bims-skolko Biomed News
on Scholarly communication
Issue of 2023–07–23
24 papers selected by
Thomas Krichel, Open Library Society
  1. Why are peer reviewers thinning out, and are there ways to enrich the peer pool?
  2. Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields.
  3. A survey to assess animal methods bias in scientific publishing.
  4. Is the Continued Claim of Indexing in Publons by Journals a Predatory Publishing Characteristic?
  5. Introducing transparent peer review to RSC Advances.
  6. What artificial intelligence can and cannot do (yet) in the scientific publishing world?
  7. Reducing the residue of retractions in evidence synthesis: ways to minimise inappropriate citation and use of retracted data.
  8. Medical students benefit from becoming peer reviewers.
  9. Recommendations for Assessing the Quality of Clinical Faculty Members' Journal Publications.
  10. Narratives in the Journal of Medical Imaging and Radiation Sciences: Publishing stories in an academic journal.
  11. Introducing article-based publishing to Modern Pathology.
  12. One female perspective on diversity in peer review.
  13. Predicting substantive biomedical citations without full text.
  14. The Journal of Adolescent Health's Editor-In-Chief Annual Reflection: A Year to Embrace Science and Compassion.
  15. Reemergence from the pandemic, annual awards, and editorial office updates: from the desk of the Editor-in-Chief, Nutrition Research.
  16. Perspectives on scientific error.
  17. Are AI-written articles the future?
  18. Reviewing Promotion Dossiers as a Professional Responsibility.
  19. A Clustering Algorithm for Polygonal Data Applied to Scientific Journal Profiles.
  20. New recommendations of the International Committee of Medical Journal Editors: use of artificial intelligence.
  21. Self-citation rates among neurosurgery journals and authors: unethical or misunderstood?
  22. Race and ethnicity reporting in endometrial cancer literature.
  23. Visibility of retracted articles: journals struggle to make retractions in the first place.
  24. ChatGPT in head and neck scientific writing: A precautionary anecdote.
  1. J Sci Med Sport. 2023 Jul;pii: S1440-2440(23)00142-1. [Epub ahead of print]26(7): 336-337
    Why are peer reviewers thinning out, and are there ways to enrich the peer pool?
    Jaime A Teixeira da Silva.
      The editorial by Meyer et al. offers a realistic reflection of the challenging state of peer review participation in some journals that hold this task to highest standards. With an increasing publishing market that is still heavily quantitatively driven by publish or perish incentives, a limited or finite peer pool of experienced sports scientists, a peer rewards scheme (Publons) that was decommissioned in mid-2022, and the lack of appetite for open peer review, sports journals are faced with challenging times to try and attract peer reviewers, and keep them incentivized. Absent an equitable trade and career-boosting rewards, the crisis in peer review might not be easily resolved.
    Keywords:  Academic publishing; Mandatory versus voluntary peer review; Sustainable peer review; Transparency
    DOI:  https://doi.org/10.1016/j.jsams.2023.06.006
  2. PeerJ. 2023 ;11 e15656
    Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields.
    Brendan Runde, Craig Harms.
      Many factors influence selection of a target journal for publishing scientific papers, including "fit" within the journal's scope, acceptance rate, readership, open access options, submission and publication costs, journal quality, and timeliness of publication. Timeliness of publication can be a critical factor affecting career development, but many journals are not transparent about turnaround times. Here we evaluated 49 journals publishing papers in zoological medicine and related fields between 2017 and 2022, and aggregated and examined distributions of turnaround time of journals that publicly provided the requisite data, in order to aid authors in selecting target journals that best meet their needs. Of 49 journals evaluated, 39 provided necessary dates for reconstructing turnaround times. Of these, median times to acceptance ranged from 37 to 338 days, and median times to publication ranged from 41 to 403.5 days. The percentage of papers published in greater than 1 year ("slow") ranged from 0 to 57.1%, while the percentage of papers published in under 6 months ("timely") ranged from 0.8 to 99.8%. Acceptance rates and times to first decision were available for only 22% and 20%, respectively, of journals evaluated. Results may prove useful for authors deciding where to submit their works, depending on how they prioritize the many factors involved.
    Keywords:  Journal selection factors; Time of first decision; Time to acceptance; Time to publication; Transparency in review times; Turnaround time
    DOI:  https://doi.org/10.7717/peerj.15656
  3. ALTEX. 2023 Jul 18.
    A survey to assess animal methods bias in scientific publishing.
    Catharine E Krebs, Ann Lam, Janine McCarthy, Helder Constantino, Kristie Sullivan.
      Publication of scientific findings is fundamental for research, pushing innovation and generating interventions that benefit society, but it is not without biases. Publication bias is generally recognized as journal's preference for publishing studies based on the direction and magnitude of results. However, early evidence of a newly recognized type of publication bias has emerged in which journal policy, peer reviewers, or editors request that animal data be provided to validate studies produced using nonanimal-based approaches. We describe herein "animal methods bias" in publishing: a preference for animal-based methods where they may not be necessary or where nonanimal-based methods may be suitable, which affects the likelihood of a manuscript being accepted for publication. To gather evidence of animal methods bias, we set out to collect the experiences and perceptions of scientists and reviewers related to animal- and nonanimal-based experiments during peer review. We created a cross-sectional survey with 33 questions that was completed by 90 respondents working in various biological fields. Twenty-one survey respondents indicated that they have carried out animal-based experiments for the sole purpose of anticipating reviewer requests. Thirty-one survey respondents indicated that they have been asked by peer reviewers to add animal experimental data to their nonanimal study; 14 of these felt the request was sometimes justified, and 11 did not think it was justified. The data presented provide preliminary evidence of animal methods bias and indicate that status quo and conservatism biases may explain such attitudes by peer reviewers and editors.
    Keywords:  nonanimal methods; peer review; validation
    DOI:  https://doi.org/10.14573/altex.2210212
  4. Curr Probl Diagn Radiol. 2023 Jul 01. pii: S0363-0188(23)00086-5. [Epub ahead of print]
    Is the Continued Claim of Indexing in Publons by Journals a Predatory Publishing Characteristic?
    Jaime A Teixeira da Silva.
      A recent article by Mathew et al. (2022) in this journal debates the important issue of honest versus predatory radiology journals. In this letter, I expand the debate by Mathew et al. (2022), focusing on the now-defunct peer reviewer rewards platform, Publons, which was phased out in 2022, but continues to be advertised as a journal's indexing location by a radiology journal of a known predatory publisher, OMICS. In 2023, can the claim of being indexed at Publons, or partnering with Publons for peer reviewer rewards be a potential predatory fingerprint?
    DOI:  https://doi.org/10.1067/j.cpradiol.2023.06.006
  5. RSC Adv. 2023 Jul 19. 13(32): 21850-21851
    Introducing transparent peer review to RSC Advances.
    Laura Fisher, Russell J Cox, Karen Faulds.
      RSC Advances is introducing the option of transparent peer review for authors. Editors-in-Chief Russell J. Cox and Karen Faulds, and Executive Editor Laura C. Fisher offer more detail on how this will work.
    DOI:  https://doi.org/10.1039/d3ra90060f
  6. Arch Argent Pediatr. 2023 Jul 27. e202310104
    What artificial intelligence can and cannot do (yet) in the scientific publishing world?
    Mariano E Ibarra.
      
    DOI:  https://doi.org/10.5546/aap.2023-10104.eng
  7. BMJ Evid Based Med. 2023 Jul 18. pii: bmjebm-2022-111921. [Epub ahead of print]
    Reducing the residue of retractions in evidence synthesis: ways to minimise inappropriate citation and use of retracted data.
    Caitlin Bakker, Stephanie Boughton, Clovis Mariano Faggion, Daniele Fanelli, Kathryn Kaiser, Jodi Schneider.
      The incorporation of publications that have been retracted is a risk in reliable evidence synthesis. Retraction is an important mechanism for correcting the literature and protecting its integrity. Within the medical literature, the continued citation of retracted publications occurs for a variety of reasons. Recent evidence suggests that systematic reviews and meta-analyses often unwittingly cite retracted publications which, at least in some cases, may significantly impact quantitative effect estimates in meta-analyses. There is strong evidence that authors of systematic reviews and meta-analyses may be unaware of the retracted status of publications and treat them as if they are not retracted. These problems are difficult to address for several reasons: identifying retracted publications is important but logistically challenging; publications may be retracted while a review is in preparation or in press and problems with a publication may also be discovered after the evidence synthesis is published. We propose a set of concrete actions that stakeholders (eg, scientists, peer-reviewers, journal editors) might take in the near-term, and that research funders, citation management systems, and databases and search engines might take in the longer term to limit the impact of retracted primary studies on evidence syntheses.
    Keywords:  Evidence-Based Practice; Information Storage and Retrieval; Publishing; Retraction of Publication as Topic; Systematic Reviews as Topic
    DOI:  https://doi.org/10.1136/bmjebm-2022-111921
  8. Can Med Educ J. 2023 Jun;14(3): 154
    Medical students benefit from becoming peer reviewers.
    Celeste Murtha.
      
    DOI:  https://doi.org/10.36834/cmej.76325
  9. Am J Pharm Educ. 2023 Jul 14. pii: S0002-9459(23)04351-6. [Epub ahead of print] 100575
    Recommendations for Assessing the Quality of Clinical Faculty Members' Journal Publications.
    Brian L Erstad.
      Evaluation of clinical faculty involves an assessment of the quality of their publications in addition to quantity (number) of publications. In contrast to assessing quantity, assessing quality is difficult. The purpose of this paper is to discuss practical considerations and provide recommendations related to quality of publications that clinical faculty members should bear in mind as part of their overall scholarship activity. College and schools of pharmacy may not provide written criteria for assessing quality of publications, so it is important that clinical faculty members seek guidance from their department chair or direct supervisor, experienced colleagues, and formal or informal mentors or advisors. One criterion for assessing quality is whether a publication was evaluated through a peer-review process although there are other considerations including dissemination of the paper via search engines such as PubMed. Clinical faculty also need to consider authorship order on their papers and potential journals for submission.
    Keywords:  academia; assessment; clinical faculty; journal publishing; publication; quality
    DOI:  https://doi.org/10.1016/j.ajpe.2023.100575
  10. J Med Imaging Radiat Sci. 2023 Jul 18. pii: S1939-8654(23)00167-4. [Epub ahead of print]
    Narratives in the Journal of Medical Imaging and Radiation Sciences: Publishing stories in an academic journal.
    Amanda Bolderston, Emma Hyde, Lelainia Lloyd, Carly McCuaig, Sue Robins, Riaan van de Venter, Caroline Wright.
      Healthcare narratives can be used for education to elicit an emotional or affective response, develop critical thinking, and gain perspective on individuals' experiences with life and illness to cultivate person-centered care. This editorial describes the recent experience of the Journal of Medical Imaging and Radiation Sciences (JMIRS) in developing a new narrative submission format. The processes of engaging and supporting patient authors as well as creating a more accessible submission and review process are presented. Finally, the paper discusses the emerging impact of published narratives and the benefit of working with patients as experts and authors.
    DOI:  https://doi.org/10.1016/j.jmir.2023.06.003
  11. Mod Pathol. 2023 Jul;pii: S0893-3952(23)00098-4. [Epub ahead of print]36(7): 100193
    Introducing article-based publishing to Modern Pathology.
    Sarah Pratta.
      
    DOI:  https://doi.org/10.1016/j.modpat.2023.100193
  12. BMJ. 2023 07 19. 382 1656
    One female perspective on diversity in peer review.
    Yali Xu.
      
    DOI:  https://doi.org/10.1136/bmj.p1656
  13. Proc Natl Acad Sci U S A. 2023 07 25. 120(30): e2213697120
    Predicting substantive biomedical citations without full text.
    Travis A Hoppe, Salsabil Arabi, B Ian Hutchins.
      Insights from biomedical citation networks can be used to identify promising avenues for accelerating research and its downstream bench-to-bedside translation. Citation analysis generally assumes that each citation documents substantive knowledge transfer that informed the conception, design, or execution of the main experiments. Citations may exist for other reasons. In this paper, we take advantage of late-stage citations added during peer review because these are less likely to represent substantive knowledge flow. Using a large, comprehensive feature set of open access data, we train a predictive model to identify late-stage citations. The model relies only on the title, abstract, and citations to previous articles but not the full-text or future citations patterns, making it suitable for publications as soon as they are released, or those behind a paywall (the vast majority). We find that high prediction scores identify late-stage citations that were likely added during the peer review process as well as those more likely to be rhetorical, such as journal self-citations added during review. Our model conversely gives low prediction scores to early-stage citations and citation classes that are known to represent substantive knowledge transfer. Using this model, we find that US federally funded biomedical research publications represent 30% of the predicted early-stage (and more likely to be substantive) knowledge transfer from basic studies to clinical research, even though these comprise only 10% of the literature. This is a threefold overrepresentation in this important type of knowledge flow.
    Keywords:  artificial intelligence; bench to bedside translation; citation analysis; machine learning; science policy
    DOI:  https://doi.org/10.1073/pnas.2213697120
  14. J Adolesc Health. 2023 08;pii: S1054-139X(23)00264-1. [Epub ahead of print]73(2): 213-216
    The Journal of Adolescent Health's Editor-In-Chief Annual Reflection: A Year to Embrace Science and Compassion.
    Carol A Ford.
      
    DOI:  https://doi.org/10.1016/j.jadohealth.2023.05.005
  15. Nutr Res. 2023 May 12. pii: S0271-5317(23)00038-6. [Epub ahead of print]
    Reemergence from the pandemic, annual awards, and editorial office updates: from the desk of the Editor-in-Chief, Nutrition Research.
    Richard S Bruno, Katie Zamary.
      
    DOI:  https://doi.org/10.1016/j.nutres.2023.05.002
  16. R Soc Open Sci. 2023 Jul;10(7): 230448
    Perspectives on scientific error.
    D van Ravenzwaaij, M Bakker, R Heesen, F Romero, N van Dongen, S Crüwell, S M Field, L Held, M R Munafò, M M Pittelkow, L Tiokhin, V A Traag, O R van den Akker, A E van 't Veer, E J Wagenmakers.
      Theoretical arguments and empirical investigations indicate that a high proportion of published findings do not replicate and are likely false. The current position paper provides a broad perspective on scientific error, which may lead to replication failures. This broad perspective focuses on reform history and on opportunities for future reform. We organize our perspective along four main themes: institutional reform, methodological reform, statistical reform and publishing reform. For each theme, we illustrate potential errors by narrating the story of a fictional researcher during the research cycle. We discuss future opportunities for reform. The resulting agenda provides a resource to usher in an era that is marked by a research culture that is less error-prone and a scientific publication landscape with fewer spurious findings.
    Keywords:  institutional reform; meta-science; methodology; publishing; scientific error
    DOI:  https://doi.org/10.1098/rsos.230448
  17. Vet Rec. 2023 Jul 22. 193(2): 58-59
    Are AI-written articles the future?
    Georgina Mills.
      Georgina Mills discusses the use of artificial intelligence tools in scientific research and literature.
    DOI:  https://doi.org/10.1002/vetr.3276
  18. Am J Pharm Educ. 2023 Jul 14. pii: S0002-9459(23)04350-4. [Epub ahead of print] 100574
    Reviewing Promotion Dossiers as a Professional Responsibility.
    William A Prescott.
      Promotion is accompanied by additional responsibility, few more important than serving as a formal external reviewer of promotion dossiers. Promotion and tenure committees rely on external peer review to provide an outside perspective regarding the impact of the candidate's work and how they compare to peers with the same or higher academic rank. What the external reviewer writes and opines impacts the promotion and/or tenure decision. When presented with this opportunity, a faculty member needs to respond to the request, familiarize themselves with the candidate and their promotion and/or tenure criteria, conduct a critical read of the dossier, and write an evaluative letter. This commentary serves as a call for faculty members at the rank of associate and full professor to engage as a reviewer when called upon, provides advice about how to approach an external review and write the letter, and discusses how schools and professional organizations can participate in this process.
    Keywords:  dossier; pharmacy; promotion
    DOI:  https://doi.org/10.1016/j.ajpe.2023.100574
  19. IEEE Trans Pattern Anal Mach Intell. 2023 Jul 19. PP
    A Clustering Algorithm for Polygonal Data Applied to Scientific Journal Profiles.
    Wagner J F Silva, Pedro J C Souza, Renata M C R Souza, Francisco Jose A Cysneiros.
      Millions of papers are submitted and published every year, but researchers often do not have much information about the journals that interest them. In this paper, we introduced the first dynamical clustering algorithm for symbolic polygonal data and this was applied to build scientific journals profiles. Dynamic clustering algorithms are a family of iterative two-step relocation algorithms involving the construction of clusters at each iteration and the identification of a suitable representation or prototype (means, axes, probability laws, groups of elements, etc.) for each cluster by locally optimizing an adequacy criterion that measures the fitting between clusters and their corresponding prototypes The application gives a powerful vision to understand the main variables that describe journals. Symbolic polygonal data can represent summarized extensive datasets taking into account variability. In addition, we developed cluster and partition interpretation indices for polygonal data that have the ability to extract insights about clustering results. From these indices, we discovered, e.g., that the number of difficult words in abstract is fundamental to building journal profiles.
    DOI:  https://doi.org/10.1109/TPAMI.2023.3297022
  20. Eur Heart J. 2023 Jul 15. pii: ehad448. [Epub ahead of print]
    New recommendations of the International Committee of Medical Journal Editors: use of artificial intelligence.
    Fernando Alfonso, Filippo Crea.
      
    DOI:  https://doi.org/10.1093/eurheartj/ehad448
  21. World Neurosurg. 2023 Jul 18. pii: S1878-8750(23)00983-X. [Epub ahead of print]
    Self-citation rates among neurosurgery journals and authors: unethical or misunderstood?
    Harsh Deora, Kristin L Kraus, William T Couldwell, Kanwaljeet Garg.
      OBJECTIVE The role of self-citation has not been discussed in the neurosurgery literature, although citations, citation indices, and impact of research may enhance funding opportunities, academic positions, fellowship opportunities, employment, and professional identity development. We sought to assess the magnitude and role of self-citation in academic neurosurgery. METHODS We performed a retrospective analysis of the citation and self-citation rates of articles published in 2001-2020 in 7 major neurosurgery journals: Acta Neurochirurgica; Journal of Neurosurgery, Journal of Neurosurgery: Pediatrics; Journal of Neurosurgery: Spine; Neurosurgery, Neurosurgical Review, and World Neurosurgery. RESULTS The total number of citations was highest for Journal of Neurosurgery and lowest for Neurosurgical Review. Journal of Neurosurgery: Spine had the highest average number of citations per article, followed closely by Journal of Neurosurgery. The self-citation rate increased for all journals over the time period 2001 to 2020. The highest number of self-citations per article during 2016-2020 was seen in Journal of Neurosurgery: Pediatrics and World Neurosurgery. Neurosurgical Review had the lowest number of self-citations per article. CONCLUSION Academic neurosurgeons must understand the ecosystem around self-citation. In our study, we found overall low levels of self citations in neurosurgery journals with a few outliers. We have, however, noticed an increasing trend in self-citations rates. Self-citation rates should be considered while evaluating the impact of an author and research productivity. Against popular belief, self-citation is not always unethical and must be understood within its circumstances.
    Keywords:  citations; h-index; impact factor; journal; self-citation
    DOI:  https://doi.org/10.1016/j.wneu.2023.07.052
  22. Int J Gynecol Cancer. 2023 Jul 21. pii: ijgc-2023-004552. [Epub ahead of print]
    Race and ethnicity reporting in endometrial cancer literature.
    Diego Raimondo, Antonio Raffone, Angelo Maria Pezzullo, Marisol Doglioli, Pierandrea De Benedetti, Pierluigi Celerino, Lucia De Meis, Manuela Maletta, Arianna Raspollini, Antonio Travaglino, Maurizio Guida, Paolo Casadio, Renato Seracchioli.
       OBJECTIVES: There is evidence that there are differences in survival outcomes among patients with endometrial cancer of different ethnic groups. We aimed to assess the quantity and quality of race/ethnicity reporting in the literature on endometrial cancer published from January 2020 to December 2020.
    METHODS: In this systematic review, electronic searches of PubMed, MEDLINE, Web of Sciences, Scopus, and Cochrane Library databases were performed for all articles published in 2020. A total of 3330 articles were reviewed, of which 949 (35%) peer-reviewed human-based articles focusing on endometrial cancer were included. Non-research-focused articles, review articles, meta-analyses, case reports, and non-human studies were excluded. We analyzed the proportion of studies reporting race/ethnicity and assessed the quality of reporting with regard to the adherence to the International Committee of Medical Journal Editors (ICMJE) recommendations. We evaluated the influence of study characteristics on race/ethnicity reporting and compared articles published in journals which adhere to the ICMJE recommendations against those that did not explicitly state that they did.
    RESULTS: Of the 949 (28.5%) included articles, 166 (17.5%) reported race/ethnicity of patients, with low quality of reporting. The reporting rate of race/ethnicity was similar when comparing articles from ICMJE and non-ICMJE journals (62 (20.4%) vs 104 (16.1%); p=0.11), prospective versus retrospective studies (53 (22.7%) vs 113 (15.8%); p=0.02), and national versus international studies (147 (17.5%) vs 19 (17.4%); p=0.99). Studies performed in the WHO region of Americas were significantly more consistent in reporting race compared with other regions (119 (44.7%) vs 23 (6.8%) European, 2 (7.4%) Eastern Mediterranean, 21 (7.1%) Western Pacific, 0 (0%) South-East Asia; p<0.001). Female corresponding authors were significantly more consistent in reporting race than male authors (94 (22.5%) vs 72 (13.6%); p<0.001).
    CONCLUSIONS: Human-based articles focusing on endometrial cancer have a low frequency and quality of race/ethnicity reporting, even in journals claiming to follow ICMJE recommendations.
    Keywords:  Carcinoma; Endometrial Neoplasms; Endometrium
    DOI:  https://doi.org/10.1136/ijgc-2023-004552
  23. BMJ. 2023 Jul 21. 382 p1669
    Visibility of retracted articles: journals struggle to make retractions in the first place.
    Christopher D Roche.
      
    DOI:  https://doi.org/10.1136/bmj.p1669
  24. Am J Otolaryngol. 2023 Jul 06. pii: S0196-0709(23)00194-1. [Epub ahead of print]44(6): 103980
    ChatGPT in head and neck scientific writing: A precautionary anecdote.
    Robin T Wu, Rushil R Dang.
       PURPOSE: To evaluate the accuracy of ChatGPT references in scientific writing relevant to head and neck surgery.
    MATERIALS AND METHODS: Five commonly researched keywords relevant to head and neck surgery were selected (osteoradionecrosis of the jaws, oral cancer, adjuvant therapy for oral cancer, TORS, and free flap reconstruction in oral cancer). The AI chatbot was then asked to provide ten complete citations for each of the keywords. Two independent authors reviewed the results for accuracy and assigned each article a numerical score based on pre-selected criteria.
    RESULTS: Among 50 total references provided by ChatGPT, only five (10 %) were found to have the correct title, journal, authors, year of publication, and DOI. Merely 14 % of the presented references had correct DOI. References regarding free flap reconstruction for oral cancer were the least accurate from all the five categories, with no correct DOI. Complete inter-rater agreement was noted while evaluating the citations.
    CONCLUSION: Only 10 % of the articles provided by ChatGPT, relevant to head and neck surgery, were correct. A high degree of academic hallucination was noted.
    Keywords:  AI; ChatGPT; Head and neck surgery; Oral cancer
    DOI:  https://doi.org/10.1016/j.amjoto.2023.103980
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