bims-skolko Biomed News
on Scholarly communication
Issue of 2024–12–22
28 papers selected by
Thomas Krichel, Open Library Society



  1. Singapore Med J. 2024 Dec 01. 65(12): 657
      
    DOI:  https://doi.org/10.4103/singaporemedj.SMJ-2024-244
  2. Eur J Cardiothorac Surg. 2024 Dec 17. pii: ezae447. [Epub ahead of print]
      
    Keywords:  academic publishing; open access journals; open science; predatory journals; predatory publishing; society publishing
    DOI:  https://doi.org/10.1093/ejcts/ezae447
  3. Bull Cancer. 2024 Dec 17. pii: S0007-4551(24)00465-X. [Epub ahead of print]
      With the advent of the author-pays business model replacing subscription, mercantile publishers have created journals. They respond to the dissatisfaction of naive researchers faced with the difficulties of publishing quickly and widely. These publishers favour commercial interests over knowledge and do not respect good publication practices. The network of science academies and UNESCO distinguish three groups of publishers: fraudulent (predatory journals), of poor quality (journals of complacency that are not to be recommended) and of good quality (legitimate journals). Good and bad articles can be found in all journals. Quality journals have created special issues with rapid reviews to remain competitive. The proliferation of these journals is a source of misinformation. Paper mills are commercial scientific writing and communication companies that sell articles to researchers in order to put their name among the authors. There are social networks accounts to promote these articles and sell the authors' positions. Review and citation mills are also scams. Five factors have influenced these abuses: the monetisation of research results; the value of publishing a lot; the shortcomings of peer review; the lack of international certification of scientific journals; and artificial intelligence with its best and worst. The system can continue as long as there are satisfied researchers and institutional leaders do nothing. Fortunately, awareness is growing, but we are all waiting for our neighbours to change their practices.
    Keywords:  Intégrité de la recherche; Misconduct; Méconduites; Paper mills; Predatory journals; Research integrity; Revues prédatrices
    DOI:  https://doi.org/10.1016/j.bulcan.2024.12.002
  4. R Soc Open Sci. 2024 Dec;11(12): 240844
      The retraction of an article is probably the most severe outcome of a scientific project. While great emphasis has been placed on articles retracted due to scientific misconduct, studies show many retractions are due to honest errors. Unfortunately, in most cases, retraction notices do not provide sufficient information to determine the specific types and causes of these errors. In our study, we explored the research data management (RDM) errors that led to retractions from the authors' perspectives. We collected responses from 97 researchers from a broad range of disciplines using a survey design. Our exploratory results suggest that just about any type of RDM error can lead to the retraction of a paper, and these errors can occur at any stage of the data management workflow. The most frequently occurring cause of an error was inattention. The retraction was an extremely stressful experience for the majority of our sample, and most surveyed researchers introduced changes to their data management workflow as a result. Based on our findings, we propose that researchers revise their data management workflows as a whole instead of focusing on certain aspects of the process, with particular emphasis on tasks vulnerable to human fallibility.
    Keywords:  honest error; research data management; retraction
    DOI:  https://doi.org/10.1098/rsos.240844
  5. J R Soc N Z. 2025 ;55(2): 267-286
      Trustworthy literature is an essential part of knowledge, evidence-based information, and science. However, publications can contain mistakes or have results from unreliable research, which may compromise their integrity. In this review, we discuss publication integrity, with a focus on our field of biomedicine, and how it could be improved. In our experience, compromised publication integrity is frequently poorly handled, and we, and others, have reported that responses to publication integrity concerns can be inefficient, inconsistent, slow, opaque, and incomplete. Checklists and tools are now available to assist in the assessment of publication integrity, but systemic changes are needed. However, this requires many of the key parties involved (journals, publishers, institutions, academic societies, and regulators) to acknowledge and engage with the problem. There is little evidence of a willingness to do this. We conclude that it has been recognised for many years that the system for dealing with publication integrity is broken, but currently, there appears little interest in trying to improve it.
    Keywords:  Publication integrity; errors; expression of concern; fabrication; fraud; questionable research practices; research integrity; retraction
    DOI:  https://doi.org/10.1080/03036758.2024.2325004
  6. Eur Arch Otorhinolaryngol. 2024 Dec 19.
       PURPOSE: The determination of authorship order in scientific publications is critical for researcher recognition and career progression. According to a recent survey's meta-analysis, the prevalence of Honorary Authorship reaches 20% of authors. This study evaluates the adoption and proficency of authorship guidelines in maxillofacial surgery and otolaryngology.
    METHODS: On March 16, 2024, a search of Scopus-indexed journals identified relevant journals in from which recent articles were sampled using a stratified random method. The author contribution alignment with actual authorship was evaluated through CalculAuthor tool and a detailed process involving large language models (LLM) and manual checks, employing statistical tests to evaluate the adoption of author contribution guidelines and agreement scores across different fields and journal quartiles.
    RESULTS: A review of 21 Scopus-indexed journals revealed that 8 adhered to the CRediT system, 7 to other systems, and 6 had no guidelines. From 147 randomly selected manuscripts, 57 reported contributions (38.8%). The mean agreement score was 65.3% (SD = 26.8), without significant differences in journal quartiles or disciplines.
    CONCLUSIONS: This study highlights the moderate to low adoption of standardized contribution systems in maxillofacial and otolaryngology journals, with a fair level of agreement between reported contributions and actual authorship. Future research should focus on larger, more diverse samples and develop prospective implementations to ensure accurate and equitable authorship credit in the context of the Artificial Intelligence's scientific writing era.
    Keywords:  Authorship; CRediT; CalculAuthor; Maxillofacial surgery; Otolaryngology
    DOI:  https://doi.org/10.1007/s00405-024-09151-5
  7. Epidemiol Serv Saude. 2024 Dec 13. pii: S2237-96222024000101000. [Epub ahead of print]33 e20241001
      
    DOI:  https://doi.org/10.1590/S2237-96222024v33e20241001.en
  8. Science. 2024 Dec 20. 386(6728): 1331-1332
      Shoddy commentaries are a quick and dirty route to higher impact numbers.
    DOI:  https://doi.org/10.1126/science.adv4101
  9. Otolaryngol Head Neck Surg. 2024 Dec 17.
      Peer review is an essential cornerstone of scientific advancement. This process involves understanding study design, data analytics, and interpretation of the evidence. For clinicians who are performing their initial peer reviews, and even for seasoned reviewers who assess complex manuscripts, it can be helpful to have a standard approach. We therefore provide a conceptual framework for peer review which builds upon experiences that are already familiar to trainees and practicing clinicians, by drawing parallels between patient encounters and peer review. This framework has been used in successive years as a didactic tool for our trainees who are being mentored toward excellence in peer review.
    Keywords:  clinical frameworks; clinician training; evidence interpretation; peer review
    DOI:  https://doi.org/10.1002/ohn.1078
  10. Int J Nurs Educ Scholarsh. 2024 Jan 01. 21(1):
       INTRODUCTION: As AI tools have become popular in academia, concerns about their impact on student originality and academic integrity have arisen.
    METHODS: This quality improvement project examined first-year nurse anesthesiology students' use of AI for an academic writing assignment. Students generated, edited, and reflected on AI-produced content. Their work was analyzed for commonalities related to the perceived ease of use, accuracy, and overall impressions.
    RESULTS: Students found AI tools easy to use with fast results, but reported concerns with inaccuracies, superficiality, and unreliable citations and formatting. Despite these issues, some saw potential in AI for brainstorming and proofreading.
    IMPLICATIONS FOR INTERNATIONAL AUDIENCE: Clear guidelines are necessary for AI use in academia. Further research should explore AI's long-term impact on academic writing and learning outcomes.
    CONCLUSIONS: While AI tools offer speed and convenience, they currently lack the depth required for rigorous academic work.
    Keywords:  AI; academic writing; artificial intelligence; machine learning; nursing
    DOI:  https://doi.org/10.1515/ijnes-2024-0050
  11. Ann Surg Oncol. 2024 Dec 18.
      This letter responds to Matsubara's discussion on preserving personal tone in the age of artificial-intelligence-assisted writing. Assistive tools such as large language models (LLMs) can be helpful for busy authors and those who struggle with the English language. Personal linguistic style in a manuscript creates a sense of true authorship. However, LLMs can enhance productivity at various stages of manuscript preparation, not just writing it. Hence, authors may use LLMs judiciously to preserve their writing style or train the chatbots to align with the authors' unique writing style.
    Keywords:  Artificial intelligence; Individuality; Language; Medical faculty; Romanticism; Writing
    DOI:  https://doi.org/10.1245/s10434-024-16711-w
  12. Neurol Clin Pract. 2025 Feb;15(1): e200419
       Objective: To describe a pragmatic process for translating quality improvement (QI) projects into published manuscripts.
    Scope: Types of QI work that are generalizable and have broad relevance (to journals and readers), design principles that are important for publishable QI work, how QI manuscript organization might differ from biomedical manuscripts, how to use and not to use Standards for Quality Improvement Reporting Excellence and other guidelines, pitfalls, and how to avoid/repair them.
    DOI:  https://doi.org/10.1212/CPJ.0000000000200419
  13. PeerJ. 2024 ;12 e18619
       Introduction: Over the years, funding for urologic diseases has witnessed a steady rise, reaching $587 million in 2020 from $541 million in 2018. In parallel, there has been a notable increase in the total number of urology journals from 2011 to 2018. This surge in research funding and journal publications calls for urologists to effectively navigate through a vast body of evidence to make the best evidence-based clinical decisions. Our primary objective was to assess the "instructions for authors" of these journals to determine the extent of endorsement of reporting guidelines for common study designs in medical research.
    Methods: Top urology journals were identified using the 2021 Scopus CiteScore and confirmed via Google Scholar Metrics h5-index. In a masked, duplicate manner, two investigators retrieved data from the "instructions for authors" webpages of the included journals. For each journal investigated in our study, the following data were extracted: journal title, 5-year impact factor, email responses of journal editors, mention of the EQUATOR Network in the "instructions for authors," mention of the ICMJE in the "instruction for authors," geographical region of publication and statements about clinical trial registration.
    Results: Of the 92 urology journals examined, only one-third (32/92) mentioned the EQUATOR network in their "instructions for authors." A total of 17 journals (17/92, 18.5%) did not mention a single reporting guideline. The most endorsed guideline was CONSORT at 67.4% (62/92). Clinical trial registration was not mentioned by 28 (30%), recommended by 27 (29%), and required by 37 journals (40%).
    Conclusion: Our findings indicate that urology journals inconsistently endorse reporting guidelines and clinical trial registration. Based on these results, we propose that urology journals adopt a standardized approach, incorporating explicit requirements for reporting guidelines such as those listed on the EQUATOR Network and clinical trial registration for all relevant study designs. Specifically, journals should consider clearly stating mandatory or recommended guidelines for clinical trials, observational studies, and systematic reviews, among others. Future efforts should focus on evaluating the implementation of these policies and identifying barriers that hinder their adoption.
    Keywords:  Adherence; Guidelines; Urology
    DOI:  https://doi.org/10.7717/peerj.18619
  14. Rev Bras Enferm. 2024 ;pii: S0034-71672024001000163. [Epub ahead of print]77(6): e20230362
       OBJECTIVES: to analyze the editorial discourses of Acta Paulista de Enfermagem from 1988 to 2017.
    METHODS: qualitative, historical, oral research, with interviews with the journal's editors. Statements were categorized and presented in three decades, discussed from Foucault's archaeological perspective.
    RESULTS: seven statements presented three discourses. In the first decade, the discourse of knowledge registration and circulation presented statements of graduate studies and professional recognition. In the second decade, knowledge internationalization was added, with statements of business and editorial panopticism, selection criteria, indexing and digitalization. Finally, the discourse of shifting scientific assessment centrality was added with statements of preprint, open science, exclusive digitalization and mediatization of science.
    FINAL CONSIDERATIONS: the journal needed to adapt to form its official discourse, which made it possible, over the years, to change its initial peripheral position to a central one within scientific communication, supporting its panoptic role.
    DOI:  https://doi.org/10.1590/0034-7167-2023-0362
  15. Psychosom Med. 2025 Jan 01. 87(1): 57-58
       ABSTRACT: In April 2023, Psychosomatic Medicine, now renamed Biopsychosocial Science and Medicine, introduced registered reports as a new article format. Registered reports are a type of scientific article in which the research methods and proposed analyses are preregistered and peer-reviewed before the data are collected or analyzed. We were excited to be joining a growing number of journals internationally to offer this format and to be aligning with the Behavioral Medicine Research Council's statement on open science, recognizing the value of publishing registered reports in our field. Recent work has shown that there is a 2-year lag between journals adopting registered reports and publishing their first registered report. Therefore, right in line with this timetable, we are delighted to be publishing our first full registered report article in this first issue that bears the Journal's new name. This article is noteworthy for several reasons, not least because the findings make an important scientific contribution to the broader early life adversity literature but also because the article applies the registered report format to secondary data analyses. We hope that you, our readership, feel inspired to give the registered report approach a chance, whether it is for primary or secondary data collection approaches, and that you send your first, or next Stage 1 registered report to Biopsychosocial Science and Medicine.
    DOI:  https://doi.org/10.1097/PSY.0000000000001364
  16. Pan Afr Med J. 2024 ;48 182
       Introduction: breaches of research integrity have risen during these years. Tunisia´s stance regarding scientific integrity remains unknown. The aim of our study was to identify the reasons for the retraction of Tunisia-affiliated publications in the biomedical field, to describe the characteristics of these retractions, and to assess the position of Tunisian legislation regarding breaches of research integrity.
    Methods: I compiled up to November 3rd, 2023, and retracted biomedical papers using the PubMed and Retraction Watch databases. For each eligible retracted article, a descriptive study of the collected variables was carried out. These included the reasons for retraction, characteristics related to the article, authors, and journal.
    Results: the search identified 22 eligible publications. Reasons for retraction were categorized into six groups. Plagiarism accounted for 45.5% of cases. The first retraction dated back to 2005, with an average number of retracted publications being 1.22 and a median retraction time of 347 days. Among the retracted publications, 77.3% included a retraction notice. A post-retraction citation was found in 81.3% of cases. None of the retracted articles were written by a single author. An international collaboration was found in 27.3% of cases. Ninety-five point five percent of journals offered open access with 81.8% using a gold open access model. In terms of bibliometrics, eleven articles were published in highly reputed journals.
    Conclusion: Tunisia is not spared from breaches of scientific integrity. The controversies relating to the categories of breaches call for standardization. The legislative framework for this phenomenon also remains to be developed in Tunisia.
    Keywords:  Ethical issue; Tunisia; plagiarism; research misconduct; scientific fraud
    DOI:  https://doi.org/10.11604/pamj.2024.48.182.44793
  17. Eur J Psychol. 2024 ;20(3): 202-219
      The value of open research data (ORD), a key feature of open science, lies in their reuse. However, the mere online availability of ORD does not guarantee their reuse by other researchers. Specifically, previous meta-scientific research has indicated that the underutilization of ORD is related to barriers at the level of the ORD themselves, potential reusers of ORD, and the broader academic ecosystem. At the same time, sharing large datasets in an understandable and transparent format that motivates researchers to explore these datasets remains a fundamental challenge. With the present work, we propose interactive data apps (IDAs) as innovative ORD supplements that provide a means to lower barriers of ORD reuse. We demonstrate the use of two open-source Python libraries (Dash, Gradio) for IDA development using two psychological research use cases. The first use case pertains to an experimental quantitative dataset acquired in a clinical psychology setting. The second use case concerns the familiarization with data analysis workflows that are characteristic of natural language processing (NLP). For both use cases, we provide easy-to-adapt Python code that can form the basis for IDA development in similar scenarios.
    Keywords:  Dash; Gradio; data reuse; innovative supplements; interactive data apps; open research data
    DOI:  https://doi.org/10.5964/ejop.12811
  18. Adv Clin Exp Med. 2024 Dec 13.
      In the last 4 years, the journal Advances in Clinical and Experimental Medicine has made significant strides in adapting to changes in scientific publishing. It has maintained high levels of citations and submitted manuscripts, publishing a considerable number of articles ahead of print releases to minimize wait times. With a solid reputation and a growing base of over 7,000 reviewers, the journal upholds rigorous ethical standards and thorough statistical verification for all manuscripts. Bibliometric indicators showcase the impact of Adv Clin Exp Med, including an increased impact factor, CiteScore, Index Copernicus Value (ICV) and recognition in indexes and bases like Scopus and PubMed Central (PMC). International cooperation support for early-career researchers are key focuses, with efforts to provide guidelines, online meetings, and social media promotion. Various materials for authors prepared by the editorial staff are discussed, including detailed instructions for authors, tips regarding graphical abstracts and choosing a checklist, as well as ethical guidelines, a brochure on the rules of statistical analysis and data presentation, and technical requirements for figures. The journal also emphasizes data sharing, detailed procedures for errata and retractions, and clear policies concerning the use of artificial intelligence (AI) tools. Calls for submissions show authors the optimal direction for creating original, innovative scientific papers. Financing from the Polish Ministry of Science and Higher Education ensures the financial stability of the journal. By adapting to the evolving landscape of scientific communication, Adv Clin Exp Med remains dedicated to facilitating open access publishing and disseminating high-quality medical research to its readers.
    Keywords:  ahead of print; bibliometrics; early-career researchers; research ethics; scientific journal
    DOI:  https://doi.org/10.17219/acem/197093