bims-skolko Biomed News
on Scholarly communication
Issue of 2025–07–20
33 papers selected by
Thomas Krichel, Open Library Society



  1. Nature. 2025 Jul 15.
      
    Keywords:  Machine learning; Medical research; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-025-02241-2
  2. Account Res. 2025 Jul 14. 1-22
       AIM: This scoping review aims to investigate the reasons for adopting the Contributor Roles Taxonomy (CRediT) in scholarly publishing, identify barriers to its implementation or concerns about its use, and propose improvements to enhance its effectiveness in attributing individual contributions to research articles.
    METHODS: A comprehensive literature search was conducted following PRISMA guidelines across multiple databases, including ProQuest, LISA, LISTA, EBSCO, PubMed, Scopus, and Web of Science Core Collection.
    RESULTS: From an initial pool of 732 papers, 45 were selected for inclusion in the review. The findings indicate that, while the adoption of CRediT promotes transparency and recognition of contributions beyond traditional authorship, several challenges remain. Key barriers include limited applicability across different research types, potential ethical concerns, and conflicts among contributors. Factors contributing to slow adoption include low awareness, inconsistent implementation, and cultural resistance within the research community. Additionally, ambiguous role definitions complicate attribution and fairness.
    CONCLUSIONS: This review highlights CRediT's potential to enhance transparency and equitable recognition of diverse contributions in scholarly publishing. However, it underscores the need to address internal challenges and promote broader acceptance within the research community. Recommendations include establishing clearer role hierarchies, standardizing adoption policies, and integrating CRediT into metadata for improved contribution tracking.
    Keywords:  Authorship; CRediT taxonomy; contributor roles; research integrity; scoping review
    DOI:  https://doi.org/10.1080/08989621.2025.2528953
  3. Ear Nose Throat J. 2025 Jul 17. 1455613251360112
      
    Keywords:  Authorship misconduct; artificial intelligence; paper mill; plagiarism; publication ethics; publish or perish; salami slicing
    DOI:  https://doi.org/10.1177/01455613251360112
  4. J Dent Res. 2025 Jul 17. 220345251349804
      In recent years, the landscape of scientific publishing has experienced exponential growth, driven in part by the increasing availability of data and advanced analytical methods, by incentives set by the scientific career system and by increasing options of publication routes, with diverging rigor in peer review. While this surge offers unprecedented opportunities for exploration and innovation, it also introduces challenges that potentially compromise the quality and accessibility of scientific literature, as the number of published articles significantly outpaces the number of scientists and, hence, available peer reviewers. Moreover, the increasing complexity of scientific outputs challenges the options for comprehensive, in-depth review and reproduction. We here examine the drivers of this phenomenon, its implications for the dental research community, and potential solutions to ensure a sustainable and rigorous publishing ecosystem. Emphasizing the importance of quality over quantity, we advocate for systemic changes in academic incentives, promoting open science, and enforcing robust peer-review standards. We further summarize the recent statement of the International Committee of Medical Journal Editors toward predatory journals; the Journal of Dental Research actively endorses this statement.
    Keywords:  big data; editorial policies; open access publishing; peer review; research; science
    DOI:  https://doi.org/10.1177/00220345251349804
  5. Nature. 2025 Jul;643(8072): 638
      
    Keywords:  Publishing; Research management
    DOI:  https://doi.org/10.1038/d41586-025-02217-2
  6. Can J Anaesth. 2025 Jul 14.
      
    Keywords:  author; authorship; authorship abuse; editor; leadership; misconduct; publishing; speaking up; whistleblower
    DOI:  https://doi.org/10.1007/s12630-025-03021-2
  7. Psychon Bull Rev. 2025 Jul 16.
      After a decade of data falsification scandals and replication failures in psychology and related empirical disciplines, there are urgent calls for open science and structural reform in the publishing industry. In the meantime, however, researchers need to learn how to recognize tell-tale signs of methodological and conceptual shortcomings that make a published claim suspect. I review four key problems and propose simple ways to detect them. First, the study may be fake; if in doubt, inspect the authors' and journal's profiles and request to see the raw data to check for inconsistencies. Second, there may be too little data; low precision of effect sizes is a clear warning sign of this. Third, the data may not be analyzed correctly; excessive flexibility in data analysis can be deduced from signs of data dredging and convoluted post hoc theorizing in the text, while violations of model assumptions can be detected by examining plots of observed data and model predictions. Fourth, the conclusions may not be justified by the data; common issues are inappropriate acceptance of the null hypothesis, biased meta-analyses, over-generalization over unmodeled variance, hidden confounds, and unspecific theoretical predictions. The main takeaways are to verify that the methodology is robust and to distinguish between what the actual results are and what the authors claim these results mean when citing empirical work. Critical evaluation of published evidence is an essential skill to develop as it can prevent researchers from pursuing unproductive avenues and ensure better trustworthiness of science as a whole.
    Keywords:  Power; Replication; Research integrity; Statistics
    DOI:  https://doi.org/10.3758/s13423-025-02740-3
  8. Rev Med Inst Mex Seguro Soc. 2025 Jul 01. 63(4): e6384
      Accuracy in bibliographic references is a fundamental aspect of scientific communication, particularly in the health sciences, where knowledge traceability carries clinical, ethical, and educational implications. This article analyzes the limitations of the Vancouver style in its editorial implementation and argues for the standardization of the NLM format as a common technical framework. Through a critical review of the literature, it identifies frequent problems resulting from the multiplicity of citation styles, such as referencing errors, ambiguity in editorial policies, and deficiencies in academic training on citation practices. Empirical studies are presented that highlight the low accuracy of references generated by reference managers without supervision, as well as the inconsistency of citation criteria among biomedical journal editors. The article proposes specific institutional actions, including incorporating reference quality into thesis evaluation rubrics, formalizing the librarian's role in the editorial review process, and developing unified citation guidelines. It also emphasizes the need for an educational approach that goes beyond mechanical style application and fosters a critical understanding of citation as an ethical and strategic practice. The article concludes that the adoption of the NLM format, supported by specialized training and institutional policies, would enhance transparency, efficiency, and reliability in biomedical scientific publishing.
    Keywords:  Data Accuracy; Ethics, Research; Scientific and Technical Publications
    DOI:  https://doi.org/10.5281/zenodo.15644343
  9. Allergy. 2025 Jul 17.
      
    Keywords:  artificial intelligence; immunology; retractions; statistical reviews
    DOI:  https://doi.org/10.1111/all.16669
  10. Nature. 2025 Jul 11.
      
    Keywords:  Machine learning; Peer review; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-025-02172-y
  11. Acad Radiol. 2025 Jul 17. pii: S1076-6332(25)00637-3. [Epub ahead of print]
       RATIONALE AND OBJECTIVES: Large language models (LLMs) show promise in radiology through various clinical applications as well as in assisting with research manuscript development. Recent studies show 52.6% of medical researchers use LLMs in manuscript development, with non-medical researchers showing similar rates. Given concerns about hallucinations, bias, etc., many publishers now require disclosure of LLM use. While most medical imaging journals have LLM policies as of 2025, the actual disclosure rates for LLM usage remain unknown. Our study examines trends in LLM disclosure by analyzing 1998 radiology publications for LLM disclosures.
    MATERIALS AND METHODS: A bibliometric analysis of nine radiology journals with LLM use disclosure requirements was performed. The study included primary investigations and secondary research while excluding short-form publications. The LLM disclosure rate was calculated overall. Logistic regression assessed temporal trends in disclosure rates, while a linear mixed effects model evaluated the relationship between disclosure status and peer review duration. Chi-square analysis examined associations between manuscript type and disclosure rates.
    RESULTS: Of 1998 manuscripts, 34 (1.7%) declared LLM use. Most disclosures involved ChatGPT (32, 94.1%), primarily for readability/grammar purposes (33, 97.1%). The majority of manuscripts disclosing LLM use originated from institutions in non-English speaking countries (22, 64.7%). No significant increase in disclosure rates over time was observed (OR: 1.06 [95% CI: 0.98, 1.16], p=0.15), and no relationship with peer review duration (coefficient: -4.85, SE=11.25, p=0.67) was found. Secondary research manuscripts disclosed LLM use more frequently (3.9% vs. 1.3%, p<0.001) with a small effect size (Cramer's V: 0.08 [0.04, 1.00]).
    CONCLUSION: Our findings demonstrate remarkably low disclosure rates in radiology manuscripts despite surveys indicating significant LLM adoption among researchers. This discrepancy may result from true non-use, fear of stigma, perceived advantages of undisclosed use, disagreement with disclosure requirements for minor editing, or policy unawareness, among other reasons. These findings suggest a need for more accepting research environments that recognize legitimate LLM benefits while developing nuanced disclosure policies addressing risks.
    Keywords:  Generative artificial intelligence; Large language models; Research disclosure
    DOI:  https://doi.org/10.1016/j.acra.2025.06.057
  12. PLoS One. 2025 ;20(7): e0328271
       BACKGROUND: Well-reported scientific abstracts are essential as they provide a concise summary of key research findings. Our study aimed to assess the completeness of reporting in abstracts of randomized controlled trials (RCTs) in dental medicine using the CONSORT for Abstracts (CONSORT-A) checklist.
    METHODS: This was a methodological cross-sectional study. We searched PubMed for RCTs published between August 2015 and August 2023 in Q1 journals from the "Dentistry, Oral Surgery & Medicine" category of the Journal Citation Reports. Two authors independently screened the records and assessed their adherence to 15 CONSORT-A items (items Authors and Recruitment were not assessed) for each abstract. All items were scored with '1' if reported adequately (in line with CONSORT-A), '0' if reported inadequately, and '0.5' if the reporting was partially adequate. We calculated each abstract's adherence (percentage) rate and median adherence across all abstracts. The adherence to CONSORT-A items was determined by dividing the number of articles that reported each item adequately by the total number of articles included. We also conducted a Jonckheere-Terpstra trend test to assess the temporal trend.
    RESULTS: The search resulted in 1691 records, of which 1564 were eligible for inclusion. We analyzed a random sample of 400 abstracts. Median adherence to CONSORT-A overall was 43.3% (95% CI 43.3 to 43.3). Items with the highest adherence scores were 'Conclusions', 'Objective', and 'Interventions', while 'Funding', 'Randomization', and 'Harms' had the lowest adherence scores. Median adherence to CONSORT-A has not improved over time (p = 0.342). For each analyzed year, mean adherence to CONSORT-A was around 40%.
    CONCLUSIONS: Reporting in abstracts of RCTs in dental medicine was suboptimal, and there was no improvement from 2015 to 2023. Improved guideline enforcement and author education are vital for enhancing abstract reporting quality and transparency.
    DOI:  https://doi.org/10.1371/journal.pone.0328271
  13. PLoS One. 2025 ;20(7): e0326754
      Materials science and engineering (MSE) research has, for the most part, escaped the doubts raised about the reliability of the scientific literature by recent large-scale replication studies in psychology and cancer biology. However, users on post-publication peer review sites have recently identified dozens of articles where the make and model of the scanning electron microscope (SEM) listed in the text of the paper does not match the instrument's metadata visible in the images in the published article. In order to systematically investigate this potential risk to the MSE literature, we develop a semi-automated approach to scan published figures for this metadata and check it against the SEM instrument identified in the text. Starting from an exhaustive set of 1,067,108 articles published since 2010 in 50 journals with impact factors ranging from 2 to 24, we identify 11,314 articles for which SEM manufacturer and model can be identified in an image's metadata. For 21.2% of those articles, the image metadata does not match the SEM manufacturer or model listed in the text and, for another 24.7%, at least some of the instruments used in the study are not reported. We find that articles with SEM misidentification are more likely to have existing observations of improprieties made on post-publication peer review site PubPeer than other MSE articles and that a subset of these articles within the subfield of electrochemistry are more likely to incorrectly estimate the optical band gap if the article features SEM misidentification. This suggests that SEM misidentification may be a tractable signature for flagging problematic MSE articles. Unexplained patterns common to many of these articles suggest the involvement of paper mills, organizations that mass-produce, sell authorship on, and publish fraudulent scientific manuscripts at scale.
    DOI:  https://doi.org/10.1371/journal.pone.0326754
  14. Res Integr Peer Rev. 2025 Jul 18. 10(1): 15
       BACKGROUND: Case reports are valuable tools that illustrate and analyze practical scenarios, novel problems, and the effectiveness of interventions. In psychiatry they often explore unique and potentially stigmatizing aspects of mental health, underscoring the importance of confidentiality and informed consent. However, journals' guidance on consent and confidentiality for case reports varies. In 2013, an international expert group developed the CAse REports (CARE) Guidelines for best practices in case reports, which include guidelines for informed consent and de-identification. In 2016, the Committee on Publication Ethics (COPE) issued ethical standards for publishing case reports, calling for written informed consent from featured patients.
    METHODS: Using a cross-sectional approach, we assessed the instructions for authors of 253 indexed psychiatry journals, of which 129 had published English-language case reports in the prior five years. Our research identified and evaluated journals' use of COPE and CARE guidelines on informed consent and de-identification in case reports.
    RESULTS: Among these 129 journals, 84 (65%) referred to COPE guidelines, and 59 (46%) referenced CARE guidelines. Furthermore, 46 (36%) required informed consent without de-identification, 7 (5%) required only de-identification, and 21 (16%) required both, specifying consent for identifying information. Notably, 40 (31%) lacked informed consent instructions. Of the 82 journals that required informed consent, 69 (85%) required documentation of consent.
    CONCLUSION: A decade after the publication of expert guidance, psychiatry journals remain inconsistent in their adherence to ethical guidelines for informed consent in case reports. More attention to clear instructions from journals on informed consent-a notable topic across different fields-would provide an important educational message about both publication ethics and fundamental respect for patients' confidentiality.
    Keywords:  Case Reports; De-identification; Informed Consent; Psychiatry Journals; Publication Ethics
    DOI:  https://doi.org/10.1186/s41073-025-00171-1
  15. Sci Data. 2025 Jul 15. 12(1): 1239
      Many cardiovascular disease (CVD) journals request data sharing statements upon trial report submission, but their compliance in publishing these statements remains unclear. We therefore performed a quantitative analysis to evaluate the current practice of the publications of data sharing statements in clinical trials by CVD journals, which included 78 CVD journals that published clinical trials from Jan 2019 to Dec 2022 and had data sharing statement request. Multivariable logistic regression analysis was used to examine the association between journal characteristics and journals' publications of statements. We also ran an online qualitative survey by sending anonymous questionnaires to editors-in-chief from CVD journals for their opinions on journals' publications of statements, trying to further explore why the journals did not publish statements. Their perspectives could provide in-depth information on and new insights into promoting publications of data sharing statements. This quantitative and qualitative analysis assessing the current practice of publishing data sharing statements by CVD journals, may generate new evidence to promote the actual data sharing and transparency in CVD trials.
    DOI:  https://doi.org/10.1038/s41597-025-05510-x
  16. J Pediatr. 2025 Jul 09. pii: S0022-3476(25)00255-0. [Epub ahead of print] 114714
       OBJECTIVE: To evaluate the prevalence of reporting guideline and clinical trial registration requirements in the "instructions for authors" pages of pediatric journals since a previously completed 2010 publication.
    STUDY DESIGN: This cross-sectional study analyzed 100 peer-reviewed pediatric journals identified through the 2021 Scopus CiteSource tool. Two investigators independently reviewed journals' "instructions for authors" pages on December 10, 2023, for references to the Enhancing the QUAlity and Transparency Of health Research (EQUATOR) Network, International Committee of Medical Journal Editors, specific reporting guidelines, and clinical trial registration requirements.
    RESULTS: Among the 100 journals analyzed, 33% (33/100) did not reference any specific reporting guidelines. Of 98 journals assessed for clinical trial registration, 43% (42/98) failed to mention study registration. EQUATOR Network guidelines were mentioned by 39% (39/100) of journals, and ICMJE was referenced by 68% (68/100). CONSORT and PRISMA were the most cited reporting guidelines, mentioned by 52% (51/98) and 41% (41/100) of journals, respectively. In contrast, 95% (94/99) of journals did not reference MOOSE, and 99% (99/100) omitted QUOROM.
    CONCLUSION: Pediatric journals inadequately endorse reporting guidelines and clinical trial registration in their author instructions. These tools are critical for improving research quality, transparency, and reproducibility. Pediatric journals should strengthen publication policies to mandate these practices. Further research is needed to explore barriers and incentives for adoption to enhance integration into clinical research.
    Keywords:  Guidelines; Pediatrics; Registration; Requirements
    DOI:  https://doi.org/10.1016/j.jpeds.2025.114714
  17. J Exp Biol. 2025 Jul 01. pii: jeb250590. [Epub ahead of print]228(13):
      The deposition of pre-peer-reviewed scientific articles in repositories as preprints has been practised for over 50 years. Recently, the popularity of this practice has surged, particularly in chemistry and physics disciplines. In the life sciences, bioRxiv is a popular preprint server; however, its usage varies greatly between fields. Preprinting is not common practice within comparative physiology, with the number of manuscripts submitted lagging far behind that seen in other fields. In this Perspective, we dig into the possible explanations for this difference. We explore common concerns regarding the deposition and use of preprints and highlight some relevant reasons why preprints are helpful to the field of comparative physiology. We strongly believe that use of preprints can help to improve transparency in the scientific publishing process and will be an important component of publishing for all fields of science in the future.
    Keywords:  Comparative physiology; Open access; Peer review; Transparency
    DOI:  https://doi.org/10.1242/jeb.250590
  18. Lancet Respir Med. 2025 Jul 10. pii: S2213-2600(25)00193-6. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1016/S2213-2600(25)00193-6
  19. Surgeon. 2025 Jul 12. pii: S1479-666X(25)00121-0. [Epub ahead of print]
       BACKGROUND: The proliferation of open access (OA) publishing has been accompanied by a rise in unsolicited academic correspondence, often originating from so-called "predatory" publishers. Early-career surgeons may be particularly vulnerable to predatory journals due to pressure to publish in order to enter and advance through training. This observational study aims to characterize the nature and volume of unsolicited emails received by a surgical trainee following the publication of a single paper.
    METHODS: All unsolicited emails received by the author between September 10th 2024 and December 31st 2024, were collated and analysed. Emails were assessed for their origin, journal/publisher, structure, requested contribution, relevance and associated Article Processing Charges (APCs). Where emails lacked this information, it was sought from journal and publisher websites. Publication legitimacy was assessed by the journal or publisher's presence on Beall's list of potential predatory journals, inclusion in the Directory of Open Access Journals (DOAJ) and the Committee on Publication Ethics (COPE).
    RESULTS: A total of 264 emails were received, 227 of which were soliciting journal articles. These represented 109 individual journals, comprising 44 publishers and 10 standalone journals. High levels of flattery (92.95 %) and poor grammar (91.19 %) were noted in the emails. In terms of legitimacy, 87.15 % (n = 95) were on Beall's list whereas 8 (7.3 %) were members of COPE and 2 (1.8 %) listed in DOAJ. APCs were mentioned in 36.56 % of emails and clearly stated in 11.45 %. The mean APC was 2006.18 USD, median APC was 1988.5 USD. Withdrawal fees were charged by 58.7 % (n = 64) of journals with a mean cost of 1039.68 USD and median cost of 680.25 USD. The remaining emails included conference invites (n = 28), editorial board invites (n = 6) and book chapter requests (n = 3).
    CONCLUSION: This study highlights the high volume and typical characteristics of predatory journal solicitations following a single publication. With increasing pressure on surgical trainees to publish, awareness of predatory practices is essential. Transparent vetting tools and guidance from training bodies are needed to safeguard academic standards in surgical training.
    Keywords:  “Open access”; “Predatory journals”; “Research integrity”
    DOI:  https://doi.org/10.1016/j.surge.2025.07.002
  20. BMJ Open. 2025 Jul 16. 15(7): e095778
       INTRODUCTION: Acknowledging equality, diversity and inclusion (EDI) in research is not only a moral imperative but also an important step in avoiding bias and ensuring generalisability of results. This protocol describes the development of STAndards for ReporTing EDI (START-EDI) in research, which will provide a set of minimum standards to help researchers improve their consistency, completeness and transparency in EDI reporting. We anticipate that these guidelines will benefit authors, reviewers, editors, funding organisations, healthcare providers, patients and the public.
    METHODS AND ANALYSIS: To create START-EDI reporting guidelines, the following five stages are proposed: (i) establish a diverse, multidisciplinary Steering Committee that will lead and coordinate guideline development; (ii) a systematic review to identify the essential principles and methodological approaches for EDI to generate preliminary checklist items; (iii) conduct an international Delphi process to reach a consensus on the checklist items; (iv) finalise the reporting guidelines and create a separate explanation and elaboration document; and (v) broad dissemination and implementation of START-EDI guidelines. We will work with patient and public involvement representatives and under-served groups in research throughout the project stages.
    ETHICS AND DISSEMINATION: The study has received ethical approval from the Imperial College London Research Ethics Committee (study ID: 7592283). The reporting guidelines will be published in open access peer-reviewed publications and presented in international conferences, and disseminated through community networks and forums.
    TRIAL REGISTRATION NUMBER: The project is pre-registered within the Open Science Framework (https://osf.io/8udbq/) and the Enhancing the Quality and Transparency of Health Research Network.
    Keywords:  Delphi Technique; Health Equity; Protocols & guidelines
    DOI:  https://doi.org/10.1136/bmjopen-2024-095778
  21. Rev Med Inst Mex Seguro Soc. 2025 Jul 01. 63(4): e6168
      Over the past decade, the Revista Médica del IMSS has established itself as a cornerstone in the dissemination of scientific health knowledge, standing out for its open-access model with no charges for authors or readers. In response to the evolving editorial landscape and equity challenges in science, the journal adopted Open Journal Systems version 3.4, enhancing its efficiency, visibility, and global integration. This modernization has significantly increased its impact, with millions of views, ranking it among the most-read publications in Latin America. With an editorial policy grounded in ethics, transparency, and quality, the journal reaffirms IMSS's commitment to open, equitable, and socially valuable science. This inclusive publishing model has positioned the Institute as a regional leader in the management and democratization of biomedical knowledge.
    Keywords:  Artificial Intelligence; Electronic Journals; Science
    DOI:  https://doi.org/10.5281/zenodo.15644206
  22. Nature. 2025 Jul;643(8072): 638
      
    Keywords:  Publishing; Research management; Scientific community
    DOI:  https://doi.org/10.1038/d41586-025-02219-0