bims-skolko Biomed News
on Scholarly communication
Issue of 2025–02–23
24 papers selected by
Thomas Krichel, Open Library Society
  1. Comments on alleged editor misconduct from editors-in-chief of anaesthesia journals.
  2. Authorship and Acknowledgment in Nursing Publications: It's a Matter of Ethics.
  3. Why retractions data could be a powerful tool for cleaning up science.
  4. Exclusive: These universities have the most retracted scientific articles.
  5. Patient partner engagement in the publication process: challenges and possible solutions.
  6. Assessing database accuracy for article retractions: A preliminary study comparing Retraction Watch Database, PubMed, and Web of Science.
  7. Open access and peer review - why do I have to pay twice?
  8. The commercialization of open access publishing: progress or predicament?
  9. Post-publication peer review and the identification of methodological and reporting issues in COVID-19 trials: a qualitative study.
  10. Peer review and Palliative Medicine: Guiding reviewers' contributions to ensuring high quality publications.
  11. Valid concerns: Considerations for reviewing manuscripts with validity arguments.
  12. Comparison of Peer Reviewer Instructions of Radiology Journals to Recommended Peer Review Checklists.
  13. Peer reviewer fatigue, or peer reviewer refusal?
  14. Threats to grant peer review: a qualitative study.
  15. The use of Generative Artificial Intelligence in Scholarly Communication.
  16. Practical Considerations and Ethical Implications of Using Artificial Intelligence in Writing Scientific Manuscripts.
  17. Roles of editors and reviewers in the modern world of actual intelligence and artificial intelligence.
  18. Discrepancies in reported results between trial registries and journal articles for AI clinical research.
  19. Interactive 3D Objects Enhance Scientific Communication of Structural Data.
  20. Top 10 Tips for Writing about AI in Radiology: A Brief Guide for Authors.
  21. How to Write a Pathology Research Paper-Basic Principles and Beyond-A Primer for Residents.
  22. When I use a word . . . Academic publishing: the impact factor.
  23. Advocating Submission of Case Reports in Family Medicine: An Analysis of Case Report Submissions in Journals Related to Family Medicine.
  24. Revisiting JMLA case reports: a publication category for driving innovation in health sciences librarianship.
  1. Br J Anaesth. 2025 Feb 13. pii: S0007-0912(24)00767-0. [Epub ahead of print]
    Comments on alleged editor misconduct from editors-in-chief of anaesthesia journals.
    Alfredo Abad Gurumeta, Andrew Davidson, Ruthi Landau, Jaideep J Pandit, James P Rathmell, André Schmidt, Stephan K W Schwarz, Brian D Sites, BobbieJean Sweitzer, Matt Wiles.
      
    Keywords:  academic publishing; authorship; editor-in-chief; editorial misconduct; publication ethics
    DOI:  https://doi.org/10.1016/j.bja.2024.12.017
  2. Clin Nurse Spec. 2025 Mar-Apr 01;39(2):39(2): 58-61
    Authorship and Acknowledgment in Nursing Publications: It's a Matter of Ethics.
    Jennifer M Quevedo, Michelle James, Christine Glaves-Smith.
      
    DOI:  https://doi.org/10.1097/NUR.0000000000000886
  3. Nature. 2025 Feb;638(8051): 581
    Why retractions data could be a powerful tool for cleaning up science.
      
    Keywords:  Authorship; Ethics; Institutions; Policy; Publishing
    DOI:  https://doi.org/10.1038/d41586-025-00509-1
  4. Nature. 2025 Feb;638(8051): 596-599
    Exclusive: These universities have the most retracted scientific articles.
    Richard Van Noorden.
      
    Keywords:  Ethics; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-025-00455-y
  5. BMC Med Res Methodol. 2025 Feb 15. 25(1): 39
    Patient partner engagement in the publication process: challenges and possible solutions.
    Krista E Cooksey, Mark Neuman, Mara Bollini, Bethany Pennington, Hugo de O Campos, Kathleen Oberst, Melissa Wurst, Mary C Politi.
      Patient engagement in research is gaining traction as an international standard, and often requirement, of many health research funding agencies. Drivers of this increase include patient interest, increased attention to and recognition of the value of patients' voices in research, and more patients leading or partnering in the conduct research. Patient engagement includes collaborating and providing insights into research question and study design, and may extend to the publication process. When patients contribute to publications, they can bring unique perspectives that may enhance the impact, reach, and utility of the research in real-world contexts. Currently, there is limited systematic guidance to support patient partners as they navigate this complex publication process. As a result, it can be difficult for patient partners to understand when and how they should be included as authors, how to collaborate in the writing process, and how to complete mandatory tasks during the submission process. In this paper, we review barriers and facilitators within existing publication practices and offer recommendations to ensure that the scientific publication process is more transparent and accessible for patient partners.
    Keywords:  Co-authorship; Co-production; Collaboration; Patient engagement; Patient partnership
    DOI:  https://doi.org/10.1186/s12874-025-02495-4
  6. Account Res. 2025 Feb 20. 1-18
    Assessing database accuracy for article retractions: A preliminary study comparing Retraction Watch Database, PubMed, and Web of Science.
    Paul Sebo, Melissa Sebo.
       OBJECTIVE: This study aimed to compare the accuracy of metadata for retracted articles in Retraction Watch Database (RWD), PubMed, and Web of Science (WoS).
    METHODS: Twenty general internal medicine journals with an impact factor > 2 were randomly selected. RWD, PubMed, and WoS were used to retrieve all retracted articles published in these journals. Eight metadata variables were examined: journal, title, type of article, author(s), country/countries of affiliation, year of publication, year of retraction, and reason(s) for retraction (assessed only for RWD, as this information was unavailable in PubMed and WoS). Descriptive analyses were conducted to document errors across databases.
    RESULTS: Thirty-five retractions were identified, and 280 metadata entries (35 × 8) were analyzed. RWD contained the most metadata errors, affecting 16 articles and 20 metadata entries, including seven errors in year of publication, six in article type, six in author names (five misspellings, one missing two authors), and one in country of affiliation. WoS had one error (a missing author), and PubMed had none.
    CONCLUSION: The relatively high error rate in RWD suggests that researchers should cross-check metadata across multiple databases. Given the preliminary nature of this study, larger-scale research is needed to confirm these findings and improve metadata reliability in retraction databases.
    Keywords:  Accuracy; PubMed; Retraction; Retraction Watch; Web of Science
    DOI:  https://doi.org/10.1080/08989621.2025.2465621
  7. Br Dent J. 2025 Feb;238(3): 151
    Open access and peer review - why do I have to pay twice?
    I G Chestnutt.
      
    DOI:  https://doi.org/10.1038/s41415-025-8398-8
  8. J Neurointerv Surg. 2025 Feb 14. 17(3): 231-232
    The commercialization of open access publishing: progress or predicament?
    Edgar A Samaniego.
      
    Keywords:  Standards
    DOI:  https://doi.org/10.1136/jnis-2025-023182
  9. BMJ Evid Based Med. 2025 Feb 20. pii: bmjebm-2024-113068. [Epub ahead of print]
    Post-publication peer review and the identification of methodological and reporting issues in COVID-19 trials: a qualitative study.
    Mauricia Davidson, Christoffer Bruun Korfitsen, Carolina Riveros, Anna Chaimani, Isabelle Boutron.
       OBJECTIVES: We aimed to determine to what extent systematic reviewers and post-preprint and post-publication peer review identified methodological and reporting issues in COVID-19 trials that could be easily resolved by the authors.
    DESIGN: Qualitative study.
    DATA SOURCES: COVID-NMA living systematic review (covid-nma.com), PubPeer, medRxiv, Research Square, SSRN.
    METHODS: We considered randomised controlled trials (RCTs) in COVID-NMA that evaluated pharmacological treatments for COVID-19 and retrieved systematic reviewers' assessments of the risk of bias and outcome reporting bias. We also searched for commentary data on PubPeer and preprint servers up to 6 November 2023. We employed qualitative content analysis to develop themes and domains of methodological and reporting issues identified by commenters.
    RESULTS: We identified 500 eligible RCTs. Systematic reviewers identified methodological and reporting issues in 446 (89%) RCTs. In 391 (78%) RCTs, the issues could be easily resolved by the trial authors; issues included incomplete reporting (49%), selection of the reported results (52%) and no access to the pre-specified plan (25%). Alternatively, 74 (15%) RCTs had received at least one comment on PubPeer or preprint servers, totalling 348 comments. In 46 (9%) RCTs, the issues identified by post-preprint and post-publication peer review comments could be easily resolved by the trial authors; the issues were related to incomplete reporting (6%), errors (5%), statistical analysis (3%), inconsistent reporting of methods and analyses (2%), spin (2%), selection of the reported results (1%) and no access to the raw data/pre-specified plan (1%).
    CONCLUSIONS: Without changing their process, systematic reviewers identified issues in most RCTs that could be easily resolved by the trial authors; however, the lack of an established author feedback mechanism represents a wasted opportunity for facilitating improvement and enhancing the overall manuscript quality. On the other hand, despite the existing feedback loop to authors present in post-publication peer review, it demonstrated limited effectiveness in identifying methodological and reporting issues.
    Keywords:  COVID-19; Environment and Public Health; Methods
    DOI:  https://doi.org/10.1136/bmjebm-2024-113068
  10. Palliat Med. 2025 Feb 21. 2692163251321082
    Peer review and Palliative Medicine: Guiding reviewers' contributions to ensuring high quality publications.
    Catherine Walshe, Kim Beernaert, Poh Heng Chong, Sonya Lowe, Sandra Martins Pereira, Sarah Yardley.
      
    DOI:  https://doi.org/10.1177/02692163251321082
  11. Anat Sci Educ. 2025 Feb 17.
    Valid concerns: Considerations for reviewing manuscripts with validity arguments.
    Georgina C Stephens, Mahbub Sarkar.
      
    Keywords:  anatomy education; health professions education; peer review; scale; survey; validity
    DOI:  https://doi.org/10.1002/ase.70006
  12. Acad Radiol. 2025 Feb 18. pii: S1076-6332(25)00018-2. [Epub ahead of print]
    Comparison of Peer Reviewer Instructions of Radiology Journals to Recommended Peer Review Checklists.
    Omar Msto Hussain Nasser, Paul Cronin, James V Rawson.
       RATIONALE AND OBJECTIVES: The objective of this study was to identify differences in peer review guidance provided to reviewer by journals, and to compare radiology journal instructions to recommended peer review checklists.
    METHODS: Peer review instructions from four prominent radiology journals (Radiology, JACR, Academic Radiology, AJR) were obtained from journal websites and instructions to reviewers in the journal. Two recommended checklists from radiology literature published by Provenzale and Stanley in 2005 with 30 items, and another by Duchesne and Jannin with 69 items published in 2008 were utilized. Journal-based instructions were compared to both recommended checklists using Excel.
    RESULTS: Variability was observed in the online available instructions for reviewers of the four radiology journals. Radiology journals' instructions for reviewers were more likely to address certain parts of the manuscript. Items that were consistently emphasized included rationale, reproducibility, results of statistical test, whether results justify the conclusion, whether the research question was addressed, and the clinical and practical applicability. Other items that were more likely to be mentioned in the instruction checklists include; if the abstract stands alone, a sufficient and concise background, logical flow of results that follows from the methods, appropriate tables and figures, and appropriate references. Items least likely to be addressed included the title, keywords, justification of study design and study methodology, unexpected results, generalizability of findings, and ethical considerations.
    CONCLUSION: Variability was observed in journals' guidelines for reviewers. This could be attributed to differences in journal aims, scopes, and article types. Radiology journals' instructions for reviewers are more likely to address certain parts of the manuscript.
    Keywords:  Peer review; Radiology; Reviewer guidelines
    DOI:  https://doi.org/10.1016/j.acra.2025.01.018
  13. Account Res. 2025 Feb 17. 1-7
    Peer reviewer fatigue, or peer reviewer refusal?
    Kate Beecher, Joshua Wang.
      Peer review processes are slowing. Existing literature and policies conceptualize this stagnation in peer review as a result of academic fatigue. Here, we instead examine an under-researched factor behind slowed peer review systems: academics refusing to voluntarily review manuscripts for for-profit journals. By synthesizing accounts of peer review refusal from scholarly blogs, journal editorials, and prominent social media movements, we provide an overview of the advantages and disadvantages of this refusal. We then offer some preliminary suggestions for academics to simultaneously safeguard the speed of peer review and voice dissatisfaction with major publishing companies. This piece contributes to the evolving field of peer review studies and provides an alternate conceptualization of the slowing peer review system.
    Keywords:  Peer review studies; higher education studies; peer reviewer refusal; reviewer fatigue; scholarly publishing
    DOI:  https://doi.org/10.1080/08989621.2025.2463977
  14. BMJ Open. 2025 Feb 20. 15(2): e091666
    Threats to grant peer review: a qualitative study.
    Joanie Sims Gould, Anne M Lasinsky, Adrian Mota, Karim M Khan, Clare L Ardern.
       BACKGROUND AND OBJECTIVES: Peer review is ubiquitous in evaluating scientific research. While peer review of manuscripts submitted to journals has been widely studied, there has been relatively less attention paid to peer review of grant applications (despite how crucial peer review is to researchers having the means and capacity to conduct research). There is spirited debate in academic community forums (including on social media) about the perceived benefits and limitations of grant peer review. The aim of our study was to understand the experiences and challenges faced by grant peer reviewers.
    METHODS: Therefore, we conducted qualitative interviews with 18 members of grant review panels-the Chairs, peer reviewers and Scientific Officers of a national funding agency-that highlight threats to the integrity of grant peer review.
    RESULTS: We identified three threats: (1) lack of training and limited opportunities to learn, (2) challenges in differentiating and rating applications of similar strength, and (3) reviewers weighting reputations and relationships in the review process to differentiate grant applications of a similar strength. These threats were compounded by reviewers' stretched resources or lack of time. Our data also highlighted the essential role of the Chair in ensuring transparency and rigorous grant peer review.
    CONCLUSIONS: As researchers continue to evaluate the threats to grant peer review, the reality of stretched resources and time must be considered. We call on funders and academic institutions to implement practices that reduce reviewer burden.
    Keywords:  peer review; research grants; time; training
    DOI:  https://doi.org/10.1136/bmjopen-2024-091666
  15. Rev Lat Am Enfermagem. 2025 Feb 17. pii: S0104-11692025000100200. [Epub ahead of print]33 e4560
    The use of Generative Artificial Intelligence in Scholarly Communication.
    Lilian Nassi-Calò.
      
    DOI:  https://doi.org/10.1590/1518-8345.0000.4560
  16. ACG Case Rep J. 2025 Feb;12(2): e01629
    Practical Considerations and Ethical Implications of Using Artificial Intelligence in Writing Scientific Manuscripts.
    Muhammad Nadeem Yousaf.
      
    DOI:  https://doi.org/10.14309/crj.0000000000001629
  17. Eur J Appl Physiol. 2025 Feb;125(2): 275-276
    Roles of editors and reviewers in the modern world of actual intelligence and artificial intelligence.
    Michael I Lindinger.
      
    DOI:  https://doi.org/10.1007/s00421-024-05690-1
  18. EClinicalMedicine. 2025 Feb;80 103066
    Discrepancies in reported results between trial registries and journal articles for AI clinical research.
    Zixuan He, Lan Yang, Xiaofan Li, Jian Du.
       Background: Complete and unbiased reporting of clinical trial results is essential for evaluating medical advances, yet publication bias and reporting discrepancies in research on the clinical application of artificial intelligence (AI) remain unknown.
    Methods: We conducted a comprehensive search of research publications and clinical trial registries focused on the application of AI in healthcare. Our search included publications in Dimensions.ai and pre-registered records from ClinicalTrials.gov and the EU Clinical Trials Registry before 31 December 2023. We linked registered trials to their corresponding publications, analysed the registration, reporting and different dissemination patterns of results, identified discrepancies between clinical trial registries and published literature, and assessed the use of these results in secondary research.
    Findings: We identified 28,248 publications related to the use of AI in clinical settings and found 1863 publications that included a clinical trial registration ID. The clinical trial registry search identified 3710 trials evaluating the use of AI in clinical settings, of which 1106 trials are completed, yet only 101 trials have published results. By linking the trials to their corresponding publications, we found that 26 trials had results available from both registries and publications. There were more results in trial registries than in articles, but researchers showed a clear preference for rapid dissemination of results through peer-reviewed articles (37.6% published within one year) over trial registries (15.8%). Discrepancies and omissions of results were common, and no complete agreement was observed between the two sources. Selective reporting of publications occurred in 53.6% of cases, and the underestimation of the incidence of adverse events is alarming.
    Interpretation: This research uncovers concerns with the registration and reporting of AI clinical trial results. While trial registries and publications serve distinct yet complementary roles in disseminating research findings, discrepancies between them may undermine the reliability of the evidence. We emphasise adherence to guidelines that promote transparency and standardisation of reporting, especially for investigator-initiated trials (IITs).
    Funding: The authors declare no source of funding.
    Keywords:  Artificial intelligence; Clinical evidence; Clinical trial; Discrepancy
    DOI:  https://doi.org/10.1016/j.eclinm.2024.103066
  19. Chembiochem. 2025 Feb 20. e202500036
    Interactive 3D Objects Enhance Scientific Communication of Structural Data.
    Daniel Mokos, Bastian Daniel.
      In scientific communication about three-dimensional structures, creating two-dimensional representations is standard practice. These representations often suffer from the drawback of losing potential information due to dimensionality reduction. Several options exist to present, share and publish 3D figures, however based on recent publications they are not widely utilized. Here we present simple ways to preserve the three-dimensionality of the structure by the creation of a custom-made model in GLTF format that is generated in the same workflow as the conventional figures. They can be published alongside a given manuscript with minimal additional effort to the authors, but a huge impact on the communicative power of the manuscript concerning the three-dimensional features of the reported structures. The scripts we adapted and published for this purpose open up new possibilities for the illustrator and allow the viewer to access the full three-dimensionality of the published structure. In future, this can simplify the publication process of protein structures or other models and be a valuable tool for scientific communication in digital or printed form.
    Keywords:  Bioinformatics; Communication; Structural biology; Structure elucidation; Structure representation
    DOI:  https://doi.org/10.1002/cbic.202500036
  20. Radiology. 2025 Feb;314(2): e243347
    Top 10 Tips for Writing about AI in Radiology: A Brief Guide for Authors.
    Sarah L Atzen.
      
    DOI:  https://doi.org/10.1148/radiol.243347
  21. APMIS. 2025 Feb;133(2): e70007
    How to Write a Pathology Research Paper-Basic Principles and Beyond-A Primer for Residents.
    Glen Kristiansen.
      Medical writing is an art but still it is usually not in the curriculum of medical students. With the beginning of scientific activity during residency, many perceive this gap increasingly, and stay behind their own expectations in their scientific productivity. Many universities offer courses to teach scientific writing and many books and article address this void, but in real life the main work to carve a readable paper out of a pile of unsorted data remains often in the hands of the scientific supervisors. This little paper tries to address this issue with a focus on typical pathology related subjects by outlining the structure of a paper and explaining typical dos and don'ts of crafting a publishable scientific paper as a pathology resident.
    Keywords:  pathology; primer; publication; scientific writing
    DOI:  https://doi.org/10.1111/apm.70007
  22. BMJ. 2025 Feb 14. 388 r333
    When I use a word . . . Academic publishing: the impact factor.
    Jeffrey K Aronson.
      
    DOI:  https://doi.org/10.1136/bmj.r333
  23. J Prim Care Community Health. 2025 Jan-Dec;16:16 21501319251320171
    Advocating Submission of Case Reports in Family Medicine: An Analysis of Case Report Submissions in Journals Related to Family Medicine.
    Apichai Wattanapisit, Kosin Sirirak, Sanhapan Wattanapisit, Chirk Jenn Ng, Chin Hai Teo, Nutchar Wiwatkunupakarn, Piyachon Aramrat, Chaisiri Angkurawaranon.
       INTRODUCTION: Family medicine embraces a wide range of principles. Identifying appropriate journals for publishing family medicine case reports can be challenging for authors. This study aims to identify journals related to family medicine that publish case reports and summarize the requirements of case report submissions.
    METHODS: Journals related to family medicine were identified from the subject categories: "family practice" in Scopus and "primary health care" in Web of Science. The author's instructions on the journal websites regarding the criteria for case report submissions were reviewed, and the specific requirements for case reports of each journal were recorded. Journals were excluded if family medicine was not the main aim and scope.
    RESULTS: Among the 80 journals focused on family medicine, 30 (37.5%) were found to accept submissions of case reports. These reports were classified into various article types, such as case reports, patient studies, clinical case studies. The length of the main text varied between 400 and 3000 words, and some journals did not mandate an abstract. However, for those that did, abstracts typically ranged from 50 to 300 words. The number of references cited ranged from 5 to 30.
    CONCLUSIONS: Less than half of the journals in the family medicine field accept case report submissions. It is advisable for authors to choose their target journal early in the preparation process, as each journal typically provides specific submission guidelines and instructions.
    Keywords:  case report; family medicine; family practice; primary health care; publication
    DOI:  https://doi.org/10.1177/21501319251320171
  24. J Med Libr Assoc. 2025 Jan 14. 113(1): 1-3
    Revisiting JMLA case reports: a publication category for driving innovation in health sciences librarianship.
    Jill T Boruff, Michelle Kraft, Alexander J Carroll.
      In the April 2019 issue (Vol. 106 No. 3), the Journal of the Medical Library Association (JMLA) debuted its Case Report publication category. In the years following this decision, the Case Reports category has grown into an integral component of JMLA. In this editorial, the JMLA Editorial Team highlights the value of case reports and outlines strategies authors can use to draft impactful manuscripts for this category.
    DOI:  https://doi.org/10.5195/jmla.2025.2099
This page is being maintained by Thomas Krichel. It was last updated on 2025‒02‒26 at 13:21.