Peer community journal最新文献

{"title":"Factors shaping vaginal microbiota long-term community dynamics in young adult women.","authors":"Tsukushi Kamiya, Nicolas Tessandier, Baptiste Elie, Claire Bernat, Vanina Boué, Sophie Grasset, Soraya Groc, Massilva Rahmoun, Christian Selinger, Michael S Humphrys, Marine Bonneau, Christelle Graf, Vinccent Foulongne, Jacques Reynes, Vincent Tribout, Michel Segondy, Nathalie Boulle, Jacques Ravel, Carmen Lía Murall, Samuel Alizon","doi":"10.24072/pcjournal.527","DOIUrl":"10.24072/pcjournal.527","url":null,"abstract":"<p><p>The vaginal microbiota is known to affect women's health. Yet, there is a notable paucity of high-resolution follow-up studies lasting several months, which would be required to interrogate the long-term dynamics and associations with demographic and behavioural covariates. Here, we present a high-resolution longitudinal cohort study of 125 women, followed for a median duration of 8.6 months, with a median of 11 samples collected per woman. Using a hierarchical Bayesian Markov model, we characterised the patterns of vaginal microbiota community persistence and transition, simultaneously estimated the impact of 16 covariates and quantified individual variability among women. We showed that \"optimal\" (Community State Type (CST) I, II, and V) and \"sub-optimal\" (CST III) communities are more stable over time than \"non-optimal\" (CST IV) ones. Furthermore, we found that some covariates - most notably alcohol consumption - impacted the probability of shifting from one CST to another. We performed counterfactual simulations to confirm that alterations of key covariates, such as alcohol consumption, could shape the prevalence of different microbiota communities in the population. Finally, our analyses indicated that there is a relatively canalised pathway leading to the deterioration of vaginal microbiota communities, whereas the paths to recovery can be highly individualised among women. In addition to providing one of the first insights into vaginal microbiota dynamics over a year, our study showcases a novel application of a hierarchical Bayesian Markov model to clinical cohort data with many covariates. Our findings pave the way for an improved mechanistic understanding of microbial dynamics in the vaginal environment and the development of novel preventative and therapeutic strategies to improve vaginal health.</p>","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4","authors":"Anton Kraege, Edgar A. Chavarro-Carrero, Nadège Guiglielmoni, Eva Schnell, Joseph Kirangwa, Stefanie Heilmann-Heimbach, Kerstin Becker, Karl Köhrer, Philipp H. Schiffer, Bart P. H. J. Thomma, Hanna Rovenich","doi":"10.24072/pcjournal.447","DOIUrl":"https://doi.org/10.24072/pcjournal.447","url":null,"abstract":"Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"57 45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecotoxicity of lanthanides to Daphnia magna: insights from elemental behavior and speciation in a standardized test medium","authors":"D. Vignati, Loïc A Martin, L. Poirier, A. Zalouk‐Vergnoux, C. Fouque, Clément Bojic, Christophe Hissler, Carole Cossu-Leguille","doi":"10.24072/pcjournal.440","DOIUrl":"https://doi.org/10.24072/pcjournal.440","url":null,"abstract":"Lanthanides (LNs) are a group of 15 elements with steadily increasing economical importance due to their multiple uses in technologies essential for sustainable ecological, digital and energetic transitions. Although knowledge on LN ecotoxicology has greatly improved over the last decade, uncertainty persists with regard to their actual hazard and risk in freshwater environments. In particular, only limited information is available on i) the actual relationships between LN speciation vs . ecotoxicological responses in standardized laboratory tests and ii) the existence of regular and predictable patterns in LN ecotoxicity (expressed as e.g. , EC 50 ) along the LN series. The present paper provides the first report on the ecotoxicity of all lanthanides (except Pm) for the freshwater crustacean Daphnia magna along with an unprecedented level of detail on LN speciation in the exposure medium. Experimental data show that exposure concentrations can decrease by up to 95 % over the test duration, with the percentage decrease being inversely related with LN atomic mass. Thermodynamic speciation calculations confirm the possible formation of insoluble species, mainly LN carbonates. However, the corresponding theoretical solubility limits do not fully agree with measured concentrations at the end of the tests. Experimental verification of exposure concentrations (as a minimum at the beginning and end of laboratory tests) remains therefore mandatory to reach proper conclusions as to the ecotoxicity of each LN. A decreasing trend in ecotoxicity can actually be observed along the LN series when temporal changes in the exposure concentrations are properly accounted for. However, this trend remains dependent on exposure time and selected exposure metrics. This and other caveats must be considered in future research to reach a community-based consensus for the proper hazard and risk assessment of LN towards daphnids and other aquatic organisms.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"123 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141821080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses","authors":"Maud Billaud, Ilias Theodorou, Quentin Lamy-Besnier, Shiraz A. Shah, François Lecointe, Luisa De Sordi, Marianne De Paepe, Marie-Agnès Petit","doi":"10.24072/pcjournal.437","DOIUrl":"https://doi.org/10.24072/pcjournal.437","url":null,"abstract":"Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre-treatment and amplification of DNA using the multiple displacement amplifica-tion (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"134 34","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141656268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in specificity, development time and virulence between two acanthocephalan parasites, infecting two cryptic species of Gammarus fossarum","authors":"Alexandre Bauer, Lucie Develay Nguyen, S. Motreuil, Maria Teixeira, Nelly Debrosse, Thierry Rigaud","doi":"10.24072/pcjournal.434","DOIUrl":"https://doi.org/10.24072/pcjournal.434","url":null,"abstract":"","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141668995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population","authors":"B. P. Bartholdy, Jørgen B. Hasselstrøm, Lambert K. Sørensen, Maia Casna, Historisch Menno Hoogland, Genootschap Beemster, Amanda G. Henry, Historisch Genootschap Beemster","doi":"10.24072/pcjournal.414","DOIUrl":"https://doi.org/10.24072/pcjournal.414","url":null,"abstract":"Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus provides direct evidence of consumption by individuals within a population. We conducted a study on 41 individuals from Middenbeemster, a 19th century rural Dutch archaeological site. Skeletal and dental analysis was performed to explore potential relationships between pathological lesions and presence of alkaloids. Dental calculus was analysed using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-ESI-MS/MS). We were able to detect nicotine, cotinine, caffeine, theophylline, and salicylic acid, suggesting the consumption of tea and coffee and smoking of tobacco on an individual scale, which is also confirmed by historic documentation and identification of pipe notches in the dentition. Nicotine and/or cotinine was present in 56% of individuals with at least one visible pipe notch. There is some influence of skeletal preservation on the detection of alkaloids, with higher quantities of compounds extracted from well-preserved individuals, and we observe a positive relationship between weight of the calculus sample and quantity of detected compounds, as well as between chronic maxillary sinusitis and the presence of multiple alkaloids. There are many limitations that will need to be addressed going forward with this type of analysis; we stress the need for more systematic research on the consumption of alkaloid-containing items and their subsequent concentration and preservation in dental calculus, in addition to how mode of consumption may affect concentrations in the dentition. Despite the limitations, this preliminary study illustrates many benefits of using calculus to target a variety of compounds that could have been consumed as medicine or diet. This method allows us to directly address specific individuals, which can be especially useful in individuals that are not always well-documented in historic documentation, such as rural populations, and especially children and women.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"132 25","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140669171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia","authors":"Brian W. Strehlow, Astrid Schuster, Warren R. Francis, Lisa K Eckford-Soper, Beate Kraft, Rob McAllen, R. Nielsen, S. Mandrup, Donald E. Canfield","doi":"10.24072/pcjournal.410","DOIUrl":"https://doi.org/10.24072/pcjournal.410","url":null,"abstract":"Deoxygenation can be fatal for many marine animals; however, some sponge species are tolerant of hypoxia and anoxia. Indeed, two sponge species, Eurypon sp. 2 and Hymeraphia stellif-era, survive seasonal anoxia for months at a time. To understand their tolerance mechanisms, we performed differential gene expression analyses on the sponges, their mitochondria and their microbial symbionts under in situ conditions of normoxia, hypoxia and anoxia. Each species","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"27 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140703084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Social Network Analysis of Ancient Japanese Obsidian Artifacts Reflecting Sampling Bias Reduction","authors":"Fumihiro Sakahira, Hiro'omi Tsumura","doi":"10.24072/pcjournal.409","DOIUrl":"https://doi.org/10.24072/pcjournal.409","url":null,"abstract":"This study aims to investigate the dynamics of obsidian trade networks during the Jomon period (15,000–2,400 years cal BP), the hunting and gathering era in Japan. To improve regional representation and reduce the distortions caused by small sample sizes, we performed clustering based on a large-scale dataset and conducted social network analysis. The research results revealed that the trade networks during the Jomon period were not constant; they expanded throughout the southern Kanto region during the Middle Jomon period (5,500–4,500 years cal BP) and ceased to function during the Late Jomon period (4,500–3,200 years cal BP). Furthermore, to enhance the readability and inter-pretability of the dataset, we implemented clustering using the density-based spatial clustering of applications with noise (DBSCAN) method. The results showed that in every time division of the Jomon period, the mean intra-cluster cosine similarity of each cluster was higher than the similarity between sites outside the clusters","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"262 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140730473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic background of body reserves in laying hens through backfat thickness phenotyping","authors":"N. Bedere, Joëlle Dupont, Y. Baumard, Christophe Staub, D. Gourichon, Elleboudt Frédéric, Pascale Le Roy, Tatiana Zerjal","doi":"10.24072/pcjournal.412","DOIUrl":"https://doi.org/10.24072/pcjournal.412","url":null,"abstract":"In this study, we pursued three primary objectives: firstly to test and validate the pheno-typing of backfat thickness as an indicator of the overall fatness of laying hens; secondly, to estimate genetic parameters for this trait; thirdly, to study the phenotypic and genetic relationships between this trait and other traits related to production and body composition. To address these questions, hens from two lines under divergent selection for residual feed intake, were phenotyped for body weight, body composition traits (backfat, total fat volume, and blood adipokines levels), and egg number. Linear mixed models enabled to estimate variance components and calculate","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140744060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dealing with post-excavation data: the Omeka S TiMMA web-database","authors":"Bastien Rueff","doi":"10.24072/pcjournal.366","DOIUrl":"https://doi.org/10.24072/pcjournal.366","url":null,"abstract":"This paper reports on the creation and use of a web database designed as part of the TiMMA project with the Content Management System Omeka S. Rather than resulting in a technical manual, its goal is to analyze the relevance of using Omeka S in the frame of a post-excavation project, gathering a wide team of researchers from several countries, working in their own language and having their own specialty. Designed to assist organizations and institutions in creating and managing digital collections, Omeka S offers a number of commodities from the perspective of both the administrator(s) and the users, the most significant being its efficiency in capitalizing on linked data standards for items description. Additionally, one of the successful achievements of this platform is to benefit the open-science tools more broadly, permitting for instance, as was done in this project, to import images with the iiiF API and bibliographical references with the Zotero module, thus avoiding the creation of new digital files and metadata. Designed with simplicity in mind, the graphic interface of Omeka S makes it a particularly appropriate tool for","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"10 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139602552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}