references.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},
  date = {2019-07-31},
  eprint = {13imDwAAQBAJ},
  eprinttype = {googlebooks},
  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.},
  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}
}

@article{alanonAssessmentFlavanol2016,
  title = {Assessment of Flavanol Stereoisomers and Caffeine and Theobromine Content in Commercial Chocolates},
  author = {Alañón, M.E. and Castle, S.M. and Siswanto, P.J. and Cifuentes-Gómez, T. and Spencer, J.P.E.},
  date = {2016-10},
  journaltitle = {Food Chemistry},
  shortjournal = {Food Chemistry},
  volume = {208},
  pages = {177--184},
  issn = {03088146},
  doi = {10.1016/j.foodchem.2016.03.116},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S030881461630499X},
  urldate = {2022-11-22},
  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 gÀ1, 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, (À)-epicatechin and (+)-catechin, was determined joint the occurrence of (+)epicatechin and (À)-catechin due to the epimerization reactions produced in chocolate manufacture. (À)-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},
  date = {2018},
  journaltitle = {The Clinical Respiratory Journal},
  volume = {12},
  number = {3},
  pages = {1283--1294},
  issn = {1752-699X},
  doi = {10.1111/crj.12662},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/crj.12662},
  urldate = {2022-12-17},
  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{arcaviCigaretteSmoking2004,
  title = {Cigarette {{Smoking}} and {{Infection}}},
  author = {Arcavi, Lidia and Benowitz, Neal L.},
  date = {2004-11-08},
  journaltitle = {Archives of Internal Medicine},
  shortjournal = {Archives of Internal Medicine},
  volume = {164},
  number = {20},
  pages = {2206--2216},
  issn = {0003-9926},
  doi = {10.1001/archinte.164.20.2206},
  url = {https://doi.org/10.1001/archinte.164.20.2206},
  urldate = {2022-12-17},
  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--{$>$}}
}

@book{aten400Jaar2012,
  title = {400 jaar Beemster: 1612-2012},
  shorttitle = {400 jaar Beemster},
  author = {Aten, D. and Bossaers, K. W. J. M. and Misset, Carly},
  date = {2012},
  publisher = {{Stichting Uitgeverij Noord-Holland}},
  location = {{Wormer}},
  abstract = {\$\$Cnote\$\$VUitg. in opdracht van de Gemeente Beemster.},
  isbn = {978-90-78381-56-3},
  langid = {dutch},
  pagetotal = {416},
  keywords = {Pieces of reclaimed land.; 15.70 history of Europe.; Beemster.; Special publications (form); 1600-1700; 1700-1800; 1800-2000; 2000-2050}
}

@article{azarpazhoohSystematicReview2006,
  title = {Systematic {{Review}} of the {{Association Between Respiratory Diseases}} and {{Oral Health}}},
  author = {Azarpazhooh, Amir and Leake, James L.},
  date = {2006},
  journaltitle = {Journal of Periodontology},
  volume = {77},
  number = {9},
  pages = {1465--1482},
  issn = {1943-3670},
  doi = {10.1902/jop.2006.060010},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1902/jop.2006.060010},
  urldate = {2022-11-22},
  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.},
  date = {2009},
  journaltitle = {Plant, Cell \& Environment},
  volume = {32},
  number = {6},
  pages = {666--681},
  issn = {1365-3040},
  doi = {10.1111/j.1365-3040.2009.01926.x},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3040.2009.01926.x},
  urldate = {2021-05-03},
  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.},
  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}
}

@misc{bartholdyDentalPathological2023,
  title = {Dental, Pathological, and {{UHPLC}} Data from {{Middenbeemster}} Archaeological Site},
  author = {Bartholdy, Bjørn Peare},
  date = {2023-02-17},
  publisher = {{Zenodo}},
  doi = {10.5281/zenodo.8061483},
  url = {https://zenodo.org/records/8061483},
  urldate = {2024-04-19},
  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).},
  langid = {english},
  version = {1.0.0},
  keywords = {dental calculus,dental caries,LC-MS/MS,paleopathology,periodontitis}
}

@software{bartholdyMB11CalculusPilot,
  title = {Bbartholdy/{{mb11CalculusPilot}}: {{Version}} of Record},
  shorttitle = {Bbartholdy/{{mb11CalculusPilot}}},
  author = {Bartholdy, Bjørn Peare},
  date = {2024-04-22},
  doi = {10.5281/zenodo.11040640},
  url = {https://zenodo.org/records/11040640},
  urldate = {2024-04-22},
  abstract = {Final published version in Peer Community Journal. Full Changelog: https://github.com/bbartholdy/mb11CalculusPilot/compare/0.3.0...1.0.0},
  organization = {{Zenodo}},
  version = {1.0.0}
}

@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.},
  date = {2002-01-01},
  journaltitle = {Journal of Chromatographic Science},
  shortjournal = {Journal of Chromatographic Science},
  volume = {40},
  number = {1},
  pages = {45--48},
  issn = {0021-9665, 1945-239X},
  doi = {10.1093/chromsci/40.1.45},
  url = {https://academic.oup.com/chromsci/article-lookup/doi/10.1093/chromsci/40.1.45},
  urldate = {2022-11-04},
  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–water–acetic acid or ethanol–water–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 µg/mL and 3.21 µg/mL to 71.2 µg/mL for caffeine; {$<$} 0.1pg/mL to 32 µg mL and {$<$} 0.1 pg/mL to 13.2 µg/mL for theobromine; {$<$} 0.1 pg/mL to 47 µg/mL and {$<$} 0.1 pg/mL to 66.3 µg/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{boocockMaxillarySinusitis1995,
  title = {Maxillary Sinusitis in {{Medieval Chichester}}, {{England}}},
  author = {Boocock, P and Roberts, C. A. and Manchester, K},
  date = {1995},
  journaltitle = {American Journal of Physical Anthropology},
  volume = {98},
  number = {4},
  pages = {483--495},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330980408},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330980408},
  urldate = {2022-12-21},
  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. © 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{boumanBegravenis2017,
  title = {De Begravenis},
  author = {Bouman, Jacobus},
  date = {2017},
  journaltitle = {De Nieuwe Schouwschuit},
  volume = {15},
  pages = {11--15},
  url = {https://www.historischgenootschapbeemster.nl/wp-content/uploads/De_Nieuwe_Schouwschuit_15e_jaargang_november_2017.pdf},
  urldate = {2022-11-18},
  entrysubtype = {magazine},
  langid = {dutch}
}

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

@book{bruinsmaBijdragenTot1872,
  title = {Bijdragen Tot de {{Geneeskundige Plaatsbeschrijving}} van {{Nederland}}},
  author = {Bruinsma, J.J.},
  date = {1872},
  publisher = {{Van Weelden en Mingelen}},
  location = {{s'Gravenhage}},
  url = {https://wellcomecollection.org/works/sttrpc2v},
  urldate = {2020-08-19}
}

@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.},
  date = {2002},
  journaltitle = {American Journal of Physical Anthropology},
  volume = {119},
  number = {3},
  pages = {231--239},
  issn = {1096-8644},
  doi = {10.1002/ajpa.10130},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.10130},
  urldate = {2021-04-08},
  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. 68:15–28), 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 119:231–239, 2002. © 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},
  date = {2014-07-16},
  journaltitle = {PLOS ONE},
  shortjournal = {PLOS ONE},
  volume = {9},
  number = {7},
  pages = {e100808},
  publisher = {{Public Library of Science}},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0100808},
  url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100808},
  urldate = {2020-06-22},
  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{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}} 1626–1866)},
  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.},
  date = {2021},
  journaltitle = {International Journal of Osteoarchaeology},
  volume = {31},
  number = {5},
  pages = {891--901},
  issn = {1099-1212},
  doi = {10.1002/oa.3006},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/oa.3006},
  urldate = {2022-11-04},
  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{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 Kuć, Joseph and Lin, Yaw‐Huei},
  date = {2001-06-01},
  journaltitle = {Journal of Experimental Botany},
  shortjournal = {Journal of Experimental Botany},
  volume = {52},
  number = {359},
  pages = {1219--1226},
  issn = {0022-0957},
  doi = {10.1093/jexbot/52.359.1219},
  url = {https://doi.org/10.1093/jexbot/52.359.1219},
  urldate = {2022-12-21},
  abstract = {14C‐salicylic acid (SA) was used to monitor SA metabolism and its regulation in tobacco cell suspension culture. Two SA concentrations (20\,μM and 200\,μM) were used for comparison. SA was quickly taken up in both treatments, and the 200\,μM‐treated cells absorbed approximately 15 times that of 20\,μM‐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\,μM and 20\,μM 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\,μM SA treatment. However, EGTA had little or no effect on SA excretion in the 20\,μM 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\,μM but not in the 20\,μM 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\,μM, but not at 20\,μM.}
}

@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.},
  date = {2008-10-01},
  journaltitle = {Journal of Analytical Toxicology},
  shortjournal = {Journal of Analytical Toxicology},
  volume = {32},
  number = {8},
  pages = {702--704},
  issn = {0146-4760},
  doi = {10.1093/jat/32.8.702},
  url = {https://doi.org/10.1093/jat/32.8.702},
  urldate = {2022-11-04},
  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},
  date = {2012-03-01},
  journaltitle = {Ethnoarchaeology},
  volume = {4},
  number = {1},
  pages = {5--36},
  publisher = {{Routledge}},
  issn = {1944-2890},
  doi = {10.1179/eth.2012.4.1.5},
  url = {https://doi.org/10.1179/eth.2012.4.1.5},
  urldate = {2022-11-08},
  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}
}

@book{clarkeCannabisEvolution2013,
  title = {Cannabis : {{Evolution}} and {{Ethnobotany}}},
  author = {Clarke, Robert},
  date = {2013},
  publisher = {{University of California Press}},
  location = {{[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 Cássia and D. Andrade, Eduardo and Rosalen, Pedro Luiz and Groppo, Francisco Carlos},
  date = {2008-06},
  journaltitle = {Canadian Journal of Microbiology},
  shortjournal = {Can. J. Microbiol.},
  volume = {54},
  number = {6},
  pages = {501--508},
  publisher = {{NRC Research Press}},
  issn = {0008-4166},
  doi = {10.1139/W08-032},
  url = {https://cdnsciencepub.com/doi/full/10.1139/W08-032},
  urldate = {2022-12-17},
  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~– F. nucleatum and F. nucleatum~– 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{coneInterpretationOral2007,
  title = {Interpretation of {{Oral Fluid Tests}} for {{Drugs}} of {{Abuse}}},
  author = {Cone, Edward J. and Huestis, Marilyn A.},
  date = {2007-03},
  journaltitle = {Annals of the New York Academy of Sciences},
  shortjournal = {Ann N Y Acad Sci},
  volume = {1098},
  eprint = {17332074},
  eprinttype = {pmid},
  pages = {51--103},
  issn = {0077-8923},
  doi = {10.1196/annals.1384.037},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700061/},
  urldate = {2022-11-19},
  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}
}

@article{coneSalivaTesting1993,
  title = {Saliva {{Testing}} for {{Drugs}} of {{Abuse}}},
  author = {Cone, Edward J.},
  date = {1993},
  journaltitle = {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{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},
  date = {2005-03-01},
  journaltitle = {Journal of Dentistry},
  shortjournal = {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},
  url = {https://www.sciencedirect.com/science/article/pii/S0300571204001721},
  urldate = {2022-05-09},
  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{duthieNaturalSalicylates2011,
  title = {Natural Salicylates: Foods , Functions and Disease Prevention},
  shorttitle = {Natural Salicylates},
  author = {Duthie, Garry G. and Wood, Adrian D.},
  date = {2011},
  journaltitle = {Food \& Function},
  volume = {2},
  number = {9},
  pages = {515--520},
  publisher = {{Royal Society of Chemistry}},
  doi = {10.1039/C1FO10128E},
  url = {http://pubs.rsc.org/en/content/articlelanding/2011/fo/c1fo10128e},
  urldate = {2022-11-22},
  langid = {english}
}

@article{echeverriaNicotineHair2013,
  title = {Nicotine in the Hair of Mummies from {{San Pedro}} de {{Atacama}} ({{Northern Chile}})},
  author = {Echeverría, Javier and Niemeyer, Hermann M.},
  date = {2013-10-01},
  journaltitle = {Journal of Archaeological Science},
  shortjournal = {Journal of Archaeological Science},
  volume = {40},
  number = {10},
  pages = {3561--3568},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2013.04.030},
  url = {https://www.sciencedirect.com/science/article/pii/S0305440313001593},
  urldate = {2022-11-19},
  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–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.–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{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.},
  date = {2018-04-01},
  journaltitle = {Journal of Archaeological Science: Reports},
  shortjournal = {Journal of Archaeological Science: Reports},
  volume = {18},
  pages = {509--515},
  issn = {2352-409X},
  doi = {10.1016/j.jasrep.2018.02.004},
  url = {https://www.sciencedirect.com/science/article/pii/S2352409X17307356},
  urldate = {2023-06-07},
  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}
}

@book{ggplot2,
  title = {Ggplot2: {{Elegant Graphics}} for {{Data Analysis}}},
  author = {Wickham, Hadley},
  date = {2016},
  publisher = {{Springer-Verlag}},
  location = {{New York}},
  url = {https://ggplot2.tidyverse.org},
  isbn = {978-3-319-24277-4}
}

@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 Müldner, Gundula and Tersch, Matthew Von and Nardi, Alessandra and Enei, Flavio and Canini, Antonella and Rickards, Olga and Alexander, Michelle and Martínez-Labarga, Cristina},
  date = {2020-01-28},
  journaltitle = {PLOS ONE},
  shortjournal = {PLOS ONE},
  volume = {15},
  number = {1},
  pages = {e0227433},
  publisher = {{Public Library of Science}},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0227433},
  url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227433},
  urldate = {2023-06-07},
  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 ω3 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}
}

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

@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.},
  date = {2005},
  journaltitle = {HOMO - Journal of Comparative Human Biology},
  volume = {56},
  number = {2},
  pages = {119--132},
  issn = {0018442X},
  doi = {10.1016/j.jchb.2005.02.002}
}

@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},
  date = {2023-01-12},
  journaltitle = {Nature Communications},
  shortjournal = {Nat Commun},
  volume = {14},
  number = {1},
  pages = {175},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-35808-6},
  url = {https://www.nature.com/articles/s41467-023-35808-6},
  urldate = {2023-10-20},
  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.},
  issue = {1},
  langid = {english},
  keywords = {Genetics research,Population genetics,Translational research}
}

@article{jangBoneInvolvement2002,
  title = {Bone Involvement in Chronic Rhinosinusitis Assessed by {{99mTc-MDP}} Bone {{SPECT}}},
  author = {Jang, Y.j. and Koo, T.w. and Chung, S.y. and Park, S.g.},
  date = {2002},
  journaltitle = {Clinical Otolaryngology \& Allied Sciences},
  volume = {27},
  number = {3},
  pages = {156--161},
  issn = {1365-2273},
  doi = {10.1046/j.1365-2273.2002.00553.x},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2273.2002.00553.x},
  urldate = {2022-12-21},
  abstract = {To investigate the clinical significance of bone involvement in chronic rhinosinusitis, 99mTc-MDP bone single photon emission computed tomography (SPECT) was studied in 43 patients diagnosed as having chronic rhinosinusitis. Quantitative isotope uptake indices calculated on SPECT were compared between the patient and a control group, and between patients with a good postoperative outcome and those with a poor outcome. The patient group showed a significantly higher isotope uptake than the control group. The uptake of isotope in the ethmoid sinus areas in patients who had a poor postoperative outcome was significantly higher than those who had a good outcome. Our study suggests that patients with chronic rhinosinusitis have apparent bony involvement, and patients with more severe bone involvement may have a poorer treatment outcome.},
  langid = {english},
  keywords = {bone involvement,rhinosinusitis,single photon emission computed tomography (SPECT)},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2273.2002.00553.x}
}

@article{jinSupragingivalCalculus2002,
  title = {Supragingival {{Calculus}}: {{Formation}} and {{Control}}},
  shorttitle = {Supragingival {{Calculus}}},
  author = {Jin, Ye and Yip, Hak-Kong},
  date = {2002},
  journaltitle = {Critical Reviews in Oral Biology \& Medicine},
  publisher = {{SAGE Publications}},
  doi = {10.1177/154411130201300506},
  url = {https://journals.sagepub.com/doi/10.1177/154411130201300506},
  urldate = {2020-05-13},
  abstract = {Dental calculus is composed of inorganic components and organic matrix. Brushite, dicalcium phosphate dihydrate, octacalcium phosphate, hydroxyapatite, and whit...},
  langid = {english}
}

@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.},
  date = {2017-09-01},
  journaltitle = {Journal of Archaeological Science},
  shortjournal = {Journal of Archaeological Science},
  volume = {85},
  pages = {30--40},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2017.06.006},
  url = {https://www.sciencedirect.com/science/article/pii/S0305440317300869},
  urldate = {2023-10-20},
  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 (900–1600 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{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},
  date = {2021-03-10},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  volume = {11},
  number = {1},
  pages = {5570},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-84348-w},
  url = {http://www.nature.com/articles/s41598-021-84348-w},
  urldate = {2022-12-17},
  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 0.39–1.21), OR of those who drink one cup was 0.67 (0.38–1.18), and OR of those who drink two or more cups was 0.50 (0.28–0.88) (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.},
  issue = {1},
  langid = {english},
  keywords = {Medical research,Risk factors}
}

@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},
  date = {2013},
  pages = {35--60},
  langid = {dutch}
}

@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},
  date = {1994},
  eprint = {2mAVkStNG5EC},
  eprinttype = {googlebooks},
  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.},
  isbn = {978-90-6299-103-7},
  langid = {english},
  pagetotal = {372},
  keywords = {cocaine,Netherlands,opium}
}

@article{lindholstLongTerm2010,
  title = {Long Term Stability of Cannabis Resin and Cannabis Extracts},
  author = {Lindholst, Christian},
  date = {2010-09-01},
  journaltitle = {Australian Journal of Forensic Sciences},
  volume = {42},
  number = {3},
  pages = {181--190},
  publisher = {{Taylor \& Francis}},
  issn = {0045-0618},
  doi = {10.1080/00450610903258144},
  url = {https://doi.org/10.1080/00450610903258144},
  urldate = {2022-11-06},
  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°C and −20°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{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},
  date = {2015-05-01},
  journaltitle = {Applied Microbiology and Biotechnology},
  shortjournal = {Appl Microbiol Biotechnol},
  volume = {99},
  number = {9},
  pages = {3775--3785},
  issn = {1432-0614},
  doi = {10.1007/s00253-015-6525-1},
  url = {https://doi.org/10.1007/s00253-015-6525-1},
  urldate = {2022-12-23},
  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{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.},
  date = {1985},
  journaltitle = {American Journal of Physical Anthropology},
  volume = {68},
  number = {1},
  pages = {15--28},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330680103},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330680103},
  urldate = {2021-04-08},
  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.},
  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.},
  date = {1976-12-01},
  journaltitle = {Calcified Tissue Research},
  shortjournal = {Calc. Tis Res.},
  volume = {21},
  number = {1},
  pages = {47--55},
  issn = {1432-0827},
  doi = {10.1007/BF02547382},
  url = {https://doi.org/10.1007/BF02547382},
  urldate = {2020-05-27},
  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},
  date = {2005},
  journaltitle = {Barge’s Anthropologica},
  number = {6}
}

@article{machtHistoryOpium1915,
  title = {The History of Opium and Some of Its Preparations and Alkaloids},
  author = {Macht, David I},
  date = {1915},
  journaltitle = {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.},
  date = {2017-01-01},
  journaltitle = {STAR: Science \& Technology of Archaeological Research},
  volume = {3},
  number = {1},
  eprint = {29098079},
  eprinttype = {pmid},
  pages = {58--70},
  publisher = {{Routledge}},
  issn = {null},
  doi = {10.1080/20548923.2017.1361629},
  url = {https://doi.org/10.1080/20548923.2017.1361629},
  urldate = {2022-06-08},
  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.},
  keywords = {Archaeology,dental calculus,destructive analysis,LC-MS/MS,protein preservation,shotgun proteomics},
  annotation = {\_eprint: https://doi.org/10.1080/20548923.2017.1361629}
}

@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.},
  date = {2017-04-01},
  journaltitle = {Journal of Food Composition and Analysis},
  shortjournal = {Journal of Food Composition and Analysis},
  volume = {57},
  pages = {31--39},
  issn = {0889-1575},
  doi = {10.1016/j.jfca.2016.12.008},
  url = {https://www.sciencedirect.com/science/article/pii/S0889157516302241},
  urldate = {2022-11-22},
  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–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 1.28–26.93 (vegetables), 2.13–36.90 (fruits), 2.80–604.97 (herbs/spices) and 2.04–51.48 (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{maughanCaffeineIngestion2003,
  title = {Caffeine Ingestion and Fluid Balance: A Review},
  shorttitle = {Caffeine Ingestion and Fluid Balance},
  author = {Maughan, R. J. and Griffin, J.},
  date = {2003},
  journaltitle = {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},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-277X.2003.00477.x},
  urldate = {2022-12-17},
  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–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 250–300 mg, equivalent to the amount found in 2–3 cups of coffee or 5–8 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}
}

@article{meillourDetectionPlantderived2023,
  title = {Detection of Plant-Derived Compounds in {{XIXth}} c. {{Dutch}} Dental Calculus},
  author = {Meillour, Louise Le},
  date = {2023-11-01},
  journaltitle = {Peer Community in Archaeology},
  shortjournal = {PCIArchaeology},
  volume = {1},
  pages = {100389},
  publisher = {{Peer Community In}},
  issn = {2742-1929},
  doi = {10.24072/pci.archaeo.100389},
  url = {https://archaeo.peercommunityin.org/articles/rec?id=389},
  urldate = {2024-04-19},
  abstract = {A recommendation of: Bartholdy, Bjørn Peare; Hasselstrøm, Jørgen B.; Sørensen, 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},
  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},
  date = {1985},
  journaltitle = {American Journal of Physical Anthropology},
  volume = {68},
  number = {1},
  pages = {57--66},
  issn = {1096-8644},
  doi = {10.1002/ajpa.1330680106},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330680106},
  urldate = {2021-04-08},
  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.},
  langid = {english},
  keywords = {Age at death,Age-determination,Demography,Forensic,Sutures},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330680106}
}

@article{milmanOralFluid2011,
  title = {Oral {{Fluid}} and {{Plasma Cannabinoid Ratios}} after {{Around-the-Clock Controlled Oral Δ9-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},
  date = {2011-11-01},
  journaltitle = {Clinical Chemistry},
  shortjournal = {Clinical Chemistry},
  volume = {57},
  number = {11},
  pages = {1597--1606},
  issn = {0009-9147},
  doi = {10.1373/clinchem.2011.169490},
  url = {https://doi.org/10.1373/clinchem.2011.169490},
  urldate = {2022-12-29},
  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 Δ9-tetrahydrocannabinol (THC, dronabinol) doses (40–120 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-μg/L, 0.5-μg/L, and 7.5-ng/L limits of quantification (LOQs), respectively. In plasma, the LOQs were 0.25 μg/L for THC and THCCOOH, and 0.5 μg/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.}
}

@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},
  date = {1901},
  publisher = {{New York, J. H. Vail \& Company}},
  url = {http://archive.org/details/peruhistoryofcoc00mortrich},
  urldate = {2021-04-23},
  abstract = {Bibliography: p. [517]-544},
  editora = {{University of California Libraries}},
  editoratype = {collaborator},
  langid = {english},
  pagetotal = {620},
  keywords = {Coca}
}

@book{nierstraszTeaTrade2015,
  title = {Rivalry for {{Trade}} in {{Tea}} and {{Textiles}}: {{The English}} and {{Dutch East India}} Companies (1700–1800)},
  shorttitle = {Rivalry for {{Trade}} in {{Tea}} and {{Textiles}}},
  author = {Nierstrasz, Chris},
  date = {2015-09-22},
  eprint = {uwtaCwAAQBAJ},
  eprinttype = {googlebooks},
  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.},
  isbn = {978-1-137-48653-0},
  langid = {english},
  pagetotal = {241},
  keywords = {Business & Economics / Economic History,Business & Economics / Industries / General,History / Asia / General,History / Europe / General,History / General,History / Modern / General,History / World}
}

@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.},
  date = {2009-02-01},
  journaltitle = {Journal of Archaeological Science},
  shortjournal = {Journal of Archaeological Science},
  volume = {36},
  number = {2},
  pages = {467--472},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2008.09.036},
  url = {https://www.sciencedirect.com/science/article/pii/S0305440308002379},
  urldate = {2022-11-19},
  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 500–1000 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–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{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.},
  date = {2016},
  journaltitle = {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 (26–49\,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 © 2014 John Wiley \& Sons, Ltd.}
}

@article{raffertyCurrentResearch2012,
  title = {Current Research on Smoking Pipe Residues},
  author = {Rafferty, Sean M. and Lednev, Igor and Virkler, Kelly and Chovanec, Zuzana},
  date = {2012-07-01},
  journaltitle = {Journal of Archaeological Science},
  shortjournal = {Journal of Archaeological Science},
  volume = {39},
  number = {7},
  pages = {1951--1959},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2012.02.001},
  url = {https://www.sciencedirect.com/science/article/pii/S0305440312000593},
  urldate = {2022-11-08},
  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}
}

@manual{Rbase,
  type = {manual},
  title = {R: {{A}} Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  date = {2020},
  publisher = {{R Foundation for Statistical Computing}},
  location = {{Vienna, Austria}},
  url = {https://www.R-project.org/}
}

@article{rehImpactTobacco2012,
  title = {Impact of {{Tobacco Smoke}} on {{Chronic Rhinosinusitis}} – {{A Review}} of the {{Literature}}},
  author = {Reh, Douglas D. and Higgins, Thomas S. and Smith, Timothy L.},
  date = {2012-09/2012-10},
  journaltitle = {International forum of allergy \& rhinology},
  volume = {2},
  number = {5},
  eprint = {22696460},
  eprinttype = {pmid},
  pages = {362},
  publisher = {{NIH Public Access}},
  doi = {10.1002/alr.21054},
  url = {http://s2443.www.ncbi.nlm.nih.gov/pmc/articles/PMC3443524/},
  urldate = {2022-12-17},
  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}
}

@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},
  date = {2000},
  edition = {1st ed},
  pages = {163--182},
  publisher = {{Cambridge University Press}},
  location = {{Cambridge}},
  isbn = {978-1-84110-046-3}
}

@manual{Rpsych,
  type = {manual},
  title = {Psych: {{Procedures}} for Psychological, Psychometric, and Personality Research},
  author = {Revelle, William},
  date = {2022},
  location = {{Evanston, Illinois}},
  url = {https://CRAN.R-project.org/package=psych},
  organization = {{Northwestern University}}
}

@manual{Rrrtools,
  type = {manual},
  title = {Rrtools: {{Creates}} a Reproducible Research Compendium},
  author = {Marwick, Ben},
  date = {2019},
  url = {https://github.com/benmarwick/rrtools}
}

@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.},
  date = {2001},
  journaltitle = {Journal of Periodontology},
  volume = {72},
  number = {1},
  pages = {50--56},
  issn = {1943-3670},
  doi = {10.1902/jop.2001.72.1.50},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1902/jop.2001.72.1.50},
  urldate = {2022-11-22},
  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 ≥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 ± 17.8 years (mean ± SD): COPD = 51.2 ± 17.9 years and subjects without COPD = 43.9 ± 17.7 years. Subjects with a history of COPD had more periodontal attachment loss than subjects without COPD (1.48 ± 1.35 mm versus 1.17 ± 1.09 mm, P = 0.0001). Subjects with mean attachment loss (MAL) ≥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.},
  date = {1999},
  journaltitle = {Journal of Periodontology},
  volume = {70},
  number = {7},
  pages = {793--802},
  issn = {1943-3670},
  doi = {10.1902/jop.1999.70.7.793},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1902/jop.1999.70.7.793},
  urldate = {2022-11-22},
  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{scheltemaOpiumTrade1907,
  title = {The {{Opium Trade}} in the {{Dutch East Indies}}. {{I}}},
  author = {Scheltema, J. F.},
  date = {1907},
  journaltitle = {American Journal of Sociology},
  volume = {13},
  number = {1},
  pages = {79--112},
  issn = {00029602, 15375390}
}

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

@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.},
  date = {2005-12-01},
  journaltitle = {Journal of Allergy and Clinical Immunology},
  shortjournal = {Journal of Allergy and Clinical Immunology},
  series = {The {{Diagnosis}} and {{Management}} of {{Sinusitis}}: {{A Practice Parameter Update}}},
  volume = {116},
  pages = {S13-S47},
  issn = {0091-6749},
  doi = {10.1016/j.jaci.2005.09.048},
  url = {https://www.sciencedirect.com/science/article/pii/S0091674905022542},
  urldate = {2022-12-17},
  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.},
  issue = {6, Supplement},
  langid = {english}
}

@article{smithDetectionOpium2018,
  title = {Detection of Opium Alkaloids in a {{Cypriot}} Base-Ring Juglet},
  author = {Smith, Rachel K. and Stacey, Rebecca J. and Bergström, Ed and Thomas-Oates, Jane},
  date = {2018},
  journaltitle = {Analyst},
  volume = {143},
  number = {21},
  pages = {5127--5136},
  publisher = {{Royal Society of Chemistry}},
  doi = {10.1039/C8AN01040D},
  url = {https://pubs.rsc.org/en/content/articlelanding/2018/an/c8an01040d},
  urldate = {2022-11-19},
  langid = {english}
}

@article{sorensenDrugsCalculus2021,
  title = {Entrapment of Drugs in Dental Calculus – {{Detection}} Validation Based on Test Results from Post-Mortem Investigations},
  author = {Sørensen, Lambert K. and Hasselstrøm, Jørgen B. and Larsen, Line S. and Bindslev, Dorthe A.},
  date = {2021-02-01},
  journaltitle = {Forensic Science International},
  shortjournal = {Forensic Science International},
  volume = {319},
  pages = {110647},
  issn = {0379-0738},
  doi = {10.1016/j.forsciint.2020.110647},
  url = {https://www.sciencedirect.com/science/article/pii/S0379073820305090},
  urldate = {2021-04-22},
  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 0.01–0.05ng 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 = {Sørensen, Lambert K. and Hasselstrøm, Jørgen B.},
  date = {2018},
  journaltitle = {Drug Testing and Analysis},
  volume = {10},
  number = {2},
  pages = {301--309},
  issn = {1942-7611},
  doi = {10.1002/dta.2221},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/dta.2221},
  urldate = {2020-07-28},
  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 Δ9-tetrahydrocannabinol (THC), cannabinol (CBN), cannabidiol (CBD), 11-hydroxy-Δ9-tetrahydrocannabinol (THC-OH), and 11-nor-9-carboxy-Δ9-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°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°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°C during the test period of 5 months. The instability at −20°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°C.},
  langid = {english},
  keywords = {antioxidants,blood,cannabinoids,stability,THC},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/dta.2221}
}

@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.},
  date = {2008-02-01},
  journaltitle = {Journal of Chromatographic Science},
  shortjournal = {Journal of Chromatographic Science},
  volume = {46},
  number = {2},
  pages = {144--149},
  issn = {0021-9665, 1945-239X},
  doi = {10.1093/chromsci/46.2.144},
  url = {https://academic.oup.com/chromsci/article-lookup/doi/10.1093/chromsci/46.2.144},
  urldate = {2022-11-18},
  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.},
  date = {1994},
  journaltitle = {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.},
  date = {1988-01},
  journaltitle = {Food and Chemical Toxicology},
  shortjournal = {Food and Chemical Toxicology},
  volume = {26},
  number = {2},
  pages = {111--118},
  issn = {02786915},
  doi = {10.1016/0278-6915(88)90107-X},
  url = {https://linkinghub.elsevier.com/retrieve/pii/027869158890107X},
  urldate = {2022-11-04},
  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{SucheyBrooks1990,
  title = {Skeletal Age Determination Based on the Os Pubis: {{A}} Comparison of the {{Acsádi-Nemeskéri}} and {{Suchey-Brooks}} Methods},
  shorttitle = {Skeletal Age Determination Based on the Os Pubis},
  author = {Brooks, S. and Suchey, J. M.},
  date = {1990-06-01},
  journaltitle = {Human Evolution},
  shortjournal = {Hum. Evol.},
  volume = {5},
  number = {3},
  pages = {227--238},
  issn = {1824-310X},
  doi = {10.1007/BF02437238},
  url = {https://doi.org/10.1007/BF02437238},
  urldate = {2021-04-08},
  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. TheAcsádi-Nemeskéri 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 theAcsádi-Nemeskéri 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},
  date = {2016-10-01},
  journaltitle = {Toxicology in Vitro},
  shortjournal = {Toxicology in Vitro},
  volume = {36},
  pages = {133--141},
  issn = {0887-2333},
  doi = {10.1016/j.tiv.2016.07.020},
  url = {https://www.sciencedirect.com/science/article/pii/S0887233316301497},
  urldate = {2022-12-23},
  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{takahashiOralMicrobiome2015,
  title = {Oral {{Microbiome Metabolism}}: {{From}} “{{Who Are They}}?” To “{{What Are They Doing}}?”},
  shorttitle = {Oral {{Microbiome Metabolism}}},
  author = {Takahashi, N.},
  date = {2015-12-01},
  journaltitle = {Journal of Dental Research},
  shortjournal = {J Dent Res},
  volume = {94},
  number = {12},
  pages = {1628--1637},
  publisher = {{SAGE Publications Inc}},
  issn = {0022-0345},
  doi = {10.1177/0022034515606045},
  url = {https://doi.org/10.1177/0022034515606045},
  urldate = {2022-12-28},
  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{tidyverse2019,
  title = {Welcome to the {{tidyverse}}},
  author = {Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and François, 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 Müller, 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},
  date = {2019},
  journaltitle = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686}
}

@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},
  date = {2013-02-01},
  journaltitle = {Journal of Archaeological Science},
  shortjournal = {Journal of Archaeological Science},
  volume = {40},
  number = {2},
  pages = {1397--1407},
  issn = {0305-4403},
  doi = {10.1016/j.jas.2012.09.019},
  url = {https://www.sciencedirect.com/science/article/pii/S0305440312004219},
  urldate = {2022-11-08},
  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—where residue is extracted directly from the stone or clay matrix of whole and fragmentary archaeological pipes—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},
  date = {2017-02-01},
  journaltitle = {Drug Metabolism and Pharmacokinetics},
  shortjournal = {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},
  url = {https://www.sciencedirect.com/science/article/pii/S1347436716305250},
  urldate = {2023-10-20},
  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 ≥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 (≥1.5-fold, P~{$<~$}0.05). Further analysis of drug-metabolizing enzyme genes indicated that expression of CYP2A6 and CYP3A4 in females in the ≥70 age group was less than in the {$<$}60 age group (≥1.5-fold, P~{$<~$}0.05), and this trend was also observed for PXR expression in males (≥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{valenDetermination212017,
  title = {Determination of 21 Drugs in Oral Fluid Using Fully Automated Supported Liquid Extraction and {{UHPLC-MS}}/{{MS}}},
  author = {Valen, Anja and Leere Øiestad, Åse Marit and Strand, Dag Helge and Skari, Ragnhild and Berg, Thomas},
  date = {2017},
  journaltitle = {Drug Testing and Analysis},
  volume = {9},
  number = {5},
  pages = {808--823},
  issn = {1942-7611},
  doi = {10.1002/dta.2045},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/dta.2045},
  urldate = {2022-12-31},
  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 μL 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 © 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{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},
  date = {2017-11},
  journaltitle = {Metabolomics},
  shortjournal = {Metabolomics},
  volume = {13},
  number = {11},
  pages = {134},
  issn = {1573-3882, 1573-3890},
  doi = {10.1007/s11306-017-1270-3},
  url = {http://link.springer.com/10.1007/s11306-017-1270-3},
  urldate = {2020-12-01},
  langid = {english},
  keywords = {dental calculus,mass spectrometry,metabolites}
}

@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},
  date = {2019-12},
  journaltitle = {Microbiome},
  shortjournal = {Microbiome},
  volume = {7},
  number = {1},
  pages = {102},
  issn = {2049-2618},
  doi = {10.1186/s40168-019-0717-3},
  url = {https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0717-3},
  urldate = {2021-08-30},
  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{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.},
  date = {2014-11-27},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  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{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.},
  date = {1997-10},
  journaltitle = {European Journal of Oral Sciences},
  shortjournal = {Eur J Oral Sci},
  volume = {105},
  number = {5},
  pages = {508--522},
  issn = {0909-8836, 1600-0722},
  doi = {10.1111/j.1600-0722.1997.tb00238.x},
  url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1600-0722.1997.tb00238.x},
  urldate = {2021-07-09},
  langid = {english}
}

@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, Asbjørg S. and Moeller, Manfred R. and Hammer, Karin P. and Verstraete, Alain G.},
  date = {2009-08},
  journaltitle = {Therapeutic Drug Monitoring},
  volume = {31},
  number = {4},
  pages = {511},
  issn = {0163-4356},
  doi = {10.1097/FTD.0b013e3181ae46ea},
  url = {https://journals.lww.com/drug-monitoring/Fulltext/2009/08000/Relationship_Between_Oral_Fluid_and_Blood.13.aspx},
  urldate = {2022-12-29},
  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 ▵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{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.},
  date = {2019},
  journaltitle = {American Journal of Physical Anthropology},
  volume = {168},
  number = {3},
  pages = {552--565},
  issn = {1096-8644},
  doi = {10.1002/ajpa.23772},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.23772},
  urldate = {2020-08-03},
  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. 1000–1540 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–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.},
  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{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.},
  date = {2015-11-13},
  journaltitle = {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, Jazmín and Mann, Allison E. and Brandt, Bernd W. and Sankaranarayanan, Krithivasan and Ozga, Andrew T. and Hoogland, Menno and Hofman, Courtney A. and Salazar‐García, 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},
  date = {2018},
  journaltitle = {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 Gmür, Rudolf and M. Harmsen, Hermie J.},
  editor = {Bereswill, Stefan},
  options = {useprefix=true},
  date = {2010-02-24},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  volume = {5},
  number = {2},
  pages = {e9321},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0009321},
  url = {https://dx.plos.org/10.1371/journal.pone.0009321},
  urldate = {2020-10-01},
  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}
}