bims-skolko Biomed News
on Scholarly communication
Issue of 2025–02–02
33 papers selected by
Thomas Krichel, Open Library Society



  1. PLoS Biol. 2025 Jan;23(1): e3002999
      Retractions are becoming increasingly common but still account for a small minority of published papers. It would be useful to generate databases where the presence of retractions can be linked to impact metrics of each scientist. We have thus incorporated retraction data in an updated Scopus-based database of highly cited scientists (top 2% in each scientific subfield according to a composite citation indicator). Using data from the Retraction Watch database (RWDB), retraction records were linked to Scopus citation data. Of 55,237 items in RWDB as of August 15, 2024, we excluded non-retractions, retractions clearly not due to any author error, retractions where the paper had been republished, and items not linkable to Scopus records. Eventually, 39,468 eligible retractions were linked to Scopus. Among 217,097 top-cited scientists in career-long impact and 223,152 in single recent year (2023) impact, 7,083 (3.3%) and 8,747 (4.0%), respectively, had at least 1 retraction. Scientists with retracted publications had younger publication age, higher self-citation rates, and larger publication volume than those without any retracted publications. Retractions were more common in the life sciences and rare or nonexistent in several other disciplines. In several developing countries, very high proportions of top-cited scientists had retractions (highest in Senegal (66.7%), Ecuador (28.6%), and Pakistan (27.8%) in career-long citation impact lists). Variability in retraction rates across fields and countries suggests differences in research practices, scrutiny, and ease of retraction. Addition of retraction data enhances the granularity of top-cited scientists' profiles, aiding in responsible research evaluation. However, caution is needed when interpreting retractions, as they do not always signify misconduct; further analysis on a case-by-case basis is essential. The database should hopefully provide a resource for meta-research and deeper insights into scientific practices.
    DOI:  https://doi.org/10.1371/journal.pbio.3002999
  2. PLoS One. 2025 ;20(1): e0309274
      This study sheds light on how journalists respond to evolving debates within academia around topics including research integrity, improper use of metrics to measure research quality and impact, and the risks and benefits of the open science movement. It does so through a codebook thematic analysis of semi-structured interviews with 19 health and science journalists from the Global North. We find that journalists' perceptions of these academic controversies vary widely, with some displaying a highly critical and nuanced understanding and others presenting a more limited awareness. Those with a more in-depth understanding report closely scrutinizing the research they report, carefully vetting the study design, methodology, and analyses. Those with a more limited awareness are more trusting of the peer review system as a quality control system and more willing to rely on researchers when determining what research to report on and how to vet and frame it. While some of these perceptions and practices may support high-quality media coverage of science, others have the potential to compromise journalists' ability to serve the public interest. Results provide some of the first insights into the nature and potential implications of journalists' internalization of the logics of science.
    DOI:  https://doi.org/10.1371/journal.pone.0309274
  3. Proc Biol Sci. 2025 Jan;292(2039): 20241487
      Publishing preprints is quickly becoming commonplace in ecology and evolutionary biology. Preprints can facilitate the rapid sharing of scientific knowledge establishing precedence and enabling feedback from the research community before peer review. Yet, significant barriers to preprint use exist, including language barriers, a lack of understanding about the benefits of preprints and a lack of diversity in the types of research outputs accepted (e.g. reports). Community-driven preprint initiatives can allow a research community to come together to break down these barriers to improve equity and coverage of global knowledge. Here, we explore the first preprints uploaded to EcoEvoRxiv (n = 1216), a community-driven preprint server for ecologists and evolutionary biologists, to characterize preprint use in ecology, evolution and conservation. Our perspective piece highlights some of the unique initiatives that EcoEvoRxiv has taken to break down barriers to scientific publishing by exploring the composition of articles, how gender and career stage influence preprint use, whether preprints are associated with greater open science practices (e.g. code and data sharing) and tracking preprint publication outcomes. Our analysis identifies areas that we still need to improve upon but highlights how community-driven initiatives, such as EcoEvoRxiv, can play a crucial role in shaping publishing practices in biology.
    Keywords:  EcoEvoRxiv; ecology; evolution; grey literature; preprints; publication; scholarly publishing
    DOI:  https://doi.org/10.1098/rspb.2024.1487
  4. iScience. 2025 Jan 17. 28(1): 111676
      Science is based on ideas that might be true or false in describing reality. In order to discern between these two, scientists conduct studies that can reveal evidence for an idea, i.e., positive findings, or not, i.e., negative or null findings. The outcome of these studies can either be true, i.e., reflecting the real world, or false. Much has been said about disentangling true from false positive findings and the danger of a publication bias toward positive findings. Here, we argue that publishing negative findings is important to provide an accurate picture of the real world. At the same time, we highlight that a cautious approach should be taken to minimize the impact of publishing false negative findings, which has received limited attention so far. We discuss sources of false negative findings, using experimental and observational animal behavior and cognition studies as examples, which often differ from those of false positive findings. We conclude by recommending strategies for rigorous studies, such as conducting positive controls, selecting diverse samples, designing engaging protocols, and clearly labeling negative findings. These practices will lead to studies that contribute to our knowledge, regardless of whether they result in positive or negative findings.
    Keywords:  Biological sciences; Biological sciences research methodologies; Health sciences; Interdisciplinary application studies; Medicine; Methodology in biological sciences; Natural sciences
    DOI:  https://doi.org/10.1016/j.isci.2024.111676
  5. Int J Gynaecol Obstet. 2025 Jan 31.
      The number of retractions of randomized clinical trials (RCTs) following post-publication allegations of misconduct is increasing. To address this issue, we aimed to establish an international multistakeholder consensus on post-publication integrity concerns related to RCTs. After prospective registration (https://osf.io/njksm), we assembled a multidisciplinary stakeholder group comprising 48 participants from 18 countries across six continents, recruited using a curated list of journal editors and snowballing. An underpinning evidence synthesis collated 89 articles related to post-publication integrity concerns. Integrity statements related to RCTs created were subjected to anonymized two-round Delphi survey. A hybrid face-to-face-online consensus development meeting was convened to consolidate the consensus. The response rates of the two Delphi survey rounds were 65% (31/48) and 67% (32/ 48), respectively. There were 101 and 41 statements in the first and second Delphi rounds, respectively. After the two Delphi rounds and the consensus development meeting, consensus was achieved on 104 statements consolidated to 84 after merging, editing, and removing duplicates. This set of statements included general aspects (n = 9), journal instructions (n = 14), editorial and peer review (n = 7), correspondence and complaints (n = 4), investigations for integrity concerns (n = 16), decisions and sanctions (n = 9), critical appraisal guidance (n = 1), systematic reviews of RCTs (n = 8), and research recommendations (n = 16). In conclusion, this international multistakeholder consensus statement aimed to underpin policies for preventing post-publication integrity concerns in RCT publications and assist in improving investigations of misconduct allegations.
    Keywords:  post‐publication; randomized clinical trial; research integrity
    DOI:  https://doi.org/10.1002/ijgo.16118
  6. Med J Armed Forces India. 2025 Jan-Feb;81(1):81(1): 32-38
       Background: An increasing number of retractions have been published in the recent past which may be conforming to the large number publications being added on a daily basis. Concerns have been flagged time and again regarding comprehensiveness and utility of retraction notices.
    Methods: Retraction notices published in PubMed in Jan 23 were analyzed for journal, publisher, article, country affiliation of authors, month of publication, who raised concern, main and additional reason for retraction, completeness of retraction notice, editors/authors requesting for retraction, agreement between authors and editors, and the number of citations received.
    Results: A total of 295 retraction notices published in PubMed in Jan 2023 by 110 journals (which included 24 publishers and 9 standalone journals) were analyzed. Sixty-four percent of journals published single retraction notice. The highest number of retractions by a single journal was 70. Only 31% of retraction notices gave complete details. Editors requested for retraction in 88% cases. Eighty-four percent of the articles received at least one citation. In 71% of cases, it is not known who raised the concern. Reasons for retraction were compromised peer review (37%), plagiarism (20%), image manipulation (13%), data reliability (8%), authorship dispute (6%), methodology issues (4%), and so on. Twenty-seven percent of cases had more than one reason. Plagiarism of figures constituted 84% of total plagiarism cases. Fifty-eight of 59 plagiarism cases were described indirectly despite clear evidence. Authors and editors agreed for retraction in 25% of cases, and no information was available in 36% cases.
    Conclusion: A substantial number of retraction notices are incomplete, vague, and euphemistic. Plagiarism of figures/images is an emerging threat.
    Keywords:  Characteristics; Euphemism; Retraction notices; Scientific publications
    DOI:  https://doi.org/10.1016/j.mjafi.2023.07.005
  7. Gac Sanit. 2025 Jan 25. pii: S0213-9111(24)00104-3. [Epub ahead of print]39 102446
    Gaceta Sanitaria Editorial Board
      
    DOI:  https://doi.org/10.1016/j.gaceta.2024.102446
  8. Proc Natl Acad Sci U S A. 2025 Feb 04. 122(5): e2401231121
      For most researchers, academic publishing serves two goals that are often misaligned-knowledge dissemination and establishing scientific credentials. While both goals can encourage research with significant depth and scope, the latter can also pressure scholars to maximize publication metrics. Commercial publishing companies have capitalized on the centrality of publishing to the scientific enterprises of knowledge dissemination and academic recognition to extract large profits from academia by leveraging unpaid services from reviewers, creating financial barriers to research dissemination, and imposing substantial fees for open access. We present a set of perspectives exploring alternative models for communicating and disseminating scientific research. Acknowledging that the success of new publishing models depends on their impact on existing approaches for assigning academic credit that often prioritize prestigious publications and metrics such as citations and impact factors, we also provide various viewpoints on reforming academic evaluation.
    Keywords:  academic journals; academic prestige economy; alternative publishing models; publication bias; publish or perish culture
    DOI:  https://doi.org/10.1073/pnas.2401231121
  9. Arq Bras Oftalmol. 2025 ;pii: S0004-27492025000300100. [Epub ahead of print]88(3):
      
    DOI:  https://doi.org/10.5935/0004-2749.2024-1015
  10. Arq Bras Oftalmol. 2025 ;pii: S0004-27492025000300700. [Epub ahead of print]88(3):
      This article systematically reviewed 327 documents in the core collection of the Web of Science database regarding ChatGPT applications in the writing domain. This study aimed to comprehensively assess the latest progress and potential applications. ChatGPT demonstrates significant potential in overcoming writing anxiety, improving writing efficiency, generating initial scientific papers, and assisting researchers and students in giving feedback. However, it still faces significant challenges in data accuracy and the ethics of generated content, including inaccurate or outdated information, plagiarism risks, gender or race biases, etc. Authorship verification is particularly important for academic writing and publishing as it relates to objectivity, accuracy, and fairness. Future studies need to explore how to address these challenges through improvements at the technical and policy levels, ensuring that ChatGPT promotes the sustainable development and application of academic writing while adhering to ethical standards.
    DOI:  https://doi.org/10.5935/0004-2749.2024-0269
  11. Proc Natl Acad Sci U S A. 2025 Feb 04. 122(5): e2401232121
      What is wrong with the peer review system? Is peer review sustainable? Useful? What other models exist? These are central yet contentious questions in today's academic discourse. This perspective critically discusses alternative models and revisions to the peer review system. The authors highlight possible changes to the peer review system, with the goal of fostering further dialog among the main stakeholders, including producers and consumers of scientific research. Neither our list of identified issues with the peer review system nor our discussed resolutions are complete. A point of agreement is that fair assessment and efficient change would require more comprehensive and rigorous data on the various aspects of the peer review system.
    Keywords:  peer review crisis; publication system; scientific community
    DOI:  https://doi.org/10.1073/pnas.2401232121
  12. Eur J Transl Myol. 2025 01 30.
      We invariably hear that Artificial Intelligence (AI), a rapidly evolving technology, does not just creatively assemble known knowledge. We are told that AI learns, processes and creates, starting from fixed points to arrive at innovative solutions. In the case of scientific work, AI can generate data without ever having entered a laboratory, (i.e., blatantly plagiarizing the existing literature, a despicable old trick). How does an editor of a scientific journal recognize when she or he is faced with something like this? The solution is for editors and referees to rigorously evaluate the track records of submitting authors and what they are doing. For example, false color evaluations of 2D and 3D CT and MRI images have been used to validate functional electrical stimulation for degenerated denervated muscle and a home Full-Body In-Bed Gym program. These have been recently published in Ejtm and other journals. The editors and referees of Ejtm can exclude the possibility that the images were invented by ChatGPT. Why? Because they know the researchers: Marco Quadrelli, Aldo Morra, Daniele Coraci, Paolo Gargiulo and their collaborators as well! Artificial intelligence is not banned by the EJTM, but when submitting their manuscripts to previous and to a new Thematic Section dedicated to Generative AI in Translational Mobility Medicine authors must openly declare whether they have used artificial intelligence, of what type and for what purposes. This will not avoid risks of plagiarism or worse, but it will better establish possible liabilities.
    DOI:  https://doi.org/10.4081/ejtm.2025.13670
  13. Nurs Educ Perspect. 2025 Jan 27.
       AIM: The aim of this study was to uncover what it is like to be a novice peer reviewer for journals that publish articles that can influence nursing education and/or practice.
    BACKGROUND: Comprehensive and effective approaches to reviewer development, based on reviewer experience, were not reported in the literature.
    METHOD: The study followed a hermeneutic phenomenological approach. Data were collected via personal interviews and a demographic questionnaire.
    RESULTS: Eleven novice reviewers, who had reviewed no more than five journal manuscripts, participated in the study. Thematic analysis uncovered five themes: sitting at the grown-up's table, building and using the toolbox, putting in the human factor, assuming this is what you're looking for, and appreciating the experience.
    CONCLUSION: This study is the first to uncover the experience of being a novice journal peer reviewer. Findings can inform the creation of comprehensive development programs to support new and continuing journal peer reviewers.
    DOI:  https://doi.org/10.1097/01.NEP.0000000000001376
  14. Am Psychol. 2025 Jan 30.
      After more than a decade of practice, registered reports (RRs) are widely adopted in psychology. However, the acceptance of RRs in terms of postpublication academic recognition and public dissemination, compared with nonregistered reports (non-RR), remained largely unexplored. This matched meta-evaluation identified and analyzed 119 pairs of original research articles (RR vs. non-RR) from 33 psychology journals, matched for the journal of publication, time of publication, and research topic. The exploratory results show that RRs significantly reduced publication bias against null results and improved method and data transparency. However, RRs had lower citation counts than non-RRs, with a small effect size when controlling for days since publication. Additional exploratory analyses found that this effect remained significant after controlling for null-result reporting, transparency, the number of studies in an article and length of method and result sections, article title perception, open access, and authorship metrics (including the number of authors, the h-index of the first or corresponding authors). The overall public impact indexed by Altmetric attention scores and the number of Twitter posts were not significantly different between RRs and non-RRs. However, Twitter posts, but not citations and Altmetric attention scores, were moderated by journal reputation, with RRs receiving more attention in lower impact journals (5-year impact factor below 4.5). These exploratory findings help generate testable hypotheses about the potential differential effects of RRs on academic recognition and public attention, informing future directions for open science practice. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
    DOI:  https://doi.org/10.1037/amp0001503
  15. J Oral Pathol Med. 2025 Jan 27.
       BACKGROUND: Cell culture studies play an important role in addressing fundamental scientific questions. However, inadequate reporting of these studies results in a lack of transparency and reproducibility. Recognizing the need for improvement, several ongoing efforts, such as CRIS guidelines and the ICLAC checklist, are focused on enhancing best practices for in vitro studies. Nonetheless, a comprehensive guideline specifically addressing the reporting of cell culture methods remains lacking. In this manner, a consensus-based approach is being undertaken to develop the Preferred and Transparent Reporting Items for Cell Culture Studies (PETRICCS) guideline. This project aims to present the protocol and the details for its development.
    METHODS: The process comprises five phases: (i) Initial Steps: a Steering Committee identifies the need for a guideline and drafts the PETRICCS protocol; (ii) Pre-meeting: an International Group of Cell Culture Experts (IGCE) reviews the draft guideline through a Delphi consensus exercise; (iii) Consensus Meeting: the steering committee presents the guideline's development, addresses concerns, and reaches consensus on the final items; (iv) Post-meeting: explanatory documents are prepared to assist authors in reporting their findings; and (v) Post-publication: PETRICCS, along with supporting documents, is published and made freely accessible.
    RESULTS AND CONCLUSIONS: PETRICCS will assist researchers in reporting and reviewing cell culture findings, enhancing transparency and reproducibility while filling a gap in this crucial scientific field. The guideline will incorporate the experiences of experts, creating a more equitable environment for authors, peer-reviewers, and editors during the publication process.
    Keywords:  Delphi technique; cell culture studies; guideline; methodological quality
    DOI:  https://doi.org/10.1111/jop.13605
  16. Women Birth. 2025 Jan 28. pii: S1871-5192(25)00012-5. [Epub ahead of print]38(2): 101878
       PROBLEM: Writing for publication can be a challenging experience. Whilst midwives develop writing skills through their university education, writing a journal article can be quite different.
    PURPOSE: To explain some basic skills of scientific writing when preparing a paper for publication to support midwives in engaging in scientific writing.
    OVERVIEW: Four basic elements of scientific writing will be presented: the importance of careful word choices, the use of active and passive voice, sentence and paragraph structures, and review and editing. Examples of poor and better writing are given to illustrate these basic elements of good academic writing. We hope potential midwifery authors will read and refer to this article when writing. As editors, the elements addressed here are common problems found when reviewing submitted manuscripts that, with guidance, can be easily overcome.
    Keywords:  Grammar; Midwifery; Scientific writing; Writing for publication
    DOI:  https://doi.org/10.1016/j.wombi.2025.101878
  17. Nature. 2025 Jan 29.
      
    Keywords:  Conservation biology; Ecology; Government; Law; Publishing
    DOI:  https://doi.org/10.1038/d41586-025-00144-w
  18. Am J Occup Ther. 2024 Nov 01. pii: 7810430010. [Epub ahead of print]78(Suppl 1):
      The American Journal of Occupational Therapy (AJOT) is the official journal of the American Occupational Therapy Association (AOTA). The primary mission of AJOT is to publish peer-reviewed research examining the effectiveness and efficacy of occupational therapy practice so that occupational therapy professionals can make informed, evidence-based decisions about best practice. In addition, the journal aims to publish (1) research documenting the reliability and validity of occupational therapy instruments; (2) studies demonstrating a relationship between occupational engagement and the facilitation of community participation and health; and (3) articles that provide a forum for scholars to debate professional issues that affect education, practice, and research. This Guidelines for Contributors to AJOT is also available at the American Journal of Occupational Therapy manuscript submission website, ScholarOne (go to https://mc04.manuscriptcentral.com/ajot and click "Instructions & Forms" in the upper right). These guidelines are published annually in a supplement to the journal; any changes implemented in the interim are published to the Author Guidelines page on the AJOT website (go to https://research.aota.org/ajot/pages/authorguidelines).
    DOI:  https://doi.org/10.5014/ajot.2024.78S109
  19. J Gen Intern Med. 2025 Jan 27.
      The Journal of General Internal Medicine (JGIM) has a long-standing history of publishing manuscripts focused on health equity and is committed to diversity, equity, and inclusion (DEI) in scientific writing and publishing. This is extremely important in the current climate where false narratives and attacks on DEI and health equity are rampant. To demonstrate their commitment to DEI and health equity, the JGIM Editors-in-Chief created an inaugural DEI Advocacy Team. Composed of four academic scholars with vast knowledge and expertise in health equity and DEI, the JGIM DEI Advocacy Team is posed to create the infrastructure for improving DEI in scientific writing and publishing within JGIM. The team strives to advocate for diversity among the editorial board and staff; foster an inclusive environment where all contributions are valued; and facilitate increased and equitable opportunities for publishing of scholarly work by underrepresented groups in medicine. To operationalize their goals, the JGIM DEI Advocacy Team created the 5TDEI Conceptual Framework (team, tools, tracking, transparency, training). This perspective provides a statement from the inaugural JGIM DEI Advocacy Team on how we envision promoting health equity, diversity, and inclusion in medical and scientific writing and publishing of research in JGIM.
    DOI:  https://doi.org/10.1007/s11606-024-09083-0
  20. Curr Probl Diagn Radiol. 2025 Jan 27. pii: S0363-0188(25)00009-X. [Epub ahead of print]
       OBJECTIVES: To assess medical student authorship in radiology research, focusing on the prevalence and impact of student articles, demographic trends, and potential barriers and opportunities for involvement.
    METHODS: We retrospectively assessed original research and review papers from 2018 to 2022 in the top five radiology journals based on their 2022 Impact Factor. Three reviewers manually validated and classified articles by medical student (MS) and non-MS authorship. Data collected included publication and authorship metrics. Thematic analysis of articles was performed from keywords and SCOPUS topic clusters. Significant associations were identified using chi-squared and two-tailed z-tests.
    RESULTS: Of the 2533 publications from all five journals, only 0.47 % were MS-authored, of which 83.3 % had a Field Weighted Citation Impact (FWCI) > 1. Of the 19 MS authors, 68.42 % had prior publications, with the same proportion holding prior first authorship. Female students averaged a higher FWCI (2.47 ± 2.31) but comprised only 26.32 % of all students. Only 16.67 % of MS articles had a female senior author (SA). This was consistent in non-MS articles, with females representing 19.9 % to 25.2 % of SAs across all journals. Of the 2521 non-MS articles, 92 % were classified into themes, revealing that 47.89 % of publications primarily focused on machine learning, while another 42.26 % incorporated some machine learning concepts.
    CONCLUSION: Compared to non-medical student publications in radiology, those by medical students were disproportionately limited but impactful. Both demographic and academic factors hinder student engagement in publishing. Hence promoting, supporting, and sponsoring student involvement in research is pivotal for the discipline.
    Keywords:  Artificial Intelligence; Authorship; Demographics; Journal Impact Factor; Medical Student
    DOI:  https://doi.org/10.1067/j.cpradiol.2025.01.007
  21. Clin Gastroenterol Hepatol. 2025 Feb;pii: S1542-3565(24)01045-0. [Epub ahead of print]23(2): 195-199.e3
      
    DOI:  https://doi.org/10.1016/j.cgh.2024.11.003
  22. Psychol Aging. 2025 Feb;40(1): 1-5
      In this editorial, I outline two key changes to the submission guidelines, and I present my vision as the new editor for Psychology and Aging, the premier outlet for psychological research on aging and adult lifespan development. To enhance the impact of research published in the journal, my editorial team and I will accept articles that make strong theoretical contributions, are methodologically rigorous and transparent, use open science practices, contribute cumulative knowledge to the field, and have important practical implications. We will continue to publish high-quality empirical articles, systematic reviews, and meta-analyses, as well as theory development and methodological articles from all areas of psychology and related disciplines that focus on basic principles of aging and adult lifespan development or that investigate these principles in applied settings. Now entering its fifth decade of publication, Psychology and Aging is the ideal outlet for theoretically and methodologically rigorous and transparent research that offers significant insights into the dynamic process of human aging and lifespan development. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
    DOI:  https://doi.org/10.1037/pag0000874