Merge pull request #7 from yasinthanvickneswaran/main

Adding Journal Names

.github/workflows/ci-pages.yml

@@ -26,6 +26,7 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install mkdocs-material 
+      - run: pip install mkdocs-material
+
 
       - run: mkdocs gh-deploy --force

docs/Albertson_1976.md

@@ -1,4 +1,7 @@
 ## The pharynx of Caenorhabditis elegans
-_Donna G. Albertson and J. N. Thompson_ 
+_Donna G. Albertson and J. N. Thompson_ <br>  _Phil. Trans. R. Soc. Lond. B275299–325_ <br> _Published: 10 August 1976  https://doi.org/10.1098/rstb.1976.0085_
 
-_Published: 10 August 1976  https://doi.org/10.1098/rstb.1976.0085_
+**Summary**
+- The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs.
+- The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections.
+- Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons.

docs/Altun_2009.md

@@ -1,6 +1,6 @@
 ## High resolution map of Caenorhabditis elegans gap junction proteins
-_Zeynep F.Altun, Bojun Chen, Zhao-Weng Wang, David. H Hall_
+_Zeynep F.Altun, Bojun Chen, Zhao-Weng Wang, David. H Hall_ <br> _Dev. Dyn., 238: 1936-1950_ <br> _Published: 17 July 2009 (https://doi.org/10.1002/dvdy.22025)_
 
-_Published: 17 July 2009 (https://doi.org/10.1002/dvdy.22025)_
-
-There are three tables of innexin expression within the paper. Table 3 is incorporated into a [dataset](https://github.com/yasinthanvickneswaran/ConnectomeToolbox/blob/main/cect/data/Modified%20celegans%20db%20dump.csv) with WormAtlas data.
+**Summary**
+- There are three tables of innexin expression within the paper.
+- Table 3 is incorporated into a [dataset](https://github.com/yasinthanvickneswaran/ConnectomeToolbox/blob/main/cect/data/Modified%20celegans%20db%20dump.csv) with WormAtlas data.

docs/Atanas_2023.md

@@ -1,7 +1,7 @@
 ## Brain-wide representations of behavior spanning multiple timescales and states in C. elegans
-_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_
+_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_ 
 
-_Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_
+_Cell, Volume 186, Issue 19, 2023, Pages 4134-4151.e31, ISSN 0092-8674_ <br> _Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_
 
 - For quantitative analaysis, the two adult datasets from Witvliet et al were averaged. (https://www.nature.com/articles/s41586-021-03778-8)
 - Self looping and single synapse edges were excluded

docs/Beets_2023.md

@@ -1,6 +1,11 @@
 ## System-wide mapping of peptide-GPCR interactions in C. elegans
 _Beets I, Zels S, Vandewyer E, Demeulemeester J, Caers J, Baytemur E, Courtney A, Golinelli L, Hasakioğulları İ, Schafer WR, Vértes PE, Mirabeau O, Schoofs L._ 
 
-_doi: 10.1016/j.celrep.2023.113058_
+_Cell Reports,
+Volume 42, Issue 9,
+2023,
+113058,
+ISSN 2211-1247,
+<br> https://doi.org/10.1016/j.celrep.2023.113058_
 
 - They report a genome-wide peptide-GPCR interaction map in _C.elegans_

docs/Bentley_2016.md

@@ -1,8 +1,6 @@
 ## The Multilayer Connectome of Caenorhabditis elegans
-*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer*
+*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer* <br> *Published: December 16, 2016* <br>*PLoS Comput Biol 12(12): e1005283. https://doi.org/10.1371/journal.pcbi.1005283*
 
-*Published: December 16, 2016
-https://doi.org/10.1371/journal.pcbi.1005283* 
 
 **Abstract:**
 - Extrasynaptic modulation (monoamines and peptides) influence neural circuits

docs/Brittin_2021.md

@@ -1,5 +1,5 @@
 ## A multi-scale brain map derived from whole-brain volumetric reconstructions
-_Brittin, C.A., Cook, S.J., Hall, D.H. et al_
+_Brittin, C.A., Cook, S.J., Hall, D.H. et al_ <br> _Nature 591, 105–110_
 
 _Published: 24 February 2021 https://doi.org/10.1038/s41586-021-03284-x_
 

docs/Cook_2019.md

@@ -1,17 +1,18 @@
-## Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes
-_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_
+# Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes
+_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_ 
 
-_Published: 3 July 2019_
+_Nature 571, 63–71 <br>Published: 3 July 2019 https://doi.org/10.1038/s41586-019-1352-7_
 
-# Abstract
+
+## Abstract
 - Present quantitative connectivity matrices that encompass all connections from sensory input to end-organ output across the entire animal.
 - Serial EM reconstructions that are based on analysis of both new and previously published EM update results and include data on male head
 - Nervous system differs between sexes at multiple levels:
   - Several sex-shared neurons that function in circuits for sexual behaviour are sexually dimorphic in structure and connectivity
   - Inputs from sex-specific circuitry to central circuitry reveal points at which sexual and non-sexual pathways converge
   - Sex-shared central pathways, a substantial no. of connections differ in strength between the sexes
 
-**Whole animal connectomes**
+### Whole animal connectomes
 - Small world, network motifs, modules and rich clubs
 - Reconstruction of circuity for the male head, including the nerve ring and retrovesicular ganglion, from a new EM series and re-annotate previously generated prints of the hermaphrodite
 - Graph of the hermaphrodite connectome has 460 nodes (302 neurons, 132 muscles and 26 non-muscle end organs)
@@ -20,7 +21,7 @@ _Published: 3 July 2019_
 - Small number (1-5) of synaptic steps between the sensory neurons and the end organs and feedforward nature of the networks
 - Placement of the nodes to the neuroanatomy of the worm reflects economical wiring, a property commonly found for nervous systems, including in C.elegans
 
-**Architecture of information flow**
+### Architecture of information flow
 - Polarity of the chemical synapses and the architecture of the physical connectivity networks to order the sex-shared neurons and end organ classes using an algorithm that detects hierarchy in a network
 - Interneurons can be categorised roughly into one of three layers that reflect preponderance of their output onto the layer below and approx the number of synaptic steps to motor neurons
 - Fourth interneuron category: consists of interneurons that interact across all layers, cannot be fitted into this layered structure
@@ -32,7 +33,7 @@ _Published: 3 July 2019_
 - Node degree: amount of convergence and divergence at single nodes in a network (number of attached edges)
   - Diverging connectivity enables information from single sensory neurons to potentially reach from 70% to 98% of all the other cells in the network within two synaptic steps
 
-**Generation of body movements**
+### Generation of body movements
 - Postural movements of C.elegans during foraging and locomotion are generated by a set of 95 body wall muscles that are arranged in four longitudinal rows, two of which are sub-dorsal and the other two are sub-ventral
 - Within each of these quadrants, adjacent muscle cells are electrically coupled by gap junctions
 - 154 neurons in 46 classes have NMJs with these somatic muscles
@@ -45,21 +46,21 @@ _Published: 3 July 2019_
   - Third is a general body curvature, corresponding to the potential effect of the sublateral motor neurons
   - Fourth includes head bending, corresponding to the head motor neurons
 
-**Reproducibility of connectivity**
+### Reproducibility of connectivity
 - Left-right homologous neuron pairs onto left-right homologous targets in the nerve ring of the hermaphrodite reconstruction to assess the amount of natural variability in connectivity
 - For chemical connections, edge weights varied by 10-40%, depending on connection strength
 - In both sexes, the gustatory neurons ASEL (left neuron of the pair) has greater chemical than the ASER (right neuron of the pair) to the olfactory neuron class AWC.
   - Known to be lateralized in its ability to sense chemosensory cues
   - We confirmed the difference in connectivity by in vivo fluorescence labelling of this synaptic connection
 
-**Comparison of the sexes**
+### Comparison of the sexes
 - Circuits controlling the sex-unique behaviours of egg laying and copulation include both sex-specific and sex-shared neurons,
 - Most notable in the male, in which the neural network that controls copulation consists of 85 male-specific and 64 shared neurons
 - Sex-specific neurons connect into the sex-shared central circuity in the head with 2 functions
   - Regulate behaviour during overt reproductive activity
   - Mediate sex specific appetitive decision making
 
-**Discussion**
+## Discussion
 - Physical connectivity matrices for the entire nervous system of an animal for both adult sexes
 - Amount of convergence and divergence of sensory input pathways is such that particular behavioural response pathways cannot be readily identified in general
 - Major motor neurons and primary premotor interneurons are highly interconnected
@@ -71,34 +72,16 @@ _Published: 3 July 2019_
   - C.elegans neurons are isopotential, properties of these neurons may be compartmentalised and signalling may not be uniform or simultaneous at all synapses
   - Modelling the functions of the nervous system at the abstracted level of the connectivity network cannot be seriously cannot be seriously undertaken if a considerable number of nodes and edges are missing
 
-**Methods**
-- Adjacency matrices: data from neuron maps are abstracted as an adjacency matrix with weights that indicate the total amount of physical connectivity between each cell pair
-
-
-
-
-
-
-
-
-
-## Significant updates and corrections to previous data (Whole-animal connectome)
-- DVB/PVT mixup.  The ventral cord processes of these neurons were crossed in MOW.  PVT extends to the head, DVB ends mid-body.  Previously reported: (WBG 16(1):24 (October 1, 1999)).
+## Significant updates and corrections to previous data
+- DVB/PVT mixup.  The ventral cord processes of these neurons were crossed in MOW.  PVT extends to the head, DVB ends mid-body.
 - PVCL and PVCR.  In MOW these were switched at N2U ventral cord section 1656.
 - Sublateral motor neurons.  MOW contained no data for the sublateral cords anterior or posterior to the nerve ring, and no neuromuscular junctions for these neurons along the body. Synapses were first noted by immunofluorescence, then confirmed by sampling multiple animals (not reconstructed).
-- Lateral nerves were closely examined in multiple animals to assess synapses for the first time (not reconstructed except for short portions) (Ramirez-Suarez N.J., Belalcazar H.M., Salazar C.J., Beyaz B., Raja B., Nguyen K.C.Q., Celestrin K., Fredens J., Færgeman N.J., Hall D.H., and Bülow H.E. (2018) Axon-dependent patterning and maintenance of somatosensory dendritic arbors, Dev Cell. 2019 Jan 28;48(2):229-244.).
+- Lateral nerves were closely examined in multiple animals to assess synapses for the first time (not reconstructed except for short portions)
 - Motor neurons re-assigned as interneurons: RIM, RMF, RMG.  nmj's reported in MOW for the adult RMF could not be verified.
 - Interneurons reassigned as motor neurons: SAB, SIA, SIB.
 - Interneuron reasssigned as sensory neuron: DVA.
 - Amphid nerves were found to contain synapses among sensory dendrites and RIP, following first discovery in Pristionchus.
 - Synapses to hypodermis, both chemical and gap junctional, were occasionally reported in MOW but were not systematically scored until now.
 - Extensive gap junctional connectivity of hmc (head mesodermal cell) to muscle was previously noted (MRC notebooks) but never systematically assessed and reported.
 - PDB is considered to be an AS class motor neuron (AS12).  It shares all the characteristics of the other members of this class, except the route taken by its commissure differs by going first posteriorly before crossing the body and progressing anteriorly (the reason behind its unique name, J. White, personal communication).  In the male it has an extensive dendritic arbor involved in mating circuitry, as does AS11.
-- Muscle arms of the bodywall muscles of the head (#1-8) were  traced to their NMJ inputs for the first time
-
-**Male-specific neurons**
-- There are two new classes of male-specific neurons: MCM (L and R) are interneurons in the head (Sammut et al. 2015, Nature 526, 385-390); PHD (L and R) are putative sensory neurons in the tail derived during the L4 larval stage by transdifferentiation of the phasmid socket cell PHso1 (Sulston et al., 1980; Molina-Garcia et al., https://www.biorxiv.org/content/early/2018/03/21/285320).
-- In Jarrell et al., the processes of PHD(L/R) were misidentified as branches of R8B.
-- In Jarrell et al., LUA and PHC were reversed.  Connectivity data given for LUA is in fact due to PHC, and vice versa.
-- AN3 of Jarrell et al. is AVF (verified by transgene expression of a synaptic marker (unpublished observations)).  AN3 was one of three interneuron processes of neurons with cell bodies in the head that could not be positiviely identified in the pre-anal ganglion.
-- The other two, AN1 and AN2, are tentatively assigned as AVH and AVJ, respectively.
+- Muscle arms of the bodywall muscles of the head (#1-8) were  traced to their NMJ inputs for the first time.

docs/Cook_2020.md

@@ -1,5 +1,5 @@
- ## The connectome of the Caenorhabditis elegans pharynx 
+## The connectome of the Caenorhabditis elegans pharynx 
 
-_Steven J. Cook, Charles M. Crouse, Eviatar Yemini, David H. Hall, Scott W. Emmons, Oliver Hobert_
-
+_Steven J. Cook, Charles M. Crouse, Eviatar Yemini, David H. Hall, Scott W. Emmons, Oliver Hobert_ <br>
+_J Comp Neurol. 2020; 528: 2767–2784_ <br>
 _First published: 30 April 2020   https://doi.org/10.1002/cne.24932_

docs/Dag_2023.md

@@ -0,0 +1,8 @@
+## Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale
+_Ugur Dag, Ijeoma Nwabudike, Di Kang, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell_ <br>
+_Cell,
+Volume 186, Issue 12,
+2023,
+Pages 2574-2592.e20,
+ISSN 0092-8674,
+https://doi.org/10.1016/j.cell.2023.04.023._

docs/Fenyves_2020.md

@@ -1,7 +1,9 @@
 ## Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network
 
-_Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Sőti, Peter Csermely
+_Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Sőti, Peter Csermely<br>
+ *PLOS Computational Biology 16(12): e1007974*<br>
 Published: December 21, 2020 https://doi.org/10.1371/journal.pcbi.1007974_
 
+**Summary**
 - Present a gene expression-based sign prediction of the ionotropic chemical synapse connectome of _C.elegans_
 - They have an open source tool (http://elegansign.linkgroup.hu) that uses three differene connectomes: WormWiring; Cook et al.; Varshney et al.

docs/Gendrel_2016.md

@@ -1 +1,2 @@
 ##  A cellular and regulatory map of the GABAergic nervous system of C. elegans 
+_Gendrel M, Atlas EG, Hobert O <br> Elife <br>  Published: 14 October 2016 https://doi.org/10.7554/eLife.17686_

docs/Hall_1991.md

@@ -1,3 +1,4 @@
 ## The Posterior Nervous System of the Nematode Caenorhabditis elegans: Serial Reconstruction of Identified Neurons and Complete Pattern of Synaptic Interactions
-_David H. Hall and Richard L. Russell_
+_David H. Hall and Richard L. Russell_ <br>
+*Journal of Neuroscience <br> 1 January 1991, 11 (1) 1-22; DOI: 10.1523/JNEUROSCI.11-01-00001.1991* 
 

docs/Pereira_2015.md

@@ -1,6 +1,7 @@
 ## A cellular and regulatory map of the cholinergic nervous system of C. elegans
-_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_
+_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_ 
 
+*eLife* <br>
 _Published: 25 December 2015 https://doi.org/10.7554/eLife.12432.001_
 
 

docs/Randi_2023.md

@@ -1 +1,4 @@
 ## Neural signal propagation atlas of Caenorhabditis elegans
+_Randi, F., Sharma, A.K., Dvali, S., Leifer, M.<br> Nature 623, 406–414 (2023) https://doi.org/10.1038/s41586-023-06683-4_
+
+**Summary**

docs/Ripoll_2023.md

@@ -1 +1,8 @@
 ## The neuropeptidergic connectome of C. elegans
+*Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM 3rd, Hobert O, Beets I, Vértes PE, Schafer WR.*<br>
+*Neuron,
+Volume 111, Issue 22,
+2023,
+Pages 3570-3589.e5,
+ISSN 0896-6273,
+https://doi.org/10.1016/j.neuron.2023.09.043.*

docs/Serrano_2013.md

@@ -1 +1,8 @@
 ##  Modular control of glutamatergic neuronal identity in C. elegans by distinct homeodomain proteins 
+_Serrano-Saiz E, Poole RJ, Felton T, Zhang F, De La Cruz ED, Hobert O._<br>
+*Cell,
+Volume 155, Issue 3,
+2013,
+Pages 659-673,
+ISSN 0092-8674,
+https://doi.org/10.1016/j.cell.2013.09.052.*

docs/Taylor_2021.md

@@ -1,8 +1,14 @@
  ## Molecular topography of an entire nervous system 
  _Seth R. Taylor, Gabriel Santpere, Alexis Weinreb, Marc Hammarlund, Oliver Hobert, David M. Miller_
 
+*Cell,
+Volume 184, Issue 16,
+2021,
+Pages 4329-4347.e23,
+ISSN 0092-8674,*<br>
 _Published: July 07, 2021 DOI:https://doi.org/10.1016/j.cell.2021.06.023_
 
+**Summary**
 - Gene expression profiles of all 118 neuron classes in the _C.elegans_ hermaphrodite
 - Each neuron type expresses a distinct code of neuropeptide genes and receptors
 - Expression profiles enable discovery of cell-type-specific _cis_-regulatory sequences