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Awards can propel academic careers. They also reflect the culture and values of the scientific community. But do awards incentivize greater transparency, inclusivity, and openness in science? Our cross-disciplinary survey of 222 awards for the "best" journal articles across all 27 SCImago subject areas revealed that journals and learned societies administering such awards generally publish little detail on their procedures and criteria. Award descriptions were brief, rarely including contact details or information on the nominations pool. Nominations of underrepresented groups were not explicitly encouraged, and concepts that align with Open Science were almost absent from the assessment criteria. At the same time, 10% of awards, especially the recently established ones, tended to use article-level impact metrics. USA-affiliated researchers dominated the winner's pool (48%), while researchers from the Global South were uncommon (11%). Sixty-one percent of individual winners were men. Overall, Best Paper awards miss the global calls for greater transparency and equitable access to academic recognition. We provide concrete and implementable recommendations for scientific awards to improve the scientific recognition system and incentives for better scientific practice., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Lagisz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

There is increasing scrutiny around how science is communicated to the public. For instance, a Twitter account @justsaysinmice (with 70.4K followers in January 2021) was created to call attention to news headlines that omit that mice, not humans, are the ones for whom the study findings apply. This is the case of many headlines reporting on Alzheimer disease (AD) research. AD is characterized by a degeneration of the human brain, loss of cognition, and behavioral changes, for which no treatment is available. Around 200 rodent models have been developed to study AD, even though AD is an exclusively human condition that does not occur naturally in other species and appears impervious to reproduction in artificial animal models, an information not always disclosed. It is not known what prompts writers of news stories to either omit or acknowledge, in the story's headlines, that the study was done in mice and not in humans. Here, we raised the hypothesis that how science is reported by scientists plays a role on the news reporting. To test this hypothesis, we investigated whether an association exists between articles' titles and news' headlines regarding the omission, or not, of mice. To this end, we analyzed a sample of 623 open-access scientific papers indexed in PubMed in 2018 and 2019 that used mice either as models or as the biological source for experimental studies in AD research. We found a significant association (p < 0.01) between articles' titles and news stories' headlines, revealing that when authors omit the species in the paper's title, writers of news stories tend to follow suit. We also found that papers not mentioning mice in their titles are more newsworthy and significantly more tweeted than papers that do. Our study shows that science reporting may affect media reporting and asks for changes in the way we report about findings obtained with animal models used to study human diseases. This study reveals that when scientists omit from the papers' title that research findings were obtained using mice, as opposed to humans, the media tend to replicate the trend by omitting the use of mice from the news stories headlines that report on these papers, thereby perpetuating the misleading omission. [ABSTRACT FROM AUTHOR]

Methods sections are often missing essential details. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included giving credit or specifying what was used (who or what citation) and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors', and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting. Methods sections often lack critical details needed to reproduce an experiment; the practice of citing previous papers instead of describing the methods in detail may contribute to this problem. An analysis of >800 papers across three fields shows that >90% of papers use at least one shortcut citation, that these significantly impair reconstruction of the original method, and that <25% of journals have policies relating to previously described methods. [ABSTRACT FROM AUTHOR]

The use of English as the common language of science represents a major impediment to maximising the contribution of non-native English speakers to science. Yet few studies have quantified the consequences of language barriers on the career development of researchers who are non-native English speakers. By surveying 908 researchers in environmental sciences, this study estimates and compares the amount of effort required to conduct scientific activities in English between researchers from different countries and, thus, different linguistic and economic backgrounds. Our survey demonstrates that non-native English speakers, especially early in their careers, spend more effort than native English speakers in conducting scientific activities, from reading and writing papers and preparing presentations in English, to disseminating research in multiple languages. Language barriers can also cause them not to attend, or give oral presentations at, international conferences conducted in English. We urge scientific communities to recognise and tackle these disadvantages to release the untapped potential of non-native English speakers in science. This study also proposes potential solutions that can be implemented today by individuals, institutions, journals, funders, and conferences. Please see the Supporting information files (S2–S6 Text) for Alternative Language Abstracts and Figs 5 and 6. This study reveals that non-native English speakers, especially early in their careers, spend more effort than native English speakers in conducting scientific activities, from reading and writing papers and preparing presentations in English, to disseminating research in multiple languages. [ABSTRACT FROM AUTHOR]

Academic journals have been publishing the results of biomedical research for more than 350 years. Reviewing their history reveals that the ways in which journals vet submissions have changed over time, culminating in the relatively recent appearance of the current peer-review process. Journal brand and Impact Factor have meanwhile become quality proxies that are widely used to filter articles and evaluate scientists in a hypercompetitive prestige economy. The Web created the potential for a more decoupled publishing system in which articles are initially disseminated by preprint servers and then undergo evaluation elsewhere. To build this future, we must first understand the roles journals currently play and consider what types of content screening and review are necessary and for which papers. A new, open ecosystem involving preprint servers, journals, independent content-vetting initiatives, and curation services could provide more multidimensional signals for papers and avoid the current conflation of trust, quality, and impact. Academia should strive to avoid the alternative scenario, however, in which stratified publisher silos lock in submissions and simply perpetuate this conflation. [ABSTRACT FROM AUTHOR]

Detailed method descriptions are essential for reproducibility, research evaluation, and effective data reuse. We summarize the key recommendations for life sciences researchers and research institutions described in the European Commission PRO-MaP report. Essential details about study methods are often missing from academic research papers in the life sciences, which can adversely affect reproducibility, undermine trust and impair researchers' ability to reuse methods and data. This Perspective article describes PRO-MaP (Promoting Reusable and Open Methods And Protocols), which aims to increase and improve the reporting of detailed, structured and open methods and reusable step-by-step protocols in the life sciences. [ABSTRACT FROM AUTHOR]

Curated scientific databases catalogue and amplify research findings to maximize their reach. Authors should write their papers with this in mind, ensuring that data are accurate, easy to extract, and presented in standardized formats. Scientific data is becoming increasingly complex, making data curation increasingly difficult. In this Perspective, a group of biocurators present some simple guidelines for data accessibility that will help to increase the reach of published studies. [ABSTRACT FROM AUTHOR]

Citation metrics are increasingly used to appraise published research. One challenge is whether and how to normalize these metrics to account for differences across scientific fields, age (year of publication), type of document, database coverage, and other factors. We discuss the pros and cons for normalizations using different approaches. Additional challenges emerge when citation metrics need to be combined across multiple papers to appraise the corpus of scientists, institutions, journals, or countries, as well as when trying to attribute credit in multiauthored papers. Different citation metrics may offer complementary insights, but one should carefully consider the assumptions that underlie their calculation. [ABSTRACT FROM AUTHOR]

Fundamental scientific advances can take decades to translate into improvements in human health. Shortening this interval would increase the rate at which scientific discoveries lead to successful treatment of human disease. One way to accomplish this would be to identify which advances in knowledge are most likely to translate into clinical research. Toward that end, we built a machine learning system that detects whether a paper is likely to be cited by a future clinical trial or guideline. Despite the noisiness of citation dynamics, as little as 2 years of postpublication data yield accurate predictions about a paper's eventual citation by a clinical article (accuracy = 84%, F1 score = 0.56; compared to 19% accuracy by chance). We found that distinct knowledge flow trajectories are linked to papers that either succeed or fail to influence clinical research. Translational progress in biomedicine can therefore be assessed and predicted in real time based on information conveyed by the scientific community's early reaction to a paper. [ABSTRACT FROM AUTHOR]

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing. [ABSTRACT FROM AUTHOR]

The Coronavirus Disease 2019 (COVID-19) pandemic has highlighted the limitations of the current scientific publication system, in which serious post-publication concerns are often addressed too slowly to be effective. In this Perspective, we offer suggestions to improve academia's willingness and ability to correct errors in an appropriate time frame. Four scientists who have identified issues in published papers struggled to get them amended or retracted; here they present evidence that these struggles are widely shared and that scientific advances are presently critically hindered. They make suggestions for academic actors that would help scientists raise concerns about submissions and improve academia's correction rate and speed. [ABSTRACT FROM AUTHOR]

Clements et al. respond to Munday's claim that his "reanalysis shows there is not an extreme decline effect in fish ocean acidification studies". They contend that extreme data reported in early studies authored by Dixson and Munday indeed result in an "extreme" decline effect in this field, and conclude that the decline effect is primarily driven by papers by particular authors. [ABSTRACT FROM AUTHOR]

The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human, animal, and environmental health. While One Health has received considerable press, its benefits remain unclear because its effects have not been quantitatively described. We systematically surveyed the published literature and used social network analysis to measure interdisciplinarity in One Health studies constructing dynamic pathogen transmission models. The number of publications fulfilling our search criteria increased by 14.6% per year, which is faster than growth rates for life sciences as a whole and for most biology subdisciplines. Surveyed publications clustered into three communities: one used by ecologists, one used by veterinarians, and a third diverse-authorship community used by population biologists, mathematicians, epidemiologists, and experts in human health. Overlap between these communities increased through time in terms of author number, diversity of co-author affiliations, and diversity of citations. However, communities continue to differ in the systems studied, questions asked, and methods employed. While the infectious disease research community has made significant progress toward integrating its participating disciplines, some segregation—especially along the veterinary/ecological research interface—remains. [ABSTRACT FROM AUTHOR]

We evaluated how the gender composition of top-cited authors within different subfields of research has evolved over time. We considered 9,071,122 authors with at least 5 full papers in Scopus as of September 1, 2022. Using a previously validated composite citation indicator, we identified the 2% top-cited authors for each of 174 science subfields (Science-Metrix classification) in 4 separate publication age cohorts (first publication pre-1992, 1992 to 2001, 2002 to 2011, and post-2011). Using NamSor, we assigned 3,784,507 authors as men and 2,011,616 as women (for 36.1% gender assignment uncertain). Men outnumbered women 1.88-fold among all authors, decreasing from 3.93-fold to 1.36-fold over time. Men outnumbered women 3.21-fold among top-cited authors, decreasing from 6.41-fold to 2.28-fold over time. In the youngest (post-2011) cohort, 32/174 (18%) subfields had > = 50% women, 97/174 (56%) subfields had > = 30% women, and 3 subfields had = <10% women among the top-cited authors. Gender imbalances in author numbers decreased sharply over time in both high-income countries (including the United States of America) and other countries, but the latter had little improvement in gender imbalances for top-cited authors. In random samples of 100 women and 100 men from the youngest (post-2011) cohort, in-depth assessment showed that most were currently (April 2023) working in academic environments. 32 women and 44 men had some faculty appointment, but only 2 women and 2 men were full professors. Our analysis shows large heterogeneity across scientific disciplines in the amelioration of gender imbalances with more prominent imbalances persisting among top-cited authors and slow promotion pathways even for the most-cited young scientists. An evaluation of the top-cited scientists across science shows a wide range in the amelioration of gender imbalances across scientific disciplines; many scientific disciplines still have fewer women among the top-cited scientists, even among the youngest age cohort. [ABSTRACT FROM AUTHOR]

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader's ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template. A systematic assessment of more than 500 articles reveals that western blot figures and methods often omit essential details. The study also provides a collection of recommendations to help scientists avoid common problems, while making their western blot figures and methods more informative, transparent and reproducible. [ABSTRACT FROM AUTHOR]

Fast-moving, competitive fields often inadvertently duplicate research. In a research environment that values being first over being robust, this results in one manuscript “scooping” ongoing research from other groups. Opportunities to demonstrate the solidity of a result through coincidental reproduction are thus lost. Here, two group leaders, one the scooper and one the scoopee, discuss their experiences under PLOS Biology’s new “complementary research” policy. In this case, submission of the second article followed publication of the first by mere days. Scooper and scoopee discuss how complementary research is good for everyone by expanding the scientific reach of studies that are overlapping but not identical, demonstrating the robustness of related results, increasing readership for both authors, and making “replication” studies cost effective by creatively using resources that have already been spent. [ABSTRACT FROM AUTHOR]

Horizontal mitochondrial transfer (HMT) has emerged as a novel phenomenon in cell biology, but it is unclear how this process of intercellular movement of mitochondria is regulated. A new study in PLOS Biology reports that ADP released by stressed cells is a signal that triggers HMT. [ABSTRACT FROM AUTHOR]

Alongside the growing concerns regarding predatory journal growth, other questionable editorial practices have gained visibility recently. Among them, we explored the usefulness of the Percentage of Papers by the Most Prolific author (PPMP) and the Gini index (level of inequality in the distribution of authorship among authors) as tools to identify journals that may show favoritism in accepting articles by specific authors. We examined whether the PPMP, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using all articles in a sample of 5,468 biomedical journals indexed in the National Library of Medicine. For articles published between 2015 and 2019, the median PPMP was 2.9%, and 5% of journal exhibited a PPMP of 10.6% or more. Among the journals with the highest PPMP or Gini index values, where a few authors were responsible for a disproportionate number of publications, a random sample was manually examined, revealing that the most prolific author was part of the editorial board in 60 cases (61%). The papers by the most prolific authors were more likely to be accepted for publication within 3 weeks of their submission. Results of analysis on a subset of articles, excluding nonresearch articles, were consistent with those of the principal analysis. In most journals, publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices. Alongside the growing concerns regarding predatory journal growth, other questionable editorial practices have gained visibility recently. This study explores the relationship between hyper-prolific authors and a journal's editorial team, finding a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. [ABSTRACT FROM AUTHOR]

Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance and posting hundreds of papers per week to preprint servers, sharing their findings with the community before embarking on the weary march through peer review. However, there are limited methods for individuals sifting through this avalanche of research to identify the preprints that are most relevant to their interests. Here, we describe , a website that indexes all preprints posted to , the largest preprint server in the life sciences, and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods. In this work, we hope to make it easier for readers to find relevant research on bioRxiv and to improve the visibility of preprints currently being read and discussed online. [ABSTRACT FROM AUTHOR]

The genetics of Parkinson's disease has been key to unravelling the PINK1-dependent mitophagy process. Here, we discuss the implications of a 2010 PLOS Biology paper that shed light on the functional importance of PINK1 in the mitophagy cascade. PINK1-dependent mitophagy is thought to be a factor in Parkinson's disease and is being investigated for therapeutic targeting. This Perspective looks back at a 2010 PLOS Biology paper that shed light on the functional importance of PINK1 in the mitophagy cascade. [ABSTRACT FROM AUTHOR]

How many species exist on Earth? Projections range from millions to trillions. A 2011 paper in PLOS Biology provided a comprehensive estimate of 9 million. How many species are there on Earth? Projections have ranged from the millions to the trillions. This Perspective looks at how a 2011 PLOS Biology study transformed this field and what is still to be done to find a definitive answer. [ABSTRACT FROM AUTHOR]

Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online. A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents. The most prevalent features that changed appear to be associated with typesetting and mentions of supporting information sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model. We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint–peer-reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint. We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer-reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish. Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape. Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review This study analyzes the full text content of the bioRxiv preprint repository, identifying field-specific patterns and changes that occur during publication, and providing a search tool that can identify the published papers that are most similar to a given bioRxiv or medRxiv preprint. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "GABAergic regulation of striatal spiny projection neurons depends upon their activity state." The correction addresses errors in Figures 3 and 4, specifically in panel E of both figures. The incorrect labeling of the inset cartoon in Figure 3E is acknowledged, and the correct labeling is provided. Additionally, in Figure 4E, the y-axis of the right panel is mislabeled and the correct labels are given. The document also provides the correct data availability statement for the paper. [Extracted from the article]

Scientific advances due to conceptual or technological innovations can be revealed by examining how research topics have evolved. But such topical evolution is difficult to uncover and quantify because of the large body of literature and the need for expert knowledge in a wide range of areas in a field. Using plant biology as an example, we used machine learning and language models to classify plant science citations into topics representing interconnected, evolving subfields. The changes in prevalence of topical records over the last 50 years reflect shifts in major research trends and recent radiation of new topics, as well as turnover of model species and vastly different plant science research trajectories among countries. Our approaches readily summarize the topical diversity and evolution of a scientific field with hundreds of thousands of relevant papers, and they can be applied broadly to other fields. Our ability to understand the progress of science through the evolution of research topics is limited by the need for specialist knowledge and the exponential growth of the literature. This study uses artificial intelligence and machine learning approaches to demonstrate how a biological field (plant science) has evolved, how the model systems have changed, and how countries differ in terms of research focus and impact. [ABSTRACT FROM AUTHOR]

Citation metrics are widely used and misused. We have created a publicly available database of 100,000 top scientists that provides standardized information on citations, h-index, coauthorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator. Separate data are shown for career-long and single-year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and 176 subfields. Field- and subfield-specific percentiles are also provided for all scientists who have published at least five papers. Career-long data are updated to end of 2017 and to end of 2018 for comparison. [ABSTRACT FROM AUTHOR]

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software. [ABSTRACT FROM AUTHOR]

Cells from most eukaryotic species make several different types of small interfering RNAs. Pioneering work in plants, published in PLOS Biology almost 20 years ago, established a framework to understand how multiple RNA interference pathways can regulate the genome in parallel. This Perspective looks back at a classic PLOS Biology paper that provided an early glimpse of the complexity of RNAi pathways in plants and how it acted as a springboard for further exploration of this extravagant universe. [ABSTRACT FROM AUTHOR]

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors. Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? This Essay reveals that every fifth published metagenome is not available to science, and asks whether data accessibility should be considered a mandatory component of manuscript submission. [ABSTRACT FROM AUTHOR]

Women comprise a minority of the Science, Technology, Engineering, Mathematics, and Medicine (STEMM) workforce. Quantifying the gender gap may identify fields that will not reach parity without intervention, reveal underappreciated biases, and inform benchmarks for gender balance among conference speakers, editors, and hiring committees. Using the PubMed and arXiv databases, we estimated the gender of 36 million authors from >100 countries publishing in >6000 journals, covering most STEMM disciplines over the last 15 years, and made a web app allowing easy access to the data (). Despite recent progress, the gender gap appears likely to persist for generations, particularly in surgery, computer science, physics, and maths. The gap is especially large in authorship positions associated with seniority, and prestigious journals have fewer women authors. Additionally, we estimate that men are invited by journals to submit papers at approximately double the rate of women. Wealthy countries, notably Japan, Germany, and Switzerland, had fewer women authors than poorer ones. We conclude that the STEMM gender gap will not close without further reforms in education, mentoring, and academic publishing. [ABSTRACT FROM AUTHOR]

The letter responds to a previous paper and discusses the inclusion of both sexes in scientific studies. The authors argue that, unless there is evidence to the contrary, it is reasonable to assume equal variance between sexes and proceed with a standard sample size. They refute the claim that heteroscedasticity (unequal variance) between sexes is the norm, citing studies that support the assumption of homoscedasticity (equal variance). The authors emphasize the importance of adapting statistical analysis and power calculations if evidence of sex-related heteroscedasticity emerges. [Extracted from the article]

A major challenge in brain organoid technologies is the lack of vasculature. In recent years, innovative approaches have been taken to meet this challenge. A 2020 paper published in PLOS Biology exemplifies the approaches used in this booming field. The development of brain organoids has been a boon to neurological research, but working out how to add blood vessels to organoids has posed a challenge. This Perspective looks at innovative approaches to brain organoid vascularization, including those put forward in a 2020 PLOS Biology paper. [ABSTRACT FROM AUTHOR]

Despite their recognized limitations, bibliometric assessments of scientific productivity have been widely adopted. We describe here an improved method to quantify the influence of a research article by making novel use of its co-citation network to field-normalize the number of citations it has received. Article citation rates are divided by an expected citation rate that is derived from performance of articles in the same field and benchmarked to a peer comparison group. The resulting Relative Citation Ratio is article level and field independent and provides an alternative to the invalid practice of using journal impact factors to identify influential papers. To illustrate one application of our method, we analyzed 88,835 articles published between 2003 and 2010 and found that the National Institutes of Health awardees who authored those papers occupy relatively stable positions of influence across all disciplines. We demonstrate that the values generated by this method strongly correlate with the opinions of subject matter experts in biomedical research and suggest that the same approach should be generally applicable to articles published in all areas of science. A beta version of iCite, our web tool for calculating Relative Citation Ratios of articles listed in PubMed, is available at . [ABSTRACT FROM AUTHOR]

This Editorial describes PLOS Biology's experiment with contextualised publication, whereby potentially controversial studies are published with an Editor’s Note and an accompanying Primer in which the Academic Editor guides the reader, dissects the study, and lays out the thinking behind the decision to publish. [ABSTRACT FROM AUTHOR]

Amid the Coronavirus Disease 2019 (COVID-19) pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press, and policymakers for the first time. This phenomenon has sharpened long-standing questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record? We assessed preprints from bioRxiv and medRxiv that had been posted and subsequently published in a journal through April 30, 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version. We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 7.2% of non-COVID-19–related and 17.2% of COVID-19–related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not qualitatively change the conclusions of the paper. During the COVID-19 pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, but can we trust them? This study reveals that the majority of preprints published within the first 4 months of the pandemic are comparable to their published version. [ABSTRACT FROM AUTHOR]

Observer bias and other “experimenter effects” occur when researchers’ expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work “blind,” meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence that blind protocols are uncommon in the life sciences and that nonblind studies tend to report higher effect sizes and more significant p-values. We discuss methods to minimize bias and urge researchers, editors, and peer reviewers to keep blind protocols in mind. [ABSTRACT FROM AUTHOR]

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries. [ABSTRACT FROM AUTHOR]

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges. Please see the Supporting information files for Alternative Language Abstracts. A survey of 419,680 peer-reviewed papers in 16 languages reveals that non-English-language studies can expand geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence on the effectiveness of biodiversity conservation interventions, especially in biodiverse regions. [ABSTRACT FROM AUTHOR]

Many fields face an increasing prevalence of multi-authorship, and this poses challenges in assessing citation metrics. Here, we explore multiple citation indicators that address total impact (number of citations, Hirsch H index [H]), co-authorship adjustment (Schreiber Hm index [Hm]), and author order (total citations to papers as single; single or first; or single, first, or last author). We demonstrate the correlation patterns between these indicators across 84,116 scientists (those among the top 30,000 for impact in a single year [2013] in at least one of these indicators) and separately across 12 scientific fields. Correlation patterns vary across these 12 fields. In physics, total citations are highly negatively correlated with indicators of co-authorship adjustment and of author order, while in other sciences the negative correlation is seen only for total citation impact and citations to papers as single author. We propose a composite score that sums standardized values of these six log-transformed indicators. Of the 1,000 top-ranked scientists with the composite score, only 322 are in the top 1,000 based on total citations. Many Nobel laureates and other extremely influential scientists rank among the top-1,000 with the composite indicator, but would rank much lower based on total citations. Conversely, many of the top 1,000 authors on total citations have had no single/first/last-authored cited paper. More Nobel laureates of 2011–2015 are among the top authors when authors are ranked by the composite score than by total citations, H index, or Hm index; 40/47 of these laureates are among the top 30,000 by at least one of the six indicators. We also explore the sensitivity of indicators to self-citation and alphabetic ordering of authors in papers across different scientific fields. Multiple indicators and their composite may give a more comprehensive picture of impact, although no citation indicator, single or composite, can be expected to select all the best scientists. [ABSTRACT FROM AUTHOR]

In 2024, all biology is computational biology. Computer-aided analysis continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities for discovery. It is currently much easier to find guidance for implementing these techniques than for reporting their use, leaving biologists to guess which details and files are relevant. In this essay, we review existing literature on the topic, summarize common tips, and link to additional resources for training. Following this overview, we then provide a set of recommendations for sharing code, with an eye toward guiding those who are comparatively new to applying open science principles to their computational work. Taken together, we provide a guide for biologists who seek to follow code sharing best practices but are unsure where to start. For those who want to share their code but don't know where to start, this Essay distils dozens of articles on reproducibility and research software, collecting the most important practical details of how to provide computational transparency even if you aren't a trained software developer. [ABSTRACT FROM AUTHOR]

The band 3 transporter is a critical integral membrane protein of the red blood cell (RBC), as it is responsible for catalyzing the exchange of bicarbonate and chloride anions across the plasma membrane. To elucidate the structural mechanism of the band 3 transporter, detergent solubilized human ghost membrane reconstituted in nanodiscs was applied to a cryo-EM holey carbon grid to define its composition. With this approach, we identified and determined structural information of the human band 3 transporter. Here, we present 5 different cryo-EM structures of the transmembrane domain of dimeric band 3, either alone or bound with chloride or bicarbonate. Interestingly, we observed that human band 3 can form both symmetric and asymmetric dimers with a different combination of outward-facing (OF) and inward-facing (IF) states. These structures also allow us to obtain the first model of a human band 3 molecule at the IF conformation. Based on the structural data of these dimers, we propose a model of ion transport that is in favor of the elevator-type mechanism. Previous studies have solved the high-resolution structures of the dimeric band 3 transporter, but the ion transport mechanism has not yet been fully elucidated. This study solves several cryo-EM structures of band 3 in different conformations indicating that the ion transport mechanism involves the concerted movement of chloride and bicarbonate ions. [ABSTRACT FROM AUTHOR]

A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann's rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a phylogenomic dataset from a single lineage with worldwide distribution, we found that body size (cell volume) was strongly correlated with genome size, which varied by 50-fold across species and was driven by differences in the amount of repetitive DNA. However, directional models identified temperature and genome size, not cell size, as having the greatest influence on maximum population growth rate. A global metabarcoding dataset further identified genome size as a strong predictor of species abundance in the ocean, but only in colder regions at high and low latitudes where diatoms with large genomes dominated, a pattern consistent with Bergmann's rule. Although species abundances are shaped by myriad interacting abiotic and biotic factors, genome size alone was a remarkably strong predictor of abundance. Taken together, these results highlight the cascading cellular and ecological consequences of macroevolutionary changes in an emergent trait, genome size, one of the most fundamental and irreducible properties of an organism. Body size is a fundamental predictor of organismal abundance, and larger-bodied organisms predominate in colder areas ("Bergmann's rule"). This study of diatoms reveals that in these unicellular organisms, genome size, rather than cell size, is a strong predictor of species abundance in the polar oceans. [ABSTRACT FROM AUTHOR]

In a new PLOS Biology paper, de Oliveira Caetano and colleagues presented an innovative method to estimate extinction risk in reptile species worldwide. The method shows a promising avenue to support Red List assessment, alongside some well-known challenges. This Primer explores the implications of a new PLOS Biology study that presents an innovative method for estimating extinction risk in reptile species worldwide; this method represents a promising avenue to support Red List assessment, alongside some well-known challenges. [ABSTRACT FROM AUTHOR]

The reproducibility crisis triggered worldwide initiatives to improve rigor, reproducibility, and transparency in biomedical research. There are many examples of scientists, journals, and funding agencies adopting responsible research practices. The QUEST (Quality-Ethics-Open Science-Translation) Center offers a unique opportunity to examine the role of institutions. The Berlin Institute of Health founded QUEST to increase the likelihood that research conducted at this large academic medical center would be trustworthy, useful for scientists and society, and ethical. QUEST researchers perform "science of science" studies to understand problems with standard practices and develop targeted solutions. The staff work with institutional leadership and local scientists to incentivize and support responsible practices in research, funding, and hiring. Some activities described in this paper focus on the institution, whereas others may benefit the national and international scientific community. Our experience, approaches, and recommendations will be informative for faculty leadership, administrators, and researchers interested in improving scientific practice. This Community Page article describes an ongoing large-scale structured initiative at the Berlin Institute of Health which aims at improving the robustness, reproducibility and transparency of research in an academic biomedical setting. [ABSTRACT FROM AUTHOR]

Scientists, public servants, and patient advocates alike increasingly question the validity of published scientific results, endangering the public’s acceptance of science. Here, I argue that emerging flaws in the integrity of the peer review system are largely responsible. Distortions in peer review are driven by economic forces and enabled by a lack of accountability of journals, editors, and authors. One approach to restoring trust in the validity of published results may be to establish basic rules that render peer review more transparent, such as publishing the reviews (a practice already embraced by some journals) and monitoring not only the track records of authors but also of editors and journals. [ABSTRACT FROM AUTHOR]

There is an ongoing debate about the value of animal experiments to inform medical practice, yet there are limited data on how well therapies developed in animal studies translate to humans. We aimed to assess 2 measures of translation across various biomedical fields: (1) The proportion of therapies which transition from animal studies to human application, including involved timeframes; and (2) the consistency between animal and human study results. Thus, we conducted an umbrella review, including English systematic reviews that evaluated the translation of therapies from animals to humans. Medline, Embase, and Web of Science Core Collection were searched from inception until August 1, 2023. We assessed the proportion of therapeutic interventions advancing to any human study, a randomized controlled trial (RCT), and regulatory approval. We meta-analyzed the concordance between animal and human studies. The risk of bias was probed using a 10-item checklist for systematic reviews. We included 122 articles, describing 54 distinct human diseases and 367 therapeutic interventions. Neurological diseases were the focus of 32% of reviews. The overall proportion of therapies progressing from animal studies was 50% to human studies, 40% to RCTs, and 5% to regulatory approval. Notably, our meta-analysis showed an 86% concordance between positive results in animal and clinical studies. The median transition times from animal studies were 5, 7, and 10 years to reach any human study, an RCT, and regulatory approval, respectively. We conclude that, contrary to widespread assertions, the rate of successful animal-to-human translation may be higher than previously reported. Nonetheless, the low rate of final approval indicates potential deficiencies in the design of both animal studies and early clinical trials. To ameliorate the efficacy of translating therapies from bench to bedside, we advocate for enhanced study design robustness and the reinforcement of generalizability. Based on the analysis of 376 therapies in 54 human diseases, this study shows that, contrary to widespread assertions, the proportion of successful animal-to-human translation may be higher than anticipated; however, the low rate of final regulatory approval indicates potential design flaws of both animal studies and early clinical trials. [ABSTRACT FROM AUTHOR]

The primate brain has unique anatomical characteristics, which translate into advanced cognitive, sensory, and motor abilities. Thus, it is important that we gain insight on its structure to provide a solid basis for models that will clarify function. Here, we report on the implementation and features of the Brain/MINDS Marmoset Connectivity Resource (BMCR), a new open-access platform that provides access to high-resolution anterograde neuronal tracer data in the marmoset brain, integrated to retrograde tracer and tractography data. Unlike other existing image explorers, the BMCR allows visualization of data from different individuals and modalities in a common reference space. This feature, allied to an unprecedented high resolution, enables analyses of features such as reciprocity, directionality, and spatial segregation of connections. The present release of the BMCR focuses on the prefrontal cortex (PFC), a uniquely developed region of the primate brain that is linked to advanced cognition, including the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset. Moreover, the inclusion of tractography data from diffusion MRI allows systematic analyses of this noninvasive modality against gold-standard cellular connectivity data, enabling detection of false positives and negatives, which provide a basis for future development of tractography. This paper introduces the BMCR image preprocessing pipeline and resources, which include new tools for exploring and reviewing the data. This study presents the Brain/MINDS Marmoset Connectivity Resource, which allows the unique visualization of high-resolution marmoset brain data from multiple individuals and modalities in a common reference space, enabling in-depth analyses of connectivity patterns such as reciprocity, directionality and spatial segregation. [ABSTRACT FROM AUTHOR]

While the malaria parasite Plasmodium falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell–infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical P. falciparum transmission bottleneck. Merozoite surface proteins expressed by the malaria parasite Plasmodium falciparum on the surface of human red-blood-cell-infecting merozoites possess exactly two deeply-diverged lineages that have seemingly not recombined. The evolutionary origin of this phenomenon remains unknown but genomic analysis of DBLMSP and DBLMSP2 reveals the answer to this long-standing puzzle. [ABSTRACT FROM AUTHOR]

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. This Consensus View issues a call to action to accelerate the growing momentum of preprint sharing and provides recommendations to empower researchers to provide open and constructive peer review for preprints. [ABSTRACT FROM AUTHOR]

Biodiversity appears to strongly suppress pathogens and pests in many plant and animal systems. However, this "dilution effect" is not consistently detected, and when present can vary strikingly in magnitude. Here, we use forest inventory data from over 25,000 plots (>1.1 million sampled trees) to quantify the strength of the dilution effect on dozens of forest pests and clarify why some pests are particularly sensitive to biodiversity. Using Bayesian hierarchical models, we show that pest prevalence is frequently lower in highly diverse forests, but there is considerable variability in the magnitude of this dilution effect among pests. The strength of dilution was not closely associated with host specialization or pest nativity. Instead, pest prevalence was lower in forests where co-occurring tree species were more distantly related to a pest's preferred hosts. Our analyses indicate that host evolutionary history and forest composition are key to understanding how species diversity may dilute the impacts of tree pests, with important implications for predicting how future biodiversity change may affect the spread and distribution of damaging forest pests. Biodiversity appears to strongly suppress pathogens and pests in many plant and animal systems, but this 'dilution effect' can vary strikingly in magnitude. This study uses forest inventory data from over 25,000 plots to show that the prevalence of tree pests is jointly controlled by the diversity and phylogenetic composition of forests. [ABSTRACT FROM AUTHOR]

Mosquitoes of the Culex pipiens complex are worldwide vectors of arbovirus, filarial nematodes, and avian malaria agents. In these hosts, the endosymbiotic bacteria Wolbachia induce cytoplasmic incompatibility (CI), i.e., reduced embryo viability in so-called incompatible crosses. Wolbachia infecting Culex pipiens (wPip) cause CI patterns of unparalleled complexity, associated with the amplification and diversification of cidA and cidB genes, with up to 6 different gene copies described in a single wPip genome. In wPip, CI is thought to function as a toxin-antidote (TA) system where compatibility relies on having the right antidotes (CidA) in the female to bind and neutralize the male's toxins (CidB). By repeating crosses between Culex isofemale lines over a 17 years period, we documented the emergence of a new compatibility type in real time and linked it to a change in cid genes genotype. We showed that loss of specific cidA gene copies in some wPip genomes results in a loss of compatibility. More precisely, we found that this lost antidote had an original sequence at its binding interface, corresponding to the original sequence at the toxin's binding interface. We showed that these original cid variants are recombinant, supporting a role for recombination rather than point mutations in rapid CI evolution. These results strongly support the TA model in natura, adding to all previous data acquired with transgenes expression. Long-term maintenance of Culex mosquito laboratory lines allowed this study to witness the emergence of novel cytoplasmic incompatibility patterns, showing that they arose from rapid evolution of Wolbachia genomes through gene loss and recombination. [ABSTRACT FROM AUTHOR]