bims-skolko Biomed News
on Scholarly communication
Issue of 2021‒10‒31
thirty papers selected by
Thomas Krichel
Open Library Society

  1. PLoS One. 2021 ;16(10): e0257340
      Despite the calls for change, there is significant consensus that when it comes to evaluating publications, review, promotion, and tenure processes should aim to reward research that is of high "quality," is published in "prestigious" journals, and has an "impact." Nevertheless, such terms are highly subjective and present challenges to ascertain precisely what such research looks like. Accordingly, this article responds to the question: how do faculty from universities in the United States and Canada define the terms quality, prestige, and impact of academic journals? We address this question by surveying 338 faculty members from 55 different institutions in the U.S. and Canada. While relying on self-reported definitions that are not linked to their behavior, this study's findings highlight that faculty often describe these distinct terms in overlapping ways. Additionally, results show that marked variance in definitions across faculty does not correspond to demographic characteristics. This study's results highlight the subjectivity of common research terms and the importance of implementing evaluation regimes that do not rely on ill-defined concepts and may be context specific.
  2. Sci Educ (Dordr). 2021 Oct 16. 1-18
      Ironically, flat-Earthers, anti-vaxxers, and climate change naysayers trust in science. Unfortunately, they trust the wrong science. That conundrum lies at the heart of scientific literacy in an age of well-funded commercial and ideological interests and overwhelming digital information. The core question for the citizen-consumer is not philosophically "why trust science?" (Oreskes 2019) but sociologically "who speaks for science?" Teachers can help students learn how to navigate the treacherous territory of inevitably mediated communication and the vulnerabilities of epistemic dependence. Students need to understand the role of science communication practices (media literacy) and the roles of credibility, expertise and honesty and the deceptive strategies used by imitators of science to seem like credible voices for science.
    Keywords:  Credibility; Deceptive practices; Expertise; Science con artist; Science media literacy
  3. Nature. 2021 Oct 26.
    Keywords:  Computer science; Databases; Publishing
  4. Microb Genom. 2021 Oct;7(10):
    Keywords:  editorial policy; parachute research; publishing; society publishing
  5. Ecol Evol. 2021 Oct;11(20): 13624-13632
      The usage of preprint servers in ecology and evolution is increasing, allowing research to be rapidly disseminated and available through open access at no cost. Early Career Researchers (ECRs) often have limited experience with the peer review process, which can be challenging when trying to build publication records and demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions. ECRs face different challenges relative to researchers with permanent positions and established research programs. These challenges might also vary according to institution size and country, which are factors associated with the availability of funding for open access journals. We predicted that the career stage and institution size impact the relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we showed that ECRs generated more preprints relative to non-ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal association between first author, institution size, and preprint usage, whereby the number of preprints tends to increase with institution size for ECRs. The United States and United Kingdom contributed the greatest number of preprints by ECRs, whereas non-Western countries contributed relatively fewer preprints. This empirical evidence that preprint usage varies with the career stage, institution size, and country helps to identify barriers surrounding large-scale adoption of preprinting in ecology and evolution.
    Keywords:  Authorea; EcoEvoArxiv; bioRxiv; career status; preprint servers
  6. Curr Opin Lipidol. 2021 Oct 25.
      PURPOSE OF REVIEW: Preprinting, or the sharing of non-peer reviewed, unpublished scholarly manuscripts, has exploded in all fields of science and medicine over the past 5 years. We searched the literature and evaluated the posting and uptake of preprint publications in the field of lipidology in bioRxiv and medRxiv servers. We also contacted the editorial offices of 20 journals that publish original research in lipidology to gauge their policies on preprints.FINDINGS: All 20 journals contacted indicated that they accepted preprints. As of 31 May 2021, 473 and 231 preprints in lipidology had been submitted to bioRxiv and medRxiv, respectively. About half of all lipidology preprints were related to cardiovascular, cardiometabolic, and/or metabolic diseases (CVMD) and their risk factors, but at least 12 other disease categories were also represented. 16.9% and 1.08% of medRxiv and bioRxiv preprints, respectively, were related to coronavirus disease 2019 (COVID-19).
    SUMMARY: All identified journals accept lipidology themed preprints for submission, removing any barriers authors may have had regarding preprinting. Based on growing experience with preprinting, this trend should encourage increased community feedback and facilitate higher quality lipidology research in the future.
  7. Food Policy. 2021 Dec;105 102167
      We use the full administrative records from four leading agricultural economics journals to study the impacts of the COVID-19 pandemic on manuscript submission, editorial desk rejection and reviewer acceptance rates, and time to editorial decision. We also test for gender differences in these impacts. Manuscript submissions increased sharply and equi-proportionately by gender. Desk rejection rates remained stable, leading to increased demand for reviews. Female reviewers became eight percentage points more likely to decline a review invitation during the early stage of the pandemic. First editorial decisions for papers sent out for peer review occurred significantly faster after pandemic lockdowns began. Overall, the initial effects of the pandemic on journal editorial tasks and review patterns appear relatively modest, despite the increased number of submissions handled by editors and reviewers. We find no evidence in agricultural economics of a generalized disruption to near-term, peer-reviewed publication.
    Keywords:  COVID-19; Decision time; Gender bias; Publishing; Review response rate; Scholarly journals; Submission rate
  8. PLoS One. 2021 ;16(10): e0258935
      BACKGROUND: Retraction of published research can reduce the dissemination of incorrect or misleading information, but concerns have been raised about the clarity and rigor of the retraction process. Failure to clearly and consistently retract research has several risks, for example discredited or erroneous research may inform health research studies (e.g. clinical trials), policies and practices, potentially rendering these unreliable.OBJECTIVE: To investigate consistency and clarity of research retraction, based on a case study of retracted Covid-19 research.
    STUDY DESIGN: A cross-sectional study of retracted Covid-19 articles reporting empirical research findings, based on searches of Medline, Embase and Scopus on 10th July and 19th December 2020.
    KEY RESULTS: We included 46 retracted Covid-19 articles. The number eligible for inclusion nearly doubled, from 26 to 46, in five months. Most articles (67%) were retracted from scientific journals and the remainder from preprint servers. Key findings: (1) reasons for retraction were not reported in 33% (15/46) of cases; (2) time from publication to retraction could not be determined in 43% (20/46) of cases; (3) More than half (59%) of retracted Covid-19 articles (27/46) remained available as original unmarked electronic documents after retraction (33% as full text and 26% as an abstract only). Sources of articles post-retraction were preprint servers, ResearchGate and, less commonly, websites including PubMed Central and the World Health Organization. A retracted journal article which controversially claimed a link between 5G technology and Covid-19 remains available in its original full text from at least 60 different websites.
    CONCLUSIONS: The retraction process is inconsistent and often ambiguous, with more than half of retracted Covid-19 research articles remaining available, unmarked, from a wide range of online sources. There is an urgent need to improve guidance on the retraction process and to extend this to cover preprint servers. We provide structured recommendations to address these concerns and to reduce the risks that arise when retracted research is inappropriately cited.
  9. Proc Biol Sci. 2021 Oct 27. 288(1961): 20211399
      Identifying reviewers is argued to improve the quality and fairness of peer review, but is generally disfavoured by reviewers. To gain some insight into the factors that influence when reviewers are willing to have their identity revealed, I examined which reviewers voluntarily reveal their identities to authors at the journal Functional Ecology, at which reviewer identities are confidential unless reviewers sign their comments to authors. I found that 5.6% of reviewers signed their comments to authors. This proportion increased slightly over time, from 4.4% in 2003-2005 to 6.7% in 2013-2015. Male reviewers were 1.8 times more likely to sign their comments to authors than were female reviewers, and this difference persisted over time. Few reviewers signed all of their reviews; reviewers were more likely to sign their reviews when their rating of the manuscript was more positive, and papers that had at least one signed review were more likely to be invited for revision. Signed reviews were, on average, longer and recommended more references to authors. My analyses cannot distinguish cause and effect for the patterns observed, but my results suggest that 'open-identities' review, in which reviewers are not permitted to be anonymous, will probably reduce the degree to which reviewers are critical in their assessment of manuscripts and will differentially affect recruitment of male and female reviewers, negatively affecting the diversity of reviewers recruited by journals.
    Keywords:  blind review; gender; open review; open-identities review; peer review; scholarly publishing
  10. Plast Reconstr Surg. 2021 Nov 01. 148(5S): 43S-45S
  11. Int J Radiat Oncol Biol Phys. 2021 Nov 01. pii: S0360-3016(21)01569-8. [Epub ahead of print]111(3S): e192
      PURPOSE/OBJECTIVE(S): We aimed to examine how the rise of open access (OA) journals in biomedicine has impacted resident research in radiation oncology.MATERIALS/METHODS: We built a comprehensive database of first-author, PubMed-searchable articles published by US radiation oncology residents who graduated between 2015 and 2019. We then classified each journal in which these manuscripts appeared as either OA or non-OA, and obtained the current article processing charge (APC) for every publication that appeared in an OA journal. Lastly, we performed a secondary analysis to identify the factors associated with publishing an article in an OA journal.
    RESULTS: The US radiation oncology residents in this study published 2,637 first-author, PubMed-searchable manuscripts, 555 (21.0%) of which appeared in 138 OA journals. The number of publications in OA journals increased from 0.47 per resident for the class of 2015 to 0.79 per resident for the class of 2019. Likewise, the number of publications in OA journals with a 2019 impact factor of zero increased from 0.14 per resident for the class of 2015 to 0.43 per resident for the class of 2019. Publications in OA journals garnered fewer citations than those in non-OA journals (8.9 versus 14.9, P < 0.01). 90.6% of OA journals levy an APC for original research reports (median $1,896), which is positively correlated with their 2019 impact factor (r = 0.63, P < 0.01). Aggregate APCs totaled $900,319.21 for all US radiation oncology residency programs and appeared to increase over the study period.
    CONCLUSION: The number of first-author, PubMed-searchable manuscripts published by graduating US radiation oncology residents in OA journals rose significantly over the study period. US radiation oncology residency programs appear to be investing increasing and significant sums of money to publish the work of their residents in these journals. A more substantive discussion about the proper role of OA journals in resident research is needed.
  12. J Geogr Syst. 2021 Oct 20. 1-18
      This paper develops the notion of "open data product". We define an open data product as the open result of the processes through which a variety of data (open and not) are turned into accessible information through a service, infrastructure, analytics or a combination of all of them, where each step of development is designed to promote open principles. Open data products are born out of a (data) need and add value beyond simply publishing existing datasets. We argue that the process of adding value should adhere to the principles of open (geographic) data science, ensuring openness, transparency and reproducibility. We also contend that outreach, in the form of active communication and dissemination through dashboards, software and publication are key to engage end-users and ensure societal impact. Open data products have major benefits. First, they enable insights from highly sensitive, controlled and/or secure data which may not be accessible otherwise. Second, they can expand the use of commercial and administrative data for the public good leveraging on their high temporal frequency and geographic granularity. We also contend that there is a compelling need for open data products as we experience the current data revolution. New, emerging data sources are unprecedented in temporal frequency and geographical resolution, but they are large, unstructured, fragmented and often hard to access due to privacy and confidentiality concerns. By transforming raw (open or "closed") data into ready to use open data products, new dimensions of human geographical processes can be captured and analysed, as we illustrate with existing examples. We conclude by arguing that several parallels exist between the role that open source software played in enabling research on spatial analysis in the 90 s and early 2000s, and the opportunities that open data products offer to unlock the potential of new forms of (geo-)data.
    Keywords:  Geographic data science; Open data; Open source
  13. Nature. 2021 Oct;598(7882): 541
    Keywords:  Publishing; Research management
  14. Nature. 2021 Oct 28.
    Keywords:  Careers; Institutions; Publishing
  15. Vis Comput Ind Biomed Art. 2021 Oct 29. 4(1): 27
      Data visualization blends art and science to convey stories from data via graphical representations. Considering different problems, applications, requirements, and design goals, it is challenging to combine these two components at their full force. While the art component involves creating visually appealing and easily interpreted graphics for users, the science component requires accurate representations of a large amount of input data. With a lack of the science component, visualization cannot serve its role of creating correct representations of the actual data, thus leading to wrong perception, interpretation, and decision. It might be even worse if incorrect visual representations were intentionally produced to deceive the viewers. To address common pitfalls in graphical representations, this paper focuses on identifying and understanding the root causes of misinformation in graphical representations. We reviewed the misleading data visualization examples in the scientific publications collected from indexing databases and then projected them onto the fundamental units of visual communication such as color, shape, size, and spatial orientation. Moreover, a text mining technique was applied to extract practical insights from common visualization pitfalls. Cochran's Q test and McNemar's test were conducted to examine if there is any difference in the proportions of common errors among color, shape, size, and spatial orientation. The findings showed that the pie chart is the most misused graphical representation, and size is the most critical issue. It was also observed that there were statistically significant differences in the proportion of errors among color, shape, size, and spatial orientation.
    Keywords:  Association rule mining; Cochran’s Q test; Data visualization; Graphical representations; McNemar’s test; Misinformation; Visual encodings; Word cloud
  16. J Urol. 2021 Oct 25. 101097JU0000000000002258
      PURPOSE: The American Urological Association (AUA) Annual Meeting serves as the premier platform for presenting unpublished research in urology. Among selected abstracts, podium presentations represent the most impactful submissions. While podium presentations receive a large audience through conference attendance and social media posts, it is unclear how often they manifest as publications in peer-reviewed journals.MATERIALS AND METHODS: Podium presentations from the 2017 AUA Annual Meeting were reviewed. Abstracts were assessed for publication between January 1, 2015 and May 31, 2020 allowing for a 3-year window of publication and accounting for publications prior to the submission deadline. Abstract authors were individually searched with key terms being added sequentially until <30 results were generated in PubMed. Abstracts were deemed published if at least 1 author and 1 conclusion matched a manuscript. Publication rate, time to publication, and 2019 journal impact factor were collected. Statistical analysis was performed by linear and logistic regression.
    RESULTS: Of 872 podium presentations, 453 (51.9%) were published within 3 years. Median time from submission to publication was 12.5 months (IQR:7.5-20.5). The number of articles published at 1-, 2- and 3-years from submission was 203, 368, and 430, respectively. The median journal impact factor of publications was 3.2 (IQR:2.0-5.8). Oncology studies (OR=1.21(95%CI:0.91-1.60), p=0.186) had similar rates of publication compared to non-oncology studies.
    CONCLUSIONS: While AUA podium presentations disseminate valuable data, approximately half were not published in peer-reviewed journals within 3 years. Therefore, care must be taken when promoting findings or adopting new practices based on these presentations alone.
    Keywords:  peer review; publications,
  17. Ethiop J Health Sci. 2021 Jul;31(4): 688
  18. J Neurosurg. 2021 Oct 29. pii: 2021.7.JNS2128. [Epub ahead of print] 1-8
      OBJECTIVE: Abstracts act as short, efficient sources of new information. This intentional brevity potentially diminishes scientific reliability of described findings. The authors' objective was to 1) determine the proportion of abstracts submitted to the American Association of Neurological Surgeons (AANS) annual meeting that subsequently are published in peer-reviewed journals, 2) assess AANS abstract publications for publication bias, and 3) assess AANS abstract publications for differing results.METHODS: The authors screened all abstracts from the annual 2012 AANS meeting and identified their corresponding full-text publication, if applicable, by searching PubMed/MEDLINE. The abstract and subsequent publication were analyzed for result type (positive or negative) and differences in results.
    RESULTS: Overall, 49.3% of abstracts were published as papers. Many (18.1%) of these published papers differed in message from their original abstract. Publication bias exists, with positive abstracts being 40% more likely to be published than negative abstracts. The top journals in which the full-text articles were published were Journal of Neurosurgery (13.1%), Neurosurgery (7.3%), and World Neurosurgery (5.4%).
    CONCLUSIONS: Here, the authors demonstrate that alone, abstracts are not reliable sources of information. Many abstracts ultimately remain unpublished; therefore, they do not attain a level of scientific scrutiny that merits alteration of clinical care. Furthermore, many that are published have differing results or conclusions. In addition, positive publication bias exists, as positive abstracts are more likely to be published than negative abstracts.
    Keywords:  American Association of Neurological Surgeons; abstract; annual meeting; national meeting; neurosurgery; oral presentation; poster; publication outcomes; scientific meeting
  19. Clin Microbiol Infect. 2021 Oct 26. pii: S1198-743X(21)00608-X. [Epub ahead of print]
    Keywords:  CMI; DOI; Editorial note; Guide for authors; references
  20. World Neurosurg. 2021 Oct 26. pii: S1878-8750(21)01640-5. [Epub ahead of print]
      BACKGROUND: Reporting quality within the neurosurgical literature is low, limiting the ability of journals to act as gatekeepers for evidence-based neurosurgical care. Journal policies during manuscript submission aim to improve reporting quality. We conducted meta-science study characterizing the reporting policies of neurosurgical journals and other related peer-reviewed publications METHODS: Journals were retrieved in 7 searches using Journal Citation Reports and Google Scholar. Characteristics, impact metrics, and submission policies were extracted.RESULTS: Of 486 results, 54 journals were included, including 27 neurosurgical, 27 related topical journals. Thirty-eight (70.4%) adopted authorship guidelines and 20 (37.0%) disclosure standards of the International Council of Medical Journal Editors. Twenty-six (48.1%) required data availability statement and 33 (61.1%) clinical trials registration. Twenty-one (38.9%) required and 11 (20.4%) recommended adherence to reporting guidelines. Twenty (37.0%) endorsed EQUATOR network guidelines. PRISMA was mentioned by 30 (55.6%) journals, CONSORT by 28 (51.9%), and STROBE by 18 (33.3%). Among neurosurgical journals, factors associated with a requirement or recommendation to follow reporting guidelines among neurosurgical journals included impact factor (p=0.0013), Article Influence Score (p=0.0236), Scimago h-index (p=0.0152), Scimago journal rank (p=0.002), and CiteScore (p=0.0023), as well as recommendations pertaining to ICMJE authorship guidelines (p=0.0085), ORCID (p=0.014), clinical trials registration (p=0.0369), or data availability statement (p=0.0047). CONSORT, PRISMA, or STROBE delineations were significantly associated with the mention of another guideline (p<0.01) CONCLUSIONS: Neurosurgical journal submission policies are inconsistent. Frameworks to improve reporting quality are uncommonly utilized. Increasing rigor and standardization of reporting policies across journals publishers may improve quality.
    Keywords:  CONSORT; EQUATOR; PRISMA; STARD; STROBE; evidence-based medicine; reporting guidelines
  21. J Oral Maxillofac Pathol. 2021 May-Aug;25(2):25(2): 215-218
      Oral pathologists or dentists in general opting for alternate career paths are very common nowadays. Financial security, lesser availability of jobs and work satisfaction are the most commonly observed reasons for this openness to switch career. While there is a multitude of alternate career options available such as medical writing and pharmacovigilance in this review, we aim to give an insight specifically on opportunities available in the medical journals aspect of the publishing industry. Oral pathologists can opt to take this field as a full-time engagement and attain a constant growth in terms of finances, knowledge and personal development. One of the authors has opted for this career path and has provided personal opinions about the scope, opportunities and perks of working in this industry.
    Keywords:  Career; medical journals; medical publishing; oral pathologist
  22. Access Microbiol. 2021 ;3(9): 000272
      Following the Microbiology Society's successful bid for a Learned Society Curation Award from the Wellcome Trust and Howard Hughes Medical Institute, the Society is converting our sound science, open access journal, Access Microbiology, to an open research platform. As part of this, we conducted a survey of our community to gauge current attitudes towards the platform and here we present some of these results. The majority of respondents (57 %) said they would always or sometimes want to remain anonymous on their peer review report, whilst 75 % of respondents said that as an author they would be happy to make the data underlying their research open. There was a clear desire for a range of research types that are often seen with sound science publications and rigorous research. An encouraging 94 % of respondents stated that the platform is somewhere they would consider publishing, demonstrating the enthusiasm in these respondents for a new publishing platform for their community. Given this data and that from our previous focus group research, the platform will launch as outlined in the original project proposal and adopt a transparent peer review model with an open data policy.
    Keywords:  Wellcome Trust; open research platform; open science; preprints; publishing; society publisher
  23. Trop Doct. 2021 Oct 25. 494755211050508