bims-skolko Biomed News
on Scholarly communication
Issue of 2023–07–02
33 papers selected by
Thomas Krichel, Open Library Society



  1. PLoS One. 2023 ;18(6): e0287611
      Double-blind peer review is considered a pillar of academic research because it is perceived to ensure a fair, unbiased, and fact-centered scientific discussion. Yet, experienced researchers can often correctly guess from which research group an anonymous submission originates, biasing the peer-review process. In this work, we present a transformer-based, neural-network architecture that only uses the text content and the author names in the bibliography to attribute an anonymous manuscript to an author. To train and evaluate our method, we created the largest authorship-identification dataset to date. It leverages all research papers publicly available on arXiv amounting to over 2 million manuscripts. In arXiv-subsets with up to 2,000 different authors, our method achieves an unprecedented authorship attribution accuracy, where up to 73% of papers are attributed correctly. We present a scaling analysis to highlight the applicability of the proposed method to even larger datasets when sufficient compute capabilities are more widely available to the academic community. Furthermore, we analyze the attribution accuracy in settings where the goal is to identify all authors of an anonymous manuscript. Thanks to our method, we are not only able to predict the author of an anonymous work but we also provide empirical evidence of the key aspects that make a paper attributable. We have open-sourced the necessary tools to reproduce our experiments.
    DOI:  https://doi.org/10.1371/journal.pone.0287611
  2. JAMA Netw Open. 2023 06 01. 6(6): e2320796
       Importance: Institutions and journals strive to promote and protect the integrity of the research record, and both groups are equally committed to ensuring the reliability of all published data.
    Observations: Three US universities coordinated a series of virtual meetings from June 2021 to March 2022 for a working group composed of senior, experienced US research integrity officers (RIOs), journal editors, and publishing staff who are familiar with managing issues of research integrity and publication ethics. The goal of the working group was to improve the collaboration and transparency between institutions and journals to ensure that research misconduct and publication ethics are managed properly and efficiently. Recommendations address the following: identifying proper contacts at institutions and journals, specifying information to share between institutions and journals, correcting the research record, reconsideration of some fundamental research misconduct concepts, and journal policy changes. The working group identified 3 key recommendations to be adopted and implemented to change the status quo for better collaboration between institutions and journals: (1) reconsideration and broadening of the interpretation by institutions of the need-to-know criteria in federal regulations (ie, confidential or sensitive information and data are not disclosed unless there is a need for an individual to know the facts to perform specific jobs or functions), (2) uncoupling the evaluation of the accuracy and validity of research data from the determination of culpability and intent of the individuals involved, and (3) initiating a widespread change for the policies of journals and publishers regarding the timing and appropriateness for contacting institutions, either before or concurrently under certain conditions, when contacting the authors.
    Conclusions and Relevance: The working group recommends specific changes to the status quo to enable effective communication between institutions and journals. Using confidentiality clauses and agreements to impede sharing does not benefit the scientific community nor the integrity of the research record. However, a careful and informed framework for improving communications and sharing information between institutions and journals can foster better working relationships, trust, transparency, and most importantly, faster resolution to data integrity issues, especially in published literature.
    DOI:  https://doi.org/10.1001/jamanetworkopen.2023.20796
  3. Sci Eng Ethics. 2023 06 28. 29(4): 24
      Irregularities in data/results of scientific research might be spotted pre-publication by co-workers and reviewers, or post-publication by readers typically with vested interest. The latter might consist of fellow researchers in the same subject area who would naturally pay closer attention to a published paper. However, it is increasingly apparent that there are readers who interrogate papers in detail with a primary intention to identify potential problems with the work. Here, we consider post-publication peer review (PPPR) by individuals, or groups of individuals, who perform PPPRs with a perceptible intention to actively identify irregularities in published data/results and to expose potential research fraud or misconduct, or intentional misconduct exposing (IME)-PPPR. On one hand, such activities, when done anonymously or pseudonymously with no formal discourse, have been deemed as lacking in accountability, or perceived to incur some degree of maleficence, and have been labelled as vigilantism. On the other, these voluntary works have unravelled many instances of research misconduct and have helped to correct the literature. We explore the tangible benefits of IME-PPPR in detecting errors in published papers and from the perspectives of moral permissibility, research ethics, and the sociological perspective of science. We posit that the benefits of IME-PPPR activities that uncover clear evidence of misconduct, even when performed anonymously or pseudonymously, outweigh their perceived deficiencies. These activities contribute to a vigilant research culture that manifests the self-correcting nature of science, and are in line with the Mertonian norms of scientific ethos.
    Keywords:  Post-publication peer review; Research ethics; Research misconduct; Whistleblowing
    DOI:  https://doi.org/10.1007/s11948-023-00447-z
  4. Mem Inst Oswaldo Cruz. 2023 ;pii: S0074-02762023000100100. [Epub ahead of print]118 e230001
      
    DOI:  https://doi.org/10.1590/0074-02760230001
  5. PLoS One. 2023 ;18(6): e0287677
      The title of an article is the main entrance for reading the full article. The aim of our work therefore is to examine differences of title content and form between original research articles and its changes over time. Using PubMed we examined title properties of 500 randomly chosen original research articles published in the general major medical journals BMJ, JAMA, Lancet, NEJM and PLOS Medicine between 2011 and 2020. Articles were manually evaluated with two independent raters. To analyze differences between journals and changes over time, we performed random effect meta-analyses and logistic regression models. Mentioning of results, providing any quantitative or semi-quantitative information, using a declarative title, a dash or a question mark were rarely used in the title in all considered journals. The use of a subtitle, methods-related items, such as mentioning of methods, clinical context or treatment increased over time (all p < 0.05), while the use of phrasal tiles decreased over time (p = 0.044). Not a single NEJM title contained a study name, while the Lancet had the highest usage of it (45%). The use of study names increased over time (per year odds ratio: 1.13 (95% CI: [1.03‒1.24]), p = 0.008). Investigating title content and form was time-consuming because some criteria could only be adequately evaluated by hand. Title content changed over time and differed substantially between the five major medical journals. Authors are advised to carefully study titles of journal articles in their target journal prior to manuscript submission.
    DOI:  https://doi.org/10.1371/journal.pone.0287677
  6. Ann Behav Med. 2023 Jun 30. 57(7): 509-510
      
    Keywords:  access to information; communications media; health communication; information dissemination; public health; publications
    DOI:  https://doi.org/10.1093/abm/kaad027
  7. Int Forum Allergy Rhinol. 2023 Jun 26.
      
    Keywords:  Image duplications; Research integrity; Research publication
    DOI:  https://doi.org/10.1002/alr.23226
  8. Front Pharmacol. 2023 ;14 1226756
      
    Keywords:  data curation and integration; data sharing; genomics; metadata; reusing public data
    DOI:  https://doi.org/10.3389/fphar.2023.1226756
  9. Complement Ther Med. 2023 Jun 24. pii: S0965-2299(23)00047-X. [Epub ahead of print] 102960
      
    Keywords:  APCs; author fees; healthcare optimization; journal quality; medical journals; page charges; scientific-information transfer
    DOI:  https://doi.org/10.1016/j.ctim.2023.102960
  10. Cureus. 2023 May;15(5): e39386
      The use of artificial intelligence (AI) in scientific publishing has gained increased attention, and one AI tool that has been the subject of much discussion is ChatGPT. It is a large language model (LLM) built on the OpenAI platform that aims to emulate human-like writing and continually improves through user interactions. In this paper, ChatGPT's performance was assessed in medical publishing by comparing it to a case report written by oral and maxillofacial radiologists. ChatGPT was tasked with writing a case report based on a drafted report written by the authors in five different prompts. The findings of this study highlight issues related to the accuracy, completeness, and readability of the generated text. These results have significant implications for the future use of AI in scientific publishing and suggest that in the current iteration of ChatGPT, scientific information must be revised by an expert.
    Keywords:  artificial hallucination; artificial intelligence; case report; chatgpt; scientific writing and artificial intelligence
    DOI:  https://doi.org/10.7759/cureus.39386
  11. Biol Psychol. 2023 Jun 24. pii: S0301-0511(23)00138-2. [Epub ahead of print] 108621
      There is increasing concern and consternation about generative artificial intelligence (AI) programs and its potential impact on academia. This editorial addresses the potential impact of such programs on scientific publishing as it relates to the journal Biological Psychology. Using chatGPT as an example, it makes the case that a prime concern is its implications for facilitating plagiarism. It briefly outlines what is known about the algorithm of the GPT text model, and also the implications of its chatGPT front end, on being able to establish appropriate credit for ideas in text that it outputs. It is concluded that, at least for Biological Psychology, the expectation is that authors will be transparent about AI usage, will declare when AI is the source of an idea, and will redouble efforts to seek out and cite prior claims to ideas in the published literature when AI is involved.
    Keywords:  Academic misconduct; Artificial intelligence; ChatGPT; Large language models; Plagiarism
    DOI:  https://doi.org/10.1016/j.biopsycho.2023.108621
  12. Res Nurs Health. 2023 Jun 26.
      
    Keywords:  artificial intelligence; language processing; nursing research; research automation; scientific writing
    DOI:  https://doi.org/10.1002/nur.22326
  13. Am J Emerg Med. 2023 Jun 14. pii: S0735-6757(23)00317-0. [Epub ahead of print]
      
    Keywords:  Artificial intelligence; ChatGPT; Ethics; Publication; Research
    DOI:  https://doi.org/10.1016/j.ajem.2023.06.023
  14. Ann Biomed Eng. 2023 Jun 27.
      This letter highlights a pressing issue regarding the absence of established editorial policies for the utilization of AI tools (e.g., ChatGPT) in the peer review process. The increasing adoption of AI tools in academic publishing necessitates the formulation of standardized guidelines to ensure fairness, transparency, and accountability. Without clear editorial policies, there is a threat of compromising the integrity of the peer review process and undermining the credibility of academic publications. Urgent attention is needed to address this gap and establish robust protocols that govern the use of AI tools in peer review.
    Keywords:  Artificial intelligence; ChatGPT; Editorial policies; Peer review
    DOI:  https://doi.org/10.1007/s10439-023-03299-7
  15. J Oral Pathol Med. 2023 Jun 26.
       BACKGROUND: Systematic reviews (SRs) have become a popular approach for evidence-based practice, being considered a lens through which evidence is viewed and applied. However, several published studies have been identified as scoping reviews rather than SRs. This methodological error can negatively impact clinical decision-making or new research conceptualization.
    AIM: This letter focuses on the increasing number of SRs in oral pathology and medicine, highlighting the most frequent methodological mistakes.
    RESULTS: We providing general guidance to help researchers conceptualize better their SRs and for the critical evaluation of SRs by scientific journal reviewers.
    CONCLUSION: Clinicians, pathologists, and reviewers, must ensure the quality of the published information.
    Keywords:  oral medicine; oral pathology; peer review; review; systematic review
    DOI:  https://doi.org/10.1111/jop.13456
  16. Health Policy Open. 2022 Dec;3 100063
    CHEERS 2022 ISPOR Good Research Practices Task Force
      Health economic evaluations are comparative analyses of alternative courses of action in terms of their costs and consequences. The Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement, published in 2013, was created to ensure health economic evaluations are identifiable, interpretable, and useful for decision making. It was intended as guidance to help authors report accurately which health interventions were being compared and in what context, how the evaluation was undertaken, what the findings were, and other details that may aid readers and reviewers in interpretation and use of the study. The new CHEERS 2022 statement replaces previous CHEERS reporting guidance. It reflects the need for guidance that can be more easily applied to all types of health economic evaluation, new methods and developments in the field, as well as the increased role of stakeholder involvement including patients and the public. It is also broadly applicable to any form of intervention intended to improve the health of individuals or the population, whether simple or complex, and without regard to context (such as health care, public health, education, social care, etc). This summary article presents the new CHEERS 2022 28-item checklist and recommendations for each item. The CHEERS 2022 statement is primarily intended for researchers reporting economic evaluations for peer reviewed journals as well as the peer reviewers and editors assessing them for publication. However, we anticipate familiarity with reporting requirements will be useful for analysts when planning studies. It may also be useful for health technology assessment bodies seeking guidance on reporting, as there is an increasing emphasis on transparency in decision making.
    Keywords:  Economic evaluation; Health economics; Health technology assessment; Reporting guidance
    DOI:  https://doi.org/10.1016/j.hpopen.2021.100063
  17. World J Gastroenterol. 2023 Jun 07. 29(21): 3379-3384
      Publication in a peer-reviewed journal is the goal of any research project. One of the most important (and possibly the least understood) aspects of the publication process is the choice of a suitable journal that is likely to accept your work. Detailed information and tips and tricks to success are given in this editorial.
    Keywords:  Altmetrics; Journal; Publication; Research
    DOI:  https://doi.org/10.3748/wjg.v29.i21.3379
  18. Am J Pharm Educ. 2023 07;pii: S0002-9459(23)00090-6. [Epub ahead of print]87(7): 100089
      The goal of this Best Practice Review is to support researchers in successfully preparing and publishing qualitative research in pharmacy education. Standard practice from the literature and journals' guidance from related fields were reviewed, and recommendations and resources applicable to qualitative research in pharmacy education were compiled for researchers planning to conduct and publish qualitative research. This review provides recommendations, not requirements, for publication in the Journal and is intended to be a guide, especially for authors and reviewers relatively new to the field of qualitative research. Additionally, researchers planning to publish their qualitative research are advised to review available best practices and standards, such as the Consolidated Criteria for Reporting Qualitative Research checklist and the Standards for Reporting Qualitative Research. Given the diverse methodology of qualitative research, it is important for authors to provide sufficient details and justifications of selected methods for transparency and to report collected results in a manner that allows reviewers and readers to adequately assess the validity of their study and the applicability of the findings.
    Keywords:  American Journal of Pharmaceutical Education; Education; Pharmacy; Publication; Qualitative research
    DOI:  https://doi.org/10.1016/j.ajpe.2023.100089
  19. J Pediatr Health Care. 2023 Jun 24. pii: S0891-5245(23)00152-9. [Epub ahead of print]
      Authors submitting a paper often receive an opportunity to revise and resubmit the paper. Authors may find addressing reviewers' comments challenging. We posit authors should welcome expert suggestions for revisions that strengthen the paper and develop a persuasive response if they disagree with the reviewer. A thoughtful, detailed response allows authors to dialogue with reviewers. Our paper uses exemplars of responses to reviewers to illustrate the effectiveness of clear and compelling author responses. Addressing reviewers' comments ultimately results in a better paper-more likely to be accepted. Developing skills in resubmitting research and clinical scholarship reports is essential to the dissemination process.
    Keywords:  Response to reviewer; dissemination; publishing; scholarly writing
    DOI:  https://doi.org/10.1016/j.pedhc.2023.06.001
  20. Nature. 2023 Jun;618(7967): 1098-1099
      
    Keywords:  Databases; Publishing; Research data
    DOI:  https://doi.org/10.1038/d41586-023-01929-7
  21. Int J Gynaecol Obstet. 2023 Jun 25.
      
    Keywords:  article processing charge; open access publishing; subscription publishing model
    DOI:  https://doi.org/10.1002/ijgo.14976
  22. Front Res Metr Anal. 2023 ;8 1233867
      
    Keywords:  Africa; barriers and facilitative factors; editorial; open access; open data; open science; policy
    DOI:  https://doi.org/10.3389/frma.2023.1233867
  23. EMBO Rep. 2023 Jun 29. e57638
      The EMBO Journal and EMBO Reports join EMBO Molecular Medicine, Molecular Systems Biology and Life Science Alliance as Open Access journals from 2024. Full Open Access at EMBO Press completes another step towards the goal of an integrated Open Science approach for the dissemination of highly selected and curated science.
    DOI:  https://doi.org/10.15252/embr.202357638
  24. Anaesthesia. 2023 Jun 26.
    Editors
      It is essential that academic publishing complies with the highest standards in terms of ethics, research conduct and manuscript preparation. This protects the rights and welfare of research participants, ensures the integrity of study results and aids the communication and dissemination of novel findings into clinical practice. This position statement outlines the current policies and practices of the Editors of Anaesthesia and Anaesthesia Reports in relation to academic medical publishing.
    Keywords:  ethics; position statement; publishing; research
    DOI:  https://doi.org/10.1111/anae.16071
  25. Acad Med. 2023 Jun 20.
       PURPOSE: Journals have begun to expand the racial diversity of editors as a first step to countering institutional racism. Given the power editors hold as gatekeepers, a diverse team helps ensure that minoritized scholars have equal opportunity to contribute. In 2021, Teaching and Learning in Medicine (TLM) created an editorial internship for racially minoritized individuals. This study examines the first 6 months of this program to better understand its creation and initial successes.
    METHOD: The authors employed critical collaborative autoethnography, a qualitative methodology, focusing on the underlying assumptions around power and hierarchy that are implicit in the design and implementation of the TLM internship. Participants included 13 TLM editorial board members (10 internship selection committee members, 3 mentors, 2 independent researchers), 3 external selection committee members, and 3 interns, with some holding multiple roles. Ten participants served as authors of this report. Data included archival emails, planning documents, and focus groups. The initial analysis explored what happened and how and was followed by a thematic analysis in which participants reflected on their responsibility for implementing an antiracist program.
    RESULTS: While the program developed interns' editorial skills, which they greatly valued, and diversified the TLM editorial board, it did not achieve the goal of fostering antiracism. Mentors focused on conducting joint peer reviews with interns, assuming that racial experiences can and should be separate from the editorial process, thus working within, rather than trying to change, the existing racist system.
    CONCLUSIONS: Given these findings, greater structural change is needed to disrupt the existing racist system. These experiences underscore the importance of recognizing the harmful impact a race-neutral lens can have on antiracist efforts. Moving forward, TLM will implement lessons learned ahead of offering the internship again with the goal of creating the transformative change intended with the creation of the program.
    DOI:  https://doi.org/10.1097/ACM.0000000000005303