bims-skolko Biomed News
on Scholarly communication
Issue of 2026–09–06
39 papers selected by
Thomas Krichel, Open Library Society



  1. BMJ. 2026 Sep 02. 394 e100460
       OBJECTIVE: To assess the number, timing, characteristics, and scholarly impact of secondary publications generated using individual participant level data (IPD) from a portfolio of clinical trials shared with external investigators through a data sharing platform.
    DESIGN: Cross sectional study.
    SETTING: Yale University Open Data Access (YODA) Project platform.
    PARTICIPANTS: Johnson & Johnson sponsored clinical trials listed on the YODA Project platform with IPD available for external sharing through 2021 and with a full length, peer reviewed publication (that is, primary publication) reporting primary endpoint results by the original trial investigators.
    MAIN OUTCOME MEASURES: Number, timing, research objectives, analysis type, and scholarly impact of secondary publications using IPD from these trials identified through Web of Science citation searches of primary publications through June 2025. Scholarly impact metrics included journal impact factor, annual citation count, and annual Altmetric Attention Score. Secondary publications were classified as internal (authored by at least one original trial investigator) or external.
    RESULTS: Among 336 eligible trials, 265 (79%) had at least one associated secondary publication, totalling 1167 publications, of which 209 (17.9%) were external. Among external publications with a reported data access mechanism (n=190; 91%), most obtained access through data sharing platforms (n=161; 85%), primarily the YODA Project (n=157; 83%). Over time, the proportion of external publications increased steadily, exceeding 50% of all secondary publications by year 11 and thereafter. Compared with internal publications, external publications were more frequently pooled analyses (151/209 (72%) v 534/958 (55.7%); P<0.001) and involved predictive or prognostic modelling (108/209 (51.7%) v 322/958 (33.6%); P<0.001), development of statistical models or algorithms (60/209 (29%) v 114/958 (11.9%); P<0.001), and validation of existing methods, models, or risk scores (32/209 (15%) v 66/958 (6.9%); P<0.001). Compared with internal publications, external publications were published in journals with higher impact factors (median 6.7 (interquartile range 3.4-16.6) v 4.6 (2.9-10.2); P=0.002) and had higher annual Altmetric Attention Scores (median 2.1 (0.7-7.1) v 0.6 (0.3-2.3); P<0.001) but had lower annual citation counts (median 2.7 (1.1-5.6) v 3.4 (1.6-7.5); P<0.001) and were less likely to be cited in clinical guidelines (21/184 (11%) v 235/805 (29.2%); P<0.001) or policy documents (14/184 (8%) v 206/805 (25.6%); P<0.001).
    CONCLUSIONS: Most trials in this portfolio of clinical trials, for which IPD were available through a data sharing platform, generated secondary research by both original trial investigators and external investigators. External investigators most often accessed data through the data sharing platform, and their publications accounted for an increasingly larger proportion of secondary publications over time. These findings suggest that structured data sharing mechanisms may support additional secondary use of clinical trial data and further enhance the scientific value of clinical trials.
    DOI:  https://doi.org/10.1136/bmj-2026-100460
  2. J Pediatr Health Care. 2026 Sep-Oct;40(5):pii: S0891-5245(26)00198-7. [Epub ahead of print]40(5): 643
      
    DOI:  https://doi.org/10.1016/j.pedhc.2026.06.002
  3. J Cell Sci. 2026 Sep 04. pii: jcs.265183. [Epub ahead of print]
      Preprints have transformed how biologists share results, yet how well a preprint reads still depends on formatting, a task that has shifted from publishers to authors. Cell biology has also become increasingly quantitative, with conclusions resting on multi-step image analysis whose figures, values, and statistics are revised repeatedly across a project. Keeping a well-formatted manuscript in step with the latest analysis is tedious and error-prone. We introduce Rxiv-Maker, an open-source framework that lets authors write in simple Markdown and produce a formatted article, as a PDF or an editable Word document, with consistent styling, automatic figure and citation numbering, and reliable cross-referencing. For quantitative work, it can optionally regenerate figures and recompute reported values directly from the data, so the text stays consistent with the analysis. Built on familiar tools such as Git and Visual Studio Code, it gives a transparent, collaborative path from analysis to a submission-ready preprint. Researchers have already used Rxiv-Maker for cell-biology studies spanning bacterial cell-cycle analysis, filopodia proteomics, and zebrafish live imaging, showing it supports reproducible reporting of genuine biological findings.
    Keywords:  Bioimage analysis; Markdown; Open-source software; Preprints; Reproducibility; Scientific publishing
    DOI:  https://doi.org/10.1242/jcs.265183
  4. Am J Med. 2026 Sep 01. pii: S0002-9343(26)00646-7. [Epub ahead of print]
      
    Keywords:  Obesity; Person-first language; Stigma
    DOI:  https://doi.org/10.1016/j.amjmed.2026.08.020
  5. Ann Coloproctol. 2026 Aug;42(4): 454-467
       PURPOSE: Article processing charges (APCs) are central to author-paid open access (OA) publishing. Disparities appear in oncology, pathology, and global surgery, but not colorectal surgery, spanning coloproctology, general surgery, gastroenterology, and oncology journals. We examined APC levels, citation-impact linkage, and authorship geography.
    METHODS: This study was a cross-sectional bibliometric analysis of 32 journals (MEDLINE/PubMed search). APCs (publisher-direct 2026) and 2024 citation metrics (Journal Impact Factor [JIF], SCImago Journal Rank [SJR], SCImago H-index) were extracted. First- and last-author countries for all 2024-2025 articles (n=31,164) were mapped to World Bank income groups. Multivariable ordinary least squares regression modeled log10(APC) on publisher group, region, OA model, and log10(JIF 2024).
    RESULTS: Median APC was US $3,980 (interquartile range, $3,580-$4,390), varying by region: $1,467 in Asia, $3,840 in the United Kingdom, $4,140 in Western Europe, and $4,175 in the United States. APC correlated with the SCImago H-index (ρ=0.51, P=0.003) but not with JIF (P=0.25) or SJR (P=0.13). Of 30,320 articles, first authors were from high-income countries in 62.5%, upper-middle-income countries in 34.7%, and lower-middle- or low-income countries in 2.8%; China (30.9%), the United States (23.1%), and Japan (8.0%) were the leading countries. First authors were more often from non-high-income countries than last authors (median difference, +0.68 percentage points; P<0.001). In multivariable regression (R2=0.90), society-direct publishing was associated with lower APCs (β=-0.44, P<0.001), whereas US-based publishing (β=+0.18, P=0.019), UK-based publishing (β=+0.16, P=0.037), and a hybrid OA model (β=+0.15, P=0.014) were associated with higher APCs. JIF was not independently associated with APC (P=0.93).
    CONCLUSION: Colorectal surgery APCs are high and decoupled from citation impact after adjustment, with underrepresentation of lower-resource-setting authors, especially at senior-author level. Society-owned and Asia-based journals offer lower-cost alternatives but remain a minority.
    Keywords:  Bibliometrics; Colorectal surgery; Healthcare disparities; Open access publishing; Publishing
    DOI:  https://doi.org/10.3393/ac.2026.00542.0077
  6. Nature. 2026 Sep;657(8130): 34-36
      
    Keywords:  Authorship; Ethics; Machine learning; Scientific community
    DOI:  https://doi.org/10.1038/d41586-026-02686-z
  7. AJR Am J Roentgenol. 2026 09 02.
      
    Keywords:  AI slop; artificial intelligence; generative AI; peer review; radiology education; research integrity
    DOI:  https://doi.org/10.2214/AJR.26.35537
  8. Digit Health. 2026 Jan-Dec;12:12 20552076261464745
       Objectives: Large language models (LLMs) are being used to facilitate academic writing. We aimed (1) to assess the quality, integrity, and factual reliability of LLM-assisted academic writing in medicine, and (2) to compare the performance of open-source versus proprietary LLMs, reflecting differences in model transparency.
    Methods: In this prospective, controlled evaluation study, an open-source model (DeepSeek-R1) and proprietary model (ChatGPT-o1) completed ten academic tasks: generating five scientific essays and five evidence-based question-answers covering clinical topics in neuroradiology. Two radiologists rated outputs using 14 Likert and 7 binary criteria across the domains of academic quality, linguistic expression, factual reliability. Paired Wilcoxon/McNemar (Holm) assessed differences; ICC/Cohen's κ assessed reliability.
    Results: DeepSeek-R1 achieved higher overall mean Likert scores than ChatGPT-o1 (mean ratings ± standard deviation: 3.23 ± 0.44 vs 3.02 ± 0.30, p = 0.021). It significantly outperformed in reasoning depth (p = 0.015), contextual coherence (p = 0.043), subtlety (p = 0.037), and evidence integration (p = 0.027). Although both models cited sources in every output, citation reliability was poor. DeepSeek-R1 cited more real publications (55.1% vs. 33.3%, p=0.053) but showed a higher confirmed fabrication rate (36.7% vs. 2.6%, p<0.001). DeepSeek-R1 respected word limits in 90%, ChatGPT-o1 only in 50%. Neither reviewer reliably noticed AI-generated text features. Inter-rater reliability was poor for Likert criteria (ICC = 0.466) and substantial for binary items (κ = 0.746).
    Conclusion: DeepSeek-R1 outperformed ChatGPT-o1 in generating academic content for neuroradiology, highlighting the potential of transparent, locally deployable models. However, moderate quality, citation errors and hallucinations indicate that LLMs are not yet sufficient for unsupervised academic writing and demand rigorous human review.
    Keywords:  artificial intelligence; natural language processing; neuroradiology; publishing/standards; reproducibility of results
    DOI:  https://doi.org/10.1177/20552076261464745
  9. Nature. 2026 Sep;657(8130): 312
      
    Keywords:  Authorship; Machine learning; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-026-02735-7
  10. J Med Internet Res. 2026 Aug 26. 28 e109605
       Unlabelled: AI is moving deeper into the realm of scholarly publishing, with tools developed to help researchers assess research and evaluate their manuscripts. In this News and Perspectives article, JMIR Correspondent Simon Spichak reports on how researchers are responding to some of these tools.
    Keywords:   preprints; artificial intelligence; bibliometrics; biomedical research ; peer review, research; scientific publication
    DOI:  https://doi.org/10.2196/109605
  11. Ann Biomed Eng. 2026 Aug 31.
      Here, we build on a letter published in 2023 in this journal ( https://doi.org/10.1007/s10439-023-03272-4 ) on prompt engineering for academic writing. Drawing on ethics literature, both new and old, we reflect on the prompting of large language models (LLMs) from three different moral perspectives: consequentialism (the ethics of outcomes), deontology (the ethics of duties), and virtue ethics (the ethics of character). While we recognize that human authors who prompt LLMs to derive text can simplify knowledge creation, the question becomes: are prompters equivalent to authors, and should they be rewarded as such? We push back against over-reliance on prompt engineering by arguing in favor of the craft of human draft as a task worth preserving in academia to encourage authors to retain control over published content that bears their name.
    Keywords:  Chatbots; Ethics; Generative artificial intelligence; Large language models
    DOI:  https://doi.org/10.1007/s10439-026-04356-7
  12. Clin Chem Lab Med. 2026 Sep 02.
      
    Keywords:  Artificial Intelligence; academic workflow; chatbots; cognitive fatigue; digital psychology; scientific publishing
    DOI:  https://doi.org/10.1515/cclm-2026-1274
  13. Science. 2026 Sep 03. 393(6815): 963-967
      As AI's capabilities grow, researchers and publishers are exploring how it can support peer review-and where it still falls short.
    DOI:  https://doi.org/10.1126/science.aem0443
  14. J Sci Med Sport. 2026 Sep;pii: S1440-2440(26)00531-1. [Epub ahead of print]29(10): 1073-1074
      
    DOI:  https://doi.org/10.1016/j.jsams.2026.08.210
  15. FEBS Open Bio. 2026 Sep;16(9): 1634-1636
      FEBS Open Bio is pleased to announce the launch of the Early Career Reviewer Hub, a new initiative designed to provide professional training and first-hand experience to Early Career Researchers (ECRs) interested in taking part in the peer-review process. We hope that, through this new programme and our focus on Research Protocols, we will continue to support and contribute to the professional development of early career molecular life scientists.
    DOI:  https://doi.org/10.1002/2211-5463.70335
  16. Am J Vet Res. 2026 Aug 24. pii: ajvr.87.09.editorial. [Epub ahead of print]87(9):
      
    DOI:  https://doi.org/10.2460/ajvr.87.09.editorial
  17. JAMA Netw Open. 2026 Sep 01. 9(9): e2632070
       Importance: Open science practices are essential for improving transparency, reproducibility, and trust in biomedical research. Journals play a critical role in promoting these practices through editorial policies, yet implementation and impact remain unclear.
    Objective: To evaluate the open science policies of leading medical journals and assess implementation and detectability of practices using automated tools.
    Design, Setting, and Participants: This cross-sectional study of journal policies and open science practices evaluated research articles published in 10 leading general medical journals from January 2020 to December 2023. Additionally, the diagnostic accuracy of automated tools was validated against manual extraction.
    Exposures: Journal policies regarding open science practices and article-level implementation of 13 core practices including registration, protocol sharing, and intention to share data.
    Main Outcomes and Measures: Journal policies were assessed using the Transparency and Openness Promotion guidelines (TOP2025). At the article level, 13 core open science practices were examined. Additionally, 9 validated automated tools were applied to detect these practices, and their performance was compared with manual extraction of articles.
    Results: Overall, 15 624 research articles published in 10 general medical journals were analyzed (validation subset, 312 articles: 103 randomized clinical trials [RCTs], 98 meta-analyses, and 111 with other designs). At the journal level, TOP2025 evaluation identified substantial heterogeneity in policies, primarily applied to clinical trials. At the article level, open science practices were more frequently implemented in RCTs than other designs: registration (RCTs: 99% [95% CI, 97%-100%]; meta-analyses: 69% [95% CI, 56%-79%]; other designs: 16% [95% CI, 9%-26%]), protocol sharing (RCTs: 96% [95% CI, 93%-98%]; meta-analyses: 67% [95% CI, 54%-78%]; other designs: 20% [95% CI, 12%-33%]), and intention to share data (RCTs: 79% [95% CI, 67%-87%]; meta-analyses: 65% [51%-77%]; other designs: 70% [95% CI, 57%-81%]). Automated tools showed variable performance (F1 scores, 0.06-1.00) and generally underestimated practices.
    Conclusions and Relevance: In this cross-sectional study of 15 624 articles in 10 leading medical journals, journal policies were only partially aligned with TOP2025, and article-level open science practices were more frequently reported for RCTs than for other designs, supporting the need for stronger journal policies.
    DOI:  https://doi.org/10.1001/jamanetworkopen.2026.32070
  18. Acad Radiol. 2026 Sep 01. pii: S1076-6332(26)00595-7. [Epub ahead of print]
      
    Keywords:  Artificial intelligence; Scientific community; Statistics
    DOI:  https://doi.org/10.1016/j.acra.2026.08.008
  19. Chiropr Man Therap. 2026 Sep 01. pii: 43. [Epub ahead of print]34(1):
      This is the first of three articles that provide step-by-step guides on how to structure the content of a scientific article to ensure a coherent and relevant text. This article deals with the Background section, with extra focus on the research objectives. We introduce the four typical elements of a Background section: (i) justification of the study topic, (ii) sufficient information for the reader to understand the research project, (iii) presentation of the research gaps that justify the research objectives, and (iv) well-constructed research objectives that indicate the study design and may include a purpose statement. Because the whole text is driven by the research objectives, we first suggest some tips for making these as informative as possible. We then provide a step-by-step approach for planning the structure and contents of the Background section as preparation for writing the full text later. We illustrate our explanations with text examples selected from this journal to show how authors have approached crucial aspects of the Background section. Finally, we discuss some pros and cons of using artificial intelligence during the writing process, and how its use can be reported. We hope that this practical guide to the structuring process will provide authors with a useful framework for the later addition of the full text and relevant references.
    Keywords:  Background section; Research objectives; Structure of a scientific article; Writing process
    DOI:  https://doi.org/10.1186/s12998-026-00643-1
  20. Chiropr Man Therap. 2026 Sep 01. pii: 45. [Epub ahead of print]34(1):
      This is the last of three articles that provide step-by-step guides on how to structure the content of a scientific article to ensure a coherent and relevant text. The current article aims to help authors produce relevant and stringent Discussion sections that reflect clarity of thought and critical analysis, with contents driven by the research objectives. We first describe the purpose of the six typical elements of the typical Discussion section: (i) Summary of Findings, (ii) Explanation of Findings, (iii) Comparison of own results with other studies, (iv) Critique of own work, (v) Perspectives, and (vi) Conclusion. We show different placements and combinations of these and explain what they should include. We then suggest how to write a simple Summary of Findings and how to avoid re-writing the Background section in the Explanation of Findings. We show how to use the previously identified research gaps when comparing own results with similar studies, suggest different approaches for Critique of own work, define the types of Perspectives that are common in clinical and epidemiological studies, and explain how to provide relevant and memorable information in the Conclusion. Examples of how authors have dealt with different elements of the Discussion section have been selected from this journal. Finally, we discuss the use of artificial intelligence in the writing process. We hope that the three articles will help authors to plan their writing in a meaningful manner, thus saving time for themselves and resulting in articles that are easy to read and understand.
    Keywords:  Discussion section; Structure of a scientific article; Writing process
    DOI:  https://doi.org/10.1186/s12998-026-00645-z
  21. Chiropr Man Therap. 2026 Sep 01. pii: 44. [Epub ahead of print]34(1):
      This is the second of three articles that provide step-by-step guides on how to structure the content of a scientific article to ensure a coherent and relevant text. This article deals with the Methods and Results sections. We start by explaining the purpose and content of these sections and then provide a practical guide for planning the structure of each section as preparation for writing the full text later. Thus, we describe ten steps for structuring the Methods section and six steps for structuring the Results section. We illustrate our explanations with text examples selected from this journal to show how authors have approached various aspects of these two sections. After some tips for constructing informative tables and figures, we discuss the use of artificial intelligence when preparing the Methods and Results sections. The Methods section is fundamental to your reader understanding your study and trusting the validity of your findings, while the Results section provides answers to your stated research objectives or questions. Transparency and completeness are essential in both sections to assist your reader and reflect your academic integrity.
    Keywords:  Methods section; Results section; Structure of a scientific article; Writing process
    DOI:  https://doi.org/10.1186/s12998-026-00644-0
  22. J Nurs Scholarsh. 2026 Sep;58(5): e70133
      
    DOI:  https://doi.org/10.1111/jnu.70133
  23. Sci Diabetes Self Manag Care. 2026 Sep 02. 26350106261484750
      
    DOI:  https://doi.org/10.1177/26350106261484750
  24. Adv Health Sci Educ Theory Pract. 2026 Aug 31.
      A comment often made by reviewers (and editors) is that, despite having an interesting topic, an appropriate methodology, and interesting findings, the 'discussion' section of the manuscript they had to review was disappointing. Instead of offering a critical interpretation of the results or findings, the discussion section did not go beyond a summary of the results, such that the reviewer struggled to see what the study added to the existing body of knowledge. In this Q&Q, the discussion section in academic writing is placed under the spotlight. The role and purpose of this important part of an academic paper are explored, and ways in which authors can do justice to their findings considered.
    DOI:  https://doi.org/10.1007/s10459-026-10578-0
  25. Lung Cancer. 2026 Aug 27. pii: S0169-5002(26)00654-9. [Epub ahead of print] 109593
      
    DOI:  https://doi.org/10.1016/j.lungcan.2026.109593
  26. Psychotherapy (Chic). 2026 Aug 31.
      In this article, Mark Hilsenroth and Jesse Owen describe the influence of Charlie Gelso on their editorial terms. Gelso was the fifth editor of our beloved journal to be followed by Hilsenroth (sixth editor) and then Owen (seventh and current editor). Gelso provided mentorship, wisdom, grace, and patience. His service as editor of Psychotherapy stands as one of the many ways he has strengthened and advanced our profession. He helped us continue the positive traditions of the journal. He embodied his work on the real relationship in his mentorship. He will be greatly missed but not forgotten. (PsycInfo Database Record (c) 2026 APA, all rights reserved).
    DOI:  https://doi.org/10.1037/pst0000635
  27. J Postgrad Med. 2026 Jul 01. 72(3): 103-104
      
    DOI:  https://doi.org/10.4103/jpgm.jpgm_654_26