bims-skolko Biomed News
on Scholarly communication
Issue of 2023‒07‒30
twenty-six papers selected by
Thomas Krichel
Open Library Society
  1. No-pay publishing: use institutional repositories.
  2. Sharp criticism of controversial ancient-human claims tests eLife's revamped peer-review model.
  3. Challenges Facing Arab Researchers in Publishing Scientific Research: A Qualitative Interview Study.
  4. Scientific publishing has a language problem.
  5. A Critical Assessment of the Peer Review Process in Life: From Submission to Final Decision.
  6. Research anomalies in criminology: How serious? How extensive over time? And who was responsible?
  7. 'A very disturbing picture': another retraction imminent for controversial physicist.
  8. The ethics of peer review process.
  9. Letter: I Asked a ChatGPT to Write an Editorial About How We Can Incorporate Chatbots Into Neurosurgical Research and Patient Care….
  10. A new policy on the use of artificial intelligence tools for manuscripts submitted to CMAJ.
  11. Chatbots, Artificial Intelligence, and the Future of Scientific Reporting.
  12. Can Artificial Intelligence Be My Coauthor?
  13. Artificial intelligence-assisted publishing in 5 prominent dermatology journals: A quantitative study of recent publications.
  14. Guidance for Authors, Peer Reviewers, and Editors on Use of AI, Language Models, and Chatbots.
  15. Leveraging large language models: transforming scholarly publishing for the better.
  16. Use of Generative Artificial Intelligence, Including Large Language Models Such as ChatGPT, in Scientific Publications: Policies of KJR and Prominent Authorities.
  17. Transparency of COVID-19-related research: A meta-research study.
  18. Data sharing implementation in top 10 ophthalmology journals in 2021.
  19. Data sharing: putting Nature's policy to the test.
  20. Exploring the use of preprints in dentistry.
  21. Readership awareness series - Paper 6: How to write a good peer review report?
  22. Consent or Permission to Publish for Case Reports.
  23. The Medical Institutional Repositories in Libraries (MIRL) Symposium: a blueprint designed in response to a community of practice need.
  24. From the internet to the COVID-19 pandemic: how technological advances and a tumultuous world have changed scientific publishing and meetings.
  25. Time and change: Scientific publishing in a postpandemic environment.
  26. Conflict of Interest and Plastic Surgery Journal Editors: The Problem and the Solution.
  1. Nature. 2023 Jul;619(7971): 698
    No-pay publishing: use institutional repositories.
    Isabel Bernal, Pandelis Perakakis.
      
    Keywords:  Publishing; Sustainability
    DOI:  https://doi.org/10.1038/d41586-023-02315-z
  2. Nature. 2023 Jul 25.
    Sharp criticism of controversial ancient-human claims tests eLife's revamped peer-review model.
    Ewen Callaway.
      
    Keywords:  Evolution; Peer review; Publishing
    DOI:  https://doi.org/10.1038/d41586-023-02415-w
  3. Res Sq. 2023 Jul 14. pii: rs.3.rs-3129329. [Epub ahead of print]
    Challenges Facing Arab Researchers in Publishing Scientific Research: A Qualitative Interview Study.
    Alya Elgamri, Zeinab Mohammed, Karima El-Rhazi, Manal Shahrouri, Mamoun Ahram, Al-Mubarak Al-Abbas, Henry Silverman.
      Background Studies have shown an underrepresentation of researchers from lower- and middle-income countries (LMICs) in the research literature compared with their counterparts in high-income countries. We aimed to explore Arab researchers' challenges regarding conducting and publishing research in peer-reviewed journals. Methods We used a descriptive qualitative study design of semi-structured in-depth interviews. Using purposive sampling, we recruited participants from four Arab countries in the Middle East and North Africa. All interviews were recorded, transcribed, and translated to English if the original language was Arabic or French. We analyzed the transcripts using reflexive thematic analysis. Several authors independently coded the transcripts and agreed on the identified codes, themes, and subthemes. Results We performed 17 interviews: three from Egypt, six from Jordan, four from Morocco, and four from Sudan. Our participants' comments were divided into three broad categories with associated themes and subthemes. The first regards the conduct of research (themes of inadequate quality of research, insufficient research resources, and nonsuppurative research environment). The second category involves the publishing process (themes of poor scientific writing skills and difficulties navigating the publishing and peer-reviewed system). The third regards international collaborations and the final category recommends methods to address the challenges. Our recommendations include: enhancing the institutional research culture, increasing funding mechanisms, establishing mentoring programs and workshops on research methodology and scientific writing, and increasing the representation of LMICs on the editorial staff. Conclusions Identifying the challenges of Arab researchers in publishing original and quality research would guide programs tailored and targeted toward Arab scholars' needs.
    DOI:  https://doi.org/10.21203/rs.3.rs-3129329/v1
  4. Nat Hum Behav. 2023 Jul;7(7): 1019-1020
    Scientific publishing has a language problem.
      
    DOI:  https://doi.org/10.1038/s41562-023-01679-6
  5. Life (Basel). 2023 Jul 21. pii: 1603. [Epub ahead of print]13(7):
    A Critical Assessment of the Peer Review Process in Life: From Submission to Final Decision.
    Pabulo Henrique Rampelotto.
      In the world of academic research and scientific publishing, the process of peer review plays a pivotal role [...].
    DOI:  https://doi.org/10.3390/life13071603
  6. Account Res. 2023 Jul 27.
    Research anomalies in criminology: How serious? How extensive over time? And who was responsible?
    Walter R Schumm, Duane W Crawford, Lorenza Lockett, Abdullah AlRashed, Asma Bin Ateeq.
      A variety of ways to detect questionable research practices in small sample social science surveys have been discussed by a variety of authors. However, some of those approaches (e.g., GRIM test, SPRITE test) do not work well for results obtained from larger samples. Here several approaches for detecting anomalies in larger samples are presented and illustrated by an analysis of 78 journal articles in the area of criminology, 59 by Dr. Eric Stewart, published since 1998 with similar methods and/or authors, finding evidence that seven of the 59 articles have been retracted or corrected and of the remaining 52, nine (17.3%) featured at least one moderate anomaly while 38 (73.1%) featured at least one major or two moderate anomalies. Of all 59 articles, 28 (47.5%, p < .001, d = 0.94) had two or more major anomalies compared to none of the 19 control group articles. Furthermore, 22 (42.3%) of the 52 articles featured at least two major anomalies (p < .001, d = 0.89). It was also found that the larger the role of Dr. Stewart in article authorship, the greater the number of anomalies detected (p < .001, d = 1.01) while for his co-authors, there were few significant relationships between their roles and total anomalies. Our results demonstrate that extensive problematic results can remain undetected for decades despite several levels of peer review and other scientific controls; however, use of two types of control groups and the use of statistical methods for measuring and evaluating anomalies can improve detection.
    Keywords:  Professor eric stewart; Research integrity; anomalies; fraud; questionable research practices; research misconduct; results; retracted articles; retractions
    DOI:  https://doi.org/10.1080/08989621.2023.2241127
  7. Nature. 2023 Jul 25.
    'A very disturbing picture': another retraction imminent for controversial physicist.
    Dan Garisto.
      
    Keywords:  Materials science; Publishing; Scientific community
    DOI:  https://doi.org/10.1038/d41586-023-02401-2
  8. Updates Surg. 2023 Jul 25.
    The ethics of peer review process.
    Giuseppe Remuzzi.
      
    DOI:  https://doi.org/10.1007/s13304-023-01602-8
  9. Neurosurgery. 2023 Jul 27.
    Letter: I Asked a ChatGPT to Write an Editorial About How We Can Incorporate Chatbots Into Neurosurgical Research and Patient Care….
    Ismail Zaed, Andrea Cardia.
      
    DOI:  https://doi.org/10.1227/neu.0000000000002619
  10. CMAJ. 2023 07 24. 195(28): E958-E959
    A new policy on the use of artificial intelligence tools for manuscripts submitted to CMAJ.
    Matthew B Stanbrook, Meredith Weinhold, Diane Kelsall.
      
    DOI:  https://doi.org/10.1503/cmaj.230949
  11. JAMA Ophthalmol. 2023 Jul 27.
    Chatbots, Artificial Intelligence, and the Future of Scientific Reporting.
    Nicholas J Volpe, Rukhsana G Mirza.
      
    DOI:  https://doi.org/10.1001/jamaophthalmol.2023.3344
  12. Simul Healthc. 2023 Jul 25.
    Can Artificial Intelligence Be My Coauthor?
    Mark W Scerbo.
      
    DOI:  https://doi.org/10.1097/SIH.0000000000000743
  13. Clin Exp Dermatol. 2023 Jul 26. pii: llad250. [Epub ahead of print]
    Artificial intelligence-assisted publishing in 5 prominent dermatology journals: A quantitative study of recent publications.
    Ida M Heerfordt.
      
    DOI:  https://doi.org/10.1093/ced/llad250
  14. JAMA. 2023 Jul 27.
    Guidance for Authors, Peer Reviewers, and Editors on Use of AI, Language Models, and Chatbots.
    Annette Flanagin, Jacob Kendall-Taylor, Kirsten Bibbins-Domingo.
      
    DOI:  https://doi.org/10.1001/jama.2023.12500
  15. J Am Vet Med Assoc. 2023 Aug 01. 261(8): 1106-1107
    Leveraging large language models: transforming scholarly publishing for the better.
    Lisa A Fortier.
      
    DOI:  https://doi.org/10.2460/javma.261.8.1106
  16. Korean J Radiol. 2023 Aug;24(8): 715-718
    Use of Generative Artificial Intelligence, Including Large Language Models Such as ChatGPT, in Scientific Publications: Policies of KJR and Prominent Authorities.
    Seong Ho Park.
      
    Keywords:  Artificial intelligence; ChatGPT; Editing; Generative; Large language model; Peer review; Policy; Publication; Writing
    DOI:  https://doi.org/10.3348/kjr.2023.0643
  17. PLoS One. 2023 ;18(7): e0288406
    Transparency of COVID-19-related research: A meta-research study.
    Ahmad Sofi-Mahmudi, Eero Raittio, Sergio E Uribe.
      BACKGROUND: We aimed to assess the adherence to five transparency practices (data availability, code availability, protocol registration and conflicts of interest (COI), and funding disclosures) from open access Coronavirus disease 2019 (COVID-19) related articles.METHODS: We searched and exported all open access COVID-19-related articles from PubMed-indexed journals in the Europe PubMed Central database published from January 2020 to June 9, 2022. With a validated and automated tool, we detected transparent practices of three paper types: research articles, randomized controlled trials (RCTs), and reviews. Basic journal- and article-related information were retrieved from the database. We used R for the descriptive analyses.
    RESULTS: The total number of articles was 258,678, of which we were able to retrieve full texts of 186,157 (72%) articles from the database Over half of the papers (55.7%, n = 103,732) were research articles, 10.9% (n = 20,229) were review articles, and less than one percent (n = 1,202) were RCTs. Approximately nine-tenths of articles (in all three paper types) had a statement to disclose COI. Funding disclosure (83.9%, confidence interval (CI): 81.7-85.8 95%) and protocol registration (53.5%, 95% CI: 50.7-56.3) were more frequent in RCTs than in reviews or research articles. Reviews shared data (2.5%, 95% CI: 2.3-2.8) and code (0.4%, 95% CI: 0.4-0.5) less frequently than RCTs or research articles. Articles published in 2022 had the highest adherence to all five transparency practices. Most of the reviews (62%) and research articles (58%) adhered to two transparency practices, whereas almost half of the RCTs (47%) adhered to three practices. There were journal- and publisher-related differences in all five practices, and articles that did not adhere to transparency practices were more likely published in lowest impact journals and were less likely cited.
    CONCLUSION: While most articles were freely available and had a COI disclosure, adherence to other transparent practices was far from acceptable. A much stronger commitment to open science practices, particularly to protocol registration, data and code sharing, is needed from all stakeholders.
    DOI:  https://doi.org/10.1371/journal.pone.0288406
  18. BMJ Open Ophthalmol. 2023 07;pii: e001276. [Epub ahead of print]8(1):
    Data sharing implementation in top 10 ophthalmology journals in 2021.
    Varis Ruamviboonsuk, Bandit Thinkhamrop, Kittisak Kulvichit, Wasee Tulvatana.
      BACKGROUND/AIMS: Deidentified individual participant data (IPD) sharing has been implemented in the International Committee of Medical Journal Editors journals since 2017. However, there were some published clinical trials that did not follow the new implemented policy. This study examines the number of clinical trials that endorsed IPD sharing policy among top ophthalmology journals.METHOD: All published original articles in 2021 in 10 highest-ranking ophthalmology journals according to the 2020 journal impact factor were included. Clinical trials were determined by the WHO definition of clinical trials. Each article was then thoroughly searched for the IPD sharing statement either in the manuscript or in the clinical trial registry. We collected the number of published clinical trials that implemented IPD sharing policy as our primary outcome.
    RESULTS: 1852 published articles in top 10 ophthalmology journals were identified, and 9.45% were clinical trials. Of these clinical trials, 44% had clinical trial registrations and 49.14% declared IPD sharing statements. Only 42 (48.83%) clinical trials were willing to share IPD, and 5 (10.21%) of these share IPD via an online repository platform. In terms of sharing period, 37 clinical trials were willing to share right after the publication and only 2 showed the ending of sharing period.
    CONCLUSION: This report shows that the number of clinical trials in top ophthalmology journals that endorsed the IPD sharing policy and the number of registrations is lower than half even though the policy has been implemented for several years. Future updates are necessary as policy evolves.
    Keywords:  Clinical Trial; Medical Education
    DOI:  https://doi.org/10.1136/bmjophth-2023-001276
  19. Nature. 2023 Jul;619(7971): 698
    Data sharing: putting Nature's policy to the test.
    Xiwei Chen, Stephanie L Dickinson, Anna L M Macagno, Chelsie M Parker, David B Allison.
      
    Keywords:  Communication; Publishing; Research data
    DOI:  https://doi.org/10.1038/d41586-023-02250-z
  20. J Dent. 2023 Jul 22. pii: S0300-5712(23)00220-8. [Epub ahead of print] 104634
    Exploring the use of preprints in dentistry.
    Rafael Sarkis-Onofre, Carolina Girotto, Bernardo Antonio Agostini.
      OBJECTIVE: This study aims to assess the use, impact, and dissemination of preprints in dentistry.METHODS: This is a meta-research study with a cross-sectional design. We included preprints published in dentistry, regardless of the year of publication. Searches were performed in the medRxiv.org and Preprints.org platforms and restricted to English. One researcher extracted the data, and another researcher verified data consistency. The following data were extracted: year of publication, country of the corresponding author, number of abstract and full-text views and downloads, Altmetric attention score, whether the preprint was mentioned in other servers such as Twitter and Publons, number of mentions in other servers, number of citations in the Dimensions database, and whether the preprint had already been published in a peer-reviewed journal. If already published, we extracted the journal's impact factor (JCR 2021) and the number of citations in the Dimensions database. We conducted a descriptive analysis of the extracted characteristics and explored relationships between metrics using the Spearman correlation.
    RESULTS: We identified 276 preprints. Most of the studies were published between 2020 and 2022 (n = 229), especially those from ten countries. The most-cited preprint and published article are the same study. Only the correlation between the number of preprint citations and peer-reviewed article citations in the Dimensions database showed a large positive association (Spearman's rho = 0.5809).
    CONCLUSION: Preprints gained popularity over the last several years due to the COVID-19 pandemic and reached a larger audience, especially on platforms such as Twitter.
    CLINICAL SIGNIFICANCE: Preprint publishing allows faster dissemination of science for the benefit of society.
    Keywords:  Open science; Platforms; Research practices
    DOI:  https://doi.org/10.1016/j.jdent.2023.104634
  21. Ocul Surf. 2023 Jul 22. pii: S1542-0124(23)00092-7. [Epub ahead of print]29 508-510
    Readership awareness series - Paper 6: How to write a good peer review report?
    Mohammad Javed Ali, Ali Djalilian.
      
    Keywords:  Ethics; Journal; Peer review; Publication; Reviews; Scientific writing
    DOI:  https://doi.org/10.1016/j.jtos.2023.07.006
  22. Prog Transplant. 2023 Jul 25. 15269248231190185
    Consent or Permission to Publish for Case Reports.
    Rebecca P Winsett.
      
    DOI:  https://doi.org/10.1177/15269248231190185
  23. J Med Libr Assoc. 2023 Jul 10. 111(3): 710-716
    The Medical Institutional Repositories in Libraries (MIRL) Symposium: a blueprint designed in response to a community of practice need.
    Brenda Fay, Lisa M Buda, Anthony J Dellureficio, Sara Hoover, Ramune K Kubilius, Steven J Moore, Lisa A Palmer.
      Background: Health sciences libraries in medical schools, academic health centers, health care networks, and hospitals have established institutional repositories (IRs) to showcase their research achievements, increase visibility, expand the reach of institutional scholarship, and disseminate unique content. Newer roles for IRs include publishing open access journals, tracking researcher productivity, and serving as repositories for data sharing. Many repository managers oversee their IR with limited assistance from others at their institution. Therefore, IR practitioners find it valuable to network and learn from colleagues at other institutions.Case Presentation: This case report describes the genesis and implementation of a new initiative specifically designed for a health sciences audience: the Medical Institutional Repositories in Libraries (MIRL) Symposium. Six medical librarians from hospitals and academic institutions in the U.S. organized the inaugural symposium held virtually in November 2021. The goal was to fill a perceived gap in conference programming for IR practitioners in health settings. Themes of the 2021 and subsequent 2022 symposium included IR management, increasing readership and engagement, and platform migration. Post-symposium surveys were completed by 73/238 attendees (31%) in 2021 and by 62/180 (34%) in 2022. Feedback was overwhelmingly positive.
    Discussion: Participant responses in post-symposium surveys rated MIRL highly. The MIRL planning group intends to continue the symposium and hopes MIRL will steadily evolve, build community among IR practitioners in the health sciences, and expand the conversation around best practices for digital archiving of institutional content. The implementation design of MIRL serves as a blueprint for collaboratively bringing together a professional community of practice.
    Keywords:  Collaboration; Community of Practice; Health Sciences Libraries; Institutional Repository; Medical Institutional Repositories in Libraries Symposium; Scholarly Communication
    DOI:  https://doi.org/10.5195/jmla.2023.1503
  24. J Nephrol. 2023 Jul 27.
    From the internet to the COVID-19 pandemic: how technological advances and a tumultuous world have changed scientific publishing and meetings.
    Massimo Torreggiani, Giorgina Barbara Piccoli, Andrew Mallett.
      
    Keywords:  COVID-19; Internet; Medical congress; Publishing
    DOI:  https://doi.org/10.1007/s40620-023-01740-7
  25. FASEB J. 2023 08;37(8): e23102
    Time and change: Scientific publishing in a postpandemic environment.
    Loren E Wold.
      
    DOI:  https://doi.org/10.1096/fj.202301378
  26. Ann Plast Surg. 2023 08 01. 91(2): 199-203
    Conflict of Interest and Plastic Surgery Journal Editors: The Problem and the Solution.
    Eric Swanson.
      ABSTRACT: Journals insist that authors disclose their financial conflicts. However, the same standard is rarely imposed on journal editors. Surprisingly, most high-impact medical journals (about 88%) do not publish editor conflicts of interest (COIs).The Sunshine Act makes it possible to query physician payments from industry. Importantly, some companies are exempted. The leading 5 US-based plastic surgery journals were investigated. Only chief editors and coeditors were included, for a total of 10 editors. The range of payments was US $0 to US $297,000 between 2015 and 2021. The mean payment was $90,890, or $12,984 per year. This amount may be compared with the average industry payments to all plastic surgeons, which is approximately $5000 annually.Examples of editor COIs are considered. In one case, an article detailing important factual deficiencies in an article defending Allergan macrotextured breast implants was rejected by coeditors that included a coeditor who received payments from Allergan. An article promoting radiofrequency treatments containing previously reported data was accepted by a chief editor with a COI, who was also a coauthor.Articles claiming improved scarring for a wound adhesive device and numerous benefits for an Allergan implant insertion funnel also found acceptance by conflicted chief editors, despite serious deficiencies.Editor COIs should be published. Attempts to manage editor COI have not been successful. No data support a dollar limit or expiry date for COIs. Relevance and breadth of COIs are unsolved problems. The ethics of industry payments to physicians are questionable at best. An alternative option is recommended-elimination of COI for journal editors. This remedy would restore editorial integrity and avoid the need for recusals. There is precedence. About half of high-impact medical journal editors have no COIs. Industry subsidies in general should be reconsidered. Abandoning them would be in the best interest of our patients and our specialty.
    DOI:  https://doi.org/10.1097/SAP.0000000000003633
This page is being maintained by Thomas Krichel. It was last updated on 2023‒07‒30 at 1:57.