bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒08‒14
twenty-one papers selected by
Thomas Krichel
Open Library Society
  1. National differences in dissemination and use of open access literature.
  2. Canadian academics' use of predatory journals.
  3. The first author takes it all? Solutions for crediting authors more visibly, transparently, and free of bias.
  4. Characteristics of Blacklisted Journals: Evidence from Chinese-language Academic Journals.
  5. Publication practices during the COVID-19 pandemic: Expedited publishing or simply an early bird effect?
  6. Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals.
  7. Peer review as a measurable responsibility of those who publish: The peer review debt index.
  8. Responding to Reviewer Needs: A Survey of JACR Reviewer Experience.
  9. neuPrint: An open access tool for EM connectomics.
  10. Shining a little light on peer review debates.
  11. Procrastination and inconsistency: expressions of concern for publications with compromised integrity.
  12. Publish or Perish but Pursue Decolonization: The Complexities of Global Surgery Authorship.
  13. Reporting and transparent research practices in sports medicine and orthopaedic clinical trials: a meta-research study.
  14. Helping the crisis in peer review.
  15. Education Descriptive Reports: How to Publish Pragmatic Studies in Education.
  16. Embracing the value of research data: Introducing the JCHLA/JABSC Data Sharing Policy.
  17. The use of the phrase "data not shown" in dental research.
  18. Equity in neurosurgical scientific publication.
  19. Translating Nursing Partnerships in Clinical Care to Scientific Publishing.
  20. Citation Bias, Diversity, and Ethics.
  21. JCHLA/JABSC editorial policies and practices to address systemic racism and improve equity, diversity, and inclusion.
  1. PLoS One. 2022 ;17(8): e0272730
    National differences in dissemination and use of open access literature.
    Marc-André Simard, Gita Ghiasi, Philippe Mongeon, Vincent Larivière.
      Open Access (OA) dissemination has been gaining a lot of momentum over the last decade, thanks to the implementation of several OA policies by funders and institutions, as well as the development of several new platforms that facilitate the publication of OA content at low or no cost. Studies have shown that nearly half of the contemporary scientific literature could be available online for free. However, few studies have compared the use of OA literature across countries. This study aims to provide a global picture of OA adoption by countries, using two indicators: publications in OA and references made to articles in OA. We find that, on average, low-income countries are publishing and citing OA at the highest rate, while upper middle-income countries and higher-income countries publish and cite OA articles at below world-average rates. These results highlight national differences in OA uptake and suggest that more OA initiatives at the institutional, national, and international levels are needed to support wider adoption of open scholarship.
    DOI:  https://doi.org/10.1371/journal.pone.0272730
  2. J Can Health Libr Assoc. 2021 Dec;42(3): 140-153
    Canadian academics' use of predatory journals.
    Maureen Babb.
      Introduction: Predatory journals have been acknowledged as an increasing concern in the scholarly literature over the last decade, but research on the subject has been sparse. Research that has focused on predatory journals in the Canadian context has been even rarer, and limited to work focused on a single university. This study explores publishing trends in predatory journals by authors affiliated with Canadian universities.Methods: Articles published by authors at 30 Canadian universities, including all universities in the U15, were pulled from select predatory journals. Key data including author affiliation, article type, discipline, and grant information were extracted from the articles.
    Results: All universities in the study were found to have publications in predatory journals. The health sciences accounted for 72% of the publications, and the sciences for 20%. Research articles accounted for 50% of the articles. Opinion, editorial, or commentary pieces accounted for 24% and 19% were review articles. Grant funding was indicated in 34% of the articles, with NSERC and CIHR being top funders. The research-intensive U15 universities were found to publish more in predatory journals than their non-U15 compatriots, even when the universities were of similar size.
    Discussion: Canadian scholars were found to publish in predatory journals, particularly those scholars from the health sciences and research-intensive U15 universities. Grant funding was common, and often came from high profile funders like NSERC and CIHR. This study suggests that policy and education initiatives may be warranted in Canadian contexts, especially in the health sciences and at research-intensive universities.
    DOI:  https://doi.org/10.29173/jchla29579
  3. Br J Soc Psychol. 2022 Aug 09.
    The first author takes it all? Solutions for crediting authors more visibly, transparently, and free of bias.
    Myriam A Baum, Moritz N Braun, Alexander Hart, Véronique I Huffer, Julia A Meßmer, Michael Weigl, Lasse Wennerhold.
      With the seventh edition of the publication manual of the American Psychological Association (APA), the APA style now prescribes bias-free language and encourages accessibility even to non-academic audiences. However, even with the newest guidelines, the way we credit authors in psychology remains anachronistic, intransparent, and prone to conflict. It still relies on a sequence-determines-credit approach in the byline, which concurrently is contradicted by the option to consider the last author as the position of the principal investigator depending on the field or journal. Scholars from various disciplines have argued that relying on such norms introduces a considerable amount of error when stakeholders rely on articles for career-relevant decisions. Given the existing recommendations towards a credit-based system, ignoring those issues will further promote bias that could be avoided with rather minor changes to the way we perceive authorship. In this article, we introduce a set of easy-to-implement changes to the manuscript layout that value contribution rather than position. Aimed at fostering transparency, accountability, and equality between authors, establishing those changes would likely benefit all stakeholders in contemporary psychological science.
    Keywords:  authorship; citation style; credit; publication; transparency
    DOI:  https://doi.org/10.1111/bjso.12569
  4. Account Res. 2022 Aug 11.
    Characteristics of Blacklisted Journals: Evidence from Chinese-language Academic Journals.
    Gengyan Tang, Jingwen Jia.
      Some institutions have issued blacklists of academic journals in China and use them as a basis for research evaluation. However, due to a lack of transparent formulation criteria, the characteristics of blacklisted journals remain unclear. Using blacklisted academic journals of the East China University of Political Science and Law, this study analyzed differences in characteristics between blacklisted and non-blacklisted journals via web surveys and statistical analyses. Statistically significant differences were detected for article review time, article processing charges (APCs), the number of editorial board members, and the journal impact factor. There was no significant difference in the number of editors. While there is scientific merit in creating and publishing a blacklist of academic journals, the list development process requires more rigorous evaluation and a public process of development.
    Keywords:  academic journals; journal blacklists; predatory journals; research evaluation
    DOI:  https://doi.org/10.1080/08989621.2022.2112953
  5. Learn Publ. 2022 Jun 30.
    Publication practices during the COVID-19 pandemic: Expedited publishing or simply an early bird effect?
    Yulia V Sevryugina, Andrew J Dicks.
      This study explores the evolution of publication practices associated with the SARS-CoV-2 research papers, namely, peer-reviewed journal and review articles indexed in PubMed and their associated preprints posted on bioRxiv and medRxiv servers: a total of 4,031 journal article-preprint pairs. Our assessment of various publication delays during the January 2020 to March 2021 period revealed the early bird effect that lies beyond the involvement of any publisher policy action and is directly linked to the emerging nature of new and 'hot' scientific topics. We found that when the early bird effect and data incompleteness are taken into account, COVID-19 related research papers show only a moderately expedited speed of dissemination as compared with the pre-pandemic era. Medians for peer-review and production stage delays were 66 and 15 days, respectively, and the entire conversion process from a preprint to its peer-reviewed journal article version took 109.5 days. The early bird effect produced an ephemeral perception of a global rush in scientific publishing during the early days of the coronavirus pandemic. We emphasize the importance of considering the early bird effect in interpreting publication data collected at the outset of a newly emerging event.
    Keywords:  COVID‐19; expedited publication practices; publication delays
    DOI:  https://doi.org/10.1002/leap.1483
  6. PLoS One. 2022 ;17(8): e0264661
    Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals.
    Jean-Francois Gehanno, Julien Grosjean, Stefan J Darmoni, Laetitia Rollin.
      INTRODUCTION: Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version.METHODS: Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.
    RESULTS: Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints.
    CONCLUSIONS: More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.
    DOI:  https://doi.org/10.1371/journal.pone.0264661
  7. J Psychosom Res. 2022 Jul 27. pii: S0022-3999(22)00282-3. [Epub ahead of print]161 110997
    Peer review as a measurable responsibility of those who publish: The peer review debt index.
    Jess G Fiedorowicz, Maria Kleinstäuber, Cédric Lemogne, Bernd Löwe, Bola Ola, Angelina Sutin, Stanley Wong, Nicholas Fabiano, Miranda Van Tilburg, Antonina Mikocka-Walus.
      
    Keywords:  Peer review; Publishing; Scientific responsibility
    DOI:  https://doi.org/10.1016/j.jpsychores.2022.110997
  8. J Am Coll Radiol. 2022 Aug 08. pii: S1546-1440(22)00550-6. [Epub ahead of print]
    Responding to Reviewer Needs: A Survey of JACR Reviewer Experience.
    Tara Catanzano.
      
    DOI:  https://doi.org/10.1016/j.jacr.2022.06.014
  9. Front Neuroinform. 2022 ;16 896292
    neuPrint: An open access tool for EM connectomics.
    Stephen M Plaza, Jody Clements, Tom Dolafi, Lowell Umayam, Nicole N Neubarth, Louis K Scheffer, Stuart Berg.
      Due to advances in electron microscopy and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the chemical synapses between them, for significant volumes of neural tissue. Smaller past reconstructions were primarily used by domain experts, could be handled by downloading data, and performance was not a serious problem. But new and much larger reconstructions upend these assumptions. These networks now contain tens of thousands of neurons and tens of millions of connections, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. Allowing other scientists to make use of this data needs more than publication-it requires new tools that are publicly available, easy to use, and efficiently handle large data. We introduce neuPrint to address these data analysis challenges. Neuprint contains two major components-a web interface and programmer APIs. The web interface is designed to allow any scientist worldwide, using only a browser, to quickly ask and answer typical biological queries about a connectome. The neuPrint APIs allow more computer-savvy scientists to make more complex or higher volume queries. NeuPrint also provides features for assessing reconstruction quality. Internally, neuPrint organizes connectome data as a graph stored in a neo4j database. This gives high performance for typical queries, provides access though a public and well documented query language Cypher, and will extend well to future larger connectomics databases. Our experience is also an experiment in open science. We find a significant fraction of the readers of the article proceed to examine the data directly. In our case preprints worked exactly as intended, with data inquiries and PDF downloads starting immediately after pre-print publication, and little affected by formal publication later. From this we deduce that many readers are more interested in our data than in our analysis of our data, suggesting that data-only papers can be well appreciated and that public data release can speed up the propagation of scientific results by many months. We also find that providing, and keeping, the data available for online access imposes substantial additional costs to connectomics research.
    Keywords:  APIs; connectomics; formal publication; open science; preprint; web access
    DOI:  https://doi.org/10.3389/fninf.2022.896292
  10. BJUI Compass. 2022 Sep;3(5): 319-323
    Shining a little light on peer review debates.
    John W Davis.
      
    DOI:  https://doi.org/10.1002/bco2.181
  11. Account Res. 2022 Aug 11.
    Procrastination and inconsistency: expressions of concern for publications with compromised integrity.
    Andrew Grey, Alison Avenell, Mark J Bolland.
      Expressions of concern (EoC) can reduce the adverse effects of unreliable publications by alerting readers to concerns about publication integrity while assessment is undertaken. We investigated the use of EoC for 463 publications by two research groups for which we notified concerns about publication integrity to 142 journals and 44 publishers between March 2013 and February 2020. By December 2021, 95 papers had had an EoC, and 83 were retracted without an EoC. Median times from notification of concerns to EoC (10.4mo) or retraction without EoC (13.1mo) were similar. Among the 95 EoCs, 29 (30.5%) were followed by retraction after a median of 5.4mo, none was lifted, and 66 (69.5%) remained in place after a median of 18.1mo. Publishers with >10 notified publications issued EoCs for 0-81.8% of papers: for several publishers the proportions of notified papers for which EoCs were issued varied considerably between the 2 research groups. EoCs were issued for >30% of notified publications of randomized clinical trials and letters to the editor, and <20% of other types of research. These results demonstrate inconsistent application of EoCs between and within publishers, and prolonged times to issue and resolve EoCs.
    Keywords:  Committee on Publication Ethics; Publication integrity; academic publishing; expression of concern; publication ethics; research integrity; retraction
    DOI:  https://doi.org/10.1080/08989621.2022.2112572
  12. World J Surg. 2022 Aug 08.
    Publish or Perish but Pursue Decolonization: The Complexities of Global Surgery Authorship.
    Felix Oyania, Tamara N Fitzgerald.
      
    DOI:  https://doi.org/10.1007/s00268-022-06698-4
  13. BMJ Open. 2022 08 08. 12(8): e059347
    Reporting and transparent research practices in sports medicine and orthopaedic clinical trials: a meta-research study.
    Robert Schulz, Georg Langen, Robert Prill, Michael Cassel, Tracey L Weissgerber.
      OBJECTIVES: Transparent reporting of clinical trials is essential to assess the risk of bias and translate research findings into clinical practice. While existing studies have shown that deficiencies are common, detailed empirical and field-specific data are scarce. Therefore, this study aimed to examine current clinical trial reporting and transparent research practices in sports medicine and orthopaedics.SETTING: Exploratory meta-research study on reporting quality and transparent research practices in orthopaedics and sports medicine clinical trials.
    PARTICIPANTS: The sample included clinical trials published in the top 25% of sports medicine and orthopaedics journals over 9 months.
    PRIMARY AND SECONDARY OUTCOME MEASURES: Two independent reviewers assessed pre-registration, open data and criteria related to scientific rigour, like randomisation, blinding, and sample size calculations, as well as the study sample, and data analysis.
    RESULTS: The sample included 163 clinical trials from 27 journals. While the majority of trials mentioned rigour criteria, essential details were often missing. Sixty per cent (95% confidence interval (CI) 53% to 68%) of trials reported sample size calculations, but only 32% (95% CI 25% to 39%) justified the expected effect size. Few trials indicated the blinding status of all main stakeholders (4%; 95% CI 1% to 7%). Only 18% (95% CI 12% to 24%) included information on randomisation type, method and concealed allocation. Most trials reported participants' sex/gender (95%; 95% CI 92% to 98%) and information on inclusion and exclusion criteria (78%; 95% CI 72% to 84%). Only 20% (95% CI 14% to 26%) of trials were pre-registered. No trials deposited data in open repositories.
    CONCLUSIONS: These results will aid the sports medicine and orthopaedics community in developing tailored interventions to improve reporting. While authors typically mention blinding, randomisation and other factors, essential details are often missing. Greater acceptance of open science practices, like pre-registration and open data, is needed. As these practices have been widely encouraged, we discuss systemic interventions that may improve clinical trial reporting.
    Keywords:  clinical trials; medical education & training; orthopaedic & trauma surgery; rehabilitation medicine; sports medicine; statistics & research methods
    DOI:  https://doi.org/10.1136/bmjopen-2021-059347
  14. J Nurs Scholarsh. 2022 Aug 10.
    Helping the crisis in peer review.
    Susan Gennaro.
      
    DOI:  https://doi.org/10.1111/jnu.12807
  15. J Chiropr Humanit. 2022 Dec;29 15-21
    Education Descriptive Reports: How to Publish Pragmatic Studies in Education.
    Claire D Johnson, Bart N Green.
      Objective: The purpose of this article is to describe the contents of an education descriptive report and to provide a useful publication format for educators in the health professions.Discussion: The education descriptive report is a pragmatic, empirical study that can contribute to the literature. Education descriptive reports describe an event or situation in an education setting, the resulting outcomes, and what new information can be learned. These reports may use quantitative, qualitative, or mixed methods and may be from organizational, academic, instructional, programmatic, or other educational perspectives.
    Conclusion: The education descriptive report gives educators in the health professions a mechanism to introduce their scholarly efforts and observations in education environments in a manner that is consistent with the academic literature. This article describes the structure of an education descriptive report and includes a helpful template for academic authors to develop their own report so they may publish observational, reflective, and hypothesis-generating articles.
    Keywords:  Education; Empirical Research; Knowledge Discovery; Research Design; Research Report
    DOI:  https://doi.org/10.1016/j.echu.2022.06.001
  16. J Can Health Libr Assoc. 2021 Apr;42(1): 6-13
    Embracing the value of research data: Introducing the JCHLA/JABSC Data Sharing Policy.
    Kevin Read, Alanna Campbell, Vanessa Kitchin, Heather MacDonald, Sandra McKeown.
      Health sciences researchers are being asked to share their data more frequently due to funder policies, journal requirements, or interest from their peers. Health sciences librarians (HSLs) have simultaneously begun to provide support to researchers in this space through training, participating in RDM efforts on research grants, and developing comprehensive data services programs. If supporting researchers' data sharing efforts is a worthwhile investment for HSLs, it is crucial that we practice data sharing in our own research endeavours. Sharing data is a positive step in the right direction, as it can increase the transparency, reliability, and reusability of HSL-related research outputs. Furthermore, being able to identify and connect with researchers in relation to the challenges associated with data sharing can help HSLs empathize with their communities and gain new perspectives on improving support in this area. To that end, the Journal of the Canadian Health Libraries Association / Journal de l'Association des bibliothèques de la santé du Canada (JCHLA/JABSC) has developed a Data Sharing Policy to improve the transparency and reusability of research data underlying the results of its publications. This paper will describe the approach taken to inform and develop this policy.
    DOI:  https://doi.org/10.29173/jchla29536
  17. PLoS One. 2022 ;17(8): e0272695
    The use of the phrase "data not shown" in dental research.
    Eero Raittio, Ahmad Sofi-Mahmudi, Erfan Shamsoddin.
      OBJECTIVE: The use of phrases such as "data/results not shown" is deemed an obscure way to represent scientific findings. Our aim was to investigate how frequently papers published in dental journals use the phrases and what kind of results the authors referred to with these phrases in 2021.METHODS: We searched the Europe PubMed Central (PMC) database for open-access articles available from studies published in PubMed-indexed dental journals until December 31st, 2021. We searched for "data/results not shown" phrases from the full texts and then calculated the proportion of articles with the phrases in all the available articles. From studies published in 2021, we evaluated whether the phrases referred to confirmatory results, negative results, peripheral results, sensitivity analysis results, future results, or other/unclear results. Journal- and publisher-related differences in publishing studies with the phrases in 2021 were tested with Fisher's exact test using the R v4.1.1 software.
    RESULTS: The percentage of studies with the relevant phrases from the total number of studies in the database decreased from 13% to 3% between 2010 and 2020. In 2021, out of 2,434 studies published in 73 different journals by eight publishers, 67 (2.8%) used the phrases. Potential journal- and publisher-related differences in publishing studies with the phrases were detected in 2021 (p = 0.001 and p = 0.005, respectively). Most commonly, the phrases referred to negative (n = 16, 24%), peripheral (n = 22, 33%) or confirmatory (n = 11, 16%) results. The significance of unpublished results to which the phrases referred considerably varied across studies.
    CONCLUSION: Over the last decade, there has been a marked decrease in the use of the phrases "data/results not shown" in dental journals. However, the phrases were still notably in use in dental studies in 2021, despite the good availability of accessible free online supplements and repositories.
    DOI:  https://doi.org/10.1371/journal.pone.0272695
  18. J Neurosurg. 2022 Aug 12. 1-2
    Equity in neurosurgical scientific publication.
    William W Ashley, Sonia V Eden, James T Rutka.
      
    DOI:  https://doi.org/10.3171/2022.7.JNS221407
  19. J Card Fail. 2022 Aug;pii: S1071-9164(22)00583-8. [Epub ahead of print]28(8): 1243-1244
    Translating Nursing Partnerships in Clinical Care to Scientific Publishing.
    Anuradha Lala, Robert J Mentz.
      
    DOI:  https://doi.org/10.1016/j.cardfail.2022.07.002
  20. Account Res. 2022 Aug 07.
    Citation Bias, Diversity, and Ethics.
    Keisha S Ray, Perry Zurn, Jordan D Dworkin, Dani S Bassett.
      How often a researcher is cited usually plays a decisive role in that person's career advancement, because academic institutions often use citation metrics, either explicitly or implicitly, to estimate research impact and productivity. Research has shown, however, that citation patterns and practices are affected by various biases, including the prestige of the authors being cited and their gender, race, and nationality, whether self-attested or perceived. Some commentators have proposed that researchers can address biases related to social identity or position by including a Citation Diversity Statement in a manuscript submitted for publication. A Citation Diversity Statement is a paragraph placed before the reference section of a manuscript in which the authors address the diversity and equitability of their references in terms of gender, race, ethnicity, or other factors and affirm a commitment to promoting equity and diversity in sources and references. The present commentary considers arguments in favor of Citation Diversity Statements, and some practical and ethical issues that they raise.
    Keywords:  bias; citation; diversity; equity; ethics
    DOI:  https://doi.org/10.1080/08989621.2022.2111257
  21. J Can Health Libr Assoc. 2021 Apr;42(1): 3-5
    JCHLA/JABSC editorial policies and practices to address systemic racism and improve equity, diversity, and inclusion.
    Sandra McKeown, Alanna Campbell, Amanda Caputo, Rachel Couban, Colleen Pawliuk.
      
    DOI:  https://doi.org/10.29173/jchla29554
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