Feasibility of an Assessment Tool as a Data-Driven Approach to Reducing Racial Bias in Biomedical Publications

The editorial independence of biomedical journals allows flexibility to meet a wide range of research interests. However, it also is a barrier for coordination between journals to solve challenging issues such as racial bias in the scientific literature. A standardized tool to screen for racial bias could prevent the publication of racially biased papers. Biomedical journals would maintain editorial autonomy while still allowing comparable data to be collected and analyzed across journals. A racially diverse research team carried out a three-phase study to generate and test a racial bias assessment tool for biomedical research. Phase 1, an in-depth, structured literature search to identify recommendations, found near complete agreement in the literature on addressing race in biomedical research. Phase 2, construction of a framework from those recommendations, provides the major innovation of this paper. The framework includes three dimensions of race: 1) context, 2) tone and terminology, and 3) analysis, which are the basis for the Race Equity Vetting Instrument for Editorial Workflow (REVIEW) tool. Phase 3, pilot testing the assessment tool, showed that the REVIEW tool was effective at flagging multiple concerns in widely criticized articles. This study demonstrates the feasibility of the proposed REVIEW tool to reduce racial bias in research. Next steps include testing this tool on a broader sample of biomedical research to determine how the tool performs on more subtle examples of racial bias.

Is Hypoxic/Altitude Training an Important Topic in the Field of Hypoxia?

Hypoxia is an essential topic in medical or biological sciences. The main aims of the present study were to examine the most important medical articles (i.e., the top 100 most cited) on hypoxia. We examine how the Nobel-prize awarded hypoxia inducible factor (HIF)-pathway discovery in the early 1990s has changed the thematic composition of this body of literature, with a special emphasis on the studies linking hypoxia and cancer. We searched Pubmed for articles with the terms #Hypox, #Altitude, or #Mountain in the title that have been published in biomedical journals and ranked the articles on their number of citations in Web of Science. A second search was performed in all journals for articles related to hypoxia and cancer. Strikingly, only 12 of the top-100 most-cited articles on hypoxia and only 3 articles of the top-100 articles related to cancer were published before 1995. Moreover, only 5 articles from prior 1995 reached 1000 citations, while 27 articles published in 1995 or later were cited more than 1000 times, most of them on the HIF-1 pathway. Eighty percent of the top-100 articles were related to the HIF pathway, while there were no articles on the application of hypoxia either for therapeutic use (i.e., hypoxic conditioning in patients) or for performance enhancement (i.e., altitude training in athletes). In conclusion, the early-1990s discovery of the HIF pathway and of its molecular regulation has shifted the focus of hypoxia research towards molecular mechanisms and consequences of tissue hypoxia, most notably in cancer. The importance of studies focusing on clinical and performance applications of systemic hypoxia is relatively lower.

A comprehensive analysis of code and data availability in biomedical research

Modern data-driven research increasingly depends on quantitative analysis, yet effectivemechanisms ensuring data and analysis transparency and reproducibility are yet to be developedand adopted widely. The importance and benefits of sharing research products has beenrecognized widely by the scientific community. In biomedical research, it is not only imperativeto publish a detailed description of the study design, methodology, results and interpretation, butthere is a pressing need to make all the research products publicly available, shareable, welldocumented to increase transparency and reproducibility. Current efforts in sharing researchproducts mostly rely on individual researchers and widely but variably enforced by theseindividuals and research organizations. However, an increasing body of evidence in recent yearsalso points to a growing problem of reproducibility across scientific disciplines, i.e. publishedresults often contain analyses that are non replicated due to lack of documentation, code anddata required to reproduce the analysis. Our results indicate that only 36% of the scientificmanuscripts published in prominent biomedical journals share raw data and 9% of the papersshare code. We hope that our analysis informs and exhorts the biomedical community to designeffective strategies to be widely adopted by the researchers to improve the current scenario oftransparency and reproducibility of data-driven biomedical research.

A comprehensive analysis of code and data availability in biomedical research

Modern data-driven research increasingly depends on quantitative analysis, yet effectivemechanisms ensuring data and analysis transparency and reproducibility are yet to be developedand adopted widely. The importance and benefits of sharing research products has beenrecognized widely by the scientific community. In biomedical research, it is not only imperativeto publish a detailed description of the study design, methodology, results and interpretation, butthere is a pressing need to make all the research products publicly available, shareable, welldocumented to increase transparency and reproducibility. Current efforts in sharing researchproducts mostly rely on individual researchers and widely but variably enforced by theseindividuals and research organizations. However, an increasing body of evidence in recent yearsalso points to a growing problem of reproducibility across scientific disciplines, i.e. publishedresults often contain analyses that are non replicated due to lack of documentation, code anddata required to reproduce the analysis. Our results indicate that only 36% of the scientificmanuscripts published in prominent biomedical journals share raw data and 9% of the papersshare code. We hope that our analysis informs and exhorts the biomedical community to designeffective strategies to be widely adopted by the researchers to improve the current scenario oftransparency and reproducibility of data-driven biomedical research.

A survey of biomedical journals to detect editorial bias and nepotistic behavior

Alongside the growing concerns regarding predatory journal growth, other questionable editorial practices have gained visibility recently. Among them, we explored the usefulness of the Percentage of Papers by the Most Prolific author (PPMP) and the Gini index (level of inequality in the distribution of authorship among authors) as tools to identify journals that may show favoritism in accepting articles by specific authors. We examined whether the PPMP, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using all articles in a sample of 5,468 biomedical journals indexed in the National Library of Medicine. For articles published between 2015 and 2019, the median PPMP was 2.9%, and 5% of journal exhibited a PPMP of 10.6% or more. Among the journals with the highest PPMP or Gini index values, where a few authors were responsible for a disproportionate number of publications, a random sample was manually examined, revealing that the most prolific author was part of the editorial board in 60 cases (61%). The papers by the most prolific authors were more likely to be accepted for publication within 3 weeks of their submission. Results of analysis on a subset of articles, excluding nonresearch articles, were consistent with those of the principal analysis. In most journals, publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

PubMed Central as a platform for the survival of open-access biomedical society journals published in Korea

Twenty-one years have passed since PubMed Central (PMC) launched. The present case study describes Korean editors’ history of participation in PMC and their contributions to PMC. The three main turning points in the history of Korean editors’ involvement with PMC were as follows: first, the production of PMC XML files and deposition starting in 2008; second, thorough evaluations of applying journals since 2014; and third, the feasibility of non-English journals being indexed in PMC starting in 2019. The importance of PMC is further shown by the fact that KoreaMed Synapse, a full-text XML database of biomedical journals in Korea that was launched in 2007, was created by benchmarking PMC. Scholarly societies or institutes publish 724 (34.2%) of the 2,119 PMC journals without embargo in June 2021. Out of those 724 journals, 127 (17.5%) are published in Korea. PMC has helped local journals receive more citations from researchers worldwide, increasing their likelihood of being indexed in international databases. The number of submissions from international researchers has increased, thereby making it possible for journals to achieve international diversity. As the best full-text platform of biomedical journals, PMC has provided an excellent opportunity for biomedical journal editors in Korea to change their journals’ language to English and produce full-text JATS (Journal Article Tag Suite) XML files. These factors have made Korea the second-ranked country in terms of no-embargo PMC journals published by academic societies or institutes.

Factors influencing acceptance or rejection by Iranian medical researchers of invitations to peer review

Background: Peer review is a necessary but costly and time-consuming process to identify good-quality and methodologically sound articles and improve them before publication. Finding good peer reviewers is often difficult. Objective: To identify the incentives that make Iranian biomedical researchers accept invitations to be a peer reviewer and factors that affect these incentives. Methods: Twelve reviewers selected at random from the reviewers pool of each of 26 biomedical journals published from Fars province, Iran, were surveyed using a questionnaire that we had developed and tested in a pilot study of 30 reviewers (Cronbach’s alpha of 0.779). The data included the reviewers’ demographics, history of their reviews, and choice of 11 reasons each for accepting or declining the invitation to review. Results: A total of 233 reviewers completed the questionnaire. The most important reasons for accepting the invitation to review were the journal’s practice to publish the names of the reviewers alongside the article they had reviewed, acknowledgement by the journals by publishing the names of reviewers once a year, free access to journals’ content, and lower publication charges as authors. The most common reasons to decline the invitation were lack of time, busy schedules, and lack of sufficient incentive to review. Conclusion: Acknowledgement by the journal, offering to publish the names of reviewers alongside the articles they had reviewed, and monetary rewards will be effective incentives for biomedical researchers in Iran to serve as peer reviewers.

Indexing of the Russian biomedical journals in MEDLINE and PubMed: analysis of the positive and negative experience

The MEDLINE database and PubMed.com web-platform are the world’s best-known and most used sources for search scientific information in biology and medicine. Indexing in MEDLINE and making a journal searchable through PubMed.com is a most powerful tool to promote it worldwide. No other databases, even Scopus and Web of Science, can be compared with MEDLINE in terms of its effect on the readability and availability in web-search results. At the same time, medical and biological journals from Russia have serious problems with the MEDLINE indexation results in an extremely low presence of publications from Russian journals in this database. Over the past decade, the number of Russian journals indexed in MEDLINE has significantly decreased. Present article discusses the main characteristics of the MEDLINE database and PubMed.com, their journal selection process and the reasons for their high importance in scientific journals promotion, as well as the experience of submitting journals for peer review to be indexed in this database. Both positive and negative experience of preparing a journal for indexing in MEDLINE is considered, this can help the editors and publishers of all biology and medicine journals in Russia in solving this task.

A scoping review on biomedical journal peer review guides for reviewers

Background Peer review is widely used in academic fields to assess a manuscript’s significance and to improve its quality for publication. This scoping review will assess existing peer review guidelines and/or checklists intended for reviewers of biomedical journals and provide an overview on the review guidelines. Methods PubMed, Embase, and Allied and Complementary Medicine (AMED) databases were searched for review guidelines from the date of inception until February 19, 2021. There was no date restriction nor article type restriction. In addition to the database search, websites of journal publishers and non-publishers were additionally hand-searched. Results Of 14,633 database publication records and 24 website records, 65 publications and 14 websites met inclusion criteria for the review (78 records in total). From the included records, a total of 1,811 checklist items were identified. The items related to Methods, Results, and Discussion were found to be the highly discussed in reviewer guidelines. Conclusion This review identified existing literature on peer review guidelines and provided an overview of the current state of peer review guides. Review guidelines were varying by journals and publishers. This calls for more research to determine the need to use uniform review standards for transparent and standardized peer review. Protocol registration The protocol for this study has been registered at Research Registry (www.researchregistry.com): reviewregistry881.