bims-skolko Biomed News
on Scholarly communication
Issue of 2021‒05‒16
eighteen papers selected by
Thomas Krichel
Open Library Society
  1. Does publication bias explain the divergent findings on menopausal hormone therapy and cardioprotection in the literature?
  2. Avoiding the High Cost of Peer Review Failures.
  3. Fraud and retraction in perioperative medicine publications: what we learned and what can be implemented to prevent future recurrence.
  4. Podcast: The super-sleuth who spots trouble in science papers.
  5. A Crossover Randomized Trial of Visual Abstracts Versus Plain-Text Tweets for Disseminating Orthopedics Research.
  6. The gender and geography of publishing: a review of sex/gender reporting and author representation in leading general medical and global health journals.
  7. A descriptive analysis of the data availability statements accompanying medRxiv preprints and a comparison with their published counterparts.
  8. A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers.
  9. Business and publication models of radiology journals.
  10. Social media platforms: a primer for researchers.
  11. Updates for contributors: Rigor and reproducibility in stem cell research.
  12. Open-access publisher PLOS pushes to extend clout beyond biomedicine.
  13. EDITORIAL The International Journal of Oncology: 30 years of progress (1992-2021).
  14. A guide to writing grant proposals for nursing research.
  15. Academic journal is criticised for publishing special issue funded by tobacco industry.
  16. The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
  17. Cochrane Rehabilitation: 2020 annual report.
  18. Bringing Policymakers to Science Through Communication: A Perspective From Latin America.
  1. Res Pract Thromb Haemost. 2021 May;5(4): e12515
    Does publication bias explain the divergent findings on menopausal hormone therapy and cardioprotection in the literature?
    Samar R El Khoudary, JoAnn E Manson.
      
    Keywords:  cardioprotection; menopausal hormone therapy; menopause; publication bias; women's health
    DOI:  https://doi.org/10.1002/rth2.12515
  2. Wilderness Environ Med. 2021 May 06. pii: S1080-6032(21)00062-4. [Epub ahead of print]
    Avoiding the High Cost of Peer Review Failures.
    Neal W Pollock.
      
    DOI:  https://doi.org/10.1016/j.wem.2021.04.001
  3. J Med Ethics. 2021 May 14. pii: medethics-2021-107252. [Epub ahead of print]
    Fraud and retraction in perioperative medicine publications: what we learned and what can be implemented to prevent future recurrence.
    Consolato Gianluca Nato, Leonardo Tabacco, Federico Bilotta.
      Fraud in medical publications is an increasing concern. In particular, disciplines related to perioperative medicine-including anaesthesia and critical care-currently hold the highest rankings in terms of retracted papers for research misconduct. The dominance of this dubious achievement is attributable to a limited number of researchers who have repeatedly committed scientific fraud. In the last three decades, six researchers have authored 303 of the 375 papers retracted in perioperative medicine. This narrative review reports on six cases of forged publication in perioperative that resulted in the paper's retraction. The process that led to unveil the fraud, the impact on clinical practice and changes in regulatory mechanisms of scientific companies and governmental agencies' policies will also be presented. Fraud in medical publications is a growing concern that affects perioperative medicine requiring a substantial number of papers to be retracted. The continuous control elicited by readers, by local institutional review boards, scientific journal reviewers, scientific societies and government agencies can play an important role in preserving the 'pact of trust' between the authors, professionals and ultimately the relationship between doctors and patients.
    Keywords:  anaesthetics / anesthesiology; applied and professional ethics; clinical ethics; education; ethics
    DOI:  https://doi.org/10.1136/medethics-2021-107252
  4. Nature. 2020 May 13.
    Podcast: The super-sleuth who spots trouble in science papers.
      
    Keywords:  Atmospheric science; Ethics; Peer review
    DOI:  https://doi.org/10.1038/d41586-020-01431-4
  5. J Arthroplasty. 2021 Apr 20. pii: S0883-5403(21)00347-8. [Epub ahead of print]
    A Crossover Randomized Trial of Visual Abstracts Versus Plain-Text Tweets for Disseminating Orthopedics Research.
    Emanuele Chisari, Zane Gouda, Mohammad Abdelaal, John Shields, Jeffrey B Stambough, Jaime Bellamy, Chad A Krueger.
      BACKGROUND: Scientists, surgeons, and trainees are increasingly taking an active role on Twitter to find, disseminate, and exchange knowledge. The purpose of this study was to determine if peer-reviewed journal articles shared on Twitter using visual abstracts (VAs) improve user engagement compared with plain-text tweets.METHODS: A two-arm randomized controlled trial with crossover was performed. Manuscripts from the Journal of Arthroplasty were allocated to one of two arms and disseminated via the journal Twitter account (@JArthroplasty) as either a text-based tweet or a VA. The primary outcome was online engagement (a composite of retweets, replies, and likes) at 7 and 30 days after posting. Univariate analysis for nonparametric and parametric data was performed using Mann-Whitney test or Student t-tests, respectively; alpha was set at 0.05.
    RESULTS: 20 in-press manuscripts were randomized to standard tweets (10) or VAs (10) the same day of online publication. The mean number of engagements was higher in the VA group at seven (412 ± 216 vs 195 ± 133; P = .016) and 30 days (495 ± 204 vs 244 ± 162; P = .007). After the crossover, similar results were reported. Overall, VAs attracted a significantly greater number of engagements than standard tweets. Most engagement for both plain-text tweets and VAs occurred shortly after the tweet is posted.
    CONCLUSION: Online, public engagement with orthopedic research is generally low. However, when VAs are used to communicate research through social media outlets such as Twitter, the overall research engagement significantly increases compared with plain-text tweets.
    Keywords:  research; science outreach; social media; twitter; visual abstracts
    DOI:  https://doi.org/10.1016/j.arth.2021.04.006
  6. BMJ Glob Health. 2021 May;pii: e005672. [Epub ahead of print]6(5):
    The gender and geography of publishing: a review of sex/gender reporting and author representation in leading general medical and global health journals.
    Rebekah Merriman, Ilaria Galizia, Sonja Tanaka, Ashley Sheffel, Kent Buse, Sarah Hawkes.
      INTRODUCTION: Diverse gender and geographical representation matters in research. We aimed to review medical and global health journals' sex/gender reporting, and the gender and geography of authorship.METHODS: 542 research and non-research articles from 14 selected journals were reviewed using a retrospective survey design. Paper screening and systematic data extraction was conducted with descriptive statistics and regression analyses calculated from the coded data. Outcome measures were journal characteristics, the extent to which published articles met sex/gender reporting guidelines, plus author gender and location of their affiliated institution.
    RESULTS: Five of the fourteen journals explicitly encourage sex/gender analysis in their author instructions, but this did not lead to increased sex/gender reporting beyond the gender of study participants (OR=3.69; p=0.000 (CI 1.79 to 7.60)). Just over half of research articles presented some level of sex/gender analysis, while 40% mentioned sex/gender in their discussion. Articles with women first and last authors were 2.4 times more likely to discuss sex/gender than articles with men in those positions (p=0.035 (CI 1.062 to 5.348)). First and last authors from high-income countries (HICs) were 19 times as prevalent as authors from low-income countries; and women from low-income and middle-income countries were at a disadvantage in terms of the impact factor of the journals they published in.
    CONCLUSION: Global health and medical research fails to consistently apply a sex/gender lens and remains largely the preserve of authors in HIC. Collaborative partnerships and funding support are needed to promote gender-sensitive research and dismantle historical power dynamics in authorship.
    Keywords:  descriptive study; public health
    DOI:  https://doi.org/10.1136/bmjgh-2021-005672
  7. PLoS One. 2021 ;16(5): e0250887
    A descriptive analysis of the data availability statements accompanying medRxiv preprints and a comparison with their published counterparts.
    Luke A McGuinness, Athena L Sheppard.
      OBJECTIVE: To determine whether medRxiv data availability statements describe open or closed data-that is, whether the data used in the study is openly available without restriction-and to examine if this changes on publication based on journal data-sharing policy. Additionally, to examine whether data availability statements are sufficient to capture code availability declarations.DESIGN: Observational study, following a pre-registered protocol, of preprints posted on the medRxiv repository between 25th June 2019 and 1st May 2020 and their published counterparts.
    MAIN OUTCOME MEASURES: Distribution of preprinted data availability statements across nine categories, determined by a prespecified classification system. Change in the percentage of data availability statements describing open data between the preprinted and published versions of the same record, stratified by journal sharing policy. Number of code availability declarations reported in the full-text preprint which were not captured in the corresponding data availability statement.
    RESULTS: 3938 medRxiv preprints with an applicable data availability statement were included in our sample, of which 911 (23.1%) were categorized as describing open data. 379 (9.6%) preprints were subsequently published, and of these published articles, only 155 contained an applicable data availability statement. Similar to the preprint stage, a minority (59 (38.1%)) of these published data availability statements described open data. Of the 151 records eligible for the comparison between preprinted and published stages, 57 (37.7%) were published in journals which mandated open data sharing. Data availability statements more frequently described open data on publication when the journal mandated data sharing (open at preprint: 33.3%, open at publication: 61.4%) compared to when the journal did not mandate data sharing (open at preprint: 20.2%, open at publication: 22.3%).
    CONCLUSION: Requiring that authors submit a data availability statement is a good first step, but is insufficient to ensure data availability. Strict editorial policies that mandate data sharing (where appropriate) as a condition of publication appear to be effective in making research data available. We would strongly encourage all journal editors to examine whether their data availability policies are sufficiently stringent and consistently enforced.
    DOI:  https://doi.org/10.1371/journal.pone.0250887
  8. Gigascience. 2021 May 13. pii: giab034. [Epub ahead of print]10(5):
    A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers.
    Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev.
      BACKGROUND: Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability.OBJECTIVE: We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript.
    METHODS: An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases.
    FINDINGS: The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing.
    CONCLUSION: The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility.
    Keywords:  FAIR principles; MINSEQE; MIxS; data; data paper; genomics; metadata; omics; standards; workflow
    DOI:  https://doi.org/10.1093/gigascience/giab034
  9. Clin Imaging. 2021 Apr 20. pii: S0899-7071(21)00159-5. [Epub ahead of print]76 222-227
    Business and publication models of radiology journals.
    Arvind Vijayasarathi, Jeffrey Ding, Richard Duszak, Faisal Khosa.
      OBJECTIVE: Traditional and open-access publication models have been increasingly scrutinized, particularly in light of the recent impasse regarding cost and access between Elsevier and the University of California. Peer-reviewed publications are the main source through which science is disseminated, yet the industry remains an enigma to most. Our aim was to determine radiology publisher market-share, access type, geographic distribution and relative research impact in order to better understand the traditionally opaque realm of academic publishing.METHODS: During April 2020, Scopus was queried to extract all entries in the "Radiology, Nuclear Medicine and Imaging" subcategory of "Medicine." Journal name, publisher, SCImago Journal Ranking (SJR) score, country and publication model were cataloged. Publishers were grouped by their ownership type and journals were grouped by their publication model. Overall trends were assessed across publisher type, publication model, and geographic location.
    RESULTS: Commercial publishers are used by 82% (239 of 293) of radiology journals. Elsevier and Springer Nature together published 40% (118/293) of journal titles within the category. Approximately one fourth (77/293) of radiology journals were open-access. On average, SJRs were highest for journals published commercially. Mean SJR across the top 10 publishers and publication model were similar (p = 0.06 and p = 0.48, respectively).
    DISCUSSION: Radiology journal publication is heavily consolidated amongst a few global commercial organizations. Most radiology journals were subscription-based, but their impact did not differ significantly from open-access counterparts. Further disputes between universities and publishers could influence future manuscript submission, review, and citation, which has the potential to destabilize traditional publication models.
    Keywords:  Journal publishers; Open access; Publication model
    DOI:  https://doi.org/10.1016/j.clinimag.2021.04.005
  10. Reumatologia. 2021 ;59(2): 68-72
    Social media platforms: a primer for researchers.
    Olena Zimba, Armen Yuri Gasparyan.
      Social media platforms play an increasingly important role in research, education, and clinical practice. As an inseparable part of open science, these platforms may increase the visibility of research outputs and facilitate scholarly networking. The editors who ethically moderate Twitter, Facebook, and other popular social media accounts for their journals may engage influential authors in the post-publication communication and expand societal implications of their publications. Several social media aggregators track and generate alternative metrics which can be used by researchers for visualizing trending articles in their fields. More and more publishers showcase their achievements by displaying such metrics along with traditional citations. The Scopus database also tracks both metrics to offer a comprehensive coverage of the indexed articles' impact. Understanding the advantages and limitations of various social media channels is essential for actively contributing to the post-publication communication, particularly in research-intensive fields such as rheumatology.
    Keywords:  periodicals as topic; publication ethics; rheumatology; social media
    DOI:  https://doi.org/10.5114/reum.2021.102707
  11. Stem Cell Reports. 2021 May 08. pii: S2213-6711(21)00218-6. [Epub ahead of print]
    Updates for contributors: Rigor and reproducibility in stem cell research.
    Martin Pera.
      
    DOI:  https://doi.org/10.1016/j.stemcr.2021.05.001
  12. Nature. 2021 May 13.
    Open-access publisher PLOS pushes to extend clout beyond biomedicine.
    Holly Else.
      
    Keywords:  Publishing
    DOI:  https://doi.org/10.1038/d41586-020-01907-3
  13. Int J Oncol. 2021 Jul;pii: 36. [Epub ahead of print]59(1):
    EDITORIAL The International Journal of Oncology: 30 years of progress (1992-2021).
    Demetrios A Spandidos.
      We are hereby very pleased to announce that the International Journal of Oncology is now celebrating its 30th year of publication since the inaugural issue in 1992. During this time span of three decades, the journal has had the pleasure of publishing a variety of research articles and reviews submitted by authors from around the world, thus bringing to light new insight into the field of oncology. The International Journal of Oncology has always aimed to publish high quality research on oncology from a diversity of international contributors. This diversity is depicted in Table I below, which presents the list of countries from which the articles have originated over the years. We would also like to take this opportunity to thank all the authors and reviewers who have contributed to the success of the journal over the years, and with their support, we look forward to an even brighter future.
    Keywords:  -
    DOI:  https://doi.org/10.3892/ijo.2021.5216
  14. Res Nurs Health. 2021 May 11.
    A guide to writing grant proposals for nursing research.
    Hyochol Ahn, Elizabeth Reifsnider.
      
    DOI:  https://doi.org/10.1002/nur.22137
  15. BMJ. 2021 May 14. 373 n1247
    Academic journal is criticised for publishing special issue funded by tobacco industry.
    Ingrid Torjesen.
      
    DOI:  https://doi.org/10.1136/bmj.n1247
  16. Nucleic Acids Res. 2021 May 12. pii: gkab346. [Epub ahead of print]
    The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
    Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets, Ash O'Farrell, Kim Cullion, Brian D O'Connor, Benedict Paten, Lincoln Stein.
      Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute's GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.
    DOI:  https://doi.org/10.1093/nar/gkab346
  17. Eur J Phys Rehabil Med. 2021 Apr;57(2): 303-308
    Cochrane Rehabilitation: 2020 annual report.
    Chiara Arienti, Carlotte Kiekens, Roberta Bettinsoli, Julia P Engkasan, Rolf Frischknecht, Francesca Gimigliano, Frane Grubisic, Tracey Howe, Valerio Iannicelli, Elena Ilieva, Stefano G Lazzarini, William M Levack, Thorsten Meyer, Aydan Oral, Michele Patrini, Elisa Pollini, Farooq A Rathore, Stefano Negrini.
      During its fourth year of existence, Cochrane Rehabilitation went on to promote evidence-informed health decision-making in rehabilitation. In 2020, the outbreak of the COVID-19 pandemic has made it necessary to alter priorities. In these challenging times, Cochrane Rehabilitation has firstly changed its internal organisation and established a new relevant project in line with pandemic needs: the REH-COVER (Rehabilitation - COVID-19 evidence-based response) action. The aim was to focus on the timely collection, review and dissemination of summarised and synthesised evidence relating to COVID-19 and rehabilitation. Cochrane Rehabilitation REH-COVER action has included in 2020 five main initiatives: 1) rapid living systematic reviews on rehabilitation and COVID-19; 2) interactive living evidence map on rehabilitation and COVID-19; 3) definition of the research topics on "rehabilitation and COVID-19" in collaboration with the World Health Organization (WHO) rehabilitation programme; 4) Cochrane Library special collection on Coronavirus (COVID-19) rehabilitation; and 5) collaboration with COVID-END for the topics "rehabilitation" and "disability." Furthermore, we are still carrying on five different special projects: Be4rehab; RCTRACK; definition of rehabilitation for research purposes; ebook project; and a prioritization exercise for Cochrane Reviews production. The Review Working Area continued to identify and "tag" the rehabilitation-relevant reviews published in the Cochrane library; the Publication Working Area went on to publish Cochrane Corners, working more closely with the Cochrane Review Groups (CRGs) and Cochrane Networks, particularly with Cochrane Musculoskeletal, Oral, Skin and Sensory Network; the Education Working Area, the most damaged in 2020, tried to continue performing educational activities such as workshops in different online meetings; the Methodology Working Area organized the third and fourth Cochrane Rehabilitation Methodological (CRM) meetings respectively in Milan and Orlando; the Communication Working Area spread rehabilitation evidences through different channels and translated the contents in different languages.
    DOI:  https://doi.org/10.23736/S1973-9087.21.06877-5
  18. Front Res Metr Anal. 2021 ;6 654191
    Bringing Policymakers to Science Through Communication: A Perspective From Latin America.
    Marta Pulido-Salgado, Fátima Antonethe Castaneda Mena.
      Scientific knowledge should be shared beyond academic circles in order to promote science in policymaking. Science communication increases the understanding of how the natural world works and the capacity to make informed decisions. However, not every researcher has the ability to master the art of communicating, and even less in a clear, concise, and easy to understand language that society representatives appreciate. Within the huge and extraordinarily diverse Latin American region, science communication has been going on for at least 200 years, when the first science stories appeared in the newspapers, as well as the first science museums and botanical gardens were founded. Nevertheless, resources are limited, and notably time, which researchers spend mostly in mentoring, ensuring funding, publication of their results and laboratory work, while science journalists are an endangered species. This perspective article aims at providing some recommendations to build bridges between science and decision-making parties through communication, by exploring how Latin American diplomats and policymakers engage with scientific knowledge.
    Keywords:  Latin America; evidence-base for policy; science advice; science communication; science diplomacy
    DOI:  https://doi.org/10.3389/frma.2021.654191
This page is being maintained by Thomas Krichel. It was last updated on 2021‒07‒23 at 10:24:22.