PLoS Biology最新文献

{"title":"Explosion of formulaic research articles, including inappropriate study designs and false discoveries, based on the NHANES US national health database.","authors":"Tulsi Suchak, Anietie E Aliu, Charlie Harrison, Reyer Zwiggelaar, Nophar Geifman, Matt Spick","doi":"10.1371/journal.pbio.3003152","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003152","url":null,"abstract":"<p><p>With the growth of artificial intelligence (AI)-ready datasets such as the National Health and Nutrition Examination Survey (NHANES), new opportunities for data-driven research are being created, but also generating risks of data exploitation by paper mills. In this work, we focus on two areas of potential concern for AI-supported research efforts. First, we describe the production of large numbers of formulaic single-factor analyses, relating single predictors to specific health conditions, where multifactorial approaches would be more appropriate. Employing AI-supported single-factor approaches removes context from research, fails to capture interactions, avoids false discovery correction, and is an approach that can easily be adopted by paper mills. Second, we identify risks of selective data usage, such as analyzing limited date ranges or cohort subsets without clear justification, suggestive of data dredging, and post-hoc hypothesis formation. Using a systematic literature search for single-factor analyses, we identified 341 NHANES-derived research papers published over the past decade, each proposing an association between a predictor and a health condition from the wide range contained within NHANES. We found evidence that research failed to take account of multifactorial relationships, that manuscripts did not account for the risks of false discoveries, and that researchers selectively extracted data from NHANES rather than utilizing the full range of data available. Given the explosion of AI-assisted productivity in published manuscripts (the systematic search strategy used here identified an average of 4 papers per annum from 2014 to 2021, but 190 in 2024-9 October alone), we highlight a set of best practices to address these concerns, aimed at researchers, data controllers, publishers, and peer reviewers, to encourage improved statistical practices and mitigate the risks of paper mills using AI-assisted workflows to introduce low-quality manuscripts to the scientific literature.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003152"},"PeriodicalIF":9.8,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12061153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A standardized nomenclature for the rods and cones of the vertebrate retina.","authors":"Tom Baden, Juan M Angueyra, Jenny M Bosten, Shaun P Collin, Bevil R Conway, Fabio Cortesi, Karin Dedek, Thomas Euler, Iñigo Novales Flamarique, Anna Franklin, Silke Haverkamp, Almut Kelber, Stephan C F Neuhauss, Wei Li, Robert J Lucas, Daniel C Osorio, Karthik Shekhar, Dario Tommasini, Takeshi Yoshimatsu, Joseph C Corbo","doi":"10.1371/journal.pbio.3003157","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003157","url":null,"abstract":"<p><p>Vertebrate photoreceptors have been studied for well over a century, but a fixed nomenclature for referring to orthologous cell types across diverse species has been lacking. Instead, photoreceptors have been variably-and often confusingly-named according to morphology, presence/absence of 'rhodopsin', spectral sensitivity, chromophore usage, and/or the gene family of the opsin(s) they express. Here, we propose a unified nomenclature for vertebrate rods and cones that aligns with the naming systems of other retinal cell classes and that is based on the photoreceptor type's putative evolutionary history. This classification is informed by the functional, anatomical, developmental, and molecular identities of the neuron as a whole, including the expression of deeply conserved transcription factors required for development. The proposed names will be applicable across all vertebrates and indicative of the widest possible range of properties, including their postsynaptic wiring, and hence will allude to their common and species-specific roles in vision. Furthermore, the naming system is open-ended to accommodate the future discovery of as-yet unknown photoreceptor types.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003157"},"PeriodicalIF":9.8,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Old cytokine, new tricks: A refined model of interferon's antiviral activity.","authors":"John W Schoggins","doi":"10.1371/journal.pbio.3003154","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003154","url":null,"abstract":"<p><p>Interferon is a central component of the vertebrate antiviral immune response, thought to act through induction of hundreds of interferon-stimulated genes, with some redundancy. Recent findings suggest a more refined 'limited set' model, in which distinct viruses are targeted by small subsets of the induced gene repertoire.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003154"},"PeriodicalIF":9.8,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circadian rhythms are more resilient to pacemaker neuron disruption in female Drosophila.","authors":"Aishwarya Ramakrishnan Iyer, Eva Scholz-Carlson, Evardra Bell, Grace Biondi, Shlesha Richhariya, Maria P Fernandez","doi":"10.1371/journal.pbio.3003146","DOIUrl":"10.1371/journal.pbio.3003146","url":null,"abstract":"<p><p>The circadian system regulates the timing of multiple molecular, physiological, metabolic, and behavioral phenomena. In Drosophila, as in other species, most of the research on how the timekeeping system in the brain controls the timing of behavioral outputs has been conducted in males, or sex has not been included as a biological variable. A critical set of circadian pacemaker neurons in Drosophila release the neuropeptide pigment-dispersing factor (PDF), which functions as a key output factor in the network with complex effects on other clock neurons. Lack of Pdf or its receptor, PdfR, results in most flies displaying arrhythmicity in activity-rest cycles under constant conditions. However, our results show that female circadian rhythms are less affected by mutations in both Pdf and PdfR. CRISPR-Cas9-mediated mutagenesis of Pdf, specifically in ventral lateral neurons (LNvs), also has a greater effect on male rhythms. We tested the influence of M-cells on the circadian network and showed that speeding up the molecular clock specifically in M-cells led to sexually dimorphic phenotypes, with a more pronounced effect on male rhythmic behavior. Our results suggest that the female circadian system is more resilient to manipulations of M-cells and the PDF pathway, suggesting that circadian timekeeping is more distributed across the clock neuron network in females.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003146"},"PeriodicalIF":9.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population genetics of plant fungal threats: Insights from wheat powdery mildew.","authors":"Sergio M Latorre","doi":"10.1371/journal.pbio.3003151","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003151","url":null,"abstract":"<p><p>Population genetics studies of microbial pathogens are demonstrating the potential of evolutionary theory to inform decisions that impact society. A recent study on wheat powdery mildew fungus in PLOS Biology uses genomic data to reveal the pathogen's population structure and to predict its continental-scale dispersion routes.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003151"},"PeriodicalIF":9.8,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12052113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved effectiveness of vaccination campaigns against rabies by reducing spatial heterogeneity in coverage.","authors":"Elaine A Ferguson, Ahmed Lugelo, Anna Czupryna, Danni Anderson, Felix Lankester, Lwitiko Sikana, Jonathan Dushoff, Katie Hampson","doi":"10.1371/journal.pbio.3002872","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002872","url":null,"abstract":"<p><p>Vaccination programs are the mainstay of control for many infectious diseases. Heterogeneous coverage is hypothesized to reduce vaccination program effectiveness, but this impact has not been quantified in real systems. We address this gap using fine-scale data from two decades of rabies contact tracing and dog vaccination campaigns in Serengeti district, Tanzania. We also aimed to identify drivers of the continued circulation of rabies in the district despite annual vaccination campaigns. Using generalized linear mixed models, we find that current focal (village-level) dog rabies incidence decreases with increasing recent focal vaccination coverage. However, current focal incidence depends most on recent incidence, both focally and in the wider district, consistent with high population connectivity. Removing the masking effects of prior non-focal incidence shows that, for the same average prior non-focal (wider-district) vaccination coverage, increased heterogeneity in coverage among the non-focal villages leads to increased focal incidence. These effects led to outbreaks following years when vaccination campaigns missed many villages, whereas when heterogeneity in coverage was reduced, incidence declined to low levels (<0.4 cases/1,000 dogs annually and no human deaths) and short vaccination lapses thereafter did not lead to resurgence. Through transmission-tree reconstruction, we inferred frequent incursions into the district each year (mean of 7). Inferred incursions substantially increased as a percentage of all cases in recent years, reaching 50% in 2022, suggesting regional connectivity is driving residual transmission. Overall, we empirically demonstrate how population connectivity and spatial heterogeneity in vaccination can impact disease outcomes, highlighting the importance of fine-scale monitoring in managing vaccination programs.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3002872"},"PeriodicalIF":9.8,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cadherin-16 regulates acoustic sensory gating in zebrafish through endocrine signaling.","authors":"Susannah S Schloss, Zackary Q Marshall, Nicholas J Santistevan, Stefani Gjorcheska, Amanda Stenzel, Lindsey Barske, Jessica C Nelson","doi":"10.1371/journal.pbio.3003164","DOIUrl":"10.1371/journal.pbio.3003164","url":null,"abstract":"<p><p>Sensory thresholds enable animals to regulate their behavioral responses to environmental threats. Despite the importance of sensory thresholds for animal behavior and human health, we do not yet have a full appreciation of the underlying molecular-genetic and circuit mechanisms. The larval zebrafish acoustic startle response provides a powerful system to identify molecular mechanisms underlying establishment of sensory thresholds and plasticity of thresholds through mechanisms like habituation. Using this system, we identify Cadherin-16 as a previously undescribed regulator of sensory gating. We demonstrate that Cadherin-16 regulates sensory thresholds via an endocrine organ, the corpuscle of Stannius (CS), which is essential in zebrafish for regulating Ca2+ homeostasis. We further show that Cadherin-16 regulates whole-body calcium and ultimately behavior through the hormone Stanniocalcin 1l (Stc1l), and the IGF-regulatory metalloprotease, Papp-aa. Finally, we demonstrate the importance of the CS through ablation experiments that reveal its role in promoting normal acoustic sensory gating. Together, our results uncover a previously undescribed brain non-autonomous pathway for the regulation of behavior and underscore Ca2+ homeostasis as a critical process underlying sensory gating in vivo.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003164"},"PeriodicalIF":9.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population genomics and molecular epidemiology of wheat powdery mildew in Europe.","authors":"Jigisha Jigisha, Jeanine Ly, Nikolaos Minadakis, Fabian Freund, Lukas Kunz, Urszula Piechota, Beyhan Akin, Virgilio Balmas, Roi Ben-David, Szilvia Bencze, Salim Bourras, Matteo Bozzoli, Otilia Cotuna, Gilles Couleaud, Mónika Cséplő, Paweł Czembor, Francesca Desiderio, Jost Dörnte, Antonín Dreiseitl, Angela Feechan, Agata Gadaleta, Kevin Gauthier, Angelica Giancaspro, Stefania L Giove, Alain Handley-Cornillet, Amelia Hubbard, George Karaoglanidis, Steven Kildea, Emrah Koc, Žilvinas Liatukas, Marta S Lopes, Fabio Mascher, Cathal McCabe, Thomas Miedaner, Fernando Martínez-Moreno, Charlotte F Nellist, Sylwia Okoń, Coraline Praz, Javier Sánchez-Martín, Veronica Sărăţeanu, Philipp Schulz, Nathalie Schwartz, Daniele Seghetta, Ignacio Solís Martel, Agrita Švarta, Stefanos Testempasis, Dolors Villegas, Victoria Widrig, Fabrizio Menardo","doi":"10.1371/journal.pbio.3003097","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003097","url":null,"abstract":"<p><p>Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt across two consecutive years, 2022 and 2023, and compiled a genomic dataset of 415 Bgt isolates from 22 countries in Europe and surrounding regions. We identified a single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003097"},"PeriodicalIF":9.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12047814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bacterial type three secretion system induces mechanoporation of vacuolar membranes.","authors":"Léa Swistak, Marvin Albert, Camila Valenzuela, Elif Begum Gokerkucuk, François Bontems, Stéphane Tachon, Keith T Egger, Anastasia D Gazi, Anna Sartori-Rupp, Cammie F Lesser, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Matthijn Vos, Jost Enninga","doi":"10.1371/journal.pbio.3003135","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003135","url":null,"abstract":"<p><p>Endomembrane breaching is a crucial strategy employed by intracellular pathogens enclosed within vacuoles to access the nutrient-rich cytosol for intracellular replication. While bacteria use various mechanisms to compromise host membranes, the specific processes and factors involved are often unknown. Shigella flexneri, a major human pathogen, accesses the cytosol relying on the Type Three Secretion System (T3SS) and secreted effectors. Using in-cell correlative light and electron microscopy, we tracked the sequential steps of Shigella host cell entry. Moreover, we captured the T3SS, which projects a needle from the bacterial surface, in the process of puncturing holes in the vacuolar membrane. This initial puncture ensures disruption of the vacuole. Together this introduces the concept of mechanoporation via a bacterial secretion system as a crucial process for bacterial pathogen-induced membrane damage.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003135"},"PeriodicalIF":9.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12045489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Removing facial features from structural MRI images biases visual quality assessment.","authors":"Céline Provins, Élodie Savary, Thomas Sanchez, Emeline Mullier, Jaime Barranco, Elda Fischi-Gómez, Yasser Alemán-Gómez, Jonas Richiardi, Russell A Poldrack, Patric Hagmann, Oscar Esteban","doi":"10.1371/journal.pbio.3003149","DOIUrl":"10.1371/journal.pbio.3003149","url":null,"abstract":"<p><p>A critical step before data-sharing of human neuroimaging is removing facial features to protect individuals' privacy. However, not only does this process redact identifiable information about individuals, but it also removes non-identifiable information. This introduces undesired variability into downstream analysis and interpretation. This registered report investigated the degree to which the so-called defacing altered the quality assessment of T1-weighted images of the human brain from the openly available \"IXI dataset\". The effect of defacing on manual quality assessment was investigated on a single-site subset of the dataset (N = 185). By comparing two linear mixed-effects models, we determined that four trained human raters' perception of quality was significantly influenced by defacing by modeling their ratings on the same set of images in two conditions: \"nondefaced\" (i.e., preserving facial features) and \"defaced\". In addition, we investigated these biases on automated quality assessments by applying repeated-measures, multivariate ANOVA (rm-MANOVA) on the image quality metrics extracted with MRIQC on the full IXI dataset (N = 581; three acquisition sites). This study found that defacing altered the quality assessments by humans and showed that MRIQC's quality metrics were mostly insensitive to defacing.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 4","pages":"e3003149"},"PeriodicalIF":9.8,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}