book.bib

@incollection{abucaCocaTrade2019,
  title = {Coca Leaf Transfers to {{Europe}}. {{Effects}} on the Consumption of Coca in {{North-western Argentina}}.},
  booktitle = {Transatlantic {{Trade}} and {{Global Cultural Transfers Since}} 1492: {{More}} than {{Commodities}}},
  author = {Abduca, Ricardo},
  editor = {Kaller, Martina and Jacob, Frank},
  year = {2019},
  month = jul,
  publisher = {{Routledge}},
  abstract = {Access to new plants and consumer goods such as sugar, tobacco, and chocolate from the beginning of the sixteenth century onwards would massively change the way people lived, especially in how and what they consumed. While global markets were consequently formed and provided access to these new commodities that increasingly became important in the `Old World', especially with regard to the establishment early modern consumer societies. This book brings together specialists from a range of historical fields to analyse the establishment of these commodity chains from the Americas to Europe as well as their cultural implications.},
  googlebooks = {13imDwAAQBAJ},
  isbn = {978-0-429-76357-1},
  langid = {english},
  keywords = {History / Americas (North; Central; South; West Indies),History / Europe / Spain \& Portugal,History / Expeditions \& Discoveries,History / General,History / Social History,History / World}
}

@book{adamsHitchhikersGuide2002,
  title = {The {{Hitchhiker}}'s {{Guide}} to the {{Galaxy}}},
  author = {Adams, Douglas},
  year = {2002},
  publisher = {{Picador}},
  address = {{London}}
}

@book{adamsLifeUniverse2002,
  title = {Life, the {{Universe}} and {{Everything}}},
  author = {Adams, Douglas},
  year = {2002},
  publisher = {{Picador}},
  address = {{London}}
}

@book{adamsLongThanks2002,
  title = {So {{Long}}, and {{Thanks}} for {{All}} the {{Fish}}},
  author = {Adams, Douglas},
  year = {2002},
  publisher = {{Picador}},
  address = {{London}}
}

@book{adamsRestaurantEnd2002,
  title = {The {{Restaurant}} at the {{End}} of the {{Universe}}},
  author = {Adams, Douglas},
  year = {2002},
  publisher = {{Picador}},
  address = {{London}}
}

@article{AdapterRemovalv2,
  title = {{{AdapterRemoval}} v2: Rapid Adapter Trimming, Identification, and Read Merging},
  shorttitle = {{{AdapterRemoval}} V2},
  author = {Schubert, Mikkel and Lindgreen, Stinus and Orlando, Ludovic},
  year = {2016},
  month = feb,
  journal = {BMC research notes},
  volume = {9},
  pages = {88},
  issn = {1756-0500},
  doi = {10.1186/s13104-016-1900-2},
  abstract = {BACKGROUND: As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run. FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support. CONCLUSIONS: We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.},
  langid = {english},
  pmcid = {PMC4751634},
  pmid = {26868221},
  keywords = {Algorithms,Base Sequence,High-Throughput Nucleotide Sequencing}
}

@article{adlerSequencingAncient2013,
  title = {Sequencing Ancient Calcified Dental Plaque Shows Changes in Oral Microbiota with Dietary Shifts of the {{Neolithic}} and {{Industrial}} Revolutions},
  author = {Adler, C. J. and Dobney, K. and Weyrich, L. S. and Kaidonis, J. and Walker, A. W. and Haak, W. and Bradshaw, C. J. and Townsend, G. and So{\l}tysiak, A. and Alt, K. W. and Parkhill, J. and Cooper, A.},
  year = {2013},
  journal = {Nature Genetics},
  volume = {45},
  number = {4},
  pages = {450--5, 455e1},
  issn = {1546-1718 (Electronic) 1061-4036 (Linking)},
  doi = {10.1038/ng.2536},
  abstract = {The importance of commensal microbes for human health is increasingly recognized, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets (beginning approximately 10,000 years before the present) and the more recent advent of industrially processed flour and sugar (in approximately 1850). Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained unexpectedly constant between Neolithic and medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in postindustrial lifestyles.},
  pmcid = {PMC3996550},
  keywords = {*Archaeology,*Diet,*Industry,Biological Evolution,Dental Plaque/*genetics/microbiology,High-Throughput Nucleotide Sequencing,Humans,Metagenome/*genetics,Mouth Mucosa/*microbiology/pathology,notion}
}

@article{akcaliDentalCalculus2018,
  title = {Dental Calculus: The Calcified Biofilm and Its Role in Disease Development},
  shorttitle = {Dental Calculus},
  author = {Akcal{\i}, Aliye and Lang, Niklaus P.},
  year = {2018},
  journal = {Periodontology 2000},
  volume = {76},
  number = {1},
  pages = {109--115},
  issn = {1600-0757},
  doi = {10.1111/prd.12151},
  abstract = {Dental calculus represents the first fossilized record of bacterial communities as a testimony of evolutionary biology. The development of dental calculus is a dynamic process that starts with a nonmineralized biofilm which eventually calcifies. Nonmineralized dental biofilm entraps particles from the oral cavity, including large amounts of oral bacteria, human proteins, viruses and food remnants, and preserves their DNA. The process of mineralization involves metabolic activities of the bacterial colonies and strengthens the attachment of nonmineralized biofilms to the tooth surface. From a clinical point of view, dental calculus always harbors a living, nonmineralized biofilm, jeopardizing the integrity of the dento-gingival or implanto-mucosal unit. This narrative review presents a brief historical overview of dental calculus formation and its clinical relevance in modern periodontal practice.},
  copyright = {\textcopyright{} 2017 John Wiley \& Sons A/S. Published by John Wiley \& Sons Ltd},
  langid = {english},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/prd.12151}
}

@article{alanonAssessmentFlavanol2016,
  title = {Assessment of Flavanol Stereoisomers and Caffeine and Theobromine Content in Commercial Chocolates},
  author = {Ala{\~n}{\'o}n, M.E. and Castle, S.M. and Siswanto, P.J. and {Cifuentes-G{\'o}mez}, T. and Spencer, J.P.E.},
  year = {2016},
  month = oct,
  journal = {Food Chemistry},
  volume = {208},
  pages = {177--184},
  issn = {03088146},
  doi = {10.1016/j.foodchem.2016.03.116},
  abstract = {Assessment of the flavanol composition of 41 commercial chocolates was by HPLC-DAD. Among individual flavonols ranged from 0.095 to 3.264 mg g\`A1, epicatechin was the predominant flavanol accounting for 32.9\%. Contrary to catechin, epicatechin was a reliable predictive value of the polyphenol content. Conversely the percentage of theobromine used as a proxy measure for nonfat cocoa solids (NFCS) was not a good predictor of epicatechin or flavanol content. In a further chiral analysis, the naturally occurring forms of cocoa flavanols, (\`A)-epicatechin and (+)-catechin, was determined joint the occurrence of (+)epicatechin and (\`A)-catechin due to the epimerization reactions produced in chocolate manufacture. (\`A)-Epicatechin, the most bioactive compound and predominant form accounted of 93\%. However, no positive correlation was found with\% cocoa solids, the most significant quality parameter.},
  langid = {english}
}

@article{alfaroChronicCoffee2018,
  title = {Chronic Coffee Consumption and Respiratory Disease: {{A}} Systematic Review},
  shorttitle = {Chronic Coffee Consumption and Respiratory Disease},
  author = {Alfaro, Tiago M. and Monteiro, Rita A. and Cunha, Rodrigo A. and Cordeiro, Carlos Robalo},
  year = {2018},
  journal = {The Clinical Respiratory Journal},
  volume = {12},
  number = {3},
  pages = {1283--1294},
  issn = {1752-699X},
  doi = {10.1111/crj.12662},
  abstract = {Purpose The widespread consumption of coffee means that any biological effects from its use can lead to significant public health consequences. Chronic pulmonary diseases are extremely prevalent and responsible for one of every six deaths on a global level. Methods Major medical databases for studies reporting on the effects of coffee or caffeine consumption on a wide range of non-malignant respiratory outcomes, including incidence, prevalence, evolution or severity of respiratory disease in adults were searched. Studies on lung function and respiratory mortality were also considered. Results Fifteen studies, including seven cohort, six cross-sectional, one case control and one randomized control trial were found. Coffee consumption was generally associated with a reduction in prevalence of asthma. The association of coffee with natural honey was an effective treatment for persistent post-infectious cough. One case-control study found higher risk of chronic obstructive pulmonary disease (COPD) with coffee consumption. No association was found with the evolution of COPD or sarcoidosis. Coffee was associated with a reduction in respiratory mortality, and one study found improved lung function in coffee consumers. Smoking was a significant confounder in most studies. Conclusions Coffee consumption was associated with some positive effects on the respiratory system. There was however limited available evidence, mostly from cross sectional and retrospective studies. The only prospective cohort studies were those reporting on respiratory mortality. These results suggest that coffee consumption may be a part of a healthy lifestyle leading to reduced respiratory morbidity.},
  langid = {english},
  keywords = {asthma,caffeine,coffee,COPD,respiratory disease,systematic review},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/crj.12662}
}

@article{ammannZurichBiofilm2012,
  title = {Advancement of the 10-Species Subgingival {{Zurich}} Biofilm Model by Examining Different Nutritional Conditions and Defining the Structure of the in Vitro Biofilms},
  author = {Ammann, Thomas W. and Gm{\"u}r, Rudolf and Thurnheer, Thomas},
  year = {2012},
  month = oct,
  journal = {BMC microbiology},
  volume = {12},
  pages = {227},
  issn = {1471-2180},
  doi = {10.1186/1471-2180-12-227},
  abstract = {BACKGROUND: Periodontitis is caused by a highly complex consortium of bacteria that establishes as biofilms in subgingival pockets. It is a disease that occurs worldwide and its consequences are a major health concern. Investigations in situ are not possible and the bacterial community varies greatly between patients and even within different loci. Due to the high complexity of the consortium and the availability of samples, a clear definition of the pathogenic bacteria and their mechanisms of pathogenicity are still not available. In the current study we addressed the need of a defined model system by advancing our previously described subgingival biofilm model towards a bacterial composition that reflects the one observed in diseased sites of patients and analysed the structure of these biofilms. RESULTS: We further developed the growth media by systematic variation of key components resulting in improved stability and the firm establishment of spirochetes in the 10-species subgingival Zurich biofilm model. A high concentration of heat-inactivated human serum allowed the best proliferation of the used species. Therefore we further investigated these biofilms by analysing their structure by confocal laser scanning microscopy following fluorescence in situ hybridisation. The species showed mutual interactions as expected from other studies. The abundances of all organisms present in this model were determined by microscopic counting following species-specific identification by both fluorescence in situ hybridisation and immunofluorescence. The newly integrated treponemes were the most abundant organisms. CONCLUSIONS: The use of 50\% of heat-inactivated human serum used in the improved growth medium resulted in significantly thicker and more stable biofilms, and the quantitative representation of the used species represents the in vivo community of periodontitis patients much closer than in biofilms grown in the two media with less or no human serum. The appearance of T. denticola, P. gingivalis, and T. forsythia in the top layer of the biofilms, and the high abundance of T. denticola, reflects well the microbial situation observed at diseased sites. The improved model biofilms will allow further investigations of interactions between individual species and of the effects of atmospheric or nutritional changes, as well as interactions with tissue cells.},
  langid = {english},
  pmcid = {PMC3561252},
  pmid = {23040057},
  keywords = {Bacteria,Bacterial Load,Bacterial Physiological Phenomena,Bacteriological Techniques,Biofilms,Culture Media,Humans,Microscopy,Models; Theoretical,Periodontitis}
}

@article{arcaviCigaretteSmoking2004,
  title = {Cigarette {{Smoking}} and {{Infection}}},
  author = {Arcavi, Lidia and Benowitz, Neal L.},
  year = {2004},
  month = nov,
  journal = {Archives of Internal Medicine},
  volume = {164},
  number = {20},
  pages = {2206--2216},
  issn = {0003-9926},
  doi = {10.1001/archinte.164.20.2206},
  abstract = {Infectious diseases may rival cancer, heart disease, and chronic lung disease as sources of morbidity and mortality from smoking. We reviewed mechanisms by which smoking increases the risk of infection and the epidemiology of smoking-related infection, and delineated implications of this increased risk of infection among cigarette smokers.The MEDLINE database was searched for articles on the mechanisms and epidemiology of smoking-related infectious diseases. English-language articles and selected cross-references were included.Mechanisms by which smoking increases the risk of infections include structural changes in the respiratory tract and a decrease in immune response. Cigarette smoking is a substantial risk factor for important bacterial and viral infections. For example, smokers incur a 2- to 4-fold increased risk of invasive pneumococcal disease. Influenza risk is severalfold higher and is much more severe in smokers than nonsmokers. Perhaps the greatest public health impact of smoking on infection is the increased risk of tuberculosis, a particular problem in underdeveloped countries where smoking rates are increasing rapidly.The clinical implications of our findings include emphasizing the importance of smoking cessation as part of the therapeutic plan for people with serious infectious diseases or periodontitis, and individuals who have positive results of tuberculin skin tests. Controlling exposure to secondhand cigarette smoke in children is important to reduce the risks of meningococcal disease and otitis media, and in adults to reduce the risk of influenza and meningococcal disease. Other recommendations include pneumococcal and influenza vaccine in all smokers and acyclovir treatment for varicella in smokers.Arch Intern Med. 2004;164:2206-2216--{$>$}}
}

@article{armitageExtractionIdentification1975,
  title = {The {{Extraction}} and {{Identification}} of {{Opal Phytoliths}} from the {{Teeth}} of {{Ungulates}}},
  author = {Armitage, Philip L.},
  year = {1975},
  journal = {Journal of Archaeological Science},
  volume = {2},
  pages = {187--197}
}

@article{aronHalfUDG2020,
  title = {Half-{{UDG}} Treated Double-Stranded Ancient {{DNA}} Library Preparation for {{Illumina}} Sequencing},
  author = {Aron, Franziska and Neumann, Gunnar and Brandt, Guido},
  year = {2020},
  month = dec,
  journal = {protocols.io},
  doi = {10.17504/protocols.io.bmh6k39e},
  abstract = {Protocol for the preparation of double-stranded genomic libraries for Illumina sequencing, optimised for ancient DNA (aDNA) with partial USER enzyme treatment. This protocol gen...},
  langid = {english}
}

@article{asscherAtomicDisorder2011,
  title = {Atomic {{Disorder}} in {{Fossil Tooth}} and {{Bone Mineral}}: {{An FTIR Study Using}} the {{Grinding Curve Method}}},
  shorttitle = {Atomic {{Disorder}} in {{Fossil Tooth}} and {{Bone Mineral}}},
  author = {Asscher, Yotam and Regev, L. and Weiner, Steve and Boaretto, Elisabetta},
  year = {2011},
  month = apr,
  journal = {ArcheoSciences. Revue d'arch\'eom\'etrie},
  number = {35},
  pages = {135--141},
  publisher = {{Presses universitaires de Rennes}},
  issn = {1960-1360},
  doi = {10.4000/archeosciences.3062},
  abstract = {Bone and tooth mineral generally undergo diagenetic changes. These changes in the carbonate hydroxyapatite structure and composition can affect the signals embedded in the mineral phase, such as migration behavior, age of the specimen and the reconstruction of past environments. Mineral preservation state can be assessed using infrared spectroscopy which provides information on crystal disorder at the atomic level and mineral composition. Here we present a new approach to evaluate carbonate hydroxyapatite atomic disorder using infrared spectroscopy and the standard KBr sample mounting method. We show that by repeated grinding of the sample and then plotting the infrared splitting factor against the width of the major phosphate absorption peak after each grinding, grinding curves with well defined trend lines can be obtained. The offsets between curves reflect differences in atomic disorder. We show that grinding curve offsets can be used to evaluate the state of preservation of bone, dentine and enamel mineral.},
  copyright = {Article L.111-1 du Code de la propri\'et\'e intellectuelle.},
  isbn = {9782753518476},
  langid = {english},
  keywords = {crystal,fossil bone,fossil teeth}
}

@article{asscherVariationsAtomic2011,
  title = {Variations in {{Atomic Disorder}} in {{Biogenic Carbonate Hydroxyapatite Using}} the {{Infrared Spectrum Grinding Curve Method}}},
  author = {Asscher, Yotam and Weiner, Steve and Boaretto, Elisabetta},
  year = {2011},
  journal = {Advanced Functional Materials},
  volume = {21},
  number = {17},
  pages = {3308--3313},
  issn = {1616-3028},
  doi = {10.1002/adfm.201100266},
  abstract = {Biogenic carbonate hydroxyapatite crystals are inherently disordered at the atomic level due mainly to the substitutions of various ions in the crystal structure, and, in the case of the bone family of materials, to the fact that these very small crystals have a very large surface-to-bulk ratio. Characterization of the extent of disorder is of much interest, as this relates to the stability and hence solubility of the crystals. Here the infrared spectrometry grinding curve approach developed for calcite, is adapted to carbonate hydroxyapatites. The infrared splitting factor is plotted against the full width at half height of the strong phosphate absorption peak as a function of increased grinding of the sample. By doing so, the contribution of particle size to the shape of the peaks is better separated from the contribution of atomic disorder to peak shape. It is shown that differences in disorder exist between dentine, cementum, and bone crystals which could reflect crystal size and/or atomic defects within the crystal. It is als shown that systematic differences exist between enamel samples from different taxa, which we assume only reflects atomic disorder differences within these large crystals. The method can be used to characterize atomic disorder in natural hydroxyapatites, as well as in the many different types of synthetic hydroxyapatites used for biomedical implants.},
  langid = {english},
  keywords = {carbonate hydroxyapatite,crystallinity,grinding curves,infrared spectrometry},
  annotation = {c \_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/adfm.201100266}
}

@book{aten400Jaar2012,
  title = {{400 jaar Beemster: 1612-2012}},
  shorttitle = {{400 jaar Beemster}},
  author = {Aten, D. and Bossaers, K. W. J. M. and Misset, Carly},
  year = {2012},
  publisher = {{Stichting Uitgeverij Noord-Holland}},
  address = {{Wormer}},
  abstract = {\$\$Cnote\$\$VUitg. in opdracht van de Gemeente Beemster.},
  isbn = {978-90-78381-56-3},
  langid = {dutch},
  lccn = {1636 G 28},
  keywords = {Pieces of reclaimed land.; 15.70 history of Europe.; Beemster.; Special publications (form); 1600-1700; 1700-1800; 1800-2000; 2000-2050}
}

@book{aufderheidePaleopathology1998,
  title = {The {{Cambridge}} Encyclopedia of Human Paleopathology},
  author = {Aufderheide, Arthur C and {Rodriguez-Martin}, Conrado and Langsjoen, Odin},
  year = {1998},
  volume = {478},
  publisher = {{Cambridge University Press Cambridge}}
}

@article{azarpazhoohSystematicReview2006,
  title = {Systematic {{Review}} of the {{Association Between Respiratory Diseases}} and {{Oral Health}}},
  author = {Azarpazhooh, Amir and Leake, James L.},
  year = {2006},
  journal = {Journal of Periodontology},
  volume = {77},
  number = {9},
  pages = {1465--1482},
  issn = {1943-3670},
  doi = {10.1902/jop.2006.060010},
  abstract = {Background: The purpose of this review was to investigate evidence for a possible etiological association between oral health and pneumonia or other respiratory diseases. Methods: The following data sources were used: Ovid MEDLINE (In-Process \& Other Non-Indexed Citations, Daily Update, and OLDMEDLINE); Cumulative Index to Nursing \& Allied Health Literature; Evidence Based Medicine of Cochrane Central Register of Controlled Trials; Cochrane Database of Systematic Reviews; Database of Abstracts of Reviews of Effects; EMBASE; Health and Psychosocial Instruments; HealthSTAR; International Pharmaceutical Abstracts; PubMed; and Google Scholar from the earliest record until July 2005. Studies were selected from randomized controlled clinical trials and longitudinal, cohort, case-control, and epidemiological studies. Searches were limited to English language and human studies. Results: A total of 728 articles were searched for relevancy, determined by article title, abstract, and full copy, resulting in a yield of 19 studies that met our inclusion criteria. These articles were read and scored independently by the reviewers to obtain the evidence for this review: 1) the potential risk factors for pneumonia were identified as the presence of cariogenic and periodontal pathogens, dental decay, and poor oral hygiene in five studies; 2) a weak association between periodontal disease and chronic obstructive pulmonary disease (COPD) was identified in four poor to fair studies; and 3) 10 studies were retained providing evidence that interventions aiming to improve oral health reduced the progression or occurrence of pneumonia. Conclusions: 1) There is fair evidence (II-2, grade B recommendation) of an association of pneumonia with oral health (odds ratio [OR] = 1.2 to 9.6 depending on oral health indicators). 2) There is poor evidence of a weak association (OR {$<$}2.0) between COPD and oral health (II-2/3, grade C recommendation). 3) There is good evidence (I, grade A recommendation) that improved oral hygiene and frequent professional oral health care reduces the progression or occurrence of respiratory diseases among high-risk elderly adults living in nursing homes and especially those in intensive care units (ICUs) (number needed to treat [NNT] = 2 to 16; relative risk reduction [RRR] = 34\% to 83\%).},
  langid = {english},
  keywords = {chronic obstructive,Dental plaque,oral health,oral hygiene,periodontal diseases,pneumonia,pulmonary disease},
  annotation = {\_eprint: https://aap.onlinelibrary.wiley.com/doi/pdf/10.1902/jop.2006.060010}
}

@article{badriRegulationFunction2009,
  title = {Regulation and Function of Root Exudates},
  author = {Badri, Dayakar V. and Vivanco, Jorge M.},
  year = {2009},
  journal = {Plant, Cell \& Environment},
  volume = {32},
  number = {6},
  pages = {666--681},
  issn = {1365-3040},
  doi = {10.1111/j.1365-3040.2009.01926.x},
  abstract = {Root-secreted chemicals mediate multi-partite interactions in the rhizosphere, where plant roots continually respond to and alter their immediate environment. Increasing evidence suggests that root exudates initiate and modulate dialogue between roots and soil microbes. For example, root exudates serve as signals that initiate symbiosis with rhizobia and mycorrhizal fungi. In addition, root exudates maintain and support a highly specific diversity of microbes in the rhizosphere of a given particular plant species, thus suggesting a close evolutionary link. In this review, we focus mainly on compiling the information available on the regulation and mechanisms of root exudation processes, and provide some ideas related to the evolutionary role of root exudates in shaping soil microbial communities.},
  copyright = {\textcopyright{} 2009 Blackwell Publishing Ltd},
  langid = {english},
  keywords = {ABC transporters,elicitors,mechanism of secretion,root system architecture,tritrophic interactions},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2009.01926.x}
}

@article{balajiUnusualPresentation2019,
  title = {An Unusual Presentation of Dental Calculus},
  author = {Balaji, Venkateshwarapuram Rengaswami and Niazi, Thanvir Mohammed and Dhanasekaran, Manikandan},
  year = {2019},
  journal = {Journal of Indian Society of Periodontology},
  volume = {23},
  number = {5},
  pages = {484--486},
  issn = {0972-124X},
  doi = {10.4103/jisp.jisp_680_18},
  abstract = {Calculus is a mineralized bacterial plaque that is formed on natural teeth surfaces where there is constant supply of saliva. Dental calculus is commonly seen over the buccal surfaces of maxillary molars and lingual surfaces of mandibular anterior teeth where the salivary duct opens into the oral cavity. This case report presents an unusual presentation of a large hard calcified mass in the left side of retromolar region associated with partially erupted tooth; hard mass was excised and examined histochemically which suggested the presence of calculus. Elimination of such nidus shall prevent formation of such calculus in such unusual position. This can also be achieved with proper oral hygiene measures.},
  pmcid = {PMC6737844},
  pmid = {31543623}
}

@misc{bartholdyAssessingValidity2023,
  title = {Assessing the Validity of a Calcifying Oral Biofilm Model as a Suitable Proxy for Dental Calculus},
  author = {Bartholdy, Bj{\o}rn Peare and Velsko, Irina M. and {Gur-Arieh}, Shira and Fagern{\"a}s, Zandra and Warinner, Christina and Henry, Amanda G.},
  year = {2023},
  month = may,
  pages = {2023.05.23.541904},
  publisher = {{bioRxiv}},
  doi = {10.1101/2023.05.23.541904},
  abstract = {Dental calculus is increasingly used by researchers to study dietary patterns in past populations. The benefits of using dental calculus for this purpose have been clearly demonstrated in previous studies, with dental calculus harbouring a wealth of microremains and biomarkers for health and diet within its mineral matrix. Previous studies have demonstrated some of the limitations and biases of how methods of processing may overlook, or even remove, some of the important information contained within the mineralised matrix. However, there are many factors that are impossible to account for *in vivo* and in archaeological material, such as exact dietary intake, and individual factors such as pH and enzyme activity, leaving some limitations that may not be addressed through these types of studies and will require a different approach. We present a protocol for creating a calcifying oral biofilm model that can be used to explore the biases and limitations of dental calculus as a medium for paleodietary reconstructions. We report the microbial and mineral composition of our model in an effort to validate the model calculus as an appropriate proxy to natural dental calculus. The microbial profile and species diversity of our model was determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, and compared to various reference samples from oral sites, including saliva, plaque, and dental calculus. We then assessed whether our model calculus mineralises in a manner similar to natural dental calculus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed a microbial profile predominantly made up of (facultative) anaerobes, with a community structure that was somewhat distinct from other oral reference samples. The core genera of the model consisted of oral species, but clustered separately from oral reference samples, with a higher abundance of anaerobes. Mineral and organic components of our model mimic that of the modern and archaeological reference calculus that was used as a comparison. There was an overall increase in the inorganic component relative to organic over the course of the experiment, with carbonated hydroxyapatite as the principal compound, consistent with natural human-derived calculus. We conclude that oral biofilm models, such as the one presented in this study, have great potential to validate current methods used in the analysis of archaeological dental calculus, and should be used to complement, rather than replace current *in vivo* studies.},
  chapter = {New Results},
  copyright = {\textcopyright{} 2023, 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/},
  langid = {english}
}

@misc{bartholdyDentalPathological2023,
  title = {Dental, Pathological, and {{UHPLC}} Data from {{Middenbeemster}} Archaeological Site},
  year = {2023},
  month = feb,
  publisher = {{Zenodo}},
  doi = {10.5281/zenodo.8061483},
  abstract = {Datasets used in 'Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population' (https://doi.org/10.5281/zenodo.7649150).},
  collaborator = {Bartholdy, Bj{\o}rn Peare},
  langid = {english},
  keywords = {dental calculus,dental caries,LC-MS/MS,paleopathology,periodontitis}
}

@article{bartholdyInvestigatingBiases2022,
  title = {Investigating {{Biases Associated With Dietary Starch Incorporation}} and {{Retention With}} an {{Oral Biofilm Model}}},
  author = {Bartholdy, Bj{\o}rn Peare and Henry, Amanda G.},
  year = {2022},
  journal = {Frontiers in Earth Science},
  volume = {10},
  issn = {2296-6463},
  doi = {10.3389/feart.2022.886512},
  abstract = {Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited to in vivo studies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted on in vitro dental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25~days growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06\% to 0.16\%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules ({$>$}20~{$\mu$}m) consistently being under-represented. We also found a positive correlation between the absolute granule counts and dry-weight of the biofilm (r = 0.659, 90\%CI[0.463, 0.794]), meaning the absolute quantity of starch granules will increase as the size of the calculus deposit increases. A similar, but weaker correlation was found between the concentration (count per mg) of granules and dry-weight (r = 0.3, 90\%CI[0.0618, 0.506]). Our results complement and reinforce previous in vivo studies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20~{$\mu$}m in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus.},
  copyright = {All rights reserved}
}

@misc{bartholdyMB11CalculusPilot,
  title = {Bbartholdy/{{mb11CalculusPilot}}: {{Version}} of Record},
  shorttitle = {Bbartholdy/{{mb11CalculusPilot}}},
  author = {Bartholdy, Bj{\o}rn Peare},
  year = {2024},
  month = apr,
  doi = {10.5281/zenodo.11040640},
  abstract = {Final published version in Peer Community Journal. Full Changelog: https://github.com/bbartholdy/mb11CalculusPilot/compare/0.3.0...1.0.0},
  howpublished = {Zenodo}
}

@techreport{bartholdyMultiproxyAnalysis2023,
  title = {Multiproxy Analysis Exploring Patterns of Diet and Disease in Dental Calculus and Skeletal Remains from a 19th Century {{Dutch}} Population},
  author = {Bartholdy, Bj{\o}rn Peare and Hasselstr{\o}m, J{\o}rgen B. and S{\o}rensen, Lambert K. and Casna, Maia and Hoogland, Menno and Beemster, Historisch Genootschap and Henry, Amanda G.},
  year = {2023},
  month = feb,
  institution = {{Zenodo}},
  doi = {10.5281/zenodo.7649151},
  abstract = {Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus provides direct evidence of consumption by individuals within a population. We conducted a study on 41 individuals from Middenbeemster, a 19th century rural Dutch archaeological site. Skeletal and dental analysis was performed to explore potential relationships between pathological conditions/lesions and the presence of alkaloids. We also explored other factors potentially affecting the detection of alkaloids, including sample weight and skeletal preservation. Dental calculus was sampled and analysed using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-ESI-MS/MS). We were able to detect nicotine, cotinine, caffeine, theophylline, and salicylic acid. By detecting these compounds we are able to show the consumption of tea and coffee and smoking of tobacco on an individual scale, which is also confirmed by historic documentation and identification of pipe notches in the dentition. Nicotine and/or cotinine was present in 60\% of individuals with at least one visible pipe notch. We find some influence of skeletal preservation on the detection of alkaloids and salicylic acid, with higher quantities of compounds extracted from well-preserved individuals, and also observe a relationship between weight of the calculus sample and raw quantity of the detected compounds, and we were able to detect alkaloids in samples as small as 2 mg. We found correlations between chronic maxillary sinusitis and the presence of multiple alkaloids.We show that there are many limitations that will need to be addressed going forward with this type of analysis, and stress the need for more systematic research on the consumption of alkaloid-containing items and their subsequent concentration and preservation in dental calculus, in addition to how mode of consumption may affect concentrations on different parts of the dentition. Despite the limitations, this preliminary study illustrates the many benefits of using calculus to target a variety of compounds that could have been ingested as medicine or diet, or consumed in a different manner. This method allows us to directly address specific individuals, which can be especially useful in individuals that are not always well-documented in historic documentation, such as rural populations, children and women.},
  copyright = {All rights reserved},
  langid = {english},
  keywords = {alkaloids,caffeine,dental calculus,dental pathology,LC-MS/MS,sinusitis,tobacco}
}

@article{bassonEstablishmentCommunity1996,
  title = {The Establishment of a Community of Oral Bacteria That Controls the Growth of {{Candida}} Albicans in a Chemostat},
  author = {Basson, N. J. and {van Wyk}, C. W.},
  year = {1996},
  journal = {Oral Microbiology and Immunology},
  volume = {11},
  number = {3},
  pages = {199--202},
  issn = {1399-302X},
  doi = {10.1111/j.1399-302X.1996.tb00358.x},
  abstract = {The purpose of this study was to establish and identify a community of oral bacteria that controls the growth of Candida albicans in the chemostat. The chemostat was operated under glucose-limiting conditions at a dilution rate of 0.05 h-1 and inoculated with a yeast-free suspension of a tongue scraping. After a steady state had been reached, it was inoculated with C. albicans to establish the yeast and determine whether its growth could be contained. The steady-state community comprised the species Streptococcus sanguis, Streptococcus sobrinus, Streptococcus mitis, Lacto-bacillus casei, Eubacterium saburreum, Veillonella dispar and Fusobacterium nucleatum. Bacteroides gracilus and Haemophilus segnis were also detected but infrequently. Yeast growth was suppressed and yeast cells were lost at the same rate as the theoretical washout rate. It is concluded that this mixed community of oral bacteria can be used to identify the parameters that maintain the equilibrium between oral bacteria and C. albicans in the oral cavity.},
  langid = {english},
  keywords = {Candida albicans,chemostat,growth,oral bacteria},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-302X.1996.tb00358.x}
}

@article{belcastroContinuityDiscontinuity2007,
  title = {Continuity or Discontinuity of the Life-Style in Central {{Italy}} during the {{Roman}} Imperial Age-Early Middle Ages Transition: {{Diet}}, Health, and Behavior},
  shorttitle = {Continuity or Discontinuity of the Life-Style in Central {{Italy}} during the {{Roman}} Imperial Age-Early Middle Ages Transition},
  author = {Belcastro, Giovanna and Rastelli, Elisa and Mariotti, Valentina and Consiglio, Chiara and Facchini, Fiorenzo and Bonfiglioli, Benedetta},
  year = {2007},
  journal = {American Journal of Physical Anthropology},
  volume = {132},
  number = {3},
  pages = {381--394},
  issn = {1096-8644},
  doi = {10.1002/ajpa.20530},
  abstract = {Dento-alveolar pathologies and alterations (dental wear, caries, abscesses, ante mortem tooth loss (AMTL), calculus, hypoplastic defects, and chipping) and skeletal markers of health (cribra orbitalia and periostitis) were analyzed in two skeletal samples from the necropolises of Quadrella (I\textendash IV c. AD) and Vicenne-Campochiaro (VII c. AD) in the Molise region of central Italy. The aim was to determine if the Roman Imperial Age-Early Middle Ages transition characterized by political, socioeconomic, and cultural transformations affected the biology of these populations, particularly their alimentation and health status. The frequencies of caries and AMTL, similar in the two samples, suggest a high consumption of carbohydrates. The higher levels of heavy wear, calculus, and interproximal chipping in the Vicenne population indicate a greater use of fibrous foods (both meat and others), in line with the dietary model of Germanic peoples. Health conditions do not appear to have been good in either period, as shown by the high frequencies of linear hypoplasia and the presence of cribra orbitalia and periostitis. The diet of the individuals buried with horses of the Vicenne population did not differ from that of the rest of the population, whereas there were evident differences in the use of the teeth for nonmasticatory activities among these individuals. Therefore, from the point of view of alimentation and health status, the profound socioeconomic and cultural transformations during the Late Antiquity-Early Middle Ages transition do not seem to have been translated into a true discontinuity of the two Molisan populations. Am J Phys Anthropol, 2007. \textcopyright{} 2006 Wiley-Liss, Inc.},
  copyright = {Copyright \textcopyright{} 2006 Wiley-Liss, Inc.},
  langid = {english},
  keywords = {dental pathologies,diet,skeletal health markers},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.20530}
}

@incollection{bernfeldAmylase1955,
  title = {Amylases, {$\alpha$} and {$\beta$}},
  booktitle = {Methods in {{Enzymology}}},
  author = {Bernfeld, Peter},
  year = {1955},
  month = jan,
  volume = {1},
  pages = {149--158},
  publisher = {{Academic Press}},
  doi = {10.1016/0076-6879(55)01021-5},
  langid = {english}
}

@article{bertranMineralizationDNA2013,
  title = {Mineralization of {{DNA}} into Nanoparticles of Hydroxyapatite},
  author = {Bertran, Oscar and del Valle, Luis J. and {Revilla-L{\'o}pez}, Guillermo and Chaves, Gustavo and Card{\'u}s, Llu{\'i}s and Casas, Mar{\'i}a T. and Casanovas, Jordi and Turon, Pau and Puiggal{\'i}, Jordi and Alem{\'a}n, Carlos},
  year = {2013},
  month = nov,
  journal = {Dalton Transactions},
  volume = {43},
  number = {1},
  pages = {317--327},
  publisher = {{The Royal Society of Chemistry}},
  issn = {1477-9234},
  doi = {10.1039/C3DT52112E},
  abstract = {Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca2+, PO43- and OH--containing aqueous solutions in the presence and absence of B-DNA has been used to conclude that the backbone of the double helix acts as a template for HAp growth. More specifically, results reveal the formation of calcium phosphate clusters at the first stages of the simulations, which subsequently re-organize to nucleate HAp. This effect is produced in the absence and, especially, presence, of DNA indicating that the biomolecules do not inhibit but even promote mineral growth. Furthermore, computer simulations suggest that the diffusion of the OH- anions through the inorganic solution is the limiting step for the nucleation of the biomineral. Nanocapsules and crystalline nanorods of HAp containing DNA molecules inside have been prepared by mixing solutions containing Ca2+ and PO43- ions with fish sperm DNA at high pH. The dimensions and morphology of such nanostructures have been examined by transmission electron microscopy, while the characterization of the biomineral has been focused on the identification of DNA inside HAp using infrared, X-ray photoelectron and UV-vis spectroscopies, as well as gel electrophoresis. The biominerals reported in this work are important for biomedical applications requiring the protection of DNA from aggressive environmental conditions.},
  langid = {english}
}

@article{bispoSimultaneousDetermination2002,
  title = {Simultaneous {{Determination}} of {{Caffeine}}, {{Theobromine}}, and {{Theophylline}} by {{High-Performance Liquid Chromatography}}},
  author = {Bispo, M. S. and Veloso, M. C. C. and Pinheiro, H. L. C. and De Oliveira, R. F. S. and Reis, J. O. N. and De Andrade, J. B.},
  year = {2002},
  month = jan,
  journal = {Journal of Chromatographic Science},
  volume = {40},
  number = {1},
  pages = {45--48},
  issn = {0021-9665, 1945-239X},
  doi = {10.1093/chromsci/40.1.45},
  abstract = {This work relates the development of an analytical methodology to simultaneously determine three methylxanthines (caffeine, theobromine, and theophylline) in beverages and urine samples based on reversed-phase high-performance liquid chromatography. Separation is made with a Bondesil C18 column using methanol\textendash water\textendash acetic acid or ethanol\textendash water\textendash acetic acid (20:75:5, v/v/v) as the mobile phase at 0.7 mL/min. Identification is made by absorbance detection at 273 nm. Under optimized conditions, the detection limit of the HPLC method is 0.1 pg/mL for all three methylxanthines. This method is applied to urine and to 25 different beverage samples, which included coffee, tea, chocolate, and coconut water. The concentration ranges determined in the beverages and urine are: {$<$} 0.1 pg/mL to 350 \textmu g/mL and 3.21 \textmu g/mL to 71.2 \textmu g/mL for caffeine; {$<$} 0.1pg/mL to 32 \textmu g mL and {$<$} 0.1 pg/mL to 13.2 \textmu g/mL for theobromine; {$<$} 0.1 pg/mL to 47 \textmu g/mL and {$<$} 0.1 pg/mL to 66.3 \textmu g/mL for theophylline. The method proposed in this study is rapid and suitable for the simultaneous quantitation of methylxanthines in beverages and human urine samples and requires no extraction step or derivatization.},
  langid = {english}
}

@article{bjarnsholtVivoBiofilm2013,
  title = {The in Vivo Biofilm},
  author = {Bjarnsholt, Thomas and Alhede, Maria and Alhede, Morten and {Eickhardt-S{\o}rensen}, Steffen R. and Moser, Claus and K{\"u}hl, Michael and Jensen, Peter {\O}strup and H{\o}iby, Niels},
  year = {2013},
  month = sep,
  journal = {Trends in Microbiology},
  volume = {21},
  number = {9},
  pages = {466--474},
  issn = {0966842X},
  doi = {10.1016/j.tim.2013.06.002},
  langid = {english}
}

@article{bjorckStarchProcessing1984,
  title = {Effects of Processing on Starch Availability {{In}} Vitro and {{In}} Vivo. {{II}}. {{Drum-drying}} of Wheat Flour},
  author = {Bj{\"o}rck, I. and Asp, N. -G. and Birkhed, D. and Eliasson, A. -C. and Sj{\"o}berg, L. -B. and Lundquist, I.},
  year = {1984},
  month = jan,
  journal = {Journal of Cereal Science},
  volume = {2},
  number = {3},
  pages = {165--178},
  issn = {0733-5210},
  doi = {10.1016/S0733-5210(84)80030-2},
  abstract = {The effect of drum-drying on starch availability in white wheat flour was studied and compared with boiling and pressure cooking. The starch in two drum-dried products was less susceptible to salivary amylase digestion in vitro than in the corresponding boiled or pressure-cooked materials. The rate of starch absorption in young rats, as reflected by the plasma glucose levels, was also lower with drum-dried products than with a boiled control. Similarly, the rise in plasma insulin was slower in drum-dried products. In addition to the conditions used during drum-drying, the method of preparation of the pre-cooked product affected starch availability, the rate of hydrolysis in vitro and, especially, the in vivo glucose response, which was higher in products that were drum-dried and then boiled. The fermentability of drum-dried and boiled wheat flour in human dental plaque was similar, resulting in approximately the same pH drop in situ. A novel type of amylose-lipid complex was formed during drum-drying. Under severe drying conditions, the apparent content of dietary fibre in wheat flour increased by about 20\%, due to formation of enzyme-resistant starch.},
  langid = {english}
}

@article{boocockMaxillarySinusitis1995,
  title = {Maxillary Sinusitis in {{Medieval Chichester}}, {{England}}},
  author = {Boocock, P and Roberts, C. A. and Manchester, K},
  year = {1995},
  journal = {American Journal of Physical Anthropology},
  volume = {98},
  number = {4},
  pages = {483--495},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330980408},
  abstract = {Maxillary sinusitis is a common medical complaint, affecting more than 30 million people per year in the United States alone. Very little palaeopathological work on this disease has been carried out, probably because of the enclosed nature of the sinuses in intact skulls and the lack of a suitable method for examination. This study tested the hypothesis that maxillary sinusitis was more common in people with leprosy than in people without it in Medieval England. The prevalence of maxillary sinusitis by age and sex was recorded in 133 individuals, some diagnosed as being leprous, derived from a later Medieval (12th to 17th centuries AD) urban hospital population at Chichester, Sussex, England using both macroscopic and endoscopic methods of examination. Of the 133 individuals with one or both sinuses available for examination, 54.9\% (73) had evidence of bone change within the sinuses. There was no difference in prevalence between those with leprosy and those without, although clinical studies suggest that over 50\% of lepromatous leprous individuals may develop sinusitis. Comparison with another study on Medieval British sites with a 3.6\% prevalence (3 of 83) indicates that the prevalence at Chichester is much greater. The problems with diagnosing sinusitis are addressed and reasons behind the high frequency in this study are discussed. Aetiological factors predisposing to maxillary sinusitis are considered with reference to possible environmental conditions prevailing in the later Medieval period in Britain. \textcopyright{} 1995 Wiley-Liss, Inc.},
  langid = {english},
  keywords = {Aetiology,Classification,Endoscope,Leprosy,Sinusitis},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330980408}
}

@article{bosHistoryLicit2006,
  title = {The {{History}} of {{Licit Cocaine}} in the {{Netherlands}}},
  author = {Bos, Annemarie},
  year = {2006},
  month = dec,
  journal = {De Economist},
  volume = {154},
  number = {4},
  pages = {581--586},
  issn = {0013-063X, 1572-9982},
  doi = {10.1007/s10645-006-9031-0},
  abstract = {This paper gives a description of the rise and fall of cocaine business in the Netherlands, between 1910 and 1930 when cocaine was a legal drug. When the anesthetic effects of cocaine were discovered demand for cocaine rose quickly. This made the production of coca leaves in the Dutch East Indies and the production of cocaine in the Netherlands a profitable business. However within the time span of two decades the introduction of synthetic replacements stimulated by international legislation to reduce drugs use caused the disappearance of the legal trade of coca and cocaine.},
  langid = {english},
  keywords = {cocaine,Netherlands}
}

@article{bosPhysicochemistryInitial1999,
  title = {Physico-Chemistry of Initial Microbial Adhesive Interactions \textendash{} Its Mechanisms and Methods for Study},
  author = {Bos, R},
  year = {1999},
  month = apr,
  journal = {FEMS Microbiology Reviews},
  volume = {23},
  number = {2},
  pages = {179--229},
  issn = {01686445},
  doi = {10.1016/S0168-6445(99)00004-2},
  abstract = {In this review, initial microbial adhesive interactions are divided into adhesion to substratum surfaces, coaggregation between microbial pairs and co-adhesion between sessile and planktonic microorganisms of different strains or species. The physico-chemical mechanisms underlying the adhesive interactions are described and a critical review is given of currently employed methods to study microbial adhesive interactions, with an emphasis on the use of the parallel plate flow chamber. Subsequently, for each of the three microbial adhesive interactions distinguished, the role of Lifshitz-van der Waals, acid-base and electrostatic interactions is described based on existing literature. \ss{} 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
  langid = {english},
  keywords = {biofilm,microbial adhesion,notion}
}

@article{boumanBegravenis2017,
  title = {{De Begravenis}},
  author = {Bouman, Jacobus},
  year = {2017},
  journal = {De Nieuwe Schouwschuit},
  volume = {15},
  pages = {11--15},
  langid = {dutch}
}

@article{bowenOralBiofilms2018,
  title = {Oral {{Biofilms}}: {{Pathogens}}, {{Matrix}} and {{Polymicrobial Interactions}} in {{Microenvironments}}},
  shorttitle = {Oral {{Biofilms}}},
  author = {Bowen, William H. and Burne, Robert A. and Wu, Hui and Koo, Hyun},
  year = {2018},
  month = mar,
  journal = {Trends in microbiology},
  volume = {26},
  number = {3},
  pages = {229--242},
  issn = {0966-842X},
  doi = {10.1016/j.tim.2017.09.008},
  abstract = {Biofilms are microbial communities embedded within an extracellular matrix, forming a highly organized structure that causes many human infections. Dental caries (tooth-decay) is a polymicrobial biofilm disease driven by the diet and microbiota-matrix interactions that occur on a solid surface. Sugars fuel the emergence of pathogens, the assembly of the matrix, and the acidification of the biofilm microenvironment, promoting ecological changes and concerted multispecies efforts that are conducive for acid damage of the mineralized tooth tissue. Here, we discuss recent advances on the role of the biofilm matrix and interactions between opportunistic pathogens and commensals in the pathogenesis of dental caries. In addition, we highlight the importance of matrix-producing organisms in fostering a pathogenic habitat where inter-species competition and synergies occur to drive the disease process, which could have implications to other infections associated with polymicrobial biofilms},
  pmcid = {PMC5834367},
  pmid = {29097091}
}

@article{boyan-salyersRelationshipProteolipids1980,
  title = {Relationship between Proteolipids and Calcium-Phospholipid-Phosphate Complexes {{inBacterionema}} Matruchotii Calcification},
  author = {{Boyan-Salyers}, B. D. and Boskey, A. L.},
  year = {1980},
  month = dec,
  journal = {Calcified Tissue International},
  volume = {30},
  number = {1},
  pages = {167--174},
  issn = {0171-967X, 1432-0827},
  doi = {10.1007/BF02408622},
  abstract = {Calcium-phospholipid-phosphate complexes (Ca-PL-P) were isolated from calcified and uncalcified Bacterionema matruchotii and its calcified lipid extracts. Similar complexes were absent from the noncalcifying bacterium Actinomyces naeshmdii. The majority of the Ca-PL-P complexes were associated with the proteolipid acidic phospholipid component. Ca-PL-P complexes isolated from B. matruchotii and from calcified proteolipid contained phosphatidylinositol, phosphatidylinositol-4-phosphate, phosphatidylinositol-4,5-diphosphate, and phosphatidylserine. They consisted of approximately 52 mole \% Ca, 32 mole \% organic P, and 15 mole \% P\textasciitilde. During Ca-PL-P extraction from B. matruchotii or its proteolipid-containing calcified lipid extracts, the proteolipid was dissociated and the apoprotein precipitated as fluff at the aqueousorganic solvent interface, thus explaining the failure to detect protein in Ca-PL-P preparations. When the ability of Ca-PL-P complexes and lipid fractions of B. matruchotii to initiate apatite formation from metastable calcium phosphate solution was compared, the yield of hydroxyapatite decreased as follows: Ca-PL-P {$>$} proteolipid acidic phospholipids {$>$} proteolipid {$>$} crude phospholipid {$>$} total lipids {$>$} whole cells.},
  langid = {english}
}

@book{brothwellDiggingBones1981,
  title = {Digging up {{Bones}}: {{The}} Excavation, Treatment and Study of Human Skeletal Remains},
  author = {Brothwell, Don},
  year = {1981},
  edition = {3rd},
  publisher = {{British Museum (Natural History)}},
  address = {{London}}
}

@book{bruinsmaBijdragenTot1872,
  title = {Bijdragen Tot de {{Geneeskundige Plaatsbeschrijving}} van {{Nederland}}},
  author = {Bruinsma, J.J.},
  year = {1872},
  publisher = {{Van Weelden en Mingelen}},
  address = {{s'Gravenhage}}
}

@article{bucchiComparisonsMethods2019,
  title = {Comparisons between Methods for Analyzing Dental Calculus Samples from {{El Mirador}} Cave ({{Sierra}} de {{Atapuerca}}, {{Spain}})},
  author = {Bucchi, Ana and {Burguet-Coca}, Aitor and Exp{\'o}sito, Isabel and Aceituno Bocanegra, Francisco Javier and Lozano, Marina},
  year = {2019},
  month = nov,
  journal = {Archaeological and Anthropological Sciences},
  volume = {11},
  number = {11},
  pages = {6305--6314},
  issn = {1866-9565},
  doi = {10.1007/s12520-019-00919-z},
  abstract = {Microremains entrapped in dental calculus are being used as a source of information to address a number of archeological questions. However, current laboratory procedures may affect the recovery of microremains and this issue has not been thoroughly investigated. This study involved the analysis of dental calculus from five Chalcolithic individuals from El Mirador cave (Sierra de Atapuerca, Spain) from a methodological perspective. Two sample processing protocols published in the archeological literature were used for this purpose, and results were compared to the El Mirador archaeobotanical record published elsewhere. Analyzed as a whole, the microremains found in the dental calculus samples are consistent with a population immersed in a farming economy, although they are not representative of the richness of the archaeobotanical record of the site. Furthermore, the two protocols delivered different results, in terms of the number of microremains identified, the time required for analysis, and associated contamination problems. This data indicates that the method selected may affect the results. We recommend further research using a larger sample set to fully understand how methodological factors affect the preservation and observation of microremains embedded in dental calculus. We also call for a discussion on the role of dental calculus in archeological research.},
  langid = {english}
}

@article{buckberryAuricular2002,
  title = {{Age estimation from the auricular surface of the ilium: A revised method}},
  shorttitle = {{Age estimation from the auricular surface of the ilium}},
  author = {Buckberry, J. L. and Chamberlain, A. T.},
  year = {2002},
  journal = {American Journal of Physical Anthropology},
  volume = {119},
  number = {3},
  pages = {231--239},
  issn = {1096-8644},
  doi = {10.1002/ajpa.10130},
  abstract = {A revised method for estimating adult age at death using the auricular surface of the ilium has been developed. It is based on the existing auricular surface aging method of Lovejoy et al. ([1985] Am. J. Phys. Anthropol. 68:15\textendash 28), but the revised technique is easier to apply, and has low levels of inter- and intraobserver error. The new method records age-related stages for different features of the auricular surface, which are then combined to provide a composite score from which an estimate of age at death is obtained. Blind tests of the method were carried out on a known-age skeletal collection from Christ Church, Spitalfields, London. These tests showed that the dispersion of age at death for a given morphological stage was large, particularly after the first decade of adult life. Statistical analysis showed that the age-related changes in auricular surface are not significantly different for males and females. The scores from the revised method have a slightly higher correlation with age than do the Suchey-Brooks pubic symphysis stages. Considering the higher survival rates of the auricular surface compared with the pubic symphysis, this method promises to be useful for biological anthropology and forensic science. Am J Phys Anthropol 119:231\textendash 239, 2002. \textcopyright{} 2002 Wiley-Liss, Inc.},
  copyright = {Copyright \textcopyright{} 2002 Wiley-Liss, Inc.},
  langid = {french},
  keywords = {auricular surface,forensic anthropology,ilium,palaeodemography,skeletal age at death,Spitalfields},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.10130}
}

@article{buckleyDentalCalculus2014,
  title = {Dental {{Calculus Reveals Unique Insights}} into {{Food Items}}, {{Cooking}} and {{Plant Processing}} in {{Prehistoric Central Sudan}}},
  author = {Buckley, Stephen and Usai, Donatella and Jakob, Tina and Radini, Anita and Hardy, Karen},
  year = {2014},
  month = jul,
  journal = {PLOS ONE},
  volume = {9},
  number = {7},
  pages = {e100808},
  publisher = {{Public Library of Science}},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0100808},
  abstract = {Accessing information on plant consumption before the adoption of agriculture is challenging. However, there is growing evidence for use of locally available wild plants from an increasing number of pre-agrarian sites, suggesting broad ecological knowledge. The extraction of chemical compounds and microfossils from dental calculus removed from ancient teeth offers an entirely new perspective on dietary reconstruction, as it provides empirical results on material that is already in the mouth. Here we present a suite of results from the multi-period Central Sudanese site of Al Khiday. We demonstrate the ingestion in both pre-agricultural and agricultural periods of Cyperus rotundus tubers. This plant is a good source of carbohydrates and has many useful medicinal and aromatic qualities, though today it is considered to be the world's most costly weed. Its ability to inhibit Streptococcus mutans may have contributed to the unexpectedly low level of caries found in the agricultural population. Other evidence extracted from the dental calculus includes smoke inhalation, dry (roasting) and wet (heating in water) cooking, a second plant possibly from the Triticaceae tribe and plant fibres suggestive of raw material preparation through chewing.},
  langid = {english},
  keywords = {Calculus,Microfossils,Neolithic period,Paleobotany,Paleozoology,Starches,Teeth,Tubers}
}

@article{burchamPatternsOral2020,
  title = {Patterns of {{Oral Microbiota Diversity}} in {{Adults}} and {{Children}}: {{A Crowdsourced Population Study}}},
  shorttitle = {Patterns of {{Oral Microbiota Diversity}} in {{Adults}} and {{Children}}},
  author = {Burcham, Zachary M. and Garneau, Nicole L. and Comstock, Sarah S. and Tucker, Robin M. and Knight, Rob and Metcalf, Jessica L. and {Genetics of Taste Lab Citizen Scientists} and Miranda, Anjelica and Reinhart, Brian and Meyers, Dani and Woltkamp, Diane and Boxer, Emma and Hutchens, Joyce and Kim, Kelly and Archer, Mike and McAteer, Mike and Huss, Phil and Defonseka, Ravin and Stahle, Sean and Babu, Sunanda and Nuessle, Tiffany and Schowinsky, Valerie and Covert, Wendy and Truman, Weston and Reusser, Willy},
  year = {2020},
  month = feb,
  journal = {Scientific Reports},
  volume = {10},
  number = {1},
  pages = {2133},
  issn = {2045-2322},
  doi = {10.1038/s41598-020-59016-0},
  abstract = {Abstract                            Oral microbiome dysbiosis has been associated with various local and systemic human diseases such as dental caries, periodontal disease, obesity, and cardiovascular disease. Bacterial composition may be affected by age, oral health, diet, and geography, although information about the natural variation found in the general public is still lacking. In this study, citizen-scientists used a crowdsourcing model to obtain oral bacterial composition data from guests at the Denver Museum of Nature \& Science to determine if previously suspected oral microbiome associations with an individual's demographics, lifestyle, and/or genetics are robust and generalizable enough to be detected within a general population. Consistent with past research, we found bacterial composition to be more diverse in youth microbiomes when compared to adults. Adult oral microbiomes were predominantly impacted by oral health habits, while youth microbiomes were impacted by biological sex and weight status. The oral pathogen               Treponema               was detected more commonly in adults without recent dentist visits and in obese youth. Additionally, oral microbiomes from participants of the same family were more similar to each other than to oral microbiomes from non-related individuals. These results suggest that previously reported oral microbiome associations are observable in a human population containing the natural variation commonly found in the general public. Furthermore, these results support the use of crowdsourced data as a valid methodology to obtain community-based microbiome data.},
  langid = {english}
}

@article{BWA,
  title = {Fast and Accurate Short Read Alignment with {{Burrows}}\textendash{{Wheeler}} Transform},
  author = {Li, Heng and Durbin, Richard},
  year = {2009},
  month = jul,
  journal = {Bioinformatics},
  volume = {25},
  number = {14},
  pages = {1754--1760},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btp324},
  abstract = {Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows\textendash Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is {$\sim$}10\textendash 20\texttimes{} faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.Availability:http://maq.sourceforge.netContact:rd@sanger.ac.uk}
}

@incollection{cabanesPhytolithAnalysis2020,
  title = {Phytolith {{Analysis}} in {{Paleoecology}} and {{Archaeology}}},
  booktitle = {Handbook for the {{Analysis}} of {{Micro-Particles}} in {{Archaeological Samples}}},
  author = {Cabanes, Dan},
  editor = {Henry, Amanda G.},
  year = {2020},
  series = {Interdisciplinary {{Contributions}} to {{Archaeology}}},
  pages = {255--288},
  publisher = {{Springer International Publishing}},
  address = {{Cham}},
  doi = {10.1007/978-3-030-42622-4_11},
  abstract = {Opaline phytoliths are formed when plants accumulate silica at the cellular level. This biomineralization process reproduces, to some extent, the original plant tissue in the form of microscopic particles that are incorporated into soils and sediments when the plant dies and decays. Phytoliths' inorganic nature makes them resistant to most pre- and post-depositional processes, including fire, and they can preserve over long periods in a different range of conditions. However, not all plants produce the same amount of phytoliths and phytolith morphologies can be redundant, impeding the identification of the original plant tissue. Phytolith assemblages can also suffer post-depositional processes that might affect their preservation and bias the interpretation. The present chapter reviews the current knowledge on phytolith formation and cycling, sampling and extraction methods, identification procedures, taphonomy, and phytolith applications in paleoecology and archaeology.},
  isbn = {978-3-030-42622-4},
  langid = {english},
  keywords = {Archaeobotany,Fire,Human–plant interactions,Paleoecology,Phytoliths,Taphonomy}
}

@article{casnaUrbanizationRespiratory2021,
  title = {Urbanization and Respiratory Stress in the {{Northern Low Countries}}: {{A}} Comparative Study of Chronic Maxillary Sinusitis in Two Early Modern Sites from the {{Netherlands}} ({{AD}} 1626\textendash 1866)},
  shorttitle = {Urbanization and Respiratory Stress in the {{Northern Low Countries}}},
  author = {Casna, Maia and Burrell, Carla L. and Schats, Rachel and Hoogland, Menno L. P. and Schrader, Sarah A.},
  year = {2021},
  journal = {International Journal of Osteoarchaeology},
  volume = {31},
  number = {5},
  pages = {891--901},
  issn = {1099-1212},
  doi = {10.1002/oa.3006},
  abstract = {The aim of this study was to investigate the relationship between urbanization and upper respiratory health in two early modern populations from the Netherlands. For this purpose, we analyzed the prevalence of chronic maxillary sinusitis in the adult urban population of Arnhem (n = 83) and in the rural village of Middenbeemster (n = 74). A slightly higher prevalence of chronic maxillary sinusitis was observed in the Arnhem sample (55.4\%) compared with the Middenbeemster sample (51.3\%), and these variations were not statistically significantly different. Although historical sources attest to the fact that life in the postmedieval settlements of Arnhem and Middenbeemster greatly differed, our results suggest that both environments exposed people to certain respiratory hazards. Furthermore, sinusitis prevalence was also investigated in correlation to sex, as urbanization in the Netherlands often involved women in factory work in direct contrast to the traditional domestic role they kept covering in rural environments. No significant differences were observed between males and females, both in an intersite (Arnhem males vs. Middenbeemster males; Arnhem females vs. Middenbeemster females) and in an intrasite (males vs. females at Arnhem; males vs. females at Middenbemster) comparison. As men and women in Arnhem worked on similar tasks, our results confirm that they were both exposed to similar risk factors. In Middenbeemster, where women mainly stayed inside taking care of the house while men worked the fields, the adverse weather conditions and continuous exposure to pollens and allergens may have enhanced men's chances of contracting chronic maxillary sinusitis. This study suggests that urbanization in the early modern Netherlands was in fact not inherently more detrimental than rural living. Future research incorporating a larger sample from other Dutch sites is being considered to better frame the complex etiology of sinusitis within the present understanding of historic regional variation in urbanization patterns.},
  langid = {english},
  keywords = {endoscope,infection,paleopathology,paranasal sinuses,urban development},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/oa.3006}
}

@article{ceriCalgaryBiofilm1999,
  title = {The {{Calgary Biofilm Device}}: {{New Technology}} for {{Rapid Determination}} of {{Antibiotic Susceptibilities}} of {{Bacterial Biofilms}}},
  shorttitle = {The {{Calgary Biofilm Device}}},
  author = {Ceri, H. and Olson, M. E. and Stremick, C. and Read, R. R. and Morck, D. and Buret, A.},
  year = {1999},
  journal = {Journal of Clinical Microbiology},
  volume = {37},
  number = {6},
  pages = {1771--1776},
  issn = {1098-660X, 0095-1137},
  doi = {10.1128/JCM.37.6.1771-1776.1999},
  abstract = {Determination of the MIC, based on the activities of antibiotics against planktonic bacteria, is the standard assay for antibiotic susceptibility testing. Adherent bacterial populations (biofilms) present with an innate lack of antibiotic susceptibility not seen in the same bacteria grown as planktonic populations. The Calgary Biofilm Device (CBD) is described as a new technology for the rapid and reproducible assay of biofilm susceptibilities to antibiotics. The CBD produces 96 equivalent biofilms for the assay of antibiotic susceptibilities by the standard 96-well technology. Biofilm formation was followed by quantitative microbiology and scanning electron microscopy. Susceptibility to a standard group of antibiotics was determined for National Committee for Clinical Laboratory Standards (NCCLS) reference strains:               Escherichia coli               ATCC 25922,               Pseudomonas aeruginosa               ATCC 27853, and               Staphylococcus aureus               ATCC 29213. Growth curves demonstrated that biofilms of a predetermined size could be formed on the CBD at specific time points and, furthermore, that no significant difference (               P               {$>$} 0.1) was seen between biofilms formed on each of the 96 pegs. The antibiotic susceptibilities for planktonic populations obtained by the NCCLS method or from the CBD were similar. Minimal biofilm eradication concentrations, derived by using the CBD, demonstrated that for biofilms of the same organisms, 100 to 1,000 times the concentration of a certain antibiotic were often required for the antibiotic to be effective, while other antibiotics were found to be effective at the MICs. The CBD offers a new technology for the rational selection of antibiotics effective against microbial biofilms and for the screening of new effective antibiotic compounds.},
  langid = {english},
  keywords = {notion}
}

@article{chambersInsteadPlaying2014,
  title = {Instead of "Playing the Game" It Is Time to Change the Rules: {{Registered Reports}} at {{AIMS Neuroscience}} and Beyond},
  shorttitle = {Instead of "Playing the Game" It Is Time to Change the Rules},
  author = {Chambers, Christopher D. and Feredoes, Eva and Muthukumaraswamy, Suresh Daniel and Etchells, Peter},
  year = {2014},
  month = may,
  journal = {AIMS Neuroscience},
  volume = {1},
  number = {1},
  pages = {4--17},
  publisher = {{AIMS Press}},
  doi = {10.3934/Neuroscience.2014.1.4},
  abstract = {The last ten years have witnessed increasing awareness of questionable research practices (QRPs) in the life sciences [1,2], including p-hacking [3], HARKing [4], lack of replication [5], publication bias [6], low statistical power [7] and lack of data sharing ([8]; see Figure 1). Concerns about such behaviours have been raised repeatedly for over half a century [9\textendash 11] but the incentive structure of academia has not changed to address them. Despite the complex motivations that drive academia, many QRPs stem from the simple fact that the incentives which offer success to individual scientists conflict with what is best for science [12]. On the one hand are a set of gold standards that centuries of the scientific method have proven to be crucial for discovery: rigour, reproducibility, and transparency. On the other hand are a set of opposing principles born out of the academic career model: the drive to produce novel and striking results, the importance of confirming prior expectations, and the need to protect research interests from competitors. Within a culture that pressures scientists to produce rather than discover, the outcome is a biased and impoverished science in which most published results are either unconfirmed genuine discoveries or unchallenged fallacies [13]. This observation implies no moral judgement of scientists, who are as much victims of this system as they are perpetrators.},
  copyright = {cc\_by},
  langid = {english}
}

@article{charlierSEMCalculus2010,
  title = {The Microscopic (Optical and {{SEM}}) Examination of Dental Calculus Deposits ({{DCD}}). {{Potential}} Interest in Forensic Anthropology of a Bio-Archaeological Method},
  author = {Charlier, Philippe and {Huynh-Charlier}, Isabelle and Munoz, Olivia and Billard, Michel and Brun, Luc and de la Grandmaison, Geoffroy Lorin},
  year = {2010},
  month = jul,
  journal = {Legal Medicine},
  volume = {12},
  number = {4},
  pages = {163--171},
  issn = {1344-6223},
  doi = {10.1016/j.legalmed.2010.03.003},
  abstract = {This article describes the potential interest in forensic anthropology of the microscopic analysis of dental calculus deposits (DCD), a calcified residue frequently found on the surface of teeth. Its sampling and analysis seem straightforward and relatively reproducible. Samples came from archaeological material (KHB-1 Ra's al-Khabbah and RH-5 Ra{${'}$}s al-Hamra, two Prehistoric graveyards located in the Sultanate of Oman, dated between the 5th and 4th millennium B.C.; Montenzio Vecchia, an Etruscan-Celtic necropolis from the north of Italy, dated between the 5th and 3rd century B.C.; body rests of Agn\`es Sorel, French royal mistress died in 1450 A.D.; skeleton of Pierre Hazard, French royal notary from the 15th century A.D.). Samples were studies by direct optical microscope (OM) or scanning electron microscopy (SEM). Many cytological, histological and elemental analyses were possible, producing precious data for the identification of these remains, the reconstitution of their alimentation and occupational habits, and propositions for manner of death.},
  langid = {english},
  keywords = {Bio-archaeology,Circumstances of death,Dental calculus,Forensic anthropology,Identification,Optical microscopy,Pathological status,SEM}
}

@article{chenCa2Dependent2001,
  title = {Ca2+-dependent and {{Ca2}}+-independent Excretion Modes of Salicylic Acid in Tobacco Cell Suspension Culture},
  author = {Chen, Hsien-Jung and Hou, Wen-Chi and Ku{\'c}, Joseph and Lin, Yaw-Huei},
  year = {2001},
  month = jun,
  journal = {Journal of Experimental Botany},
  volume = {52},
  number = {359},
  pages = {1219--1226},
  issn = {0022-0957},
  doi = {10.1093/jexbot/52.359.1219},
  abstract = {14C-salicylic acid (SA) was used to monitor SA metabolism and its regulation in tobacco cell suspension culture. Two SA concentrations (20\,{$\mu$}M and 200\,{$\mu$}M) were used for comparison. SA was quickly taken up in both treatments, and the 200\,{$\mu$}M-treated cells absorbed approximately 15 times that of 20\,{$\mu$}M-treated cells within 5\,min. More than 85\% and 50\% of the absorbed SA were excreted in free form to the culture medium within 5\,h from cells treated with 200\,{$\mu$}M and 20\,{$\mu$}M SA, respectively. SA excretion was significantly inhibited by EGTA and the inhibition could be reversed by the addition of exogenous Ca2+to the culture medium in the 200\,{$\mu$}M SA treatment. However, EGTA had little or no effect on SA excretion in the 20\,{$\mu$}M SA treatment. The data suggest that tobacco suspension-cultured cells may contain both Ca2+-dependent and Ca2+-independent pathways for SA excretion. Reduced glutathione (an active oxygen species scavenger), staurosporine (a protein kinase inhibitor), and cycloheximide (an inhibitor of de novo protein synthesis) also blocked intracellular SA excretion to the culture medium in the 200\,{$\mu$}M but not in the 20\,{$\mu$}M SA treatment. These data support the existence of alternative SA excretion pathways in tobacco suspension-cultured cells. Tobacco cells may use both Ca2+-dependent and Ca2+-independent excretion pathways to cope with different intracellular SA status, and the pathway influenced by EGTA, reduced glutathione, staurosporine, and cycloheximide is activated by SA at 200\,{$\mu$}M, but not at 20\,{$\mu$}M.}
}

@article{chenSpecificGenes1999,
  title = {The {{Specific Genes}} for {{Lantibiotic Mutacin II Biosynthesis}} in {{Streptococcus}} Mutans {{T8 Are Clustered}} and {{Can Be}}  {{Transferred En Bloc}}},
  author = {Chen, Ping and Qi, FengXia and Novak, Jan and Caufield, Page W.},
  year = {1999},
  month = mar,
  journal = {Applied and Environmental Microbiology},
  volume = {65},
  number = {3},
  pages = {1356--1360},
  issn = {0099-2240},
  abstract = {Mutacin II is a ribosomally synthesized peptide lantibiotic produced by group II Streptococcus mutans. DNA sequencing has revealed that the mutacin II biosynthetic gene cluster consists of seven specific open reading frames: a regulator (mutR), the prepromutacin structural gene (mutA), a modifying protein (mutM), an ABC transporter (mutT), and an immunity cluster (mutFEG). Transformations of a non-mutacin-producing strain, S. mutans UA159, and a mutacin I-producing strain, S. mutans UA140, with chromosomal DNA from S. mutans T8 with an aphIII marker inserted upstream of the mutacin II structural gene yielded transformants producing mutacin II and mutacins I and II, respectively.},
  pmcid = {PMC91190},
  pmid = {10049909}
}

@article{chenStarchGrains2021,
  title = {Starch Grains from Human Teeth Reveal the Plant Consumption of Proto-{{Shang}} People (c. 2000\textendash 1600 {{BC}}) from {{Nancheng}} Site, {{Hebei}}, {{China}}},
  author = {Chen, Tao and Hou, Liangliang and Jiang, Hongen and Wu, Yan and Henry, Amanda G.},
  year = {2021},
  month = aug,
  journal = {Archaeological and Anthropological Sciences},
  volume = {13},
  number = {9},
  pages = {153},
  issn = {1866-9565},
  doi = {10.1007/s12520-021-01416-y},
  abstract = {The founding processes of the first state of ancient China with a known written record, the Shang dynasty (3600\textendash 3046~cal BP), have been poorly understood. Recent discoveries of a host of archaeological sites dating to the proto-Shang culture (4000\textendash 3600~cal BP) have helped elucidate the transition to the Shang culture. Nevertheless, there are few investigations about the mode of subsistence and economy of the proto-Shang culture, and how this might have shaped the transition to statehood. In this present study, we analyzed the starch grains preserved in dental calculus and teeth surfaces from 16 samples from the site of Nancheng in order to gain a better understanding of the subsistence strategy and plant consumption of proto-Shang people. We also performed experiments to test how different cooking methods may lead to size changes in the starches of four Poaceae plants, in order to identify the processing methods used by the proto-Shang people. The results indicate that Triticum aestivum, Coix lacryma-jobi, Setaria italica and some yet-unidentified roots and tubers were consumed by these individuals. These data indicate a broader spectrum of plant consumption than that seen by previous archaeobotanical and stable isotope analyses. Such a broad spectrum of plant consumption provided a substantial economic base for proto-Shang people and might be one of the factors supporting the subsequent development of the Shang state culture.},
  langid = {english}
}

@article{chinCaffeineContent2008,
  title = {Caffeine {{Content}} of {{Brewed Teas}}},
  author = {Chin, Jenna M. and Merves, Michele L. and Goldberger, Bruce A. and {Sampson-Cone}, Angela and Cone, Edward J.},
  year = {2008},
  month = oct,
  journal = {Journal of Analytical Toxicology},
  volume = {32},
  number = {8},
  pages = {702--704},
  issn = {0146-4760},
  doi = {10.1093/jat/32.8.702},
  abstract = {Caffeine is the world's most popular drug and can be found in many beverages including tea. It is a psychostimulant that is widely used to enhance alertness and improve performance. This study was conducted to determine the concentration of caffeine in 20 assorted commercial tea products. The teas were brewed under a variety of conditions including different serving sizes and steep-times. Caffeine was isolated from the teas with liquid-liquid extraction and quantitated by gas chromatography with nitrogen-phosphorus detection. Caffeine concentrations in white, green, and black teas ranged from 14 to 61 mg per serving (6 or 8 oz) with no observable trend in caffeine concentration due to the variety of tea. The decaffeinated teas contained less than 12 mg of caffeine per serving, and caffeine was not detected in the herbal tea varieties. In most instances, the 6- and 8-oz serving sizes contained similar caffeine concentrations per ounce, but the steep-time affected the caffeine concentration of the tea. These findings indicate that most brewed teas contain less caffeine per serving than brewed coffee.}
}

@article{chovanecOpiumMasses2012,
  title = {Opium for the {{Masses}}},
  author = {Chovanec, Zuzana and Rafferty, Sean and Swiny, Stuart},
  year = {2012},
  month = mar,
  journal = {Ethnoarchaeology},
  volume = {4},
  number = {1},
  pages = {5--36},
  publisher = {{Routledge}},
  issn = {1944-2890},
  doi = {10.1179/eth.2012.4.1.5},
  abstract = {The opium poppy, Papaver somniferum L., constitutes one of the most widely exploited psychoactive substances in human history. Hitherto, the investigation of the antiquity of the opium poppy's use by humans for narcotic purposes has predominantly relied on implicit archaeological data that suggests, but does not demonstrate such a use. In acknowledgment of the various geochemical processes involved in the creation, preservation, and decomposition of residues in archaeological contexts, an experimental archaeological approach was utilized to model the degradation of opium alkaloids. Procedures of the controlled creation, artificial aging, and the molecular characterization by gas chromatography/mass spectrometry of opium residues are presented. Experimental results and implications are also discussed.},
  annotation = {\_eprint: https://doi.org/10.1179/eth.2012.4.1.5}
}

@article{ciochonOpalPhytoliths1990,
  title = {Opal Phytoliths Found on the Teeth of the Extinct Ape {{Gigantopithecus}} Blacki: Implications for Paleodietary Studies.},
  shorttitle = {Opal Phytoliths Found on the Teeth of the Extinct Ape {{Gigantopithecus}} Blacki},
  author = {Ciochon, R L and Piperno, D R and Thompson, R G},
  year = {1990},
  month = oct,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {87},
  number = {20},
  pages = {8120--8124},
  publisher = {{Proceedings of the National Academy of Sciences}},
  doi = {10.1073/pnas.87.20.8120}
}

@book{clarkeCannabisEvolution2013,
  title = {Cannabis : {{Evolution}} and {{Ethnobotany}}},
  author = {Clarke, Robert},
  year = {2013},
  publisher = {{University of California Press}},
  address = {{[N.p.]}},
  abstract = {Cannabis: Evolution and Ethnobotany is a comprehensive, interdisciplinary exploration of the natural origins and early evolution of this famous plant, highlighting its historic role in the development of human societies. Cannabis has long been prized for the strong and durable fiber in its stalks, its edible and oil-rich seeds, and the psychoactive and medicinal compounds produced by its female flowers. The culturally valuable and often irreplaceable goods derived from cannabis deeply influenced the commercial, medical, ritual, and religious practices of cultures throughout the ages, and human desire for these commodities directed the evolution of the plant toward its contemporary varieties. As interest in cannabis grows and public debate over its many uses rises, this book will help us understand why humanity continues to rely on this plant and adapts it to suit our needs.},
  isbn = {978-0-520-27048-0 978-0-520-29248-2 978-0-520-95457-1},
  langid = {english},
  keywords = {Cannabis,Cannabis--Evolution,Cannabis--Utilization,Human-plant relationships,SCIENCE / Life Sciences / Botany}
}

@article{cogoVitroEvaluation2008,
  title = {In Vitro Evaluation of the Effect of Nicotine, Cotinine, and Caffeine on Oral Microorganisms},
  author = {Cogo, Karina and Montan, Michelle Franz and Bergamaschi, Cristiane de C{\'a}ssia and D. Andrade, Eduardo and Rosalen, Pedro Luiz and Groppo, Francisco Carlos},
  year = {2008},
  month = jun,
  journal = {Canadian Journal of Microbiology},
  volume = {54},
  number = {6},
  pages = {501--508},
  publisher = {{NRC Research Press}},
  issn = {0008-4166},
  doi = {10.1139/W08-032},
  abstract = {The aim of this in vitro study was to evaluate the effects of nicotine, cotinine, and caffeine on the viability of some oral bacterial species. It also evaluated the ability of these bacteria to metabolize those substances. Single-species biofilms of Streptococcus gordonii, Porphyromonas gingivalis, or Fusobacterium nucleatum and dual-species biofilms of S.~gordonii~\textendash{} F. nucleatum and F. nucleatum~\textendash{} P.~gingivalis were grown on hydroxyapatite discs. Seven species were studied as planktonic cells, including Streptococcus oralis, Streptococcus mitis, Propionibacterium acnes, Actinomyces naeslundii, and the species mentioned above. The viability of planktonic cells and biofilms was analyzed by susceptibility tests and time-kill assays, respectively, against different concentrations of nicotine, cotinine, and caffeine. High-performance liquid chromatography was performed to quantify nicotine, cotinine, and caffeine concentrations in the culture media after the assays. Susceptibility tests and viability assays showed that nicotine, cotinine, and caffeine cannot reduce or stimulate bacterial growth. High-performance liquid chromatography results showed that nicotine, cotinine, and caffeine concentrations were not altered after bacteria exposure. These findings indicate that nicotine, cotinine, and caffeine, in the concentrations used, cannot affect significantly the growth of these oral bacterial strains. Moreover, these species do not seem to metabolize these substances.},
  keywords = {notion}
}

@article{collinsHomelessDental2007,
  title = {Homeless in {{North}} and {{West Belfast}}: An Oral Health Needs Assessment},
  shorttitle = {Homeless in {{North}} and {{West Belfast}}},
  author = {Collins, J. and Freeman, R.},
  year = {2007},
  month = jun,
  journal = {British Dental Journal},
  volume = {202},
  number = {12},
  pages = {E31-E31},
  publisher = {{Nature Publishing Group}},
  issn = {1476-5373},
  doi = {10.1038/bdj.2007.473},
  abstract = {This is the first assessment of the oral health needs of single homeless adults in North and West Belfast.The study population had greater experience of dental caries and periodontal disease compared with adults in Northern Ireland (NI) who took part in the 1998 Adult Dental Health Survey.The widespread use of smoking and use and abuse of alcohol marked the study population as a high-risk group for oral cancer, with the increased risk calculated as 95 times greater than the NI population as a whole.Homeless people are not a homogeneous population, therefore social exclusion and psycho-social functioning should be considered when planning appropriate oral healthcare services for this diverse client group.},
  copyright = {2007 Nature Publishing Group},
  langid = {english},
  keywords = {Dentistry}
}

@article{coneInterpretationOral2007,
  title = {Interpretation of {{Oral Fluid Tests}} for {{Drugs}} of {{Abuse}}},
  author = {Cone, Edward J. and Huestis, Marilyn A.},
  year = {2007},
  month = mar,
  journal = {Annals of the New York Academy of Sciences},
  volume = {1098},
  pages = {51--103},
  issn = {0077-8923},
  doi = {10.1196/annals.1384.037},
  abstract = {Oral fluid testing for drugs of abuse offers significant advantages over urine as a test matrix. Collection can be performed under direct observation with reduced risk of adulteration and substitution. Drugs generally appear in oral fluid by passive diffusion from blood, but also may be deposited in the oral cavity during oral, smoked, and intranasal administration. Drug metabolites also can be detected in oral fluid. Unlike urine testing, there may be a close correspondence between drug and metabolite concentrations in oral fluid and in blood. Interpretation of oral fluid results for drugs of abuse should be an iterative process whereby one considers the test results in the context of program requirements and a broad scientific knowledge of the many factors involved in determining test outcome. This review delineates many of the chemical and metabolic processes involved in the disposition of drugs and metabolites in oral fluid that are important to the appropriate interpretation of oral fluid tests. Chemical, metabolic, kinetic, and analytic parameters are summarized for selected drugs of abuse, and general guidelines are offered for understanding the significance of oral fluid tests.},
  pmcid = {PMC2700061},
  pmid = {17332074}
}

@article{coneSalivaTesting1993,
  title = {Saliva {{Testing}} for {{Drugs}} of {{Abuse}}},
  author = {Cone, Edward J.},
  year = {1993},
  journal = {Annals of the New York Academy of Sciences},
  volume = {694},
  number = {1},
  pages = {91--127},
  issn = {1749-6632},
  doi = {10.1111/j.1749-6632.1993.tb18346.x}
}

@article{cooperAncientDNA2000,
  title = {Ancient {{DNA}}: {{Do}} It Right or {{Not}} at All},
  shorttitle = {Ancient {{DNA}}},
  author = {Cooper, Alan and Poinar, Hendrik N.},
  year = {2000},
  journal = {Science},
  volume = {289},
  doi = {10.1126/science.289.5482.1139b},
  langid = {english}
}

@article{cornejo-ramirezStructuralCharacteristics2018,
  title = {The Structural Characteristics of Starches and Their Functional Properties},
  author = {{Cornejo-Ram{\'i}rez}, Yaeel Isbeth and {Mart{\'i}nez-Cruz}, Oliviert and {Del Toro-S{\'a}nchez}, Carmen Lizette and {Wong-Corral}, Francisco Javier and {Borboa-Flores}, Jes{\'u}s and {Cinco-Moroyoqui}, Francisco Javier},
  year = {2018},
  month = jan,
  journal = {CyTA - Journal of Food},
  volume = {16},
  number = {1},
  pages = {1003--1017},
  publisher = {{Taylor \& Francis}},
  issn = {1947-6337},
  doi = {10.1080/19476337.2018.1518343},
  abstract = {Starch is composed of amylose and amylopectin and deposited as granules of different sizes and shapes with semi-crystalline and amorphous concentric layers that show the `maltese cross'. Starches from different sources show variable chemical composition as well as the structure of their components that are involved in thermal properties. Amylose, lipids, phosphorylated residues and long lateral chain amylopectin interact among them avoiding water uptake. In contrast, high amylopectin contents, especially with short lateral chains, allow hydration via hydrogen bonds to form gels with the tendency to retrogradation. Smaller starch granules have a larger superficial area, surface pores, and channels that enhance water uptake. High hydration increases the swelling, viscosity, and gelatinization ability of starch granules. The knowledge of those properties allows the selection of the most appropriate starch for a specific end use. This review discusses the relationship between the physicochemical composition of the starch and their rheological properties.},
  keywords = {chemical composition,composición química,cristalinidad,crystallinity,Estructura del almidón,propiedades térmicas,reología del almidón,retrogradación,retrogradation,starch rheology,Starch structure,thermal properties},
  annotation = {\_eprint: https://doi.org/10.1080/19476337.2018.1518343}
}

@article{costertonBacterialBiofilms1987,
  title = {Bacterial {{Biofilms}} in {{Nature}} and {{Disease}}},
  author = {Costerton, J. William and Cheng, K J and Geesey, G G and Ladd, T I and Nickel, J C and Dasgupta, M and Marrie, T J},
  year = {1987},
  month = oct,
  journal = {Annual Review of Microbiology},
  volume = {41},
  number = {1},
  pages = {435--464},
  issn = {0066-4227, 1545-3251},
  doi = {10.1146/annurev.mi.41.100187.002251},
  langid = {english}
}

@article{costertonMicrobialBiofilms1995,
  title = {Microbial {{Biofilms}}},
  author = {Costerton, J. William and Lewandowski, Zbigniew and Caldwell, Douglas E. and Korber, Darren R. and {Lappin-Scott}, Hilary M.},
  year = {1995},
  month = oct,
  journal = {Annual Review of Microbiology},
  volume = {49},
  number = {1},
  pages = {711--745},
  issn = {0066-4227, 1545-3251},
  doi = {10.1146/annurev.mi.49.100195.003431},
  langid = {english}
}

@article{crowtherDocumentingContamination2014,
  title = {Documenting Contamination in Ancient Starch Laboratories},
  author = {Crowther, Alison and Haslam, Michael and Oakden, Nikki and Walde, Dale and Mercader, Julio},
  year = {2014},
  journal = {Journal of Archaeological Science},
  volume = {49},
  pages = {90--104},
  issn = {03054403},
  doi = {10.1016/j.jas.2014.04.023}
}

@incollection{cummingsMayanCalculus1997,
  title = {A Phytolith and Starch Record of Food and Grit in {{Mayan}} Human Tooth Tartar},
  booktitle = {The {{State-of-the-Art}} of {{Phytoliths}} in {{Soils}} and {{Plants}}},
  author = {Scott Cummings, L. and Magennis, A.},
  editor = {Pinilla, A. and {Juan-Tresserras}, J. and Machado, M.J.},
  year = {1997},
  publisher = {{CSIC Press}},
  address = {{Spain}},
  googlebooks = {j66CDVfVhwEC},
  isbn = {978-84-00-07674-0},
  langid = {english},
  keywords = {calculus; plant microremains}
}

@article{curtisRoleMicrobiota2020,
  title = {The Role of the Microbiota in Periodontal Disease},
  author = {Curtis, Mike A. and Diaz, Patricia I. and Dyke, Thomas E. Van},
  year = {2020},
  journal = {Periodontology 2000},
  volume = {83},
  number = {1},
  pages = {14--25},
  issn = {1600-0757},
  doi = {10.1111/prd.12296},
  abstract = {The last decade has witnessed unparalleled advances in our understanding of the complexity of the oral microbiome and the compositional changes that occur in subgingival biofilms in the transition from health to gingivitis and to destructive periodontal disease. The traditional view, which has held sway for the last 2 decades, that disease is characterized by the outgrowth of a consortium, or consortia, of a limited number of potentially pathogenic organisms, has given way to an alternative paradigm. In this new view, the microbiological changes associated with disease represent whole-scale alterations to the overall microbial population structure and to the functional properties of the entire community. Thus, and in common with other microbially mediated diseases of the gastrointestinal tract, the normally balanced, symbiotic, and generally benign commensal microbiome of the tooth-associated biofilm undergoes dysbiosis to a potentially deleterious microbiota. Coincident with progress in defining the microbiology of these diseases, there have been equally important advances in our understanding of the inflammatory systems of the periodontal tissues, their control, and how inflammation may contribute both to the development of dysbiosis and, in a deregulated state, the destructive disease process. One can therefore speculate that the inflammatory response and the periodontal microbiome are in a bidirectional balance in oral health and a bidirectional imbalance in periodontitis. However, despite these clear insights into both sides of the host/microbe balance in periodontal disease, there remain several unresolved issues concerning the role of the microbiota in disease. These include, but are not limited to, the factors which determine progression from gingivitis to periodontitis in a proportion of the population, whether dysbiosis causes disease or results from disease, and the molecular details of the microbial stimulus responsible for driving the destructive inflammatory response. Further progress in resolving these issues may provide significant benefit to diagnosis, treatment, and prevention.},
  langid = {english},
  keywords = {destructive periodontal disease,dysbiosis,gingivitis,inflammatory response,periodontal microbiota},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/prd.12296}
}

@misc{daaDentalAnthropology,
  title = {Dental {{Anthropology Association}}},
  journal = {Dental Anthropology Association},
  abstract = {Dental Anthropology Association},
  howpublished = {http://www.dentalanthropology.org},
  langid = {american}
}

@article{dahlenMicrobiologicalStudy2010,
  title = {A Microbiological Study in Relation to the Presence of Caries and Calculus},
  author = {Dahl{\'e}n, Gunnar and Konradsson, Karolina and Eriksson, Sophia and Teanpaisan, Rawee and Piwat, Supatcharin and Carl{\'e}n, Anette},
  year = {2010},
  month = jul,
  journal = {Acta Odontologica Scandinavica},
  volume = {68},
  number = {4},
  pages = {199--206},
  publisher = {{Taylor \& Francis}},
  issn = {0001-6357},
  doi = {10.3109/00016351003745514},
  abstract = {Objective. To examine whether oral microflora in individuals with caries differs from that of individuals with calculus in Thai adolescents with poor oral hygiene. Material and methods. One hundred 13-year-old schoolchildren from Southern Thailand were examined for the presence of caries, calculus and plaque and saliva pH was also determined. Saliva samples were analysed by culture and approximal supragingival plaque samples were analysed with the DNA\textendash DNA hybridization method (`checkerboard'). Results. Among the 100 children, mean DMFS was 3.43 [standard deviation (SD) 2.82] and 90\% had calculus. The correlation between DMFS and the calculus index was 0.064. A total of 36 children were caries-free and 56 had calculus including teeth other than those in the lower anterior region (calculus score {$\geq$}3). A total of 23 caries-free children with a high calculus score ({$\geq$}3) were compared with 22 children with the highest DMFS [mean 11.19 (SD 5.58)] and a calculus score {$<$} 3. No significant difference was obtained for saliva and plaque pH. The salivary levels of mutans Streptococci and Lactobacilli were low. Significantly more children in the caries group had high levels of glycolytic Prevotella nigrescens and Filifactor alocis in plaque compared with the calculus group. Calculus cases had a significantly higher total viable count in saliva. Conclusions. There was no inverse correlation between the presence of caries and calculus at a population level and a high calculus score only marginally reduced the individual likelihood of having caries. Several glycolytic bacteria were related to caries, while no specific bacteria could be related to calculus formation. Calculus seemed to be more closely related to poor oral hygiene.},
  keywords = {Calculus,caries,oral microbiota},
  annotation = {\_eprint: https://doi.org/10.3109/00016351003745514}
}

@article{damenSilicicAcid1989,
  title = {The {{Effect}} of {{Silicic Acid}} on {{Calcium Phosphate Precipitation}}},
  author = {Damen, J.J.M. and Ten Cate, J.M.},
  year = {1989},
  month = sep,
  journal = {Journal of Dental Research},
  volume = {68},
  number = {9},
  pages = {1355--1359},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/00220345890680091301},
  abstract = {So that a possible involvement in the mineralization of dental plaque could be investigated, the effects of silicic acid on calcium phosphate precipitation were assessed in vitro. By measuring the decrease in Ca2+ concentration (by means of ion-selective electrodes), we determined both spontaneous precipitation and seeded crystal growth from solutions that contained 1 mmol/L calcium, 7.5 mmol/L phosphate, 50 mmol/L Hepes pH 7.2, and various amounts of silicic acid. Polymerized silicic acid, but not its monomer, was found both to cause a 60\% reduction in the lag period that precedes spontaneous precipitation and to enhance the growth rate of seeded hydroxyapatite crystals. Silica suspensions showed effects similar to those of polysilicic acid. In all cases, the precipitated material was found to be hydroxyapatite. Whereas seeded brushite crystals grew slowly without silicic acid, hydroxyapatite was the only mineral detected after crystal growth in the presence of silicic acid. Apparently, polysilicic acid acted as a substrate for hydroxyapatite nucleation, inducing secondary nuclei on both hydroxyapatite and brushite crystals. The finding that polysilicic acid could overcome part of the inhibitory effect of a phosphoprotein on calcium phosphate precipitation gave additional support for the idea that polysilicic acid and silica may promote the formation of dental calculus.},
  langid = {english}
}

@article{dawBacteriocinsNature1996,
  title = {Bacteriocins: Nature, Function and Structure},
  shorttitle = {Bacteriocins},
  author = {Daw, M. A. and Falkiner, F. R.},
  year = {1996},
  month = dec,
  journal = {Micron (Oxford, England: 1993)},
  volume = {27},
  number = {6},
  pages = {467--479},
  issn = {0968-4328},
  doi = {10.1016/s0968-4328(96)00028-5},
  abstract = {Bacteriocins are extracellular substances produced by different types of bacteria, including both Gram positive and Gram negative species. They can be produced spontaneously or induced by certain chemicals such as mitomycin C. They are biologically one of the important substances, and have been found to be useful in membrane studies and also in typing pathogenic microorganisms causing serious nosocomial infections. Bacteriocins are a heterogeneous group of particles with different morphological and biochemical entities. They range from a simple protein to a high molecular weight complex: the active moiety of each molecule in all cases seems to be protein in nature. The genetic determinants of most of the bacteriocins are located on the plasmids, apart from few which are chromosomally encoded. These bactericidal particles are species specific. They exert their lethal activity through adsorption to specific receptors located on the external surface of sensitive bacteria, followed by metabolic, biological and morphological changes resulting in the killing of such bacteria. This review summarises the classification, biochemical nature, morphology and mode of action of bacteriocins as well as their genetic determinants and the microbiological relevance of these bactericidal agents.},
  langid = {english},
  pmid = {9168627},
  keywords = {Bacteria,Bacteriocins,Enterobacter cloacae,Lysogeny,Microscopy; Electron,Molecular Structure,Pseudomonas aeruginosa}
}

@article{dawesCircadianRhythms1972,
  title = {Circadian Rhythms in Human Salivary Flow Rate and Composition},
  author = {Dawes, C.},
  year = {1972},
  month = feb,
  journal = {The Journal of Physiology},
  volume = {220},
  number = {3},
  pages = {529--545},
  issn = {0022-3751},
  abstract = {1. Unstimulated whole saliva and parotid saliva stimulated at a constant flow rate of 1{$\cdot$}0 ml./min were collected from eight subjects at about 07.00, 11.00, 14.00, 17.00 and 22.00 hr and oral temperature was recorded several times daily for time spans of between 4 and 26 days. A least-squares cosine wave was fitted to the data to test for the presence and characteristics of circadian rhythms., 2. Estimates of mean level, amplitude, acrophase and period were obtained for different components and the results were subjected to cosinor analysis., 3. Unstimulated whole saliva showed significant circadian rhythms in flow rate and in the concentrations of sodium and chloride but not in protein, potassium, calcium, phosphate or urea., 4. Stimulated parotid saliva showed significant circadian rhythms in the concentrations of protein, sodium, potassium, calcium and chloride but not in phosphate or urea, 5. Oral temperature showed a circadian rhythm which, like the salivary rhythms, was of a 24.0 hr periodicity.},
  pmcid = {PMC1331668},
  pmid = {5016036}
}

@article{dawesEffectsDiet1970,
  title = {Effects of {{Diet}} on {{Salivary Secretion}} and {{Composition}}},
  author = {Dawes, C.},
  year = {1970},
  journal = {Journal of Dental Research},
  volume = {49},
  pages = {1263--1272}
}

@article{delafuenteDNAHuman2013,
  title = {{{DNA From Human Ancient Bacteria}}: {{A}} Novel Source of Genetic Evidence from Archaeological Dental Calculus},
  shorttitle = {{{DNA FROM HUMAN ANCIENT BACTERIA}}},
  author = {De La Fuente, C. and Flores, S. and Moraga, M.},
  year = {2013},
  month = aug,
  journal = {Archaeometry},
  volume = {55},
  number = {4},
  pages = {767--778},
  issn = {0003813X},
  doi = {10.1111/j.1475-4754.2012.00707.x},
  abstract = {We report a molecular methodology to obtain and analyse ancient bacterial DNA from archaeological dental calculus. Recent and archaeological DNA samples, as old as 4000 BP, were successfully extracted and amplified with species-specific PCR primers. We propose this approach in order to: detect the presence of specific bacterial species infecting past human populations; compare the composition of ancient oral microbiomes among human populations; and analyse the genetic variability and covariation of bacteria and human host populations. Genomic analysis of bacteria from dental calculus is a promising source of evidence for palaeopathological and micro-evolutionary studies, focused either on micro-organisms or their human hosts.},
  langid = {english}
}

@article{delaneyMoreWhat2023,
  title = {More than What We Eat: {{Investigating}} an Alternative Pathway for Intact Starch Granules in Dental Calculus Using {{Experimental Archaeology}}},
  shorttitle = {More than What We Eat},
  author = {Delaney, Sarah and Alexander, Michelle and Radini, Anita},
  year = {2023},
  month = apr,
  journal = {Quaternary International},
  series = {From {{Food}} to {{Environments}}: {{Advances}} in {{Ancient Human Dental Calculus Research}}},
  volume = {653--654},
  pages = {19--32},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2022.03.004},
  abstract = {Starch granules and other plant tissues are commonly found as part of the microdebris assemblage analysed within dental calculus. These are often interpreted as evidence of past diets. However, many of the starch granules extracted from dental calculus are intact, and do not show evidence of alterations as a result of being processed for consumption. This research examines if plant material can accidently enter the mouth while being processed for a meal, with a focus on starch granules. Grinding experiments were performed on three types of cereal grains (wheat, oat and millet). We compare the presence of intact and altered starch granules in mouthwash samples (in place of dental calculus samples) from individuals involved in grinding and also from samples in the environment surrounding the grinding activity. This experiment is a proof of concept aimed to expand experimental research in the field of dental calculus analysis and to encourage the exploration of pathways beyond direct and deliberate consumption.},
  langid = {english},
  keywords = {Ancient starch,Dental calculus,Food processing,Medieval archaeology}
}

@article{dibdinDiffusionSugars1981,
  title = {Diffusion of Sugars and Carboxylic Acids through Human Dental Plaque in Vitro},
  author = {Dibdin, G. H.},
  year = {1981},
  month = jan,
  journal = {Archives of Oral Biology},
  volume = {26},
  number = {6},
  pages = {515--523},
  issn = {0003-9969},
  doi = {10.1016/0003-9969(81)90010-8},
  abstract = {Diffusion through plaque was measured with an apparatus consisting of 3 identical diffusion cells contained in an aluminium alloy block thermostatically controlled at 35 \textdegree C. In two of the cells, measurements were made of diffusion through a composite membrane consisting of 18 h dental plaque contained between bacteriological grade filters and support screens. In the third cell, diffusion occurred through a reference membrane from which the bulk of the plaque was absent. Subtraction of the diffusion resistance of this reference membrane allowed calculation of apparent tracer diffusion coefficients in the bulk of the plaque alone. Diffusion of 14C-labelled sugars and carboxylic acids was compared with that of tritiated water using dual-channel liquid scintillation counting. The diffusion coefficient of tritiated water in the plaque samples varied from 0.81 to 1.02 \texttimes{} 10-9 m2s-1 depending on the wet wt used, with coefficients of variation of \textasciitilde{} 15 per cent. This is between 14 and 13 of the value in aqueous solution. Diffusion coefficients relative to that of tritiated water in plaque ranged from 0.154 {$\pm$} 0.014 for sucrose to 0.363 {$\pm$} 0.029 for acetate. Permselectivity was low, and diffusion coefficients of I he test molecules were all between 14 and 15 of their values in free aqueous solution.},
  langid = {english}
}

@article{dibdinOralUrea1998,
  title = {A {{Mathematical Model}} of the {{Influence}} of {{Salivary Urea}} on the {{pH}} of {{Fasted Dental Plaque}} and on the {{Changes Occurring}} during a {{Cariogenic Challenge}}},
  author = {Dibdin, G.H. and Dawes, C.},
  year = {1998},
  journal = {Caries Research},
  volume = {32},
  number = {1},
  pages = {70--74},
  issn = {0008-6568, 1421-976X},
  doi = {10.1159/000016432},
  abstract = {Urea diffusing from saliva into dental plaque is converted to ammonia and carbon dioxide by bacterial ureases. The influence of normal salivary urea levels on the pH of fasted plaque and on the depth and duration of a Stephan curve is uncertain. A numerical model which simulates a cariogenic challenge (a 10\% sucrose rinse alone or one followed by use of chewing-gum with or without sugar) was modified to include salivary urea levels from 0 to 30 mmol/l. It incorporated: site-dependent exchange between bulk saliva and plaque surfaces via a salivary film; sugar and urea diffusion into plaque; pH-dependent rates of acid formation and urea breakdown; diffusion and dissociation of end-products and other buffers (acetate, lactate, phosphate, ammonia and carbonate); diffusion of protons and other ions; equilibration with fixed and mobile buffers; and chargecoupling between ionic flows. The Km (2.12 mmol/l) and Vmax (0.11 \textmu mol urea/ min/mg dry weight) values for urease activity and the pH dependence of Vmax were taken from the literature. From the results, it is predicted that urea concentrations normally present in saliva (3\textendash 5 mmol/l) will increase the pH at the base of a 0.5-mm-thick fasted plaque by up to 1 pH unit, and raise the pH minimum after a sucrose rinse or sugar-containing chewing-gum by at least half a pH unit. The results suggest that plaque cariogenicity may be inversely related to salivary urea concentrations, not only when the latter are elevated because of disease, but even when they are in the normal range.},
  langid = {english}
}

@article{dobneyMethodEvaluating1987,
  title = {A Method for Evaluating the Amount of Dental Calculus on Teeth from Archaeological Sites},
  author = {Dobney, Keith and Brothwell, Don},
  year = {1987},
  month = jul,
  journal = {Journal of Archaeological Science},
  volume = {14},
  number = {4},
  pages = {343--351},
  issn = {0305-4403},
  doi = {10.1016/0305-4403(87)90024-0},
  abstract = {A series of archaeological teeth, both human and animal, were scanned with a view to establishing a quick and reliable method of recording the extent and severity of dental calculus. The method involved allocating each dentition or tooth a general score, one of five grades: 0 (normal) to 4 (gross). Each tooth was then divided into morphological zones, depending upon species, and the percentage covering of calculus for each zone was recorded. Thickness was also assessed using a five-grade scoring system and was based on radiographs of affected teeth. This gave an idea of the severity of the calculus deposit.},
  langid = {english},
  keywords = {buttress,dental calculus,grade,infolding,involution,scoring,sub-gingival,supra-gingival}
}

@article{doddsCarbohydrateRetention1988,
  title = {The {{Relationship Between Plaque pH}}, {{Plaque Acid Anion Profiles}}, and {{Oral Carbohydrate Retention After Ingestion}} of {{Several}} '{{Reference Foods}}' by {{Human Subjects}}},
  author = {Dodds, Michael W. J. and Edgar, W.M.},
  year = {1988},
  month = may,
  journal = {Journal of Dental Research},
  volume = {67},
  number = {5},
  pages = {861--865},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/00220345880670051301},
  abstract = {The primary aim of this study was to rank several reference foods (apple drink, caramel, chocolate, cookie, skimmed milk powder, snack cracker, and wheat flake) according to their plaque pH response as monitored in a panel of 12 volunteers by the plaque-sampling method for comparison with data previously reported with other methods used to assess cariogenicity potential. Secondary experiments (using subsets of the panel of subjects) were undertaken in an attempt to elucidate some of the reasons for the observed plaque pH changes. Oral carbohydrate retention was measured at a single time period after food use as total anthrone-positive carbohydrate material, and as specific acidogenic sugars by gas-liquid chromatography after gel-exclusion chromatography. The concentrations of acid anions in the plaque fluid after food consumption were measured by isotachophoresis eight min after food use. According to the plaque pH response, apple-flavored fruit drink and chocolate were the most acidogenic foods and skimmed milk powder the least acidogenic. There were significant correlations (p {$<$} 0.05) between the plaque pH data and lactate-plus-acetate concentrations in plaque fluid, but the correlations between the pH data and any of the carbohydrate retention parameters were not significant.},
  langid = {english}
}

@article{doddsHealthBenefits2005,
  title = {Health Benefits of Saliva: A Review},
  shorttitle = {Health Benefits of Saliva},
  author = {Dodds, Michael W. J. and Johnson, Dorthea A. and Yeh, Chih-Ko},
  year = {2005},
  month = mar,
  journal = {Journal of Dentistry},
  series = {Symposium in Honour of the Work of {{Professor W M Edgar}}},
  volume = {33},
  number = {3},
  pages = {223--233},
  issn = {0300-5712},
  doi = {10.1016/j.jdent.2004.10.009},
  abstract = {Objective The aim is to present a review of the literature on human saliva composition, flow rates and some of the health benefits of saliva, with emphasis on studies from our laboratory that have looked at effects of age and age-related diseases on saliva output and composition. Data Saliva influences oral health both through its non-specific physico-chemical properties, as well as through more specific effects. The proline-rich proteins, statherin and the histatins are salivary proteins that influence calcium phosphate chemistry, initial plaque formation and candida infection. Increases or decreases in mastication may affect saliva output. Our cross-sectional studies of saliva in a large population-based study cohort (N=1130) indicate that there is an age-related decline in saliva output for unstimulated whole, stimulated parotid, unstimulated submandibular/sublingual and stimulated submandibular/sublingual saliva, as well as some compositional alterations in anti-microbial and other proteins. Some of these alterations also appear to be specific for certain age-related medical conditions, such as diabetes mellitus. Conclusions These studies and data presented confirm the importance of saliva in maintaining a healthy oral environment; the practitioner is encouraged to consider saliva output and medical conditions that may compromise it as part of routine dental treatment planning.},
  langid = {english},
  keywords = {Aging,Diabetes,Hypertension,notion,Saliva}
}

@article{drewettExcavationOval1975,
  title = {The {{Excavation}} of an {{Oval Burial Mound}} of the {{Third Millennium}} Be at {{Alfriston}}, {{East Sussex}}, 1974},
  author = {Drewett, Peter},
  year = {1975},
  pages = {38},
  abstract = {The small oval burial mound at Alfriston, East Sussex, being one of only twelve certain burial structures of the 3rd millennium be in Sussex, was totally excavated in 1974 prior to its final obliteration by ploughing. The barrow was found to consist of a simple dump mound derived from material out of flanking ditches. It covered a single burial pit containing the crouched skeleton of a young female. Information concerning the post-Neolithic land use of Alfriston Down was obtained from the ditch silts and expanded by an intensive field survey.},
  langid = {english}
}

@article{duarteInfluencesStarch2008,
  title = {Influences of Starch and Sucrose on {{Streptococcus}} Mutans Biofilms},
  author = {Duarte, S. and Klein, M. I. and Aires, C. P. and Cury, J. A. and Bowen, W. H. and Koo, H.},
  year = {2008},
  month = jun,
  journal = {Oral Microbiology and Immunology},
  volume = {23},
  number = {3},
  pages = {206--212},
  issn = {0902-0055, 1399-302X},
  doi = {10.1111/j.1399-302X.2007.00412.x},
  abstract = {Introduction: The combination of starch and sucrose has been shown to be potentially more cariogenic than either alone. The aim of this study was to examine the influence of starch and sucrose, alone or in combinations, on formation, polysaccharide composition, gene expression, and acidogenicity of Streptococcus mutans biofilms. Methods: S. mutans UA159 biofilms were formed on saliva-coated hydroxyapatite (sHA) discs in batch culture for 5 days in the presence of 1\% (weight/volume) starch, 1\% sucrose, 1\% starch plus 1\% sucrose, 1\% starch plus 0.5\% fructose plus 0.5\% glucose, or 1\% sucrose plus 1\% glucose. Results: Amylase activity from sHA disks was detected up to 48 h, thereby increasing the availability of reducing sugars and acidogenicity in the early stages of biofilm development. S. mutans grown in the presence of sucrose alone or in combinations formed well-defined and tightly adherent biofilms comprised of mostly water-insoluble polysaccharides (INS); in contrast, the presence of starch or starch + glucose + fructose resulted in little biofilm formation with minimal amounts of INS. However, the combination of starch + sucrose produced biofilms with more biomass and acidogenicity, and a higher content of INS than those grown in sucrose or sucrose + glucose (P {$<$} 0.05). The INS extracted from biofilms formed in the presence of starch + sucrose displayed a higher percentage of 3-linked branching (3,4-, 3,6-, and 3,4,6-linked glucose) compared to those from biofilms grown in sucrose or sucrose + glucose. Furthermore, biofilms grown in starch + sucrose expressed significantly higher levels of gtfB messenger RNA than sucrose-grown or sucrose + glucose-grown biofilms (P {$<$} 0.05). Conclusion: The combination of starch and sucrose has profound effects not only on the composition and structure of the polysaccharide matrix but also on gene expression of S. mutans within biofilms, which may enhance the cariogenic potential of dental biofilms.},
  langid = {english}
}

@article{dudgeonDietGeography2014,
  title = {Diet, {{Geography}} and {{Drinking Water}} in {{Polynesia}}: {{Microfossil Research}} from {{Archaeological Human Dental Calculus}}, {{Rapa Nui}} ({{Easter Island}})},
  shorttitle = {Diet, {{Geography}} and {{Drinking Water}} in {{Polynesia}}},
  author = {Dudgeon, John V. and Tromp, Monica},
  year = {2014},
  journal = {International Journal of Osteoarchaeology},
  volume = {24},
  number = {5},
  pages = {634--648},
  issn = {1099-1212},
  doi = {10.1002/oa.2249},
  abstract = {Microfossil analysis of human dental calculus provides consumption-specific and archaeologically relevant data for evaluating diet and subsistence in past populations. Calculus was extracted from 114 teeth representing 104 unique individuals from a late 16th to early 18th century skeletal series on Rapa Nui (Easter Island) to address questions of human\textendash environment interactions and possible dietary preference. Scanning electron microscopy was used in lieu of optical microscopy for its superior depth of field and resolution of surface detail. The calculus microfossil recovery produced 16,377 total biogenic silica microfossils: 4733 phytoliths and 11,644 diatoms. The majority of phytoliths correspond with the Arecaceae or palm family (n = 4,456) and the minority corresponds to the Poaceae or grass family (n = 277). Because of the relatively large sample size, we were able to test hypotheses related to age cohort, sex, dental element and geographic region. Results indicate no significant difference in phytolith or diatom recovery based on age cohort or sex. The high frequency and proportion of Arecaceae phytoliths found in calculus extracted from the anterior dentition suggests consumption of soft or cooked foods containing palm phytoliths and the high frequency of diatoms recovered from the southern part of the island argue for different sources of drinking water. Copyright \textcopyright{} 2012 John Wiley \& Sons, Ltd.},
  copyright = {Copyright \textcopyright{} 2012 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {dental calculus,diatoms,Easter Island,microfossils,phytoliths,Polynesia,Rapa Nui},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/oa.2249}
}

@article{duthieNaturalSalicylates2011,
  title = {Natural Salicylates: Foods , Functions and Disease Prevention},
  shorttitle = {Natural Salicylates},
  author = {Duthie, Garry G. and Wood, Adrian D.},
  year = {2011},
  journal = {Food \& Function},
  volume = {2},
  number = {9},
  pages = {515--520},
  publisher = {{Royal Society of Chemistry}},
  doi = {10.1039/C1FO10128E},
  langid = {english}
}

@article{echeverriaNicotineHair2013,
  title = {Nicotine in the Hair of Mummies from {{San Pedro}} de {{Atacama}} ({{Northern Chile}})},
  author = {Echeverr{\'i}a, Javier and Niemeyer, Hermann M.},
  year = {2013},
  month = oct,
  journal = {Journal of Archaeological Science},
  volume = {40},
  number = {10},
  pages = {3561--3568},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2013.04.030},
  abstract = {The consumption of plant-derived hallucinogenic substances through smoking and snuffing is a long-standing tradition in the south-central Andes. Chemical and archaeobotanical evidence point to the consumption of nicotine and tryptamine alkaloids in Northwestern Argentina and of tryptamine alkaloids in San Pedro de Atacama (SPA), in prehispanic times. In this paper, results are reported of gas chromatography\textendash mass spectrometry (GC/MS) analyses aimed at identifying nicotine and tryptamine alkaloids in the hair of mummies from different cultural periods of SPA. Fifty-six samples were examined. While tryptamines were not found in any of the samples, nicotine was found in 35 samples, assigned to the Late Formative (1 of 1 sample from this period), Late Formative or Middle (1 of 2 samples from either of these periods), Middle (4 of 6 samples from this period) and Late Intermediate periods (8 of 12 samples from this period), or without assignment to period due to lack of contextual information (21 of 35 samples unassigned to a period). These results show a continuous consumption of nicotine from the Late Formative to the Late Intermediate periods of SPA (ca. 100 B.C.\textendash 1450 A.D.). No associations were found between presence of nicotine in the hair of mummies and presence of snuffing trays or of other snuffing paraphernalia in the corresponding tomb; furthermore, neither the diversity of the funerary context, measured in terms of the number of types of objects, nor the presence of gemstone necklaces differed between tombs with mummies with or without nicotine in their hair. Overall, these results suggest that consumption of nicotine was performed by members of the society at large, irrespective of their social and wealth status.},
  langid = {english},
  keywords = {Bufotenine,Dimethyltryptamines,Hair analysis,Hallucinogenic substances,Nicotine,Northern Chile mummies,Psychoactive alkaloids,San Pedro de Atacama}
}

@article{edlundBiofilmModel2013,
  title = {An in Vitrobiofilm Model System Maintaining a Highly Reproducible Species and Metabolic Diversity Approaching That of the Human Oral Microbiome},
  author = {Edlund, Anna and Yang, Youngik and Hall, Adam P. and Guo, Lihong and Lux, Renate and He, Xuesong and Nelson, Karen E. and Nealson, Kenneth H. and Yooseph, Shibu and Shi, Wenyuan and McLean, Jeffrey S.},
  year = {2013},
  month = oct,
  journal = {Microbiome},
  volume = {1},
  number = {1},
  pages = {25},
  issn = {2049-2618},
  doi = {10.1186/2049-2618-1-25},
  abstract = {Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level.},
  keywords = {Biofilm,In vitro model,Lactobacillus,notion,Oral microbiome,Saliva,Streptococcus,Uncultivated bacteria}
}

@article{edlundUncoveringComplex2018,
  title = {Uncovering Complex Microbiome Activities via Metatranscriptomics during 24 Hours of Oral Biofilm Assembly and Maturation},
  author = {Edlund, Anna and Yang, Youngik and Yooseph, Shibu and He, Xuesong and Shi, Wenyuan and McLean, Jeffrey S.},
  year = {2018},
  month = dec,
  journal = {Microbiome},
  volume = {6},
  number = {1},
  pages = {217},
  issn = {2049-2618},
  doi = {10.1186/s40168-018-0591-4},
  abstract = {Background: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation. Results: Time course analysis of the biofilm maturation was performed by parallel sampling every 2\textendash 3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum. Conclusion: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.},
  langid = {english},
  keywords = {In vitro biofilm,notion,oral biofilm model}
}

@article{eerkensDentalCalculus2018,
  title = {Dental Calculus as a Source of Ancient Alkaloids: {{Detection}} of Nicotine by {{LC-MS}} in Calculus Samples from the {{Americas}}},
  shorttitle = {Dental Calculus as a Source of Ancient Alkaloids},
  author = {Eerkens, Jelmer W. and Tushingham, Shannon and Brownstein, Korey J. and Garibay, Ramona and Perez, Katherine and Murga, Engel and Kaijankoski, Phil and Rosenthal, Jeffrey S. and Gang, David R.},
  year = {2018},
  month = apr,
  journal = {Journal of Archaeological Science: Reports},
  volume = {18},
  pages = {509--515},
  issn = {2352-409X},
  doi = {10.1016/j.jasrep.2018.02.004},
  abstract = {Dental calculus has been shown to be a repository of a variety of exogenous organic materials, including bacterial DNA, proteins, phytoliths, and starch grains. Here we show that certain alkaloids, nicotine in this case, can also be trapped and preserved in ancient dental calculus. We present Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) results of analyses of ten archaeological calculus samples from eight individuals from Central California. Two samples tested positive for the presence of nicotine, including one from an individual buried with a pipe. UPLC-MS analyses of dental calculus could provide an alternative means to trace the spread and consumption of tobacco and other plants with distinctive alkaloid products in ancient societies. As shown here for the first time in ancient samples, the ability to detect nicotine alkaloids in calculus has enormous potential to help us better understand the consumption of intoxicant plants by ancient humans on the individual level, for example by giving us the ability to test assumptions about the age, sex, and status of individual tobacco users in the past.},
  langid = {english}
}

@article{enneverCharacterizationBacterionema1978,
  title = {Characterization of {{Bacterionema}} Matruchotii {{Calcification Nucleator}}},
  author = {Ennever, J. and Riggan, L.J. and Vogel, J.J. and {Boyan-Salyers}, B.},
  year = {1978},
  month = apr,
  journal = {Journal of Dental Research},
  volume = {57},
  number = {4},
  pages = {637--642},
  issn = {0022-0345, 1544-0591},
  doi = {10.1177/00220345780570041901},
  abstract = {The nucleator of Bacterionema matruchotii calcification was characterized. Parameters examined were: proteolipid purity and singularity, amino acid composition and relative polarity, phospholipid composition, apoprotein homogeneity, essentiality of the complex for nucleation, and ordered structure. The data fulfill a requirement for comparisons among apatite-nucleating proteolipids.},
  langid = {english}
}

@article{enneverIntracellularCalcification1960,
  title = {Intracellular {{Calcification}} by {{Oral Filamentous Microorganisms}}},
  author = {Ennever, J.},
  year = {1960},
  journal = {The Journal of Periodontology},
  volume = {31},
  number = {4},
  pages = {304--307},
  issn = {1943-3670},
  doi = {10.1902/jop.1960.31.4.304},
  langid = {english},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1902/jop.1960.31.4.304}
}

@article{enneverMicrobiologicCalcification1967,
  title = {Microbiologic Calcification: {{Bone}} Mineral and Bacteria},
  shorttitle = {Microbiologic Calcification},
  author = {Ennever, J. and Creamer, H.},
  year = {1967},
  month = dec,
  journal = {Calcified Tissue Research},
  volume = {1},
  number = {1},
  pages = {87--93},
  issn = {0008-0594, 1432-0827},
  doi = {10.1007/BF02008078},
  langid = {english}
}

@article{extercateAAA2010,
  title = {Different {{Response}} to {{Amine Fluoride}} by {{Streptococcus}} Mutans and {{Polymicrobial Biofilms}} in a {{Novel High-Throughput Active Attachment Model}}},
  author = {Exterkate, R.A.M. and Crielaard, W. and Ten Cate, J.M.},
  year = {2010},
  journal = {Caries Research},
  volume = {44},
  number = {4},
  pages = {372--379},
  issn = {1421-976X, 0008-6568},
  doi = {10.1159/000316541},
  langid = {english},
  keywords = {notion}
}

@incollection{fagernasDentalCalculus2023,
  title = {Dental {{Calculus}}},
  booktitle = {Handbook of {{Archaeological Sciences}}},
  author = {Fagern{\"a}s, Zandra and Warinner, Christina},
  editor = {Pollard, A.M. and Armitage, Ruth Ann and Makarevicz, Cheryl},
  year = {2023},
  edition = {Second edition},
  isbn = {978-1-119-59204-4},
  langid = {english}
}

@article{fagernasMicrobialBiogeography2021,
  title = {Understanding the Microbial Biogeography of Ancient Human Dentitions to Guide Study Design and Interpretation},
  author = {Fagern{\"a}s, Zandra and {Salazar-Garc{\'i}a}, Domingo C. and Avil{\'e}s, Azucena and Haber, Mar{\'i}a and Henry, Amanda and Maurandi, Joaqu{\'i}n Lomba and Ozga, Andrew and Velsko, Irina M. and Warinner, Christina},
  year = {2021},
  month = jan,
  journal = {bioRxiv},
  pages = {2021.08.16.456492},
  doi = {10.1101/2021.08.16.456492},
  abstract = {The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Inter-individual differences in microbial composition are found to be much larger than intra-individual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples may be of environmental origin, showing the importance of including environmental controls or several lines of biomolecular evidence.Competing Interest StatementThe authors have declared no competing interest.}
}

@article{fagernasMicrobialBiogeography2022,
  title = {Understanding the Microbial Biogeography of Ancient Human Dentitions to Guide Study Design and Interpretation},
  author = {Fagern{\"a}s, Zandra and {Salazar-Garc{\'i}a}, Domingo C and Haber~Uriarte, Mar{\'i}a and Avil{\'e}s~Fern{\'a}ndez, Azucena and Henry, Amanda G and Lomba~Maurandi, Joaqu{\'i}n and Ozga, Andrew T and Velsko, Irina M. and Warinner, Christina},
  year = {2022},
  month = jan,
  journal = {FEMS Microbes},
  volume = {3},
  pages = {xtac006},
  issn = {2633-6685},
  doi = {10.1093/femsmc/xtac006},
  abstract = {The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500\textendash 5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.}
}

@article{fagernasUnifiedProtocol2020,
  title = {A Unified Protocol for Simultaneous Extraction of {{DNA}} and Proteins from Archaeological Dental Calculus},
  author = {Fagern{\"a}s, Zandra and {Garc{\'i}a-Collado}, Maite I. and Hendy, Jessica and Hofman, Courtney A. and Speller, Camilla and Velsko, Irina M. and Warinner, Christina},
  year = {2020},
  month = jun,
  journal = {Journal of Archaeological Science},
  volume = {118},
  pages = {105135},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2020.105135},
  abstract = {Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43\%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource.},
  langid = {english},
  keywords = {Ancient DNA,Dental plaque,eager,Metagenomics,Oral microbiome,Palaeoproteomics}
}

@misc{fdiOralHealth,
  title = {{{FDI}}'s Definition of Oral Health | {{FDI}}},
  journal = {FDI World Dental Federation},
  howpublished = {https://www.fdiworlddental.org/fdis-definition-oral-health}
}

@article{fehrVitroCalculus1960,
  title = {In Vitro Calculus Formation},
  author = {von der Fehr, Frithjof and Brudevold, F.},
  year = {1960},
  month = sep,
  journal = {J Dent Res},
  volume = {39},
  pages = {1041--8},
  issn = {0022-0345 (Print) 0022-0345 (Linking)},
  doi = {10.1177/00220345600390050801},
  keywords = {*Calculi,*Teeth,*Tooth,Humans,In Vitro Techniques}
}

@article{filocheFluorescenceAssay2007,
  title = {A Fluorescence Assay to Determine the Viable Biomass of Microcosm Dental Plaque Biofilms},
  author = {Filoche, Sara K. and Coleman, Megan J. and Angker, Linny and Sissons, Chris H.},
  year = {2007},
  month = jun,
  journal = {Journal of Microbiological Methods},
  volume = {69},
  number = {3},
  pages = {489--496},
  issn = {01677012},
  doi = {10.1016/j.mimet.2007.02.015},
  abstract = {Dental plaque bacteria form complex and robust cell aggregates which cannot be counted accurately using epifluorescence microscopy. This causes a significant problem for quantifying their viability. The aim of the investigation was to develop a fluorescence assay to quantify the viable biomass of dental plaque biofilms. Using an artificial mouth system, microcosm plaques were grown under a range of fluoride and mineralizing conditions, and were treated with the oral antiseptics chlorhexidine (CHX) and Listerine\textregistered. Plaques were harvested, made into suspension and stained in microtitre plates with a di-chromatic fluorescent stain (Live/Dead\textregistered{} BacLight\texttrademark ). The percentage of viable biomass was calculated from the regression data generated from a viability standard. The standard was constructed using different proportions of viable (green fluorescence) and non-viable (red fluorescence) plaque bacteria, and growth conditions for optimizing green fluorescence were investigated. The results from the assay showed that fluoride at 1000 and 3000 ppm promoted plaque viability by at least 15\%, from {$\sim$} 45 to 60\%, and at 5000 ppm to {$\sim$} 87\% (P b 0.05). Plaques treated with Listerine\textregistered{} and CHX from d 0 yielded insufficient biomass to be tested for viability, however 14 d post-treatment, viability was comparable to untreated plaques ({$\sim$} 55\%, P N 0.05). Treatment with Listerine\textregistered{} and CHX from d 3 reduced biomass but not viability. Development of this assay enabled viability of plaque bacteria which cannot be resolved with epifluorescence microscopy to be evaluated. It offers a rapid alternative to epifluorescence microscopy and could be applied to nonoral bacteria.},
  langid = {english},
  keywords = {notion}
}

@article{filochePlaqueMicrocosm2007,
  title = {Caries-Related Plaque Microcosm Biofilms Developed in Microplates},
  author = {Filoche, S. K. and Soma, K. J. and Sissons, C. H.},
  year = {2007},
  journal = {Oral Microbiology and Immunology},
  volume = {22},
  number = {2},
  pages = {73--79},
  issn = {1399-302X},
  doi = {10.1111/j.1399-302X.2007.00323.x},
  abstract = {In vivo dental plaque biofilms consist of complex communities of oral bacteria that are a challenge to replicate in vitro. The aim of this investigation was to establish human dental plaque microcosms in microplates to reflect conditions that are relevant to dental caries. Microcosm plaque biofilms were initiated from the saliva of two different donors, grown for up to 10 days in 24-welled microplates on ThermanoxTM coverslips in various types of artificial saliva with and without sucrose, which were replaced daily. Microbiota composition of 40 species associated with oral health and dental caries was monitored in the plaques using Checkerboard DNA\textendash DNA hybridization analysis. pH was measured as an indicator of cariogenic potential. The composition of the saliva inocula was different, and yielded plaque microcosms with different composition and growth responses to sucrose. Artificial saliva type and presence of sucrose, and the resulting growth and pH conditions, modified the growth of individual species and hence the ecological profile of the microplate plaques during development. Complex population shifts were observed during development, and older plaques comprised predominantly facultative anaerobic species. Sucrose supplementation limited the decline of Streptococci over time but did not increase the abundance of mutans Streptococci. Sucrose at 0.15\% increased levels of caries-associated species including Lactobacillus fermentum, Lactobacillus acidophilus and Actinomyces gerensceriae; these were further increased with sucrose at 0.5\%, in addition to Actinomyces israelii, Rothia dentocariosa and Capnocytophaga gingivalis. The microplate plaques demonstrated complex community dynamics that appeared to reflect the maturation of natural plaques, and sucrose induced a cariogenic plaque composition and pH.},
  langid = {english},
  keywords = {caries,microcosm,microplates,notion,oral biofilm,plaque},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-302X.2007.00323.x}
}

@article{fiorinCombiningDental2021,
  title = {Combining Dental Calculus with Isotope Analysis in the {{Alps}}: {{New}} Evidence from the {{Roman}} and Medieval Cemeteries of {{Lamon}}, Northern {{Italy}}},
  shorttitle = {Combining Dental Calculus with Isotope Analysis in the {{Alps}}},
  author = {Fiorin, Elena and Moore, Joanna and Montgomery, Janet and Lippi, Marta Mariotti and Nowell, Geoff and Forlin, Paolo},
  year = {2021},
  month = nov,
  journal = {Quaternary International},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2021.11.022},
  abstract = {This study presents the results of complementary isotopic and dental calculus analyses of a number of individuals buried in two cemeteries of Roman and medieval chronology in Lamon, northern Italy. Eleven individuals from the Roman cemetery of San Donato and six from the medieval cemetery of San Pietro are presented and discussed. The results suggest a distinctive stability of the two populations, with most of the analysed individuals showing a local or regional origin. Carbon and nitrogen isotopes are indicative of a diet based on a mixed C3/C4 plant consumption and rich in animal proteins, with no significant difference between the Roman and the medieval populations. The consumption of C4 plants, more resilient to the Alpine climate, is consistently documented both by isotopes and dental calculus. Dental calculus results permit the characterisation of the typology of the crop consumed, namely millet, barley/wheat and legumes and may also suggest differing cooking processes between the Roman and the medieval periods. Phytoliths, vascular elements, fungal spores and animal remains from dental calculus provide new insights into the diet of the analysed individuals but also, hypothetically, into possible medicinal treatments. The presence of birds such as fowls and ducks in the medieval diet of some individuals from San Pietro has also emerged. Overall, the results of this study open a new window into the biographies of the individuals analysed, their diet, mobility, habits, and environment, thus stimulating further and more systematic investigation on the populations occupying an Alpine sector which is still poorly understood from an archaeological perspective.},
  langid = {english},
  keywords = {Alps,Dental calculus,Isotopes,Middle ages,Roman period}
}

@article{flemmingBiofilmMatrix2010,
  title = {The Biofilm Matrix},
  author = {Flemming, Hans-Curt and Wingender, Jost},
  year = {2010},
  month = sep,
  journal = {Nature Reviews Microbiology},
  volume = {8},
  number = {9},
  pages = {623--633},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro2415},
  abstract = {The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.},
  langid = {english}
}

@article{flemmingBiofilmsEmergent2016,
  title = {Biofilms: An Emergent Form of Bacterial Life},
  shorttitle = {Biofilms},
  author = {Flemming, Hans-Curt and Wingender, Jost and Szewzyk, Ulrich and Steinberg, Peter and Rice, Scott A. and Kjelleberg, Staffan},
  year = {2016},
  month = sep,
  journal = {Nature Reviews Microbiology},
  volume = {14},
  number = {9},
  pages = {563--575},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro.2016.94},
  abstract = {Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of `emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms \textemdash{} such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials \textemdash{} all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.},
  langid = {english},
  keywords = {notion}
}

@article{foxPhytolithCalculus1996,
  title = {Phytolith Analysis on Dental Calculus, Enamel Surface, and Burial Soil: {{Information}} about Diet and Paleoenvironment},
  author = {Fox, Carles Lalueza and Juan, Jordi and Albert, Rosa M.},
  year = {1996},
  journal = {American Journal of Physical Anthropology},
  volume = {101},
  number = {1},
  pages = {101--113},
  issn = {1096-8644},
  doi = {10.1002/(SICI)1096-8644(199609)101:1<101::AID-AJPA7>3.0.CO;2-Y},
  abstract = {Silica phytoliths (microscopic remains originating in plant tissues) have been identified on the enamel surface and dental calculus of a sample of teeth selected from well preserved skeletons from a Late Roman necropolis in Tarragona (Spain). Phytoliths were observed by scanning electron microscopy (SEM) and their siliceous nature was confirmed by X-ray microanalysis. The phytoliths were compared to those of soil samples from both the areas of the tombs corresponding to the abdomen and the periphery of the skeletons, and were classified taxonomically by comparison with a large collection of silica particles from modern plants in the Mediterranean area. Most of the phytoliths identified on the enamel and the dental calculus belong to the family of Poaceae, while the phytoliths from the abdominal area belong to Poaceae, Leguminosae, Cyperaceae, and Chenopodiaceae. Results are concordant with archaeological, ecological, and historical data from the same site, and with the human Mediterranean diet. If done properly, the study of phytoliths can provide direct information about the vegetable diet of past human populations, and could be applied to the study of human fossils. \textcopyright{} 1996 Wiley-Liss, Inc.}
}

@article{francoStarchDegradation1992,
  title = {Factors That {{Affect}} the {{Enzymatic Degradation}} of {{Natural Starch Granules}} -{{Effect}} of the {{Size}} of the {{Granules}}},
  author = {Franco, Celia M. L. and Preto, S{\~a}o Jos{\'e} do Rio and Ciacco, C{\'e}sar F.},
  year = {1992},
  journal = {Starch - St\"arke},
  volume = {44},
  number = {11},
  pages = {422--426},
  issn = {1521-379X},
  doi = {10.1002/star.19920441106},
  abstract = {In this study the relationship between the enzymatic susceptibility and the size of the corn and cassava starch granules was studied. The starch granules were separated by size and classified according to their average diameter in: a) larger than 16 urn: b) between 15 and 10 um and c) smaller than 10 um. The starch granules of various sizes were hydrolyzed by bacterial alpha-amylase and fungal amyloglucosidase. The results showed a relationship between the enzymatic susceptibility and the size of the starch granules: smaller size of the starch granules resulted in a higher percentage of hydrolysis. A basic difference in the mode of action of enzymes on small and large granules was observed. Enzymatic attack on the large granules was characterized by considerable surface corrosion, mainly at the radial axis. For small granules, the enzymatic action occurred on the surface of the granules and was characterized by an erosion with solubilization of the granules. Chemical and physical analysis of the starches suggested that hydrolysis should occur mainly at the amorphous areas of the granules.},
  langid = {english},
  annotation = {\_eprint: https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/star.19920441106}
}

@article{friskoppComparativeScanning1980,
  title = {A {{Comparative}}, {{Scanning Electron Microscopic Study}} of {{Supragingival}} and {{Subgingival Calculus}}},
  author = {Friskopp, Johan and Hammarstr{\"o}m, Lars},
  year = {1980},
  journal = {Journal of Periodontology},
  volume = {51},
  number = {10},
  pages = {553--562},
  issn = {1943-3670},
  doi = {10.1902/jop.1980.51.10.553},
  abstract = {The morphology of supragingival and subgingival calculus on extracted teeth was studied with the scanning electron microscope. Oral, crevicular, and fracture surfaces were examined. Both subgingival and supragingival calculus had a heterogenous core covered by a soft, loose layer of microorganisms. On supragingival calculus this layer was dominated by filamentous microorganisms while subgingival calculus was covered by a mixture of cocci, rods and filaments. The supragingival covering of filaments was oriented with the filaments approximately perpendicular to and in direct contact with the underlying dense calculus. This arrangement was rarely seen subgingivally where there was no distinct pattern of orientation. Some of the specimens of sub- and supragingival calculus were treated with sodium-hypochlorite. These lost the soft covering, and channels the same size as the filamentous organisms were found penetrating into the calculus. They were oriented perpendicular to the surface in supragingival calculus but had no specific direction in subgingival calculus. The appearance of the channels supports the concept that calcification starts between the microorganisms in both subgingival and supragingival calculus.},
  langid = {english},
  annotation = {\_eprint: https://aap.onlinelibrary.wiley.com/doi/pdf/10.1902/jop.1980.51.10.553}
}

@article{friskoppUltrastructureNondecalcified1983,
  title = {Ultrastructure of {{Nondecalcified Supragingival}} and {{Subgingival Calculus}}},
  author = {Friskopp, Johan},
  year = {1983},
  month = sep,
  journal = {Journal of Periodontology},
  volume = {54},
  number = {9},
  pages = {542--550},
  issn = {0022-3492, 1943-3670},
  doi = {10.1902/jop.1983.54.9.542},
  langid = {english}
}

@article{froehlichEffectOral1987,
  title = {The Effect of Oral Stimulation on Human Parotid Salivary Flow Rate and Alpha-Amylase Secretion},
  author = {Froehlich, Deborah A. and Pangborn, Rose Marie and Whitaker, John R.},
  year = {1987},
  month = jan,
  journal = {Physiology \& Behavior},
  volume = {41},
  number = {3},
  pages = {209--217},
  issn = {0031-9384},
  doi = {10.1016/0031-9384(87)90355-6},
  abstract = {Unilateral parotid saliva was collected from ten subjects following oral stimulation with water as baseline, and aqueous solutions of starch (2.5, 5.0, and 10\%), sucrose (0.1, 0.2, and 0.4 M) sodium chloride (0.075, 0.15, and 0.30 M), and citric acid (0.005, 0.01, and 0.02 M). Salivary flow rate increased with increasing levels of each taste stimulus. At concentrations of equal taste intensity, citric acid evoked the highest flow rate, followed by sodium chloride and sucrose, while starch, in solution, had a minimal effect. Secretion rate patterns for total protein and alpha-amylase mirrored those of flow rate. The total protein and alpha-amylase concentrations of the saliva, and specific activity of alpha-amylase, were influenced by the type but not the concentration of stimulus, with citric acid stimulation resulting in the lowest concentrations and highest specific activity. Sodium ion (Na+) concentration generally increased with increasing stimulated flow rate, while K+, Ca++, and Mg++ concentrations remained relatively constant. Subjects with lower flow rates had a more concentrated saliva than those with high flow, except for Na+ concentration. Oral stimulation resulted in similar changes in protein and alpha-amylase secretion rates for the two groups.},
  langid = {english},
  keywords = {Gustatory stimulation,Human parotid saliva,Oral stimulation,Salivary alpha-amylase,Salivary secretion}
}

@book{ggplot2,
  title = {Ggplot2: {{Elegant Graphics}} for {{Data Analysis}}},
  author = {Wickham, Hadley},
  year = {2016},
  publisher = {{Springer-Verlag}},
  address = {{New York}},
  isbn = {978-3-319-24277-4}
}

@article{gilbertAssessingAncient2005,
  title = {Assessing Ancient {{DNA}} Studies},
  author = {Gilbert, M. Thomas P. and Bandelt, Hans-J{\"u}rgen and Hofreiter, Michael and Barnes, Ian},
  year = {2005},
  month = oct,
  journal = {Trends in Ecology \& Evolution},
  volume = {20},
  number = {10},
  pages = {541--544},
  issn = {0169-5347},
  doi = {10.1016/j.tree.2005.07.005},
  abstract = {The study of ancient DNA has the potential to make significant and unique contributions to ecology and evolution. However, the techniques used contain inherent problems, particularly with regards to the generation of authentic and useful data. The solution currently advocated to reduce contamination and artefactual results is to adopt criteria for authentication. Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies. We argue here that researchers in this field must take a more cognitive and self-critical approach. Specifically, in place of checking criteria off lists, researchers must explain, in sufficient enough detail to dispel doubt, how the data were obtained, and why they should be believed to be authentic.},
  langid = {english}
}

@article{gilbertBiochemicalPhysical2005,
  title = {Biochemical and Physical Correlates of {{DNA}} Contamination in Archaeological Human Bones and Teeth Excavated at {{Matera}}, {{Italy}}},
  author = {Gilbert, M. Thomas P. and Rudbeck, Lars and Willerslev, Eske and Hansen, Anders J. and Smith, Colin and Penkman, Kirsty E. H. and Prangenberg, Kurt and {Nielsen-Marsh}, Christina M. and Jans, Miranda E. and Arthur, Paul and Lynnerup, Niels and {Turner-Walker}, Gordon and Biddle, Martin and {Kj{\o}lbye-Biddle}, Birthe and Collins, Matthew J.},
  year = {2005},
  month = may,
  journal = {Journal of Archaeological Science},
  volume = {32},
  number = {5},
  pages = {785--793},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2004.12.008},
  abstract = {The majority of ancient DNA studies on human specimens have utilised teeth and bone as a source of genetic material. In this study the levels of endogenous contamination (i.e. present within the sample prior to sampling for the DNA analysis) are assessed within human bone and teeth specimens sampled from the cemetery of Santa Lucia alle Malve, Matera, Italy. This site is of exceptional interest, because the samples have been assayed for 18 measures of biochemical and physical preservation, and it is the only one identified in a study of more than 107 animal and 154 human bones from 43 sites across Europe, where a significant number of human bones was well preserved. The findings demonstrate several important issues: (a) although teeth are more resilient to contamination than bone, both are readily contaminated (presumably through handling or washing), and (b) once contaminated in this way, both are difficult (if not impossible) to decontaminate. Furthermore, although assessed on bone samples, several of the specific biochemical and physical characteristics that describe overall sample preservation, levels of microbial attack and related increases in sample porosity directly correlate with the presence of observable contamination in both bone and teeth samples from individual samples. While we can only speculate on the cause of this relationship, we posit that they provide useful guides for the assessment of whether samples are likely to be contaminated or not.},
  langid = {english},
  keywords = {Ancient DNA,Biopreservation,Bone,Contamination,Diagenesis,Human,Teeth}
}

@article{gismondiMultidisciplinaryApproach2020,
  title = {A Multidisciplinary Approach for Investigating Dietary and Medicinal Habits of the {{Medieval}} Population of {{Santa Severa}} (7th-15th Centuries, {{Rome}}, {{Italy}})},
  author = {Gismondi, Angelo and Baldoni, Marica and Gnes, Micaela and Scorrano, Gabriele and D'Agostino, Alessia and Marco, Gabriele Di and Calabria, Giulietta and Petrucci, Michela and M{\"u}ldner, Gundula and Tersch, Matthew Von and Nardi, Alessandra and Enei, Flavio and Canini, Antonella and Rickards, Olga and Alexander, Michelle and {Mart{\'i}nez-Labarga}, Cristina},
  year = {2020},
  month = jan,
  journal = {PLOS ONE},
  volume = {15},
  number = {1},
  pages = {e0227433},
  publisher = {{Public Library of Science}},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0227433},
  abstract = {A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of {$\omega$}3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.},
  langid = {english},
  keywords = {Diet,Food,Italy,Marine fish,Medicinal plants,Polymerase chain reaction,Ribs,Starches}
}

@article{gismondiStarchGranules2019,
  title = {Starch Granules: A Data Collection of 40 Food Species},
  shorttitle = {Starch Granules},
  author = {Gismondi, Angelo and D'Agostino, Alessia and Canuti, Lorena and Di Marco, Gabriele and Basoli, Francesco and Canini, Antonella},
  year = {2019},
  month = mar,
  journal = {Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology},
  volume = {153},
  number = {2},
  pages = {273--279},
  issn = {1126-3504, 1724-5575},
  doi = {10.1080/11263504.2018.1473523},
  abstract = {A collection of starch granules synthesized in 40 food plants was assembled. After extraction and purification, samples were subjected to optic and scanning electron microscopy investigations. Detailed images and descriptions of the starch granules are provided, evidencing all their morphological and structural features. In particular, shape, size, position and visibility of the hilum, organization of the lamellae, presence of fissures and surface elements (i.e. pores, pressure facets), density of granules per mg of sample and percentage of amylose content were reported. Generally, the results showed that starch synthesis in organisms belonging to the same species or genus follows conserved patterns, although some differences can be always detected. In conclusion, the present work represents a starch Botanical Atlas fundamental for botanic, archaeological and food quality researches.},
  langid = {english}
}

@article{glasBiophysicalStudies1962,
  title = {Biophysical {{Studies}} on {{Dental Calculus}} from {{Germfree}} and {{Conventional Rats}}},
  author = {Glas, Jan-Erik and Krasse, Bo},
  year = {1962},
  month = jan,
  journal = {Acta Odontologica Scandinavica},
  volume = {20},
  number = {2},
  pages = {127--134},
  issn = {0001-6357, 1502-3850},
  doi = {10.3109/00016356209026100},
  langid = {english},
  annotation = {glasGermfreeCalculus1962}
}

@article{gloorMicrobiomeDatasets2017,
  title = {Microbiome {{Datasets Are Compositional}}: {{And This Is Not Optional}}},
  shorttitle = {Microbiome {{Datasets Are Compositional}}},
  author = {Gloor, Gregory B. and Macklaim, Jean M. and {Pawlowsky-Glahn}, Vera and Egozcue, Juan J.},
  year = {2017},
  month = nov,
  journal = {Frontiers in Microbiology},
  volume = {8},
  pages = {2224},
  issn = {1664-302X},
  doi = {10.3389/fmicb.2017.02224},
  abstract = {Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data. The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis. We briefly introduce compositional data, illustrate the pathologies that occur when compositional data are analyzed inappropriately, and finally give guidance and point to resources and examples for the analysis of microbiome datasets using compositional data analysis.},
  pmcid = {PMC5695134},
  pmid = {29187837}
}

@book{goodmanTobaccoHistory1994,
  title = {Tobacco in History: The Cultures of Dependence},
  author = {Goodman, Jordan},
  year = {1994},
  publisher = {{Routledge}},
  address = {{London}},
  isbn = {0-415-11669-4}
}

@article{grahamEnterococcusFaecalis2017,
  title = {Enterococcus Faecalis Bacteriocin {{EntV}} Inhibits Hyphal Morphogenesis, Biofilm Formation, and Virulence of {{Candida}} Albicans},
  author = {Graham, Carrie E. and Cruz, Melissa R. and Garsin, Danielle A. and Lorenz, Michael C.},
  year = {2017},
  month = apr,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {114},
  number = {17},
  pages = {4507--4512},
  publisher = {{Proceedings of the National Academy of Sciences}},
  doi = {10.1073/pnas.1620432114}
}

@article{graneroStarchTaphonomy2020,
  title = {Starch Taphonomy, Equifinality and the Importance of Context: {{Some}} Notes on the Identification of Food Processing through Starch Grain Analysis},
  shorttitle = {Starch Taphonomy, Equifinality and the Importance of Context},
  author = {{Garc{\'i}a-Granero}, Juan Jos{\'e}},
  year = {2020},
  month = dec,
  journal = {Journal of Archaeological Science},
  volume = {124},
  pages = {105267},
  issn = {03054403},
  doi = {10.1016/j.jas.2020.105267},
  abstract = {The analysis of starch grains from food-related archaeological artefacts and human dental calculus has provided evidence for the consumption of plant resources worldwide. Recently, and based on experimental research, starch grain analysis has also been used as a proxy to reconstruct food transformation in the archaeological record through the analysis of the damage produced on starch grains by different food-processing techniques such as grinding, boiling and fermentation. The prospect of identifying food transformation through starch grain analysis opens exciting avenues for exploring the cultural factors underlying culinary practices. However, the structural integrity of starch grains may be affected by a variety of depositional and post-depositional processes, including but not limited to food processing, so that in order to identify damage produced by food processing one would first need to discard potential damage occurred at later stages (e.g., in the burial environment, during laboratory processing and analysis, etc.). The identification of food processing through the analysis of the damage produced on starch grains is further obscured by equifinality and multifinality, as exemplified by un\- cooked modern reference material presented here showing damage patterns consistent with ``boiling'', ``spouting'' and ``fermenting''. Consequently, the identification of food transformation in the archaeological record through the analysis of the damage produced on starch grains needs to be supported by reliable contextual information, a representative number of samples and the existence of alternative sources of evidence (i.e., a multi-proxy approach).},
  langid = {english}
}

@article{greeneQuantifyingCalculus2005,
  title = {Quantifying Calculus: {{A}} Suggested New Approach for Recording an Important Indicator of Diet and Dental Health},
  author = {Greene, T. R. and Kuba, C. L. and Irish, J. D.},
  year = {2005},
  journal = {HOMO - Journal of Comparative Human Biology},
  volume = {56},
  number = {2},
  pages = {119--132},
  issn = {0018442X},
  doi = {10.1016/j.jchb.2005.02.002}
}

@article{greeneSimplifiedOral1964,
  title = {The {{Simplified Oral Hygiene Index}}},
  author = {Greene, John G. and Vermillion, Jack R.},
  year = {1964},
  month = jan,
  journal = {The Journal of the American Dental Association},
  volume = {68},
  number = {1},
  pages = {7--13},
  issn = {0002-8177},
  doi = {10.14219/jada.archive.1964.0034},
  abstract = {Delayed-onset infection is defined as infectious swelling and trismus accompanied by pain or the presence of suppuration starting approximately 30 days after surgery. This study aimed to describe the occurrence and potential predisposing factors of delayed-onset infection. A retrospective case-control study of 223 lower third molar surgeries was performed. Participants were selected from among 1102 outpatients who underwent surgery between January 2013 and June 2018 at Semmelweis University. The inclusion criterion for the case group was inflammation of the operated area after suture removal. Patients in the control group were healthy nonsmokers {$<$}26 years old who healed without complication. Statistical analysis was performed using the Shapiro-Wilk test, the Mann-Whitney U test, and Fisher's exact test. Complications occurred only in patients {$<$}26 years old approximately 29.5 days after surgery. A significantly higher risk was observed for younger age, total soft tissue coverage, deeper impaction, lower Nolla stage (P {$<$} .001), mesioangular direction (P = .002), and full bone coverage (P {$<$} .05). Distal space was inversely correlated with complications (P {$<$} .001). Lower Nolla stage, total soft tissue coverage, lack of distal space, deeper impaction, or mesioangular tilt may promote delayed-onset infection. Follow-up of at-risk patients and the maintenance of oral hygiene are recommended. To investigate the effect of mogroside, palatinose, erythritol, and xylitol on the dental plaque pH of children and to compare the plaque pH change between caries-active and caries-free children caused by these sweeteners. Thirty-six children (mean age 6.2 {$\pm$} 2.9-year-old), caries-active and caries-free, were included. After refraining from practicing oral hygiene, the accessible plaque was collected and equally divided for challenging with 6 different solutions: mogroside, palatinose, erythritol, xylitol, 10\% sucrose, and deionized water. The pH of each solution was measured using a digital pH meter at 0, 5, 10, 15, 20, 25, and 30 min. Mogroside, erythritol, xylitol, and water did not significantly lower the dental plaque pH, however, palatinose reduced dental plaque pH comparable to sucrose (p {$<$} 0.05). Comparing the caries-active and caries-free groups, only sucrose produced significantly different pH value at min 5 and 10. Mogroside, erythritol, and xylitol did not lower the dental plaque pH in caries-active or caries-free children. However, palatinose affected the dental plaque pH similar to sucrose.},
  langid = {english}
}

@article{haaseComparativeGenomics2017,
  title = {Comparative Genomics and Evolution of the Amylase-Binding Proteins of Oral Streptococci},
  author = {Haase, Elaine M. and Kou, Yurong and Sabharwal, Amarpreet and Liao, Yu-Chieh and Lan, Tianying and Lindqvist, Charlotte and Scannapieco, Frank A.},
  year = {2017},
  month = apr,
  journal = {BMC Microbiology},
  volume = {17},
  number = {1},
  pages = {94},
  issn = {1471-2180},
  doi = {10.1186/s12866-017-1005-7},
  abstract = {Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adapted to life in the oral cavity by binding salivary {$\alpha$}-amylase, which hydrolyzes dietary starch, thus providing a source of nutrition. Oral streptococcal species bind {$\alpha$}-amylase by expressing a variety of amylase-binding proteins (ABPs). Here we determine the genotypic basis of amylase binding where proteins of diverse size and function share a common phenotype.},
  keywords = {Adaptation,Amylase,Commensal,Horizontal gene transfer,Phylogenetics}
}

@article{haffajeeBiofilmPosition2009,
  title = {Factors Affecting Human Supragingival Biofilm Composition. {{II}}. {{Tooth}} Position},
  author = {Haffajee, A. D. and Teles, R. P. and Patel, M. R. and Song, X. and Yaskell, T. and Socransky, S. S.},
  year = {2009},
  journal = {Journal of Periodontal Research},
  volume = {44},
  number = {4},
  pages = {520--528},
  issn = {1600-0765},
  doi = {10.1111/j.1600-0765.2008.01155.x},
  abstract = {Background and Objective: Little is known regarding the factors that affect the microbial composition of supragingival biofilms. This study was designed to test the hypothesis that tooth location affects the microbial composition of supragingival plaque beyond the effect due to plaque mass as reflected by total DNA probe count. Material and Methods: Supragingival plaque samples were taken from the mesiobuccal aspect of each tooth in 187 subjects (n = 4745 samples). All samples were individually analyzed for their content of 40 bacterial species using checkerboard DNA\textendash DNA hybridization. Significance of differences in mean species counts and proportions were determined among tooth surfaces and six tooth type categories: molars, bicuspids, incisors/canines in the mandible and maxilla separately using the Kruskal\textendash Wallis test. Stepwise multiple linear regression was employed to examine the relationship between species proportions and total DNA probe count, tooth location, periodontal and smoking status, age and sex. Results: All species differed significantly among tooth types and among the six tooth categories. Higher plaque levels were seen on molars and lower incisors. Some differences observed between tooth types could be partly explained by the level of plaque. Teeth with high plaque mass exhibited high levels of Capnocytophaga gingivalis, Actinomyces naeslundii genospecies 2, Campylobacter rectus and Campylobacter showae. However, certain species, such as Veillonella parvula and Streptococcus sanguinis, differed significantly at different tooth locations despite similarities in plaque mass. Twenty of the test species exhibited a significant association with tooth location after adjusting for total DNA probe count and subject level factors. Conclusion: While plaque mass was associated with differences in proportions of many species in supragingival biofilms, tooth location also was strongly associated with species proportions in both univariate and multivariate analyses.},
  langid = {english},
  keywords = {bacteria,plaque mass,supragingival plaque,tooth type},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0765.2008.01155.x}
}

@article{hardyDentalCalculus2016,
  title = {Dental Calculus Reveals Potential Respiratory Irritants and Ingestion of Essential Plant-Based Nutrients at {{Lower Palaeolithic Qesem Cave Israel}}},
  author = {Hardy, Karen and Radini, Anita and Buckley, Stephen and Sarig, Rachel and Copeland, Les and Gopher, Avi and Barkai, Ran},
  year = {2016},
  month = apr,
  journal = {Quaternary International},
  series = {State of the Art of the Multidisciplinary Research at the {{Middle Pleistocene Qesem Cave}}, {{Israel}}, 2015},
  volume = {398},
  pages = {129--135},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2015.04.033},
  abstract = {Reconstructing detailed aspects of the lives of Lower Palaeolithic hominins, who lived during the Middle Pleistocene, is challenging due to the restricted nature of the surviving evidence, predominantly animal bones and stone tools. Qesem Cave, Israel (420\textendash 200~ka) is a site that has produced evidence for a wealth of innovative features including controlled use of fire, represented by a repeatedly used hearth. Numerous charred bone and stone tools as well as wood ash have been found throughout the ten metres of archaeological deposits. Here, we describe the presence of a range of potentially inhaled, and ingested, materials extracted from samples of dental calculus from the Qesem Cave hominins. These finds offer an insight into the environment in and around the cave, while micro-charcoal highlights the need for smoke management in enclosed environments. Plant fibres and a phytolith may be evidence of oral hygiene activities or of using the teeth to work raw materials. Starch granules and chemical compounds provide a direct link to ingested plant food items. This extends the evidence for consumption of plant foods containing essential nutrients including polyunsaturated fatty acids and carbohydrates, into the Lower Palaeolithic. Together, these results represent a significant breakthrough towards a better understanding of Middle Pleistocene dietary breadth and highlight some of the challenges facing the adoption of the habitual use of fire for cooking by the Qesem Cave hominins, as well as offering an insight into their ecological knowledge and technological adaptability.},
  langid = {english},
  keywords = {Dental calculus,Diet,Lower Palaeolithic,Plants,Respiratory irritants}
}

@article{hardyNeanderthalMedics2012,
  title = {Neanderthal Medics? {{Evidence}} for Food, Cooking, and Medicinal Plants Entrapped in Dental Calculus},
  shorttitle = {Neanderthal Medics?},
  author = {Hardy, Karen and Buckley, Stephen and Collins, Matthew J. and Estalrrich, Almudena and Brothwell, Don and Copeland, Les and {Garc{\'i}a-Tabernero}, Antonio and {Garc{\'i}a-Vargas}, Samuel and {de la Rasilla}, Marco and {Lalueza-Fox}, Carles and Huguet, Rosa and Bastir, Markus and Santamar{\'i}a, David and Madella, Marco and Wilson, Julie and Cort{\'e}s, {\'A}ngel Fern{\'a}ndez and Rosas, Antonio},
  year = {2012},
  month = aug,
  journal = {Naturwissenschaften},
  volume = {99},
  number = {8},
  pages = {617--626},
  issn = {1432-1904},
  doi = {10.1007/s00114-012-0942-0},
  abstract = {Neanderthals disappeared sometime between 30,000 and 24,000~years ago. Until recently, Neanderthals were understood to have been predominantly meat-eaters; however, a growing body of evidence suggests their diet also included plants. We present the results of a study, in which sequential thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) were combined with morphological analysis of plant microfossils, to identify material entrapped in dental calculus from five Neanderthal individuals from the north Spanish site of El Sidr\'on. Our results provide the first molecular evidence for inhalation of wood-fire smoke and bitumen or oil shale and ingestion of a range of cooked plant foods. We also offer the first evidence for the use of medicinal plants by a Neanderthal individual. The varied use of plants that we have identified suggests that the Neanderthal occupants of El Sidr\'on had a sophisticated knowledge of their natural surroundings which included the ability to select and use certain plants.},
  langid = {english}
}

@article{hardyRecoveringInformation2018,
  title = {Pleistocene Dental Calculus: {{Recovering}} Information on {{Paleolithic}} Food Items, Medicines, Paleoenvironment and Microbes},
  shorttitle = {Pleistocene Dental Calculus},
  author = {Hardy, Karen and Buckley, Stephen and Copeland, Les},
  year = {2018},
  month = sep,
  journal = {Evolutionary Anthropology: Issues, News, and Reviews},
  volume = {27},
  number = {5},
  pages = {234--246},
  issn = {10601538},
  doi = {10.1002/evan.21718},
  abstract = {Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.},
  langid = {english}
}

@article{hardyStarchGranules2009,
  title = {Starch Granules, Dental Calculus and New Perspectives on Ancient Diet},
  author = {Hardy, Karen and Blakeney, Tony and Copeland, Les and Kirkham, Jennifer and Wrangham, Richard and Collins, Matthew},
  year = {2009},
  journal = {Journal of Archaeological Science},
  volume = {36},
  number = {2},
  pages = {248--255},
  issn = {03054403},
  doi = {10.1016/j.jas.2008.09.015}
}

@article{haslamDecompositionStarch2004,
  title = {The Decomposition of Starch Grains in Soils: Implications for Archaeological Residue Analyses},
  shorttitle = {The Decomposition of Starch Grains in Soils},
  author = {Haslam, Michael},
  year = {2004},
  month = dec,
  journal = {Journal of Archaeological Science},
  volume = {31},
  number = {12},
  pages = {1715--1734},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2004.05.006},
  abstract = {Recent research involving starch grains recovered from archaeological contexts has highlighted the need for a review of the mechanisms and consequences of starch degradation specifically relevant to archaeology. This paper presents a review of the plant physiological and soil biochemical literature pertinent to the archaeological investigation of starch grains found as residues on artefacts and in archaeological sediments. Preservative and destructive factors affecting starch survival, including enzymes, clays, metals and soil properties, as well as differential degradation of starches of varying sizes and amylose content, were considered. The synthesis and character of chloroplast-formed `transitory' starch grains, and the differentiation of these from `storage' starches formed in tubers and seeds were also addressed. Findings of the review include the higher susceptibility of small starch grains to biotic degradation, and that protective mechanisms are provided to starch by both soil aggregates and artefact surfaces. These findings suggest that current reasoning which equates higher numbers of starch grains on an artefact than in associated sediments with the use of the artefact for processing starchy plants needs to be reconsidered. It is argued that an increased understanding of starch decomposition processes is necessary to accurately reconstruct both archaeological activities involving starchy plants and environmental change investigated through starch analysis.},
  langid = {english},
  keywords = {Archaeology,Residue analysis,Soil,Starch grains,Taphonomy,Transitory starch}
}

@article{hayashizakiSiteSpecific2008,
  title = {Site Specific Mineral Composition and Microstructure of Human Supra-Gingival Dental Calculus},
  author = {Hayashizaki, Junko and Ban, Seiji and Nakagaki, Haruo and Okumura, Akihiko and Yoshii, Saori and Robinson, Colin},
  year = {2008},
  month = feb,
  journal = {Archives of Oral Biology},
  volume = {53},
  number = {2},
  pages = {168--174},
  issn = {00039969},
  doi = {10.1016/j.archoralbio.2007.09.003},
  abstract = {Dental calculus has been implicated in the aetiology of several periodontal conditions. Its prevention and removal are therefore desirable clinical goals. While it is known that calculus is very variable in chemical composition, crystallinity and crystallite size little is known about site specific variability within a dentition and between individuals. With this in mind, a study was undertaken to investigate the comparative site specific nature and composition of human dental supra-gingival dental calculus obtained from 66 male patients visiting for their dental check-up using fluorescent X-ray spectroscopy, X-ray diffractometry and Fourier transform infrared spectroscopy. The supra-gingival dental calculus formed on the lingual surfaces of lower anterior teeth and the buccal surfaces of upper molar teeth were classified into four types based on calcium phosphate phases present. There was significant difference in composition of the crystal phase types between lower and upper teeth ( p {$<$} 0.01). There was no significant difference in crystal size between dental calculus on anterior or molar teeth of all samples. The degree of crystallinity of dental calculus formed on the upper molar teeth was higher than that formed on the lower anterior teeth ( p {$<$} 0.01). The CO32\`A contents in dental calculus formed on the lower anterior teeth were higher than on upper molar teeth ( p {$<$} 0.05) which might explain the difference in crystallinity. Magnesium and Si contents and Ca:P ratio on the other hand showed no significant difference between lower and upper teeth. It was concluded that the crystal phases, crystallinity and CO32\`A contents of human dental supra-gingival dental calculus is related to its location in the mouth.},
  langid = {english}
}

@article{hendyAncientProtein2021,
  title = {Ancient Protein Analysis in Archaeology},
  author = {Hendy, Jessica},
  year = {2021},
  month = jan,
  journal = {Science Advances},
  volume = {7},
  number = {3},
  pages = {eabb9314},
  publisher = {{American Association for the Advancement of Science}},
  doi = {10.1126/sciadv.abb9314},
  abstract = {The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.},
  keywords = {paleoproteomics,review}
}

@article{hendyProteomicCalculus2018,
  title = {Proteomic Evidence of Dietary Sources in Ancient Dental Calculus},
  author = {Hendy, Jessica and Warinner, Christina and Bouwman, Abigail and Collins, Matthew J. and Fiddyment, Sarah and Fischer, Roman and Hagan, Richard and Hofman, Courtney A. and Holst, Malin and Chaves, Eros and Klaus, Lauren and Larson, Greger and Mackie, Meaghan and McGrath, Krista and Mundorff, Amy Z. and Radini, Anita and Rao, Huiyun and Trachsel, Christian and Velsko, Irina M. and Speller, Camilla F.},
  year = {2018},
  month = jul,
  journal = {Proceedings. Biological Sciences},
  volume = {285},
  number = {1883},
  pages = {20180977},
  issn = {1471-2954},
  doi = {10.1098/rspb.2018.0977},
  abstract = {Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein {$\beta$}-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.},
  langid = {english},
  pmcid = {PMC6083251},
  pmid = {30051838},
  keywords = {Archaeology,dental calculus,Dental Calculus,Diet,dietary reconstruction,DNA; Ancient,England,History; 15th Century,History; 16th Century,History; 17th Century,History; 18th Century,History; 19th Century,History; Ancient,History; Medieval,mass spectrometry,Proteome,proteomics}
}

@article{henryCalculusSyria2008,
  title = {Using Plant Microfossils from Dental Calculus to Recover Human Diet: A Case Study from {{Tell}} al-{{Raq\=a}}'i, {{Syria}}},
  author = {Henry, Amanda G. and Piperno, Dolores R.},
  year = {2008},
  journal = {Journal of Archaeological Science},
  volume = {35},
  number = {7},
  pages = {1943--1950},
  issn = {03054403},
  doi = {10.1016/j.jas.2007.12.005}
}

@article{henryCookingStarch2009,
  title = {Changes in Starch Grain Morphologies from Cooking},
  author = {Henry, Amanda G. and Hudson, Holly F. and Piperno, Dolores R.},
  year = {2009},
  journal = {Journal of Archaeological Science},
  volume = {36},
  number = {3},
  pages = {915--922},
  issn = {03054403},
  doi = {10.1016/j.jas.2008.11.008}
}

@article{henryDietAustralopithecus2012,
  title = {The Diet of {{Australopithecus}} Sediba},
  author = {Henry, Amanda G. and Ungar, Peter S. and Passey, Benjamin H. and Sponheimer, Matt and Rossouw, Lloyd and Bamford, Marion and Sandberg, Paul and {de Ruiter}, Darryl J. and Berger, Lee},
  year = {2012},
  month = jul,
  journal = {Nature},
  volume = {487},
  number = {7405},
  pages = {90--93},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/nature11185},
  abstract = {Phytolith, stable carbon isotope, and dental microwear texture data for two individuals of Au. sediba, 2-million-year-old hominins from South Africa, show that they consumed a mostly C3 diet that probably included harder foods, and both dicotyledons (for example, tree leaves, fruits, and wood or bark) and monocotyledons (for example, grasses and sedges); this diet contrasts with previously described diets of other early hominin species.},
  copyright = {2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  langid = {english},
  keywords = {Archaeology}
}

@article{henryNeanderthalCalculus2014,
  title = {Plant Foods and the Dietary Ecology of {{Neanderthals}} and Early Modern Humans},
  author = {Henry, Amanda G. and Brooks, Alison S. and Piperno, Dolores R.},
  year = {2014},
  month = apr,
  journal = {Journal of Human Evolution},
  volume = {69},
  pages = {44--54},
  issn = {0047-2484},
  doi = {10.1016/j.jhevol.2013.12.014},
  abstract = {One of the most important challenges in anthropology is understanding the disappearance of Neanderthals. Previous research suggests that Neanderthals had a narrower diet than early modern humans, in part because they lacked various social and technological advances that lead to greater dietary variety, such as a sexual division of labor and the use of complex projectile weapons. The wider diet of early modern humans would have provided more calories and nutrients, increasing fertility, decreasing mortality and supporting large population sizes, allowing them to out-compete Neanderthals. However, this model for Neanderthal dietary behavior is based on analysis of animal remains, stable isotopes, and other methods that provide evidence only of animal food in the diet. This model does not take into account the potential role of plant food. Here we present results from the first broad comparison of plant foods in the diets of Neanderthals and early modern humans from several populations in Europe, the Near East, and Africa. Our data comes from the analysis of plant microremains (starch grains and phytoliths) in dental calculus and on stone tools. Our results suggest that both species consumed a similarly wide array of plant foods, including foods that are often considered low-ranked, like underground storage organs and grass seeds. Plants were consumed across the entire range of individuals and sites we examined, and none of the expected predictors of variation (species, geographic region, or associated stone tool technology) had a strong influence on the number of plant species consumed. Our data suggest that Neanderthal dietary ecology was more complex than previously thought. This implies that the relationship between Neanderthal technology, social behavior, and food acquisition strategies must be better explored.},
  langid = {english},
  keywords = {Dental calculus,Microfossil,Microremain,Neanderthal diet,Phytolith,Starch grain}
}

@article{hidakaDietCalculus2007,
  title = {An in Vitro Study of the Effect of Some Dietary Components on Calculus Formation: Regulation of Calcium Phosphate Precipitation},
  author = {Hidaka, S. and Oishi, A.},
  year = {2007},
  month = may,
  journal = {Oral Diseases},
  volume = {13},
  number = {3},
  pages = {296--302},
  issn = {1354-523X (Print) 1354-523X (Linking)},
  doi = {10.1111/j.1601-0825.2006.01283.x},
  abstract = {OBJECTIVE: We studied the effects of food components on the in vitro formation of calcium phosphate precipitates. MATERIALS AND METHODS: The effects of food components, such as starch, soybean flour, fish meal, rapeseed oil, and coconut oil, on calcium phosphate precipitation were studied using a pH drop method. RESULTS: Although the addition of starch had no effect on the rate of precipitation of amorphous calcium phosphate (ACP), it increased both the rate of transformation of ACP to hydroxyapatite (HAP) and the induction time (i.e. time for the initiation of transformation of ACP to HAP to occur); this was irrespective of the heat treatment of the starch. Amylopectin (insoluble constituent of starch) was effective in increasing the rate of HAP transformation, but amylose (soluble constituent of starch) was not. Oil specimen obtained from rapeseed (400 microl ml(-1)) increased the entire reaction of calcium phosphate precipitation, but that from coconut did not. Protein food, such as soybean flour and fish meal, decreased the rate of transformation of ACP to HAP and increased the induction time, while they had no effect on the rate of ACP precipitation. CONCLUSION: These results suggest that carbohydrate and oil (both are staple diets for the humans) enhance oral calcification (dental calculus formation or re-mineralization of tooth enamel), while side dishes of protein food would decrease it.},
  keywords = {Calcium Phosphates/chemistry,Chemical Precipitation,Dental Calculus/*metabolism,Dietary Carbohydrates/*metabolism,Dietary Fats/*metabolism,Dietary Proteins/adverse effects/*metabolism,Fish Products/adverse effects,Hydrogen-Ion Concentration,Hydroxyapatites/metabolism,Plant Oils/metabolism,Soybeans/adverse effects/metabolism,Starch/metabolism,Tooth Calcification/*physiology,Tooth Remineralization}
}

@article{hidakaStarchRole2008,
  title = {The {{Possible Role}} of {{Starch}} in {{Oral Calcification}}: {{The In Vitro Formation}} of {{Hydroxyapatite}} Is {{Regulated}} by a {{Combination}} of {{Protein}} and {{Mineral Content}} in {{Dietary Starch Flour}}},
  shorttitle = {The {{Possible Role}} of {{Starch}} in {{Oral Calcification}}},
  author = {Hidaka, Saburo and Okamoto, Yoshizo and Tsukamoto, Suehiro and Oishi, Akiko},
  year = {2008},
  month = apr,
  journal = {The Open Food Science Journal},
  volume = {2},
  number = {1},
  pages = {10--22},
  issn = {18742564},
  doi = {10.2174/1874256400802010010},
  abstract = {The effects of twelve kinds of dietary starch flour, i.e. rice (non-glutinous and glutinous), wheat (soft, medium, and hard), barley (roasted), buckwheat (inner layer and straight), corn, sweet potato, kudzu, and tapioca on in vitro calcium phosphate precipitation were investigated using the pH drop method. The induction time was elongated by the addition of all of the kinds of flour. Although the rate of amorphous calcium phosphate (ACP) formation was not affected, the rate of transformation of ACP to hydroxyapatite (HAP) was either stimulated or inhibited by the different types of flour. The following observations were made: (1) When the lipid content below 0.2\% (w/w), any of the types of starch had a stimulatory effect on the transformation of ACP to HAP. (2) When the lipid content around or above 1.0\% (w/w), the value of the product of (protein content)   (mineral content) seems to determine the effect of starch.},
  langid = {english}
}

@book{hillsonDentalAnthropology1996,
  title = {Dental {{Anthropology}}},
  author = {Hillson, Simon},
  year = {1996},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}},
  isbn = {978-1-107-07826-0}
}

@article{honraetModifiedRobbins2006,
  title = {Use of the Modified Robbins Device and Fluorescent Staining to Screen Plant Extracts for the Inhibition of {{S}}. Mutans Biofilm Formation},
  author = {Honraet, K. and Nelis, H.J.},
  year = {2006},
  month = feb,
  journal = {Journal of Microbiological Methods},
  volume = {64},
  number = {2},
  pages = {217--224},
  issn = {01677012},
  doi = {10.1016/j.mimet.2005.05.005},
  abstract = {Streptococcus mutans plays an important role in the formation of dental plaque. To study biofilm growth on hydroxyapatite (HA) in vitro, a flow system based on a Modified Robbins Device (MRD) and a method for the quantification of the biomass using fluorescent staining with SYTOR 9 were developed. The combined approach was used to assess the inhibitory effect of plant extracts on biofilm formation in concentrations below their minimal inhibitory concentrations.},
  langid = {english},
  keywords = {notion}
}

@article{huangDecipheringGenetic2023,
  title = {Deciphering Genetic Causes for Sex Differences in Human Health through Drug Metabolism and Transporter Genes},
  author = {Huang, Yingbo and Shan, Yuting and Zhang, Weijie and Lee, Adam M. and Li, Feng and Stranger, Barbara E. and Huang, R. Stephanie},
  year = {2023},
  month = jan,
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {175},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-35808-6},
  abstract = {Sex differences have been widely observed in human health. However, little is known about the underlying mechanism behind these observed sex differences. We hypothesize that sex-differentiated genetic effects are contributors of these phenotypic differences. Focusing on a collection of drug metabolism enzymes and transporters (DMET) genes, we discover sex-differentiated genetic regulatory mechanisms between these genes and human complex traits. Here, we show that sex-differentiated genetic effects were present at genome-level and at DMET gene regions for many human complex traits. These sex-differentiated regulatory mechanisms are reflected in the levels of gene expression and endogenous serum biomarkers. Through Mendelian Randomization analysis, we identify putative sex-differentiated causal effects in each sex separately. Furthermore, we identify and validate sex differential gene expression of a subset of DMET genes in human liver samples. We observe higher protein abundance and enzyme activity of CYP1A2 in male-derived liver microsomes, which leads to higher level of an active metabolite formation of clozapine, a commonly prescribed antipsychotic drug. Taken together, our results demonstrate the presence of sex-differentiated genetic effects on DMET gene regulation, which manifest in various phenotypic traits including disease risks and drug responses.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Genetics research,Population genetics,Translational research}
}

@article{huangEffectArginine2017,
  title = {Effect of Arginine on the Growth and Biofilm Formation of Oral Bacteria},
  author = {Huang, Xuelian and Zhang, Keke and Deng, Meng and Exterkate, Robertus A.M. and Liu, Chengcheng and Zhou, Xuedong and Cheng, Lei and {ten Cate}, Jacob M.},
  year = {2017},
  month = oct,
  journal = {Archives of Oral Biology},
  volume = {82},
  pages = {256--262},
  issn = {00039969},
  doi = {10.1016/j.archoralbio.2017.06.026},
  abstract = {Background: Alkali production via arginine deiminase system (ADS) of oral bacteria plays a significant role in oral ecology, pH homeostasis and inhibition of dental caries. ADS activity in dental plaque varies greatly between individuals, which may profoundly affect their susceptibility to caries. Objective: To investigate the effect of arginine on the growth and biofilm formation of oral bacteria. Methods and results: Polymicrobial dental biofilms derived from saliva were formed in a high-throughput active attachment biofilm model and L-arginine (Arg) was shown to reduce the colony forming units (CFU) counts of such biofilms grown for various periods or biofilms derived from saliva of subjects with different caries status. Arg hardly disturbed bacterial growth of Streptococcus mutans, Streptococcus sobrinus, Streptococcus sanguinis and Streptococcus gordonii in BHI medium, but only inhibited biofilm formation of S. mutans. Scanning electron microscope (SEM) showed S. mutans biofilms harboured fewer cells grown with Arg than that without Arg, even in the initial 2 h and 8 h phase. Confocal laser scanning microscope (CLSM) images of poly-microbial dental and S. mutans biofilms revealed the biofilms grown with Arg had lower exopolysaccharide (EPS)/bacteria ratios than those without Arg (P = 0.004, 0.002, respectively). Arg could significantly reduce the production of waterinsoluble EPS in S. mutans biofilms (P {$<$} 0.001); however, quantitative real-time PCR (qRT-PCR) did not show significantly influence in gene expression of gtfB, gtfC or gtfD (P = 0.32, 0.06, 0.44 respectively). Conclusions: Arg could reduce the biomass of poly-microbial dental biofilms and S. mutans biofilms, which may be due to the impact of Arg on water-insoluble EPS. Considering the contribution to pH homeostasis in dental biofilms, Arg may serve as an important agent keeping oral biofilms healthy thus prevent dental caries.},
  langid = {english}
}

@article{huangFactorsAssociated2012,
  title = {Factors {{Associated}} with {{Alkali Production}} from {{Arginine}} in {{Dental Biofilms}}},
  author = {Huang, Xuelian and Exterkate, Robertus A.M. and {ten Cate}, Jacob M.},
  year = {2012},
  month = dec,
  journal = {Journal of Dental Research},
  volume = {91},
  number = {12},
  pages = {1130--1134},
  issn = {0022-0345, 1544-0591},
  doi = {10.1177/0022034512461652},
  abstract = {Alkali production by oral bacteria in the oral cavity has been linked to protection against dental caries. The current study assessed various parameters associated with ammonium produced during arginine catabolism in dental biofilms. Polymicrobial biofilms were formed with saliva as the inoculum. The NH3 level and the pH of the spent medium were used to monitor and quantitate the bacterial reactions. The presence of sucrose, a low buffer capacity, and a low pH ({$\leq$} pH 4.5) were found to hamper alkali production from arginine. The rate of alkali production exhibited an optimum around pH 5.5. Biofilms were found to produce NH3 also from polypeptides and proteins in the medium. The biofilm age affected these processes. The experimental model proved valuable for the assessment of the collective bacterial reactions determining the overall pH outcome. This experimental approach could bridge the gap in our knowledge between pH-rise phenomena and caries susceptibility from clinical observations and studies performed on alkali-producing bacteria in wellcontrolled, though simplified, in vitro models. Analysis of our data supports the hypothesis that the initiation and progression of dental caries may be influenced by the relative rates of acid and base formation, which critically depend on the aforementioned parameters.},
  langid = {english}
}

@article{hublerHOPSAutomated2019,
  title = {{{HOPS}}: Automated Detection and Authentication of Pathogen {{DNA}} in Archaeological Remains},
  shorttitle = {{{HOPS}}},
  author = {H{\"u}bler, Ron and Key, Felix M. and Warinner, Christina and Bos, Kirsten I. and Krause, Johannes and Herbig, Alexander},
  year = {2019},
  month = dec,
  journal = {Genome Biology},
  volume = {20},
  number = {1},
  pages = {280},
  issn = {1474-760X},
  doi = {10.1186/s13059-019-1903-0},
  abstract = {High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.},
  keywords = {Ancient bacteria,Ancient DNA,Archaeogenetics,Metagenomics,Microbial archaeology,Paleopathology,Pathogen detection}
}

@article{immelEffectXray2016,
  title = {Effect of {{X-ray}} Irradiation on Ancient {{DNA}} in Sub-Fossil Bones \textendash{} {{Guidelines}} for Safe {{X-ray}} Imaging},
  author = {Immel, Alexander and Le Cabec, Adeline and Bonazzi, Marion and Herbig, Alexander and Temming, Heiko and Schuenemann, Verena J. and Bos, Kirsten I. and Langbein, Frauke and Harvati, Katerina and Bridault, Anne and Pion, Gilbert and Julien, Marie-Anne and Krotova, Oleksandra and Conard, Nicholas J. and M{\"u}nzel, Susanne C. and Drucker, Doroth{\'e}e G. and Viola, Bence and Hublin, Jean-Jacques and Tafforeau, Paul and Krause, Johannes},
  year = {2016},
  month = sep,
  journal = {Scientific Reports},
  volume = {6},
  number = {1},
  pages = {32969},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/srep32969},
  abstract = {Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([{$\mu$}]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000\,Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200\,Gy. Dosimetry shows that conventional {$\mu$}CT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies.},
  copyright = {2016 The Author(s)},
  langid = {english},
  keywords = {DNA,Double-strand DNA breaks,X-ray tomography}
}

@article{indriatiCocaPrehistoric2001,
  title = {Coca Chewing in Prehistoric Coastal {{Peru}}: {{Dental}} Evidence},
  shorttitle = {Coca Chewing in Prehistoric Coastal {{Peru}}},
  author = {Indriati, Etty and Buikstra, Jane E.},
  year = {2001},
  journal = {American Journal of Physical Anthropology},
  volume = {114},
  number = {3},
  pages = {242--257},
  issn = {1096-8644},
  doi = {10.1002/1096-8644(200103)114:3<242::AID-AJPA1023>3.0.CO;2-J},
  abstract = {In this study, we describe the dental health of four prehistoric human populations from the southern coast of Peru, an area in which independent archaeological evidence suggests that the practice of coca-leaf chewing was relatively common. A repeated pattern of cervical-root caries accompanying root exposure was found on the buccal surfaces of the posterior dentition, coinciding with the typical placement of coca quids during mastication. To further examine the association between caries patterning and coca chewing, caries site characteristics of molar teeth were utilized as indicators for estimating the likelihood of coca chewing for adults within each of the study samples. Likelihood estimates were then compared with results of a test for coca use derived from hair samples from the same individuals. The hair and dental studies exhibited an 85.7\% agreement. Thus, we have demonstrated the validity of a hard-tissue technique for identifying the presence of habitual coca-leaf chewing in ancient human remains, which is useful in archaeological contexts where hair is not preserved. These data can be used to explore the distribution of coca chewing in prehistoric times. Simultaneously, we document the dental health associated with this traditional Andean cultural practice. Am J Phys Anthropol 114:242\textendash 257, 2001. \textcopyright{} 2001 Wiley-Liss, Inc.},
  copyright = {Copyright \textcopyright{} 2001 Wiley-Liss, Inc.},
  langid = {english},
  keywords = {cervical-root caries,coca chewing,oral pathology,Peru,posterior teeth},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/1096-8644\%28200103\%29114\%3A3\%3C242\%3A\%3AAID-AJPA1023\%3E3.0.CO\%3B2-J}
}

@incollection{irishIntroductionDental2015,
  title = {Introduction to {{Dental Anthropology}}},
  booktitle = {A {{Companion}} to {{Dental Anthropology}}},
  author = {Irish, Joel D. and Scott, G. Richard},
  editor = {Irish, Joel D. and Scott, G. Richard},
  year = {2015},
  pages = {3--6},
  publisher = {{John Wiley \& Sons, Ltd}},
  address = {{Chichester}},
  doi = {10.1002/9781118845486.ch18},
  chapter = {18},
  isbn = {978-1-118-84548-6},
  langid = {english},
  keywords = {Arizona State University Dental Anthropology System,distance statistics,genetic relatedness,P henetic affinities,qualitative and quantitative analyses},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781118845486.ch18}
}

@article{jainIsolationCharacterization2013,
  title = {Isolation and Characterization of Biofilm-Forming Bacteria and Associated Extracellular Polymeric Substances from Oral Cavity},
  author = {Jain, Kirti and Parida, Sheetal and Mangwani, Neelam and Dash, Hirak R. and Das, Surajit},
  year = {2013},
  month = dec,
  journal = {Annals of Microbiology},
  volume = {63},
  number = {4},
  pages = {1553--1562},
  issn = {1590-4261, 1869-2044},
  doi = {10.1007/s13213-013-0618-9},
  abstract = {The current work deals with the studies on characterization of two biofilm-forming bacteria isolated from the oral cavity. The major constituent of biofilm other than bacterial cells is the extracellular polymeric substance (EPS) matrix, which is secreted by the bacterial cells themselves. Physical properties of biofilms such as attachment, mechanical strength, antibiotic resistance can be attributed to EPS matrix. Molecular phylogeny confirmed these two isolates as Pseudomonas aeruginosa and Bacillus subtilis. It was observed that cell attachment in both the strains was maximal when xylose was used as the sole carbon source. The EPS characterization result indicated the presence of a macromolecular complex constituting of carbohydrate, protein, lipids and nucleic acids. Test for biofilm formation in the presence of metal salts of iron and zinc showed moderate to high inhibition of biofilm formation. However, calcium, iron and copper have been found to enhance biofilm growth significantly. There was more than 50 \% increase in biofilm growth by P. aeruginosa with an increase in calcium concentration up to 80 ppm (Two tailed t-test P{$<$}0.05), whereas {$\geq$} 15 \% increase in biofilm growth by B. subtilis was observed in the presence of 80 ppm of calcium. However, variations were significant (Two way ANOVA, P{$<$}0.01) between different metals in different concentrations. In this study, attempts have been made to examine the effect of different carbon sources and physiological conditions on biofilm growth.},
  langid = {english},
  keywords = {FTIR,oral biofilm}
}

@article{janeAnthologyStarch1994,
  title = {Anthology of {{Starch Granule Morphology}} by {{Scanning Electron Microscopy}}},
  author = {Jane, Jay-Lin and Kasemsuwan, Tunyawat and Leas, Sharon and Zobel, Henzy and Robyt, John F.},
  year = {1994},
  journal = {Starch - St\"arke},
  volume = {46},
  number = {4},
  pages = {121--129},
  issn = {00389056, 1521379X},
  doi = {10.1002/star.19940460402},
  langid = {english}
}

@article{jepsenCalculusRemoval2011,
  title = {Calculus Removal and the Prevention of Its Formation},
  author = {Jepsen, S{\o}ren and Deschner, James and Braun, Andreas and Schwarz, Frank and Eberhard, J{\"o}rg},
  year = {2011},
  journal = {Periodontology 2000},
  volume = {55},
  number = {1},
  pages = {167--188},
  issn = {1600-0757},
  doi = {10.1111/j.1600-0757.2010.00382.x},
  langid = {english},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0757.2010.00382.x}
}

@article{jiFluorideMagnesium2000,
  title = {Fluoride and Magnesium Concentrations in Human Dental Calculus Obtained from {{Japanese}} and {{Chinese}} Patients},
  author = {Ji, Haixiang and Nakagaki, Haruo and Hayashizaki, Junko and Tsuboi, Shinji and Kato, Kazuo and Toyama, Atsushi and Arai, Koji and Thuy, Tran Thu and Ha, Nguyen Thi Thanh and Kameyama, Yoichiro and Kirkham, Jennifer and Robinson, Colin},
  year = {2000},
  month = jul,
  journal = {Archives of Oral Biology},
  volume = {45},
  number = {7},
  pages = {611--615},
  issn = {00039969},
  doi = {10.1016/S0003-9969(00)00021-2},
  abstract = {Calculus deposited on a total of 68 permanent teeth from patients 30{$\pm$}60 years old from Nagoya in Japan and Beijing in China was investigated. An abrasive microsampling method was used to examine the \textasciimacron uoride (F) and magnesium (Mg) distribution, using a \textasciimacron uoride ion-speci\textregistered c electrode and atomic absorption spectrophotometry, respectively. F concentrations decreased from the surface towards the interior of the calculus. Mg concentrations, however, gradually rose towards the innermost surface adjacent to the tooth. In all parts of the depth pro\textregistered les, the average concentrations of both magnesium and \textasciimacron uoride were higher in the Japanese than in the Chinese calculus. Towards the inner surface of the calculus, F and Mg concentrations were also much higher in the Japanese than in the Chinese group. A greater intake of sea foods and greater use of \textasciimacron uoride dentifrices are possible reasons for the higher F and Mg concentrations in the Japanese individuals. 7 2000 Elsevier Science Ltd. All rights reserved.},
  langid = {english}
}

@article{jinSupragingivalCalculus2002,
  title = {Supragingival {{Calculus}}: {{Formation}} and {{Control}}},
  shorttitle = {Supragingival {{Calculus}}},
  author = {Jin, Ye and Yip, Hak-Kong},
  year = {2002},
  journal = {Critical Reviews in Oral Biology \& Medicine},
  publisher = {{SAGE Publications}},
  doi = {10.1177/154411130201300506},
  abstract = {Dental calculus is composed of inorganic components and organic matrix. Brushite, dicalcium phosphate dihydrate, octacalcium phosphate, hydroxyapatite, and whit...},
  langid = {english}
}

@article{jovanovicNeolithicCalculus2021,
  title = {Microbotanical Evidence for the Spread of Cereal Use during the {{Mesolithic-Neolithic}} Transition in the {{Southeastern Europe}} ({{Danube Gorges}}): {{Data}} from Dental Calculus Analysis},
  shorttitle = {Microbotanical Evidence for the Spread of Cereal Use during the {{Mesolithic-Neolithic}} Transition in the {{Southeastern Europe}} ({{Danube Gorges}})},
  author = {Jovanovi{\'c}, Jelena and Power, Robert C. and {de Becdeli{\`e}vre}, Camille and Goude, Gwena{\"e}lle and Stefanovi{\'c}, Sofija},
  year = {2021},
  month = jan,
  journal = {Journal of Archaeological Science},
  volume = {125},
  pages = {105288},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2020.105288},
  abstract = {Research increasingly suggests that natural and social environments shaped the Neolithic expansion of the farming niche into Europe. The Danube Gorges, on account of its position between the Mediterranean and more temperate regions and the presence of archaeological sites with continuous Mesolithic and Neolithic layers of occupation associated with vast burial grounds is ideal for studying the modality of Neolithization. Previous dietary stable isotope (carbon, nitrogen, and sulphur) studies in the Central Balkan area indicate that many Neolithic humans remained reliant on foraged aquatic resources in the Gorges. Until now, there is no unambiguous evidence of cereal consumption in this region. The possibility that the rich aquatic resources of the Danube river habitats within Central Balkans influenced diet and thus delayed uptake of Neolithic cultigens is unanswered. The extensive skeletal record from sites in the Danube Gorges (Central Balkans) with its long temporal sequence, provides the opportunity to reconstruct plant use during Mesolithic and the Neolithic. To assess when cereals and possibly cultivated plants spread to the region, we analysed the microbotanical remains (starch grains and phytoliths) entrapped in the dental calculus of 81 individuals dating from 9100 to 5500~cal BC, recovered from five sites in the Danube Gorges. This study marks the largest study of dental calculus from this period so far conducted. Added to this, we present new radiocarbon dates (n~=~17), bone collagen stable isotope data ({$\delta$}13C and {$\delta$}15N; n~=~5) and data on caries frequency. This dietary study identifies that the growing of crops commenced in the Early Neolithic circa 6000~cal BC and was brought by farming migrants of north-western Anatolian ancestry into the Danube Gorges. Despite bringing a Neolithic agro-pastoral subsistence practices and cultural novelties in the Gorges, these migrants and their descendants adopted some of the local dietary and cultural traditions, suggesting a mosaic pattern of Neolithization. The resulting data provides a better understanding of the tempo and spread of cereal agriculture practices and the role of cereals in the diet of Danube Gorges inhabitants.},
  langid = {english},
  keywords = {Cereals,Danube Gorges,Dental calculus analyses,Diet,Mesolithic-Neolithic transition}
}

@article{kashketFoodParticles1996,
  title = {Accumulation of {{Fermentable Sugars}} and {{Metabolic Acids}} in {{Food Particles}} That {{Become Entrapped}} on the {{Dentition}}},
  author = {Kashket, S and Zhang, J and Houte, J Van},
  year = {1996},
  journal = {Journal of Dental Research},
  pages = {8},
  abstract = {Earlier studies (Kashket et al., 1991) showed that particles of high-starch snack foods remained longer on the teeth than those of high-sucrose, low-starch foods. The question arose whether the prolonged presence of food particles enhances cariogenicity. A study was undertaken to measure sugars, starches, and metabolic acids in retained food particles. Subjects consumed portions of different foods, and particles were removed from all bicuspids and first molars at defined times after swallowing. Dry weights, sugars, and short-chain carboxylic acids were determined. High-sucrose foods were cleared rapidly from the teeth, while high-starch foods were retained for up to 20 min. Sucrose, glucose, and fructose persisted in the retained particles. Particles of high-starch foods accumulated maltose and maltotriose, presumably from the breakdown of starch by salivary amylase. At maximum, maltose plus maltotriose constituted 94\% of total sugars in particles of potato chips; corresponding values in doughnuts, peanut butter cookies, and salted crackers were 43, 51, and 61\%, respectively. Total fermentable sugars in the particles of high-starch foods were similar to those for the high-sucrose confectionery products. Carboxylic acids accumulated within the particles, presumably due to the fermentation of the sugars by entrapped salivary micro-organisms. At maximum (5 to 7 min), acetic, formic, lactic, and propionic acids rose 17-, 30-, 15-, and 1.3-fold, respectively, in dough-nuts, and to smaller degrees in potato chips, salted crackers, and chocolatecaramel-peanut bars. In summary, the study demonstrated the persistence of sugars, the progressive accumulation of starch breakdown products, and the fermentation of the accumulated sugars in retained food particles. The findings support the view that high-starch foods contribute to the development of caries lesions.},
  langid = {english}
}

@article{kashketFoodRetention1991,
  title = {Lack of {{Correlation Between Food Retention}} on the {{Human Dentition}} and {{Consumer Perception}} of {{Food Stickiness}}},
  author = {Kashket, S. and Van Houte, J. and Lopez, L.R. and Stocks, S.},
  year = {1991},
  month = oct,
  journal = {Journal of Dental Research},
  volume = {70},
  number = {10},
  pages = {1314--1319},
  issn = {0022-0345, 1544-0591},
  doi = {10.1177/00220345910700100101},
  abstract = {When dental health professionals advise that sticky foods be avoided, it is left to the consumer to choose correctly among different foods. In this study, comparisons were made among consumer ratings of stickiness of 21 commercially available foods and objective measurements of tooth retention of each of the foods. No correlation was found between the two, and neither the rates of clearance of food particles from the teeth nor the rates of clearance of food-derived sugars from the saliva correlated with ratings of food stickiness. Cookies, crackers, and potato chips were most retentive, whereas caramels, jelly beans, raisins, and milk chocolate bars were among those poorly retained. Clearance rates appeared to vary inversely with initial retention. However, chocolate-caramel bars exhibited high initial retention and a very rapid rate of clearance from the teeth. The findings show that consumers cannot accurately assess the retentiveness of foods and, thus, the advice simply to avoid sticky ones is inadequate.},
  langid = {english}
}

@incollection{katzenbergStableIsotope2008,
  title = {Stable {{Isotope Analysis}}: {{A Tool}} for {{Studying Past Diet}}, {{Demography}}, and {{Life History}}},
  booktitle = {Biological {{Anthropology}} of the {{Human Skeleton}}},
  author = {Katzenberg, M. A.},
  editor = {Katzenberg, M. A. and Saunders, S. R.},
  year = {2008},
  pages = {301--340},
  publisher = {{John Wiley and Sons}},
  address = {{Hoboken}}
}

@article{kazarinaPostmedievalMicrobial2021,
  title = {The {{Postmedieval Latvian Oral Microbiome}} in the {{Context}} of {{Modern Dental Calculus}} and {{Modern Dental Plaque Microbial Profiles}}},
  author = {Kazarina, Alisa and {Petersone-Gordina}, Elina and Kimsis, Janis and Kuzmicka, Jevgenija and Zayakin, Pawel and Gri{\v s}kjans, {\v Z}ans and Gerhards, Guntis and Ranka, Renate},
  year = {2021},
  month = feb,
  journal = {Genes},
  volume = {12},
  number = {2},
  pages = {309},
  issn = {2073-4425},
  doi = {10.3390/genes12020309},
  abstract = {Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16\textendash 17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.},
  langid = {english},
  keywords = {dental calculus,kraken}
}

@article{kearnsMasterRegulator2005,
  title = {A Master Regulator for Biofilm Formation by {{Bacillus}} Subtilis},
  author = {Kearns, Daniel B. and Chu, Frances and Branda, Steven S. and Kolter, Roberto and Losick, Richard},
  year = {2005},
  journal = {Molecular Microbiology},
  volume = {55},
  number = {3},
  pages = {739--749},
  issn = {1365-2958},
  doi = {10.1111/j.1365-2958.2004.04440.x},
  abstract = {Wild strains of Bacillus subtilis are capable of forming architecturally complex communities of cells known as biofilms. Critical to biofilm formation is the eps operon, which is believed to be responsible for the biosynthesis of an exopolysaccharide that binds chains of cells together in bundles. We report that transcription of eps is under the negative regulation of SinR, a repressor that was found to bind to multiple sites in the regulatory region of the operon. Mutations in sinR bypassed the requirement in biofilm formation of two genes of unknown function, ylbF and ymcA, and sinI, which is known to encode an antagonist of SinR. We propose that these genes are members of a pathway that is responsible for counteracting SinR-mediated repression. We further propose that SinR is a master regulator that governs the transition between a planktonic state in which the bacteria swim as single cells in liquid or swarm in small groups over surfaces, and a sessile state in which the bacteria adhere to each other to form bundled chains and assemble into multicellular communities.},
  langid = {english},
  keywords = {agar,biofilm},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2004.04440.x}
}

@incollection{kinastonOrtnerDentition2019,
  title = {The {{Dentition}}: {{Development}}, {{Disturbances}}, {{Disease}}, {{Diet}}, and {{Chemistry}}},
  shorttitle = {Chapter 21 - {{The Dentition}}},
  booktitle = {Ortner's {{Identification}} of {{Pathological Conditions}} in {{Human Skeletal Remains}} ({{Third Edition}})},
  author = {Kinaston, Rebecca and Willis, Anna and Miszkiewicz, Justyna J. and Tromp, Monica and Oxenham, Marc F.},
  editor = {Buikstra, Jane E.},
  year = {2019},
  month = jan,
  pages = {749--797},
  publisher = {{Academic Press}},
  address = {{San Diego}},
  doi = {10.1016/B978-0-12-809738-0.00021-1},
  abstract = {The chief focus of this chapter is the dentition, with reviews of associated structures where relevant. Dental development, including the dentin and enamel, is discussed in the first section, followed by disturbances in the dentin and enamel in the second section. The third section looks at the identification of oral disease, including caries, alveolar lesions, antemortem tooth loss (AMTL), and periodontal disease. The fourth section focuses on interpreting oral health, particularly in the context of sex differences and major demographic transitions. The fifth discusses dental chemistry in terms of paleodietary reconstruction, breastfeeding and weaning, stress and disease, and finally mobility and migration. The final section examines dental calculus in the context of microparticles and then chemical analyses of calculus, with aDNA and protein analyses of dental calculus also reviewed.},
  isbn = {978-0-12-809738-0},
  langid = {english},
  keywords = {aDNA,alveolar lesions,antemortem tooth loss,breastfeeding and weaning,caries,dental calculus,dental chemistry,dental development,dentin,Dentition,enamel,interpreting oral health,migration,mobility,paleodietary reconstruction,periodontal disease}
}

@article{kingCautionaryTales2017,
  title = {Cautionary Tales on the Identification of Caffeinated Beverages in {{North America}}},
  author = {King, Adam and Powis, Terry G. and Cheong, Kong F. and Gaikwad, Nilesh W.},
  year = {2017},
  month = sep,
  journal = {Journal of Archaeological Science},
  volume = {85},
  pages = {30--40},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2017.06.006},
  abstract = {In recent years several studies have attempted to understand the use of caffeinated beverages in North America before the coming of Europeans using absorbed residues. These studies have focused on the two key plant sources of caffeine in North America: Theobroma cacao (cacao) and Ilex vomitoria (yaupon holly). The authors initiated a study to explore the possibility that one or both plants were used at the Mississippian period (900\textendash 1600 CE) center of Etowah in northern Georgia. In the process, a series of problems with methodologies in use were revealed. Key among those were limitations on the methods used to identify ancient caffeinated beverage residues, distinguish them from modern contamination, and differentiate residues made by each plant. In this paper we explore what our data from the Etowah site reveal about methodologies currently in use and make suggestions for future studies of residues created by caffeinated beverages in North America.},
  keywords = {Absorbed residues,Cacao,Mass spectrometry,Ultra performance liquid chromatography,Yaupon holly}
}

@article{kitabaBlackCeramic2017,
  title = {Black Ceramic Spheres as Marker Grains for Microfossil Analyses, with Improved Chemical, Physical, and Optical Properties},
  author = {Kitaba, Ikuko and Nakagawa, Takeshi},
  year = {2017},
  month = oct,
  journal = {Quaternary International},
  series = {Japanese {{Quaternary Studies}} 2 ({{Part I}})},
  volume = {455},
  pages = {166--169},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2017.08.052},
  abstract = {Marker grain method is commonly used by palynologists to quantify absolute pollen concentration in sediments. DuPont NEM plastic microbeads and Lycopodium spore tablets are two of the most commonly used marker grains. The DuPont NEM series has an obvious advantage over Lycopodium tablets because Lycopodium is not guaranteed `exotic' in many ecosystems (especially in the past). Moreover, NEM also has high visibility, easily identifiable spherical shape, and availability in different size ranges. However, the production of NEM has been discontinuous since more than a decade, and palynologists of the world are using the precious remainders of their own stock in very small (=suboptimal) quantities. Here we propose a solution. Microspheres of black ceramic can be used as marker grains for a wide range of microfossil analyses (in this paper, however, we mainly discuss the use of the material for pollen analysis because of the expertise of the authors). The ceramic spheres are tolerant to all chemicals commonly used during pollen extraction processes and is extremely resistant to physical stresses. The particles are matt black, spherical, available in a wide range of size clusters, have a density very close to that of fossil pollen grains (1.424~g/cm3 vs. 1.494~g/cm3 in average), and don't change color and density over a long storage in acidic liquids. The behavior of ceramic spheres was closer to the pollen grains than the Lycopodium spores regardless of the pollen concentration and composition in sediments. In combination, these properties make the black ceramic spheres an even better solution for palynologists than DuPont NEM microbeads or Lycopodium spore tablets. The absolute pollen concentrations estimated from ceramic spheres and those estimated from volume method were indistinguishable within errors. On the other hand, when the samples were relatively poor in fossil pollen grains, the concentrations calculated by Lycopodium method tended to be significantly overestimated. The ceramic microbeads are available either as a dry powder in different size ranges, or as a mixture of two size ranges blended in a defined ratio and dispersed in a buoyancy-neutral liquid, ready to be added to sediment samples. Mixing two different size ranges in a known ratio serves to detect any laboratory failures that differentially favor recovery of larger or smaller pollen types.},
  langid = {english},
  keywords = {Absolute pollen concentration,Black ceramic spheres,Marker grains,Microbeads,Microfossil analysis,Pollen analysis}
}

@article{knappSettingStage2012,
  title = {Setting the Stage \textendash{} {{Building}} and Working in an Ancient {{DNA}} Laboratory},
  author = {Knapp, Michael and Clarke, Andrew C. and Horsburgh, K. Ann and {Matisoo-Smith}, Elizabeth A.},
  year = {2012},
  month = jan,
  journal = {Annals of Anatomy - Anatomischer Anzeiger},
  series = {Special {{Issue}}: {{Ancient DNA}}},
  volume = {194},
  number = {1},
  pages = {3--6},
  issn = {0940-9602},
  doi = {10.1016/j.aanat.2011.03.008},
  abstract = {With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process.},
  langid = {english},
  keywords = {aDNA,Contamination,Next generation sequencing}
}

@article{knightsSourceTracker2011,
  title = {Bayesian Community-Wide Culture-Independent Microbial Source Tracking},
  author = {Knights, Dan and Kuczynski, Justin and Charlson, Emily S and Zaneveld, Jesse and Mozer, Michael C and Collman, Ronald G and Bushman, Frederic D and Knight, Rob and Kelley, Scott T},
  year = {2011},
  month = sep,
  journal = {Nature Methods},
  volume = {8},
  number = {9},
  pages = {761--763},
  issn = {1548-7091, 1548-7105},
  doi = {10.1038/nmeth.1650},
  abstract = {Contamination is a critical issue in high-throughput metagenomic studies, yet progress towards a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments. We apply SourceTracker to new microbial surveys from neonatal intensive care units (NICUs), offices, and molecular biology laboratories, and provide a database of known contaminants for future testing.},
  langid = {english}
}

@article{kolenbranderAdhereToday1993,
  title = {Adhere Today, Here Tomorrow: Oral Bacterial Adherence},
  shorttitle = {Adhere Today, Here Tomorrow},
  author = {Kolenbrander, Paul E. and London, J.},
  year = {1993},
  month = jun,
  journal = {Journal of Bacteriology},
  volume = {175},
  number = {11},
  pages = {3247--3252},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/jb.175.11.3247-3252.1993},
  langid = {english}
}

@article{kolenbranderOralMultispecies2010,
  title = {Oral Multispecies Biofilm Development and the Key Role of Cell\textendash Cell Distance},
  author = {Kolenbrander, Paul E. and Palmer, Robert J. and Periasamy, Saravanan and Jakubovics, Nicholas S.},
  year = {2010},
  month = jul,
  journal = {Nature Reviews Microbiology},
  volume = {8},
  number = {7},
  pages = {471--480},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro2381},
  abstract = {Growth of oral bacteria in situ requires adhesion to a surface because the constant flow of host secretions thwarts the ability of planktonic cells to grow before they are swallowed. Therefore, oral bacteria evolved to form biofilms on hard tooth surfaces and on soft epithelial tissues, which often contain multiple bacterial species. Because these biofilms are easy to study, they have become the paradigm of multispecies biofilms. In this Review we describe the factors involved in the formation of these biofilms, including the initial adherence to the oral tissues and teeth, cooperation between bacterial species in the biofilm, signalling between the bacteria and its role in pathogenesis, and the transfer of DNA between bacteria. In all these aspects distance between cells of different species is integral for oral biofilm growth.},
  langid = {english},
  keywords = {notion,oral biofilm,oral microbiome}
}

@article{kondoAssociationCoffee2021,
  title = {Association between Coffee and Green Tea Intake and Pneumonia among the {{Japanese}} Elderly: A Case-Control Study},
  shorttitle = {Association between Coffee and Green Tea Intake and Pneumonia among the {{Japanese}} Elderly},
  author = {Kondo, Kyoko and Suzuki, Kanzo and Washio, Masakazu and Ohfuji, Satoko and Adachi, Satoru and Kan, Sakae and Imai, Seiichiro and Yoshimura, Kunihiko and Miyashita, Naoyuki and Fujisawa, Nobumitsu and Maeda, Akiko and Fukushima, Wakaba and Hirota, Yoshio},
  year = {2021},
  month = mar,
  journal = {Scientific Reports},
  volume = {11},
  number = {1},
  pages = {5570},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-84348-w},
  abstract = {A large prospective cohort study in the United States examined the association between coffee intake and overall and cause-specific mortality and showed a inverse association between pneumonia and influenza deaths and coffee intake. In Japan, the mortality rate of pneumonia in elderly people is high, and its prevention is an important issue. The present study investigated the association between coffee and green tea intake and pneumonia among the elderly. The design was a hospital-based case control study. The cases were patients over 65~years old newly diagnosed as pneumonia. As a control, patients with the same sex and age (range of 5~years) who visited the same medical institution around the same time (within 2~months after examination of the case) for a disease other than pneumonia were selected. There were two controls per case. Odds ratio (OR) and 95\% confidence interval (CI) for pneumonia of coffee and green tea intake during the past month were calculated using a conditional logistic regression model. A total of 199 cases and 374 controls were enrolled. When compared to those who do not drink coffee, the OR for pneumonia of those who drink less than one cup of coffee per day was 0.69 (95\% CI 0.39\textendash 1.21), OR of those who drink one cup was 0.67 (0.38\textendash 1.18), and OR of those who drink two or more cups was 0.50 (0.28\textendash 0.88) (Trend p\,=\,0.024). No association was found between pneumonia and green tea consumption. This study suggested a preventive association between coffee intake over 2 cups per day and pneumonia in the elderly.},
  copyright = {2021 The Author(s)},
  langid = {english},
  keywords = {Medical research,Risk factors}
}

@article{kraken2,
  title = {Improved Metagenomic Analysis with {{Kraken}} 2},
  author = {Wood, Derrick E. and Lu, Jennifer and Langmead, Ben},
  year = {2019},
  month = nov,
  journal = {Genome Biology},
  volume = {20},
  number = {1},
  pages = {257},
  issn = {1474-760X},
  doi = {10.1186/s13059-019-1891-0},
  abstract = {Although Kraken's k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85\%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.},
  keywords = {Alignment-free methods,Metagenomics,Metagenomics classification,Microbiome,Minimizers,Probabilistic data structures}
}

@article{langejansRemainsDay2010,
  title = {Remains of the Day-Preservation of Organic Micro-Residues on Stone Tools},
  author = {Langejans, Geeske H. J.},
  year = {2010},
  month = may,
  journal = {Journal of Archaeological Science},
  volume = {37},
  number = {5},
  pages = {971--985},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2009.11.030},
  abstract = {Here I report on the decay processes of microscopic organic residues left on stone tool surfaces after their use. Residue analysis on ancient stone tools facilitates reconstruction of past activities. This study enables predictions about the circumstances under which ancient residues preserve. Experimental tool sets with modern residues were buried for a year in separate deposits at Sterkfontein, Sibudu (South Africa) and Zelhem (the Netherlands) whose pH and geomorphology varied, they were then analysed using light microscopy. Biological weathering mainly causes residue decay. In unstable environments rich in microbes and micro-organisms, residues decay quickly. From an archaeological perspective this means that sites that are stable, desiccated, waterlogged, extremely acidic or alkaline and extremely cold or hot sites. Different residue types have different preservation optima and this may lead to a preservation and perhaps interpretation bias. The preliminary predictive models presented in this paper could aid in the considered selection of sites and samples.},
  langid = {english},
  keywords = {Conservation,Decay,Experimental archaeology,Micro-remains,Preservation,Replication,Residue analysis,Stone tools,Taphonomy}
}

@article{leeOralFluid2011,
  title = {Oral {{Fluid Cannabinoids}} in {{Chronic}}, {{Daily Cannabis Smokers}} during {{Sustained}}, {{Monitored Abstinence}}},
  author = {Lee, Dayong and Milman, Garry and Barnes, Allan J and Goodwin, Robert S and Hirvonen, Jussi and Huestis, Marilyn A},
  year = {2011},
  month = aug,
  journal = {Clinical Chemistry},
  volume = {57},
  number = {8},
  pages = {1127--1136},
  issn = {0009-9147},
  doi = {10.1373/clinchem.2011.164822},
  abstract = {Oral fluid (OF) is an accepted alternative biological matrix for drug treatment, workplace, and DUID (driving under the influence of drugs) investigations, but establishing the cannabinoid OF detection window and concentration cutoff criteria are important.Cannabinoid concentrations were quantified in OF from chronic, daily cannabis smokers during monitored abstinence. {$\Delta$}9-tetrahydrocannabinol (THC)3, cannabidiol (CBD), cannabinol (CBN), and 11-nor-9-carboxy-THC (THCCOOH) were determined in daily OF samples collected with the Quantisal\texttrademark{} device. GC-MS limits of quantification (LOQ) were 0.5 {$\mu$}g/L for THC and CBD, 1 {$\mu$}g/L for CBN, and 7.5 ng/L for THCCOOH.After providing written informed consent for this institutional review board\textendash approved study, 28 participants resided from 4 to 33 days on the secure research unit and provided 577 OF specimens. At the LOQ, THC was generally quantifiable for 48 h, whereas CBD and CBN were detected only at admission. Median THCCOOH detection time was 13 days (CI 6.4\textendash 19.6 days). Mean THC detection rates decreased from 89.3\% at admission to 17.9\% after 48 h, whereas THCCOOH gradually decreased from 89.3\% to 64.3\% within 4 days. Criteria of THC {$\geq$}2 {$\mu$}g/L and THCCOOH {$\geq$}20 ng/L reduced detection to \&lt;48 h in chronic cannabis smokers. An OF THCCOOH/THC ratio {$\leq$}4 ng/{$\mu$}g or presence of CBD or CBN may indicate more recent smoking.THC, THCCOOH, CBD, and CBN quantification in confirmatory OF cannabinoid testing is recommended. Inclusion of multiple cannabinoid cutoffs accounted for residual cannabinoid excretion in OF from chronic, daily cannabis smokers and could reduce the potential for positive test results from passive cannabis smoke exposure and lead to greatly improved test interpretation.}
}

@incollection{lemmersMiddenbeemster2013,
  title = {{Fysisch antropologische analyse Middenbeemster}},
  booktitle = {{De begravingen bij de Keyserkerk te Middenbeemster}},
  author = {Lemmers, S. A. M. and Schats, Rachel and Hoogland, M. L. P. and {Waters-Rist}, Andrea},
  year = {2013},
  pages = {35--60},
  langid = {dutch}
}

@article{lemoyneCalculusPretreatments2021,
  title = {Effects of Chemical Pre-Treatments on Modified Starch Granules: {{Recommendations}} for Dental Calculus Decalcification for Ancient Starch Research},
  shorttitle = {Effects of Chemical Pre-Treatments on Modified Starch Granules},
  author = {Le Moyne, Charles and Crowther, Alison},
  year = {2021},
  month = feb,
  journal = {Journal of Archaeological Science: Reports},
  volume = {35},
  pages = {102762},
  issn = {2352-409X},
  doi = {10.1016/j.jasrep.2020.102762},
  abstract = {Starch granules and other plant microremains embedded in dental calculus provide information about the diet and culinary practices of past individuals. While most researchers use either hydrochloric acid (HCl) or ethylenediaminetetraacetic acid (EDTA) to demineralise samples and release embedded microremains, protocols vary significantly in regard to chemical concentration and duration. Furthermore, there are conflicting reports concerning the suitability of these chemicals for archaeological starch analyses, particularly when granules are modified (damaged) such as from food processing or enzymatic digestion. This study tests 0.5~M HCl and 0.5~M EDTA on modified modern wheat, chickpea and potato starch with direct observation of individual starch granules over 168~h, the maximum duration reported so far for full decalcification of archaeological calculus samples. While there were no observable changes to gross morphological characteristics of any granules, metric analysis indicates slight changes to average granule size in milled potato and wheat starch in all solutions. Furthermore, interactions between the chemical reagent and ions released from the calculus matrix have the potential to result in the diminished recovery of archaeological starch from HCl extractions. We recommend that of these two chemical decalcification options, EDTA is more suitable for processing archaeological dental calculus for starch microremains as it chelates ions released during decalcification of the calculus matrix that might otherwise adversely affect archaeological starch granules.},
  langid = {english},
  keywords = {Diet,Ethylenediaminetetraacetic acid,Hydrochloric acid,Plant microremains,Starch analysis}
}

@article{leonardPlantMicroremains2015,
  title = {Plant Microremains in Dental Calculus as a Record of Plant Consumption: {{A}} Test with {{Twe}} Forager-Horticulturalists},
  shorttitle = {Plant Microremains in Dental Calculus as a Record of Plant Consumption},
  author = {Leonard, Chelsea and Vashro, Layne and O'Connell, James F. and Henry, Amanda G.},
  year = {2015},
  month = jun,
  journal = {Journal of Archaeological Science: Reports},
  volume = {2},
  pages = {449--457},
  issn = {2352-409X},
  doi = {10.1016/j.jasrep.2015.03.009},
  abstract = {Starch granules and phytoliths trapped in dental calculus preserve a record of plant consumption. Analysis of these microscopic plant remains has increased in popularity in recent years, providing information on diet that complements dental microwear and stable isotope studies. However, it is unclear how accurately these microremains reflect plant consumption. This study examines how well starch granules and phytoliths in dental calculus from a living population (the Twe) with a well-documented diet capture the range and intensity of plant consumption. We find that plant microremains are a poor predictor of plant consumption on an individual level, but may provide a good signal of plant consumption across a population, as well as evidence for plant processing in the mouth. This is the first study to test how well plant microremains in dental calculus reflect plant consumption in a population with a known diet. Results from this project have implications for interpreting plant microremain data from archaeological dental calculus samples.},
  langid = {english},
  keywords = {Dental calculus,Foragers,Phytolith,Plant foods,Starch}
}

@book{leuwProhibitionLegalization1994,
  title = {Between {{Prohibition}} and {{Legalization}}: {{The Dutch Experiment}} in {{Drug Policy}}},
  shorttitle = {Between {{Prohibition}} and {{Legalization}}},
  author = {Leuw, Ed and Marshall, Ineke Haen},
  year = {1994},
  publisher = {{Kugler Publications}},
  abstract = {In a period of two decades Dutch drug policy has evolved in partial opposition to the internationally dominant ideology of prohibitionism. The "normalizing" home policy, together with the compliance to law enforcement in the international arena, make up a rather complicated and ambivalent Dutch position in drug policy. The Dutch drug policy is fully in line with the international control practices against wholesale drug trafficking. In regards to its social drug policy, however, it has become a rare dissenter within an increasingly unifying and compelling international drug policy context. This book gives an account of the national Dutch drug control strategy.},
  googlebooks = {2mAVkStNG5EC},
  isbn = {978-90-6299-103-7},
  langid = {english},
  keywords = {cocaine,Netherlands,opium}
}

@article{lieverseDentalHealth2007,
  title = {Dental Health Indicators of Hunter\textendash Gatherer Adaptation and Cultural Change in {{Siberia}}'s {{Cis-Baikal}}},
  author = {Lieverse, Angela R. and Link, David W. and Bazaliiskiy, Vladimir Ivanovich and Goriunova, Olga Ivanovna and Weber, Andzrej W.},
  year = {2007},
  journal = {American Journal of Physical Anthropology},
  volume = {134},
  number = {3},
  pages = {323--339},
  issn = {1096-8644},
  doi = {10.1002/ajpa.20672},
  abstract = {This investigation of the Cis-Baikal dental record focuses on health and lifestyle reconstruction of the region's mid-Holocene foragers, with particular interest in an apparent fifth millennium BC biocultural hiatus. The four cemetery populations considered represent two distinct biological and cultural groups separated by an apparent 700-year hiatus: the late Mesolithic-early Neolithic Kitoi culture (6800\textendash 4900 BC) and the middle Neolithic-early Bronze Age Serovo\textendash Glaskovo cultural complex (4200\textendash 1000 BC). Research focuses on the frequency and severity of seven dental health indicators: enamel hypoplasia, caries, alveolar defects, periodontitis, antemortem tooth loss, dental calculus, and dental attrition. Together, these seven indicators provide a basis not only for better understanding mid-Holocene lifeways in the Cis-Baikal but also for independently assessing the relative effectiveness of the different adaptive strategies employed by pre- and posthiatus peoples. Results reveal some discrepancies between the Kitoi and Serovo\textendash Glaskovo, specifically in their relative vulnerability to physiological stress, providing evidence to support previous interpretations of their distinct adaptive regimes (namely the narrower resource base and decreased mobility of the former). Results also suggest that some of the differences observed among the four sites may reflect geographical or environmental factors rather than simply cultural ones. However, despite these distinctions, the overriding trend appears to be one of general continuity, social equality, and good health among all mid-Holocene occupants of the Cis-Baikal, pre- and posthiatus alike. Am J Phys Anthropol 2007. \textcopyright{} 2007 Wiley-Liss, Inc.},
  langid = {english},
  keywords = {alveolar defect,antemortem tooth loss,calculus,caries,dental attrition,enamel hypoplasia,forager,Middle Holocene,periodontitis},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.20672}
}

@article{lieverseDietAetiology1999,
  title = {Diet and the Aetiology of Dental Calculus},
  author = {Lieverse, Angela R.},
  year = {1999},
  journal = {International Journal of Osteoarchaeology},
  volume = {9},
  number = {4},
  pages = {219--232},
  issn = {1099-1212},
  doi = {10.1002/(SICI)1099-1212(199907/08)9:4<219::AID-OA475>3.0.CO;2-V},
  abstract = {The aetiology of dental calculus formation is not fully understood, but it is known that a number of factors play a role. Generally, anthropologists have overlooked the role of other causative factors in the formation of dental calculus, attributing it almost exclusively to diet, particularly protein consumption. Anthropologists have also oversimplified the role of diet in the formation of dental calculus. This may be due to a general paucity on research on dietary effects on calculus formation, as well as a lack of integration between anthropological and non-anthropological data. Copyright \textcopyright{} 1999 John Wiley \& Sons, Ltd.},
  copyright = {Copyright \textcopyright{} 1999 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {dental calculus,dental plaque,mineralization,tartar},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/\%28SICI\%291099-1212\%28199907/08\%299\%3A4\%3C219\%3A\%3AAID-OA475\%3E3.0.CO\%3B2-V}
}

@article{liInfluenceGrinding2020,
  title = {Influence of Grinding on the Preservation of Starch Grains from Rice},
  author = {Li, W. and {Pag{\'a}n-Jim{\'e}nez}, J. R. and Tsoraki, C. and Yao, L. and Van Gijn, A.},
  year = {2020},
  journal = {Archaeometry},
  volume = {62},
  number = {1},
  pages = {157--171},
  issn = {1475-4754},
  doi = {10.1111/arcm.12510},
  abstract = {China is a major centre for rice domestication, where starch grain analysis has been widely applied to archaeological grinding tools to gain information about plant use by ancient Chinese societies. However, few rice starch grains have been identified to date. To understand this apparent scarcity of starch grains from rice, dry- and wet-grinding experiments with stone tools were carried out on four types of cereals: rice (Oryza sativa L.), foxtail millet (Setaria italica), Job's tears (Coix lacryma-jobi L.) and barley (Hordeum vulgare L.). The results reveal that dry-grinding produces significant damage to starches to the point where they may be undetected in archaeological samples, while wet-grinding causes only slight morphological changes to the starch grains. Moreover, rice starch grains have the most substantial alterations from dry-grinding, possibly impeding their identification. These findings provide a possible means to explain the relative scarcity of rice starch grains recovered from archaeological grinding tools, which it is suggested was caused by the use of the dry-grinding technique. Therefore, it is suggested that rice starch grains have been likely underrepresented in the archaeological record, and previous interpretations of starch analyses need to be reconsidered.},
  copyright = {\textcopyright{} 2019 The Authors. Archaeometry published by John Wiley \& Sons Ltd on behalf of University of Oxford},
  langid = {english},
  keywords = {archaeologyNeolithic,China,grainsexperimental,ricegrinding,techniquestarch},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/arcm.12510}
}

@article{limSalivaMicrobiome2017,
  title = {The Saliva Microbiome Profiles Are Minimally Affected by Collection Method or {{DNA}} Extraction Protocols},
  author = {Lim, Yenkai and Totsika, Makrina and Morrison, Mark and Punyadeera, Chamindie},
  year = {2017},
  month = aug,
  journal = {Scientific Reports},
  volume = {7},
  number = {1},
  pages = {8523},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-017-07885-3},
  abstract = {Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human {$\beta$}-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.},
  copyright = {2017 The Author(s)},
  langid = {english},
  keywords = {Bacterial techniques and applications,Microbiome}
}

@article{linANCOMBC2020,
  title = {Analysis of Compositions of Microbiomes with Bias Correction},
  author = {Lin, Huang and Peddada, Shyamal Das},
  year = {2020},
  month = jul,
  journal = {Nature Communications},
  volume = {11},
  number = {1},
  pages = {3514},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-020-17041-7},
  abstract = {Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of ``sampling fraction'' and demonstrate a major hurdle in performing DA analysis of microbiome data is the bias introduced by differences in the sampling fractions across samples. We introduce a methodology called Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework. This formulation makes a fundamental advancement in the field because, unlike the existing methods, it (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement.},
  copyright = {2020 The Author(s)},
  langid = {english},
  keywords = {Computational biology and bioinformatics,Ecology,Microbiology}
}

@article{lindholstLongTerm2010,
  title = {Long Term Stability of Cannabis Resin and Cannabis Extracts},
  author = {Lindholst, Christian},
  year = {2010},
  month = sep,
  journal = {Australian Journal of Forensic Sciences},
  volume = {42},
  number = {3},
  pages = {181--190},
  publisher = {{Taylor \& Francis}},
  issn = {0045-0618},
  doi = {10.1080/00450610903258144},
  abstract = {The aim of the present study was to investigate the stability of cannabinoids in cannabis resin slabs and cannabis extracts upon long-term storage. The levels of tetrahydrocannabinol (THC), cannabinol (CBN), cannabidiol (CBD) and cannabigerol (CBG) on both neutral and acidic form were measured at room temperature, 4\textdegree C and -20\textdegree C for up to 4 years. Acidic THC degrades exponentially via decarboxylation with concentration halve-lives of approximately 330 and 462 days in daylight and darkness, respectively. The degradation of neutral THC seems to occur somewhat slower. When cannabinoids were stored in extracted form at room temperature the degradation rate of acidic THC increased significantly relative to resin material with concentration halve-lives of 35 and 91 days in daylight and darkness, respectively. Once cannabis material is extracted into organic solvents, care should be taken to avoid the influence of sunlight.},
  keywords = {cannabis,extracts,forensic science,resin,stability study,THC},
  annotation = {\_eprint: https://doi.org/10.1080/00450610903258144}
}

@article{lingstromStarchyFood1994,
  title = {Effect of {{Frequent Consumption}} of {{Starchy Food Items}} on {{Enamel}} and {{Dentin Demineralization}} and on {{Plaque pH}} in Situ},
  author = {Lingstrom, P. and Birkhed, D. and Ruben, J. and Arends, J.},
  year = {1994},
  month = mar,
  journal = {Journal of Dental Research},
  volume = {73},
  number = {3},
  pages = {652--660},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/00220345940730031101},
  abstract = {The aim of this cross-over study was to determine the cariogenic potential of starchy food items as between-meal snacks. This was done by measuring demineralization of human enamel and dentin as well as the pH of dental plaque in situ. Eight volunteers with complete dentures carried two enamel and two dentin specimens, mounted in the molar regions of their mandibular prostheses. There were three test periods, each lasting for 21 days, followed in a randomized order: (1) consumption of starchy food products, 12-15 times a day, in addition to the normal diet (starch period); (2) consumption of sucrose products, 12-15 times a day, in addition to the normal diet (sucrose period); and (3) no addition of test products to the normal diet (control period). Both the starch and the sucrose diets increased the demineralization of enamel and dentin compared with the control period. However, only the sucrose period resulted in significant demineralization of dentin compared with the control period. The plaque pH, followed during 60 min after a one-minute mouthrinse with 10\% sucrose, was lower at all time points after both the starch and the sucrose periods compared with the control period.},
  langid = {english},
  keywords = {Carbohydrates,Demineralization (tooth),Dental Plaque,pH,Plaque pH,Starch.}
}

@article{liuNicotinedegradingMicroorganisms2015,
  title = {Nicotine-Degrading Microorganisms and Their Potential Applications},
  author = {Liu, Jianli and Ma, Guanghui and Chen, Tao and Hou, Ying and Yang, Shihua and Zhang, Ke-Qin and Yang, Jinkui},
  year = {2015},
  month = may,
  journal = {Applied Microbiology and Biotechnology},
  volume = {99},
  number = {9},
  pages = {3775--3785},
  issn = {1432-0614},
  doi = {10.1007/s00253-015-6525-1},
  abstract = {Nicotine-degrading microorganisms (NDMs) are a special microbial group which can use nicotine as the sole carbon and nitrogen source for growth. Since the 1950s, the bioconversion of nicotine by microbes has received increasing attention, and several NDMs have been identified, such as Arthrobacter nicotinovorans, Microsporum gypseum, Pellicularia filamentosa JTS-208, and Pseudomonas sp. 41. In recent years, increasing numbers of NDMs have been isolated and identified from tobacco plantation soil, leaf, and tobacco waste. Meanwhile, the metabolic pathway and degradation mechanism of nicotine have been elucidated in several NDMs, such as A. nicotinovorans, Agrobacterium tumefaciens S33, Aspergillus oryzae, and Pseudomonas putida S16. Moreover, several NDMs have been used in improving the quality of cigarettes, treating tobacco waste, and producing valuable intermediates of nicotine. Here, we summarize the diversity, phylogenetic analysis, and potential applications of NDMs.},
  langid = {english},
  keywords = {Metabolic pathways,Nicotine,Nicotine-degrading microorganisms (NDMs),Phylogenetic analysis,Potential application}
}

@article{llamasFieldLaboratory2017,
  title = {From the Field to the Laboratory: {{Controlling DNA}} Contamination in Human Ancient {{DNA}} Research in the High-Throughput Sequencing Era},
  shorttitle = {From the Field to the Laboratory},
  author = {Llamas, Bastien and Valverde, Guido and {Fehren-Schmitz}, Lars and Weyrich, Laura S and Cooper, Alan and Haak, Wolfgang},
  year = {2017},
  month = jan,
  journal = {STAR: Science \& Technology of Archaeological Research},
  volume = {3},
  number = {1},
  pages = {1--14},
  publisher = {{Routledge}},
  issn = {null},
  doi = {10.1080/20548923.2016.1258824},
  abstract = {High-Throughput DNA Sequencing (HTS) technologies have changed the way in which we detect and assess DNA contamination in ancient DNA studies. Researchers use computational methods to mine the large quantity of sequencing data to detect characteristic patterns of DNA damage, and to evaluate the authenticity of the results. We argue that unless computational methods can confidently separate authentic ancient DNA sequences from contaminating DNA that displays damage patterns under independent decay processes, prevention and control of DNA contamination should remain a central and critical aspect of ancient human DNA studies. Ideally, DNA contamination can be prevented early on by following minimal guidelines during excavation, sample collection and/or subsequent handling. Contaminating DNA should also be monitored or minimised in the ancient DNA laboratory using specialised facilities and strict experimental procedures. In this paper, we update recommendations to control for DNA contamination from the field to the laboratory, in an attempt to facilitate communication between field archaeologists, anthropologists and ancient DNA researchers. We also provide updated criteria of ancient DNA authenticity for HTS-based studies. We are confident that the procedures outlined here will increase the retrieval of higher proportions of authentic genetic information from valuable archaeological human remains in the future.},
  keywords = {ancient DNA,archaeological sampling,contaminating DNA},
  annotation = {\_eprint: https://doi.org/10.1080/20548923.2016.1258824}
}

@article{lovejoyAuricular1985,
  title = {Chronological Metamorphosis of the Auricular Surface of the Ilium: {{A}} New Method for the Determination of Adult Skeletal Age at Death},
  shorttitle = {Chronological Metamorphosis of the Auricular Surface of the Ilium},
  author = {Lovejoy, C. Owen and Meindl, Richard S. and Pryzbeck, Thomas R. and Mensforth, Robert P.},
  year = {1985},
  journal = {American Journal of Physical Anthropology},
  volume = {68},
  number = {1},
  pages = {15--28},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330680103},
  abstract = {A new method for the determination of adult skeletal age at death based upon chronological changes in the auricular surface of the ilium is presented. Formal stages have been constructed following extensive tests and refinements in observations made of such changes. Two completely ``blind'' tests were conducted to assess the accuracy and bias of the new method. Results show that the system is equally accurate to pubic symphyseal aging (although somewhat more difficult to apply), and also carries the advantages of a higher preservation rate for the auricular surface in archaeological populations and continued age-related change beyond the fifth decade.},
  copyright = {Copyright \textcopyright{} 1985 Wiley-Liss, Inc., A Wiley Company},
  langid = {english},
  keywords = {Age-determination,Auricular,Demography,Forensic,Ilium,Sacroiliac},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330680103}
}

@article{lustmannScanningElectron1976,
  title = {Scanning Electron Microscopy of Dental Calculus},
  author = {Lustmann, J. and {Lewin-Epstein}, J. and Shteyer, A.},
  year = {1976},
  month = dec,
  journal = {Calcified Tissue Research},
  volume = {21},
  number = {1},
  pages = {47--55},
  issn = {1432-0827},
  doi = {10.1007/BF02547382},
  abstract = {The morphologic structure of anorganic dental calculus was studied by means of the scanning electron microscope. From surface observations, calculus is apparently composed of two components with distinguishable patterns of calcification. One component is formed by the precipitation of minute calcific crystals on microorganisms and intermicrobial substances (plaque matrix). Such calcified masses, often spherical in shape, have a sponge-like appearance with empty spaces representing the former sites of entombed and degenerated organisms. Thus, intracellular calcification is not evident at this stage of calculus development.},
  langid = {english}
}

@article{maatManualPhysical2005,
  title = {Manual for the Physical Anthropological Report},
  author = {Maat, GJR and Mastwijk, RW},
  year = {2005},
  journal = {Barge's Anthropologica},
  number = {6}
}

@article{machtHistoryOpium1915,
  title = {The History of Opium and Some of Its Preparations and Alkaloids},
  author = {Macht, David I},
  year = {1915},
  journal = {The Journal of the American Medical Association},
  volume = {LXIV},
  number = {6},
  pages = {5},
  langid = {english},
  annotation = {https://ia600708.us.archive.org/view\_archive.php?archive=/28/items/crossref-pre-1923-scholarly-works/10.1001\%252Fjama.1915.02570280038011.zip\&file=10.1001\%252Fjama.1915.02570320001001.pdf}
}

@article{mackiePreservationMetaproteome2017,
  title = {Preservation of the Metaproteome: Variability of Protein Preservation in Ancient Dental Calculus},
  shorttitle = {Preservation of the Metaproteome},
  author = {Mackie, Meaghan and Hendy, Jessica and Lowe, Abigail D. and Sperduti, Alessandra and Holst, Malin and Collins, Matthew J. and Speller, Camilla F.},
  year = {2017},
  month = jan,
  journal = {STAR: Science \& Technology of Archaeological Research},
  volume = {3},
  number = {1},
  pages = {58--70},
  publisher = {{Routledge}},
  issn = {null},
  doi = {10.1080/20548923.2017.1361629},
  abstract = {Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.},
  pmid = {29098079},
  keywords = {Archaeology,dental calculus,destructive analysis,LC-MS/MS,protein preservation,shotgun proteomics},
  annotation = {\_eprint: https://doi.org/10.1080/20548923.2017.1361629}
}

@article{maHumanDiet2022,
  title = {Human {{Diet Patterns During}} the {{Qijia Cultural Period}}: {{Integrated Evidence}} of {{Stable Isotopes}} and {{Plant Micro-remains From}} the {{Lajia Site}}, {{Northwest China}}},
  shorttitle = {Human {{Diet Patterns During}} the {{Qijia Cultural Period}}},
  author = {Ma, Zhikun and Liu, Shu and Li, Zhao and Ye, Maolin and Huan, Xiujia},
  year = {2022},
  journal = {Frontiers in Earth Science},
  volume = {10},
  issn = {2296-6463},
  abstract = {The diet of prehistoric humans in the Qijia period (4,400\textendash 3,500~BP) was significantly changed by the advent of dry agriculture and food globalization. However, it is yet to be proven whether wild plants were exploited despite the cultivation of millet, and whether wheat crops, cattle, and sheep originating from southwestern Asia were adopted into the regional human diet. This study presents stable isotope, starch grain, and phytolith analyses of 24 human teeth from the Lajia site in Qinghai, which is a representative Qijia culture settlement site. The carbon and nitrogen isotope results show that the subjects primarily ate C4 plants and had a high protein diet. Starch grain and phytolith results showed that the inhabitants consumed broomcorn millet (Panicum miliaceum), foxtail millet (Setaria italica), Triticeae, tubers and roots, along with other Pooideae and Poaceae plants. This data proves that although broomcorn and foxtail millet formed the mainstay of the Qijia diet, it also included a wide range of plants, such as the tribe Triticeae, tubers and roots, which would have been foraged rather than grown. Compared with the other three contemporaneous sites in Northern China, the proportion of millet starches was highest at the Lajia site, while the type and proportion of foraged plants were the lowest. This was probably because of the arid environment in the region, which could not have supported sufficient plant resources for foraging, which in turn might have led to enhanced millet cultivation and/or a greater reliance on hunting. No wheat or barley traces were found in human teeth in Lajia, and the high proportion of nitrogen was possibly related to the consumption of sheep because sheep bones were found in a zooarchaeological study. This study enhances our understanding of the subsistence strategies present in Qijia culture and of prehistoric food globalization, which is of pivotal significance for a deeper understanding of interactions between east and west Asia during the Neolithic and Bronze ages.}
}

@article{malakarNaturallyOccurring2017,
  title = {Naturally Occurring Dietary Salicylates: {{A}} Closer Look at Common {{Australian}} Foods},
  shorttitle = {Naturally Occurring Dietary Salicylates},
  author = {Malakar, Sreepurna and Gibson, Peter R. and Barrett, Jacqueline S. and Muir, Jane G.},
  year = {2017},
  month = apr,
  journal = {Journal of Food Composition and Analysis},
  volume = {57},
  pages = {31--39},
  issn = {0889-1575},
  doi = {10.1016/j.jfca.2016.12.008},
  abstract = {Dietary salicylates may have similar benefits and/or adverse symptoms as documented for Aspirin. To develop dietary strategies, data on salicylate content of food is essential, but the available literature is limited and controversial. Hence the aims of this study are to apply and validate a reliable methodology to determine the salicylate content of common foods, and compare with recently published data. Gas chromatography-mass spectrometry (GC\textendash MS) was used with SA-d6 (deuterated salicylic acid) as an internal standard to analyse 112 common Australian food items pooled from ten different sources. Technical sextuplicates show a coefficient of variation of 3.03\%. SA content ranged from 1.28\textendash 26.93 (vegetables), 2.13\textendash 36.90 (fruits), 2.80\textendash 604.97 (herbs/spices) and 2.04\textendash 51.48 (beverages) mg/kg. SA was undetected in oils, sugars and cereals analysed. The results reveal inconsistencies within the extant literature and a pressing need for further research extending the analysis to a broader range of food items.},
  langid = {english},
  keywords = {Cereals,Diet,Food analysis,Food composition,Fruits,Gas chromatography-mass spectrometry,Herbs,Salicylates,Spices,Sugar,Vegetables}
}

@article{maModelingDiffusion2010,
  title = {Modeling of {{Diffusion Transport}} through {{Oral Biofilms}} with the {{Inverse Problem Method}}},
  author = {Ma, Rui and Liu, Jie and Jiang, Yun-tao and Liu, Zheng and Tang, Zi-sheng and Ye, Dong-xia and Zeng, Jin and Huang, Zheng-wei},
  year = {2010},
  month = dec,
  journal = {International Journal of Oral Science},
  volume = {2},
  number = {4},
  pages = {190--197},
  publisher = {{Nature Publishing Group}},
  issn = {2049-3169},
  doi = {10.4248/IJOS10075},
  abstract = {The purpose of this study was to develop a mathematical model to quantitatively describe the passive transport of macromolecules within dental biofilms.},
  copyright = {2010 West China School of Stomatology},
  langid = {english},
  keywords = {Dentistry,Oral and Maxillofacial Surgery,Orthopedics,Surgical Orthopedics}
}

@article{maMorphologicalChanges2019,
  title = {Morphological Changes in Starch Grains after Dehusking and Grinding with Stone Tools},
  author = {Ma, Zhikun and Perry, Linda and Li, Quan and Yang, Xiaoyan},
  year = {2019},
  month = feb,
  journal = {Scientific Reports},
  volume = {9},
  number = {1},
  pages = {2355},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-38758-6},
  abstract = {Research on the manufacture, use, and use-wear of grinding stones (including slabs and mullers) can provide a wealth of information on ancient subsistence strategy and plant food utilization. Ancient residues extracted from stone tools frequently exhibit damage from processing methods, and modern experiments can replicate these morphological changes so that they can be better understood. Here, experiments have been undertaken to dehusk and grind grass grain using stone artifacts. To replicate ancient activities in northern China, we used modern stone tools to dehusk and grind twelve cultivars of foxtail millet (Setaria italica), two cultivars of broomcorn millet (Panicum miliaceum) and three varieties of green bristlegrass (Setaira viridis). The residues from both used and unused facets of the stone tools were then extracted, and the starch grains studied for morphological features and changes from the native states. The results show that (1) Dehusking did not significantly change the size and morphology of millet starch grains; (2) After grinding, the size of millet starch grains increases up to 1.2 times larger than native grains, and a quarter of the ground millet starch grains bore surface damage and also exhibited distortion of the extinction cross. This indicator will be of significance in improving the application of starch grains to research in the functional inference of grinding stone tools, but we are unable to yet distinguish dehusked forms from native.},
  copyright = {2019 The Author(s)},
  langid = {english},
  keywords = {Archaeology,Evolutionary ecology}
}

@article{mannDifferentialPreservation2018,
  title = {Differential Preservation of Endogenous Human and Microbial {{DNA}} in Dental Calculus and Dentin},
  author = {Mann, Allison E. and Sabin, Susanna and Ziesemer, Kirsten and V{\aa}gene, {\AA}shild J. and Schroeder, Hannes and Ozga, Andrew T. and Sankaranarayanan, Krithivasan and Hofman, Courtney A. and Fellows Yates, James A. and {Salazar-Garc{\'i}a}, Domingo C. and Frohlich, Bruno and Aldenderfer, Mark and Hoogland, Menno and Read, Christopher and Milner, George R. and Stone, Anne C. and Lewis, Cecil M. and Krause, Johannes and Hofman, Corinne and Bos, Kirsten I. and Warinner, Christina},
  year = {2018},
  month = jun,
  journal = {Scientific Reports},
  volume = {8},
  number = {1},
  pages = {9822},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-018-28091-9},
  abstract = {Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is~a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08\,{$\pm$}\,0.08\%, range 0.007\textendash 0.47\%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70\,{$\pm$}\,18.62\%, range 0.003\textendash 70.14\%), and for a subset of dentin samples (15.21\%), oral bacteria contribute\,{$>$}\,20\% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.},
  copyright = {2018 The Author(s)},
  langid = {english},
  keywords = {Archaeology,Genetics,Microbial ecology}
}

@article{mannHaveSomething2023,
  title = {Do {{I}} Have Something in My Teeth? {{The}} Trouble with Genetic Analyses of Diet from Archaeological Dental Calculus},
  shorttitle = {Do {{I}} Have Something in My Teeth?},
  author = {Mann, Allison E. and Fellows Yates, James A. and Fagern{\"a}s, Zandra and Austin, Rita M. and Nelson, Elizabeth A. and Hofman, Courtney A.},
  year = {2023},
  month = apr,
  journal = {Quaternary International},
  series = {From {{Food}} to {{Environments}}: {{Advances}} in {{Ancient Human Dental Calculus Research}}},
  volume = {653--654},
  pages = {33--46},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2020.11.019},
  abstract = {Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a relatively stable environment for DNA preservation, the detection of plants and animals possibly consumed by an individual through DNA analysis is primarily hindered by microbial richness and incomplete reference databases. Moreover, high genomic similarity within eukaryotic groups - such as mammals - can obfuscate precise taxonomic identification. In the current study we demonstrate the challenges associated with accurate taxonomic identification and authentication of dietary taxa in ancient DNA data using both synthetic and ancient dental calculus datasets. We highlight common errors and sources of contamination across ancient DNA datasets, provide recommendations for dietary DNA validation, and call for caution in the interpretation of diet from dental calculus and other archaeological microbiome substrates.},
  langid = {english},
  keywords = {Ancient DNA,Dental calculus,Diet,Metagenomics}
}

@book{marianiCoca1886,
  title = {Coca {{Erythroxylon}}: {{Its Uses}} in the {{Treatment}} of {{Disease}}},
  author = {Mariani Company},
  year = {1886},
  edition = {Fourth},
  publisher = {{Mariani \& Co.}},
  address = {{Paris}}
}

@article{marshDentalPlaque2005,
  title = {Dental Plaque: Biological Significance of a Biofilm and Community Life-Style},
  shorttitle = {Dental Plaque},
  author = {Marsh, Philip D.},
  year = {2005},
  journal = {Journal of Clinical Periodontology},
  volume = {32},
  number = {s6},
  pages = {7--15},
  issn = {1600-051X},
  doi = {10.1111/j.1600-051X.2005.00790.x},
  abstract = {Background: Most microorganisms in nature attach to surfaces and form matrix-embedded biofilms. Biofilms are highly structured and spatially organized, and are often composed of consortia of interacting microorganisms, termed microbial communities, the properties of which are more than the sum of the component species. Microbial gene expression alters markedly in biofilms; organisms communicate by gene transfer and by secretion of diffusible signalling molecules. Cells in biofilms are less susceptible to antimicrobial agents. Aim and Materials \& Methods: To comprehensively review the literature to determine whether dental plaque displays properties consistent with those of a typical biofilm and microbial community. Results: Novel microscopic and molecular techniques have demonstrated that plaque has a structured architecture with an extracellular matrix, and a diverse composition (around 50\% of cells are unculturable). The constituent species communicate by gene transfer, by secreted peptides (Gram-positive bacteria) and autoinducer-2 (Gram-positive and Gram-negative bacteria). These organisms are functionally organized for increased metabolic efficiency, greater resistance to stress and for enhanced virulence. Plaque formation has direct and indirect effects on gene expression. Conclusion: Dental plaque displays properties that are typical of biofilms and microbial communities in general, a clinical consequence of which is a reduced susceptibility to antimicrobial agents as well as pathogenic synergism.},
  langid = {english},
  keywords = {antimicrobial resistance,biofilm,cell signalling,dental plaque,ecology,gene expression,gene transfer,microbial community,review},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-051X.2005.00790.x}
}

@article{marshDentalPlaque2006,
  title = {Dental Plaque as a Biofilm and a Microbial Community \textendash{} Implications for Health and Disease},
  author = {Marsh, Philip D.},
  year = {2006},
  month = jun,
  journal = {BMC Oral Health},
  volume = {6},
  number = {S1},
  pages = {S14},
  issn = {1472-6831},
  doi = {10.1186/1472-6831-6-S1-S14},
  abstract = {Dental plaque is a structurally- and functionally-organized biofilm. Plaque forms in an ordered way and has a diverse microbial composition that, in health, remains relatively stable over time (microbial homeostasis). The predominant species from diseased sites are different from those found in healthy sites, although the putative pathogens can often be detected in low numbers at normal sites. In dental caries, there is a shift toward community dominance by acidogenic and acidtolerating species such as mutans streptococci and lactobacilli, although other species with relevant traits may be involved. Strategies to control caries could include inhibition of biofilm development (e.g. prevention of attachment of cariogenic bacteria, manipulation of cell signaling mechanisms, delivery of effective antimicrobials, etc.), or enhancement of the host defenses. Additionally, these more conventional approaches could be augmented by interference with the factors that enable the cariogenic bacteria to escape from the normal homeostatic mechanisms that restrict their growth in plaque and out compete the organisms associated with health. Evidence suggests that regular conditions of low pH in plaque select for mutans streptococci and lactobacilli. Therefore, the suppression of sugar catabolism and acid production by the use of metabolic inhibitors and nonfermentable artificial sweeteners in snacks, or the stimulation of saliva flow, could assist in the maintenance of homeostasis in plaque. Arguments will be presented that an appreciation of ecological principles will enable a more holistic approach to be taken in caries control.},
  langid = {english}
}

@incollection{marshDentalPlaque2016,
  title = {Dental {{Plaque}}},
  booktitle = {Marsh and {{Martin}}'s {{Oral Microbiology}}},
  author = {Marsh, Philip D. and Lewis, Michael A. O. and Rogers, Helen and Williams, David W. and Wilson, Melanie},
  year = {2016},
  month = may,
  edition = {6th Edition},
  pages = {81--111},
  publisher = {{Elsevier Health Sciences}},
  abstract = {Now expanded with the latest information of relevance to current dental practice, Oral Microbiology retains its unique ecological approach to the subject which helps the reader determine whether an organism will have a pathogenic or commensal relationship at a given site.  In the new edition, greater emphasis is placed on the role of current molecular biology techniques in the understanding of oral microbes. The book also provides insight into current therapeutic and prophylactic antibiotic use, infection control, and the relationships between oral and general health.   Oral Microbiology provides comprehensive coverage of the subject which will be essential to readers with a specific interest in dentistry as well as those with a more general interest in host-microbe interactions and in microbial ecology. The book is suitable for undergraduate and postgraduate dental students, research workers, and a wide range of clinical dental professionals. Full coverage of the latest molecular biology techniques which have revolutionized our knowledge of oral microbes  Exploration of the biological and clinical significance of the oral microflora in the form of a biofilm on dental and mucosal surfaces  Contemporary views on therapeutic and prophylactic antibiotic use, infection control, and the relationships between oral and general health},
  isbn = {978-0-7020-6174-5},
  langid = {english},
  keywords = {Medical / Dentistry / General,Medical / Infectious Diseases}
}

@article{marshMicrobiologyDental2010,
  title = {Microbiology of {{Dental Plaque Biofilms}} and {{Their Role}} in {{Oral Health}} and {{Caries}}},
  author = {Marsh, Philip D.},
  year = {2010},
  month = jul,
  journal = {Dental Clinics of North America},
  volume = {54},
  number = {3},
  pages = {441--454},
  issn = {00118532},
  doi = {10.1016/j.cden.2010.03.002},
  langid = {english}
}

@article{marshPhysiologicalApproaches1997,
  title = {Physiological {{Approaches}} to the {{Control}} of {{Oral Biofilms}}},
  author = {Marsh, Philip D. and Bradshaw, David J.},
  year = {1997},
  month = apr,
  journal = {Advances in Dental Research},
  volume = {11},
  number = {1},
  pages = {176--185},
  publisher = {{SAGE Publications Inc}},
  issn = {0895-9374},
  doi = {10.1177/08959374970110010901},
  abstract = {Evidence that physiological strategies may be potential routes for oral biofilm control has come from (i) observations of the variations in the intra-oral distribution of members of the resident oral microflora, (ii) changes in plaque composition in health and disease, and (iii) data from laboratory model systems. Key physiological factors that were identified as significant in modulating the microflora included the local pH, redox potential (Eh), and nutrient availability. Increases in mutans streptococci and lactobacilli occur at sites with caries; growth of these species is selectively enhanced at low pH. In contrast, periodontal diseases are associated with plaque accumulation, followed by an inflammatory host response. The increases in Gram-negative, proteolytic, and obligately anaerobic bacteria reflect a low redox potential and a change in nutrient status due to the increased flow of gingival crevicular fluid (GCF). Consequently, physiological strategies for oral biofilm control should focus on reducing the frequency of low pH in plaque by (i) inhibiting acid production, (ii) using sugar substitutes, and (iii) promoting alkali generation from arginine or urea supplements. Similarly, strategies to make the pocket environment less favorable to periodontopathogens include (i) anti-inflammatory agents to reduce the flow of (and hence nutrient supply by) GCF, (ii) bacterial protease inhibitors, and (iii) redox agents to raise the Ehh locally. Most laboratory and clinical findings support the concept of physiological control. However, some data suggest that the ordered structure and metabolically interactive organization of mature dental plaque could generate a community with a high level of homeostasis that is relatively resistant to deliberate external manipulation.},
  langid = {english},
  keywords = {antimicrobial agents,arginine,biofilm,ecology,fluoride,homeostasis.,pH,redox potential,urea}
}

@article{marshRoleMicrobiology1995,
  title = {The {{Role}} of {{Microbiology}} in {{Models}} of {{Dental Caries}}},
  author = {Marsh, Philip D.},
  year = {1995},
  month = nov,
  journal = {Advances in Dental Research},
  volume = {9},
  number = {3},
  pages = {244--254},
  issn = {0895-9374, 1544-0737},
  doi = {10.1177/08959374950090030901},
  abstract = {Models of dental caries (laboratory, animal, and human in situ models) vary markedly in their microbiological complexity. Laboratory models range from mono-cultures of cariogenic species providing an acidic challenge to enamel, to the development of diverse mixed cultures growing on a habitatsimulating medium in an artificial mouth or chemostat. The latter systems are of value in determining either mechanisms of action or cause-and-effect relationships\textemdash e.g., between dietary components or antimicrobial agents and the microflora. Laboratory models have also shown that the sensitivity of oral bacteria to inhibitors is markedly reduced when growing in biofilms such as dental plaque. Animal models have proved unequivocally that caries is an infectious and transmissible disease. Their use has enabled comparisons to be made of (a) the cariogenic potential of different bacterial species, (b) the role of the diet, and (c) the effects of potential anti-caries agents. It has been claimed that no caries-protective agent currently in use has failed a rodent test. In situ human models have been designed to permit the development of "natural" plaque on standardized enamel surfaces freely exposed to the human oral environment. The microflora that develops on unadulterated surfaces is similar in composition to that found at comparable sites on vital teeth. Demineralization can be accelerated by the inoculation of additional cariogenic bacteria coupled with either intra- or extra-oral sucrose rinses. The increased realism associated with the transition from laboratory to human in situ models is countered by a reduced ability to control or manipulate the system for experimental purposes. Thus, a hierarchy of tests is needed for the study of anti-caries agents, each requiring a varying degree of microbiological complexity.},
  langid = {english}
}

@article{maughanCaffeineIngestion2003,
  title = {Caffeine Ingestion and Fluid Balance: A Review},
  shorttitle = {Caffeine Ingestion and Fluid Balance},
  author = {Maughan, R. J. and Griffin, J.},
  year = {2003},
  journal = {Journal of Human Nutrition and Dietetics},
  volume = {16},
  number = {6},
  pages = {411--420},
  issn = {1365-277X},
  doi = {10.1046/j.1365-277X.2003.00477.x},
  abstract = {Background Caffeine and related methylxanthine compounds are recognized as having a diuretic action, and consumers are often advised to avoid beverages containing these compounds in situations where fluid balance may be compromised. The aim of this review is to evaluate the available literature concerning the effect of caffeine ingestion on fluid balance and to formulate targeted and evidence-based advice on caffeinated beverages in the context of optimum hydration. Method A literature search was performed using the Medline database of articles published in the medical and scientific literature for the period of January 1966\textendash March 2002. Subject headings and key words used in this search were: tea, coffee, caffeine, diuresis, fluid balance and water-electrolyte balance. A secondary search was performed using the bibliographies of publications identified in the initial search. Results The available literature suggests that acute ingestion of caffeine in large doses (at least 250\textendash 300 mg, equivalent to the amount found in 2\textendash 3 cups of coffee or 5\textendash 8 cups of tea) results in a short-term stimulation of urine output in individuals who have been deprived of caffeine for a period of days or weeks. A profound tolerance to the diuretic and other effects of caffeine develops, however, and the actions are much diminished in individuals who regularly consume tea or coffee. Doses of caffeine equivalent to the amount normally found in standard servings of tea, coffee and carbonated soft drinks appear to have no diuretic action. Conclusion The most ecologically valid of the published studies offers no support for the suggestion that consumption of caffeine-containing beverages as part of a normal lifestyle leads to fluid loss in excess of the volume ingested or is associated with poor hydration status. Therefore, there would appear to be no clear basis for refraining from caffeine containing drinks in situations where fluid balance might be compromised.},
  langid = {english},
  keywords = {body water,caffeine,diuresis,fluid balance,hydration},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-277X.2003.00477.x}
}

@incollection{mcbainBiofilmModels2009,
  title = {In {{Vitro Biofilm Models}}: {{An Overview}}},
  shorttitle = {In {{Vitro Biofilm Models}}},
  booktitle = {Advances in {{Applied Microbiology}}},
  author = {McBain, Andrew J.},
  year = {2009},
  month = jan,
  series = {Advances in {{Applied Microbiology}}},
  volume = {69},
  pages = {99--132},
  publisher = {{Academic Press}},
  doi = {10.1016/S0065-2164(09)69004-3},
  abstract = {Observing naturally occurring biofilms in situ or ex situ has revealed the wide distribution of sessile microbial communities. The ubiquity, variety and complexity of biofilms is now widely accepted by microbiologists. While they are associated with many beneficial functions such as nutrient cycling, bioremediation and colonization resistance, adverse effects including recalcitrance, their involvement in industrial fouling, contamination and infection have made biofilms a priority research topic. We know that most biofilms, other than within certain infections and laboratory flasks, are composed of multiple species and that there is arguably no unifying biofilm architecture. Biofilms do however share certain properties including the presence of gradients of nutrients, gasses and metabolic products, relatively increased cell density, deposition of extracellular polymeric substances and marked recalcitrance towards antimicrobial treatments. Much of our understanding of biofilm physiology and micro-ecology originates from experiments using in vitro biofilm models. Broadly speaking, such models may be used to replicate environmental conditions within the laboratory or to focus on selected variables such a growth rate or fluid flow, etc. This chapter provides an overview of some commonly used biofilm models including microtitre plate systems, flow cells, the constant depth film fermenter, annular reactors and the perfused biofilm fermenter. While perfused biofilm fermenters, in particular, enable growth rate to be controlled within thin, relatively homogenous, quasi steady-state biofilms through modulation of flow rate nutrient availability, other models provide representative modelling of in situ conditions where steady states may be uncommon.},
  langid = {english},
  keywords = {Baby machine,Biofilm,CDC reactor,CDFF,Drip flow reactor,Flow cell,Microcosm,oral biofilm model,Perfused biofilm fermenter,Sorbarod,Sorbarod device,Substratum}
}

@article{meillourDetectionPlantderived2023,
  title = {Detection of Plant-Derived Compounds in {{XIXth}} c. {{Dutch}} Dental Calculus},
  author = {Meillour, Louise Le},
  year = {2023},
  month = nov,
  journal = {Peer Community in Archaeology},
  volume = {1},
  pages = {100389},
  publisher = {{Peer Community In}},
  issn = {2742-1929},
  doi = {10.24072/pci.archaeo.100389},
  abstract = {A recommendation of: Bartholdy, Bj\o rn Peare; Hasselstr\o m, J\o rgen B.; S\o rensen, Lambert K.; Casna, Maia; Hoogland, Menno; Historisch Genootschap Beemster; Henry, Amanda G. Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population https://doi.org/10.5281/zenodo.7649150},
  copyright = {(C) Peer Community in Archaeology, 2023},
  langid = {english}
}

@article{meindlSutureClosure1985,
  title = {Ectocranial Suture Closure: {{A}} Revised Method for the Determination of Skeletal Age at Death Based on the Lateral-Anterior Sutures},
  shorttitle = {Ectocranial Suture Closure},
  author = {Meindl, Richard S. and Lovejoy, C. Owen},
  year = {1985},
  journal = {American Journal of Physical Anthropology},
  volume = {68},
  number = {1},
  pages = {57--66},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330680106},
  abstract = {A new method for estimation of age-at-death based on the degree of suture closure is presented. The method employs simple ectocranial scoring of specific sites on the external table. Composite scores for two groups of sutures, lateral-anterior and vault systems, which are used to provide estimates of age-at-death, have been developed from a sample of 236 crania from the Hamann-Todd Collection. A variety of tests show that the lateralanterior sutures are superior to the sutures of the vault, that ectocranial is superior to endocranial observation, and that age estimates are independent of race and sex. It is concluded that suture closure can provide valuable estimates of age-at-death in both archaeological and forensic contexts when used in conjunction with other skeletal age indicators.},
  copyright = {Copyright \textcopyright{} 1985 Wiley-Liss, Inc., A Wiley Company},
  langid = {english},
  keywords = {Age at death,Age-determination,Demography,Forensic,Sutures},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330680106}
}

@inproceedings{mentzerDistributionAuthigenic2014,
  title = {The Distribution of Authigenic Minerals in the {{Middle Stone Age}} Deposits of {{Sibudu}} ({{South Africa}}), and Implications for the Preservation of Archaeological Features},
  booktitle = {European Society for the Study of Human Evolution, {{4thAnnual}} Meeting, Florence, Italy},
  author = {Mentzer, Susan M and Miller, Christopher E and Kloos, Peter and Wadley, Lyn and Conard, Nicholas J},
  year = {2014}
}

@article{mercaderExaggeratedExpectations2018,
  title = {Exaggerated Expectations in Ancient Starch Research and the Need for New Taphonomic and Authenticity Criteria},
  author = {Mercader, Julio and Akeju, Tolutope and Brown, Melisa and Bundala, Mariam and Collins, Matthew J. and Copeland, Les and Crowther, Alison and Dunfield, Peter and Henry, Amanda and Inwood, Jamie and Itambu, Makarius and Kim, Joong-Jae and Larter, Steve and Longo, Laura and Oldenburg, Thomas and Patalano, Robert and Sammynaiken, Ramaswami and Soto, Mar{\'i}a and Tyler, Robert and Xhauflair, Hermine},
  editor = {Al, Tom A.},
  year = {2018},
  month = oct,
  journal = {FACETS},
  volume = {3},
  number = {1},
  pages = {777--798},
  issn = {2371-1671},
  doi = {10.1139/facets-2017-0126},
  abstract = {Ancient starch research illuminates aspects of human ecology and economic botany that drove human evolution and cultural complexity over time, with a special emphasis on past technology, diet, health, and adaptation to changing environments and socio-economic systems. However, lapses in prevailing starch research demonstrate the exaggerated expectations for the field that have been generated over the last few decades. This includes an absence of explanation for the millennial-scale survivability of a biochemically degradable polymer, and difficulties in establishing authenticity and taxonomic identification. This paper outlines new taphonomic and authenticity criteria to guide future work toward designing research programs that fully exploit the potential of ancient starch while considering growing demands from readers, editors, and reviewers that look for objective compositional identification of putatively ancient starch granules.},
  langid = {english}
}

@article{mickleburghNewInsights2012,
  title = {New Insights into the Consumption of Maize and Other Food Plants in the Pre-{{Columbian Caribbean}} from Starch Grains Trapped in Human Dental Calculus},
  author = {Mickleburgh, Hayley L. and {Pag{\'a}n-Jim{\'e}nez}, Jaime R.},
  year = {2012},
  journal = {Journal of Archaeological Science},
  volume = {39},
  number = {7},
  pages = {2468--2478},
  issn = {03054403},
  doi = {10.1016/j.jas.2012.02.020}
}

@article{middletonImprovedMethod1990,
  title = {An {{Improved Method}} for {{Extraction}} of {{Opal Phytoliths}} from {{Tartar Residues}} on {{Herbivore Teeth}}},
  author = {Middleton, William D.},
  year = {1990},
  journal = {Phytolitharien Newsletter},
  volume = {6},
  number = {3},
  pages = {2--5}
}

@article{middletonOpalPhytoliths1994,
  title = {Extraction of {{Opal Phytoliths}} from {{Herbivore Dental Calculus}}},
  author = {Middleton, William D. and Rovner, Irwin},
  year = {1994},
  month = jul,
  journal = {Journal of Archaeological Science},
  volume = {21},
  number = {4},
  pages = {469--473},
  issn = {0305-4403},
  doi = {10.1006/jasc.1994.1046},
  abstract = {Opal phytoliths can easily be extracted from herbivore dental calculus and examined to gain data for the reconstruction of prehistoric herbivore diet. The extraction process is a simple, quick and inexpensive three-step procedure. It consists of one or two distilled water washes to control and assess contamination and a final wash with dilute hydrochloric acid. A pilot study conducted on barnyard animals (cow, sheep and pig) from the American Colonial period site of Hampton, Virginia, demonstrates that dental calculus phytolith assemblages can provide data on herbivore diet that can be used to reconstruct livestock management practices and ecological change.},
  langid = {english},
  keywords = {Dental Calculus,Palaeodiet,Phytoliths}
}

@article{middletonVitroCalculus1965,
  title = {Human Salivary Proteins and Artificial Calculus Formation in Vitro},
  author = {Middleton, J.D.},
  year = {1965},
  month = mar,
  journal = {Archives of Oral Biology},
  volume = {10},
  number = {2},
  pages = {227--235},
  issn = {00039969},
  doi = {10.1016/0003-9969(65)90024-5},
  langid = {english}
}

@article{milmanOralFluid2011,
  title = {Oral {{Fluid}} and {{Plasma Cannabinoid Ratios}} after {{Around-the-Clock Controlled Oral $\Delta$9-Tetrahydrocannabinol Administration}}},
  author = {Milman, Garry and Schwope, David M and Schwilke, Eugene W and Darwin, William D and Kelly, Deanna L and Goodwin, Robert S and Gorelick, David A and Huestis, Marilyn A},
  year = {2011},
  month = nov,
  journal = {Clinical Chemistry},
  volume = {57},
  number = {11},
  pages = {1597--1606},
  issn = {0009-9147},
  doi = {10.1373/clinchem.2011.169490},
  abstract = {Oral fluid (OF) testing is increasingly important for drug treatment, workplace, and drugged-driving programs. There is interest in predicting plasma or whole-blood concentrations from OF concentrations; however, the relationship between these matrices is incompletely characterized because of few controlled drug-administration studies.Ten male daily cannabis smokers received around-the-clock escalating 20-mg oral {$\Delta$}9-tetrahydrocannabinol (THC, dronabinol) doses (40\textendash 120 mg/day) for 8 days. Plasma and OF samples were simultaneously collected before, during, and after dosing. OF THC, 11-hydroxy-THC and 11-nor-9-carboxy-THC (THCCOOH) were quantified by GC-MS at 0.5-{$\mu$}g/L, 0.5-{$\mu$}g/L, and 7.5-ng/L limits of quantification (LOQs), respectively. In plasma, the LOQs were 0.25 {$\mu$}g/L for THC and THCCOOH, and 0.5 {$\mu$}g/L for 11-hydroxy-THC.Despite multiple oral THC administrations each day and increasing plasma THC concentrations, OF THC concentrations generally decreased over time, reflecting primarily previously self-administered smoked cannabis. The logarithms of the THC concentrations in oral fluid and plasma were not significantly correlated (r = -0.10; P = 0.065). The OF and plasma THCCOOH concentrations, albeit with 1000-fold higher concentrations in plasma, increased throughout dosing. The logarithms of OF and plasma THCCOOH concentrations were significantly correlated (r = 0.63; P \&lt; 0.001), although there was high interindividual variation. A high OF/plasma THC ratio and a high OF THC/THCCOOH ratio indicated recent cannabis smoking.OF monitoring does not reliably detect oral dronabinol intake. The time courses of THC and THCCOOH concentrations in plasma and OF were different after repeated oral THC doses, and high interindividual variation was observed. For these reasons, OF cannabinoid concentrations cannot predict concurrent plasma concentrations.}
}

@article{modiCalculusMethodologies2020,
  title = {Combined Methodologies for Gaining Much Information from Ancient Dental Calculus: Testing Experimental Strategies for Simultaneously Analysing {{DNA}} and Food Residues},
  shorttitle = {Combined Methodologies for Gaining Much Information from Ancient Dental Calculus},
  author = {Modi, Alessandra and Pisaneschi, Lisa and Zaro, Valentina and Vai, Stefania and Vergata, Chiara and Casalone, Enrico and Caramelli, David and {Moggi-Cecchi}, Jacopo and Mariotti Lippi, Marta and Lari, Martina},
  year = {2020},
  month = jan,
  journal = {Archaeological and Anthropological Sciences},
  volume = {12},
  number = {1},
  pages = {10},
  issn = {1866-9565},
  doi = {10.1007/s12520-019-00983-5},
  abstract = {Dental calculus from archaeological samples is a rich source of ancient biomolecules, such as DNA, proteins, and microremains, mainly related to food. Focusing on different contents, laboratory procedures require specific treatments that necessitate the same material and are generally mutually exclusive; therefore, the low quantity of the starting material is often the main limiting factor for gathering data. Here, we compare different combinations of laboratory procedures in order to identify the best strategy for simultaneously extracting DNA and isolating plant residue. Preliminary tests were performed on fresh plant materials to verify the effects of the DNA extraction protocols on starch grains and phytoliths. Different combined experimental procedures were successively applied to the dental calculus of three medieval individuals. Our results confirmed that authentic genetic data could be recovered from ancient dental calculus using protocols commonly used for extracting DNA from ancient bones and teeth, and the residual pellet could be successfully used for morphological characterization of plant residues. In addition, we confirmed that, although most DNA within calculus is microbial, the whole human mitochondrial genome could be reconstructed using target enrichment techniques.},
  langid = {english}
}

@article{moorerCalcificationCariogenic1993,
  title = {Calcification of a {{Cariogenic Streptococcus}} and of {{Corynebacterium}} ({{Bacterionema}}) Matruchotii},
  author = {Moorer, W. R. and Ten Cate, J. M. and Buijs, J. F.},
  year = {1993},
  journal = {Journal of Dental Research},
  volume = {72},
  number = {6},
  pages = {1021--1026},
  doi = {10.1177/00220345930720060501},
  abstract = {The main aim of this investigation was to challenge the idea that cariogenic streptococci do not calcify. Calcium uptake or calcification of Streptococcus mutans C180-2, proven to be an acidogenic and cariogenic strain, was compared with calcium uptake and calcification of Corynebacterium (Bacterionema) matruchotii, known as a ready calcifier. Bacteria were grown on Brain Heart Infusion Agar (BHIA) and on well-buffered semi-synthetic E-agar, both containing 1.4 mmol/L calcium, 2 g/L glucose, initial pH 7.4. Calcium uptake from BHIA by C. matruchotii (25 mmol Ca/kg wet bacterial cell mass), but not by S. mutans, was found. Grown as a plaque-like lawn on E-agar, the S. mutans cell mass concentrated calcium to 63 {$\pm$} 11 mmol/ kg compared with 145 {$\pm$} 61 mmol/kg in C. matruchotii. X-ray diffraction confirmed the presence of crystalline apatite in the bacterial cell masses. Electron microscopy revealed crystals and mineralized deposits in both organisms. Heavy calcifications in some cells of S. mutans were seen. Calcification was partly inhibited by magnesium ion and by methanehydroxybisphosphonate. S. sobrinus 6715, as well as freshly isolated S. mutans and S. sobrinus from patients, concentrated very large quantities of calcium, up to 500-fold from the medium, when maintained for several weeks on E-agar of initial pH 7.6. Our observations widen the view on acidogenic bacteria as mineralization agents and support the notion that members of the mutans group of streptococci may be involved in events that trigger heavy intracellular calcifications and, possibly, dental calculus formation.}
}

@book{mortimerHistoryCoca1901,
  title = {Peru. {{History}} of Coca, "the Divine Plant" of the {{Incas}}; with an Introductory Account of the {{Incas}}, and of the {{Andean Indians}} of to-Day},
  author = {Mortimer, William Golden},
  year = {1901},
  publisher = {{New York, J. H. Vail \& Company}},
  abstract = {Bibliography: p. [517]-544},
  collaborator = {{University of California Libraries}},
  langid = {english},
  lccn = {ucb\_banc:GLAD-84097281},
  keywords = {Coca}
}

@article{naterHumanAmylase2005,
  title = {Human Salivary Alpha-Amylase Reactivity in a Psychosocial Stress Paradigm},
  author = {Nater, Urs M. and Rohleder, Nicolas and Gaab, Jens and Berger, Simona and Jud, Andreas and Kirschbaum, Clemens and Ehlert, Ulrike},
  year = {2005},
  month = mar,
  journal = {International Journal of Psychophysiology},
  volume = {55},
  number = {3},
  pages = {333--342},
  issn = {0167-8760},
  doi = {10.1016/j.ijpsycho.2004.09.009},
  abstract = {Biological indicators for stress reactions are valuable markers in psychophysiological research and clinical practice. Since the release of salivary enzyme alpha-amylase was reported to react to physiological and psychological stressors, we set out to investigate human salivary alpha-amylase changes employing a reliable laboratory stress protocol to investigate the reactivity of salivary alpha-amylase to a brief period of psychosocial stress. In a within-subject repeated-measures design, 24 healthy adults were exposed to the TSST and a control condition on separate days with randomized sequence. Salivary alpha-amylase, salivary cortisol and heart rate were repeatedly measured before, during and after both conditions. Significant differences between psychosocial stress and the rest condition in alpha-amylase activity [F(3.74,86.06)=4.52; P=0.003], cortisol levels [F(4.21,88.32)=12.48; P{$<$}0.001] and heart rate [F(1,22)=81.15; P{$<$}0.001] were observed, with marked increases before and after stress. The data corroborate findings from other studies that showed increased levels of alpha-amylase before and after psychological stress. We discuss the role of salivary alpha-amylase as a promising candidate for a reliable, noninvasive marker of psychosocial stress.},
  langid = {english},
  keywords = {Cortisol,Heart rate,HPA axis,Psychosocial stress test,Salivary alpha-amylase,SAM system}
}

@article{nearingAssessingVariation2020,
  title = {Assessing the {{Variation}} within the {{Oral Microbiome}} of {{Healthy Adults}}},
  author = {Nearing, Jacob T. and DeClercq, Vanessa and Van Limbergen, Johan and Langille, Morgan G. I.},
  year = {2020},
  month = sep,
  journal = {mSphere},
  volume = {5},
  number = {5},
  pages = {e00451-20},
  publisher = {{American Society for Microbiology}},
  doi = {10.1128/mSphere.00451-20},
  abstract = {More than 1,000 different species of microbes have been found to live within the human oral cavity, where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community; however, the factors that determine oral microbiome composition are not well understood. In this study, we exam the salivary oral microbiome of 1,049 Atlantic Canadians using 16S rRNA gene sequencing to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition. Features that were identified as being significantly associated with overall composition then were additionally examined for genera, amplicon sequence variants, and predicted pathway abundances that were associated with these features. Several associations were replicated in an additional secondary validation data set. Overall, we found that several anthropometric measurements, including waist-hip ratio (WHR), height, and fat-free mass, as well as age and sex, were associated with overall oral microbiome structure in both our exploratory and validation data sets. We were unable to validate any dietary impacts on overall taxonomic oral microbiome composition but did find evidence to suggest potential contributions from factors such as the number of vegetable and refined grain servings an individual consumes. Interestingly, each one of these factors on its own was associated with only minor shifts in the overall taxonomic composition of the oral microbiome, suggesting that future biomarker identification for several diseases associated with the oral microbiome can be undertaken without the worry of confounding factors obscuring biological signals. IMPORTANCE The human oral cavity is inhabited by a diverse community of microbes, known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and, as such, have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. In this report, we investigate the oral microbiome of 1,049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition, no single biological factor explained a variation larger than 2\%. These results indicate that future work on biomarker detection may be encouraged by the lack of strong confounding factors.}
}

@article{nessEpidemiologicStudy1977,
  title = {An Epidemiologic Study of Factors Affecting Extrinsic Staining of Teeth in an {{English}} Population},
  author = {Ness, Leslie and Rosekrans, Davidde L. and Welford, John F.},
  year = {1977},
  journal = {Community Dentistry and Oral Epidemiology},
  volume = {5},
  number = {1},
  pages = {55--60},
  issn = {1600-0528},
  doi = {10.1111/j.1600-0528.1977.tb01617.x},
  abstract = {A survey is described in which extrinsic staining of teeth was assessed by practising dentists during routine clinical examinations. Habits information was also supplied by patients. The results show that extrinsic staining is markedly influenced by smoking habits and age, and that males tend to have more staining than females. The effect of tea and coffee consumption was not pronounced. No effect attributable to the use of a stannous fluoride toothpaste was observed.},
  langid = {english},
  keywords = {dental deposits,fluorides},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0528.1977.tb01617.x}
}

@book{nierstraszTeaTrade2015,
  title = {Rivalry for {{Trade}} in {{Tea}} and {{Textiles}}: {{The English}} and {{Dutch East India}} Companies (1700\textendash 1800)},
  shorttitle = {Rivalry for {{Trade}} in {{Tea}} and {{Textiles}}},
  author = {Nierstrasz, Chris},
  year = {2015},
  month = sep,
  publisher = {{Springer}},
  abstract = {The rivalry for trade in tea and textiles between the English and Dutch East India companies is very much a global history. This trade is strongly connected to emblematic events such as the opening of Western trade with China, the Boston Tea Party, the establishment of British Empire in Bengal and the Industrial Revolution.},
  googlebooks = {uwtaCwAAQBAJ},
  isbn = {978-1-137-48653-0},
  langid = {english},
  keywords = {Business \& Economics / Economic History,Business \& Economics / Industries / General,History / Asia / General,History / Europe / General,History / General,History / Modern / General,History / World}
}

@article{nikitkovaEffectStarch2012,
  title = {Effect of Starch and Amylase on the Expression of Amylase-Binding Protein {{A}} in {{Streptococcus}} Gordonii},
  author = {Nikitkova, Anna E. and Haase, Elaine M. and Scannapieco, Frank A.},
  year = {2012},
  journal = {Molecular Oral Microbiology},
  volume = {27},
  number = {4},
  pages = {284--294},
  issn = {2041-1014},
  doi = {10.1111/j.2041-1014.2012.00644.x},
  abstract = {Streptococcus gordonii is a common oral commensal bacterial species in tooth biofilm (dental plaque) and specifically binds to salivary amylase through the surface exposed amylase-binding protein A (AbpA). When S. gordonii cells are pretreated with amylase, amylase bound to AbpA facilitates growth with starch as a primary nutrition source. The goal of this study was to explore possible regulatory effects of starch, starch metabolites and amylase on the expression of S. gordonii AbpA. An amylase ligand-binding assay was used to assess the expression of AbpA in culture supernatants and on bacterial cells from S. gordonii grown in defined medium supplemented with 1\% starch, 0.5 mg ml-1 amylase, with starch and amylase together, or with various linear malto-oligosaccharides. Transcription of abpA was determined by reverse transcription quantitative polymerase chain reaction. AbpA was not detectable in culture supernatants containing either starch alone or amylase alone. In contrast, the amount of AbpA was notably increased when starch and amylase were both present in the medium. The expression of abpA was significantly increased (P {$<$} 0.05) following 40 min of incubation in defined medium supplemented with starch and amylase. Similar results were obtained in the presence of maltose and other short-chain malto-oligosacchrides. These results suggest that the products of starch hydrolysis produced from the action of salivary {$\alpha$}-amylase, particularly maltose and maltotriose, up-regulate AbpA expression in S. gordonii.},
  langid = {english},
  keywords = {amylase-binding protein A,dental plaque,oral cavity,saliva},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-1014.2012.00644.x}
}

@article{nikitkovaStarchBiofilms2013,
  title = {Taking the {{Starch}} out of {{Oral Biofilm Formation}}: {{Molecular Basis}} and {{Functional Significance}} of {{Salivary}} {$\alpha$}-{{Amylase Binding}} to {{Oral Streptococci}}},
  shorttitle = {Taking the {{Starch}} out of {{Oral Biofilm Formation}}},
  author = {Nikitkova, Anna E. and Haase, Elaine M. and Scannapieco, Frank A.},
  year = {2013},
  month = jan,
  journal = {Applied and Environmental Microbiology},
  volume = {79},
  number = {2},
  pages = {416--423},
  publisher = {{American Society for Microbiology}},
  issn = {0099-2240, 1098-5336},
  doi = {10.1128/AEM.02581-12},
  abstract = {{$\alpha$}-Amylase-binding streptococci (ABS) are a heterogeneous group of commensal oral bacterial species that comprise a significant proportion of dental plaque microfloras. Salivary {$\alpha$}-amylase, one of the most abundant proteins in human saliva, binds to the surface of these bacteria via specific surface-exposed {$\alpha$}-amylase-binding proteins. The functional significance of {$\alpha$}-amylase-binding proteins in oral colonization by streptococci is important for understanding how salivary components influence oral biofilm formation by these important dental plaque species. This review summarizes the results of an extensive series of studies that have sought to define the molecular basis for {$\alpha$}-amylase binding to the surface of the bacterium as well as the biological significance of this phenomenon in dental plaque biofilm formation.},
  chapter = {Minireview},
  copyright = {Copyright \textcopyright{} 2013, American Society for Microbiology. All Rights Reserved.},
  langid = {english},
  pmid = {23144140}
}

@article{nobbsStreptococcusAdherence2009,
  title = {Streptococcus {{Adherence}} and {{Colonization}}},
  author = {Nobbs, Angela H. and Lamont, Richard J. and Jenkinson, Howard F.},
  year = {2009},
  month = sep,
  journal = {Microbiology and Molecular Biology Reviews},
  volume = {73},
  number = {3},
  pages = {407--450},
  publisher = {{American Society for Microbiology}},
  doi = {10.1128/MMBR.00014-09},
  keywords = {notion}
}

@article{nosekRegisteredReports2014,
  title = {Registered {{Reports}}},
  author = {Nosek, Brian A. and Lakens, Dani{\"e}l},
  year = {2014},
  month = may,
  journal = {Social Psychology},
  volume = {45},
  number = {3},
  pages = {137--141},
  publisher = {{Hogrefe Publishing}},
  issn = {1864-9335},
  doi = {10.1027/1864-9335/a000192}
}

@article{novakDentalHealth2015,
  title = {Dental Health and Diet in Early Medieval {{Ireland}}},
  author = {Novak, Mario},
  year = {2015},
  month = sep,
  journal = {Archives of Oral Biology},
  volume = {60},
  number = {9},
  pages = {1299--1309},
  issn = {0003-9969},
  doi = {10.1016/j.archoralbio.2015.06.004},
  abstract = {Objective With the aim to get a better picture of dental health, diet and nutrition in early medieval Ireland a population-based study focusing on several attributes of oral health in adult individuals was conducted. The study focused on possible differences between sexes and age groups in terms of frequency and distribution of studied pathologies in order to determine whether these differences result from different diets, cultural practices or are age-related. Design Permanent dentitions belonging to adult individuals from five Irish early medieval sites were examined for the evidence of caries, ante-mortem tooth loss, abscesses, calculus, alveolar bone resorption and tooth wear. All pathologies were analysed and presented by teeth and alveoli. Results A total of 3233 teeth and 3649 alveoli belonging to 167 individuals (85 males and 82 females) were included into the analysis. Males exhibited significantly higher prevalence of abscesses, heavy wear and alveolar bone resorption, while females exhibited significantly higher prevalence of calculus. All studied dento-alveolar pathologies showed a strong correlation with advanced age, except calculus in females. Additionally, dental wear associated with habitual activities was observed in two females. Conclusion The results of the present study confirm the data gained by written sources and stable isotopes analyses suggesting the diet of the early Irish was rich in carbohydrates with only occasional use of meat. Furthermore, significant differences between the sexes in terms of recorded pathologies strongly suggest different nutritional patterns with females consuming foods mostly based on carbohydrates in comparison to males. The observed sex-differences might also occur due to differences between male and female sex such as reproductive biology and pregnancy, a somewhat different age distributions, but also as a result of different cultural practices between the sexes.},
  langid = {english},
  keywords = {Archaeological populations,Diet,Ireland,Permanent dentition,Sex-differences}
}

@article{ogaldeIdentificationPsychoactive2009,
  title = {Identification of Psychoactive Alkaloids in Ancient {{Andean}} Human Hair by Gas Chromatography/Mass Spectrometry},
  author = {Ogalde, Juan P. and Arriaza, Bernardo T. and Soto, Elia C.},
  year = {2009},
  month = feb,
  journal = {Journal of Archaeological Science},
  volume = {36},
  number = {2},
  pages = {467--472},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2008.09.036},
  abstract = {Various ethnographic sources have demonstrated the symbolic and ritualistic importance of psychoactive plants in Native American societies. The social milieu of these mind- altering plants appears to be ancient. Archaeological evidence during the Tiwanaku empire expansion along the Atacama Desert of Chile, circa 500\textendash 1000 A.D., shows the presence of highly decorated snuffing tablets and tubes as grave goods. The preservation of mummified human bodies in the Azapa Valley, northern Chile, provided an opportunity to test the exact nature of the psychoactive plants used in this region. Using gas chromatography/mass spectrometry (GC\textendash MS), here we show that ancient Andean populations from northern Chile consumed Banisteriopsis, a vine that contains harmine. This is the first direct archaeological evidence of hallucinogenic and medicinal ethnographic practices. Interestingly enough, this rainforest plant does not grow along the Atacama coast, thus our findings suggest extensive plant trade networks in antiquity as far as the Amazon.},
  langid = {english},
  keywords = {Azapa valley,Gas chromatography/mass spectrometry,Hair analysis,Psychoactive alkaloids,Tiwanaku Horizon}
}

@article{omelonReviewPhosphate2013,
  title = {A {{Review}} of {{Phosphate Mineral Nucleation}} in {{Biology}} and {{Geobiology}}},
  author = {Omelon, Sidney and Ariganello, Marianne and Bonucci, Ermanno and Grynpas, Marc and Nanci, Antonio},
  year = {2013},
  month = oct,
  journal = {Calcified Tissue International},
  volume = {93},
  number = {4},
  pages = {382--396},
  issn = {1432-0827},
  doi = {10.1007/s00223-013-9784-9},
  abstract = {Relationships between geological phosphorite deposition and biological apatite nucleation have often been overlooked. However, similarities in biological apatite and phosphorite mineralogy suggest that their chemical formation mechanisms may be similar. This review serves to draw parallels between two newly described phosphorite mineralization processes, and proposes a similar novel mechanism for biologically controlled apatite mineral nucleation. This mechanism integrates polyphosphate biochemistry with crystal nucleation theory. Recently, the roles of polyphosphates in the nucleation of marine phosphorites were discovered. Marine bacteria and diatoms have been shown to store and concentrate inorganic phosphate (Pi) as amorphous, polyphosphate granules. Subsequent release of these P reserves into the local marine environment as Pi results in biologically induced phosphorite nucleation. Pi storage and release through an intracellular polyphosphate intermediate may also occur in mineralizing oral bacteria. Polyphosphates may be associated with biologically controlled apatite nucleation within vertebrates and invertebrates. Historically, biological apatite nucleation has been attributed to either a biochemical increase in local Pi concentration or matrix-mediated apatite nucleation control. This review proposes a mechanism that integrates both theories. Intracellular and extracellular amorphous granules, rich in both calcium and phosphorus, have been observed in apatite-biomineralizing vertebrates, protists, and atremate brachiopods. These granules may represent stores of calcium-polyphosphate. Not unlike phosphorite nucleation by bacteria and diatoms, polyphosphate depolymerization to Pi would be controlled by phosphatase activity. Enzymatic polyphosphate depolymerization would increase apatite saturation to the level required for mineral nucleation, while matrix proteins would simultaneously control the progression of new biological apatite formation.},
  langid = {english},
  keywords = {biomineralisation,Biomineralization: mechanisms,Bone and cartilage development,Crystal structure/crystallinity}
}

@article{omoriComparativeEvaluation2021,
  title = {Comparative Evaluation of Microbial Profiles of Oral Samples Obtained at Different Collection Time Points and Using Different Methods},
  author = {Omori, Michi and {Kato-Kogoe}, Nahoko and Sakaguchi, Shoichi and Fukui, Nozomu and Yamamoto, Kayoko and Nakajima, Yoichiro and Inoue, Kazuya and Nakano, Hiroyuki and Motooka, Daisuke and Nakano, Takashi and Nakamura, Shota and Ueno, Takaaki},
  year = {2021},
  month = may,
  journal = {Clinical Oral Investigations},
  volume = {25},
  number = {5},
  pages = {2779--2789},
  issn = {1436-3771},
  doi = {10.1007/s00784-020-03592-y},
  abstract = {Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis.},
  langid = {english},
  keywords = {Human,Metagenome,Methods,Microbiota,Saliva}
}

@book{ortnerIdentificationPathological2003,
  title = {Identification of {{Pathological Conditions}} in {{Human Skeletal Remains}}},
  author = {Ortner, Donald J.},
  year = {2003},
  publisher = {{Academic Press}},
  address = {{London}}
}

@article{palmerActivityReconstruction2016,
  title = {Activity {{Reconstruction}} of {{Post}}-{{Medieval Dutch Rural Villagers}} from {{Upper Limb Osteoarthritis}} and {{Entheseal Changes}}},
  author = {Palmer, J. L. A. and Hoogland, M. H. L. and Waters-Rist, A. L.},
  year = {2016},
  journal = {International Journal of Osteoarchaeology},
  volume = {26},
  number = {1},
  pages = {78--92},
  issn = {1099-1212},
  doi = {10.1002/oa.2397},
  abstract = {The first objective of this study is to reconstruct levels and types of physical activity and associated sexual and social differences using human skeletal remains from the predominately 19th century Dutch cemetery of Middenbeemster. For most individuals, life in the Beemster centred around dairy farming and was heavily based on manual labor, with a purported higher class of wealthier individuals performing less manual labor. Two skeletal markers of activity are examined in the upper limb of late young adult and middle-aged adults of both sexes (26\textendash 49\,years, n\,=\,69): osteoarthritis (OA) and entheseal changes (EC). Results support the hypothesis that the majority of the population engaged in high levels of physical activity; however, a group with a clearly lower or different pattern of activity, possibly representing a higher, less active class, was not discernible. This may be due to a low number of less active individuals in the analysed sample and/or the heterogeneity of occupations and activities. A gendered division of labour was evident in the EC data with males having more pronounced muscle attachments in almost all sites, especially the biceps brachii, used primarily in lifting. Females had more pronounced triceps brachii, which may be due to activities that required pushing or pulling with the elbow in a flexed position. The prevalence and severity of OA did not differ between the sexes. While this could be interpreted to indicate men and women engaged in a similar level of strenuous activity, hormonal and anatomical differences limit the strength of the comparison. The second objective of this study is to evaluate the concordance of OA and EC as activity markers. The correlation between OA and EC is very low, illustrating their variable and complex etiologies. Etiological factors need further research for OA and EC to become more reliable activity markers. Copyright \textcopyright{} 2014 John Wiley \& Sons, Ltd.}
}

@article{palmerCoaggregationInteractions2003,
  title = {Coaggregation-{{Mediated Interactions}} of {{Streptococci}} and {{Actinomyces Detected}} in {{Initial Human Dental Plaque}}},
  author = {Palmer, Robert J. and Gordon, Sharon M. and Cisar, John O. and Kolenbrander, Paul E.},
  year = {2003},
  month = jun,
  journal = {Journal of Bacteriology},
  volume = {185},
  number = {11},
  pages = {3400--3409},
  issn = {0021-9193},
  doi = {10.1128/JB.185.11.3400-3409.2003},
  abstract = {Streptococci and actinomyces that initiate colonization of the tooth surface frequently coaggregate with each other as well as with other oral bacteria. These observations have led to the hypothesis that interbacterial adhesion influences spatiotemporal development of plaque. To assess the role of such interactions in oral biofilm formation in vivo, antibodies directed against bacterial surface components that mediate coaggregation interactions were used as direct immunofluorescent probes in conjunction with laser confocal microscopy to determine the distribution and spatial arrangement of bacteria within intact human plaque formed on retrievable enamel chips. In intrageneric coaggregation, streptococci such as Streptococcus gordonii DL1 recognize receptor polysaccharides (RPS) borne on other streptococci such as Streptococcus oralis 34. To define potentially interactive subsets of streptococci in the developing plaque, an antibody against RPS (anti-RPS) was used together with an antibody against S. gordonii DL1 (anti-DL1). These antibodies reacted primarily with single cells in 4-h-old plaque and with mixed-species microcolonies in 8-h-old plaque. Anti-RPS-reactive bacteria frequently formed microcolonies with anti-DL1-reactive bacteria and with other bacteria distinguished by general nucleic acid stains. In intergeneric coaggregation between streptococci and actinomyces, type 2 fimbriae of actinomyces recognize RPS on the streptococci. Cells reactive with antibody against type 2 fimbriae of Actinomyces naeslundii T14V (anti-type-2) were much less frequent than either subset of streptococci. However, bacteria reactive with anti-type-2 were seen in intimate association with anti-RPS-reactive cells. These results are the first direct demonstration of coaggregation-mediated interactions during initial plaque accumulation in vivo. Further, these results demonstrate the spatiotemporal development and prevalence of mixed-species communities in early dental plaque.},
  pmcid = {PMC155391},
  pmid = {12754239}
}

@article{palmerComparingUse2021,
  title = {Comparing the {{Use}} of {{Magnetic Beads}} with {{Ultrafiltration}} for {{Ancient Dental Calculus Proteomics}}},
  author = {Palmer, Karren S. and Makarewicz, Cheryl A. and Tishkin, Alexey A. and Tur, Svetlana S. and Chunag, Amartuvshin and Diimajav, Erdenebaatar and Jamsranjav, Bayarsaikhan and Buckley, Michael},
  year = {2021},
  month = mar,
  journal = {Journal of Proteome Research},
  volume = {20},
  number = {3},
  pages = {1689--1704},
  publisher = {{American Chemical Society}},
  issn = {1535-3893},
  doi = {10.1021/acs.jproteome.0c00862},
  abstract = {Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC\textendash MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins {$\beta$}-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.}
}

@article{palmerInterbacterialAdhesion2017,
  title = {Interbacterial {{Adhesion Networks}} within {{Early Oral Biofilms}} of {{Single Human Hosts}}},
  author = {Palmer, Robert J. and Shah, Nehal and Valm, Alex and Paster, Bruce and Dewhirst, Floyd and Inui, Taichi and Cisar, John O.},
  year = {2017},
  month = may,
  journal = {Applied and Environmental Microbiology},
  volume = {83},
  number = {11},
  pages = {e00407-17},
  issn = {0099-2240},
  doi = {10.1128/AEM.00407-17},
  abstract = {Specific interbacterial adhesion, termed coaggregation, is well established for three early colonizers of the plaque biofilm: streptococci, actinomyces, and veillonellae. However, little is known about interactions of other early colonizers and about the extent of interactions within the bacterial community from a single host. To address these gaps, subject-specific culture collections from two individuals were established using an intraoral biofilm retrieval device. Molecular taxonomy (Human Oral Microbe Identification Microarray [HOMIM]) analysis of biofilm samples confirmed the integrity and completeness of the collections. HOMIM analysis verified the isolation of Streptococcus gordonii and S. anginosus from only one subject, as well as isolation of a previously uncultivated streptococcal phylotype from the other subject. Strains representative of clonal diversity within each collection were further characterized. Greater than 70\% of these streptococcal strains from each subject coaggregated with at least one other coisolate. One-third of the strains carry a known coaggregation mediator: receptor polysaccharide (RPS). Almost all nonstreptococcal isolates coaggregated with other coisolates. Importantly, certain Rothia strains demonstrated more coaggregations with their coisolated bacteria than did any Streptococcus or Actinomyces strain, and certain Haemophilus isolates participated in twice as many. Confocal microscopy of undisturbed biofilms showed that Rothia and Haemophilus each occur in small multispecies microcolonies. However, in confluent high-biomass regions, Rothia occurred in islands whereas Haemophilus was distributed throughout. Together, the data demonstrate that coaggregation networks within an individual's oral microflora are extensive and that Rothia and Haemophilus can be important initiators of cell-cell interactions in the early biofilm., IMPORTANCE Extensive involvement of specific interbacterial adhesion in dental plaque biofilm formation has been postulated based on in vitro coaggregation between oral bacteria from culture collections that are not subject specific. In the present study, subject-specific culture collections were obtained from early plaque biofilm of two volunteers, and coaggregations within each culture collection were assayed. Coaggregations, several of which involved a coaggregation-mediating cell surface molecule known from well-studied streptococci, were widespread. Unexpectedly, the little-studied organisms Haemophilus and Rothia participated in the greatest numbers of interactions with community members; these two organisms showed different distributions within the undisturbed biofilm. The data show that coaggregation networks encompass most organisms within the biofilm community of each individual, and they indicate prominent participation of organisms such as Haemophilus and Rothia in early plaque biofilm formation.},
  pmcid = {PMC5440702},
  pmid = {28341674}
}

@article{pearceConcomitantDeposition1987,
  title = {The {{Concomitant Deposition}} of {{Strontium}} and {{Fluoride}} in {{Dental Plaque}}},
  author = {Pearce, E.I.F. and Sissons, C.H.},
  year = {1987},
  month = oct,
  journal = {Journal of Dental Research},
  volume = {66},
  number = {10},
  pages = {1518--1522},
  issn = {0022-0345, 1544-0591},
  doi = {10.1177/00220345870660100101},
  langid = {english}
}

@incollection{petersConstantDepth1988,
  title = {A {{Constant-Depth Laboratory Model Film Fermenter}}},
  booktitle = {{{CRC Handbook}} of {{Laboratory Model Systems}} for {{Microbial Ecosystems}}},
  author = {Peters, Adrian and Wimpenny, Julian W. T.},
  year = {1988},
  publisher = {{CRC Press}},
  abstract = {This chapter discusses the use of a generalized microbial film fermenter capable of operating under quasi-steady-state conditions. The importance of microbial film and its complexity as an ecosystem make it a most interesting area for ecological study. This very complexity makes in situ investigation extremely difficult, suggesting that laboratory model systems are needed if the fundamental processes of microbial film are to be understood. The constant-depth film fermenter maintains a steady-state by physically removing growth once a predetermined depth of film has been generated. A variety of surfaces may become colonized by microbial film, and characteristic properties of a given film may be determined by the nature of the substratum material. Microbial films are responsible for so much economic damage that a brief discussion of economic applications of film fermenters seems important. The resulting microbial film is a complex heterogeneous ecosystem with bacteria held in a matrix of polymeric substances produced by one or more of the species involved.},
  isbn = {978-1-315-15079-6}
}

@article{petersonViscoelasticityBiofilms2015,
  title = {Viscoelasticity of Biofilms and Their Recalcitrance to Mechanical and Chemical Challenges},
  author = {Peterson, Brandon W. and He, Yan and Ren, Yijin and Zerdoum, Aidan and Libera, Matthew R. and Sharma, Prashant K. and {van Winkelhoff}, Arie-Jan and Neut, Danielle and Stoodley, Paul and {van der Mei}, Henny C. and Busscher, Henk J.},
  year = {2015},
  month = mar,
  journal = {FEMS Microbiology Reviews},
  volume = {39},
  number = {2},
  pages = {234--245},
  issn = {1574-6976},
  doi = {10.1093/femsre/fuu008},
  langid = {english},
  keywords = {biofilm,detachment,extracellular polymeric substances,structure}
}

@article{petrovaEscapingBiofilm2016,
  title = {Escaping the Biofilm in More than One Way: Desorption, Detachment or Dispersion},
  shorttitle = {Escaping the Biofilm in More than One Way},
  author = {Petrova, Olga E and Sauer, Karin},
  year = {2016},
  month = apr,
  journal = {Current Opinion in Microbiology},
  series = {Cell Regulation},
  volume = {30},
  pages = {67--78},
  issn = {1369-5274},
  doi = {10.1016/j.mib.2016.01.004},
  abstract = {Biofilm bacteria have developed escape strategies to avoid stresses associated with biofilm growth, respond to changing environmental conditions, and disseminate to new locations. An ever-expanding body of research suggests that cellular release from biofilms is distinct from a simple reversal of attachment and reversion to a planktonic mode of growth, with biofilm dispersion involving sensing of specific cues, regulatory signal transduction, and consequent physiological alterations. However, dispersion is only one of many ways to escape the biofilm mode of growth. The present review is aimed at distinguishing this active and regulated process of dispersion from the passive processes of desorption and detachment by highlighting the regulatory processes and distinct phenotypes specific to dispersed cells.},
  langid = {english}
}

@article{pilloudOutliningDefinition2019,
  title = {Outlining a {{Definition}} of {{Oral Health}} within the {{Study}} of {{Human Skeletal Remains}}: {{Defining Oral Health}}},
  shorttitle = {Outlining a {{Definition}} of {{Oral Health}} within the {{Study}} of {{Human Skeletal Remains}}},
  author = {Pilloud, Marin A. and Fancher, J. P.},
  year = {2019},
  month = jul,
  journal = {Dental Anthropology Journal},
  volume = {32},
  number = {2},
  pages = {3--11},
  issn = {1096-9411},
  doi = {10.26575/daj.v32i2.297},
  abstract = {The term oral health is regularly used in bioarchaeological research to discuss a myriad of pathological conditions of the oral cavity. However, there is very little consensus on what conditions should be included in such a study, and some of the conditions are at odds with those in the clinical literature. \&nbsp;In this manuscript, we outline the clinical definition of oral health and develop a strategy in which bioarchaeology can address this type of research.\&nbsp; We argue that the terms dental disease and/or pathological conditions of the oral cavity should be used in lieu of oral health.\&nbsp; Various conditions that can be included in such research are outlined.\&nbsp; Finally, definitions, clinical etiologies, and recording schema for these conditions are discussed as relevant to bioarchaeological studies.},
  copyright = {Copyright (c) 2019 {$<$}a rel="license" href="http://creativecommons.org/licenses/by/4.0/"{$><$}img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /{$><$}/a{$><$}br /{$>$}This work is licensed under a {$<$}a rel="license" href="http://creativecommons.org/licenses/by/4.0/"{$>$}Creative Commons Attribution 4.0 International License{$<$}/a{$>$}.},
  langid = {english},
  keywords = {antemortem tooth loss,calculus,dental caries,hypercementosis,linear enamel hypoplasia,periapical lesions,periodontal disease}
}

@article{pipernoStarchGrains2008,
  title = {Starch Grains on Human Teeth Reveal Early Broad Crop Diet in Northern {{Peru}}},
  author = {Piperno, D. R. and Dillehay, T. D.},
  year = {2008},
  month = dec,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {105},
  number = {50},
  pages = {19622--19627},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0808752105},
  langid = {english}
}

@article{powerChimpCalculus2015,
  title = {Dental Calculus Evidence of {{Tai Forest Chimpanzee}} Plant Consumption and Life History Transitions},
  author = {Power, R.C. and {Salazar-Garcia}, D.C. and Wittig, R.M. and Freiberg, M. and Henry, A.G.},
  year = {2015},
  month = oct,
  journal = {Scientific Reports},
  volume = {5},
  pages = {15161},
  issn = {2045-2322 (Electronic) 2045-2322 (Linking)},
  doi = {10.1038/srep15161},
  abstract = {Dental calculus (calcified dental plaque) is a source of multiple types of data on life history. Recent research has targeted the plant microremains preserved in this mineralised deposit as a source of dietary and health information for recent and past populations. However, it is unclear to what extent we can interpret behaviour from microremains. Few studies to date have directly compared the microremain record from dental calculus to dietary records, and none with long-term observation dietary records, thus limiting how we can interpret diet, food acquisition and behaviour. Here we present a high-resolution analysis of calculus microremains from wild chimpanzees (Pan troglodytes verus) of Tai National Park, Cote d'Ivoire. We test microremain assemblages against more than two decades of field behavioural observations to establish the ability of calculus to capture the composition of diet. Our results show that some microremain classes accumulate as long-lived dietary markers. Phytolith abundance in calculus can reflect the proportions of plants in the diet, yet this pattern is not true for starches. We also report microremains can record information about other dietary behaviours, such as the age of weaning and learned food processing techniques like nut-cracking.},
  pmcid = {PMC4611876},
  keywords = {*Dental Calculus,*Herbivory,*Pan troglodytes,Animal Feed,Animals,Behavior; Animal,Cote d'Ivoire,Female,Male,Models; Theoretical}
}

@article{powerRepresentativenessDental2021,
  title = {The Representativeness of the Dental Calculus Dietary Record: Insights from {{Ta\"i}} Chimpanzee Faecal Phytoliths},
  shorttitle = {The Representativeness of the Dental Calculus Dietary Record},
  author = {Power, Robert C. and Wittig, Roman M. and Stone, Jeffery R. and Kupczik, Kornelius and {Schulz-Kornas}, Ellen},
  year = {2021},
  month = may,
  journal = {Archaeological and Anthropological Sciences},
  volume = {13},
  number = {6},
  pages = {104},
  issn = {1866-9565},
  doi = {10.1007/s12520-021-01342-z},
  abstract = {In recent years, new applications of microremain dietary analysis using dental calculus as a source of dietary data on ancient human subsistence and behaviours have accelerated. The dental calculus of contemporary human and non-human populations with known diets have been used as reference datasets, including the chimpanzees of Ta\"i National Park (C\^ote d'Ivoire), but explaining the preservation mechanism involved is challenged by our incomplete knowledge of the microremain content within the diets of these reference populations and our rudimentary information on microremain incorporation into dental calculus. Here, we analyse phytoliths in faecal samples to assess to what extent plant phytoliths of a diet are reflected in the dental calculus as well as in the egested faeces. In this study, we identify and document the faecal phytolith assemblages as an indicator of plant consumption in two Western chimpanzees of the Ta\"i National Park (C\^ote d'Ivoire) before (wet season), during (dry season) and after (dry season) a dust-rich period. Moreover, observational dietary records of these two individuals were compiled to improve the interpretability of this dental calculus phytolith dataset. The faecal phytolith assemblages vary significantly across samples in terms of abundance and diversity. The most common phytolith morphotypes were eudicot plates, single-cell and multi-cell tracheids, monocot rugulose and echinate spheroids and, to a lesser extent, unspecified thick and thin elongates. High loads of grit and other micro-remains (e.g. diatoms) are found during the dry period. Using observational dietary records as a starting point and our faecal results as a terminus, we consider how dental calculus can accumulate phytoliths. Our findings enable identification of the phytolith morphotypes that are under-represented in dental calculus, which is highly informative for future dental calculus research strategies.},
  langid = {english},
  lccn = {faro}
}

@article{powerSEMCalculus2014,
  title = {Assessing Use and Suitability of Scanning Electron Microscopy in the Analysis of Micro Remains in Dental Calculus},
  author = {Power, R.C. and {Salazar-Garc{\'i}a}, D.C. and Wittig, R.M. and Henry, A.G.},
  year = {2014},
  journal = {Journal of Archaeological Science},
  volume = {49},
  pages = {160--169},
  issn = {03054403},
  doi = {10.1016/j.jas.2014.04.016},
  keywords = {dental calculus,SEM}
}

@article{powerSynchrotronRadiationbased2022,
  title = {Synchrotron Radiation-Based Phase-Contrast Microtomography of Human Dental Calculus Allows Nondestructive Analysis of Inclusions: Implications for Archeological Samples},
  shorttitle = {Synchrotron Radiation-Based Phase-Contrast Microtomography of Human Dental Calculus Allows Nondestructive Analysis of Inclusions},
  author = {Power, Robert C. and Henry, Amanda G. and Moosmann, Julian and Beckmann, Felix and Temming, Heiko and Roberts, Anthony and Cabec, Adeline Le},
  year = {2022},
  month = mar,
  journal = {Journal of Medical Imaging},
  volume = {9},
  number = {3},
  pages = {031505},
  publisher = {{SPIE}},
  issn = {2329-4302, 2329-4310},
  doi = {10.1117/1.JMI.9.3.031505},
  abstract = {Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified. Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR-{$\mu$}CT) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples. Results: The virtual histological exploration of the samples shows that PPC-SR-{$\mu$}CT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains. Conclusions: PPC-SR-{$\mu$}CT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions.}
}

@article{prattenVitroStudies1998,
  title = {In Vitro Studies of the Effect of Antiseptic-Containing Mouthwashes on the Formation and Viability of {{Streptococcus}} Sanguis Biofilms},
  author = {{Pratten} and {Wills} and {Barnett} and {Wilson}},
  year = {1998},
  journal = {Journal of Applied Microbiology},
  volume = {84},
  number = {6},
  pages = {1149--1155},
  issn = {1365-2672},
  doi = {10.1046/j.1365-2672.1998.00462.x},
  abstract = {The aims of this study were to evaluate the growth of Streptococcus sanguis on hydroxyapatite, bovine enamel and polytetrafluoroethylene substrata in a constant depth film fermentor, and to determine the effects of three antimicrobial-containing mouthwashes on biofilm formation and bacterial viability on hydroxyapatite and enamel. There was little difference in the final cell density (5 \texttimes{} 104 cfu mm-2) of the Strep. sanguis biofilm on the three substrata. When hydroxyapatite-grown biofilms were exposed to the mouthwashes for 1 min, the one containing triclosan (T) proved the most effective. The chlorhexidine-containing mouthwash (CX) also achieved significant kills. The T-containing mouthwash was the most effective at killing biofilms grown on enamel. Pre-treatment of hydroxyapatite with CX, cetylpyridium chloride (CPC) or T for 1 min resulted in undetectable biofilm formation after 8 h. After 8 h of growth, only biofilms grown on enamel discs pre-treated with CX showed a reduction in the number of viable organisms. In conclusion, the results of this study have shown that while growth of Strep. sanguis on hydroxyapatite and enamel were similar, the ability of antimicrobial agents to prevent the accumulation of viable bacteria depended on the nature of the substratum.},
  langid = {english},
  annotation = {\_eprint: https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2672.1998.00462.x}
}

@article{priceTestingValidity2018,
  title = {Testing the Validity of Stable Isotope Analyses of Dental Calculus as a Proxy in Paleodietary Studies},
  author = {Price, Samantha D. R. and Keenleyside, Anne and Schwarcz, Henry P.},
  year = {2018},
  month = mar,
  journal = {Journal of Archaeological Science},
  volume = {91},
  pages = {92--103},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2018.01.008},
  abstract = {Stable isotopic analyses ({$\delta$}13C, {$\delta$}15N) of dental calculus have been suggested as a proxy for the study of diet of ancient populations but questions about their validity have been raised. Here we test this question, introducing significant improvements in the analysis of {$\delta$}13C and comparing our results for {$\delta$}13C and {$\delta$}15N of calculus with corresponding analyses of associated well-preserved bone which are widely believed to provide reliable paleodiet values. The content of organic material in calculus is decreased by {$\sim$}75\% compared with modern calculus, resulting in diagenetic changes to {$\delta$}13C and {$\delta$}15N of organic matter. Neither {$\delta$}13C nor {$\delta$}15N analyses of the organic component of calculus provide accurate estimates of paleodiet. Although {$\delta$}15N values of dental calculus are correlated with {$\delta$}15N values of bone collagen from the same individual, it is clear that they have been greatly affected by diagenesis, as shown by a correlation between C/N ratio and {$\delta$}15N. The inorganic (mineral-bound) carbon component of calculus, analyzed separately from the organic component, gave {$\delta$}13C values slightly offset from {$\delta$}13C values of CO3 in bone mineral. Thus it alone appears to have potential as a dietary proxy.},
  langid = {english},
  keywords = {Apatite,Carbon,Dental calculus,Diagenesis,Nitrogen,Paleodiet,Plaque,Stable isotopes}
}

@article{proctorSpatialGradient2018,
  title = {A Spatial Gradient of Bacterial Diversity in the Human Oral Cavity Shaped by Salivary Flow},
  author = {Proctor, Diana M. and Fukuyama, Julia A. and Loomer, Peter M. and Armitage, Gary C. and Lee, Stacey A. and Davis, Nicole M. and Ryder, Mark I. and Holmes, Susan P. and Relman, David A.},
  year = {2018},
  month = feb,
  journal = {Nature Communications},
  volume = {9},
  number = {1},
  pages = {681},
  issn = {2041-1723},
  doi = {10.1038/s41467-018-02900-1},
  abstract = {Spatial and temporal patterns in microbial communities provide insights into the forces that shape them, their functions and roles in health and disease. Here, we used spatial and ecological statistics to analyze the role that saliva plays in structuring bacterial communities of the human mouth using {$>$}9000 dental and mucosal samples. We show that regardless of tissue type (teeth, alveolar mucosa, keratinized gingiva, or buccal mucosa), surface-associated bacterial communities vary along an ecological gradient from the front to the back of the mouth, and that on exposed tooth surfaces, the gradient is pronounced on lingual compared to buccal surfaces. Furthermore, our data suggest that this gradient is attenuated in individuals with low salivary flow due to Sj\"ogren's syndrome. Taken together, our findings imply that salivary flow influences the spatial organization of microbial communities and that biogeographical patterns may be useful for understanding host physiological processes and for predicting disease.},
  langid = {english},
  pmcid = {PMC5813034},
  pmid = {29445174},
  keywords = {Adult,Aged,Bacteria,Biodiversity,Female,Genetic Variation,Humans,Male,Middle Aged,Mouth,Mouth Mucosa,RNA; Ribosomal; 16S,Saliva,Salivation,Sjogren's Syndrome,Tongue,Tooth,Xerostomia,Young Adult}
}

@article{radiniDirtyTeeth2022,
  title = {Beyond Dirty Teeth: {{Integrating}} Dental Calculus Studies with Osteoarchaeological Parameters},
  shorttitle = {Beyond Dirty Teeth},
  author = {Radini, Anita and Nikita, Efthymia},
  year = {2022},
  month = mar,
  journal = {Quaternary International},
  issn = {1040-6182},
  doi = {10.1016/j.quaint.2022.03.003},
  abstract = {The study of ancient human dental calculus (mineralized dental plaque, also known as tartar) is becoming increasingly important in osteoarchaeology, human palaeoecology and environmental archaeology. Microremains of different origin (e.g. starch granules, pollen, phytoliths, feather barbules) as well as biomolecules and chemical compounds retrieved from its mineral matrix may represent an important link between past humans and their physical, biological and social environment, but they are rarely fully linked to the evidence from skeletal remains. This paper critically reviews the lines of evidence retrieved from dental calculus in relation to osteoarchaeological parameters, employing macroscopic, microscopic and biomolecular approaches, assessing synergy potential and limitations. The scope of this paper is also to contribute to the building of a much needed theoretical framework in this emerging subfield.},
  langid = {english},
  keywords = {Dental calculus,Environment,Life history,Osteoarchaeology}
}

@article{radiniFoodPathways2017,
  title = {Beyond Food: {{The}} Multiple Pathways for Inclusion of Materials into Ancient Dental Calculus},
  author = {Radini, Anita and Nikita, E. and Buckley, S. and Copeland, L. and Hardy, K.},
  year = {2017},
  month = jan,
  journal = {American Journal of Physical Anthropology},
  volume = {162},
  pages = {71--83},
  issn = {1096-8644 (Electronic) 0002-9483 (Linking)},
  doi = {10.1002/ajpa.23147},
  abstract = {Dental calculus (mineralized dental plaque) was first recognised as a potentially useful archaeological deposit in the 1970s, though interest in human dental calculus as a resource material has increased sharply in the past few years. The majority of recent research has focused on the retrieval of plant microfossils embedded in its matrix and interpretation of these finds as largely the result of deliberate consumption of plant-derived food. However, while most of the material described in published works does represent food, dental calculus is in fact a "depositional environment" as material can enter the mouth from a range of sources. In this respect, it therefore represents an archaeological deposit that can also contain extensive non-dietary debris. This can comprise a wide variety of cultural and environmental material which reaches the mouth and can become embedded in dental calculus through alternative pathways. Here, we explore the human behaviors and activities besides eating that can generate a flux of particles into the human mouth, the broad range of additional cultural and environmental information that can be obtained through the analysis and contextualisation of this material, and the implications of the additional pathways by which material can become embedded in dental calculus.},
  keywords = {*Dental Calculus,Archaeology,dental calculus,diet,Diet/*history,Environment,Food/*history,Fossils,History; Ancient,Humans,microfossils}
}

@article{radiniMedievalWomen2019,
  title = {Medieval Women's Early Involvement in Manuscript Production Suggested by Lapis Lazuli Identification in Dental Calculus},
  author = {Radini, Anita and Tromp, M. and Beach, A. and Tong, E. and Speller, C. and McCormick, M. and Dudgeon, J. V. and Collins, M. J. and R{\"u}hli, F. and Kr{\"o}ger, R. and Warinner, C.},
  year = {2019},
  month = jan,
  journal = {Science Advances},
  volume = {5},
  number = {1},
  pages = {eaau7126},
  publisher = {{American Association for the Advancement of Science}},
  doi = {10.1126/sciadv.aau7126},
  abstract = {During the European Middle Ages, the opening of long-distance Asian trade routes introduced exotic goods, including ultramarine, a brilliant blue pigment produced from lapis lazuli stone mined only in Afghanistan. Rare and as expensive as gold, this pigment transformed the European color palette, but little is known about its early trade or use. Here, we report the discovery of lapis lazuli pigment preserved in the dental calculus of a religious woman in Germany radiocarbon-dated to the 11th or early 12th century. The early use of this pigment by a religious woman challenges widespread assumptions about its limited availability in medieval Europe and the gendered production of illuminated texts.}
}

@article{raffertyCurrentResearch2012,
  title = {Current Research on Smoking Pipe Residues},
  author = {Rafferty, Sean M. and Lednev, Igor and Virkler, Kelly and Chovanec, Zuzana},
  year = {2012},
  month = jul,
  journal = {Journal of Archaeological Science},
  volume = {39},
  number = {7},
  pages = {1951--1959},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2012.02.001},
  abstract = {This paper presents research into the identification of tobacco residues in ancient smoking pipes. Two techniques have been used so far: gas chromatography/mass spectroscopy (GC/MS), and Raman microscopy. GC/MS has been used successful in the past by the author to identify ancient tobacco residues, and the results of this round of analysis support prior research. Raman microscopy, which has the advantage of working on dry samples without solvents, was not successful. It appears that combustion products overwhelm any useful signal that would identify the substance smoked. We are pursuing the use of Raman in non-combusted samples.},
  langid = {english},
  keywords = {GC–MS,Raman microscopy,Residue analysis,Tobacco}
}

@article{ramsoeDeamiDATESitespecific2020,
  title = {{{DeamiDATE}} 1.0: {{Site-specific}} Deamidation as a Tool to Assess Authenticity of Members of Ancient Proteomes},
  shorttitle = {{{DeamiDATE}} 1.0},
  author = {Rams{\o}e, Abigail and {van Heekeren}, Vivian and Ponce, Paola and Fischer, Roman and Barnes, Ian and Speller, Camilla and Collins, Matthew J.},
  year = {2020},
  month = mar,
  journal = {Journal of Archaeological Science},
  volume = {115},
  pages = {105080},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2020.105080},
  abstract = {Contamination is a potential problem in the study of ancient proteins, either from prior handling of the sample, laboratory consumables, or cross-sample carryover from mass spectrometers. Recently, deamidation of glutamine has been proposed as a measure for assessing the degradation of ancient proteins. Here, we present deamiDATE 1.0, a method for the authentication of ancient proteins using measure of site-specific deamidation rates. We test this approach on shotgun proteomic data derived from bone collagen from modern, archaeological and extinct taxa. We further demonstrate how this method may be used to differentiate between modern contaminants and authentic ancient proteins using a case study from Neolithic dental calculus.},
  langid = {english},
  keywords = {Authentication,Bioinformatics,Contamination,Palaeoproteomics}
}

@manual{Rbase,
  type = {Manual},
  title = {R: {{A}} Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  year = {2020},
  address = {{Vienna, Austria}},
  institution = {{R Foundation for Statistical Computing}}
}

@manual{Rbroom,
  type = {Manual},
  title = {Broom: {{Convert}} Statistical Objects into Tidy Tibbles},
  author = {Robinson, David and Hayes, Alex and Couch, Simon},
  year = {2021}
}

@article{Rdecontam,
  title = {Simple Statistical Identification and Removal of Contaminant Sequences in Marker-Gene and Metagenomics Data},
  author = {Davis, Nicole M. and Proctor, Diana M. and Holmes, Susan P. and Relman, David A. and Callahan, Benjamin J.},
  year = {2018},
  month = dec,
  journal = {Microbiome},
  volume = {6},
  number = {1},
  pages = {226},
  issn = {2049-2618},
  doi = {10.1186/s40168-018-0605-2},
  abstract = {The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants\textemdash DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.},
  keywords = {16S rRNA gene,DNA contamination,Marker-gene,Metagenomics,Microbiome}
}

@article{rehImpactTobacco2012,
  title = {Impact of {{Tobacco Smoke}} on {{Chronic Rhinosinusitis}} \textendash{} {{A Review}} of the {{Literature}}},
  author = {Reh, Douglas D. and Higgins, Thomas S. and Smith, Timothy L.},
  year = {2012},
  month = sep,
  journal = {International forum of allergy \& rhinology},
  volume = {2},
  number = {5},
  pages = {362},
  publisher = {{NIH Public Access}},
  doi = {10.1002/alr.21054},
  abstract = {Environmental factors such as inhaled pollutants like cigarette smoke may play a significant role in diseases of the upper airway including chronic rhinosinusitis (CRS). The objectives of this review are to summarize prior studies that describe the correlation ...},
  langid = {english},
  pmid = {22696460}
}

@book{reichertStarchBible1913b,
  title = {The Differentiation and Specificity of Starches in Relation to Genera, Species, Etc: Stereochemistry Applied to Protoplasmic Processes and Products, and as a Strictly Scientific Basis for the Classification of Plants and Animals},
  author = {Reichert, Edward Tyson},
  year = {1913},
  volume = {2},
  publisher = {{Carnegie institution of Washington}},
  address = {{Washington, D.C.}}
}

@article{reimerBacDive2022,
  title = {{{BacDive}} in 2022: The Knowledge Base for Standardized Bacterial and Archaeal Data},
  shorttitle = {{{BacDive}} in 2022},
  author = {Reimer, Lorenz Christian and Sard{\`a}~Carbasse, Joaquim and Koblitz, Julia and Ebeling, Christian and Podstawka, Adam and Overmann, J{\"o}rg},
  year = {2022},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {D1},
  pages = {D741-D746},
  issn = {0305-1048},
  doi = {10.1093/nar/gkab961},
  abstract = {The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30\% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.}
}

@article{renduelesMechanismsCompetition2015,
  title = {Mechanisms of {{Competition}} in {{Biofilm Communities}}},
  author = {Rendueles, Olaya and Ghigo, Jean-Marc},
  year = {2015},
  month = jun,
  journal = {Microbiology Spectrum},
  volume = {3},
  number = {3},
  pages = {3.3.28},
  publisher = {{American Society for Microbiology}},
  doi = {10.1128/microbiolspec.MB-0009-2014},
  keywords = {bacterial competition,oral biofilm}
}

@article{rennerPhysicochemicalRegulation2011,
  title = {Physicochemical Regulation of Biofilm Formation},
  author = {Renner, Lars D. and Weibel, Douglas B.},
  year = {2011},
  month = may,
  journal = {MRS Bulletin},
  volume = {36},
  number = {5},
  pages = {347--355},
  issn = {1938-1425},
  doi = {10.1557/mrs.2011.65},
  abstract = {This article reviews the physical and chemical constraints of environments on biofilm formation. We provide a perspective on how materials science and engineering can address fundamental questions and unmet technological challenges in this area of microbiology, such as biofilm prevention. Specifically, we discuss three factors that impact the development and organization of bacterial communities. (1) Physical properties of surfaces regulate cell attachment and physiology and affect early stages of biofilm formation. (2) Chemical properties influence the adhesion of cells to surfaces and their development into biofilms and communities. (3) Chemical communication between cells attenuates growth and influences the organization of communities. Mechanisms of spatial and temporal confinement control the dimensions of communities and the diffusion path length for chemical communication between biofilms, which, in turn, influences biofilm phenotypes. Armed with a detailed understanding of biofilm formation, researchers are applying the tools and techniques of materials science and engineering to revolutionize the study and control of bacterial communities growing at interfaces.},
  langid = {english}
}

@manual{Rhere,
  type = {Manual},
  title = {Here: {{A}} Simpler Way to Find Your Files},
  author = {M{\"u}ller, Kirill},
  year = {2020}
}

@article{RmixOmics,
  title = {{{mixOmics}}: {{An R}} Package for 'omics Feature Selection and Multiple Data Integration},
  author = {Rohart, F and Gautier, B and Singh, A and Le Cao, K-A},
  year = {2017},
  journal = {PLoS computational biology},
  volume = {13},
  number = {11},
  pages = {e1005752},
  publisher = {{Public Library of Science}}
}

@incollection{robertsDentalDisease2007,
  title = {Dental {{Disease}}},
  booktitle = {The {{Archaeology}} of {{Disease}}},
  author = {Roberts, Charlotte A and Manchester, Keith},
  year = {2007},
  edition = {3rd Edition},
  pages = {63--83},
  publisher = {{Cornell University Press}}
}

@article{roderStudyingBacterial2016,
  title = {Studying {{Bacterial Multispecies Biofilms}}: {{Where}} to {{Start}}?},
  shorttitle = {Studying {{Bacterial Multispecies Biofilms}}},
  author = {R{\o}der, Henriette L. and S{\o}rensen, S{\o}ren J. and Burm{\o}lle, Mette},
  year = {2016},
  month = jun,
  journal = {Trends in Microbiology},
  volume = {24},
  number = {6},
  pages = {503--513},
  issn = {0966-842X},
  doi = {10.1016/j.tim.2016.02.019},
  abstract = {The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating the approaches used to study these complex communities. This review focuses on the establishment of multispecies biofilms in vitro, interspecies interactions in microhabitats, and how to select communities for evaluation. Studies have used different experimental approaches; here we evaluate the benefits and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions.},
  langid = {english},
  keywords = {bacterial interactions,biofilm,communities,multispecies,notion}
}

@incollection{rogersPalaeopathologyJoint2000,
  title = {The Palaeopathology of Joint Disease},
  booktitle = {Human Osteology : {{In}} Archaeology and Forensic Science.},
  author = {Rogers, Juliet},
  editor = {Cox, Margaret and Mays, Simon},
  year = {2000},
  edition = {1st ed},
  pages = {163--182},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}},
  isbn = {978-1-84110-046-3}
}

@article{rogersRoleStreptococcus2001,
  title = {Role of {{Streptococcus}} Gordonii {{Amylase-Binding Protein A}} in {{Adhesion}} to {{Hydroxyapatite}}, {{Starch Metabolism}},  and {{Biofilm Formation}}},
  author = {Rogers, Jeffrey D. and Palmer, Robert J. and Kolenbrander, Paul E. and Scannapieco, Frank A.},
  year = {2001},
  month = nov,
  journal = {Infection and Immunity},
  volume = {69},
  number = {11},
  pages = {7046--7056},
  issn = {0019-9567},
  doi = {10.1128/IAI.69.11.7046-7056.2001},
  abstract = {Interactions between bacteria and salivary components are thought to be important in the establishment and ecology of the oral microflora. {$\alpha$}-Amylase, the predominant salivary enzyme in humans, binds to Streptococcus gordonii, a primary colonizer of the tooth. Previous studies have implicated this interaction in adhesion of the bacteria to salivary pellicles, catabolism of dietary starches, and biofilm formation. Amylase binding is mediated at least in part by the amylase-binding protein A (AbpA). To study the function of this protein, an erythromycin resistance determinant [erm(AM)] was inserted within the abpA gene of S. gordonii strains Challis and FAS4 by allelic exchange, resulting in abpA mutant strains Challis-E1 and FAS4-E1. Comparison of the wild-type and mutant strains did not reveal any significant differences in colony morphology, biochemical metabolic profiles, growth in complex or defined media, surface hydrophobicity, or coaggregation properties. Scatchard analysis of adhesion isotherms demonstrated that the wild-type strains adhered better to human parotid-saliva- and amylase-coated hydroxyapatite than did the AbpA mutants. In contrast, the mutant strains bound to whole-saliva-coated hydroxyapatite to a greater extent than did the wild-type strains. While the wild-type strains preincubated with purified salivary amylase grew well in defined medium with potato starch as the sole carbohydrate source, the AbpA mutants did not grow under the same conditions even after preincubation with amylase. In addition, the wild-type strain produced large microcolonies in a flow cell biofilm model, while the abpA mutant strains grew much more poorly and produced relatively small microcolonies. Taken together, these results suggest that AbpA of S. gordonii functions as an adhesin to amylase-coated hydroxyapatite, in salivary-amylase-mediated catabolism of dietary starches and in human saliva-supported biofilm formation by S. gordonii.},
  pmcid = {PMC100085},
  pmid = {11598080}
}

@article{rohanizadehUltrastructuralStudy2005,
  title = {Ultrastructural Study of Calculus\textendash Enamel and Calculus\textendash Root Interfaces},
  author = {Rohanizadeh, Ramin and LeGeros, Racquel Z.},
  year = {2005},
  month = jan,
  journal = {Archives of Oral Biology},
  volume = {50},
  number = {1},
  pages = {89--96},
  issn = {0003-9969},
  doi = {10.1016/j.archoralbio.2004.07.001},
  abstract = {The attachment of dental calculus to the tooth (enamel or cementum) surface affects the ease or difficulty of its removal. Understanding the ultrastructural features of the calculus\textendash tooth interface will help in the development of efficient strategies for efficient removal of dental calculus. Objective: The aim of this study was to determine the ultrastructural characteristics of the calculus\textendash tooth interface in relation to the occurrence of calculus fracture. Design: Investigation of the ultrastructural characteristics of the calculus\textendash tooth interface was made on eight human molars with mature supragingival and subgingival calculus using scanning electron microscopy (SEM), transmission electron microscopy (TEM) and fourier transform infra-red (FT-IR) spectroscopy. Results: Fractures were shown by SEM to consistently occur within the calculus itself, but not at the calculus\textendash tooth interface. Higher magnification revealed that the enamel apatite crystals (in the case of supragingival calculus) or the cementum apatite crystals (in the case of subgingival calculus) appeared intimately connected with the calculus crystals at the calculus\textendash enamel or calculus\textendash cementum interface. TEM micrographs confirmed this intimate direct connection or fusion (epitaxial growth) of calculus crystals with enamel and cementum apatite crystals. FT-IR showed lower concentrations of organic phase attributed to microorganisms and higher concentrations of collagen at the calculus\textendash cementum interface compared to that in the calculus away from the interface. Conclusion: Difficulty in complete calculus removal from tooth surfaces (especially from cementum or dentin) may be due in part to the intimate contact between the calculus and the tooth, due to the chemical bonding between the calculus crystals and the tooth apatite crystals and occasional fusion (i.e., epitaxial growth) of the calculus calcium phosphate crystals with the enamel, dentin or apatite crystals. This cohesive bonding results in fracture planes occurring within the calculus instead of at the calculus\textendash tooth interface.},
  langid = {english},
  keywords = {Calcium phosphates,Calculus,Calculus–tooth interface,Cementum apatite,Enamel apatite,FTIR,Ultrastructure}
}

@manual{Rpatchwork,
  type = {Manual},
  title = {Patchwork: {{The}} Composer of Plots},
  author = {Pedersen, Thomas Lin},
  year = {2020}
}

@manual{Rpsych,
  type = {Manual},
  title = {Psych: {{Procedures}} for Psychological, Psychometric, and Personality Research},
  author = {Revelle, William},
  year = {2022},
  address = {{Evanston, Illinois}},
  organization = {{Northwestern University}}
}

@manual{Rrrtools,
  type = {Manual},
  title = {Rrtools: {{Creates}} a Reproducible Research Compendium},
  author = {Marwick, Ben},
  year = {2019}
}

@article{rustichelliSimultaneousSeparation1996,
  title = {Simultaneous Separation and Identification of Hashish Constituents by Coupled Liquid Chromatography-Mass Spectrometry ({{HPLC-MS}})},
  author = {Rustichelli, C. and Ferioli, V. and Vezzalini, F. and Rossi, M. C. and Gamberini, G.},
  year = {1996},
  month = aug,
  journal = {Chromatographia},
  volume = {43},
  number = {3},
  pages = {129--134},
  issn = {1612-1112},
  doi = {10.1007/BF02292940},
  abstract = {This paper reports the use of liquid chromatography for the separation and determination of the major cannabinoids extracted from hashish samples. The direct coupling to the mass spectrometer enables the selective identification both of neutral and acidic cannabinoids. The developed method does not require any preliminary derivatization and should, therefore, be of interest in forensic analysis for simple and unequivocal determination of hashish constituents.},
  langid = {english},
  keywords = {Column liquid chromatography,Hashish samples,Neutral and acidic cannabinoids,On-line liquid chromatography-mass spectrometry}
}

@manual{Rvegan,
  type = {Manual},
  title = {Vegan: {{Community}} Ecology Package},
  author = {Oksanen, Jari and Simpson, Gavin L. and Blanchet, F. Guillaume and Kindt, Roeland and Legendre, Pierre and Minchin, Peter R. and O'Hara, R.B. and Solymos, Peter and Stevens, M. Henry H. and Szoecs, Eduard and Wagner, Helene and Barbour, Matt and Bedward, Michael and Bolker, Ben and Borcard, Daniel and Carvalho, Gustavo and Chirico, Michael and De Caceres, Miquel and Durand, Sebastien and Evangelista, Heloisa Beatriz Antoniazi and FitzJohn, Rich and Friendly, Michael and Furneaux, Brendan and Hannigan, Geoffrey and Hill, Mark O. and Lahti, Leo and McGlinn, Dan and Ouellette, Marie-Helene and Ribeiro Cunha, Eduardo and Smith, Tyler and Stier, Adrian and Ter Braak, Cajo J.F. and Weedon, James},
  year = {2022}
}

@article{sagneStudiesPeriodontal1977,
  title = {Studies of the {{Periodontal Status}} of a {{Medieval Population}}},
  author = {Sagne, S. and Olsson, G.},
  year = {1977},
  month = jan,
  journal = {Dentomaxillofacial Radiology},
  volume = {6},
  number = {1},
  pages = {46--52},
  issn = {0250-832X, 1476-542X},
  doi = {10.1259/dmfr.1977.0006},
  langid = {english}
}

@article{salazar-garciaDentalCalculus2014,
  title = {Dental Calculus Is Not Equivalent to Bone Collagen for Isotope Analysis: A Comparison between Carbon and Nitrogen Stable Isotope Analysis of Bulk Dental Calculus, Bone and Dentine Collagen from Same Individuals from the {{Medieval}} Site of {{El Raval}} ({{Alicante}}, {{Spain}})},
  shorttitle = {Dental Calculus Is Not Equivalent to Bone Collagen for Isotope Analysis},
  author = {{Salazar-Garc{\'i}a}, D. C. and Richards, M. P. and Nehlich, O. and Henry, A. G.},
  year = {2014},
  month = jul,
  journal = {Journal of Archaeological Science},
  volume = {47},
  pages = {70--77},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2014.03.026},
  abstract = {Palaeodietary reconstruction using the carbon and nitrogen isotope values of bone and dentine collagen is a well-established method and the biochemical processes involved are well known. Researchers have recently explored using bulk samples of dental calculus as a substitute for bone and dentine collagen in dietary analyses, because calculus can be sampled without causing damage to the teeth, and may be useful in situations where more destructive analyses are not possible, or where collagen is poorly preserved. Several questions remain about the use of bulk calculus as a source of carbon and nitrogen isotope data, however. It is not yet clear how much of an individual's life span dental calculus represents, what portions of the diet it records, and how diagenesis effects the carbon and nitrogen isotope values of this material. Most importantly, there have been no comparative studies of collagen and calculus isotope values, which are necessary to establish the value of bulk calculus as a source of accurate isotope values. Here we report the comparison of carbon and nitrogen stable isotope analyses of bulk calculus to those from bone and dentine collagen. These analyses have been performed on individuals from the El Raval Mud\'ejar Medieval Cemetery (Eastern Iberia, 15th century A.D.). Although calculus isotope values may be broadly similar to expected values at the population level, we report here no correlation between collagen and bulk dental calculus values at the individual level. As a result, we recommend that carbon and nitrogen analysis on bulk dental calculus should only be used as a last resource archaeological dietary marker, if at all.},
  langid = {english},
  keywords = {Collagen,Dental calculus,Diet,Medieval period,Stable isotopes}
}

@article{scannapiecoPotentialAssociations2001,
  title = {Potential {{Associations Between Chronic Respiratory Disease}} and {{Periodontal Disease}}: {{Analysis}} of {{National Health}} and {{Nutrition Examination Survey III}}},
  shorttitle = {Potential {{Associations Between Chronic Respiratory Disease}} and {{Periodontal Disease}}},
  author = {Scannapieco, Frank A. and Ho, Alex W.},
  year = {2001},
  journal = {Journal of Periodontology},
  volume = {72},
  number = {1},
  pages = {50--56},
  issn = {1943-3670},
  doi = {10.1902/jop.2001.72.1.50},
  abstract = {Background: Associations between poor oral health and chronic lung disease have recently been reported. The present study evaluated these potential associations by analyzing data from the National Health and Nutrition Examination Survey III (NHANES III), which documents the general health and nutritional status of randomly selected United States subjects from 1988 to 1994. Methods: This cross-sectional, retrospective study of the NHANES III database included a study population of 13,792 subjects {$\geq$}20 years of age with at least 6 natural teeth. A history of bronchitis and/or emphysema was recorded from the medical questionnaire, and a dichotomized variable combined those with either chronic bronchitis and/or emphysema, together considered as chronic obstructive pulmonary disease (COPD). Subject lung function was estimated by calculating the ratio of forced expiratory volume (FEV) after 1 second (FEV1)/forced vital capacity (FVC). Oral health status was assessed from the DMFS/T index (summary of cumulative caries experience), gingival bleeding, gingival recession, gingival probing depth, and periodontal attachment level. Unweighted analyses were used for initial examination of the data, and a weighted analysis was performed in a final logistic regression model adjusting for age, gender, race and ethnicity, education, income, frequency of dental visits, diabetes mellitus, smoking, and alcohol use. Results: The mean age of all subjects was 44.4 {$\pm$} 17.8 years (mean {$\pm$} SD): COPD = 51.2 {$\pm$} 17.9 years and subjects without COPD = 43.9 {$\pm$} 17.7 years. Subjects with a history of COPD had more periodontal attachment loss than subjects without COPD (1.48 {$\pm$} 1.35 mm versus 1.17 {$\pm$} 1.09 mm, P = 0.0001). Subjects with mean attachment loss (MAL) {$\geq$}3.0 mm had a higher risk of COPD than those having MAL {$<$}3.0 mm (odds ratio, 1.45; 95\% CI, 1.02 to 2.05). A trend was noted in that lung function appeared to diminish with increasing periodontal attachment loss. Conclusions: The findings of the present analysis support recently published reports that suggest an association between periodontal disease and COPD. J Periodontol 2001;72:50-56.},
  langid = {english},
  keywords = {cross-sectional studies,Lung diseases,National Health and Nutrition Examination Survey III,obstructive,oral health,periodontal attachment loss/complications,periodontal diseases/complications,risk factors},
  annotation = {\_eprint: https://aap.onlinelibrary.wiley.com/doi/pdf/10.1902/jop.2001.72.1.50}
}

@article{scannapiecoRoleOral1999,
  title = {Role of {{Oral Bacteria}} in {{Respiratory Infection}}},
  author = {Scannapieco, Frank A.},
  year = {1999},
  journal = {Journal of Periodontology},
  volume = {70},
  number = {7},
  pages = {793--802},
  issn = {1943-3670},
  doi = {10.1902/jop.1999.70.7.793},
  abstract = {An association between oral conditions such as periodontal disease and several respiratory conditions has been noted. For example, recent evidence has suggested a central role for the oral cavity in the process of respiratory infection. Oral periodontopathic bacteria can be aspirated into the lung to cause aspiration pneumonia. The teeth may also serve as a reservoir for respiratory pathogen colonization and subsequent nosocomial pneumonia. Typical respiratory pathogens have been shown to colonize the dental plaque of hospitalized intensive care and nursing home patients. Once established in the mouth, these pathogens may be aspirated into the lung to cause infection. Other epidemiologic studies have noted a relationship between poor oral hygiene or periodontal bone loss and chronic obstructive pulmonary disease. Several mechanisms are proposed to explain the potential role of oral bacteria in the pathogenesis of respiratory infection: 1. aspiration of oral pathogens (such as Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, etc.) into the lung to cause infection; 2. periodontal disease-associated enzymes in saliva may modify mucosal surfaces to promote adhesion and colonization by respiratory pathogens, which are then aspirated into the lung; 3. periodontal disease-associated enzymes may destroy salivary pellicles on pathogenic bacteria to hinder their clearance from the mucosal surface; and 4. cytokines originating from periodontal tissues may alter respiratory epithelium to promote infection by respiratory pathogens. J Periodontol 1999;70:793-802.},
  langid = {english},
  keywords = {cytokines,Enzymes/adverse effects,oral hygiene,periodontal diseases/microbiology,periodontal diseases/pathogenicity,respiratory tract infections/pathogenicity,saliva/enzymology,saliva/physiology},
  annotation = {\_eprint: https://aap.onlinelibrary.wiley.com/doi/pdf/10.1902/jop.1999.70.7.793}
}

@article{scannapiecoSalivaryAmylase1993,
  title = {Salivary {$\alpha$}-Amylase: Role in Dental Plaque and Caries Formation},
  author = {Scannapieco, Frank A. and Torres, Guillermo and Levine, Michael J.},
  year = {1993},
  journal = {Critical Reviews in Oral Biology \& Medicine},
  volume = {4},
  number = {3},
  pages = {301--307},
  issn = {1045-4411}
}

@article{scheltemaOpiumTrade1907,
  title = {The {{Opium Trade}} in the {{Dutch East Indies}}. {{I}}},
  author = {Scheltema, J. F.},
  year = {1907},
  journal = {American Journal of Sociology},
  volume = {13},
  number = {1},
  pages = {79--112},
  issn = {00029602, 15375390}
}

@article{schuijtemakerTeTheegasten2011,
  title = {{Te Theegasten}},
  author = {Schuijtemaker, D.},
  year = {2011},
  journal = {De Nieuwe Schouwschuit},
  volume = {9},
  pages = {16--17},
  langid = {dutch}
}

@incollection{scottBriefHistory2015,
  title = {A {{Brief History}} of {{Dental Anthropology}}},
  booktitle = {A {{Companion}} to {{Dental Anthropology}}},
  author = {Scott, G. Richard},
  editor = {Irish, J. D. and Scott, G. Richard},
  year = {2015},
  pages = {7--17},
  publisher = {{John Wiley \& Sons, Ltd}},
  address = {{Chichester}},
  doi = {10.1002/9781118845486.ch18},
  chapter = {18},
  isbn = {978-1-118-84548-6},
  langid = {english},
  keywords = {Arizona State University Dental Anthropology System,distance statistics,genetic relatedness,P henetic affinities,qualitative and quantitative analyses},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781118845486.ch18}
}

@article{scottExoticFoods2021,
  title = {Exotic Foods Reveal Contact between {{South Asia}} and the {{Near East}} during the Second Millennium {{BCE}}},
  author = {Scott, Ashley and Power, Robert C. and {Altmann-Wendling}, Victoria and Artzy, Michal and Martin, Mario A. S. and Eisenmann, Stefanie and Hagan, Richard and {Salazar-Garc{\'i}a}, Domingo C. and Salmon, Yossi and Yegorov, Dmitry and Milevski, Ianir and Finkelstein, Israel and Stockhammer, Philipp W. and Warinner, Christina},
  year = {2021},
  month = jan,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {118},
  number = {2},
  pages = {e2014956117},
  publisher = {{Proceedings of the National Academy of Sciences}},
  doi = {10.1073/pnas.2014956117},
  abstract = {Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum), and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine.}
}

@book{seidemannStarchAtlas1966,
  title = {St\{\textbackslash "a\}rke-{{Atlas}}: {{Grundlagen}} Der {{St}}\{\textbackslash "a\}rke-{{Mikroskopie}} Und {{Beschreibung}} Der Wichtigsten {{St}}\{\textbackslash "a\}rkearten},
  author = {Seidemann, Johannes},
  year = {1966},
  publisher = {{Parey}},
  address = {{Berlin}}
}

@article{shawCommonalityElastic2004,
  title = {Commonality of {{Elastic Relaxation Times}} in {{Biofilms}}},
  author = {Shaw, T. and Winston, M. and Rupp, C. J. and Klapper, I. and Stoodley, P.},
  year = {2004},
  month = aug,
  journal = {Physical Review Letters},
  volume = {93},
  number = {9},
  pages = {098102},
  publisher = {{American Physical Society}},
  doi = {10.1103/PhysRevLett.93.098102},
  abstract = {Biofilms, sticky conglomerations of microorganisms and extracellular polymers, are among the Earth's most common life forms. One component for their survival is an ability to withstand external mechanical stress. Measurements indicate that biofilm elastic relaxation times are approximately the same (about 18 min) over a wide sample of biofilms though other material properties vary significantly. A possible survival significance of this time scale is that it is the shortest period over which a biofilm can mount a phenotypic response to transient mechanical stress.}
}

@article{shellisSyntheticSaliva1978,
  title = {A Synthetic Saliva for Cultural Studies of Dental Plaque},
  author = {Shellis, R. P.},
  year = {1978},
  month = jan,
  journal = {Archives of Oral Biology},
  volume = {23},
  number = {6},
  pages = {485--489},
  issn = {0003-9969},
  doi = {10.1016/0003-9969(78)90081-X},
  abstract = {The synthetic solution described is intended as a substitute for natural saliva in continuous culture of plaque in artificial-mouth apparatus. The solution contains bovine submandibular glycoprotein, has a composition based on published analyses of human saliva, is readily sterilised by filtration and is stable. The viscosity and buffering properties are similar to those of natural saliva and it resembles natural saliva more closely than previous formulations.},
  langid = {english}
}

@article{sidawayMicrobiologicalStudy1978a,
  title = {A Microbiological Study of Dental Calculus},
  author = {Sidaway, D. A.},
  year = {1978},
  month = aug,
  journal = {Journal of Periodontal Research},
  volume = {13},
  number = {4},
  pages = {360--366},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {1600-0765},
  doi = {10.1111/j.1600-0765.1978.tb00190.x},
  abstract = {A simple in vitro system has been used to culture 34 species of microorganisms derived from human calculus. A confluent growth on the surface of an agar dise, was subjected to a daily 4 hr incubation...},
  langid = {english}
}

@article{simonsoroOralGeography2013,
  title = {Microbial Geography of the Oral Cavity},
  author = {{Sim{\'o}n-Soro}, A. and Tom{\'a}s, I. and {Cabrera-Rubio}, R. and Catalan, M. D. and Nyvad, B. and Mira, A.},
  year = {2013},
  month = jul,
  journal = {Journal of Dental Research},
  volume = {92},
  number = {7},
  pages = {616--621},
  issn = {1544-0591},
  doi = {10.1177/0022034513488119},
  abstract = {We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40\% to 70\% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.},
  langid = {english},
  pmid = {23674263},
  keywords = {Actinobacillus,Actinomycetaceae,Adult,Bacteria,Bicuspid,Capnocytophaga,Cuspid,dental plaque,Dental Plaque,DNA; Bacterial,Fusobacterium,Gingiva,gingival sulcus,Haemophilus,human microbiome,Humans,Incisor,Male,massively parallel sequencing,Molar,Mouth,Mouth Mucosa,Palate,Polymerase Chain Reaction,Prevotella,RNA; Bacterial,RNA; Ribosomal; 16S,saliva,Saliva,sampling,Streptococcus,Tongue,Veillonella,Young Adult}
}

@article{sissonsArtificialPlaque1997,
  title = {Artificial {{Dental Plaque Biofilm Model Systems}}},
  author = {Sissons, C.H.},
  year = {1997},
  month = apr,
  journal = {Advances in Dental Research},
  volume = {11},
  number = {1},
  pages = {110--126},
  issn = {0895-9374, 1544-0737},
  doi = {10.1177/08959374970110010201},
  abstract = {Difficulties with in vivo studies of natural plaque and its complex, heterogeneous structure have led to development of laboratory biofilm plaque model systems. Technologies for their culture are outlined, and the rationale, strengths, and relative uses of two complementary approaches to microbial models with a focus on plaque biodiversity are analyzed. Construction of synthetic consortia biofilms of major plaque species has established a variety of bacterial interactions important in plaque development. In particular, the 'Marsh' nine-species biofilm consortia systems are powerful quasi steady-state models which can be closely specified, modified, and analyzed. In the second approach, microcosm plaque biofilms are evolved in vitro from the natural oral microflora to the laboratory model most closely related to plaque in vivo. Functionally reproducible microcosm plaques are attainable with a biodiverse microbiota, heterogeneous structure, and pH behavior consistent with those of natural plaque. The resting pH can be controlled by urea supply. Their growth patterns, pH gradient formation, control of urease levels by environmental effectors, and plaque mineralization have been investigated. Microcosm biofilms may be the only useful in vitro systems where the identity of the microbes and processes involved is uncertain. Together, these two approaches begin to capture the complexity of plaque biofilm development, ecology, behavior, and pathology. They facilitate hypothesis testing across almost the whole range of plaque biology and the investigation of antiplaque procedures yielding accurate predictions of plaque behavior in vivo.},
  langid = {english}
}

@article{sissonsMultistationPlaque1991,
  title = {A {{Multi-station Dental Plaque Microcosm}} ({{Artificial Mouth}}) for the {{Study}} of {{Plaque Growth}}, {{Metabolism}}, {{pH}}, and {{Mineralization}}:},
  shorttitle = {A {{Multi-station Dental Plaque Microcosm}} ({{Artificial Mouth}}) for the {{Study}} of {{Plaque Growth}}, {{Metabolism}}, {{pH}}, and {{Mineralization}}},
  author = {Sissons, C. H. and Cutress, T. W. and Hoffman, M. P. and Wakefield, J. St J.},
  year = {1991},
  journal = {Journal of Dental Research},
  publisher = {{SAGE PublicationsSage CA: Los Angeles, CA}},
  doi = {10.1177/00220345910700110301},
  abstract = {A plaque growth chamber was developed for long-term growth of five separate plaques from the same plaque or saliva sample under identical conditions of temperat...},
  langid = {english},
  keywords = {notion}
}

@article{sissonsPHResponse1994,
  title = {The {{pH}} Response to Urea and the Effect of Liquid Flow in `Artificial Mouth' Microcosm Plaques},
  author = {Sissons, C. H. and Wong, L. and Hancock, E. M. and Cutress, T. W.},
  year = {1994},
  month = jun,
  journal = {Archives of Oral Biology},
  volume = {39},
  number = {6},
  pages = {497--505},
  issn = {0003-9969},
  doi = {10.1016/0003-9969(94)90146-5},
  abstract = {This study examined in detailed the pH response of mircrocosm plaque biofilms to the application of 500 mmol/l urea, and the effect of modifying the flow rate of BMM (a basal medium containing 0.25\% mucin). Microcosm plaques were cultured from the mixed salivary bacteria in a multi-plaque `artificial mouth' supplied continuously with BMM at 3.6 ml/h per plaque, and periodically with sucrose (5 or 10\%). Urea (500 mmol/l) induced a pH response that was the inverse of the Stephan pH curve induced by sucrose. In thicker plaques the ureolytic pH response was delayed and slower. With no BMM flow, the urea-induced pH curve reached a maximum and then slowly decreased indicating loss of ammonia. A flow of BMM reduced the magnitude of the pH response. Urea dilution explained (r2 = 0.97) the reduction in the maximum rate of pH rise caused by an increasing BMM flow. There were, however, additional flow-rate effects on the magnitude of the pH rise, the curve areas and the maximum rate of pH decrease back to the resting pH. These effects were greatest at low BMM flow rates, indicating that ammonia clearance may be limited at higher flow rates by the rate of intraplaque diffusion and metabolism. Application of 50 instead of 500 mmol/l urea reduced the rate of pH rise about 10-fold, and the area of the curve about seven fold. Metabolism of arginine (50 mmol/l) generated only about half the pH response of the same amount of urea. Simple metabolism of urea to ammonia and carbon dioxide therefore generates a complex pH response that cannot be adequately described by any single pH change variable. The magnitude of the pH change depends more on urea concentration than the total amount applied. The pH response to urea is delayed and slower in thicker plaques, and the ammonia formed is cleared only slowly over many hours at a rate that is greatly affected by liquid flow over the plaque.},
  langid = {english},
  keywords = {microcosm plaque,notion,pH,urea}
}

@article{skoglundSeparatingEndogenous2014,
  title = {Separating Endogenous Ancient {{DNA}} from Modern Day Contamination in a {{Siberian Neandertal}}},
  author = {Skoglund, Pontus and Northoff, Bernd H. and Shunkov, Michael V. and Derevianko, Anatoli P. and P{\"a}{\"a}bo, Svante and Krause, Johannes and Jakobsson, Mattias},
  year = {2014},
  month = feb,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  number = {6},
  pages = {2229--2234},
  publisher = {{Proceedings of the National Academy of Sciences}},
  doi = {10.1073/pnas.1318934111},
  abstract = {One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation\textemdash summarized in a postmortem degradation score\textemdash which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.}
}

@article{slausDentalHealth2011,
  title = {Dental Health at the Transition from the {{Late Antique}} to the Early {{Medieval}} Period on {{Croatia}}'s Eastern {{Adriatic}} Coast},
  author = {{\v S}laus, Mario and Bedi{\'c}, {\v Z}eljka and Raji{\'c} {\v S}ikanji{\'c}, Petra and Vodanovi{\'c}, Marin and Domi{\'c} Kuni{\'c}, Alka},
  year = {2011},
  journal = {International Journal of Osteoarchaeology},
  volume = {21},
  number = {5},
  pages = {577--590},
  issn = {1099-1212},
  doi = {10.1002/oa.1163},
  abstract = {Dento-alveolar pathologies: caries, ante mortem tooth loss, abscesses, calculus, alveolar resorption and tooth wear were analysed in two composite skeletal series from Croatia's eastern Adriatic coast (Dalmatia). The first consists of 103 skeletons from seven Late Antique (3rd\textendash 6th century AD) sites, the second of 151 skeletons from three Early Medieval (7th\textendash 11th centuries AD) sites. As recent bioarhaeological studies (\v{S}laus, 2008) showed a significant increase of disease loads and trauma frequencies in Dalmatia during the Early Medieval period, the aim of this study was to investigate whether dental health was equally adversely affected by the Late Antique/Early Medieval transition. The results of our analyses show that the frequencies of carious lesions, ante mortem tooth loss, abscesses and alveolar resorption increased significantly during the Early Medieval period, as did the degree of heavy occlusal wear on posterior teeth. These data suggest a change in alimentary habits, with a significantly higher dependence on carbohydrates and a greater reliance on hard, fibrous foods requiring vigorous mastication in the Early Medieval diet. The combination of higher calculus and lower caries rates in the Late Antique series similarly suggests more protein in the Late Antique diet and is, therefore, also consistent with the hypothesised change in alimentary habits. In general (the two exceptions are male caries and female alveolar resorption frequencies) lesion frequencies increased uniformly in both sexes suggesting that the deterioration of dental health during the Early Medieval period equally affected males and females. Cumulatively, the collected data suggest that the political, social, economic and religious changes that characterised the Late Antique/Early Medieval transition in Dalmatia resulted in a clear discontinuity, not only from the cultural, but also from the biological point of view with an evident deterioration of oral health during the Early Medieval period. Copyright \textcopyright{} 2010 John Wiley \& Sons, Ltd.},
  copyright = {Copyright \textcopyright{} 2010 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {ante mortem tooth loss,bioarchaeology,calculus,dental abscess,dental caries,dental wear,early medieval,late antique},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/oa.1163}
}

@article{slavinDiagnosisManagement2005,
  title = {The Diagnosis and Management of Sinusitis: {{A}} Practice Parameter Update},
  shorttitle = {The Diagnosis and Management of Sinusitis},
  author = {Slavin, Raymond G. and Spector, Sheldon L. and Bernstein, I. Leonard and Slavin, Raymond G. and Kaliner, Michael A. and Kennedy, David W. and Virant, Frank S. and Wald, Ellen R. and Khan, David A. and {Blessing-Moore}, Joann and Lang, David M. and Nicklas, Richard A. and Oppenheimer, John J. and Portnoy, Jay M. and Schuller, Diane E. and Tilles, Stephen A. and Borish, Larry and Nathan, Robert A. and Smart, Brian A. and Vandewalker, Mark L.},
  year = {2005},
  month = dec,
  journal = {Journal of Allergy and Clinical Immunology},
  series = {The {{Diagnosis}} and {{Management}} of {{Sinusitis}}: {{A Practice Parameter Update}}},
  volume = {116},
  number = {6, Supplement},
  pages = {S13-S47},
  issn = {0091-6749},
  doi = {10.1016/j.jaci.2005.09.048},
  abstract = {These parameters were developed by the Joint Task Force on Practice Parameters, representing the American Academy of Allergy, Asthma and Immunology; the American College of Allergy, Asthma and Immunology; and the Joint Council of Allergy, Asthma and Immunology. The American Academy of Allergy, Asthma and Immunology (AAAAI) and the American College of Allergy, Asthma and Immunology (ACAAI) have jointly accepted responsibility for establishing ``The diagnosis and management of sinusitis: a practice parameter update.'' This is a complete and comprehensive document at the current time. The medical environment is a changing environment, and not all recommendations will be appropriate for all patients. Because this document incorporated the efforts of many participants, no single individual, including those who served on the Joint Task force, is authorized to provide an official AAAAI or ACAAI interpretation of these practice parameters. Any request for information about or an interpretation of these practice parameters by the AAAAI or the ACAAI should be directed to the Executive Offices of the AAAAI, the ACAAI, and the Joint Council of Allergy, Asthma and Immunology. These parameters are not designed for use by pharmaceutical companies in drug promotion.},
  langid = {english}
}

@article{smithDetectionOpium2018,
  title = {Detection of Opium Alkaloids in a {{Cypriot}} Base-Ring Juglet},
  author = {Smith, Rachel K. and Stacey, Rebecca J. and Bergstr{\"o}m, Ed and {Thomas-Oates}, Jane},
  year = {2018},
  journal = {Analyst},
  volume = {143},
  number = {21},
  pages = {5127--5136},
  publisher = {{Royal Society of Chemistry}},
  doi = {10.1039/C8AN01040D},
  langid = {english}
}

@article{songEffectsMaterial2015,
  title = {Effects of {{Material Properties}} on {{Bacterial Adhesion}} and {{Biofilm Formation}}},
  author = {Song, F. and Koo, H. and Ren, D.},
  year = {2015},
  month = aug,
  journal = {Journal of Dental Research},
  volume = {94},
  number = {8},
  pages = {1027--1034},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/0022034515587690},
  abstract = {Adhesion of microbes, such as bacteria and fungi, to surfaces and the subsequent formation of biofilms cause multidrug-tolerant infections in humans and fouling of medical devices. To address these challenges, it is important to understand how material properties affect microbe-surface interactions and engineer better nonfouling materials. Here we review the recent progresses in this field and discuss the main challenges and opportunities. In particular, we focus on bacterial biofilms and review the effects of surface energy, charge, topography, and stiffness of substratum material on bacterial adhesion. We summarize how these surface properties influence oral biofilm formation, and we discuss the important findings from nondental systems that have potential applications in dental medicine.},
  langid = {english}
}

@article{sorensenDrugsCalculus2021,
  title = {Entrapment of Drugs in Dental Calculus \textendash{} {{Detection}} Validation Based on Test Results from Post-Mortem Investigations},
  author = {S{\o}rensen, Lambert K. and Hasselstr{\o}m, J{\o}rgen B. and Larsen, Line S. and Bindslev, Dorthe A.},
  year = {2021},
  month = feb,
  journal = {Forensic Science International},
  volume = {319},
  pages = {110647},
  issn = {0379-0738},
  doi = {10.1016/j.forsciint.2020.110647},
  abstract = {For prospective investigation of drugs and metabolites in archaeological and contemporary dental calculus, a sensitive, broadly applicable ultra-high-performance liquid chromatography-tandem mass spectrometry method using pneumatically assisted electrospray ionisation (UHPLC-ESI-MS/MS) was developed. The dental calculus was treated with citric acid and the dissolution extracts were cleaned using weak and strong polymeric cation-exchange sorbents. The method was validated on hydroxyapatite for the analysis of 67 drugs and metabolites. Typically, the lower limits of quantification were in the range of 0.01\textendash 0.05ng for the sample mass extracted. The general applicability of the method was tested using dental calculus material sampled from 10 corpses undergoing forensic autopsy. The calculus material was washed several times before dissolution to remove residual substances originating from saliva, gingival crevicular fluid and blood. The wash extracts and the calculus samples (cleaned calculus material) were analysed using the same instrumental conditions. The dry mass of the calculus samples ranged from 1 to 10mg. The total number of drug detections was 131 in the dental calculus samples and 117 in the whole blood samples. From the analyses of the wash extracts and calculus samples, it was proven that drug residues were trapped in the interior of the calculus material. In 82 of the drug detections, the drug concentrations were higher in the dental calculus than in the blood. Among substances detected in the dental calculus but not in the blood were cocaine, heroin, 6-MAM and THCA-A.},
  langid = {english},
  keywords = {Alkaloids,Caffeine,Cannabinoids,Cocaine,Dental calculus,Drugs,LC-MS/MS,Nicotine,Opioids}
}

@article{sorensenEffectAntioxidants2018,
  title = {The Effect of Antioxidants on the Long-Term Stability of {{THC}} and Related Cannabinoids in Sampled Whole Blood},
  author = {S{\o}rensen, Lambert K. and Hasselstr{\o}m, J{\o}rgen B.},
  year = {2018},
  journal = {Drug Testing and Analysis},
  volume = {10},
  number = {2},
  pages = {301--309},
  issn = {1942-7611},
  doi = {10.1002/dta.2221},
  abstract = {The stability of cannabinoids is complex and crucial for the assessment of impaired driving caused by cannabis. Therefore, the effect of antioxidants on the long-term stability of {$\Delta$}9-tetrahydrocannabinol (THC), cannabinol (CBN), cannabidiol (CBD), 11-hydroxy-{$\Delta$}9-tetrahydrocannabinol (THC-OH), and 11-nor-9-carboxy-{$\Delta$}9-tetrahydrocannabinol (THC-COOH) in whole blood samples preserved with fluoride citrate (FC) and fluoride oxalate (FX) mixtures was investigated at different temperatures. The measured concentrations of the cannabinoids in authentic whole blood preserved solely with FC or FX mixtures decreased significantly during prolonged storage at -20\textdegree C. On average, less than 5\% of the initial concentrations of THC and CBD were recovered after 19 weeks of storage interrupted by 5 thawing/freezing cycles. The rate of decrease was greatest in FC-preserved blood. The repeated thawing/freezing of the samples accelerated the instability progression. At 5\textdegree C approximately 60\% of the initial concentrations of THC and CBD were recovered after 19 weeks of storage. No significant decrease was observed in samples stored at -80\textdegree C during the test period of 5 months. The instability at -20\textdegree C was to a great extend avoided by adding 30 mM ascorbic acid (ASC) to the samples before storage. Samples preserved with a combination of the FX mixture and ASC showed no significant decrease in the recovered concentrations during a 5-month storage period interrupted by 6 thawing/freezing cycles. Samples preserved with a combination of the FC mixture and ASC showed almost similar improvements in cannabinoid stability. Other reducing agents such as sodium metabisulfite and glutathione also improved the stability in FX-preserved blood stored at -20\textdegree C.},
  copyright = {Copyright \textcopyright{} 2017 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {antioxidants,blood,cannabinoids,stability,THC},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/dta.2221}
}

@article{sorensenSensitiveDetermination2017,
  title = {Sensitive {{Determination}} of {{Cannabinoids}} in {{Whole Blood}} by {{LC}}\textendash{{MS-MS After Rapid Removal}} of {{Phospholipids}} by {{Filtration}}},
  author = {S{\o}rensen, Lambert K. and Hasselstr{\o}m, J{\o}rgen B.},
  year = {2017},
  month = jun,
  journal = {Journal of Analytical Toxicology},
  volume = {41},
  number = {5},
  pages = {382--391},
  issn = {0146-4760},
  doi = {10.1093/jat/bkx030},
  abstract = {Direct analysis of {$\Delta$}9-tetrahydrocannabinol (THC) and other cannabinoids in crude acetonitrile extracts of whole blood by liquid chromatography\textendash tandem mass spectrometry using pneumatically assisted electrospray ionization (LC\textendash ESI\textendash MS-MS) was subjected to pronounced ion suppression from co-eluting phospholipids (PLs). The interferences were mainly caused by the lysophosphatidylcholine and lysophosphatidylethanolamine classes of PLs. The PLs were easily removed from crude extracts by filtration through a sorbent with Lewis acid properties, which typically increased the THC and cannabinol (CBN) signal intensities by a factor of 5. Based on this technique, a simple high-throughput LC\textendash MS-MS method was developed for the determination of cannabinoids in 100 {$\mu$}L samples of whole blood. The lower limits of quantification were 0.2 {$\mu$}g/L for THC, CBN, cannabidiol (CBD) and {$\Delta$}9-tetrahydrocannabinolic acid A (THCA-A) and 0.5 {$\mu$}g/L for 11-hydroxy-{$\Delta$}9-tetrahydrocannabinol (THC-OH) and 11-nor-9-carboxy-{$\Delta$}9-tetrahydrocannabinol (THC-COOH). The mean ion suppression levels after clean-up were 10\% (THC), 9\% (CBN), 17\% (CBD), 0\% (THC-OH), 2\% (THC-COOH) and 9\% (THCA-A) at blood concentration levels of 1\textendash 10 {$\mu$}g/L. The mean true extraction recoveries were 97\% (THC), 101\% (CBN), 101\% (CBD), 98\% (THC-OH), 95\% (THC-COOH) and 90\% (THCA-A) at the same concentration levels. The relative intra-laboratory reproducibility standard deviations were \&lt;9\% at concentrations of 1 {$\mu$}g/L or higher. The trueness expressed as the relative bias of the test results was within {$\pm$}4\% at concentrations of 1 {$\mu$}g/L or higher.}
}

@article{sotoCharacterizationDecontamination2019,
  title = {Structural Characterization and Decontamination of Dental Calculus for Ancient Starch Research},
  author = {Soto, Mar{\'i}a and Inwood, Jamie and Clarke, Siobh{\'a}n and Crowther, Alison and Covelli, Danielle and Favreau, Julien and Itambu, Makarius and Larter, Steve and Lee, Patrick and Lozano, Marina and Maley, Jason and Mwambwiga, Aloyce and Patalano, Robert and Sammynaiken, Ramaswami and Verg{\`e}s, Josep M. and Zhu, Jianfeng and Mercader, Julio},
  year = {2019},
  month = sep,
  journal = {Archaeological and Anthropological Sciences},
  volume = {11},
  number = {9},
  pages = {4847--4872},
  issn = {1866-9565},
  doi = {10.1007/s12520-019-00830-7},
  abstract = {Ancient dental calculus research currently relies on destructive techniques whereby archeological specimens are broken down to determine their contents. Two strategies that could partly remediate a permanent loss of the original sample and enhance future analysis and reproducibility include (1) structural surface characterization through spectroscopy along with crystallographic and spectroscopic analysis of its molecular structure, and (2) surface decontamination protocols in which the efficacy of cleaning dental calculus prior to extraction is demonstrated. Dental calculus provides ancient starch research a niche where granules may be adsorbed to minerals, coated, overgrown, entrapped, and/or protected from chemical degradation. While encapsulation offers protection from degradation, it does not shield the sample's surface from contamination. The most common approach to retrieving microbotanical particles from archeological calculus has been the direct decalcification of the sample, after a cleaning stage variously consisting of immersion in water, acids, and mechanical dislodgment via gas, sonication, and/or toothbrushes. Little is known about the efficiency of these methods for a complete removal of sediment/soil and unrelated microbotanical matter. In this paper, controlled laboratory experimentation leads to chemical structural characterization and a decontamination protocol to eradicate starch granules. Several concentrations of acids, bases, and enzymes were tested at intervals to understand their potential to gelatinize and fully destroy starch granules; arriving at a procedure that effectively eradicates modern starch prior to dissolution without damaging the matrix or entrapped starch microremains. This is the first attempt at creating synthetic calculus to understand and systematically test effective decontamination protocols for ancient starch research.},
  langid = {english},
  keywords = {Ancient dental calculus,Ancient starch research,Decontamination prior to decalcification,P-XRD,Raman,Starch contamination,Structural chemical characterization,XPS}
}

@article{springfieldCocaineMetabolites1993,
  title = {Cocaine and Metabolites in the Hair of Ancient {{Peruvian}} Coca Leaf Chewers},
  author = {Springfield, Angela C and Cartmell, Larry W and Aufderheide, Arthur C and Buikstra, Jane and Ho, Joyce},
  year = {1993},
  month = dec,
  journal = {Forensic Science International},
  volume = {63},
  number = {1-3},
  pages = {269--275},
  issn = {03790738},
  doi = {10.1016/0379-0738(93)90280-N},
  abstract = {Cocaine and its metabolites, benzoylecgonine (BZE) and ecgonine methylester (EME), were found in hair samples from ancient Peruvian coca-leaf chewers dating back to AD 1000. Hair was analyzed by gas chromatography/mass spectrometry (GUMS) to quantitate the concentrations. The two metabolites were found in higher concentration than the parent drug. The metabolite levels appear to be below that of modern cocaine abusers. Gender does not appear to be a factor in the incorporation of drug into hair.},
  langid = {english}
}

@incollection{squierOralMucosa1998,
  title = {Oral {{Mucosa}}},
  booktitle = {Oral {{Histology}}: {{Development}}, {{Structure}}, and {{Function}}},
  author = {Squier, C. A. and Finkelstein, M. W.},
  editor = {Ten Cate, A. R.},
  year = {1998},
  edition = {Fifth},
  pages = {345--385},
  publisher = {{Mosby}},
  address = {{London}},
  isbn = {0-8151-2952-1},
  langid = {english}
}

@article{srdjenovicSimultaneousHPLC2008,
  title = {Simultaneous {{HPLC Determination}} of {{Caffeine}}, {{Theobromine}}, and {{Theophylline}} in {{Food}}, {{Drinks}}, and {{Herbal Products}}},
  author = {Srdjenovic, B. and {Djordjevic-Milic}, V. and Grujic, N. and Injac, R. and Lepojevic, Z.},
  year = {2008},
  month = feb,
  journal = {Journal of Chromatographic Science},
  volume = {46},
  number = {2},
  pages = {144--149},
  issn = {0021-9665, 1945-239X},
  doi = {10.1093/chromsci/46.2.144},
  langid = {english}
}

@article{stahlDoublestrandedIndexing2019,
  title = {Illumina Double-Stranded {{DNA}} Dual Indexing for Ancient {{DNA}}},
  author = {Stahl, Raphaela and Warinner, Christina and Velsko, Irina and Orfanou, Eleftheria and Aron, Franziska and Brandt, Guido},
  year = {2020},
  month = dec,
  journal = {protocols.io},
  doi = {10.17504/protocols.io.4r3l287x3l1y/v3},
  abstract = {This protocol converts partially completed double-stranded DNA libraries e.g. from:  Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing (dx....},
  langid = {english}
}

@article{Standards1994,
  title = {Standards for Data Collection from Human Skeletal Remains: {{Proceedings}} of a Seminar at the {{Field Museum}} of {{Natural History}} ({{Arkansas Archaeology Research Series}} 44)},
  author = {Buikstra, Jane E. and Ubelaker, Douglas H.},
  year = {1994},
  journal = {Fayetteville Arkansas Archaeological Survey}
}

@article{stavricVariabilityCaffeine1988,
  title = {Variability in Caffeine Consumption from Coffee and Tea: {{Possible}} Significance for Epidemiological Studies},
  shorttitle = {Variability in Caffeine Consumption from Coffee and Tea},
  author = {Stavric, B. and Klassen, R. and Watkinson, B. and Karpinski, K. and Stapley, R. and Fried, P.},
  year = {1988},
  month = jan,
  journal = {Food and Chemical Toxicology},
  volume = {26},
  number = {2},
  pages = {111--118},
  issn = {02786915},
  doi = {10.1016/0278-6915(88)90107-X},
  abstract = {Five surveys, using a previously developed high-performance liquid chromatography procedure to measure caffeine concentrations, indicated great variations in the concentrations of caffeine in tea and coffee. In the study of beverages prepared at home, data on caffeine concentrations in 58 samples of tea and coffee, volumes of cups, and numbers of cups consumed/day, indicated that the range of caffeine intakes for the women participating was 49-1022 mg/day. There were considerable day-to-day variations in caffeine contents in coffee samples from some commercial coffee shops. When 17 samples of five national brands of instant coffee were made into beverages in the laboratory, variations in caffeine concentrations between lots were small but between brands were significant. A considerable range of caffeine concentrations was also found when 12 samples of coffee prepared at work by different individuals using the same jar of instant coffee were analysed. Analysis of tea samples prepared in the laboratory indicated that steeping time had an important influence on resulting caffeine and theobromine concentrations. People preparing their own beverages were found to drink more liquid than the volume offered commercially. The mean caffeine 'contents' of home-made coffee and of coffee prepared by individuals at work were 79.4 and 81.7mg/cup respectively, indicating a mean intake of approximately 80mg caffeine/cup. When this amount (80 mg/cup) was used to estimate daily intakes of caffeine from coffee, on the basis of the number of reported cups/day, and the values obtained were compared with the amounts actually consumed by individuals, the potential for misrepresentation of individual consumption became obvious. For example, for subjects consuming three cups of coffee, only 25\% would have been correctly categorized in the expected range for the daily intake of caffeine, 39\% would have been overestimated and 36\% underestimated for the amount of caffeine consumed. These variations in caffeine concentrations and in the volume of coffee consumed have frequently been ignored in examinations of the possible relationship between coffee consumption and various health problems, and this could perhaps partly explain some conflicting results seen in epidemiological studies.},
  langid = {english},
  keywords = {caffeine,hplc,theophylline}
}

@article{stephanStudiesChanges1947,
  title = {Studies of Changes in {{pH}} Produced by Pure Cultures of Oral Micro-Organisms; Effects of Varying the Microbic Cell Concentration; Comparison of Different Micro-Organisms and Different Substrates; Some Effects of Mixing Certain Micro-Organisms},
  author = {Stephan, R. M. and Hemmens, E. S.},
  year = {1947},
  month = feb,
  journal = {Journal of Dental Research},
  volume = {26},
  number = {1},
  pages = {15--41},
  issn = {0022-0345},
  doi = {10.1177/00220345470260010201},
  langid = {english},
  pmid = {20287951},
  keywords = {Bacteriology,Face,Mouth,MOUTH/bacteriology}
}

@article{stewartAntimicrobialTolerance2015,
  title = {Antimicrobial {{Tolerance}} in {{Biofilms}}},
  author = {Stewart, Philip S.},
  year = {2015},
  month = jun,
  journal = {Microbiology Spectrum},
  volume = {3},
  number = {3},
  pages = {10.1128/microbiolspec.mb-0010-2014},
  publisher = {{American Society for Microbiology}},
  doi = {10.1128/microbiolspec.mb-0010-2014},
  abstract = {The tolerance of microorganisms in biofilms to antimicrobial agents is examined through a meta-analysis of literature data. A numerical tolerance factor comparing the rates of killing in the planktonic and biofilm states is defined to provide a quantitative basis for the analysis. Tolerance factors for biocides and antibiotics range over three orders of magnitude. This variation is not explained by taking into account the molecular weight of the agent, the chemistry of the agent, the substratum material, or the speciation of the microorganisms. Tolerance factors do depend on the areal cell density of the biofilm at the time of treatment and on the age of the biofilm as grown in a particular experimental system. This suggests that there is something that happens during biofilm maturation, either physical or physiological, that is essential for full biofilm tolerance. Experimental measurements of antimicrobial penetration times in biofilms range over orders of magnitude, with slower penetration ({$>$}12 min) observed for reactive oxidants and cationic molecules. These agents are retarded through the interaction of reaction, sorption, and diffusion. The specific physiological status of microbial cells in a biofilm contributes to antimicrobial tolerance. A conceptual framework for categorizing physiological cell states is discussed in the context of antimicrobial susceptibility. It is likely that biofilms harbor cells in multiple states simultaneously (e.g., growing, stress-adapted, dormant, inactive) and that this physiological heterogeneity is an important factor in the tolerance of the biofilm state.}
}

@article{storeyPaleopathologyOrigins1986,
  title = {Paleopathology at the {{Origins}} of {{Agriculture}}. {{Mark Nathan Cohen}} and {{George J}}. {{Armelagos}}, Editors. {{Academic Press}}, {{Inc}}., {{Orlando}}, 1984. Xx + 615 Pp., Figures, Tables, References, Index. \$59.00 (Cloth).},
  author = {Storey, Rebecca},
  year = {1986},
  month = jul,
  journal = {American Antiquity},
  volume = {51},
  number = {3},
  pages = {661--662},
  publisher = {{Cambridge University Press}},
  issn = {0002-7316, 2325-5064},
  doi = {10.2307/281762},
  abstract = {//static.cambridge.org/content/id/urn\%3Acambridge.org\%3Aid\%3Aarticle\%3AS0002731600062144/resource/name/firstPage-S0002731600062144a.jpg},
  langid = {english}
}

@article{SucheyBrooks1990,
  title = {Skeletal Age Determination Based on the Os Pubis: {{A}} Comparison of the {{Acs\'adi-Nemesk\'eri}} and {{Suchey-Brooks}} Methods},
  shorttitle = {Skeletal Age Determination Based on the Os Pubis},
  author = {Brooks, S. and Suchey, J. M.},
  year = {1990},
  month = jun,
  journal = {Human Evolution},
  volume = {5},
  number = {3},
  pages = {227--238},
  issn = {1824-310X},
  doi = {10.1007/BF02437238},
  abstract = {After reviewing various systems of age determination based on analysis of the pubic bone, the discussion concentrates on the collection and preparation of an extensive autopsy sample (n=1225) of pubic bones from modern individuals with legal documentation of age at death (death and/or birth certificates). TheSuchey-Brooks method derived from this sample is described. TheAcs\'adi-Nemesk\'eri system is evaluated in terms of the documented collection and it is seen that their five stage method focuses only on the early and late morphological changes. The intermediate stages, in which the ventral rampart is in process of completion, are not described. Their suggested age ranges do not correspond with the documented modern sample. Based on these limitations of theAcs\'adi-Nemesk\'eri method, applications of theSuchey-Brooks system are discussed.},
  langid = {english}
}

@article{sunMetabolomicsEvaluation2016,
  title = {Metabolomics Evaluation of the Impact of Smokeless Tobacco Exposure on the Oral Bacterium {{Capnocytophaga}} Sputigena},
  author = {Sun, Jinchun and Jin, Jinshan and Beger, Richard D. and Cerniglia, Carl E. and Yang, Maocheng and Chen, Huizhong},
  year = {2016},
  month = oct,
  journal = {Toxicology in Vitro},
  volume = {36},
  pages = {133--141},
  issn = {0887-2333},
  doi = {10.1016/j.tiv.2016.07.020},
  abstract = {The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the arginine-nitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine.},
  langid = {english},
  keywords = {Metabolomics,Oral bacteria,Smokeless tobacco,Toxicology}
}

@article{sutherlandBiofilmMatrix2001,
  title = {The Biofilm Matrix \textendash{} an Immobilized but Dynamic Microbial Environment},
  author = {Sutherland, Ian W},
  year = {2001},
  month = may,
  journal = {Trends in Microbiology},
  volume = {9},
  number = {5},
  pages = {222--227},
  issn = {0966-842X},
  doi = {10.1016/S0966-842X(01)02012-1},
  abstract = {The biofilm matrix is a dynamic environment in which the component microbial cells appear to reach homeostasis and are optimally organized to make use of all available nutrients. The major matrix components are microbial cells, polysaccharides and water, together with excreted cellular products. The matrix therefore shows great microheterogeneity, within which numerous microenvironments can exist. Although exopolysaccharides provide the matrix framework, a wide range of enzyme activities can be found within the biofilm, some of which will greatly affect structural integrity and stability.},
  langid = {english},
  keywords = {biofilm,biosurfacant,commensalim,dextran,exopolysaccharides,gels,matrix,plaque}
}

@article{takahashiOralMicrobiome2015,
  title = {Oral {{Microbiome Metabolism}}: {{From}} ``{{Who Are They}}?'' To ``{{What Are They Doing}}?''},
  shorttitle = {Oral {{Microbiome Metabolism}}},
  author = {Takahashi, N.},
  year = {2015},
  month = dec,
  journal = {Journal of Dental Research},
  volume = {94},
  number = {12},
  pages = {1628--1637},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/0022034515606045},
  abstract = {Recent advances in molecular biology have facilitated analyses of the oral microbiome (?Who are they??); however, its functions (e.g., metabolic activities) are poorly understood (?What are they doing??). This review aims to summarize our current understanding of the metabolism of the oral microbiome. Saccharolytic bacteria?including Streptococcus, Actinomyces, and Lactobacillus species?degrade carbohydrates into organic acids via the Embden-Meyerhof-Parnas pathway and several of its branch pathways, resulting in dental caries, while alkalization and acid neutralization via the arginine deiminase system, urease, and so on, counteract acidification. Proteolytic/amino acid?degrading bacteria, including Prevotella and Porphyromonas species, break down proteins and peptides into amino acids and degrade them further via specific pathways to produce short-chain fatty acids, ammonia, sulfur compounds, and indole/skatole, which act as virulent and modifying factors in periodontitis and oral malodor. Furthermore, it is suggested that ethanol-derived acetaldehyde can cause oral cancer, while nitrate-derived nitrite can aid caries prevention and systemic health. Microbial metabolic activity is influenced by the oral environment; however, it can also modify the oral environment, enhance the pathogenicity of bacteria, and induce microbial selection to create more pathogenic microbiome. Taking a metabolomic approach to analyzing the oral microbiome is crucial to improving our understanding of the functions of the oral microbiome.},
  langid = {english}
}

@article{takazoeCalciumHydroxyapatite1970,
  title = {Calcium {{Hydroxyapatite Nucleation}} by {{Lipid Extract}} of {{Bacterionema}} Matruchotii},
  author = {Takazoe, I. and Vogel, J. and Ennever, J.},
  year = {1970},
  month = feb,
  journal = {Journal of Dental Research},
  volume = {49},
  number = {2},
  pages = {395--398},
  issn = {0022-0345, 1544-0591},
  doi = {10.1177/00220345700490023301},
  langid = {english}
}

@article{takenakaDiffusionMacromolecules2009,
  title = {Diffusion of {{Macromolecules}} in {{Model Oral Biofilms}}},
  author = {Takenaka, Shoji and Pitts, Betsey and Trivedi, Harsh M. and Stewart, Philip S.},
  year = {2009},
  month = mar,
  journal = {Applied and Environmental Microbiology},
  volume = {75},
  number = {6},
  pages = {1750--1753},
  issn = {0099-2240},
  doi = {10.1128/AEM.02279-08},
  abstract = {The diffusive penetration of fluorescently tagged macromolecular solutes into model oral biofilms was visualized by time-lapse microscopy. All of the solutes tested, including dextrans, proteases, green fluorescent protein, and immunoglobulin G, accessed the interior of cell clusters 100 to 200 {$\mu$}m in diameter within 3 min or less.},
  pmcid = {PMC2655469},
  pmid = {19168660}
}

@article{tanAllTogether2017,
  title = {All Together Now: Experimental Multispecies Biofilm Model Systems},
  shorttitle = {All Together Now},
  author = {Tan, Chuan Hao and Lee, Kai Wei Kelvin and Burm{\o}lle, Mette and Kjelleberg, Staffan and Rice, Scott A.},
  year = {2017},
  journal = {Environmental Microbiology},
  volume = {19},
  number = {1},
  pages = {42--53},
  issn = {1462-2920},
  doi = {10.1111/1462-2920.13594},
  abstract = {Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta-omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community-based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.},
  langid = {english},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13594}
}

@article{tanBacterialViability2004,
  title = {Study of {{Bacterial Viability}} within {{Human Supragingival Dental Calculus}}},
  author = {Tan, Benjamin T. K. and Mordan, Nicola J. and Embleton, Jason and Pratten, Jonathan and Galgut, Peter N.},
  year = {2004},
  journal = {Journal of Periodontology},
  volume = {75},
  number = {1},
  pages = {23--29},
  issn = {1943-3670},
  doi = {10.1902/jop.2004.75.1.23},
  abstract = {Background: There is evidence that supragingival calculus contains unmineralized channels and lacunae. The purpose of this study was to investigate the viability of bacteria within these areas. Methods: Supragingival calculus harvested from patients with moderate to severe chronic periodontitis was immediately frozen to \textendash 70\textdegree C. Six samples were cryosectioned, stained with a bacterial viability kit, and examined with fluorescence microscopy. Controls comprised heat treatment of cryosections prior to staining. Four additional samples were stained and examined whole a confocal laser scanning microscope (CLSM). Nine additional samples were prepared for bacterial culture, after initial irradiation with ultraviolet light to kill viable organisms on the covering plaque layer. Test samples were crushed to expose internal bacteria, while two controls were used without crushing. Results: Viable bacteria, as identified using the bacterial viability stain, were found within cavities/lacunae in supragingival calculus cryosections. Similar results were obtained from whole calculus samples using CLSM. Of the nine experimental samples where bacterial culture was attempted, five provided positive bacterial culture under both aerobic and anaerobic conditions; one showed positive growth under aerobic conditions only; while one showed no bacterial growth. The controls showed no bacterial growth. Conclusions: From this study, it appears that viable aerobic and anaerobic bacteria may be present within supragingival calculus, specifically within the internal channels and lacunae. Clinically, this may be important, since incomplete removal of supragingival calculus may expose these reservoirs of possible pathogenic bacteria and be a factor in the recurrence of periodontal diseases after treatment. J Periodontol 2004;75:23-29.},
  langid = {english},
  keywords = {aerobic/growth,anaerobic/growth,bacteria,Bacteria,dental calculus,supragingival},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1902/jop.2004.75.1.23}
}

@article{tanCalculusUltrastructure2004,
  title = {A Preliminary Investigation into the Ultrastructure of Dental Calculus and Associated Bacteria},
  author = {Tan, Benjamin T. K. and Gillam, David G. and Mordan, N. J. and Galgut, P. N.},
  year = {2004},
  journal = {Journal of Clinical Periodontology},
  volume = {31},
  number = {5},
  pages = {364--369},
  issn = {1600-051X},
  doi = {10.1111/j.1600-051X.2004.00484.x},
  abstract = {Introduction: Though dental calculus is generally recognised as comprising mineralised bacteria, areas of non-mineralised bacteria may be present. Aim: To investigate the ultrastructure of non-decalcified young and mature supragingival calculus and subgingival calculus, and the possible presence of internal viable bacteria. Materials and methods: Supragingival calculus was harvested from five patients, 9\textendash 10 weeks after scaling and root debridement. Five samples of mature supragingival and subgingival calculus were taken from patients presenting with adult periodontitis. Specimens were fixed and embedded for transmission electron microscopy. Results: The ultrastructure of young and mature supragingival calculus was similar with various large and small crystal types. Non-mineralised channels were observed extending into the calculus, often joining extensive lacunae, both containing intact non-mineralised coccoid and rod-shaped microorganisms. Subgingival calculus possessed more uniform mineralisation without non-mineralised channels and lacunae. Conclusion: Supragingival calculus contains non-mineralised areas which contain bacteria and other debris. The viability of the bacteria, and their identification could not be determined in this preliminary investigation. As viable bacteria within these lacunae may provide a source of re-infection, further work needs to be done to identify the bacteria in the lacunae, and to determine their viability.},
  langid = {english},
  keywords = {bacteria,calculus,plaque,subgingival,supragingival}
}

@article{taoWheatCalculus2020,
  title = {Investigating Wheat Consumption Based on Multiple Evidences: {{Stable}} Isotope Analysis on Human Bone and Starch Grain Analysis on Dental Calculus of Humans from the {{Laodaojing}} Cemetery, {{Central Plains}}, {{China}}},
  shorttitle = {Investigating Wheat Consumption Based on Multiple Evidences},
  author = {Tao, Dawei and Zhang, Guowen and Zhou, Yawei and Zhao, Haizhou},
  year = {2020},
  journal = {International Journal of Osteoarchaeology},
  volume = {30},
  number = {5},
  pages = {594--606},
  issn = {1099-1212},
  doi = {10.1002/oa.2884},
  abstract = {The introduction and spread of wheat contributed to the transformation of the tradition millets agriculture in North China. However, when and how wheat came to be a staple crop in China is still unclear. Stable isotope data from some archaeological sites suggested that the dietary change from C4 based diet to C3/C4 mixed diet occurred during the Eastern Zhou Dynasty (770\textendash 221 BC) on the Central Plains of China. However, the role of each C3 crop (wheat, rice and soybean) in human diet is not well understood in this key period. Some scholars have argued that wheat made the biggest contribution to human diet among the C3 crops. To further investigate the dietary role of wheat and agricultural economy in the Eastern Zhou on the Central Plains of China, combined methods of stable isotope analysis on human bones and starch grain analysis on human dental calculus were conducted at Laodaojing cemetery during the Warring States period. The mean {$\delta$}13C values (-14.7 {$\pm$} 2\textperthousand, n = 24) and mean {$\delta$}15N values (9.1 {$\pm$} 0.9\textperthousand, n = 24) of individuals from Laodaojing cemetery suggest that Laodaojing humans had a reliance on the mixture of C3/C4 foods and a certain proportion of animal protein was consumed. Given that the small elevation of {$\delta$}15N values ({$<$}3\textperthousand ) of Laodaojing humans, the contribution of domesticated animals to the mixed C3/C4 diet of Laodaojing population is relatively limited. Combined with starch grains extracted from human dental calculus, we argue that C3 and C4 foods at Laodaojing were mainly derived from wheat and millets respectively. Temporal investigations of stable isotope data and archaeobotanical evidences from the late Longshan period to Eastern Zhou Dynasty show the importance of wheat increased in agricultural economy slowly since its introduction into the Central Plains of China. Until the Eastern Zhou Dynasty, wheat as a C3 crop played an important dietary role in human diet of the Central Plains. A transformation from millet-based to millets/wheat-based agricultural economy occurred along with the shift of dietary pattern during this period.},
  copyright = {\textcopyright{} 2020 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {Central Plains,dental calculus,Laodaojing cemetery,stable isotope,starch grain},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/oa.2884}
}

@article{theiladeGermfreeCalculus1964,
  title = {Electron Microscopic Observations of Dental Calculus in Germfree and Conventional Rats},
  author = {Theilade, J. and Fitzgerald, R.J. and Scott, D.B. and Nylen, M.U.},
  year = {1964},
  month = jan,
  journal = {Archives of Oral Biology},
  volume = {9},
  number = {1},
  pages = {97-IN17},
  issn = {00039969},
  doi = {10.1016/0003-9969(64)90051-2},
  langid = {english}
}

@article{tianUsingDGGE2010,
  title = {Using {{DGGE}} Profiling to Develop a Novel Culture Medium Suitable for Oral Microbial Communities},
  author = {Tian, Y. and He, X. and Torralba, M. and Yooseph, S. and Nelson, K.e. and Lux, R. and McLean, J.s. and Yu, G. and Shi, W.},
  year = {2010},
  journal = {Molecular Oral Microbiology},
  volume = {25},
  number = {5},
  pages = {357--367},
  issn = {2041-1014},
  doi = {10.1111/j.2041-1014.2010.00585.x},
  abstract = {More than 700 bacterial species have been detected in the human oral cavity. They form highly organized microbial communities and are responsible for many oral infectious diseases, such as dental caries and periodontal disease. The prevention and treatment of these diseases require a comprehensive knowledge of oral microbial communities, which largely relies on culture-dependent methods to provide detailed phenotypic and physiological analysis of these communities. However, most of the currently available laboratory media can only selectively support the growth of a limited number of bacterial species within these communities, and fail to sustain the original oral microbial diversity. In this study, using denaturing gradient gel electrophoresis (DGGE) as an index to systematically survey and analyse the selectivity of commonly used laboratory media, we developed a new medium (SHI medium) by combining the ingredients of several selected media that can support different subpopulations within the original oral microbial community derived from pooled saliva. DGGE and 454 pyrosequencing analysis showed that SHI medium was capable of supporting a more diversified community with a microbial profile closer to that of the original oral microbiota. Furthermore, 454 pyrosequencing revealed that SHI medium supported the growth of many oral species that have not before been cultured. Crystal violet assay and the confocal laser scanning microscope analysis indicated that, compared with other media, SHI medium is able to support a more complex saliva-derived biofilm with higher biomass yield and more diverse species. This DGGE-guided method could also be used to develop novel media for other complex microbial communities.},
  langid = {english},
  keywords = {454 pyrosequencing,growth medium,oral microbial community},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-1014.2010.00585.x}
}

@article{tidyverse2019,
  title = {Welcome to the {{tidyverse}}},
  author = {Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Fran{\c c}ois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and Kuhn, Max and Pedersen, Thomas Lin and Miller, Evan and Bache, Stephan Milton and M{\"u}ller, Kirill and Ooms, Jeroen and Robinson, David and Seidel, Dana Paige and Spinu, Vitalie and Takahashi, Kohske and Vaughan, Davis and Wilke, Claus and Woo, Kara and Yutani, Hiroaki},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686}
}

@incollection{tonjumNeisseria2017,
  title = {179 - {{Neisseria}}},
  booktitle = {Infectious {{Diseases}} ({{Fourth Edition}})},
  author = {T{\o}njum, Tone and {van Putten}, Jos},
  editor = {Cohen, Jonathan and Powderly, William G. and Opal, Steven M.},
  year = {2017},
  month = jan,
  pages = {1553-1564.e1},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-7020-6285-8.00179-9},
  isbn = {978-0-7020-6285-8},
  langid = {english}
}

@article{toppingResistantStarch2003,
  title = {Resistant Starch as a Prebiotic and Synbiotic: State of the Art},
  shorttitle = {Resistant Starch as a Prebiotic and Synbiotic},
  author = {Topping, David L. and Fukushima, Michihiro and Bird, Anthony R.},
  year = {2003},
  month = feb,
  journal = {Proceedings of the Nutrition Society},
  volume = {62},
  number = {1},
  pages = {171--176},
  publisher = {{Cambridge University Press}},
  issn = {1475-2719, 0029-6651},
  doi = {10.1079/PNS2002224},
  abstract = {Non-infectious diseases such as CHD and certain cancers have become major causes of death and disability in affluent countries. Probiotics (principally lactic acid bacteria; LAB) may assist in lowering the risk of these diseases. Experimental studies with probiotics have given generally inconclusive outcomes for infectious disease and for biomarkers for non-infectious disease. In part this situation may reflect their inability to colonise the adult human gut effectively. Prebiotics can assist in promoting colonisation, and resistant starch (RS), as a high-amylose starch, is a prebiotic and synbiotic. This starch exerts its synbiotic action through adhesion of the bacteria to the granule surface. Consumption of RS assists in recovery from infectious diarrhoea in man and animals. A rice porridge, high in RS, appears to modify the autochthonous porcine large-bowel microflora favourably through lowering Escherichia coli and coliform numbers. Many of the beneficial effects of RS on large-bowel function appear to beexerted through short-chain fatty acids (SCFA) formed by bacterial fermentation. In man LAB are found in relatively highest numbers in milk-fed infants where theprofile of fermentation products differs quite markedly from that in adults. It appearsunlikely that ingestion of current probiotics will alter either total SCFA or the proportions of the major acids. More emphasis needs to be given to the investigation of the effects of complex carbohydrates, including RS, on the autochthonous microflora of the human large bowel.},
  langid = {english},
  keywords = {Prebiotics,Probiotics,Resistant starch,Synbiotics}
}

@book{townsendDentalAnthropology2012,
  title = {New {{Directions}} in {{Dental Anthropology}}: {{Paradigms}}, {{Methodologies}} and {{Outcomes}}},
  shorttitle = {New {{Directions}} in {{Dental Anthropology}}},
  editor = {Townsend, Grant and Kanazawa, Eisaku and Takayama, Hiroshi},
  year = {2012},
  publisher = {{The University of Adelaide Press}},
  doi = {10.1017/9780987171870},
  abstract = {In recent years, migration, as well as increases and decreases in the size of different human populations, have been evident as a result of globalisation.  Dental features are also changing associated with changes in nutritional status, different economic or social circumstances, and intermarriage between peoples.  Dental anthropological studies have explored these changes with the use of advanced techniques and refined methodologies.  New paradigms are also evolving in the field of dental anthropology.},
  isbn = {978-0-9871718-8-7},
  keywords = {dental anthropology}
}

@article{trompDietaryNondietary2015,
  title = {Differentiating Dietary and Non-Dietary Microfossils Extracted from Human Dental Calculus: The Importance of Sweet Potato to Ancient Diet on {{Rapa Nui}}},
  shorttitle = {Differentiating Dietary and Non-Dietary Microfossils Extracted from Human Dental Calculus},
  author = {Tromp, Monica and Dudgeon, John V.},
  year = {2015},
  month = feb,
  journal = {Journal of Archaeological Science},
  volume = {54},
  pages = {54--63},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2014.11.024},
  abstract = {Human dental calculus is an excellent target for examining the plant component of ancient diets. Microfossils become imbedded within dental calculus throughout life, providing an overall picture of plant foods available (at least those that produce recoverable microfossils). Here we evaluate previous phytolith results (Dudgeon and Tromp, 2012) by examining starch grains from 30 human dental calculus samples from 10 archaeological sites throughout Rapa Nui (Easter Island), dating between AD 1330\textendash 1900. The unobscured starch grains recovered are consistent with descriptions of modern reference samples of sweet potato (Ipomoea batatas). These results indicate the importance of sweet potato to the Rapanui diet prior to European contact in 1722. The analysis of modern sweet potato skins show that they incorporate phytoliths as they grow in phytolith rich sediment, and we argue that the high frequency of palm phytoliths recovered from dental calculus, in conjunction with our starch results points to the consumption of sweet potato.},
  langid = {english},
  keywords = {Easter Island,Phytolith,Polynesia,Starch}
}

@article{trompEDTACalculus2017,
  title = {{{EDTA}} Decalcification of Dental Calculus as an Alternate Means of Microparticle Extraction from Archaeological Samples},
  author = {Tromp, Monica and Buckley, Hallie and Geber, Jonny and {Matisoo-Smith}, Elizabeth},
  year = {2017},
  month = aug,
  journal = {Journal of Archaeological Science: Reports},
  volume = {14},
  pages = {461--466},
  issn = {2352-409X},
  doi = {10.1016/j.jasrep.2017.06.035},
  abstract = {Dental calculus studies, though becoming more common for addressing a range of archaeological questions, are still in their infancy. Dental calculus is a mineralised biofilm that forms on the surface of teeth, with the potential to encase anything that comes into contact with the mouth. Dental calculus has provided information on the lifeways of past people including diet, health, disease, trade and fabrication. To extract this microarchaeological information from dental calculus it must first be processed, either mechanically (with a mortar and pestle) or chemically (generally with hydrochloric acid or HCl), in order to free the microparticles and biomolecular structures encased within. Until now, ethylenediaminetetraacetic acid (EDTA) has not been used for microparticle extraction. Here we present data that demonstrate EDTA is an equally and potentially more effective decalcifying agent for extracting microparticles than previous methods using samples from the Southwest Pacific and Ireland. EDTA has the added benefit of being an appropriate for the first step in genomic and proteomic sample processing.},
  langid = {english}
}

@article{tushinghamHuntergathererTobacco2013,
  title = {Hunter-Gatherer Tobacco Smoking: Earliest Evidence from the {{Pacific Northwest Coast}} of {{North America}}},
  shorttitle = {Hunter-Gatherer Tobacco Smoking},
  author = {Tushingham, Shannon and Ardura, Dominique and Eerkens, Jelmer W. and Palazoglu, Mine and Shahbaz, Sevini and Fiehn, Oliver},
  year = {2013},
  month = feb,
  journal = {Journal of Archaeological Science},
  volume = {40},
  number = {2},
  pages = {1397--1407},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2012.09.019},
  abstract = {Chemical analysis of residue extracted from stone pipes and pipe fragments excavated at sites in the southern Pacific Northwest Coast of North America demonstrate that hunter-gatherers smoked the psychostimulant tobacco (Nicotiana sp.) by at least AD 860. Non-farming ethno-historic Native Americans throughout the west gathered and sometimes cultivated tobacco for ritual and religious purposes, but until now the antiquity of the practice on this part of the continent was unknown. Method validation includes chemical characterization of a suite of smoke plants and experimental reproduction of ``smoked'' pipe chemistry; results indicate biomarkers are traceable for several species commonly smoked by ethnographic native peoples, including tobacco (nicotine, cotinine), tree tobacco (anabasine), and kinnikinnick (arbutin). Developed methods\textemdash where residue is extracted directly from the stone or clay matrix of whole and fragmentary archaeological pipes\textemdash may be applied in similar studies investigating the spread and use of ritual smoke plants in the ancient Americas and elsewhere.},
  langid = {english},
  keywords = {California,GC–MS,Hunter-gatherers,Pacific Northwest Coast,Plant management,Residue analysis,Tobacco}
}

@article{unoSexAgedependent2017,
  title = {Sex- and Age-Dependent Gene Expression in Human Liver: {{An}} Implication for Drug-Metabolizing Enzymes},
  shorttitle = {Sex- and Age-Dependent Gene Expression in Human Liver},
  author = {Uno, Yasuhiro and Takata, Ryo and Kito, Go and Yamazaki, Hiroshi and Nakagawa, Kazuko and Nakamura, Yusuke and Kamataki, Tetsuya and Katagiri, Toyomasa},
  year = {2017},
  month = feb,
  journal = {Drug Metabolism and Pharmacokinetics},
  series = {Prediction of the {{Potential Risk}} of {{Idiosyncratic Drug Toxicity}}},
  volume = {32},
  number = {1},
  pages = {100--107},
  issn = {1347-4367},
  doi = {10.1016/j.dmpk.2016.10.409},
  abstract = {Sex and age differences in hepatic expression of drug-metabolizing enzyme genes could cause variations in drug metabolism, but has not been fully elucidated, especially in Asian population. In this study, the global expression of human hepatic genes was analyzed by microarrays in 40 Japanese subjects (27 males and 13 females). Thirty-five sex-biased genes were identified (P~{$<~$}0.005). Whereas, 60 age-biased genes in two age groups, {$<$}60 years and {$\geq$}70 years (P~{$<~$}0.001), were identified in males. By Gene Ontology analysis, the sex-biased genes were related to protein catabolism and modification, while the age-biased genes were related to transcription regulation and cell death. Quantitative polymerase chain reaction confirmed the female-biased expression of drug-metabolizing enzyme genes BChE, CYP4X1, and SULT1E1 ({$\geq$}1.5-fold, P~{$<~$}0.05). Further analysis of drug-metabolizing enzyme genes indicated that expression of CYP2A6 and CYP3A4 in females in the {$\geq$}70 age group was less than in the {$<$}60 age group ({$\geq$}1.5-fold, P~{$<~$}0.05), and this trend was also observed for PXR expression in males ({$\geq$}1.5-fold, P~{$<~$}0.05). The results presented provide important insights into hepatic physiology and function, especially drug metabolism, with respect to sex and age.},
  keywords = {Age,Cytochrome P450,Drug metabolism,Gene expression,Liver,Sex}
}

@article{uzelMicrobialShifts2011,
  title = {Microbial Shifts during Dental Biofilm Re-Development in the Absence of Oral Hygiene in Periodontal Health and Disease},
  author = {Uzel, Naciye G. and Teles, Flavia R. and Teles, Ricardo P. and Song, Xiaoging Q. and Torresyap, Gay and Socransky, Sigmund S. and Haffajee, Anne D.},
  year = {2011},
  journal = {Journal of Clinical Periodontology},
  volume = {38},
  number = {7},
  pages = {612--620},
  issn = {1600-051X},
  doi = {10.1111/j.1600-051X.2011.01730.x},
  abstract = {Uzel NG, Teles FR, Teles RP, Song XQ, Torresyap G, Socransky SS, Haffajee AD. Microbial shifts during dental biofilm re-development in the absence of oral hygiene in periodontal health and disease. J Clin Peridontol 2011; doi: 10.1111/j.1600-051X.2011.01730.x. Abstract Aim: To monitor microbial shifts during dental biofilm re-development. Materials and methods: Supra- and subgingival plaque samples were taken separately from 28 teeth in 38 healthy and 17 periodontitis subjects at baseline and immediately after tooth cleaning. Samples were taken again from seven teeth in randomly selected quadrants during 1, 2, 4 and 7 days of no oral hygiene. Samples were analysed using checkerboard DNA\textendash DNA hybridization. Species counts were averaged within subjects at each time point. Significant differences in the counts between healthy and periodontitis subjects were determined using the Mann\textendash Whitney test. Results: The total supra- and subgingival counts were significantly higher in periodontitis on entry and reached or exceeded the baseline values after day 2. Supragingival counts of Veillonella parvula, Fusobacterium nucleatum ss vincentii and Neisseria mucosa increased from 2 to 7 days. Subgingival counts were greater for Actinomyces, green and orange complex species. Significant differences between groups in supragingival counts occurred for 17 of 41 species at entry, 0 at day 7; for subgingival plaque, these values were 39/41 taxa at entry, 17/41 at day 7. Conclusions: Supragingival plaque re-development was similar in periodontitis and health, but subgingival species recolonization was more marked in periodontitis.},
  langid = {english},
  keywords = {biofilms,health,oral bacteria,periodontal,periodontitis,subgingival,supragingival},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-051X.2011.01730.x}
}

@article{valenDetermination212017,
  title = {Determination of 21 Drugs in Oral Fluid Using Fully Automated Supported Liquid Extraction and {{UHPLC-MS}}/{{MS}}},
  author = {Valen, Anja and Leere {\O}iestad, {\AA}se Marit and Strand, Dag Helge and Skari, Ragnhild and Berg, Thomas},
  year = {2017},
  journal = {Drug Testing and Analysis},
  volume = {9},
  number = {5},
  pages = {808--823},
  issn = {1942-7611},
  doi = {10.1002/dta.2045},
  abstract = {Collection of oral fluid (OF) is easy and non-invasive compared to the collection of urine and blood, and interest in OF for drug screening and diagnostic purposes is increasing. A high-throughput ultra-high-performance liquid chromatography-tandem mass spectrometry method for determination of 21 drugs in OF using fully automated 96-well plate supported liquid extraction for sample preparation is presented. The method contains a selection of classic drugs of abuse, including amphetamines, cocaine, cannabis, opioids, and benzodiazepines. The method was fully validated for 200 {$\mu$}L OF/buffer mix using an Intercept OF sampling kit; validation included linearity, sensitivity, precision, accuracy, extraction recovery, matrix effects, stability, and carry-over. Inter-assay precision (RSD) and accuracy (relative error) were {$<$}15\% and 13 to 5\%, respectively, for all compounds at concentrations equal to or higher than the lower limit of quantification. Extraction recoveries were between 58 and 76\% (RSD {$<$} 8\%), except for tetrahydrocannabinol and three 7-amino benzodiazepine metabolites with recoveries between 23 and 33\% (RSD between 51 and 52 \% and 11 and 25\%, respectively). Ion enhancement or ion suppression effects were observed for a few compounds; however, to a large degree they were compensated for by the internal standards used. Deuterium-labelled and 13C-labelled internal standards were used for 8 and 11 of the compounds, respectively. In a comparison between Intercept and Quantisal OF kits, better recoveries and fewer matrix effects were observed for some compounds using Quantisal. The method is sensitive and robust for its purposes and has been used successfully since February 2015 for analysis of Intercept OF samples from 2600 cases in a 12-month period. Copyright \textcopyright{} 2016 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {13C-labelled internal standards,automated supported liquid extraction,drugs of abuse,oral fluid,UHPLC-MS/MS},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/dta.2045}
}

@article{vandermeerschMiddlePaleolithic1994,
  title = {Middle {{Paleolithic Dental Bacteria From Kebara}}, {{Israel}}},
  author = {Vandermeersch, B. and Arensburg, B. and Tillier, A.M. and Rak, Y. and Weiner, S. and Spiers, M. and Aspillaga, E.},
  year = {1994},
  journal = {Comptes Rendus De L Academie Des Sciences Serie Ii},
  volume = {319},
  number = {6},
  pages = {727--731}
}

@article{vandeveldeStarchMorphology2002,
  title = {Visualisation of Starch Granule Morphologies Using Confocal Scanning Laser Microscopy ({{CSLM}})},
  author = {{van de Velde}, Fred and {van Riel}, Jan and Tromp, R Hans},
  year = {2002},
  journal = {Journal of the Science of Food and Agriculture},
  volume = {82},
  number = {13},
  pages = {1528--1536},
  issn = {1097-0010},
  doi = {10.1002/jsfa.1165},
  abstract = {Confocal scanning laser microscopy (CSLM) is a powerful tool for the visualisation of starch granules from their botanical source, during processing into their final application. CSLM allows the visualisation of the starch gelatinisation process and of granule remnants in starch pastes in their original environment and without modification. In this study, CSLM has been used to study the granule morphology of starch from different botanical sources. CSLM is a suitable technique to obtain, under mild conditions, 2D and 3D images of the granules. The samples for observation by CSLM do not require complicated preparations such as drying and metal coating as in the case of electron microscopy. Moreover, the CSLM technique is not limited to the observation of native starch granules, as the gelatinisation process and the remnants of granules in starch pastes can be monitored in their original environment. In this way, starch granules can be visualised from their botanical sources to the final application with a single microscopic technique. \textcopyright{} 2002 Society of Chemical Industry},
  langid = {english},
  keywords = {confocal scanning laser microscopy,fluorescent staining,gelatinisation,granules,potato tissue,remnants,starch,structure},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.1165}
}

@article{velskoConsistentReproducible2018,
  title = {Consistent and Reproducible Long-Term in Vitro Growth of Health and Disease-Associated Oral Subgingival Biofilms},
  author = {Velsko, Irina M. and Shaddox, Luciana M.},
  year = {2018},
  month = jul,
  journal = {BMC Microbiology},
  volume = {18},
  number = {1},
  pages = {70},
  issn = {1471-2180},
  doi = {10.1186/s12866-018-1212-x},
  abstract = {Several in vitro oral biofilm growth systems can reliably construct oral microbiome communities in culture, yet their stability and reproducibility through time has not been well characterized. Long-term in vitro growth of natural biofilms would enable use of these biofilms in both in vitro and in vivo studies that require complex microbial communities with minimal variation over a period of time. Understanding biofilm community dynamics in continuous culture, and whether they maintain distinct signatures of health and disease, is necessary to determine the reliability and applicability of such models to broader studies. To this end, we performed next-generation sequencing on biofilms grown from healthy and disease-site subgingival plaque for 80~days to assess stability and reliability of continuous oral biofilm growth.},
  keywords = {Biofilm growth,Dental plaque,In vitro model,Model system,Oral microbiome,Periodontal disease,Subgingival plaque}
}

@article{velskoCytokineResponse2017,
  title = {Cytokine Response Patterns to Complex Biofilms by Mononuclear Cells Discriminate Patient Disease Status and Biofilm Dysbiosis},
  author = {Velsko, Irina M. and {Cruz-Almeida}, Y. and Huang, H. and Wallet, S. M. and Shaddox, Luciana M.},
  year = {2017},
  month = jan,
  journal = {Journal of Oral Microbiology},
  volume = {9},
  number = {1},
  pages = {1330645},
  publisher = {{Taylor \& Francis}},
  issn = {null},
  doi = {10.1080/20002297.2017.1330645},
  abstract = {Localized aggressive periodontitis (LAP) is a rare form of periodontal disease with site-specific rapid tissue destruction. A lipopolysaccharide (LPS) hyper-inflammatory response was shown in LAP using peripheral whole blood, although responses to other bacterial surface components or complex oral biofilms have not been evaluated. Peripheral blood mononuclear cells (PBMCs) from 14 LAP patients, 15 healthy siblings (HS), and 13 unrelated healthy controls (HC) were stimulated with: LPS, lipoteichoic acid, or peptidoglycan; intact or sonically dispersed in vitro\textendash grown biofilms from a LAP disease site, a LAP healthy site, or a healthy control site. Cell culture supernatants were assayed for 14 cyto/chemokines. Discriminant function analysis determined cyto/chemokines that discriminate disease status by response patterns to different stimuli. Qualitative differences in the cytokine response pattern among patient groups were observed to intact and dispersed biofilms, yet responses to healthy and diseased biofilms could not be discriminated. Despite an equivalent magnitude of response, LAP-derived PBMCs demonstrated a qualitatively different pattern of response to LPS and dispersed biofilms. PMBCs from each group responded distinctly to stimulation withsubgingival biofilms. Multiple underlying mechanisms related to bacterial-induced inflammatory responses can culminate in LAP disease initiation and/or progression, and biofilm homeostasis could play an important role.},
  pmid = {28748035},
  keywords = {biofilm homeostasis,cytokine,host–pathogen interaction,inflammatory response,localized aggressive periodontitis,Periodontal disease,subgingival biofilm,unread},
  annotation = {\_eprint: https://doi.org/10.1080/20002297.2017.1330645}
}

@article{velskoDentalCalculus2017,
  title = {The Dental Calculus Metabolome in Modern and Historic Samples},
  author = {Velsko, Irina M. and Overmyer, Katherine A. and Speller, Camilla and Klaus, Lauren and Collins, Matthew J. and Loe, Louise and Frantz, Laurent A. F. and Sankaranarayanan, Krithivasan and Lewis, Cecil M. and Martinez, Juan Bautista Rodriguez and Chaves, Eros and Coon, Joshua J. and Larson, Greger and Warinner, Christina},
  year = {2017},
  month = nov,
  journal = {Metabolomics},
  volume = {13},
  number = {11},
  pages = {134},
  issn = {1573-3882, 1573-3890},
  doi = {10.1007/s11306-017-1270-3},
  langid = {english},
  keywords = {dental calculus,mass spectrometry,metabolites}
}

@article{velskoHighConservation2023,
  title = {High Conservation of the Dental Plaque Microbiome across Populations with Differing Subsistence Strategies and Levels of Market Integration},
  author = {Velsko, Irina M. and Gallois, Sandrine and Stahl, Raphaela and Henry, Amanda G. and Warinner, Christina},
  year = {2023},
  journal = {Molecular Ecology},
  issn = {1365-294X},
  doi = {10.1111/mec.16988},
  abstract = {Industrialization\textemdash including urbanization, participation in the global food chain and consumption of heavily processed foods\textemdash is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.},
  langid = {english},
  keywords = {Baka,dental plaque,diet,industrialization,Nzime,oral microbiome,subsistence},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16988}
}

@article{velskoMicrobialDifferences2019,
  title = {Microbial Differences between Dental Plaque and Historic Dental Calculus Are Related to Oral Biofilm Maturation Stage},
  author = {Velsko, Irina M. and Fellows Yates, James A. and Aron, Franziska and Hagan, Richard W. and Frantz, Laurent A. F. and Loe, Louise and Martinez, Juan Bautista Rodriguez and Chaves, Eros and Gosden, Chris and Larson, Greger and Warinner, Christina},
  year = {2019},
  month = dec,
  journal = {Microbiome},
  volume = {7},
  number = {1},
  pages = {102},
  issn = {2049-2618},
  doi = {10.1186/s40168-019-0717-3},
  abstract = {Background: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. Results: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. Conclusions: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.},
  langid = {english}
}

@article{vigeantReversibleIrreversible2002,
  title = {Reversible and {{Irreversible Adhesion}} of {{Motile Escherichia}} Coli {{Cells Analyzed}} by {{Total Internal Reflection Aqueous Fluorescence Microscopy}}},
  author = {Vigeant, Margot A.-S. and Ford, Roseanne M. and Wagner, Michael and Tamm, Lukas K.},
  year = {2002},
  month = jun,
  journal = {Applied and Environmental Microbiology},
  volume = {68},
  number = {6},
  pages = {2794--2801},
  publisher = {{American Society for Microbiology}},
  doi = {10.1128/AEM.68.6.2794-2801.2002}
}

@book{waldronPalaeopathology2020,
  title = {Palaeopathology},
  author = {Waldron, Tony},
  year = {2020},
  publisher = {{Cambridge University Press}}
}

@article{warinnerEvidenceMilk2014,
  title = {Direct Evidence of Milk Consumption from Ancient Human Dental Calculus},
  author = {Warinner, Christina and Hendy, J. and Speller, C. and Cappellini, E. and Fischer, R. and Trachsel, C. and Arneborg, J. and Lynnerup, N. and Craig, O. E. and Swallow, D. M. and Fotakis, A. and Christensen, R. J. and Olsen, J. V. and Liebert, A. and Montalva, N. and Fiddyment, S. and Charlton, S. and Mackie, M. and Canci, A. and Bouwman, A. and Ruhli, F. and Gilbert, M. T. and Collins, M. J.},
  year = {2014},
  month = nov,
  journal = {Scientific Reports},
  volume = {4},
  pages = {7104},
  issn = {2045-2322 (Electronic) 2045-2322 (Linking)},
  doi = {10.1038/srep07104},
  abstract = {Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein beta-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15(th) century CE.},
  pmcid = {PMC4245811},
  keywords = {Animals,Archaeology,Biological Evolution,Cattle,Dairy Products,Dental Calculus/*metabolism,Humans,Lactoglobulins/metabolism,Milk/*metabolism,Sheep,Tandem Mass Spectrometry}
}

@article{warinnerNewEra2015,
  title = {A New Era in Palaeomicrobiology: Prospects for Ancient Dental Calculus as a Long-Term Record of the Human Oral Microbiome},
  shorttitle = {A New Era in Palaeomicrobiology},
  author = {Warinner, Christina and Speller, Camilla and Collins, Matthew J.},
  year = {2015},
  month = jan,
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume = {370},
  number = {1660},
  pages = {20130376},
  publisher = {{Royal Society}},
  doi = {10.1098/rstb.2013.0376},
  abstract = {The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.},
  keywords = {ancient DNA,dental calculus,metagenomics,metaproteomics,oral microbiome,palaeomicrobiology},
  annotation = {c}
}

@article{warinnerPathogensHost2014,
  title = {Pathogens and Host Immunity in the Ancient Human Oral Cavity},
  author = {Warinner, Christina and Rodrigues, J. F. and Vyas, R. and Trachsel, C. and Shved, N. and Grossmann, J. and Radini, A. and Hancock, Y. and Tito, R. Y. and Fiddyment, S. and Speller, C. and Hendy, J. and Charlton, S. and Luder, H. U. and {Salazar-Garcia}, D. C. and Eppler, E. and Seiler, R. and Hansen, L. H. and Castruita, J. A. and {Barkow-Oesterreicher}, S. and Teoh, K. Y. and Kelstrup, C. D. and Olsen, J. V. and Nanni, P. and Kawai, T. and Willerslev, E. and {von Mering}, C. and Lewis, C. M. and Collins, M. J. and Gilbert, M. T. and Ruhli, F. and Cappellini, E.},
  year = {2014},
  month = apr,
  journal = {Nature Genetics},
  volume = {46},
  number = {4},
  pages = {336--44},
  issn = {1546-1718 (Electronic) 1061-4036 (Linking)},
  doi = {10.1038/ng.2906},
  abstract = {Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.},
  pmcid = {PMC3969750},
  keywords = {Archaeology,Bacteroidetes/*genetics,Base Sequence,Dental Calculus/history/*microbiology,Food Analysis,Genome; Bacterial/*genetics,Germany,History; Medieval,Humans,Microbiota/*genetics,Molecular Sequence Data,Mouth/immunology/*microbiology,Phylogeny,Proteome/*genetics,RNA; Ribosomal; 16S/genetics,Sequence Analysis; DNA,Tandem Mass Spectrometry}
}

@incollection{weinerBiologicalMaterials2010,
  title = {Biological {{Materials}}: {{Bones}} and {{Teeth}}},
  booktitle = {Microarchaeology: {{Beyond}} the {{Visible Archaeological Record}}},
  author = {Weiner, Stephen},
  year = {2010},
  pages = {99--134},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}},
  isbn = {978-0-511-81121-0}
}

@incollection{weinerInfraredSpectroscopy2010,
  title = {Infrared {{Spectroscopy}} in {{Archaeology}}},
  booktitle = {Microarchaeology: {{Beyond}} the {{Visible Archaeological Record}}},
  author = {Weiner, Stephen},
  year = {2010},
  month = feb,
  edition = {First},
  pages = {275--316},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}},
  doi = {10.1017/CBO9780511811210},
  abstract = {The archaeological record is a combination of what is seen by eye, as well as the microscopic record revealed with the help of instrumentation. The information embedded in the microscopic record can significantly add to our understanding of past human behaviour, provided this information has not been altered by the passage of time. Microarchaeology seeks to understand the microscopic record in terms of the type of information embedded in this record, the materials in which this information resides, and the conditions under which a reliable signal can be extracted. This book highlights the concepts needed to extract information from the microscopic record. Intended for all archaeologists and archaeological scientists, it will be of particular interest to students who have some background in the natural sciences as well as archaeology.},
  isbn = {978-0-521-88003-9 978-0-521-70584-4 978-0-511-81121-0},
  langid = {english}
}

@article{weinerStatesPreservation1990,
  title = {States of Preservation of Bones from Prehistoric Sites in the {{Near East}}: {{A}} Survey},
  shorttitle = {States of Preservation of Bones from Prehistoric Sites in the {{Near East}}},
  author = {Weiner, Stephen and {Bar-Yosef}, Ofer},
  year = {1990},
  month = mar,
  journal = {Journal of Archaeological Science},
  volume = {17},
  number = {2},
  pages = {187--196},
  issn = {0305-4403},
  doi = {10.1016/0305-4403(90)90058-D},
  abstract = {A survey of the states of preservation of organic material in 30 fossil bones from 16 different prehistoric sites in the Near East shows that whereas almost all the bones have little or no collagen preserved, they do, with few exceptions, contain non-collagenous proteins. These macromolecules, therefore, represent an important reservoir of indigenous fossil bone constituents.},
  langid = {english},
  keywords = {Collagen,Diagenesis,Fossil bone,Fossil proteins,Mineral crystallinity,State of preservation}
}

@article{wesolowskiEvaluatingMicrofossil2010,
  title = {Evaluating Microfossil Content of Dental Calculus from {{Brazilian}} Sambaquis},
  author = {Wesolowski, Ver{\^o}nica and {Ferraz Mendon{\c c}a de Souza}, Sheila Maria and Reinhard, Karl J. and Ceccantini, Greg{\'o}rio},
  year = {2010},
  month = jun,
  journal = {Journal of Archaeological Science},
  volume = {37},
  number = {6},
  pages = {1326--1338},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2009.12.037},
  abstract = {To date, limited numbers of dental calculus samples have been analyzed by researchers in diverse parts of the world. The combined analyses of these have provided some general guidelines for the analysis of calculus that is non-destructive to archaeological teeth. There is still a need for a quantitative study of large numbers of calculus samples to establish protocols, assess the level of contamination, evaluate the quantity of microfossils in dental calculus, and to compare analysis results with the literature concerning the biology of calculus formation. We analyzed dental calculus from 53 teeth from four Brazilian sambaquis. Sambaquis are the shell-mounds that were established prehistorically along the Brazilian coast. The analysis of sambaqui dental calculi shows that there are relatively high concentrations of microfossils (phytoliths and starch), mineral fragments, and charcoal in dental calculus. Mineral fragments and charcoal are possibly contaminants. The largest dental calculi have the lowest concentrations of microfossils. Biologically, this is explained by individual variation in calculus formation between people. Importantly, starch is ubiquitous in dental calculus. The starch and phytoliths show that certainly Dioscorea (yam) and Araucaria angustifolia (Paran\'a pine) were eaten by sambaqui people. Araceae (arum family), Ipomoea batatas (sweet potato) and Zea mays (maize) were probably in their diet.},
  langid = {english},
  keywords = {Archaeobotany,Bioarchaeology,Brazil,Calculus,Dental,Dental Anthropology,Paleonutrition,Phytolith,Sambaquis,Starch}
}

@book{whiteBoneManual2005,
  title = {The {{Human Bone Manual}}},
  author = {White, Tim D. and Folkens, Pieter A.},
  year = {2005},
  month = oct,
  edition = {1st edition},
  publisher = {{Academic Press}},
  address = {{Amsterdam ; Boston}},
  isbn = {978-0-12-088467-4},
  langid = {english}
}

@article{whiteDentalCalculus1997,
  title = {Dental Calculus: Recent Insights into Occurrence, Formation, Prevention, Removal and Oral Health Effects of Supragingival and Subgingival Deposits},
  shorttitle = {Dental Calculus},
  author = {White, Donald J.},
  year = {1997},
  month = oct,
  journal = {European Journal of Oral Sciences},
  volume = {105},
  number = {5},
  pages = {508--522},
  issn = {0909-8836, 1600-0722},
  doi = {10.1111/j.1600-0722.1997.tb00238.x},
  langid = {english}
}

@book{whiteHumanOsteology2011,
  title = {Human {{Osteology}}},
  author = {White, Tim D. and Black, Michael T. and Folkens, Pieter A.},
  year = {2011},
  month = mar,
  edition = {3rd edition},
  publisher = {{Academic Press}},
  address = {{San Diego, Calif}},
  isbn = {978-0-12-374134-9},
  langid = {english}
}

@misc{whoOralHealth,
  title = {Oral Health},
  journal = {World Health Organization},
  howpublished = {https://www.who.int/news-room/fact-sheets/detail/oral-health},
  langid = {english}
}

@article{wilkinsonFAIRGuiding2016,
  title = {The {{FAIR Guiding Principles}} for Scientific Data Management and Stewardship},
  author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and {da Silva Santos}, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and {Gonzalez-Beltran}, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and {'t Hoen}, Peter A. C. and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and {Rocca-Serra}, Philippe and Roos, Marco and {van Schaik}, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and {van der Lei}, Johan and {van Mulligen}, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
  year = {2016},
  month = mar,
  journal = {Scientific Data},
  volume = {3},
  number = {1},
  pages = {160018},
  publisher = {{Nature Publishing Group}},
  issn = {2052-4463},
  doi = {10.1038/sdata.2016.18},
  abstract = {There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders\textemdash representing academia, industry, funding agencies, and scholarly publishers\textemdash have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.},
  copyright = {2016 The Author(s)},
  langid = {english},
  keywords = {Publication characteristics,Research data}
}

@article{willeRelationshipOral2009,
  title = {Relationship {{Between Oral Fluid}} and {{Blood Concentrations}} of {{Drugs}} of {{Abuse}} in {{Drivers Suspected}} of {{Driving Under}} the {{Influence}} of {{Drugs}}},
  author = {Wille, Sarah M. R. and Raes, Elke and Lillsunde, Pirjo and Gunnar, Teemu and Laloup, Marleen and Samyn, Nele and Christophersen, Asbj{\o}rg S. and Moeller, Manfred R. and Hammer, Karin P. and Verstraete, Alain G.},
  year = {2009},
  month = aug,
  journal = {Therapeutic Drug Monitoring},
  volume = {31},
  number = {4},
  pages = {511},
  issn = {0163-4356},
  doi = {10.1097/FTD.0b013e3181ae46ea},
  abstract = {In recent years, the interest in the use of oral fluid as a biological matrix has increased significantly, particularly for detecting driving under the influence of drugs (DUID). In this study, the relationship between the oral fluid and the blood concentrations of drugs of abuse in drivers suspected of DUID is discussed. Blood and oral fluid samples were collected from drivers suspected of DUID or stopped during random controls by the police in Belgium, Germany, Finland, and Norway for the ROSITA-2 project. The blood samples were analyzed by gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS), sometimes preceded by immunoassay screening of blood or urine samples. The oral fluid samples were analyzed by GC-MS or LC-MS(/MS). Scatter plots and trend lines of the blood and oral fluid concentrations and the median, mean, range, and SD of the oral fluid to blood (OF:B) ratios were calculated for amphetamines, benzodiazepines, cocaine, opiates, and {$\vartriangle$}9-2 tetrahydrocannabinol. The ratios found in this study were comparable with those that were published previously, but the range was wider. The OF:B ratios of basic drugs such as amphetamines, cocaine, and opiates were {$>$}1 [amphetamine: median (range) 13 (0.5-182), methylenedioxyamphetamine: 4 (1-15), methylenedioxymethamphetamine: 6 (0.9-88), methamphetamine: 5 (2-23), cocaine: 22 (4-119), benzoylecgonine: 1 (0.2-11), morphine: 2 (0.8-6), and codeine: 10 (0.8-39)]. The ratios for benzodiazepines were very low, as could be expected as they are highly protein bound and weakly acidic, leading to low oral fluid concentrations [diazepam: 0.02 (0.01-0.15), nordiazepam: 0.04 (0.01-0.23), oxazepam: 0.05 (0.03-0.14), and temazepam: 0.1 (0.06-0.54)]. For tetrahydrocannabinol, an OF:B ratio of 15 was found (range 0.01-569). In this study, the time of last administration, the dose, and the route of administration were unknown. Nevertheless, the data reflect the variability of the OF:B ratios in drivers thought to be under the influence of drugs. The wide range of the ratios, however, does not allow reliable calculation of the blood concentrations from oral fluid concentrations.},
  langid = {american}
}

@article{wongCalciumPhosphate2002,
  title = {Calcium Phosphate Deposition in Human Dental Plaque Microcosm Biofilms Induced by a Ureolytic {{pH-rise}} Procedure},
  author = {Wong, L and Sissons, C. H and Pearce, E. I. F and Cutress, T. W},
  year = {2002},
  month = nov,
  journal = {Archives of Oral Biology},
  volume = {47},
  number = {11},
  pages = {779--790},
  issn = {0003-9969},
  doi = {10.1016/S0003-9969(02)00114-0},
  abstract = {The objectives were to develop and characterize a procedure based on a ureolytic pH rise to deposit calcium phosphate into microcosm dental plaque biofilms and to test the importance of the plaque pH range. Plaque biofilms were cultured in a multiplaque culture system (`artificial mouth') with a continuous supply of a simulated oral fluid (basal medium mucin; BMM) with 146mmol/l (5\% w/v) sucrose periodically applied over 6min every 8h. After initial plaque growth, the biofilms were periodically exposed for up to 16 days to 6-min applications of calcium phosphate monofluorophosphate urea (CPMU) solution containing 20mmol/l CaCl2, 12mmol/l NaH2PO4, 5mmol/l monofluorophosphate and 500mmol/l urea (pH 5.0). Three application regimes were examined, one included a sucrose-induced acidic pH fluctuation. Plaque hydrolysis of the urea in CPMU caused the pH to rise to between 8.2 and 8.8, depositing fluoridated and carbonated calcium phosphates, and possibly some calcium carbonate, into the plaque. Calcium, phosphate and fluoride deposition was rapid for about 4 days and then slowed. After 10 days' treatment under standard conditions (BMM containing 1mmol/l urea and 1mmol/l arginine), plaque calcium and phosphate concentrations had increased up to 50-fold and 10-fold to approximately 2\textendash 4 and 1\textendash 2mmol/g plaque protein, respectively. The calcium, phosphate and fluoride content increased steadily. Calcium phosphate deposition was proportional to the plaque resting pH, increasing over four-fold when the BMM urea concentration was increased from 0 to 20mmol/l, which raised the resting pH from 6.4 to 7.2 and yielded a mean plaque calcium concentration of 14.3mmol/g protein, one subsample reaching 20.8mmol/g protein. Supplementation of BMM with 20\% human serum inhibited deposition. These results support the hypothesis that an alkaline pH in plaque is critical in promoting plaque mineralization and that mineral deposition is modulated by serum. These factors are likely to be important in regulating calculus formation.},
  langid = {english},
  keywords = {Biofilm,Dental calculus,Dental plaque,Mineralization,Plaque pH,Urea}
}

@article{wrightAdvancingRefining2021,
  title = {Advancing and Refining Archaeological Dental Calculus Research Using Multiomic Frameworks},
  author = {Wright, Sterling L. and Dobney, Keith and Weyrich, Laura S.},
  year = {2021},
  month = jan,
  journal = {STAR: Science \& Technology of Archaeological Research},
  volume = {7},
  number = {1},
  pages = {13--30},
  publisher = {{Routledge}},
  issn = {null},
  doi = {10.1080/20548923.2021.1882122},
  abstract = {Dental calculus (calcified dental plaque) is a cross-cultural biological matrix that is emerging as a critical source of information for anthropologists and oral health professionals. It contains a multitude of diverse biomolecules, providing information about an individual's culture, diet, ancestry, and health. Most researchers who study archaeological dental calculus use genomic or proteomic approaches, although a wide range of other techniques are now available. However, few studies have utilized efficient multiomic protocols. This lack of integration is problematic, as such approaches in other fields have proven to improve results and strengthen interpretations. Our review discusses three multiomic approaches: (1) interactions between the metaproteome and metagenome; (2) relationships between the host genome and oral metagenome; and, (3) associations between the epigenome and metagenome. We draw from multiomic studies on soil, plant, gut, and modern oral microbiomes to demonstrate how such integration can provide insights that are not attainable with single-omic approaches.},
  keywords = {ancient DNA,Dental calculus,multiomics,oral microbiome},
  annotation = {\_eprint: https://doi.org/10.1080/20548923.2021.1882122}
}

@techreport{wuDietEarliest2021,
  type = {Preprint},
  title = {Diet of the Earliest Modern Humans in {{East Asia}}},
  author = {Wu, Yan and Tao, Dawei and Wu, Xiujie and Liu, Wu},
  year = {2021},
  month = may,
  institution = {{In Review}},
  doi = {10.21203/rs.3.rs-442096/v1},
  abstract = {Abstract           Reconstructing diet can offer an improved understanding of the origin and evolution of modern humans. However, the diet of early modern humans in East Asia is poorly understood. Starch analysis of dental calculus is harmless to precious fossil hominins and provides the most direct evidence of plant food sources in early modern human dietary records. In this paper, we examined starch grains in dental calculus from Fuyan Cave hominins in Daoxian (South China), which were the earliest modern humans in East Asia. Our results reveal the earliest direct evidence of a hominin diet made of acorns, roots, tubers, grass seeds, and other yet-unidentified plants in marine isotope stage 5 between 120\textendash 80 ka. Our study also provides the earliest evidence that acorns may have played an important role in subsistence strategies. There may have been a long-lasting tradition of using these plants during the Late Pleistocene in China. Plant foods would have been a plentiful source of carbohydrates that greatly increased energy availability to human tissues with high glucose demands, such as the brain, red blood cells, and developing fetuses. Furthermore, a variety of starch grains retrieved from dental calculus revealed that Fuyan cave hominins were able to consume a diet that fulfilled their physiological requirements in the late Middle and early Upper Pleistocene. Our study both provides the earliest direct dietary evidence from modern humans in China and helps elucidate the evolutionary advantages of early modern humans in the late Middle and early Upper Pleistocene.},
  langid = {english}
}

@article{yaoIdentificationProtein2003,
  title = {Identification of Protein Components in Human Acquired Enamel Pellicle and Whole Saliva Using Novel Proteomics Approaches},
  author = {Yao, Y. and Berg, E. A. and Costello, C. E. and Troxler, R. F. and Oppenheim, F. G.},
  year = {2003},
  month = feb,
  journal = {J Biol Chem},
  volume = {278},
  number = {7},
  pages = {5300--8},
  issn = {0021-9258 (Print) 0021-9258 (Linking)},
  doi = {10.1074/jbc.M206333200},
  abstract = {Precursor proteins of the acquired enamel pellicle derive from glandular and non-glandular secretions, which are components of whole saliva. The purpose of this investigation was to gain further insights into the characteristics of proteins in whole saliva and in vivo formed pellicle components. To maximize separation and resolution using only micro-amounts of protein, a two-dimensional gel electrophoresis system was employed. Protein samples from parotid secretion, submandibular/sublingual secretion, whole saliva, and pellicle were subjected to isoelectric focusing followed by SDS-PAGE. Selected protein spots were excised, subjected to "in-gel" trypsin digestion, and examined by mass spectrometry (MS). The data generated, including peptide maps and tandem MS spectra, were analyzed using protein data base searches. Components identified in whole saliva include cystatins (SA-III, SA, and SN), statherin, albumin, amylase, and calgranulin A. Components identified in pellicle included histatins, lysozyme, statherin, cytokeratins, and calgranulin B. The results showed that whole saliva and pellicle have more complex protein patterns than those of glandular secretions. There are some similarities and also distinct differences between the patterns of proteins present in whole saliva and pellicle. MS approaches allowed identification of not only well characterized salivary proteins but also novel proteins not previously identified in pellicle.},
  keywords = {*Proteomics/methods,Dental Enamel Proteins/*analysis,Dental Pellicle,Electrophoresis; Gel; Two-Dimensional,Humans,Protein Precursors/analysis,Salivary Proteins and Peptides/*analysis,Sensitivity and Specificity}
}

@article{yatesEAGER2020,
  title = {Reproducible, Portable, and Efficient Ancient Genome Reconstruction with Nf-Core/Eager},
  author = {Fellows Yates, James A. and Lamnidis, Thiseas C. and Borry, Maxime and Valtue{\~n}a, Aida Andrades and Fagern{\"a}s, Zandra and Clayton, Stephen and Garcia, Maxime U. and Neukamm, Judith and Peltzer, Alexander},
  year = {2020},
  month = oct,
  journal = {bioRxiv},
  pages = {2020.06.11.145615},
  publisher = {{Cold Spring Harbor Laboratory}},
  doi = {10.1101/2020.06.11.145615},
  abstract = {{$<$}h3{$>$}Abstract{$<$}/h3{$>$} {$<$}p{$>$}The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practises. This new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term lifecycle for the pipeline. nf-core/eager will assist in ensuring that ancient DNA sequencing data can be used by a diverse range of research groups and fields.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {\textcopyright{} 2020, 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/},
  langid = {english},
  keywords = {eager}
}

@article{yatesOralMicrobiome2021,
  title = {The Evolution and Changing Ecology of the {{African}} Hominid Oral Microbiome},
  author = {Fellows Yates, James A. and Velsko, Irina M. and Aron, Franziska and Posth, Cosimo and Hofman, Courtney A. and Austin, Rita M. and Parker, Cody E. and Mann, Allison E. and N{\"a}gele, Kathrin and Arthur, Kathryn Weedman and Arthur, John W. and Bauer, Catherine C. and Crevecoeur, Isabelle and Cupillard, Christophe and Curtis, Matthew C. and Dal{\'e}n, Love and Bonilla, Marta D{\'i}az-Zorita and {Fern{\'a}ndez-Lomana}, J. Carlos D{\'i}ez and Drucker, Doroth{\'e}e G. and Escriv{\'a}, Elena Escribano and Francken, Michael and Gibbon, Victoria E. and Morales, Manuel R. Gonz{\'a}lez and Mateu, Ana Grande and Harvati, Katerina and Henry, Amanda G. and Humphrey, Louise and Men{\'e}ndez, Mario and Mihailovi{\'c}, Du{\v s}an and Peresani, Marco and Moroder, Sof{\'i}a Rodr{\'i}guez and Roksandic, Mirjana and Rougier, H{\'e}l{\`e}ne and S{\'a}zelov{\'a}, Sandra and Stock, Jay T. and Straus, Lawrence Guy and Svoboda, Ji{\v r}{\'i} and Te{\ss}mann, Barbara and Walker, Michael J. and Power, Robert C. and Lewis, Cecil M. and Sankaranarayanan, Krithivasan and Guschanski, Katerina and Wrangham, Richard W. and Dewhirst, Floyd E. and {Salazar-Garc{\'i}a}, Domingo C. and Krause, Johannes and Herbig, Alexander and Warinner, Christina},
  year = {2021},
  month = may,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {118},
  number = {20},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.2021655118},
  abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine\textendash platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},
  chapter = {Biological Sciences},
  copyright = {Copyright \textcopyright{} 2021 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).},
  langid = {english},
  pmid = {33972424},
  keywords = {dental calculus,microbiome,Neanderthal,primate,salivary amylase}
}

@article{yaussyCalculusSurvivorship2019,
  title = {Calculus and Survivorship in Medieval {{London}}: {{The}} Association between Dental Disease and a Demographic Measure of General Health},
  shorttitle = {Calculus and Survivorship in Medieval {{London}}},
  author = {Yaussy, Samantha L. and DeWitte, Sharon N.},
  year = {2019},
  journal = {American Journal of Physical Anthropology},
  volume = {168},
  number = {3},
  pages = {552--565},
  issn = {1096-8644},
  doi = {10.1002/ajpa.23772},
  abstract = {Objectives Dental plaque is associated with a variety of systemic diseases and mortality risks in living populations. However, bioarchaeologists have not fully investigated the mortality risks associated with plaque (or its mineralized form, calculus) in the past. This study examines the relationship between survivorship and calculus in a medieval skeletal sample. Materials and methods Our sample (n = 1,098) from four medieval London cemeteries, c. 1000\textendash 1540 CE, includes people who died under attritional (normal) and catastrophic (famine and plague) conditions. The associations between age and the presence of dental calculus on the permanent left first mandibular molar are assessed using binary logistic regression and Kaplan\textendash Meier survival analysis. Results The regression results indicate a significant negative relationship between age and calculus presence for individuals of all ages who died under normal mortality conditions and for adults who died under both normal and catastrophic conditions. Survival analysis reveals decreased survivorship for people of all ages with calculus under normal mortality conditions. Similarly, during conditions of catastrophic mortality, adult males with calculus suffered reduced survivorship compared to males without it, though there was no difference in survivorship between adult females with and without calculus. Conclusions These results suggest that, as in modern populations, calculus accumulation in the inhabitants of medieval London reflects a greater risk of premature death. The evaluation of calculus, a potential measure of underlying frailty, in the context of a demographic measure of general health suggests that it might provide insights into health in past populations.},
  copyright = {\textcopyright{} 2019 Wiley Periodicals, Inc.},
  langid = {english},
  keywords = {binary logistic regression,bioarchaeology,mortality,paleodemography,paleopathology,survival analysis},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.23772}
}

@article{zeroSituCaries1995,
  title = {In {{Situ Caries Models}}},
  author = {Zero, D.T.},
  year = {1995},
  month = nov,
  journal = {Advances in Dental Research},
  volume = {9},
  number = {3},
  pages = {214--230},
  publisher = {{SAGE Publications Inc}},
  issn = {0895-9374},
  doi = {10.1177/08959374950090030501},
  abstract = {By using in situ models, we have the potential to study both fundamental aspects of the caries process as well as more applied research problems such as the effect of food on dental caries and the role of fluoride in caries prevention in human subjects without actually causing caries in the natural dentition. The key experimental parameters that need to be considered in the development of an in situ model are the characteristics of the subject panel, the physical design of the model, the type of hard tissue substrate and the method of assessing mineral status, and the study design and clinical protocol. Each parameter must be carefully considered in relation to the objectives of the research, study design requirements, ethical considerations, impact on clinical relevance, and impact on the control of variation. The major source of variation associated with in situ models should be of biological and not experimental origin. The design and conduct of proper  in situ model studies require a clear understanding of the caries process, sound analytical support, and a knowledge of how to work with research subjects to achieve a high level of compliance. Given the complex nature of caries, a combination of hard tissue substrates-including sound, surface-softened lesions and subsurface lesions-may be necessary to model all aspects of caries progression and prevention successfully. Internal validation of in situ models using fluoride dose-response controls is considered to be necessary for studies evaluating the efficacy of new fluoride dentifrice formulations.},
  langid = {english},
  keywords = {Dental caries,dentifrices,fluorides,tooth demineralization,tooth remineralization.}
}

@article{zhangDentalDisease1982,
  title = {Dental Disease of Neolithic Age Skulls Excavated in Shaanxi Province},
  author = {Zhang, Yu-zhu},
  year = {1982},
  month = jan,
  journal = {Chinese Medical Journal},
  volume = {95},
  number = {06},
  pages = {391--396},
  publisher = {{Chinese Medical Association Publishing House}},
  doi = {10.5555/cmj.0366-6999.95.06.p391.01}
}

@article{zhangMeasurementPolysaccharides1998,
  title = {Measurement of Polysaccharides and Proteins in Biofilm Extracellular Polymers},
  author = {Zhang, Xiaoqi and Bishop, Paul L. and Kupferle, Margaret J.},
  year = {1998},
  month = jan,
  journal = {Water Science and Technology},
  series = {Microorganisms in {{Activated Sludge}} and {{Biofilm Processes II}}},
  volume = {37},
  number = {4},
  pages = {345--348},
  issn = {0273-1223},
  doi = {10.1016/S0273-1223(98)00127-9},
  abstract = {The structure of biofilm extracellular polymers (ECPs) was studied by measuring their polysaccharide and protein spatial distributions along biofilm depth. Biofilm was collected from two aerobic heterotrophic biofilm reactors, which were seeded with Sphingomonas sp. and Sphingomonas sp. plus mixed liquor, respectively, and operated under toxic organic (in this case, azo dye) degrading conditions. Complete mixing conditions in the two reactors were verified by measuring water content, and polysaccharide and protein quantities from three vertical sampling positions over time. Experimental results showed that: (1) the biofilm water content of either reactor did not change with sample position or biofilm age, with an average biofilm water content m both reactors of 97\%; (2) polysaccharides and proteins in the ECPs did not change with sample position; (3) the profiles of polysaccharides and proteins along the biofilm depth showed a stratified biofilm structure, with their ratio (proteins/polysaccharides) being relatively stable over the depth. Oxygen and substrate transport and interactions among species were considered to be the main reasons for producing such a non-uniform biofilm structure; and (4) Sphingomonas sp. could not compete well with microorganisms derived from the mixed liquor of a wastewater treatment plant aeration basin.},
  langid = {english},
  keywords = {Biofilm,extracellular polymers (ECPs),polysaccharides,proteins,reactors,spatial distribution,structure}
}

@article{ziesemer16SChallenges2015,
  title = {Intrinsic Challenges in Ancient Microbiome Reconstruction Using {{16S rRNA}} Gene Amplification},
  author = {Ziesemer, Kirsten A. and Mann, A. E. and Sankaranarayanan, K. and Schroeder, H. and Ozga, A. T. and Brandt, B. W. and Zaura, E. and {Waters-Rist}, A. and Hoogland, M. and {Salazar-Garcia}, D. C. and Aldenderfer, M. and Speller, C. and Hendy, J. and Weston, D. A. and MacDonald, S. J. and Thomas, G. H. and Collins, M. J. and Lewis, C. M. and Hofman, C. and Warinner, C.},
  year = {2015},
  month = nov,
  journal = {Sci Rep},
  volume = {5},
  pages = {16498},
  issn = {2045-2322 (Electronic) 2045-2322 (Linking)},
  doi = {10.1038/srep16498},
  abstract = {To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.},
  pmcid = {PMC4643231},
  keywords = {*Gene Amplification,Archaeology,Bacteria/classification/genetics,Dental Calculus/microbiology,Female,Gastrointestinal Microbiome/genetics,High-Throughput Nucleotide Sequencing/methods,Humans,Male,Metagenome/*genetics,Metagenomics/*methods,Methanobrevibacter/classification/genetics,Microbiota/*genetics,Nucleic Acid Conformation,Phylogeny,RNA; Ribosomal; 16S/chemistry/*genetics}
}

@article{ziesemerGenomeCalculus2018,
  title = {The Efficacy of Whole Human Genome Capture on Ancient Dental Calculus and Dentin},
  author = {Ziesemer, Kirsten A. and Ramos-Madrigal, Jazm{\'i}n and Mann, Allison E. and Brandt, Bernd W. and Sankaranarayanan, Krithivasan and Ozga, Andrew T. and Hoogland, Menno and Hofman, Courtney A. and Salazar-Garc{\'i}a, Domingo C. and Frohlich, Bruno and Milner, George R. and Stone, Anne C. and Aldenderfer, Mark and Lewis, Cecil M. and Hofman, Corinne L. and Warinner, Christina and Schroeder, Hannes},
  year = {2018},
  journal = {American Journal of Physical Anthropology},
  issn = {0002-9483},
  doi = {10.1002/ajpa.23763},
  abstract = {Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.}
}

@article{zijngeBiofilmArchitecture2010,
  title = {Oral {{Biofilm Architecture}} on {{Natural Teeth}}},
  author = {Zijnge, Vincent and {van Leeuwen}, M. Barbara M. and Degener, John E. and Abbas, Frank and Thurnheer, Thomas and Gm{\"u}r, Rudolf and M. Harmsen, Hermie J.},
  editor = {Bereswill, Stefan},
  year = {2010},
  month = feb,
  journal = {PLoS ONE},
  volume = {5},
  number = {2},
  pages = {e9321},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0009321},
  abstract = {Periodontitis and caries are infectious diseases of the oral cavity in which oral biofilms play a causative role. Moreover, oral biofilms are widely studied as model systems for bacterial adhesion, biofilm development, and biofilm resistance to antibiotics, due to their widespread presence and accessibility. Despite descriptions of initial plaque formation on the tooth surface, studies on mature plaque and plaque structure below the gum are limited to landmark studies from the 1970s, without appreciating the breadth of microbial diversity in the plaque. We used fluorescent in situ hybridization to localize in vivo the most abundant species from different phyla and species associated with periodontitis on seven embedded teeth obtained from four different subjects. The data showed convincingly the dominance of Actinomyces sp., Tannerella forsythia, Fusobacterium nucleatum, Spirochaetes, and Synergistetes in subgingival plaque. The latter proved to be new with a possibly important role in host-pathogen interaction due to its localization in close proximity to immune cells. The present study identified for the first time in vivo that Lactobacillus sp. are the central cells of bacterial aggregates in subgingival plaque, and that Streptococcus sp. and the yeast Candida albicans form corncob structures in supragingival plaque. Finally, periodontal pathogens colonize already formed biofilms and form microcolonies therein. These in vivo observations on oral biofilms provide a clear vision on biofilm architecture and the spatial distribution of predominant species.},
  langid = {english},
  keywords = {oral biofilm,oral microbiome}
}

@incollection{zimmermanBiomolecularArchaeology2023,
  title = {The {{Biomolecular Archaeology}} of {{Psychoactive Substances}}},
  booktitle = {Handbook of {{Archaeological Sciences}}},
  author = {Zimmerman, Mario and Tushingham, Shannon},
  editor = {Pollard, A.M. and Armitage, Ruth Ann and Makarevicz, Cheryl},
  year = {2023},
  edition = {Second edition},
  abstract = {"The Handbook of Archaeological Sciences brings together all branches of archaeological science in one place. The book is organised under 10 broad headings: dating, quaternary palaeoenvironments, human bioarchaeology, biomolecular archaeology, archaeogenetics, biological resource exploitation, inorganic resource exploitation, archaeological prospection, conservation science in the archaeological context and statistical and computer applications. The contributors, who are all well-known in their own areas of expertise, bring together in each chapter the basic science and the relevance of this science to the overall goal of archaeology - understanding humans in the past. This book is an invaluable source of reference for those interested in archaeology, anthropology, quaternary studies, geography, palaeoecology, computing, biology, chemistry and physics, those involved in commercial and local authority field archaeology units, museums and archaeological organisations"\textendash},
  isbn = {978-1-119-59204-4},
  langid = {english},
  lccn = {2022047005},
  keywords = {Archaeology,Archaeology – Methodology,CC75,CC75 .H36 2023}
}