Peer community journal最新文献

{"title":"General encoding of canonical k-mers","authors":"Roland Wittler","doi":"10.24072/pcjournal.323","DOIUrl":"https://doi.org/10.24072/pcjournal.323","url":null,"abstract":"To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308887","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":"Combining several indicators to assess the effectiveness of tailor-made health plans in pig farms","authors":"Pierre Levallois, Mily Leblanc-Maridor, Annalisa Scollo, Paolo Ferrari, Catherine Belloc, Christine Fourichon","doi":"10.24072/pcjournal.318","DOIUrl":"https://doi.org/10.24072/pcjournal.318","url":null,"abstract":"A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective ( > 50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance ( > 50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136312831","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":"Provision of essential resources as a persistence strategy in food webs","authors":"Michael Raatz","doi":"10.24072/pcjournal.315","DOIUrl":"https://doi.org/10.24072/pcjournal.315","url":null,"abstract":"Pairwise interactions in food webs, including those between predator and prey are often modulated by a third species. Such higher-order interactions are important structural components of natural food webs that can increase the stability of communities against perturbations and ensure continued ecosystem functioning. Particularly the flux of rare organic and inorganic compounds that are essential to species in the community can create higher-order interactions. Even though many such compounds exist, their effect on structuring communities is little understood. In this study, I perform invasion analyses on a general food web model that depicts apparent and exploitative competition. Introducing the provision of essential resources by a prey species to either its competitor or its predator as a higher-order interaction, I find that this mechanism can ensure the focal prey’s persistence. Larger dietary essentiality, i.e. a stronger dependence of the predator or the competitor on the essential resource can increase the invasion growth rate of the focal prey to positive values, thus promoting its persistence when it would go extinct for low essentiality. This research shows that essential resources and the higher-order interactions created by them should be considered in community ecology.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135827574","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":"Life Thinning and Gaming Disorder: A Longitudinal Qualitative Registered Report","authors":"Veli-Matti Karhulahti, Miia Siutila, Jukka Vahlo, Raine Koskimaa","doi":"10.24072/pcjournal.313","DOIUrl":"https://doi.org/10.24072/pcjournal.313","url":null,"abstract":"The academic debates regarding the psychiatric relevance of gaming disorder continue largely because the lived experiences of treatment-seekers remain mostly unstudied. This registered report addresses the above research gap with a longitudinal design that pursues a comparative descriptive understanding of how intensive gaming experiences evolve in both clinical and non-clinical life situations. Accompanied by a rich health survey, interpretative phenomenological analysis was adapted to understand in-depth interview data from treatment-seeking (n=5) and esports-playing (n=4) participants, the latter of which did not experience any gaming-related health problems. The interviews were carried out as a 1-year follow-up. The study finds intensive relationships with gaming to be experienced through","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135884194","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":"The distribution, phenology, host range and pathogen prevalence of Ixodes ricinus in France: a systematic map and narrative review","authors":"Grégoire Perez, Laure Bournez, Nathalie Boulanger, Johanna Fite, Barbara Livoreil, Karen D. McCoy, Elsa Quillery, Magalie René-Martellet, Sarah I. Bonnet","doi":"10.24072/pcjournal.291","DOIUrl":"https://doi.org/10.24072/pcjournal.291","url":null,"abstract":"The tick Ixodes ricinus is the most important vector species of infectious diseases in European France. Understanding its distribution, phenology, and host species use, along with the distribution and prevalence of associated pathogens at a national scale is essential for developing prevention strategies. The aim of this paper is to provide a systematic map and narrative review of the existing knowledge on the eco-epidemiology of I. ricinus in France. Using literature published up to 2020, the present paper provides a distribution map for the species and a summary of environmental factors explaining observed geographical differences in phenology and temporal differences in abundance. The diversity of vertebrate host species used by this tick, along with their degree of infestation when available, are presented and discussed with respect to their potential contribution to the population dynamics of I. ricinus and the circulation of tick-borne zoonotic pathogens. Prevalence data of detected pathogens are summarised in different maps. Results from 187 identified references show that the species is present in most departments, but scarce under Mediterranean climates and in coastal habitats. Its phenology is generally bimodal with climate-associated variations. Abundance seems positively influenced by forest cover and host abundance. Rodents and ruminants are the most studied species groups, but the diversity of sampling protocols (e.g., location, season, exhaustivity of inspection) precluded direct comparisons between groups. Data on pathogens are patchy, with most studies conducted near research laboratories. Among pathogens, Borrelia burgdorferi sensu lato is the most examined and seems most prevalent in north-eastern and central France. The review highlights the gaps in our knowledge of tick-host-pathogen interactions, their ecologies and their distributions, and demonstrates the need to address these gaps in order to optimize tick and tick-borne diseases prevention and control.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136362808","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":"Geometric morphometric analysis of projectile points from the Southwest United States","authors":"Robert J. Bischoff","doi":"10.24072/pcjournal.312","DOIUrl":"https://doi.org/10.24072/pcjournal.312","url":null,"abstract":"Traditional analyses of projectile points often use visual identification, the presence or absence of discrete characteristics, or linear measurements and angles to classify points into distinct types. Geometric morphometrics provides additional tools for analyzing, visualizing","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45251079","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":"Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii","authors":"Mathieu Gautier","doi":"10.24072/pcjournal.309","DOIUrl":"https://doi.org/10.24072/pcjournal.309","url":null,"abstract":"Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136355055","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":"Modelling the growth stress in tree branches: eccentric growth vs. reaction wood","authors":"Arnoul Van Rooij, É. Badel, J. Barczi, Y. Caraglio, T. Alméras, J. Gril","doi":"10.24072/pcjournal.308","DOIUrl":"https://doi.org/10.24072/pcjournal.308","url":null,"abstract":"9 This work aims to model the mechanical processes used by tree branches to control their posture despite 10 their increasing weight loading. The two known options for a branch to maintain its orientation are the 11 asymmetry of maturation stress, including reaction wood formation, and eccentric radial growth. Both 12 options can be observed in nature and influence the stress distribution developed in the branch each 13 year. This so-called \"growth stress\" reflects the mechanical state of the branch. In this work, a growth 14 stress model was developed at the cross-section level in order to quantify and study the bio-mechanical 15 impact of each process. For illustration, this model was applied to branches of two 50-year-old trees, 16 one softwood Pinus pinaster and one hardwood Prunus avium (wild cherry tree), both simulated with 17 the AmapSim discrete element software. For the wild cherry tree, the computed ouputs enlightened that 18 the eccentricity of radial growth seems to be as efficient as the formation of reaction wood to maintain 19 the postural control despite the increasing gravity. err The computed outputs enlightened that, for both 20 Prunus avium and Pinus pinaster , eccentric radial growth appears less efficient than the formation of 21 reaction wood to counter the increasing gravity stress applied to the branch. err For the pine tree, eccentric 22 radial growth appears to be less efficient than the formation of reaction wood err . But although eccentric 23 growth err it err does not necessarily act as a relevant lever for postural control, it greatly modifies the","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44762174","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":"Comparing habit-behaviour relationships for organised versus leisure time physical activity.","authors":"Katerina Newman, Cyril Forestier, Boris Cheval, Zachary Zenko, Margaux de Chanaleilles, Benjamin Gardner, Amanda L Rebar","doi":"10.24072/pcjournal.311","DOIUrl":"10.24072/pcjournal.311","url":null,"abstract":"<p><p>Evidence shows that people with strong physical activity habits tend to engage in more physical activity than those with weaker habits, but little is known about how habit influences specific types of physical activity. This study aimed to test whether mean level of habit strength and magnitude of the habit strength - behaviour association differed as a function of physical activity modality. Participants (N = 120; M age = 25 years, 75% female) who reported engaging in organised sport separately reported their habit strength for organised sport and leisure time physical activity as well as the time they spent engaging in these physical activity behaviours. Means comparisons and multilevel modelling revealed that people had significantly stronger habit for organised sport than for leisure time physical activity. Crucially, no significant difference was found in the magnitude of the sport-habit and leisure-habit link. Post-hoc analyses revealed that habit was stronger for team sport compared to individual sport, but that there was no significant difference in sport-habit association between team and individual sports. Research should therefore focus on identifying the characteristics of team sports-based activity that are particularly conducive to habit formation as a precursor to developing interventions to promote performance of leisure time activity in a way that would attain such characteristics.</p>","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45648624","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":"A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence","authors":"Mélanie Hennart, Chiara Crestani, Sébastien Bridel, Nathalie Armatys, Sylvie Brémont, Annick Carmi-Leroy, Annie Landier, Virginie Passet, Laure Fonteneau, Sophie Vaux, Julie Toubiana, Edgar Badell, Sylvain Brisse","doi":"10.24072/pcjournal.307","DOIUrl":"https://doi.org/10.24072/pcjournal.307","url":null,"abstract":"Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135890669","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}