those with access to electricity, and this was also related to earlier bedtimes and sleep onsets than participants in the community with electricity. In both communities, daily sleep duration was longer during the winter than during the summer. Our field study supports the notion that access to inexpensive sources of artificial light and the ability to create artificially lit environments must have been key factors in reducing sleep in industrialized human societies.},
  language = {en},
  number = {4},
  journal = {Journal of Biological Rhythms},
  author = {{de la Iglesia}, Horacio O. and {Fern\'andez-Duque}, Eduardo and Golombek, Diego A. and Lanza, Norberto and Duffy, Jeanne F. and Czeisler, Charles A. and Valeggia, Claudia R.},
  month = aug,
  year = {2015},
  pages = {342-350},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GTXDEGTA/de la Iglesia et al. - 2015 - Access to Electric Light Is Associated with Shorte.pdf}
}

@article{lilly_animals_1964,
  title = {Animals in Aquatic Environments: Adaptation of Mammals to the Ocean},
  journal = {Handbook of Physiology--Environment},
  author = {Lilly, John C},
  year = {1964},
  pages = {741-747},
  publisher = {{American Physiology Society Washington, DC}}
}

@article{mukhametov_black_1997,
  title = {The {{Black Sea}} Bottlenose Dolphin: The Conditions of Rest and Activity},
  journal = {The Black Sea Bottlenose Dolphin. Nauka, Moscow},
  author = {Mukhametov, LM and Lyamin, OI},
  year = {1997},
  pages = {650-668}
}

@article{sekiguchi_sleep_2006,
  title = {Sleep Behaviour: {{Sleep}} in Continuously Active Dolphins},
  volume = {441},
  copyright = {2006 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {Sleep Behaviour},
  doi = {10.1038/nature04898},
  abstract = {Arising from: O. Lyamin, J. Pryaslova, V. Lance \& J. Siegel Nature 435, 1177 (2005); see also communication from Gnone et al.; Lyamin et al. reply.Sleep has been assumed to be necessary for development and to be a vital function in mammals1,2 and other animals3,4. However, Lyamin et al.5 claim that in bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), neonates and their mothers show almost no sleep behaviour for the first month after birth; this conclusion is based on their observation that the cetaceans keep swimming, avoid obstacles and rarely close their eyes for 24 hours a day throughout that period. Here we analyse the behaviour and eye closure of three neonate\textendash{}mother pairs of bottlenose dolphins and find that, although the animals tend to open both eyes when surfacing to breathe, one or both eyes are closed during `swim rest', an underwater sleeping behaviour that is associated with continuous activity. This observation calls into question the conclusions of Lyamin et al.5, who overlooked this type of sleep by analysing the animals' eye state only when they surfaced to breathe.},
  language = {en},
  number = {7096},
  journal = {Nature},
  author = {Sekiguchi, Yuske and Arai, Kazutoshi and Kohshima, Shiro},
  month = jun,
  year = {2006},
  pages = {E9-E10},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IJDMLN29/Sekiguchi et al. - 2006 - Sleep behaviour Sleep in continuously active dolp.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SFZ2EAFU/nature04898.html}
}

@article{lyamin_relationship_2004,
  title = {Relationship between Sleep and Eye State in {{Cetaceans}} and {{Pinnipeds}}.},
  volume = {142},
  copyright = {Copyright (c)},
  issn = {0003-9829},
  doi = {10.4449/aib.v142i4.427},
  abstract = {We recorded EEG from both hemispheres and documented the state of the two eyes in two species of Cetaceans (one beluga and one bottlenose dolphin) and one species of Pinnipeds (two northern fur seals). In the dolphin and beluga we found that episodes of unihemispheric slow wave sleep (USWS) were associated with asymmetry in eye state. During USWS and asymmetrical SWS the eye contralateral to the sleeping hemisphere was mostly closed or in an intermediate state while the eye contralateral to the waking hemisphere was more often open or in an intermediate state. Bilateral eye opening indicated waking in about 80\% cases and unilateral eye closure indicated USWS with an accuracy of about 75\%. Bilateral eye closure was rare (less than 2\% of the observation time) and was not necessarily associated with high amplitude SWS. In fur seals, episodes of one eye briefly opening usually occurred in the beginning of sleep episodes and lasted several minutes. Those episodes were frequently associated with lower amplitude EEG slow waves in the contralateral brain hemisphere. During most of their sleep on land, fur seals had both eyes tightly closed. No EEG asymmetry was recorded at this time. Although eye state and EEG stage are correlated in the bottlenose dolphin, beluga and fur seals, short episodes of EEG synchrony (less then 1 min) occur contralateral to an open eye and waking (a more activated EEG) activity can be present contralateral to a closed eye. The available data suggest that two functions of USWS/EEG asymmetry during SWS in Cetaceans and fur seals are multisensory control of the environment and maintenance of motion and postures of sleep. The adaptive advantages of USWS throughout the evolution of Cetaceans and Pinnipeds from terrestrial mammals to present forms could include 1) the avoidance of predators and maintenance of contact with other animals of the same species; 2) continuance of regular breathing; 3) and effective thermoregulation in the water environment.},
  language = {en},
  number = {4},
  journal = {Archives Italiennes de Biologie},
  author = {Lyamin, O. I. and Mukhametov, L. M. and Siegel, J. M.},
  month = jul,
  year = {2004},
  pages = {557-568},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9GQ6J3HP/Lyamin et al. - 2004 - Relationship between sleep and eye state in Cetace.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UNFGCI4P/427.html}
}

@article{cande_optogenetic_2018,
  title = {Optogenetic Dissection of Descending Behavioral Control in {{Drosophila}}},
  volume = {7},
  copyright = {\textcopyright{} 2018 Cande et al.. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  doi = {10.7554/eLife.34275},
  language = {en},
  journal = {eLife},
  author = {Cande, Jessica and Namiki, Shigehiro and Qiu, Jirui and Korff, Wyatt and Card, Gwyneth M. and Shaevitz, Josh W. and Stern, David L. and Berman, Gordon J.},
  month = jun,
  year = {2018},
  pages = {e34275},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8SAGUBK2/Cande et al. - 2018 - Optogenetic dissection of descending behavioral co.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EYE6JHCC/34275.html}
}

@book{greenspan_fly_2004,
  title = {Fly {{Pushing}}: {{The Theory}} and {{Practice}} of {{Drosophila Genetics}}},
  isbn = {978-0-87969-711-2},
  shorttitle = {Fly {{Pushing}}},
  abstract = {A second edition of the classic handbook has become a standard in the Drosophila field. This edition is expanded to include topics in which classical genetic strategies have been augmented with new molecular tools. Included are such new techniques as homologous recombination, RNAi, new mapping techniques, and new mosaic marking techniques.},
  language = {en},
  publisher = {{CSHL Press}},
  author = {Greenspan, Ralph J.},
  year = {2004},
  keywords = {Science / Life Sciences / Genetics \& Genomics}
}

@book{mohr_first_2018,
  title = {First in {{Fly}}: {{Drosophila Research}} and {{Biological Discovery}}},
  isbn = {978-0-674-98473-8},
  shorttitle = {First in {{Fly}}},
  abstract = {A single species of fly, Drosophila melanogaster, has been the subject of scientific research for more than one hundred years. Why does this tiny insect merit such intense scrutiny? Drosophila's importance as a research organism began with its short life cycle, ability to reproduce in large numbers, and easy-to-see mutant phenotypes. Over time, laboratory investigation revealed surprising similarities between flies and other animals at the level of genes, gene networks, cell interactions, physiology, immunity, and behavior. Like humans, flies learn and remember, fight microbial infection, and slow down as they age. Scientists use Drosophila to investigate complex biological activities in a simple but intact living system. Fly research provides answers to some of the most challenging questions in biology and biomedicine, including how cells transmit signals and form ordered structures, how we can interpret the wealth of human genome data now available, and how we can develop effective treatments for cancer, diabetes, and neurodegenerative diseases. Written by a leader in the Drosophila research community, First in Fly celebrates key insights uncovered by investigators using this model organism. Stephanie Elizabeth Mohr draws on these ``first in fly'' findings to introduce fundamental biological concepts gained over the last century and explore how research in the common fruit fly has expanded our understanding of human health and disease.},
  language = {en},
  publisher = {{Harvard University Press}},
  author = {Mohr, Stephanie Elizabeth},
  month = mar,
  year = {2018},
  keywords = {Science / Life Sciences / Biology,Science / Life Sciences / Zoology / Entomology,Science / Life Sciences / Genetics \& Genomics}
}

@article{meunier_regulation_2007,
  title = {Regulation of Feeding Behaviour and Locomotor Activity by Takeout in {{Drosophila}}},
  volume = {210},
  issn = {0022-0949},
  doi = {10.1242/jeb.02755},
  abstract = {The hormonal regulation of feeding behaviour is well known in vertebrates, whereas it remains poorly understood in insects. Here, we report that the takeout gene is an essential component of nutritional homeostasis in Drosophila. takeout encodes a putative juvenile hormone (JH) binding protein and has been described as a link between circadian rhythm and feeding behaviour. However, the physiological role of takeout and its putative link to JH remain unknown. In this study, we show that takeout (to(1)) flies failed to adapt their food intake according to food availability and that most defects could be genetically rescued. When food is abundant, to(1) are hyperphagic, yielding to hypertrophy of the fat body. When food reappears after a starvation period, to(1) flies do not increase their food intake as much as wild-type flies. This defect in food intake regulation is partly based on the action of Takeout on taste neurons, because the sensitivity of to(1) gustatory neurons to sugars does not increase after starvation, as in wild-type neurons. This lack of regulation is also evident at the locomotor activity, which normally increases during starvation, a behaviour related to food foraging. In addition, to(1) flies lack sexual dimorphism of locomotor activity, which has previously been linked to the JH circulating level. Moreover, application of the JH analog methoprene rescues the phenotype. These results suggest that takeout plays a central role as a feeding regulator and may act by modulating the circulating JH level.},
  language = {eng},
  number = {Pt 8},
  journal = {The Journal of Experimental Biology},
  author = {Meunier, Nicolas and Belgacem, Yesser Hadj and Martin, Jean-Ren\'e},
  month = apr,
  year = {2007},
  keywords = {Video Recording,Animals,Electrophysiology,Drosophila Proteins,Drosophila melanogaster,Locomotion,Analysis of Variance,Eating,Feeding Behavior,Juvenile Hormones,Receptors; Cell Surface,Triglycerides},
  pages = {1424-1434},
  pmid = {17401125}
}

@article{barnes_feeding_2008,
  title = {Feeding, Fecundity and Lifespan in Female {{Drosophila}} Melanogaster},
  volume = {275},
  issn = {0962-8452},
  doi = {10.1098/rspb.2008.0139},
  abstract = {Male seminal fluid proteins induce a profound remodelling of behavioural, physiological and gene signalling pathways in females of many taxa, and typically cause elevated egg production and decreased sexual receptivity. In Drosophila melanogaster, these effects can be mediated by an ejaculate 'sex peptide' (SP), which, in addition, contributes significantly to the cost of mating in females. Recent research has revealed that SP can stimulate female post-copulatory feeding, raising the possibility that the widespread female cost of mating could be due to over-feeding. In this study, we used D. melanogaster as a model to test this hypothesis. We first show that elevated post-mating feeding is dependent upon egg production and does not occur in sterile ovoD1 mutant females. This conclusion was also supported by the increase in feeding of virgin females whose egg production was experimentally elevated. We then demonstrated that sterile ovoD1 and fertile females experienced identical survival costs of mating, related to their frequency of mating and not to female feeding rate or to egg production. We conclude that female mating costs are not the result of over-feeding, but may be due to other, potentially more direct, effects of ejaculate molecules.},
  language = {eng},
  number = {1643},
  journal = {Proceedings. Biological Sciences},
  author = {Barnes, Andrew I. and Wigby, Stuart and Boone, James M. and Partridge, Linda and Chapman, Tracey},
  month = jul,
  year = {2008},
  keywords = {Models; Animal,Animals; Genetically Modified,Sexual Behavior; Animal,Female,Male,Neurons,Animals,Drosophila Proteins,Drosophila melanogaster,Nerve Tissue Proteins,Longevity,Peptides,Fertility,Feeding Behavior,Transcription Factors},
  pages = {1675-1683},
  pmid = {18430646},
  pmcid = {PMC2452982}
}

@article{blumberg_spatiotemporal_2013,
  title = {Spatiotemporal Structure of {{REM}} Sleep Twitching Reveals Developmental Origins of Motor Synergies},
  volume = {23},
  issn = {1879-0445},
  doi = {10.1016/j.cub.2013.08.055},
  abstract = {BACKGROUND: During active (or REM) sleep, infant mammals exhibit myoclonic twitches of skeletal muscles throughout the body, generating jerky, discrete movements of the distal limbs. Hundreds of thousands of limb twitches are produced daily, and sensory feedback from these movements is a substantial driver of infant brain activity, suggesting that they contribute to motor learning and sensorimotor integration. It is not known whether the production of twitches is random or spatiotemporally structured, or whether the patterning of twitching changes with age; such information is critical for understanding how twitches contribute to development.
RESULTS: We used high-speed videography and 3D motion tracking to assess the spatiotemporal structure of twitching at forelimb joints in 2- and 8-day-old rats. At both ages, twitches exhibited highly structured spatiotemporal properties at multiple timescales, including synergistic and multijoint movements within and across forelimbs. Hierarchical cluster analysis and latent class analysis revealed developmental changes in twitching quantity and patterning. Critically, we found evidence for a selectionist process whereby movement patterns at the early age compete for retention and expression over development.
CONCLUSIONS: These findings indicate that twitches are not produced randomly but are highly structured at multiple timescales. This structure has important implications for understanding brain and spinal mechanisms that produce twitching, and the role that sensory feedback from twitching plays in sensorimotor system development. We propose that twitches represent a heretofore-overlooked form of motor exploration that helps animals probe the biomechanics of their limbs, build motor synergies, and lay a foundation for complex, automatic, and goal-directed wake movements.},
  language = {eng},
  number = {21},
  journal = {Current biology: CB},
  author = {Blumberg, Mark S. and Coleman, Cassandra M. and Gerth, Ashlynn I. and McMurray, Bob},
  month = nov,
  year = {2013},
  keywords = {Video Recording,Female,Male,Brain,Animals,Rats,Motor Activity,Sleep; REM,Animals; Newborn,Feedback; Sensory,Muscle Development,Rats; Sprague-Dawley},
  pages = {2100-2109},
  pmid = {24139739},
  pmcid = {PMC3823644}
}

@article{hasegawa_circadian_nodate,
  title = {{{CIRCADIAN RHYTHM OF LOCOMOTOR BEHAVIOR IN A POPULATION OF Paramecium}} Multimicronucleatum: {{ITS CHARACTERISTICS AS DERIVED FROM CIRCADIAN CHANGES IN THE SWIMMING SPEEDS AND THE FREQUENCIES OF AVOIDING RESPONSE AMONG INDIVIDUAL CELLS}}},
  volume = {40},
  issn = {1751-1097},
  shorttitle = {{{CIRCADIAN RHYTHM OF LOCOMOTOR BEHAVIOR IN A POPULATION OF Paramecium}} Multimicronucleatum},
  doi = {10.1111/j.1751-1097.1984.tb04560.x},
  abstract = {The locomotor behavior of Paramecium is determined by two components: swimming speed and the frequency of avoiding responses. The circadian oscillations of these two components were examined in order to interpret characteristics of the circadian locomotor rhythm, previously found in a Paramecium population using an originally defined parameter, ``traverse frequency'' (Hasegawa et al., 1978, 1982). In our present study, a modified version of the previously developed, fully computerized, close-up video/photoamplifier system was used. Results indicate that individual specimens swam fast and unidirectionally during the day, while at night, in a light\textendash{}dark cycle, they swam slowly and frequently turned. This oscillatory pattern was sustained in continuous darkness, where fluctuation in the frequency of avoiding responses was a dominant characteristic. The time structure of the ``random walk'' of Paramecium behavior was also examined by constructing and stochastically testing histograms of the interval times between specimens consecutively traversing beneath an observation point. Statistical analyses of observation data indicated that the circadian organization of the two components by individual specimens resulted in a circadian accumulation/dispersal rhythm of the entire population. It was concluded that the circadian ``traverse frequency'' rhythm principally represented this circadian accumulation/dispersal rhythm.},
  language = {en},
  number = {1},
  journal = {Photochemistry and Photobiology},
  author = {Hasegawa, Kenji and Tanakadate, Akihiro},
  pages = {105-112},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KEHBSULU/j.1751-1097.1984.tb04560.html}
}

@article{hinrichsen_frequency_2010,
  title = {The Frequency of the Behavioral Response in {{Paramecium}} Tetraurelia Displays an Ultradian Rhythm: A Regulatory Role for the Inositol Signaling Pathway},
  volume = {41},
  issn = {0929-1016},
  shorttitle = {The Frequency of the Behavioral Response in {{Paramecium}} Tetraurelia Displays an Ultradian Rhythm},
  doi = {10.1080/09291010903411500},
  abstract = {Paramecium tetraurelia displays a behavioral response to environmental stimuli that involves changes in the direction and speed of swimming. This paper demonstrates that there are periodic variations in the frequency of behavioral responses of individual cells. The frequency of the backward swimming response undergoes repeated oscillations with a period (tau) between 40 and 50 minutes; these oscillations are only slightly affected by the temperature at which the cells have been grown. These data indicate the presence of an ultradian clock that underlies this cellular process. However, growing cells in the presence of low concentrations of LiCl perturbs the ultradian rhythm, with the periodicity being reduced to approximately 11 minutes. The LiCl effect is seen within 10\textendash{}45 minutes, depending on the concentration of LiCl used, and is completely reversible. In order to determine if the LiCl effect was due to a depletion of inositol, cells were grown in 10 mM myo-inositol for 24 hours prior to the addition of LiCl. It was found that the presence of excess inositol inhibited the perturbation of the periodicity caused by the LiCl. These results signify that Paramecium tetraurelia possesses an endogenous ultradian clock that influences the strength of the behavioral response, and the inositol signaling pathway is most likely involved in the generation of the ultradian rhythm. Therefore, the Paramecium behavioral response is an excellent model system for elucidation of the molecular mechanisms underlying the ultradian rhythms.},
  number = {6},
  journal = {Biological Rhythm Research},
  author = {Hinrichsen, Robert D.},
  month = dec,
  year = {2010},
  keywords = {behavioral response,ciliary beat,inositol,inositol signaling pathway,lithium,Paramecium,ultradian rhythms},
  pages = {457-475},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IV85THVQ/Hinrichsen - 2010 - The frequency of the behavioral response in Parame.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4ALI3QIA/09291010903411500.html}
}

@article{diehn_terminology_nodate,
  title = {Terminology of {{Behavioral Responses}} of {{Motile Microorganisms}}*},
  volume = {26},
  issn = {1751-1097},
  doi = {10.1111/j.1751-1097.1977.tb07532.x},
  language = {en},
  number = {6},
  journal = {Photochemistry and Photobiology},
  author = {Diehn, B. and Feinleib, M. and Haupt, W. and Hildebrand, E. and Lenci, F. and Nultsch, W.},
  pages = {559-560},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JEZKEVY7/j.1751-1097.1977.tb07532.html}
}

@article{yacobovitch_motility_2004,
  title = {Motility of Zooxanthellae Isolated from the {{Red Sea}} Soft Coral {{Heteroxenia}} Fuscescens ({{Cnidaria}})},
  volume = {298},
  issn = {0022-0981},
  doi = {10.1016/j.jembe.2003.08.003},
  abstract = {Unicellular dinoflagellate algae are among the best examples of organisms that exhibit biological clocks. This study examined the effect of light regime on rhythmicity of motility in the symbiotic dinoflagellate Symbiodinium sp., freshly isolated from the soft coral Heteroxenia fuscescens (Ehrenberg). Freshly isolated algal cells, placed under a 12-h L:12-h D cycle, exhibited motility with a diel rhythm. This motility occurred only during the period of illumination and lasted 8\textendash{}9 h, with a peak at 2.5\textendash{}4 h after lights on. Algal cells placed in an inverted light regime inverted their motility pattern. The response to the L/D regime was very precise, and even a 1-h shift backward or forward affected initiation of motility and time of its maximal peak. When placed in either constant light or dark, algal motility ceased until the L/D cycle was restored. These findings suggest that the rhythm is entrained by light cues and is not due to an endogenous circadian rhythm. Further, we provide evidence that the presence of juvenile hosts does not affect the algal motility pattern. These results offer the first evidence for the lack of impact by the host on rhythmicity of motility of free-living algal cells. The motility pattern found in freshly isolated algae may indicate the presence of light-induced diel rhythmicity in yet-to-be described free-living Symbiodinium.},
  number = {1},
  journal = {Journal of Experimental Marine Biology and Ecology},
  author = {Yacobovitch, Tali and Benayahu, Yehuda and Weis, Virginia M.},
  month = jan,
  year = {2004},
  keywords = {Circadian rhythm,Dinoflagellate,Motility,Primary polyp,Red Sea,Soft coral,Symbiosis,Zooxanthellae},
  pages = {35-48},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/98BRDT2E/Yacobovitch et al. - 2004 - Motility of zooxanthellae isolated from the Red Se.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KEZSANRW/S0022098103004180.html}
}

@article{werner_chlamydomonas_2002,
  title = {Chlamydomonas Reinhardtii as a Unicellular Model for Circadian Rhythm Analysis},
  volume = {19},
  issn = {0742-0528},
  doi = {10.1081/CBI-120002981},
  abstract = {Chlamydomonas reinhardtii has been used as an experimental model organism for circadian rhythm research for more than 30 yr. Some of the physiological rhythms of this alga are well established, and several clock mutants have been isolated. The cloning of clock genes from these mutant strains by positional cloning is under way and should give new insights into the mechanism of the circadian clock. In a spectacular space experiment, the question of the existence of an endogenous clock vs. an exogenous mechanism has been studied in this organism. With the emergence of molecular analysis of circadian rhythms in plants in 1985, a circadian gene expression pattern of several nuclear and chloroplast genes was detected. Evidence is now accumulating that shows circadian control at the translational level. In addition, the gating of the cell cycle by the circadian clock has been analyzed. This review focuses on the different aspects of circadian rhythm research in C. reinhardtii over the past 30 yr. The suitability of Chlamydomonas as a model system in chronobiology research and the adaptive significance of the observed rhythms will be discussed.},
  number = {2},
  journal = {Chronobiology International},
  author = {Werner, Ralf},
  month = jan,
  year = {2002},
  keywords = {Circadian clock,Chlamydomonas reinhardtii,Light perception,mRNA accumulation of nuclear and chloroplast genes,Physiological rhythms,Translational control},
  pages = {325-343},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3PA3HKUH/Werner - 2002 - Chlamydomonas reinhardtii as a unicellular model f.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6D89U79C/CBI-120002981.html}
}

@article{akritas_bootstrapping_1986,
  title = {Bootstrapping the {{Kaplan}}-{{Meier Estimator}}},
  volume = {81},
  issn = {0162-1459},
  doi = {10.2307/2289079},
  abstract = {Randomly censored data consist of $<$tex-math$>$\$$\backslash$operatorname\{iid\}\$$<$/tex-math$>$ pairs of observations (X\textsubscript{i}, $\delta$\textsubscript{i}), i = 1, ..., n; if $\delta$\textsubscript{i} = 0, X\textsubscript{i} denotes a censored observation, and if $\delta$\textsubscript{i} = 1, X\textsubscript{i} denotes an exact "survival" time, which is the variable of interest. For estimating the distribution F of the survival times, the product-limit estimator proposed by Kaplan and Meier (1958) has been studied extensively and it has been shown to enjoy a number of optimality properties (Wellner 1982). See Gill (1980, chaps. 1-4; 1983) for a modern treatment and for references. With censored data, bootstrapping can be carried out using two different resampling plans introduced by Efron (1981) and Reid (1981), respectively. With Efron's plan one takes a random sample with replacement from (X\textsubscript{1}, $\delta$\textsubscript{1}), ..., (X\textsubscript{n}, $\delta$\textsubscript{n}), whereas with Reid's plan one takes a random sample from the Kaplan-Meier estimator. The purpose of this article is to study the asymptotic behavior of the bootstrapped Kaplan-Meier estimator with both resampling plans. The approach adopted uses the theory of martingales for point processes. This extends our understanding of the asymptotic behavior of bootstrapped estimated distribution functions to the situation in which random censoring occurs. The uncensored case has been studied by Bickel and Freedman (1981) and Shorack (1982). The new result is used to obtain bootstrap confidence bands for a survival distribution under random censoring using Efron's approach. These bands are the only available ones that are valid even when the survival distribution has a discrete component. Further, it is demonstrated that Reid's proposal for bootstrapping does not produce asymptotically correct confidence bands. Results from simulation studies assessing the finite sample performance of the bootstrap confidence bands are included.},
  number = {396},
  journal = {Journal of the American Statistical Association},
  author = {Akritas, Michael G.},
  year = {1986},
  pages = {1032-1038}
}

@book{kuhn_structure_1962,
  title = {The Structure of Scientific Revolutions},
  publisher = {{University of Chicago press}},
  author = {Kuhn, Thomas S},
  year = {1962},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5KZGSVSG/Kuhn - 1962 - The structure of scientific revolutions.pdf}
}

@article{guo_robust_2018,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1806.11011},
  primaryClass = {cs},
  title = {Robust Pose Tracking with a Joint Model of Appearance and Shape},
  abstract = {We present a novel approach for estimating the 2D pose of an articulated object with an application to automated video analysis of small laboratory animals. We have found that deformable part models developed for humans, exemplified by the flexible mixture of parts (FMP) model, typically fail on challenging animal poses. We argue that beyond encoding appearance and spatial relations, shape is needed to overcome the lack of distinctive landmarks on laboratory animal bodies. In our approach, a shape consistent FMP (scFMP) model computes promising pose candidates after a standard FMP model is used to rapidly discard false part detections. This "cascaded" approach combines the relative strengths of spatial-relations, appearance and shape representations and is shown to yield significant improvements over the original FMP model as well as a representative deep neural network baseline.},
  journal = {arXiv:1806.11011 [cs]},
  author = {Guo, Yuliang and Govindarajan, Lakshmi Narasimhan and Kimia, Benjamin and Serre, Thomas},
  month = jun,
  year = {2018},
  keywords = {Computer Science - Computer Vision and Pattern Recognition},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/A4T229YB/Guo et al. - 2018 - Robust pose tracking with a joint model of appeara.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QY6Y2LJK/1806.html}
}

@article{rezaval_sexually_2014,
  title = {Sexually Dimorphic Octopaminergic Neurons Modulate Female Postmating Behaviors in {{Drosophila}}},
  volume = {24},
  issn = {1879-0445},
  doi = {10.1016/j.cub.2013.12.051},
  abstract = {Mating elicits profound behavioral and physiological changes in many species that are crucial for reproductive success. After copulation, Drosophila melanogaster females reduce their sexual receptivity and increase egg laying [1, 2]. Transfer of male sex peptide (SP) during copulation mediates these postmating responses [1, 3-6] via SP sensory neurons in the uterus defined by coexpression of the proprioceptive neuronal marker pickpocket (ppk) and the sex-determination genes doublesex (dsx) and fruitless (fru) [7-9]. Although neurons expressing dsx downstream of SP signaling have been shown to regulate postmating behaviors [9], how the female nervous system coordinates the change from pre- to postcopulatory states is unknown. Here, we show a role of the neuromodulator octopamine (OA) in the female postmating response. Lack of OA disrupts postmating responses in mated females, while increase of OA induces postmating responses in virgin females. Using a novel dsx(FLP) allele, we uncovered dsx neuronal elements associated with OA signaling involved in modulation of postmating responses. We identified a small subset of sexually dimorphic OA/dsx(+) neurons (approximately nine cells in females) in the abdominal ganglion. Our results are consistent with a model whereby OA neuronal signaling increases after copulation, which in turn modulates changes in female behavior and physiology in response to reproductive state.},
  language = {eng},
  number = {7},
  journal = {Current biology: CB},
  author = {Rez\'aval, Carolina and Nojima, Tetsuya and Neville, Megan C. and Lin, Andrew C. and Goodwin, Stephen F.},
  month = mar,
  year = {2014},
  keywords = {Sexual Behavior; Animal,Female,Animals,Molecular Sequence Data,Drosophila,Drosophila Proteins,Sex Characteristics,Octopamine},
  pages = {725-730},
  pmid = {24631243}
}

@article{ayroles_behavioral_2015,
  title = {Behavioral Idiosyncrasy Reveals Genetic Control of Phenotypic Variability},
  volume = {112},
  issn = {0027-8424},
  doi = {10.1073/pnas.1503830112},
  abstract = {If we could rear genetically identical individuals from a variety of genetic backgrounds and rear them in the same environment, how much phenotypic variation between individuals of the same genotype would we see? Would different genetic backgrounds differ in their degree of variability? What would account for these differences? We used Drosophila inbred lines to address these questions focusing on variability in locomotor handedness. We show that different genotypes vary dramatically in their propensity for variability, that phenotypic variability itself, as a trait, can be heritable, and that loci affecting variability can be mapped. The genetic control of variability has received little attention in quantitative genetics despite the important role variability plays in explaining phenotypic variation between individuals., Quantitative genetics has primarily focused on describing genetic effects on trait means and largely ignored the effect of alternative alleles on trait variability, potentially missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study the genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability), we used Drosophila inbred lines and measured the spontaneous locomotor behavior of flies walking individually in Y-shaped mazes, focusing on variability in locomotor handedness, an assay optimized to measure variability. We discovered that some lines had consistently high levels of intragenotypic variability among individuals, whereas lines with low variability behaved as although they tossed a coin at each left/right turn decision. We demonstrate that the degree of variability is itself heritable. Using a genome-wide association study (GWAS) for the degree of intragenotypic variability as the phenotype across lines, we identified several genes expressed in the brain that affect variability in handedness without affecting the mean. One of these genes, Ten-a, implicates a neuropil in the central complex of the fly brain as influencing the magnitude of behavioral variability, a brain region involved in sensory integration and locomotor coordination. We validated these results using genetic deficiencies, null alleles, and inducible RNAi transgenes. Our study reveals the constellation of phenotypes that can arise from a single genotype and shows that different genetic backgrounds differ dramatically in their propensity for phenotypic variabililty. Because traditional mean-focused GWASs ignore the contribution of variability to overall phenotypic variation, current methods may miss important links between genotype and phenotype.},
  number = {21},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Ayroles, Julien F. and Buchanan, Sean M. and O'Leary, Chelsea and {Skutt-Kakaria}, Kyobi and Grenier, Jennifer K. and Clark, Andrew G. and Hartl, Daniel L. and {de Bivort}, Benjamin L.},
  month = may,
  year = {2015},
  pages = {6706-6711},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6S65FUWQ/Ayroles et al. - 2015 - Behavioral idiosyncrasy reveals genetic control of.pdf},
  pmid = {25953335},
  pmcid = {PMC4450409}
}

@article{kain_phototactic_2012,
  title = {Phototactic Personality in Fruit Flies and Its Suppression by Serotonin and White},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1211988109},
  abstract = {Drosophila typically move toward light (phototax positively) when startled. The various species of Drosophila exhibit some variation in their respective mean phototactic behaviors; however, it is not clear to what extent genetically identical individuals within each species behave idiosyncratically. Such behavioral individuality has indeed been observed in laboratory arthropods; however, the neurobiological factors underlying individual-to-individual behavioral differences are unknown. We developed ``FlyVac,'' a high-throughput device for automatically assessing phototaxis in single animals in parallel. We observed surprising variability within every species and strain tested, including identically reared, isogenic strains. In an extreme example, a domesticated strain of Drosophila simulans harbored both strongly photopositive and strongly photonegative individuals. The particular behavior of an individual fly is not heritable and, because it persists for its lifetime, constitutes a model system for elucidating the molecular mechanisms of personality. Although all strains assayed had greater than expected variation (assuming binomial sampling), some had more than others, implying a genetic basis. Using genetics and pharmacology, we identified the metabolite transporter White and white-dependent serotonin as suppressors of phototactic personality. Because we observed behavioral idiosyncrasy in all experimental groups, we suspect it is present in most behaviors of most animals.},
  language = {en},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Kain, Jamey S. and Stokes, Chris and de Bivort, Benjamin L.},
  month = nov,
  year = {2012},
  keywords = {bet-hedging,ethology,Ischnopterapion virens,stochasticity},
  pages = {201211988},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/W5QY6F5P/Kain et al. - 2012 - Phototactic personality in fruit flies and its sup.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZSFXMM4K/1211988109.html},
  pmid = {23150588}
}

@article{kaern_stochasticity_2005,
  title = {Stochasticity in Gene Expression: From Theories to Phenotypes},
  volume = {6},
  copyright = {2005 Nature Publishing Group},
  issn = {1471-0064},
  shorttitle = {Stochasticity in Gene Expression},
  doi = {10.1038/nrg1615},
  abstract = {Genetically identical cells exposed to the same environmental conditions can show significant variation in molecular content and marked differences in phenotypic characteristics. This variability is linked to stochasticity in gene expression, which is generally viewed as having detrimental effects on cellular function with potential implications for disease. However, stochasticity in gene expression can also be advantageous. It can provide the flexibility needed by cells to adapt to fluctuating environments or respond to sudden stresses, and a mechanism by which population heterogeneity can be established during cellular differentiation and development.},
  language = {en},
  number = {6},
  journal = {Nature Reviews Genetics},
  author = {K\ae{}rn, Mads and Elston, Timothy C. and Blake, William J. and Collins, James J.},
  month = jun,
  year = {2005},
  pages = {451-464},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NGY8CJWP/Kærn et al. - 2005 - Stochasticity in gene expression from theories to.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QQU722AS/nrg1615.html}
}

@article{yampolsky_developmental_1994,
  title = {Developmental {{Noise}}, {{Phenotypic Plasticity}}, and {{Allozyme Heterozygosity}} in {{Daphnia}}},
  volume = {48},
  issn = {0014-3820},
  doi = {10.2307/2410259},
  abstract = {Previous theories and studies have postulated negative correlations between allozyme heterozygosity and developmental noise and between heterozygosity and phenotypic plasticity. We examined these relationships for morphological and life-history traits of Daphnia magna in four independent experiments using two different Moscow populations and one German population. Clones were raised under a range of food levels or individual densities. Heterozygosity was scored at five allozyme loci in two experiments and at three loci in two others. Relative differences in developmental noise among clones with different heterozygosity levels were estimated as the pooled residual variation from an analysis of variation that removed the effects of macroenvironment, clones, and their interaction. Plasticity was measured as the amount of macroenvironmental variation plus genotype-by-environment interaction variation. We found a positive correlation between developmental noise and heterozygosity, although this correlation varied among traits and experiments. This result contradicts most previous claims about these relationships. In contrast, we found that phenotypic plasticity and heterozygosity were negatively correlated for some traits. Developmental noise and phenotypic plasticity were correlated for only two traits in two different experiments. This trait-specific relationship is in concordance with previous studies. Our results could not be explained by effects of developmental time, a previously hypothesized mechanism. We propose several explanations for our results and the disparate results of others that do not require that heterozygosity be the actual cause of variation in developmental noise.},
  number = {5},
  journal = {Evolution},
  author = {Yampolsky, Lev Yu. and Scheiner, Samuel M.},
  year = {1994},
  pages = {1715-1722}
}

@article{grenier_phenotypic_2016,
  title = {Phenotypic {{Plasticity}} and {{Selection}}: {{Nonexclusive Mechanisms}} of {{Adaptation}}},
  volume = {2016},
  issn = {2090-908X},
  shorttitle = {Phenotypic {{Plasticity}} and {{Selection}}},
  doi = {10.1155/2016/7021701},
  abstract = {Selection and plasticity are two mechanisms that allow the adaptation of a population to a changing environment. Interaction between these nonexclusive mechanisms must be considered if we are to understand population survival. This review discusses the ways in which plasticity and selection can interact, based on a review of the literature on selection and phenotypic plasticity in the evolution of populations. The link between selection and phenotypic plasticity is analysed at the level of the individual. Plasticity can affect an individual's response to selection and so may modify the end result of genetic diversity evolution at population level. Genetic diversity increases the ability of populations or communities to adapt to new environmental conditions. Adaptive plasticity increases individual fitness. However this effect must be viewed from the perspective of the costs of plasticity, although these are not easy to estimate. It is becoming necessary to engage in new experimental research to demonstrate the combined effects of selection and plasticity for adaptation and their consequences on the evolution of genetic diversity.},
  journal = {Scientifica},
  author = {Grenier, S. and Barre, P. and Litrico, I.},
  year = {2016},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZBW8W4PV/Grenier et al. - 2016 - Phenotypic Plasticity and Selection Nonexclusive .pdf},
  pmid = {27313957},
  pmcid = {PMC4895053}
}

@article{veening_bistability_2008,
  title = {Bistability, {{Epigenetics}}, and {{Bet}}-{{Hedging}} in {{Bacteria}}},
  volume = {62},
  doi = {10.1146/annurev.micro.62.081307.163002},
  abstract = {Clonal populations of microbial cells often show a high degree of phenotypic variability under homogeneous conditions. Stochastic fluctuations in the cellular components that determine cellular states can cause two distinct subpopulations, a property called bistability. Phenotypic heterogeneity can be readily obtained by interlinking multiple gene regulatory pathways, effectively resulting in a genetic logic-AND gate. Although switching between states can occur within the cells' lifetime, cells can also pass their cellular state over to the next generation by a mechanism known as epigenetic inheritance and thus perpetuate the phenotypic state. Importantly, heterogeneous populations can demonstrate increased fitness compared with homogeneous populations. This suggests that microbial cells employ bet-hedging strategies to maximize survival. Here, we discuss the possible roles of interlinked bistable networks, epigenetic inheritance, and bet-hedging in bacteria.},
  number = {1},
  journal = {Annual Review of Microbiology},
  author = {Veening, Jan-Willem and Smits, Wiep Klaas and Kuipers, Oscar P.},
  year = {2008},
  pages = {193-210},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/BITKJL8T/Veening et al. - 2008 - Bistability, Epigenetics, and Bet-Hedging in Bacte.pdf},
  pmid = {18537474}
}

@article{debat_mapping_2001,
  title = {Mapping Phenotypes: Canalization, Plasticity and Developmental Stability},
  volume = {16},
  issn = {0169-5347},
  shorttitle = {Mapping Phenotypes},
  doi = {10.1016/S0169-5347(01)02266-2},
  abstract = {The relationship between genotype and phenotype is not one to one. This statement is central to our understanding of how natural selection shapes phenotypic evolution. Here, we clarify the links between canalization, plasticity and developmental stability, the three major processes involved in the control of phenotypic variability. We present a short historical review, including the original definitions of these concepts, and then summarize their current meaning and use, highlighting possible sources of confusion. Some of the perspectives allowed by a more synthetic conceptual framework are presented, in the light of the recent advances in molecular and developmental genetics.},
  number = {10},
  journal = {Trends in Ecology \& Evolution},
  author = {Debat, Vincent and David, Patrice},
  month = oct,
  year = {2001},
  keywords = {phenotypes,adaptation,canalization,developmental stability,fluctuating asymmetry,geometric morphometrics,phenotypic plasticity},
  pages = {555-561},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GFHM3WLG/Debat and David - 2001 - Mapping phenotypes canalization, plasticity and d.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TGCSBHDJ/S0169534701022662.html}
}

@article{geissmann_most_2018,
  title = {Most Sleep Does Not Serve a Vital Function. {{Evidence}} from {{Drosophila}} Melanogaster},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  doi = {10.1101/361667},
  abstract = {Sleep appears to be a universally conserved phenomenon among the animal kingdom but whether this striking evolutionary conservation underlies a basic vital function is still an open question. Using novel technologies, we conducted an unprecedentedly detailed high-throughput analysis of sleep in the fruit fly Drosophila melanogaster, coupled with a life-long chronic and specific sleep restriction. Our results show that some wild-type flies are virtually sleepless in baseline conditions and that complete, forced sleep restriction is not necessarily a lethal treatment in wild-type Drosophila melanogaster. We also show that circadian drive, and not homeostatic regulation, is the main contributor to sleep pressure in flies. We propose a three-partite model framework of sleep function, according to which, total sleep accounts for three components: a vital component, a useful component, and an accessory component.},
  language = {en},
  journal = {bioRxiv},
  author = {Geissmann, Quentin and Beckwith, Esteban J. and Gilestro, Giorgio F.},
  month = jul,
  year = {2018},
  pages = {361667},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DHBN4Q9B/Geissmann et al. - 2018 - Most sleep does not serve a vital function. Eviden.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VQGQFHGB/361667.html}
}

@article{yurgel_ade2_2018,
  title = {Ade2 Functions in the {{Drosophila}} Fat Body to Promote Sleep},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  doi = {10.1101/361055},
  abstract = {Metabolic state is a potent modulator of sleep and circadian behavior and animals acutely modulate their sleep in accordance with internal energy stores and food availability. Across phyla, hormones secreted from adipose tissue act in the brain to control neural physiology and behavior to modulate sleep and metabolic state. Growing evidence suggests the fat body is a critical regulator of complex behaviors, but little is known about the genes that function within the fat body to regulate sleep. To identify molecular factors functioning in the periphery to regulate sleep, we performed an RNAi screen selectively knocking down genes in the fat body. We found that knockdown of Phosphoribosylformylglycinamidine synthase/Pfas(Ade2), a highly conserved gene involved the biosynthesis of purines, reduces sleep and energy stores. Flies heterozygous for multiple Ade2 mutations are also short sleepers and this effect is partially rescued by restoring Ade2 to the fat body. Targeted knockdown of Ade2 in the fat body does not alter arousal threshold or the homeostatic response to sleep deprivation, suggesting a specific role in modulating baseline sleep duration. Together, these findings suggest Ade2 functions within the fat body to promote both sleep and energy storage, providing a functional link between these processes.},
  language = {en},
  journal = {bioRxiv},
  author = {Yurgel, Maria E. and Shah, Kreesha and Bennick, Ryan A. and DiAngelo, Justin and Keene, Alex},
  month = jul,
  year = {2018},
  pages = {361055},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UJUPFHD8/Yurgel et al. - 2018 - Ade2 functions in the Drosophila fat body to promo.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8FUSL4QR/361055.html}
}

@article{chen_genetic_2017,
  title = {Genetic and Neuronal Mechanisms Governing the Sex-Specific Interaction between Sleep and Sexual Behaviors in {{Drosophila}}},
  volume = {8},
  copyright = {2017 The Author(s)},
  issn = {2041-1723},
  doi = {10.1038/s41467-017-00087-5},
  abstract = {Genes and circuits involved in sleep and sexual arousal have been extensively studied in Drosophila. Here the authors identify the sex determination genes fruitless and doublesex, and a sex-specific P1-DN1 neuronal feedback that governs the interaction between these competing behaviors},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  author = {Chen, Dandan and Sitaraman, Divya and Chen, Nan and Jin, Xin and Han, Caihong and Chen, Jie and Sun, Mengshi and Baker, Bruce S. and Nitabach, Michael N. and Pan, Yufeng},
  month = jul,
  year = {2017},
  pages = {154},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/87QQ3RZG/Chen et al. - 2017 - Genetic and neuronal mechanisms governing the sex-.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/U7V4ATAY/s41467-017-00087-5.html}
}

@article{dove_mechanisms_2017,
  title = {Mechanisms of Sleep Plasticity Due to Sexual Experience in {{Drosophila}} Melanogaster},
  volume = {180},
  issn = {0031-9384},
  doi = {10.1016/j.physbeh.2017.08.020},
  abstract = {Sleep can be altered by an organism's previous experience. For instance, female Drosophila melanogaster experience a post-mating reduction in daytime sleep that is purportedly mediated by sex peptide (SP), one of many seminal fluid proteins (SFPs) transferred from male to female during mating. In the present study, we first characterized this mating effect on sleep more fully, as it had previously only been tested in young flies under 12h light/12h dark conditions. We found that mating reduced sleep equivalently in 3-day-old or 14-day-old females, and could even occur in females who had been mated previously, suggesting that there is not a developmental critical period for the suppression of sleep by mating. In conditions of constant darkness, circadian rhythms were not affected by prior mating. In either constant darkness or constant light, the sleep reduction due to mating was no longer confined to the subjective day but could be observed throughout the 24-hour period. This suggests that the endogenous clock may dictate the timing of when the mating effect on sleep is expressed. We recently reported that genetic elimination of SP only partially blocked the post-mating female siesta sleep reduction, suggesting that the effect was unlikely to be governed solely by SP. We found here that the daytime sleep reduction was also reduced but not eliminated in females mated to mutant males lacking the vast majority of SFPs. This suggested that SFPs other than SP play a minimal role in the mating effect on sleep, and that additional non-SFP signals from the male might be involved. Males lacking sperm were able to induce a normal initial mating effect on female sleep, although the effect declined more rapidly in these females. This result indicated that neither the presence of sperm within the female reproductive tract nor female impregnation are required for the initial mating effect on sleep to occur, although sperm may serve to prolong the effect. Finally, we tested for contributions from other aspects of the mating experience. NorpA and eya2 mutants with disrupted vision showed normal mating effects on sleep. By separating males from females with a mesh, we found that visual and olfactory stimuli from male exposure, in the absence of physical contact, could not replicate the mating effect. Further, in ken/barbie male flies lacking external genitalia, courtship and physical contact without ejaculation were also unable to replicate the mating effect. These findings confirmed that the influence of mating on sleep does in fact require male/female contact including copulation, but may not be mediated exclusively by SP transfer.},
  journal = {Physiology \& Behavior},
  author = {Dove, Abigail E. and Cook, Brianne L. and Irgebay, Zhazira and Vecsey, Christopher G.},
  month = oct,
  year = {2017},
  keywords = {Sleep,Drosophila melanogaster,Plasticity,Sex peptide,Circadian rhythm,Post-mating response},
  pages = {146-158},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UWY25UM9/S0031938417302688.html}
}

@article{seidner_identification_2015,
  title = {Identification of {{Neurons}} with a {{Privileged Role}} in {{Sleep Homeostasis}} in {{Drosophila}} Melanogaster},
  volume = {25},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2015.10.006},
  abstract = {Summary
Sleep is thought to be controlled by two main processes: a circadian clock that primarily regulates sleep timing and a homeostatic mechanism that detects and responds to sleep need. Whereas abundant experimental evidence suggests that sleep need increases with time spent awake, the contributions of different brain arousal systems have not been assessed independently of each other to determine whether certain neural circuits, rather than waking per se, selectively contribute to sleep homeostasis. Using the fruit fly, Drosophila melanogaster, we found that sustained thermogenetic activation of three independent neurotransmitter systems promoted nighttime wakefulness. However, only sleep deprivation resulting from activation of cholinergic neurons was sufficient to elicit subsequent homeostatic recovery sleep, as assessed by multiple~behavioral criteria. In contrast, sleep deprivation resulting from activation of octopaminergic neurons suppressed homeostatic recovery sleep, indicating that wakefulness can be dissociated from accrual of sleep need. Neurons that promote sleep homeostasis were found to innervate the central brain and motor control regions of the thoracic ganglion. Blocking activity of these neurons suppressed recovery sleep but did not alter baseline sleep, further differentiating between neural control of sleep homeostasis and daily fluctuations in the sleep/wake cycle. Importantly, selective activation of wake-promoting neurons without engaging the sleep homeostat impaired subsequent short-term memory, thus providing evidence that neural circuits that regulate~sleep homeostasis are important for behavioral plasticity. Together, our data suggest a neural circuit model involving distinct populations of wake-promoting neurons, some of which are involved in homeostatic control of sleep and cognition.},
  number = {22},
  journal = {Current Biology},
  author = {Seidner, Glen and Robinson, James E. and Wu, Meilin and Worden, Kurtresha and Masek, Pavel and Roberts, Stephen W. and Keene, Alex C. and Joiner, William J.},
  month = nov,
  year = {2015},
  pages = {2928-2938},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/G57WR679/Seidner et al. - 2015 - Identification of Neurons with a Privileged Role i.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8FA6QUCP/S0960982215012348.html}
}

@article{murphy_simultaneous_2017,
  title = {Simultaneous Measurement of Sleep and Feeding in Individual {{{\emph{Drosophila}}}}},
  volume = {12},
  copyright = {2017 Nature Publishing Group},
  issn = {1750-2799},
  doi = {10.1038/nprot.2017.096},
  abstract = {Drosophila is widely used for the dissection of genetic and neuronal mechanisms of behavior. Recently, flies have emerged as a model for investigating the regulation of feeding and sleep. Although typically studied in isolation, increasing evidence points to a fundamental connection between these behaviors. Thus, a system for measuring sleep and feeding simultaneously in a single integrated system is important for interpreting behavioral shifts of either state. Here, we describe the construction and use of the Activity Recording Capillary Feeder or CAFE (ARC), a machine-vision (automated image tracking)-based system for the integrated measurement of sleep and feeding in individual Drosophila. Flies feed on liquid food from a microcapillary, and consumption is measured by tracking the liquid meniscus over time. Sleep measurements are obtained from positional tracking of individual animals, and arousal threshold can be determined by vibrational stimulus response. Using this system, a single computer and experimenter can track diverse behaviors from up to 60 individual flies in a single integrated system. The ARC is efficiently assembled with minimal training, and each experiment can be run for up to $\sim$7 d, with a total setup and breakdown time of $\sim$2 h.},
  language = {en},
  number = {11},
  journal = {Nature Protocols},
  author = {Murphy, Keith R. and Park, Jin Hong and Huber, Robert and Ja, William W.},
  month = nov,
  year = {2017},
  pages = {2355-2366},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/3XMUB5X9/Murphy et al. - 2017 - Simultaneous measurement of sleep and feeding in i.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZFE2QZVY/nprot.2017.html}
}

@article{wong_quantification_2009,
  title = {Quantification of {{Food Intake}} in {{Drosophila}}},
  volume = {4},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0006063},
  abstract = {Measurement of food intake in the fruit fly Drosophila melanogaster is often necessary for studies of behaviour, nutrition and drug administration. There is no reliable and agreed method for measuring food intake of flies in undisturbed, steady state, and normal culture conditions. We report such a method, based on measurement of feeding frequency by proboscis-extension, validated by short-term measurements of food dye intake. We used the method to demonstrate that (a) female flies feed more frequently than males, (b) flies feed more often when housed in larger groups and (c) fly feeding varies at different times of the day. We also show that alterations in food intake are not induced by dietary restriction or by a null mutation of the fly insulin receptor substrate chico. In contrast, mutation of takeout increases food intake by increasing feeding frequency while mutation of ovoD increases food intake by increasing the volume of food consumed per proboscis-extension. This approach provides a practical and reliable method for quantification of food intake in Drosophila under normal, undisturbed culture conditions.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  author = {Wong, Richard and Piper, Matthew D. W. and Wertheim, Bregje and Partridge, Linda},
  year = {26-Jun-2009},
  keywords = {Drosophila melanogaster,Diet,Nutrients,Food consumption,Yeast,Food,Generalized linear model,Ingestion},
  pages = {e6063},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/93WSHZ27/Wong et al. - 2009 - Quantification of Food Intake in Drosophila.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/YCV62IV8/article.html}
}

@article{mair_calories_2005,
  title = {Calories {{Do Not Explain Extension}} of {{Life Span}} by {{Dietary Restriction}} in {{Drosophila}}},
  volume = {3},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.0030223},
  abstract = {Dietary restriction (DR) extends life span in diverse organisms, including mammals, and common mechanisms may be at work. DR is often known as calorie restriction, because it has been suggested that reduction of calories, rather than of particular nutrients in the diet, mediates extension of life span in rodents. We here demonstrate that extension of life span by DR in Drosophila is not attributable to the reduction in calorie intake. Reduction of either dietary yeast or sugar can reduce mortality and extend life span, but by an amount that is unrelated to the calorie content of the food, and with yeast having a much greater effect per calorie than does sugar. Calorie intake is therefore not the key factor in the reduction of mortality rate by DR in this species.},
  language = {en},
  number = {7},
  journal = {PLOS Biology},
  author = {Mair, William and Piper, Matthew D. W. and Partridge, Linda},
  year = {31-May-2005},
  keywords = {Drosophila melanogaster,Diet,Nutrients,Antibiotics,Death rates,Yeast,Food,Tetracyclines},
  pages = {e223},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/X5V976GS/Mair et al. - 2005 - Calories Do Not Explain Extension of Life Span by .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/XRMLVAWS/article.html}
}

@article{dauwalder_drosophila_2002,
  title = {The {{Drosophila}} Takeout Gene Is Regulated by the Somatic Sex-Determination Pathway and Affects Male Courtship Behavior},
  volume = {16},
  issn = {0890-9369},
  doi = {10.1101/gad.1010302},
  abstract = {The Drosophila somatic sex-determination regulatory pathway has been well studied, but little is known about the target genes that it ultimately controls. In a differential screen for sex-specific transcripts expressed in fly heads, we identified a highly male-enriched transcript encoding Takeout, a protein related to a superfamily of factors that bind small lipophilic molecules. We show that sex-specific takeout transcripts derive from fat body tissue closely associated with the adult brain and are dependent on the sex determination genes doublesex (dsx) and fruitless (fru). The male-specific Doublesex and Fruitless proteins together activate Takeout expression, whereas the female-specific Doublesex protein represses takeout independently of Fru. When cells that normally express takeout are feminized by expression of the Transformer-F protein, male courtship behavior is dramatically reduced, suggesting that male identity in these cells is necessary for behavior. A loss-of-function mutation in the takeout gene reduces male courtship and synergizes with fruitless mutations, suggesting that takeout plays a redundant role with other fru-dependent factors involved in male mating behavior. Comparison of Takeout sequences to the Drosophila genome reveals a family of 20 related secreted factors. Expression analysis of a subset of these genes suggests that the takeout gene family encodes multiple factors with sex-specific functions.},
  language = {eng},
  number = {22},
  journal = {Genes \& Development},
  author = {Dauwalder, Brigitte and Tsujimoto, Susan and Moss, Jason and Mattox, William},
  month = nov,
  year = {2002},
  keywords = {Behavior; Animal,Animals; Genetically Modified,Female,Male,Brain,Animals,Amino Acid Sequence,Molecular Sequence Data,Drosophila,Circadian Rhythm,Drosophila Proteins,Insect Proteins,Mutation,Nerve Tissue Proteins,DNA-Binding Proteins,Transcription Factors,Courtship,Fat Body,Gene Expression Regulation; Developmental,Ribonucleoproteins,Sequence Homology; Amino Acid,Sex Determination Processes},
  pages = {2879-2892},
  pmid = {12435630},
  pmcid = {PMC187483}
}

@article{mann_pair_2013,
  title = {A {{Pair}} of {{Interneurons Influences}} the {{Choice}} between {{Feeding}} and {{Locomotion}} in {{Drosophila}}},
  volume = {79},
  issn = {0896-6273},
  doi = {10.1016/j.neuron.2013.06.018},
  abstract = {Summary
The decision to engage in one behavior often precludes the selection of others, suggesting cross-inhibition between incompatible behaviors. For example, the likelihood to initiate feeding might be influenced by an animal's commitment to other behaviors. Here, we examine the modulation of feeding behavior in the fruit fly, Drosophila melanogaster, and identify a pair of interneurons in the ventral nerve cord that is activated by stimulation of mechanosensory neurons and inhibits feeding initiation, suggesting that these neurons suppress feeding while the fly is walking. Conversely, inhibiting activity in these neurons promotes feeding initiation and inhibits locomotion. These studies demonstrate the mutual exclusivity between locomotion and feeding initiation in the fly, isolate interneurons that influence this behavioral choice, and provide a framework for studying the neural basis for behavioral exclusivity in Drosophila.},
  number = {4},
  journal = {Neuron},
  author = {Mann, Kevin and Gordon, Michael D. and Scott, Kristin},
  month = aug,
  year = {2013},
  pages = {754-765},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NHTSAU8P/Mann et al. - 2013 - A Pair of Interneurons Influences the Choice betwe.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q4NNUSA8/S0896627313005345.html}
}

@incollection{djawdan_metabolic_2004,
  title = {Metabolic {{Aspects}} of the {{Trade}}-{{Off}} between {{Fecundity}} and {{Longevity}} in {{Drosophila}} Melanogaster},
  isbn = {978-981-238-741-7},
  booktitle = {Methuselah {{Flies}}},
  publisher = {{WORLD SCIENTIFIC}},
  author = {Djawdan, Minou and Sugiyama, Tina T. and Schlaeger, Lisa K. and Bradley, Timothy J. and Rose, Michael R.},
  month = jun,
  year = {2004},
  pages = {145-164},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/VTAZ4AXJ/9789812567222_0014.html},
  doi = {10.1142/9789812567222_0014}
}

@article{flatt_juvenile_2007,
  title = {Juvenile {{Hormone}} as a {{Regulator}} of the {{Trade}}-{{Off Between Reproduction}} and {{Life Span}} in {{Drosophila Melanogaster}}},
  volume = {61},
  issn = {1558-5646},
  doi = {10.1111/j.1558-5646.2007.00151.x},
  abstract = {Trade-offs between reproduction and life span are ubiquitous, but little is known about their underlying mechanisms. Here we combine treatment with the juvenile hormone analog (JHa) methoprene and experimental evolution in Drosophila melanogaster to study the potential role of juvenile hormone (JH) in mediating such trade-offs at both the physiological and evolutionary level. Exposure to JHa in the larval medium (and up to 24 h posteclosion) increased early life fecundity but reduced life span of normal (unselected) flies, supporting the physiological role of JH in mediating the trade-off. This effect was much smaller for life span, and not detectable for fecundity, in fly lines previously bred for 19 generations on a medium containing JHa. Furthermore, these selection lines lived longer than unselected controls even in the absence of JHa treatment, without a detectable reduction in early life fecundity. Thus, selection for resistance to JHa apparently induced some evolutionary changes in JH metabolism or signaling, which led to longer life span as a correlated response. This supports the hypothesis that JH may mediate evolution of longer life span, but\textemdash{}contrary to our expectation\textemdash{}this apparently does not need to trade-off with fecundity.},
  language = {en},
  number = {8},
  journal = {Evolution},
  author = {Flatt, Thomas and Kawecki, Tadeusz J.},
  year = {2007},
  keywords = {Aging,Drosophila,reproduction,antagonistic pleiotropy,cost of reproduction,experimental evolution,juvenile hormone,life span,trade-off},
  pages = {1980-1991},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FCQWEL3K/Flatt and Kawecki - Juvenile Hormone as a Regulator of the Trade-Off B.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZI5C2L4B/j.1558-5646.2007.00151.html}
}

@article{libert_trade-offs_2006,
  title = {Trade-Offs between Longevity and Pathogen Resistance in {{Drosophila}} Melanogaster Are Mediated by {{NF$\kappa$B}} Signaling},
  volume = {5},
  issn = {1474-9726},
  doi = {10.1111/j.1474-9726.2006.00251.x},
  abstract = {The innate immune response protects numerous organisms, including humans, from the universe of pathogenic molecules, viruses and micro-organisms. Despite its role in promoting pathogen resistance, inappropriate activation and expression of NF$\kappa$B and other immunity-related effector molecules can lead to cancer, inflammation, and other diseases of aging. Understanding the mechanisms leading to immune system activation as well as the short- and long-term consequences of such activation on health and lifespan is therefore critical for the development of beneficial immuno-modulating and longevity-promoting interventions. Mechanisms of innate immunity are highly conserved across species, and we take advantage of genetic tools in the model organism, Drosophila melanogaster, to study the effects of acute and chronic activation of immunity pathways on pathogen resistance and general fitness of adult flies. Our findings indicate that fat body specific overexpression of a putative pathogen recognition molecule, peptidoglycan recognition protein (PGRP-LE), is sufficient for constitutive up-regulation of the immune response and for enhanced pathogen resistance. Primary components of fitness are unaffected by acute activation, but chronic activation leads to an inflammatory state and reduced lifespan. These phenotypes are dependent on the NF$\kappa$B-related transcriptional factor, Relish, and they establish a mechanistic basis for a link between immunity, inflammation, and longevity.},
  language = {en},
  number = {6},
  journal = {Aging Cell},
  author = {Libert, Sergiy and Chao, Yufang and Chu, Xiaowen and Pletcher, Scott D.},
  year = {2006},
  keywords = {aging,NFκB,innate immunity,infection,inflammation},
  pages = {533-543},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/HQJWLKZR/Libert et al. - Trade-offs between longevity and pathogen resistan.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/76BVCC33/j.1474-9726.2006.00251.html}
}

@article{lochmiller_trade-offs_2000,
  title = {Trade-Offs in Evolutionary Immunology: Just What Is the Cost of Immunity?},
  volume = {88},
  issn = {1600-0706},
  shorttitle = {Trade-Offs in Evolutionary Immunology},
  doi = {10.1034/j.1600-0706.2000.880110.x},
  abstract = {It has become increasingly clear that life-history patterns among the vertebrates have been shaped by the plethora and variety of immunological risks associated with parasitic faunas in their environments. Immunological competence could very well be the most important determinant of life-time reproductive success and fitness for many species. It is generally assumed by evolutionary ecologists that providing immunological defences to minimise such risks to the host is costly in terms of necessitating trade-offs with other nutrient-demanding processes such as growth, reproduction, and thermoregulation. Studies devoted to providing assessments of such costs and how they may force evolutionary trade-offs among life-history characters are few, especially for wild vertebrate species, and their results are widely scattered throughout the literature. In this paper we attempt to review this literature to obtain a better understanding of energetic and nutritional costs for maintaining a normal immune system and examine how costly it might be for a host who is forced to up-regulate its immunological defence mechanisms. The significance of these various costs to ecology and life history trade-offs among the vertebrates is explored. It is concluded that sufficient evidence exists to support the primary assumption that immunological defences are costly to the vertebrate host.},
  language = {en},
  number = {1},
  journal = {Oikos},
  author = {Lochmiller, Robert L. and Deerenberg, Charlotte},
  year = {2000},
  pages = {87-98},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UW2ILEJQ/Lochmiller and Deerenberg - Trade-offs in evolutionary immunology just what i.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LTJ8BRXH/j.1600-0706.2000.880110.html}
}

@article{rogina_longevity_2002,
  title = {Longevity {{Regulation}} by {{Drosophila Rpd3 Deacetylase}} and {{Caloric Restriction}}},
  volume = {298},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1078986},
  abstract = {Genetic studies of single gene mutations are revealing mechanisms and pathways that regulate longevity across distant species ([1][1]). One such mechanism is an alteration in histone deacetylase activity. Abolishing expression of the Rpd3 deacetylase ([2][2]) or increasing expression of the Sir2},
  language = {en},
  number = {5599},
  journal = {Science},
  author = {Rogina, Blanka and Helfand, Stephen L. and Frankel, Stewart},
  month = nov,
  year = {2002},
  pages = {1745-1745},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ZG69C7A3/Rogina et al. - 2002 - Longevity Regulation by Drosophila Rpd3 Deacetylas.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/KKH92ALJ/1745.html},
  pmid = {12459580}
}

@article{masoro_overview_2005,
  series = {Dietary restriction, longevity and ageing - the current state of our knowledge and ignorance},
  title = {Overview of Caloric Restriction and Ageing},
  volume = {126},
  issn = {0047-6374},
  doi = {10.1016/j.mad.2005.03.012},
  abstract = {It has been known for some 70 years that restricting the food intake of laboratory rats extends their mean and maximum life span. In addition, such life extension has been observed over the years in many other species, including mice, hamsters, dogs, fish, invertebrate animals, and yeast. Since this life-extending action appears to be due to a restricted intake of energy, this dietary manipulation is referred to as caloric restriction (CR). CR extends life by slowing and/or delaying the ageing processes. The underlying biological mechanism responsible for the life extension is still not known, although many hypotheses have been proposed. The Growth Retardation Hypothesis, the first proposed, has been tested and found wanting. Although there is strong evidence against the Reduction of Body Fat Hypothesis, efforts have recently been made to resurrect it. While the Reduction of Metabolic Rate Hypothesis is not supported by experimental findings, it nevertheless still has advocates. Currently, the most popular concept is the Oxidative Damage Attenuation Hypothesis; the results of several studies provide support for this hypothesis, while those of other studies do not. The Altered Glucose\textendash{}Insulin System Hypothesis and the Alteration of the Growth Hormone\textendash{}IGF-1 Axis Hypothesis have been gaining favor, and data have emerged that link these two hypotheses as one. Thus, it may now be more appropriate to refer to them as the Attenuation of Insulin-Like Signaling Hypothesis. Finally, the Hormesis Hypothesis may provide an overarching concept that embraces several of the other hypotheses as merely specific examples of hormetic processes. For example, the Oxidative Damage Attenuation Hypothesis probably addresses only one of likely many damaging processes that underlie aging. It is proposed that low-intensity stressors, such as CR, activate ancient hormetic defense mechanisms in organisms ranging from yeast to mammals, defending them against a variety of adversities and, when long-term, retarding senescent processes.},
  number = {9},
  journal = {Mechanisms of Ageing and Development},
  author = {Masoro, Edward J.},
  month = sep,
  year = {2005},
  keywords = {Hormesis,Insulin-like signaling,Life extension,Oxidative damage,Senescence},
  pages = {913-922},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Z9HB5CLH/Masoro - 2005 - Overview of caloric restriction and ageing.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ITXTXMM3/S0047637405000783.html}
}

@article{oxenkrug_extended_2010,
  title = {The Extended Life Span of {{Drosophila}} Melanogaster Eye-Color (White and Vermilion) Mutants with Impaired Formation of Kynurenine},
  volume = {117},
  issn = {0300-9564, 1435-1463},
  doi = {10.1007/s00702-009-0341-7},
  abstract = {Animal and human studies suggest that aging is associated with increased formation of kynurenine (KYN) from tryptophan (TRY). The rate-limiting factors of TRY\textendash{}KYN metabolism are transmembrane transport of TRY, and activity of enzyme, TRY 2,3-dioxygenase (TDO2). Eye-color mutants, white (w1118) (impaired TRY transport) and vermilion (v48a and v2) (deficient TDO activity), were compared with wild-type Oregon-R (Ore-R) strain of Drosophila melanogaster. Female 1-day-old adult flies maintained on a standard medium, and acclimatized to 12-h light:12-h dark cycle were collected, and then regularly transferred to fresh medium every 3\textendash{}4 days. The number of dead flies was recorded at the time of transfer. Forty flies were studied in each experimental group. The life span of w1118 (mean = 45.5 days), and v48a (mean = 47.6 days) and v2 (mean = 43.8 days), were significantly longer than of wild-type Ore-R flies (27.1 days) (p $<$ 0.001, Logrank test). There were no differences in life span between w1118 and v48a and v2 mutants. Present results suggest that prolongation of life span may be associated with slow rate of KYN formation from TRY.},
  language = {en},
  number = {1},
  journal = {Journal of Neural Transmission},
  author = {Oxenkrug, Gregory F.},
  month = jan,
  year = {2010},
  pages = {23},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PACJIX9C/Oxenkrug - 2010 - The extended life span of Emphasis Type=Italic.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UVBLGH2T/10.html}
}

@article{borbely1980sleep,
  title = {Sleep: Circadian Rhythm versus Recovery Process},
  journal = {Functional states of the brain: Their determinants},
  author = {Borb\'ely, AA},
  year = {1980},
  pages = {151-161},
  publisher = {{Elsevier Amsterdam}}
}

@article{gavrilets_quantitative-genetic_1994,
  title = {A {{Quantitative}}-{{Genetic Model}} for {{Selection}} on {{Developmental Noise}}},
  volume = {48},
  copyright = {\textcopyright{} 1994 The Society for the Study of Evolution},
  issn = {1558-5646},
  doi = {10.1111/j.1558-5646.1994.tb02190.x},
  abstract = {We propose a simple model for analyzing the effects of microenvironmental variation in quantitative genetics. Our model assumes that the sensitivity of the phenotype to fluctuations in microenvironment has a genetic basis and allows for genetic correlation between trait value and microenvironmental sensitivity. We analyze the effects of short-term stabilizing and directional selection on the genotypic and microenvironmental components of phenotypic variance. Our model predicts that stabilizing selection on a quantitative trait increases developmental canalization. We show that stabilizing selection can result in an increase in the heritability. Our findings may provide an explanation for the results of selection experiments in which artificial stabilizing selection did not change the heritability coefficient or increased it.},
  language = {en},
  number = {5},
  journal = {Evolution},
  author = {Gavrilets, Sergey and Hastings, Alan},
  year = {1994},
  keywords = {selection,Developmental noise,quantitative-genetic model},
  pages = {1478-1486},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PBSZLY7U/Gavrilets and Hastings - A Quantitative-Genetic Model for Selection on Deve.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/J5DH5X76/j.1558-5646.1994.tb02190.html}
}

@article{tenaillon_second-order_2001,
  title = {Second-Order Selection in Bacterial Evolution: Selection Acting on Mutation and Recombination Rates in the Course of Adaptation},
  volume = {152},
  issn = {0923-2508},
  shorttitle = {Second-Order Selection in Bacterial Evolution},
  abstract = {The increase in genetic variability of a population can be selected during adaptation, as demonstrated by the selection of mutator alleles. The dynamics of this phenomenon, named second-order selection, can result in an improved adaptability of bacteria through regulation of all facets of mutation and recombination processes.},
  language = {eng},
  number = {1},
  journal = {Research in Microbiology},
  author = {Tenaillon, O. and Taddei, F. and Radmian, M. and Matic, I.},
  year = {2001 Jan-Feb},
  keywords = {Mutation,Biological Evolution,Bacteria,Recombination; Genetic,Selection; Genetic,Adaptation; Physiological},
  pages = {11-16},
  pmid = {11281320}
}

@article{cichewicz_shinyr-dam_2018,
  title = {{{ShinyR}}-{{DAM}}: A Program Analyzing {{Drosophila}} Activity, Sleep and Circadian Rhythms},
  volume = {1},
  copyright = {2018 The Author(s)},
  issn = {2399-3642},
  shorttitle = {{{ShinyR}}-{{DAM}}},
  doi = {10.1038/s42003-018-0031-9},
  abstract = {Karol Cichewicz and Jay Hirsh developed a free, open-source, cloud-based application called ShinyR-DAM for analyzing Drosophila activity, sleep and circadian rhythms. ShinyR-DAM allows users to analyze their data quickly in customizable ways, improving the productivity of researchers.},
  language = {en},
  number = {1},
  journal = {Communications Biology},
  author = {Cichewicz, Karol and Hirsh, Jay},
  month = apr,
  year = {2018},
  pages = {25},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/I2LMRJTW/Cichewicz and Hirsh - 2018 - ShinyR-DAM a program analyzing Drosophila activit.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/DXGZ4MVY/s42003-018-0031-9.html}
}

@book{wilkinson_grammar_2005,
  address = {New York},
  edition = {2},
  series = {Statistics and Computing},
  title = {The {{Grammar}} of {{Graphics}}},
  isbn = {978-0-387-24544-7},
  abstract = {This book was written for statisticians, computer scientists, geographers, researchers, and others interested in visualizing data. It presents a unique foundation for producing almost every quantitative graphic found in scientific journals, newspapers, statistical packages, and data visualization systems. While the tangible results of this work have been several visualization software libraries, this book focuses on the deep structures involved in producing quantitative graphics from data. What are the rules that underlie the production of pie charts, bar charts, scatterplots, function plots, maps, mosaics, and radar charts? Those less interested in the theoretical and mathematical foundations can still get a sense of the richness and structure of the system by examining the numerous and often unique color graphics it can produce. The second edition is almost twice the size of the original, with six new chapters and substantial revision. Much of the added material makes this book suitable for survey courses in visualization and statistical graphics. From reviews of the first edition: "Destined to become a landmark in statistical graphics, this book provides a formal description of graphics, particularly static graphics, playing much the same role for graphics as probability theory played for statistics." Journal of the American Statistical Association "Wilkinson's careful scholarship shows around every corner. This is a tour de force of the highest order." Psychometrika "All geography and map libraries should add this book to their collections; the serious scholar of quantitative data graphics will place this book on the same shelf with those by Edward Tufte, and volumes by Cleveland, Bertin, Monmonier, MacEachren, among others, and continue the unending task of proselytizing for the best in statistical data presentation by example and through scholarship like that of Leland Wilkinson." Cartographic Perspectives "In summary, this is certainly a remarkable book and a new ambitious step for the development and application of statistical graphics." Computational Statistics and Data Analysis About the author: Leland Wilkinson is Senior VP, SPSS Inc. and Adjunct Professor of Statistics at Northwestern University. He is also affiliated with the Computer Science department at The University of Illinois at Chicago. He wrote the SYSTAT statistical package and founded SYSTAT Inc. in 1984. Wilkinson joined SPSS in a 1994 acquisition and now works on research and development of visual analytics and statistics. He is a Fellow of the ASA. In addition to journal articles and the original SYSTAT computer program and manuals, Wilkinson is the author (with Grant Blank and Chris Gruber) of Desktop Data Analysis with SYSTAT.},
  language = {en},
  publisher = {{Springer-Verlag}},
  author = {Wilkinson, Leland},
  year = {2005},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/T34UCUMG/9780387245447.html}
}

@article{cirelli_sleep_2008-1,
  title = {Sleep and Wakefulness in {{Drosophila}} Melanogaster},
  volume = {1129},
  issn = {0077-8923},
  doi = {10.1196/annals.1417.017},
  abstract = {Sleep is present and tightly regulated in every vertebrate species in which it has been carefully investigated, but what sleep is for remains a mystery. Sleep is also present in invertebrates, and an extensive analysis in Drosophila melanogaster has shown that sleep in fruit flies show most of the fundamental features that characterize sleep in mammals. In Drosophila, fly sleep consists of sustained periods of quiescence associated with an increased arousal threshold. Fly sleep is modulated by several of the same stimulants and hypnotics that affect mammalian sleep. Moreover, like in mammals, fly sleep shows remarkable interindividual variability. The expression of several genes involved in energy metabolism, synaptic plasticity, and the response to cellular stress varies in Drosophila between sleep and wakefulness, and the same occurs in rodents. Brain activity also changes in flies as a function of behavioral state. Furthermore, Drosophila sleep is tightly regulated in a circadian and homeostatic manner, and the homeostatic regulation is largely independent of the circadian regulation. After sleep deprivation recovery sleep in flies is longer in duration and more consolidated, as indicated by an increase in arousal threshold and fewer brief awakenings. Finally, sleep deprivation in flies impairs vigilance and performance. Because of the extensive similarities between flies and mammals, Drosophila is now being used as a promising model system for the genetic dissection of sleep. Over the last few years, mutagenesis screens have isolated several short sleeping mutants, a demonstration that that single genes can have a powerful effect on a complex trait like sleep.},
  journal = {Annals of the New York Academy of Sciences},
  author = {Cirelli, Chiara and Bushey, Daniel},
  year = {2008},
  pages = {323-329},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/54578PRN/Cirelli and Bushey - 2008 - Sleep and wakefulness in Drosophila melanogaster.pdf},
  pmid = {18591491},
  pmcid = {PMC2715168}
}

@article{bushey_sleep-_2015,
  title = {Sleep- and Wake-Dependent Changes in Neuronal Activity and Reactivity Demonstrated in Fly Neurons Using in Vivo Calcium Imaging},
  volume = {112},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1419603112},
  abstract = {Sleep in Drosophila shares many features with mammalian sleep, but it remains unknown whether spontaneous and evoked activity of individual neurons change with the sleep/wake cycle in flies as they do in mammals. Here we used calcium imaging to assess how the Kenyon cells in the fly mushroom bodies change their activity and reactivity to stimuli during sleep, wake, and after short or long sleep deprivation. As before, sleep was defined as a period of immobility of $>$5 min associated with a reduced behavioral response to a stimulus. We found that calcium levels in Kenyon cells decline when flies fall asleep and increase when they wake up. Moreover, calcium transients in response to two different stimuli are larger in awake flies than in sleeping flies. The activity of Kenyon cells is also affected by sleep/wake history: in awake flies, more cells are spontaneously active and responding to stimuli if the last several hours (5\textendash{}8 h) before imaging were spent awake rather than asleep. By contrast, long wake ($\geq$29 h) reduces both baseline and evoked neural activity and decreases the ability of neurons to respond consistently to the same repeated stimulus. The latter finding may underlie some of the negative effects of sleep deprivation on cognitive performance and is consistent with the occurrence of local sleep during wake as described in behaving rats. Thus, calcium imaging uncovers new similarities between fly and mammalian sleep: fly neurons are more active and reactive in wake than in sleep, and their activity tracks sleep/wake history.},
  language = {en},
  number = {15},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Bushey, Daniel and Tononi, Giulio and Cirelli, Chiara},
  month = apr,
  year = {2015},
  keywords = {GCaMP5,Kenyon cells,sleep deprivation,mushroom bodies},
  pages = {4785-4790},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/IVMUPBKE/Bushey et al. - 2015 - Sleep- and wake-dependent changes in neuronal acti.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/EPIHET2D/4785.html},
  pmid = {25825756}
}

@article{flexer_reliable_2005,
  title = {A Reliable Probabilistic Sleep Stager Based on a Single {{EEG}} Signal},
  volume = {33},
  issn = {0933-3657},
  doi = {10.1016/j.artmed.2004.04.004},
  abstract = {Objective: We developed a probabilistic continuous sleep stager based on Hidden Markov models using only a single EEG signal. It offers the advantage of being objective by not relying on human scorers, having much finer temporal resolution (1s instead of 30s), and being based on solid probabilistic principles rather than a predefined set of rules (Rechtschaffen \& Kales) Methods and material: Sixty-eight whole night sleep recordings from two different sleep labs are analysed using Gaussian observation Hidden Markov models. Results: Our unsupervised approach detects the cornerstones of human sleep (wakefulness, deep and rem sleep) with around 80\% accuracy based on data from a single EEG channel. There are some difficulties in generalizing results across sleep labs. Conclusion: Using data from a single electrode is sufficient for reliable continuous sleep staging. Sleep recordings from different sleep labs are not directly comparable. Training of separate models for the sleep labs is necessary.},
  number = {3},
  journal = {Artificial Intelligence in Medicine},
  author = {Flexer, Arthur and Gruber, Georg and Dorffner, Georg},
  month = mar,
  year = {2005},
  keywords = {EEG,Hidden Markov models,Sleep analysis,Time series processing},
  pages = {199-207},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FH7YLMZT/Flexer et al. - 2005 - A reliable probabilistic sleep stager based on a s.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GBAGDUNU/S093336570400079X.html}
}

@article{yang_use_1973,
  title = {The {{Use}} of a {{Semi}}-{{Markov Model}} for {{Describing Sleep Patterns}}},
  volume = {29},
  issn = {0006-341X},
  doi = {10.2307/2529133},
  abstract = {The Markov chain model proposed by Zung et al. [1965] for sleep patterns was tested with more data, and found inadequate for describing sleep stage sequences because the data do not fit the geometric distribution required by the model. Instead, a semi-Markov process was shown to adequately represent the data. Predictive ability was illustrated. The parameters generated by a semi-Markov model correctly distinguished 11 out of 12 insomniacs from 11 out of 12 normal subjects. The transition probability for the progression from stage 1 to stage 2 is consistent over the night for subjects age 3 to 69. The transition probability for progression from stage 2 to stage 3, however, changes each hour during the night for the ages tested (20 to 69). The curve of these changes has the same general form except for ages 40-49 years. This age is well known for a high incidence of insomnia.},
  number = {4},
  journal = {Biometrics},
  author = {Yang, Mark C. K. and Hursch, Carolyn J.},
  year = {1973},
  pages = {667-676}
}

@inproceedings{tokuda_speech_2000,
  title = {Speech Parameter Generation Algorithms for {{HMM}}-Based Speech Synthesis},
  volume = {3},
  doi = {10.1109/ICASSP.2000.861820},
  abstract = {This paper derives a speech parameter generation algorithm for HMM-based speech synthesis, in which the speech parameter sequence is generated from HMMs whose observation vector consists of a spectral parameter vector and its dynamic feature vectors. In the algorithm, we assume that the state sequence (state and mixture sequence for the multi-mixture case) or a part of the state sequence is unobservable (i.e., hidden or latent). As a result, the algorithm iterates the forward-backward algorithm and the parameter generation algorithm for the case where the state sequence is given. Experimental results show that by using the algorithm, we can reproduce clear formant structure from multi-mixture HMMs as compared with that produced from single-mixture HMMs},
  booktitle = {2000 {{IEEE International Conference}} on {{Acoustics}}, {{Speech}}, and {{Signal Processing}}. {{Proceedings}} ({{Cat}}. {{No}}.{{00CH37100}})},
  author = {Tokuda, K. and Yoshimura, T. and Masuko, T. and Kobayashi, T. and Kitamura, T.},
  year = {2000},
  keywords = {Databases,Hidden Markov models,Cepstral analysis,Character generation,Computer science,Context modeling,dynamic feature vector,formant structure,forward-backward algorithm,hidden Markov models,HMM-based speech synthesis,Interpolation,maximum likelihood estimation,multi-mixture HMM,observation vector,Runtime,spectral parameter vector,speech parameter generation algorithms,speech parameter sequence,speech synthesis,Speech synthesis,state sequence},
  pages = {1315-1318 vol.3},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CGLL7AZ5/861820.html}
}

@article{perez-atencio_four-state_2018,
  title = {A Four-State {{Markov}} Model of Sleep-Wakefulness Dynamics along Light/Dark Cycle in Mice},
  volume = {13},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0189931},
  abstract = {Behavioral states alternate between wakefulness (wk), rapid eye movement (rem) and non-rem (nrem) sleep at time scale of hours i.e., light and dark cycle rhythms and from several tens of minutes to seconds (i.e., brief awakenings during sleep). Using statistical analysis of bout duration, Markov chains of sleep-wk dynamics and quantitative EEG analysis, we evaluated the influence of light/dark (ld) changes on brain function along the sleep-wk cycle. Bout duration (bd) histograms and Kaplan-Meier (km) survival curves of wk showed a bimodal statistical distribution, suggesting that two types of wk do exist: brief-wk (wkb) and long-wk (wkl). Light changes modulated specifically wkl bouts, increasing its duration during active/dark period. In contrast, wkb, nrem and rem bd histograms and km curves did not change significantly along ld cycle. Hippocampal eeg of both types of wk were different: in comparison wkb showed a lower spectral power in fast gamma and fast theta bands and less emg tone. After fitting a four-states Markov chain to mice hypnograms, moreover in states transition probabilities matrix was found that: in dark/active period, state-maintenance probability of wkl increased, and probability of wkl to nrem transition decreased; the opposite was found in light period, favoring the hypothesis of the participation of brief wk into nrem-rem intrinsic sleep cycle, and the role of wkl in SWS homeostasis. In conclusion, we propose an extended Markov model of sleep using four stages (wkl, nrem, rem, wkb) as a fully adequate model accounting for both modulation of sleep-wake dynamics based on the differential regulation of long-wk (high gamma/theta) epochs during dark and light phases.},
  language = {en},
  number = {1},
  journal = {PLOS ONE},
  author = {{Perez-Atencio}, Leonel and {Garcia-Aracil}, Nicolas and Fernandez, Eduardo and Barrio, Luis C. and Barios, Juan A.},
  year = {05-Jan-2018},
  keywords = {Hippocampus,Sleep,Light,Electroencephalography,Homeostasis,Chronobiology,Markov models,Mouse models},
  pages = {e0189931},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/L63JJFW4/Perez-Atencio et al. - 2018 - A four-state Markov model of sleep-wakefulness dyn.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5C2M7I38/article.html}
}

@article{brown_dictionary_2013,
  title = {A Dictionary of Behavioral Motifs Reveals Clusters of Genes Affecting {{Caenorhabditis}} Elegans Locomotion},
  volume = {110},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1211447110},
  abstract = {Visible phenotypes based on locomotion and posture have played a critical role in understanding the molecular basis of behavior and development in Caenorhabditis elegans and other model organisms. However, it is not known whether these human-defined features capture the most important aspects of behavior for phenotypic comparison or whether they are sufficient to discover new behaviors. Here we show that four basic shapes, or eigenworms, previously described for wild-type worms, also capture mutant shapes, and that this representation can be used to build a dictionary of repetitive behavioral motifs in an unbiased way. By measuring the distance between each individual's behavior and the elements in the motif dictionary, we create a fingerprint that can be used to compare mutants to wild type and to each other. This analysis has revealed phenotypes not previously detected by real-time observation and has allowed clustering of mutants into related groups. Behavioral motifs provide a compact and intuitive representation of behavioral phenotypes.},
  language = {en},
  number = {2},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Brown, Andr\'e E. X. and Yemini, Eviatar I. and Grundy, Laura J. and Jucikas, Tadas and Schafer, William R.},
  month = jan,
  year = {2013},
  keywords = {ethology,imaging,nematode,phenotyping},
  pages = {791-796},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4QRI7Y8I/Brown et al. - 2013 - A dictionary of behavioral motifs reveals clusters.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/FVY3PVYU/791.html},
  pmid = {23267063}
}

@article{fulcher_highly_2014,
  title = {Highly {{Comparative Feature}}-{{Based Time}}-{{Series Classification}}},
  volume = {26},
  issn = {1041-4347},
  doi = {10.1109/TKDE.2014.2316504},
  abstract = {A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across the scientific time-series analysis literature, and include summaries of time series in terms of their correlation structure, distribution, entropy, stationarity, scaling properties, and fits to a range of time-series models. After computing thousands of features for each time series in a training set, those that are most informative of the class structure are selected using greedy forward feature selection with a linear classifier. The resulting feature-based classifiers automatically learn the differences between classes using a reduced number of time-series properties, and circumvent the need to calculate distances between time series. Representing time series in this way results in orders of magnitude of dimensionality reduction, allowing the method to perform well on very large data sets containing long time series or time series of different lengths. For many of the data sets studied, classification performance exceeded that of conventional instance-based classifiers, including one nearest neighbor classifiers using euclidean distances and dynamic time warping and, most importantly, the features selected provide an understanding of the properties of the data set, insight that can guide further scientific investigation.},
  number = {12},
  journal = {IEEE Transactions on Knowledge and Data Engineering},
  author = {Fulcher, B. D. and Jones, N. S.},
  month = dec,
  year = {2014},
  keywords = {data mining,learning (artificial intelligence),time series,Databases,Data mining,Time series analysis,feature extraction,classification,dimensionality reduction,dynamic time warping,Euclidean distances,extensive database,Feature extraction,feature selection,feature-based classifiers,greedy algorithms,greedy forward feature selection,highly comparative feature-based time-series classification,instance-based classifiers,interpretable feature extraction,linear classifier,Market research,nearest neighbor classifiers,pattern classification,scientific time-series analysis literature,Time measurement,Time-series analysis,training set,very large data sets},
  pages = {3026-3037},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ASF2TGYZ/Fulcher and Jones - 2014 - Highly Comparative Feature-Based Time-Series Class.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/AK52S3Z2/6786425.html}
}

@article{fulcher_hctsa_2017,
  title = {Hctsa: {{A Computational Framework}} for {{Automated Time}}-{{Series Phenotyping Using Massive Feature Extraction}}},
  volume = {5},
  issn = {2405-4712},
  shorttitle = {Hctsa},
  doi = {10.1016/j.cels.2017.10.001},
  abstract = {Summary
Phenotype measurements frequently take the form of time series, but we currently lack a systematic method for relating these complex data streams to scientifically meaningful outcomes, such as relating the movement dynamics of organisms to their genotype or measurements of brain dynamics of a patient to their disease diagnosis. Previous work addressed this problem by comparing implementations of thousands of diverse scientific time-series analysis methods in an approach termed highly comparative time-series analysis. Here, we introduce hctsa, a software tool for applying this methodological approach to data. hctsa includes an architecture for computing over 7,700 time-series features and a suite of analysis and visualization algorithms to automatically select useful and interpretable time-series features for a given application. Using exemplar applications to high-throughput phenotyping experiments, we show how hctsa allows researchers to leverage decades of time-series research to quantify and understand informative structure in time-series data.},
  number = {5},
  journal = {Cell Systems},
  author = {Fulcher, Ben D. and Jones, Nick S.},
  month = nov,
  year = {2017},
  keywords = {high-throughput phenotyping,time-series analysis},
  pages = {527-531.e3},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/2NEXQMEM/Fulcher and Jones - 2017 - hctsa A Computational Framework for Automated Tim.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/NL4JIBSC/S2405471217304386.html}
}

@article{riemensperger_optogenetics_2016,
  title = {Optogenetics in {{Drosophila Neuroscience}}},
  volume = {1408},
  issn = {1940-6029},
  doi = {10.1007/978-1-4939-3512-3_11},
  abstract = {Optogenetic techniques enable one to target specific neurons with light-sensitive proteins, e.g., ion channels, ion pumps, or enzymes, and to manipulate their physiological state through illumination. Such artificial interference with selected elements of complex neuronal circuits can help to determine causal relationships between neuronal activity and the effect on the functioning of neuronal circuits controlling animal behavior. The advantages of optogenetics can best be exploited in genetically tractable animals whose nervous systems are, on the one hand, small enough in terms of cell numbers and to a certain degree stereotypically organized, such that distinct and identifiable neurons can be targeted reproducibly. On the other hand, the neuronal circuitry and the behavioral repertoire should be complex enough to enable one to address interesting questions. The fruit fly Drosophila melanogaster is a favorable model organism in this regard. However, the application of optogenetic tools to depolarize or hyperpolarize neurons through light-induced ionic currents has been difficult in adult flies. Only recently, several variants of Channelrhodopsin-2 (ChR2) have been introduced that provide sufficient light sensitivity, expression, and stability to depolarize central brain neurons efficiently in adult Drosophila. Here, we focus on the version currently providing highest photostimulation efficiency, ChR2-XXL. We exemplify the use of this optogenetic tool by applying it to a widely used aversive olfactory learning paradigm. Optogenetic activation of a population of dopamine-releasing neurons mimics the reinforcing properties of a punitive electric shock typically used as an unconditioned stimulus. In temporal coincidence with an odor stimulus this artificially induced neuronal activity causes learning of the odor signal, thereby creating a light-induced memory.},
  language = {eng},
  journal = {Methods in Molecular Biology (Clifton, N.J.)},
  author = {Riemensperger, Thomas and Kittel, Robert J. and Fiala, Andr\'e},
  year = {2016},
  keywords = {Animals; Genetically Modified,Memory,Brain,Photic Stimulation,Animals,Drosophila melanogaster,Dopamine,Neurosciences,Dopaminergic Neurons,Optogenetics,Learning and memory,Gene Expression,Channelrhodopsins,ChR2-XXL,Mushroom body,Neuronal circuits},
  pages = {167-175},
  pmid = {26965122}
}

@article{lewontin_general_1958,
  title = {A {{General Method}} for {{Investigating}} the {{Equilibrium}} of {{Gene Frequency}} in a {{Population}}},
  volume = {43},
  issn = {0016-6731},
  number = {3},
  journal = {Genetics},
  author = {Lewontin, R. C.},
  month = may,
  year = {1958},
  pages = {419-434},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LH9Z4R57/Lewontin - 1958 - A General Method for Investigating the Equilibrium.pdf},
  pmid = {17247767},
  pmcid = {PMC1209891}
}

@article{fitzpatrick_maintaining_2007,
  title = {Maintaining a Behaviour Polymorphism by Frequency-Dependent Selection on a Single Gene},
  volume = {447},
  copyright = {2007 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature05764},
  abstract = {Accounting for the abundance of genetic variation in the face of natural selection remains a central problem of evolutionary biology1,2. Genetic polymorphisms are constantly arising through mutation, and although most are promptly eliminated3, polymorphisms in functionally important traits are common. One mechanism that can maintain polymorphisms is negative frequency-dependent selection on alternative alleles, whereby the fitness of each decreases as its frequency increases4,5. Examples of frequency-dependent selection are rare, especially when attempting to describe the genetic basis of the phenotype under selection. Here we show frequency-dependent selection in a well-known natural genetic polymorphism affecting fruitfly foraging behaviour. When raised in low nutrient conditions, both of the naturally occurring alleles of the foraging gene (fors and forR) have their highest fitness when rare\textemdash{}the hallmark of negative frequency-dependent selection. This effect disappears at higher resources levels, demonstrating the role of larval competition. We are able to confirm the involvement of the foraging gene by showing that a sitter-like mutant allele on a rover background has similar frequency-dependent fitness as the natural sitter allele. Our study represents a clear demonstration of frequency-dependent selection, and we are able to attribute this effect to a single, naturally polymorphic gene known to affect behaviour.},
  language = {en},
  number = {7141},
  journal = {Nature},
  author = {Fitzpatrick, Mark J. and Feder, Elah and Rowe, Locke and Sokolowski, Marla B.},
  month = may,
  year = {2007},
  pages = {210-212},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JF8X93CY/Fitzpatrick et al. - 2007 - Maintaining a behaviour polymorphism by frequency-.pdf}
}

@article{monge_sommeil_2005,
  series = {Sommeil et sujet \^ag\'e},
  title = {Sommeil et Mythologie},
  volume = {2},
  issn = {1769-4493},
  doi = {10.1016/S1769-4493(05)70141-2},
  number = {5},
  journal = {M\'edecine du Sommeil},
  author = {Monge, P.},
  month = sep,
  year = {2005},
  pages = {51-54},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/MDMTZ45C/S1769449305701412.html}
}

@book{hohne_mythology_2009,
  title = {The {{Mythology}} of {{Sleep}}: {{The Waking Power}} of {{Dreams}}},
  isbn = {978-0-9819779-0-4},
  shorttitle = {The {{Mythology}} of {{Sleep}}},
  abstract = {There are timeless healing messages hidden in our ancient stories. The Mythology of Sleep: The Waking Power of Dreams is a groundbreaking look at the hero's journey through the dreamscape. Just as myths are stories about heroes in search of their destiny, the fantastic landscapes and cryptic symbols appearing in dreams present clues about our real identity. As if some aspect of the mind has an understanding that transcends time and self-awareness, the journey always awakens us to our full potential. Approaching dreams as the hero's journey through a landscape of wellness, this self-help book makes healing an adventure, and presents a new dimension in the study of dream interpretation.},
  language = {en},
  publisher = {{Way of Tao Books}},
  author = {Hohne, Kari},
  month = may,
  year = {2009}
}

@incollection{sanford_stress_2014,
  series = {Current Topics in Behavioral Neurosciences},
  title = {Stress, {{Arousal}}, and {{Sleep}}},
  isbn = {978-3-662-46877-7 978-3-662-46878-4},
  abstract = {Stress is considered to be an important cause of disrupted sleep and insomnia. However, controlled and experimental studies in rodents indicate that effects of stress on sleep\textendash{}wake regulation are complex and may strongly depend on the nature of the stressor. While most stressors are associated with at least a brief period of arousal and wakefulness, the subsequent amount and architecture of recovery sleep can vary dramatically across conditions even though classical markers of acute stress such as corticosterone are virtually the same. Sleep after stress appears to be highly influenced by situational variables including whether the stressor was controllable and/or predictable, whether the individual had the possibility to learn and adapt, and by the relative resilience and vulnerability of the individual experiencing stress. There are multiple brain regions and neurochemical systems linking stress and sleep, and the specific balance and interactions between these systems may ultimately determine the alterations in sleep\textendash{}wake architecture. Factors that appear to play an important role in stress-induced wakefulness and sleep changes include various monominergic neurotransmitters, hypocretins, corticotropin releasing factor, and prolactin. In addition to the brain regions directly involved in stress responses such as the hypothalamus, the locus coeruleus, and the amygdala, differential effects of stressor controllability on behavior and sleep may be mediated by the medial prefrontal cortex. These various brain regions interact and influence each other and in turn affect the activity of sleep\textendash{}wake controlling centers in the brain. Also, these regions likely play significant roles in memory processes and participate in the way stressful memories may affect arousal and sleep. Finally, stress-induced changes in sleep-architecture may affect sleep-related neuronal plasticity processes and thereby contribute to cognitive dysfunction and psychiatric disorders.},
  language = {en},
  booktitle = {Sleep, {{Neuronal Plasticity}} and {{Brain Function}}},
  publisher = {{Springer, Berlin, Heidelberg}},
  author = {Sanford, Larry D. and Suchecki, Deborah and Meerlo, Peter},
  year = {2014},
  pages = {379-410},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TQ2YYMZD/7854_2014_314.html},
  doi = {10.1007/7854_2014_314}
}

@article{krause_sleep-deprived_2017,
  title = {The Sleep-Deprived Human Brain},
  volume = {18},
  copyright = {2017 Nature Publishing Group},
  issn = {1471-0048},
  doi = {10.1038/nrn.2017.55},
  abstract = {How does a lack of sleep affect our brains? In contrast to the benefits of sleep, frameworks exploring the impact of sleep loss are relatively lacking. Importantly, the effects of sleep deprivation (SD) do not simply reflect the absence of sleep and the benefits attributed to it; rather, they reflect the consequences of several additional factors, including extended wakefulness. With a focus on neuroimaging studies, we review the consequences of SD on attention and working memory, positive and negative emotion, and hippocampal learning. We explore how this evidence informs our mechanistic understanding of the known changes in cognition and emotion associated with SD, and the insights it provides regarding clinical conditions associated with sleep disruption.},
  language = {en},
  number = {7},
  journal = {Nature Reviews Neuroscience},
  author = {Krause, Adam J. and Simon, Eti Ben and Mander, Bryce A. and Greer, Stephanie M. and Saletin, Jared M. and {Goldstein-Piekarski}, Andrea N. and Walker, Matthew P.},
  month = jul,
  year = {2017},
  pages = {404-418},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TXDZDJEY/Krause et al. - 2017 - The sleep-deprived human brain.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/8B7HJFCX/nrn.2017.html}
}

@article{wit_laboratory_2013,
  title = {Laboratory Selection for Increased Longevity in {{Drosophila}} Melanogaster Reduces Field Performance},
  volume = {48},
  issn = {0531-5565},
  doi = {10.1016/j.exger.2013.07.012},
  abstract = {Drosophila melanogaster is frequently used in ageing studies to elucidate which mechanisms determine the onset and progress of senescence. Lines selected for increased longevity have often been shown to perform as well as or superior to control lines in life history, stress resistance and behavioural traits when tested in the laboratory. Functional senescence in longevity selected lines has also been shown to occur at a slower rate. However, it is known that performance in a controlled laboratory setting is not necessarily representative of performance in nature. In this study the effect of ageing, environmental temperature and longevity selection on performance in the field was tested. Flies from longevity selected and control lines of different ages (2, 5, 10 and 15days) were released in an environment free of natural food sources. Control flies were tested at low, intermediate and high temperatures, while longevity selected flies were tested at the intermediate temperature only. The ability of flies to locate and reach a food source was tested. Flies of intermediate age were generally better at locating resources than both younger and older flies, where hot and cold environments accelerate the senescent decline in performance. Control lines were better able to locate a resource compared to longevity selected lines of the same age, suggesting that longevity comes at a cost in early life field fitness, supporting the antagonistic pleiotropy theory of ageing.},
  number = {11},
  journal = {Experimental Gerontology},
  author = {Wit, Janneke and Kristensen, Torsten Nygaard and Sarup, Pernille and Frydenberg, Jane and Loeschcke, Volker},
  month = nov,
  year = {2013},
  keywords = {Ageing,Environmental temperature,Fitness in the field,Functional senescence,Longevity selection,Release–capture},
  pages = {1189-1195},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/TX94LPBM/Wit et al. - 2013 - Laboratory selection for increased longevity in Dr.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PBLHQSDP/S0531556513002337.html}
}

@article{chandegra_sexually_2017,
  title = {Sexually Dimorphic Effects of Dietary Sugar on Lifespan, Feeding and Starvation Resistance in {{Drosophila}}},
  volume = {9},
  issn = {1945-4589},
  doi = {10.18632/aging.101335},
  abstract = {Lifespan and health in older age are strongly influenced by diet. Feeding Drosophila melanogaster diets high in sugar has increasingly been used as an experimental model to understand the physiological effects of unhealthy, contemporary human diets. Several metabolic parameters and physiological responses to nutrition are known to be dependent on the sex of the animal. However, sexual dimorphism in the responses to high-sugar diets in fruit flies has not been examined. Here we show that a high-sugar diet in Drosophila melanogaster elicits sexually dimorphic effects on feeding behaviour, starvation resistance and lifespan. Females feed less on such diets, while males feed more, and these feeding responses may have secondary consequences. Females, more than males, gain the ability to resist periods of starvation from high-sugar diets, indicating that the female response to excess sugar may be geared towards surviving food shortages in early life. At the same time, female lifespan is more susceptible to the detrimental effects of high sugar diets. Our study reveals differences between Drosophila sexes in their responses to sugar-rich diets, indicating the fruit fly could be used as a model to understand the sexually dimorphic features of human metabolic health.},
  number = {12},
  journal = {Aging (Albany NY)},
  author = {Chandegra, Bhakti and Tang, Jocelyn Lok Yee and Chi, Haoyu and Alic, Nazif},
  month = dec,
  year = {2017},
  pages = {2521-2528},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UAXAYE8V/Chandegra et al. - 2017 - Sexually dimorphic effects of dietary sugar on lif.pdf},
  pmid = {29207375},
  pmcid = {PMC5764390}
}

@article{rolff_batemans_2002,
  title = {Bateman's Principle and Immunity},
  volume = {269},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2002.1959},
  abstract = {The immunocompetence handicap hypothesis (ICHH) of Folstad and Karter has inspired a large number of studies that have tried to understand the causal basis of parasite\textendash{}mediated sexual selection. Even though this hypothesis is based on the double function of testosterone, a hormone restricted to vertebrates, studies of invertebrates have tended to provide central support for specific predictions of the ICHH. I propose an alternative hypothesis that explains many of the findings without relying on testosterone or other biochemical feedback loops. This alternative is based on Bateman's principle, that males gain fitness by increasing their mating success whilst females increase fitness through longevity because their reproductive effort is much higher. Consequently, I predict that females should invest more in immunity than males. The extent of this dimorphism is determined by the mating system and the genetic correlation between males and females in immune traits. In support of my arguments, I mainly use studies on insects that share innate immunity with vertebrates and have the advantage that they are easier to study.},
  language = {en},
  number = {1493},
  journal = {Proceedings of the Royal Society of London B: Biological Sciences},
  author = {Rolff, Jens},
  month = apr,
  year = {2002},
  pages = {867-872},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/QHK5FSMI/Rolff - 2002 - Bateman's principle and immunity.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/CX3JBPKC/867.html},
  pmid = {11958720}
}

@article{jaillon_sexual_2017,
  title = {Sexual {{Dimorphism}} in {{Innate Immunity}}.},
  issn = {1080-0549},
  doi = {10.1007/s12016-017-8648-x},
  abstract = {Abstract: Sexual dimorphisms account for differences in clinical manifestations or incidence of infectious or autoimmune diseases and malignancy between...},
  language = {eng},
  journal = {Clinical reviews in allergy \& immunology},
  author = {Jaillon, S. and Berthenet, K. and Garlanda, C.},
  month = sep,
  year = {2017},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/7MNCCLEG/28963611.html},
  pmid = {28963611}
}

@article{hill-burns_x-linked_2009,
  title = {X-{{Linked Variation}} in {{Immune Response}} in {{Drosophila}} Melanogaster},
  volume = {183},
  copyright = {Copyright \textcopyright{} 2009 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.108.093971},
  abstract = {This study quantifies the effects of naturally occurring X-linked variation on immune response in Drosophila melanogaster to assess associations between immunity genotypes and innate immune response. We constructed a set of 168 X-chromosomal extraction lines, incorporating X chromosomes from a natural population into co-isogenic autosomal backgrounds, and genotyped the lines at 88 SNPs in 20 X-linked immune genes. We find that genetic variation in many of the genes is associated with immune response phenotypes, including bacterial load and immune gene expression. Many of the associations act in a sex-specific or sexually antagonistic manner, supporting the theory that with the selective pressures facing genes on the X chromosome, sexually antagonistic variation may be more easily maintained.},
  language = {en},
  number = {4},
  journal = {Genetics},
  author = {{Hill-Burns}, Erin M. and Clark, Andrew G.},
  month = dec,
  year = {2009},
  pages = {1477-1491},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/UXVKD73R/Hill-Burns and Clark - 2009 - X-Linked Variation in Immune Response in Drosophil.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/F9EU5E35/1477.html},
  pmid = {19822734}
}

@article{connolly_rejection_1973,
  title = {Rejection {{Responses By Female Drosophila Melanogaster}} : {{Their Ontogeny}}, {{Causality}} and {{Effects Upon}} the {{Behaviour}} of the {{Courting Male}}},
  volume = {44},
  issn = {1568-539X},
  shorttitle = {Rejection {{Responses By Female Drosophila Melanogaster}}},
  doi = {10.1163/156853973X00364},
  abstract = {1. The experiments reported were designed to study the causes and consequences of various responses emitted by female Drosophila melanogaster in relation to the behaviour of the courting male. 2. The female responses studied were: flicking, kicking, curling, extruding and fending. These were recorded simultaneously with male behaviours, from single pair courtships, onto a multi-channel time-event recorder. The male behaviours recorded were: orientation, vibration, licking, attempted copulation, locomotor activity, preening and male stationary. 3. Four groups of female were examined for modal response and the associated pattern of male behaviour. The groups were selected in order to elucidate developmental changes in the nature of the rejection response and any changes consequent upon fertilisation. 4. Three methods of analysis were employed. A description of the frequency response for each group of females was followed by an analysis of the temporal pattern of male behaviours associated with the modal response. 5. A finer resolution of the relationship between male and female behaviour was obtained by a transitional analysis of the females\&apos; responses with the various male activities. 6. Both fertilised females and aging virgins showed extrusion of the ovipositor as the modal response. 7. Fending and curling occurred rarely and did not lead to any changes in male behaviour. 8. Kicking and flicking were deduced to be responses to different aspects, or intensities of courtship. Kicking was largely contingent upon attempted copulation, whereas flicking resulted from licking and sometimes non-courtship behaviours. Flicking is also correlated with a high level of locomotor activity. 9. Extrusion by aged virgins and fertilised females was associated with the wing vibration display of the male, and in both groups was followed, rather than preceded, by attempted copulation. However, the aged virgins were receptive, whereas the fertilised females were not. Extrusion was interpreted as a means of physically preventing copulation, rather then producing long term inhibition of courtship. 10. It is suggested that the ontogeny of extrusion is associated with development in the female\&apos;s egg producing system. 11. The temporary reluctance of the 3 day old virgin females, exemplified by their kicking, was discussed in the context of EWING\&apos;S (1969) concept of a \&apos;reference oscillator\&apos; used by the female to identify the auditory signals produced by a conspecific.},
  language = {en},
  number = {1},
  journal = {Behaviour},
  author = {Connolly, Kevin and Cook, Robert},
  month = jan,
  year = {1973},
  pages = {142-165},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/6U3JEGSC/Connolly and Cook - 1973 - Rejection Responses By Female Drosophila Melanogas.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/PEV3LYIS/156853973x00364.html}
}

@article{yang_drosophila_2008,
  title = {Drosophila {{Egg}}-{{Laying Site Selection}} as a {{System}} to {{Study Simple Decision}}-{{Making Processes}}},
  volume = {319},
  copyright = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1151842},
  abstract = {The ability to select a better option from multiple acceptable ones is important for animals to optimize their resources. The mechanisms that underlie such decision-making processes are not well understood. We found that selection of egg-laying site in Drosophila melanogaster is a suitable system to probe the neural circuit that governs simple decision-making processes. First, Drosophila females pursue active probing of the environment before depositing each egg, apparently to evaluate site quality for every egg. Second, Drosophila females can either accept or reject a sucrose-containing medium, depending on the context. Last, communication of the ``acceptability'' of the sucrose-containing medium as an egg-laying option to the reproductive system depends on the function of a group of insulin-like peptide 7 (ILP7)\textendash{}producing neurons. These findings suggest that selection of egg-laying site involves a simple decision-making process and provide an entry point toward a systematic dissection of this process.
Experiments show how flies make complex decisions when laying eggs, choosing surfaces containing sucrose only when other options are not available.
Experiments show how flies make complex decisions when laying eggs, choosing surfaces containing sucrose only when other options are not available.},
  language = {en},
  number = {5870},
  journal = {Science},
  author = {Yang, Chung-hui and Belawat, Priyanka and Hafen, Ernst and Jan, Lily Y. and Jan, Yuh-Nung},
  month = mar,
  year = {2008},
  pages = {1679-1683},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/LTUTHS2D/Yang et al. - 2008 - Drosophila Egg-Laying Site Selection as a System t.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/4PC5UYKB/1679.html},
  pmid = {18356529}
}

@article{zaninovich_single-fly_2013,
  title = {A {{Single}}-Fly {{Assay}} for {{Foraging Behavior}} in {{Drosophila}}},
  issn = {1940-087X},
  doi = {10.3791/50801},
  abstract = {For many animals, hunger promotes changes in the olfactory system in a manner that facilitates the search for appropriate food sources. In this video article, we describe an automated assay to measure the effect of hunger or satiety on olfactory dependent food search behavior in the adult fruit fly Drosophila melanogaster. In a light-tight box illuminated by red light that is invisible to fruit flies, a camera linked to custom data acquisition software monitors the position of six flies simultaneously. Each fly is confined to walk in individual arenas containing a food odor at the center. The testing arenas rest on a porous floor that functions to prevent odor accumulation. Latency to locate the odor source, a metric that reflects olfactory sensitivity under different physiological states, is determined by software analysis. Here, we discuss the critical mechanics of running this behavioral paradigm and cover specific issues regarding fly loading, odor contamination, assay temperature, data quality, and statistical analysis.},
  number = {81},
  journal = {Journal of Visualized Experiments : JoVE},
  author = {Zaninovich, Orel A. and Kim, Susy M. and Root, Cory R. and Green, David S. and Ko, Kang I. and Wang, Jing W.},
  month = nov,
  year = {2013},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/5MZ43A9T/Zaninovich et al. - 2013 - A Single-fly Assay for Foraging Behavior in Drosop.pdf},
  pmid = {24299900},
  pmcid = {PMC3969902}
}

@article{wollheim_logic_nodate,
  title = {The {{Logic}} of {{Scientific Discovery}}},
  language = {en},
  author = {Wollheim, Richard and Bliven, Naomi},
  pages = {545},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/JKN9RLS7/Wollheim and Bliven - The Logic of Scientific Discovery.pdf}
}

@book{baird_thing_2004,
  address = {Berkeley, Calif},
  title = {Thing {{Knowledge}}: {{A Philosophy}} of {{Scientific Instruments}}},
  isbn = {978-0-520-23249-5},
  shorttitle = {Thing {{Knowledge}}},
  abstract = {Western philosophers have traditionally concentrated on theory as the means for expressing knowledge about a variety of phenomena. This absorbing book challenges this fundamental notion by showing how objects themselves, specifically scientific instruments, can express knowledge. As he considers numerous intriguing examples, Davis Baird gives us the tools to "read" the material products of science and technology and to understand their place in culture. Making a provocative and original challenge to our conception of knowledge itself, Thing Knowledge demands that we take a new look at theories of science and technology, knowledge, progress, and change. Baird considers a wide range of instruments, including Faraday's first electric motor, eighteenth-century mechanical models of the solar system, the cyclotron, various instruments developed by analytical chemists between 1930 and 1960, spectrometers, and more.},
  language = {English},
  publisher = {{University of California Press}},
  author = {Baird, Davis},
  month = mar,
  year = {2004}
}

@book{gooding_uses_1989,
  title = {The {{Uses}} of {{Experiment}}: {{Studies}} in the {{Natural Sciences}}},
  isbn = {978-0-521-33768-7},
  shorttitle = {The {{Uses}} of {{Experiment}}},
  abstract = {Experiment is widely regarded as the most distinctive feature of natural science and essential to the way scientists find out about the world. Yet there has been little study of the way scientists actually make and use experiments. The Uses of Experiment fills this gap in our knowledge about how science is practised. Presenting 14 original case studies of important and often famous experiments, the book asks the questions: What tools do experimenters use? How do scientists argue from experiments? What happens when an experiment is challenged? How do scientists check that their experiments are working? Are there differences between experiments in the physical sciences and technology? Leading scholars in the fields of history, sociology and philosophy of science consider topics such as the interaction of experiment; instruments and theory; accuracy and reliability as hallmarks of experiment in science and technology; realising new phenomena; the believability of experiments and the sort of knowledge they produce; and the wider contexts on which experimentalists draw to develop and win support for their work. Drawing on examples as diverse as Galilean mechanics, Victorian experiments on electricity, experiments on cloud formation, and testing of nuclear missiles, a new view of experiment emerges. This view emphasises that experiments always involve choice, tactics and strategy in persuading audiences that Nature resembles the picture experimenters create.},
  language = {en},
  publisher = {{Cambridge University Press}},
  author = {Gooding, David and Pinch, Trevor and Schaffer, Simon},
  month = may,
  year = {1989},
  keywords = {Science / History,Science / Experiments \& Projects,Science / Research \& Methodology,Technology \& Engineering / History}
}

@book{kaplan_conduct_1964,
  title = {The Conduct of Inquiry: Methodology for Behavioral Science},
  shorttitle = {The Conduct of Inquiry},
  language = {en},
  publisher = {{Chandler Pub. Co.}},
  author = {Kaplan, Abraham},
  year = {1964},
  keywords = {Behavioral sciences,Inquiry (Theory of knowledge),Social Science / Methodology,Social Science / Research,Social sciences,Social Sciences}
}

@article{mathis_markerless_2018,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1804.03142},
  primaryClass = {cs, q-bio, stat},
  title = {Markerless Tracking of User-Defined Features with Deep Learning},
  abstract = {Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, yet markers are intrusive (especially for smaller animals), and the number and location of the markers must be determined a priori. Here, we present a highly efficient method for markerless tracking based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in a broad collection of experimental settings: mice odor trail-tracking, egg-laying behavior in drosophila, and mouse hand articulation in a skilled forelimb task. For example, during the skilled reaching behavior, individual joints can be automatically tracked (and a confidence score is reported). Remarkably, even when a small number of frames are labeled (\$$\backslash$approx 200\$), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.},
  journal = {arXiv:1804.03142 [cs, q-bio, stat]},
  author = {Mathis, Alexander and Mamidanna, Pranav and Abe, Taiga and Cury, Kevin M. and Murthy, Venkatesh N. and Mathis, Mackenzie W. and Bethge, Matthias},
  month = apr,
  year = {2018},
  keywords = {Computer Science - Computer Vision and Pattern Recognition,Quantitative Biology - Neurons and Cognition,Quantitative Biology - Quantitative Methods,Statistics - Machine Learning},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/GEGRZGVR/Mathis et al. - 2018 - Markerless tracking of user-defined features with .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/ITSFZ8GV/1804.html}
}

@article{stephens_dimensionality_2008,
  title = {Dimensionality and {{Dynamics}} in the {{Behavior}} of {{C}}. Elegans},
  volume = {4},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1000028},
  abstract = {A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here, we show that the space of shapes adopted by the nematode Caenorhabditis elegans is low dimensional, with just four dimensions accounting for 95\% of the shape variance. These dimensions provide a quantitative description of worm behavior, and we partially reconstruct ``equations of motion'' for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively ``steering'' the worm in real time.},
  language = {en},
  number = {4},
  journal = {PLOS Computational Biology},
  author = {Stephens, Greg J. and {Johnson-Kerner}, Bethany and Bialek, William and Ryu, William S.},
  year = {25-Apr-2008},
  keywords = {Behavior,Caenorhabditis elegans,Covariance,Crawling,Eigenvalues,Equations of motion,Lasers,Motion},
  pages = {e1000028},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/Q2X5XSJF/Stephens et al. - 2008 - Dimensionality and Dynamics in the Behavior of C. .pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/A5TV7EXQ/article.html}
}

@article{giardina_estimating_nodate,
  title = {Estimating Mating Rates in Wild {{Drosophila}} Melanogaster Females by Decay Rates of Male Reproductive Proteins in Their Reproductive Tracts},
  volume = {17},
  copyright = {\textcopyright{} 2017 John Wiley \& Sons Ltd},
  issn = {1755-0998},
  doi = {10.1111/1755-0998.12661},
  abstract = {Female Drosophila melanogaster frequently mate with multiple males in nature as shown through parentage analysis. Although polyandry is well documented, we know little about the timing between mating events in wild Drosophila populations due to the challenge of following behaviours of individual females. In this study, we used the presence of a male reproductive protein that is transferred to the female during mating (Sex Peptide, SP) to determine whether she had recently mated. We sampled females throughout the day, conducted control matings to determine the decay rate of SP within the female reproductive tract and performed computer simulations to fit the observed proportion of mated females to a nonhomogenous Poisson process that defined the expected time between successive matings for a given female. In our control matings, 100\% of mated females tested positive for SP 0.5 h after the start of mating (ASM), but only 24\% tested positive 24 h ASM. Overall, 35\% of wild-caught females tested positive for the presence of SP. Fitting our observed data to our simple nonhomogenous Poisson model provided the inference that females are mating, on average, approximately every 27 h (with 95\% credibility interval 23\textendash{}31 h). Thus, it appears that females are mating a bit less frequently that once per day in this natural population and that mating events tend to occur either early in the morning or late in the afternoon.},
  language = {en},
  number = {6},
  journal = {Molecular Ecology Resources},
  author = {Giardina, Thomas J. and Clark, Andrew G. and Fiumera, Anthony C.},
  keywords = {sex peptide,accessory gland protein,mating systems,parentage,polyandry,sexual selection},
  pages = {1202-1209},
  file = {/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/9IRR4XLA/Giardina et al. - Estimating mating rates in wild Drosophila melanog.pdf;/home/quentin/.mozilla/firefox/kkgy4t0w.default/zotero/storage/SNM6STNL/1755-0998.html}
}

@book{maslow_psychology_1966,
  title = {The Psychology of Science: A Reconnaissance},
  shorttitle = {The Psychology of Science},
  language = {en},
  publisher = {{Harper \& Row}},
  author = {Maslow, Abraham Harold},
  year = {1966}
}

@article{gumustekin_effects_2004,
  title = {Effects of Sleep Deprivation, Nicotine, and Selenium on Wound Healing in Rats},
  volume = {114},
  issn = {0020-7454},
  abstract = {Effects of sleep deprivation (SD), nicotine, and selenium (Se) on wound healing were studied in 50 male rats (Sprague-Dawley strain). Full-skin-thickness burns were produced in animals. Then, SD, nicotine, and Se administrations were applied to animals in different groups. Wound healing was assessed by pathological analysis of wound by counting fibroblasts, capillary vessels, polymorphonuclear leucocytes (PNLs), and by measuring radiolabeled immunoglobulin G (IgG) amount in wound area by radio-pharmaceutical and immunoscintigraphic procedures. The number of fibroblasts and capillary vessels were higher in control and Se groups than in sleep deprivation and nicotine groups, and the number of PNLs and the radiolabeled polyvalent IgG levels were higher in SD and nicotine groups than in control and Se groups. The results suggest that SD and nicotine may delay wound healing and that Se supplementation may accelerate wound healing by preventing nicotine-induced oxidative stress and lipid peroxidation.},
  language = {eng},
  number = {11},
  journal = {The International Journal of Neuroscience},
  author = {G\"um\"u{\c s}tek\'in, Kenan and Seven, Bedr\'i and Karabulut, Nez\'ihe and Akta{\c s}, Omer and G\"ursan, Nesr\'in and Aslan, Sah\'in and Kele{\c s}, Mustafa and Varoglu, Erhan and Dane, Senol},
  month = nov,
  year = {2004},
  keywords = {Animals,Antioxidants,Disease Models; Animal,Drug Interactions,Fibroblasts,Immunoglobulin G,Male,Neovascularization; Physiologic,Neutrophils,Nicotine,Nicotinic Agonists,Radioimmunodetection,Rats,Rats; Sprague-Dawley,Selenium,Skin,Sleep Deprivation,Wound Healing},
  pages = {1433-1442},
  pmid = {15636354}
}

@article{benzer_behavioral_1967-1,
  title = {Behavioral {{Mutants}} of {{Drosophila Isolated}} by {{Countercurrent Distribution}}},
  volume = {58},
  issn = {0027-8424},
  number = {3},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Benzer, Seymour},
  year = {1967},
  pages = {1112-1119}
}