bims-skolko Biomed News
on Scholarly communication
Issue of 2024–09–22
29 papers selected by
Thomas Krichel, Open Library Society



  1. Account Res. 2024 Sep 18. 1-19
      Given animal research is challenged with inadequacies, e.g., animal-to-human knowledge translation, ethical considerations, and cost:benefit, new approach methodologies (NAMs) have been proposed as a replacement. With reference to the field of nutrition and dietetics, our aim was to examine the policies of its leading journals regarding human-based vs. traditional animal-based research; and to explore emerging NAMs that provide alternatives to animal experimentation. We reviewed 100 leading journals from an established database (SCImago Journal Rankings) in the nutrition and dietetics category for the year 2022. Eighty-three journals met the inclusion criteria. NAMs were extracted from a range of established sources. 9.6% (n = 8) of journals state they do not publish animal-based studies; 4.8% (n = 4) consider animal studies with qualifications, whereas the remaining 85.5% (n = 71) publish animal studies without qualification. Across sources, NAMs commonalities were identified including in vitro, in chemico, and in silico methods; and individual and population-based studies. Of leading nutrition/dietetic journals, relatively few have shifted to strictly non-animal methods. Greater attention to the increasing range of NAMs may not only reduce the need for animal research in the field, but may provide superior human-relevant outcomes. Studies are needed to establish their potential superiority.
    Keywords:  Animal experimentation; benchmark; human-relevant research; new approach methodologies; scientific paradigms
    DOI:  https://doi.org/10.1080/08989621.2024.2398104
  2. Perspect Med Educ. 2024 ;13(1): 442-451
       Introduction: For authors, selecting a target journal to submit a manuscript is a critical decision with career implications. In the discipline of medical education, research conducted in 2016 found that authors were influenced by multiple factors such as a journal's prestige and its mission. However, since this research was conducted the publishing landscape has shifted to include a broader variety of journals, an increased threat of predatory journals, and new publishing models. This study updates and expands upon how medical education authors decide which journal to submit to with the aim of describing the motivational factors and journal characteristics that guide authors' decision making.
    Methods: The authors conducted five qualitative focus groups in which twenty-two medical education authors and editors participated. During the focus groups participants were engaged in a discussion about how they select a journal to submit their manuscripts. Audio from all focus groups was transcribed. Transcripts were analyzed using codebook thematic analysis.
    Results: Participants considered multiple factors when selecting a target journal. Factors included a journal's impact, the scope of a journal, journal quality, and technical factors (e.g., word limits). Participants also described how social factors influenced their process and that open access plays a role that could both encourage or deter submission.
    Discussion: The findings describe the motivational factors and influential signals that guide authors in their journal selection decision making. These findings confirm, extend, and update journal selection factors reported in medical education and other disciplines. Notably, these findings emphasize the role of social factors, relationships and personal experiences, which were absent from previous work. Additionally, we observed increased consideration of open acces and a shift away from an emphasis on journal prestige.
    DOI:  https://doi.org/10.5334/pme.1517
  3. J Undergrad Neurosci Educ. 2024 ;22(2): A116-A119
      microPublication Biology (micropublication.org) is a non-profit, community-focused, peer-reviewed journal dedicated to publishing small (single-figure) reports of data, methods and software related to a variety of model organisms. A workshop on microPublications at the Faculty for Undergraduate Neuroscience (FUN) conference in Summer 2023 focused on 1) publishing data-especially student research experiences, and data gathered through course-based research, and 2) using the microPublication platform and article template in teaching and learning. In this article, we further describe the microPublication platform and workflow and how PI's can use this venue to publish student work. We also provide examples of how the microPublication format can be adapted and adopted as tools for undergraduate teaching and learning.
    Keywords:  course-based undergraduate research experience (CURE); microPublication; peer-review; undergraduate research; undergraduate teaching
    DOI:  https://doi.org/10.59390/AUIV7625
  4. Nature. 2024 Sep;633(8030): 525
      
    Keywords:  Ethics; Intellectual-property rights; Lab life; Publishing
    DOI:  https://doi.org/10.1038/d41586-024-03024-x
  5. Med Hist. 2024 Sep 13. 1-21
      Medical practitioners, inevitably scattered across the country, need frequent periodicals to communicate the latest medical information. Journals are an essential component of the infrastructure of modern medicine, yet they were slow to achieve firm roots in Britain during the eighteenth century, with few sustained quarterly periodicals and the only attempt at a monthly lasting a year. Then in 1799, Richard Phillips, owner of the Monthly Magazine, published the Medical and Physical Journal, the first sustained monthly medical journal, which lasted for thirty-four years. Ever since, Britain has never been without a monthly or weekly general medical journal. Responding to the need for a strong commercial focus, the Journal used a magazine format which blended reviews and abstracts of already published material with original contributions and medical news, and it quickly achieved a national circulation by close engagement with all types of practitioners across the country.Contrary to the historiography, the Journal was distinctly different from the contemporaneous monthly science journals. The key to success was two-way communication with all practitioners, especially the numerous surgeons and surgeon-apothecaries who were increasingly better trained and confident of their status. Much of the content of the Journal was written by these readers, and with rapid, reliable distribution and quick publication of correspondence, controversial topics could be bounced back and forth between all practitioners, including the distinguished. Initially, the editors tried to maximise circulation by avoiding any controversy, but this started to change in the first few years of the next century.
    Keywords:  London Medical Journal; Medical and Physical Journal; Medical journals; Medical readers; Richard Phillips; Surgeons
    DOI:  https://doi.org/10.1017/mdh.2024.19
  6. Science. 2024 Sep 20. 385(6715): 1263
      In first regulatory overhaul in 20 years, Office of Research Integrity takes modest steps toward greater transparency.
    DOI:  https://doi.org/10.1126/science.adt2251
  7. Arq Bras Oftalmol. 2024 ;pii: S0004-27492024000500909. [Epub ahead of print]87(5): e20240177
      
    DOI:  https://doi.org/10.5935/0004-2749.2024-0177
  8. Nature. 2024 Sep;633(8030): S5
      
    Keywords:  Machine learning; Publishing; Society; Technology
    DOI:  https://doi.org/10.1038/d41586-024-02984-4
  9. Account Res. 2024 Sep 18. 1-7
       PURPOSE: The increasing use of AI tools, particularly large language models like ChatGPT, in academic research has raised significant questions about authorship and transparency. This commentary emphasizes the need for a standardized AI contributions taxonomy to clarify AI's role in producing and publishing research outputs, ensuring ethical standards and maintaining academic integrity.
    APPROACH: We propose adapting the NIST AI Use Taxonomy and incorporating categories that reflect AI's use in tasks such as hypothesis generation, data analysis, manuscript preparation, and ethical oversight. Findings: Establishing an AI contributions taxonomy for the production and publication of research output would address inconsistencies in AI disclosure, enhance transparency, and uphold accountability in research. It would help differentiate between AI-assisted and human-led tasks, providing more explicit attribution of contributions.
    FINDINGS: Establishing an AI contributions taxonomy for the production and publication of research output would address inconsistencies in AI disclosure, enhance transparency, and uphold accountability in research. It would help differentiate between AI-assisted and human-led tasks, providing more explicit attribution of contributions.
    PRACTICAL IMPLICATIONS: The proposed taxonomy would offer researchers and journals a standardized method for disclosing AI's role in academic work, promoting responsible and transparent reporting aligned with ethical guidelines from COPE and ICMJE.
    VALUE: A well-defined AI contributions taxonomy for the production and publication of research output would foster transparency and trust in using AI in research, ensuring that AI's role is appropriately acknowledged while preserving academic integrity.
    Keywords:  AI contributions taxonomy; Artificial intelligence (AI); NIST AI use taxonomy; ethics; publishing
    DOI:  https://doi.org/10.1080/08989621.2024.2405039
  10. AJNR Am J Neuroradiol. 2024 Sep 17. pii: ajnr.A8505. [Epub ahead of print]
       BACKGROUND AND PURPOSE: We aimed to evaluate GPT-4's ability to write radiology editorials and to compare these with human-written counterparts, thereby determining their real-world applicability for scientific writing.
    MATERIALS AND METHODS: Sixteen editorials from eight journals were included. To generate the AI-written editorials, the summary of 16 human-written editorials was fed into GPT-4. Six experienced editors reviewed the articles. First, an unpaired approach was used. The raters were asked to evaluate the content of each article using a 1-5 Likert scale across specified metrics. Then, they determined whether the editorials were written by humans or AI. The articles were then evaluated in pairs to determine which article was generated by AI and which should be published. Finally, the articles were analyzed with an AI detector and for plagiarism.
    RESULTS: The human-written articles had a median AI probability score of 2.0%, whereas the AI-written articles had 58%. The median similarity score among AI-written articles was 3%. 58% of unpaired articles were correctly classified regarding authorship. Rating accuracy was increased to 70% in the paired setting. AI-written articles received slightly higher scores in most metrics. When stratified by perception, human-written perceived articles were rated higher in most categories. In the paired setting, raters strongly preferred publishing the article they perceived as human-written (82%).
    CONCLUSIONS: GPT-4 can write high-quality articles that iThenticate does not flag as plagiarized, which may go undetected by editors, and that detection tools can detect to a limited extent. Editors showed a positive bias toward human-written articles.
    ABBREVIATIONS: AI = Artificial intelligence; LLM = large language model; SD = standard deviation.
    DOI:  https://doi.org/10.3174/ajnr.A8505
  11. Nature. 2024 Sep;633(8030): S18-S20
      
    Keywords:  Careers; Machine learning; Peer review; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-024-02989-z
  12. Res Synth Methods. 2024 Sep 14.
       BACKGROUND: Data sharing improves the value, synthesis, and integrity of research, but rates are low. Data sharing might be improved if data sharing policies were prominent and actionable at every stage of research. We aimed to systematically describe the epidemiology of data sharing policies across the health research lifecycle.
    METHODS: This was a cross-sectional analysis of the data sharing policies of the largest health research funders, all national ethics committees, all clinical trial registries, the highest-impact medical journals, and all medical research data repositories. Stakeholders' official websites, online reports, and other records were reviewed up to May 2022. The strength and characteristics of their data sharing policies were assessed, including their policies on data sharing intention statements (a.k.a. data accessibility statements) and on data sharing specifically for coronavirus disease studies. Data were manually extracted in duplicate, and policies were descriptively analysed by their stakeholder and characteristics.
    RESULTS: Nine hundred and thirty-five eligible stakeholders were identified: 110 funders, 124 ethics committees, 18 trial registries, 273 journals, and 410 data repositories. Data sharing was required by 41% (45/110) of funders, no ethics committees or trial registries, 19% (52/273) of journals and 6% (24/410) of data repositories. Among funder types, a higher proportion of private (63%, 35/55) and philanthropic (67%, 4/6) funders required data sharing than public funders (12%, 6/49).
    CONCLUSION: Data sharing requirements, and even recommendations, were insufficient across health research. Where data sharing was required or recommended, there was limited guidance on implementation. We describe multiple pathways to improve the implementation of data sharing. Public funders and ethics committees are two stakeholders with particularly important untapped opportunities.
    DOI:  https://doi.org/10.1002/jrsm.1757
  13. mBio. 2024 Sep 20. e0250624
      Microbiologists, like scientists in any other biomedical field, are too engrossed in writing research papers. Aided by both expanding research programs and shrinking resources, this will continue for the foreseeable time. In this editorial, I discuss a compelling need for all microbiologists to dedicate some time to writing non-research publications such as minireviews, perspectives, commentary, opinion/hypothesis, and other non-research article types. I also list the benefits to the field, of review articles and how they can have the potential to change the field. I have provided a handful of classic examples of reviews that clearly changed the field in a remarkable way as well as a number of reviews that clarified the field and facilitated future research.
    Keywords:  editorial; minireviews; non-primary research
    DOI:  https://doi.org/10.1128/mbio.02506-24
  14. Circ Cardiovasc Qual Outcomes. 2024 Sep;17(9): e010257
      
    Keywords:  goals; humans; information dissemination; prospective studies; public health
    DOI:  https://doi.org/10.1161/CIRCOUTCOMES.124.010257
  15. Arq Bras Oftalmol. 2024 ;pii: S0004-27492024000500100. [Epub ahead of print]87(5): e20241011
      
    DOI:  https://doi.org/10.5935/0004-2749.2024-1011
  16. Cureus. 2024 Aug;16(8): e66970
      Journal selection is very important for any researcher in every field. Publication in a reputable journal not only has a higher reach among a greater number of people but also sets a benchmark for significance and quality. This primer aims to guide researchers in the field of cardiothoracic research, including medicine, surgery, and imaging, to assist in journal selection for their respective articles. Journal selection depends on a variety of factors, such as impact factors, publication charges, review processes, article types that a journal accepts, and indexing. This primer highlights all these factors in detail that are essential for the selection of a suitable journal. The article emphasizes the importance of these factors in making a reasoned decision about journal selection. This article also focuses on different types of publication models and their implications, including hybrid open access, gold open access, and diamond open access. In conclusion, this primer aims to provide insights to researchers in the fields of cardiothoracic surgery, medicine, and imaging about the publication landscapes and guide them to strategically plan their submissions.
    Keywords:  article types; cardiology; cardiothoracic; case reports; impact factor; indexing; publication model
    DOI:  https://doi.org/10.7759/cureus.66970
  17. SAGE Open Med. 2024 ;12 20503121241274710
       Background: In the realm of academia, the publication of scientific research is not merely an act of dissemination; it serves as a pivotal milestone that signifies the culmination of rigorous investigation, critical analysis, and intellectual contribution.
    Aim: To examine the challenges and barriers encountered by faculty members in the process of publishing their work.
    Methods: The study utilized a descriptive cross-sectional design and was conducted from 1 March to 1 May 2022. A convenience sample of 358 faculty members from eight universities in Egypt, representing a diverse range of faculties. These faculties comprised five practical disciplines, namely, Nursing, Medicine, Science, Pharmacy, and Engineering, as well as three theoretical faculties including Al-Alsun (Languages), Arts, and Commerce. The universities involved in the study included Ain Shams, Cairo, Mansoura, Benha, Assiut, 6th of October, British University in Egypt (BUE), among others. Data were collected through an online questionnaire that included staff characteristics and barriers to scientific research and publishing. Hypothesis testing was conducted using appropriate statistical analysis methods (e.g., Chi-square test) to assess the relationships between faculty members' characteristics and barriers to publishing.
    Results: The faculty staff in our study reported the highest barriers to publishing scientific research in the domains of the reviewing process (74%), institutional support (67%), and scientific publishing process (60.9%). Conversely, the lowest barriers were found in the domains of frustration after rejection (55.1%), scientific writing barriers (46.1%), and loss of passion and causation of publishing barriers (41.3%).
    Conclusions: The results highlighted the need for increased support and resources to overcome these barriers and foster a positive culture of research and publishing in Egyptian universities.
    Keywords:  Scientific research; academic publishing; barriers; faculty member
    DOI:  https://doi.org/10.1177/20503121241274710
  18. Clin Exp Dermatol. 2024 Sep 14. pii: llae371. [Epub ahead of print]
      Although much has been written about peer review science, practical advice on HOW to peer review articles is lacking, especially for Dermatology. This article aims to provide a practical, stepwise framework to support new reviewers. Step 1 involves a rapid read of the manuscript to get a feel of the topic and to clarify the study question and design. Step 2 is a thorough slower read, using an appropriate EQUATOR checklist. Step 3 is to organise your comments to authors into major and minor points in a constructive way, focusing on clarity of question, internal validity, external validity and whether interpretation fits with the results. Finally, make a recommendation to the editor, indicating whether the study is publishable with suitable revision or whether it contains some fatal flaws. We hope that this practical guide will encourage and help new reviewers to take on this rewarding and important scientific task for patient benefit.
    DOI:  https://doi.org/10.1093/ced/llae371
  19. Int Endod J. 2024 Sep 19.
      The Preferred Reporting Items for Diagnostic Accuracy Studies in Endodontics (PRIDASE) 2024 guidelines are based on the Standards for Reporting of Diagnostic Accuracy Studies (STARD) 2015 guidelines and the Clinical and Laboratory Images in Publications (CLIP) principles, with the addition of items specifically related to endodontics. The use of the PRIDASE 2024 guidelines by authors and their application by journals during the peer review process will reduce the possibility of bias and enhance the quality of future diagnostic accuracy studies. The PRIDASE 2024 guidelines consist of a checklist containing 11 domains and 66 individual items. The purpose of the current document is to provide an explanation for each item on the PRIDASE 2024 checklist, along with examples from the literature to help readers understand their importance and offer advice to those developing manuscripts. A link to the PRIDASE 2024 explanation and elaboration document is available on the Preferred Reporting Items for study Designs in Endodontology (PRIDE) website (https://pride-endodonticguidelines.org/pridase/) and on the International Endodontic Journal website (https://onlinelibrary.wiley.com/page/journal/13652591/homepage/pride-guidelines.htm).
    Keywords:  PRIDASE 2024; diagnostic accuracy studies; endodontics; reporting guidelines; root canal treatment
    DOI:  https://doi.org/10.1111/iej.14148
  20. FEBS Lett. 2024 Sep 16.
      Although publication in scholarly peer-reviewed journals remains the gold standard for communication of findings in the life sciences, the gold has been debased in the digital age by various impurities, including (a) reviewer fatigue, (b) fraud, paper mills, and the perils of artificial intelligence, (c) predatory journals, (d) the ongoing use of journal impact factor as a proxy for individual article quality, and (e) salami-slicing and other unethical practices. In this article, I present a detailed overview of these problems, as well as solutions proposed and implemented to counter them. Finally, I suggest that these are all symptomatic of a wider problem, namely the culture of 'publish or perish' and ongoing issues with how researcher performance is evaluated for grant, hiring, and promotion decisions. Only by working towards a global shift in the way scientists view the purpose of publication can we finally remove the impurities and refine the gold.
    Keywords:  impact factor; paper mills; peer review; scholarly publishing
    DOI:  https://doi.org/10.1002/1873-3468.15018
  21. Psychiatry Res. 2024 Sep 11. pii: S0165-1781(24)00479-7. [Epub ahead of print]342 116194
      
    Keywords:  Abstract; Artificial intelligence; ChatGPT; Manuscript; Writing
    DOI:  https://doi.org/10.1016/j.psychres.2024.116194