bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒11‒06
25 papers selected by
Thomas Krichel
Open Library Society


  1. Sci Rep. 2022 Oct 31. 12(1): 18306
      A great deal of the images found in scientific publications are retouched, reused, or composed to enhance the quality of the presentation. In most instances, these edits are benign and help the reader better understand the material in a paper. However, some edits are instances of scientific misconduct and undermine the integrity of the presented research. Determining the legitimacy of edits made to scientific images is an open problem that no current technology can perform satisfactorily in a fully automated fashion. It thus remains up to human experts to inspect images as part of the peer-review process. Nonetheless, image analysis technologies promise to become helpful to experts to perform such an essential yet arduous task. Therefore, we introduce SILA, a system that makes image analysis tools available to reviewers and editors in a principled way. Further, SILA is the first human-in-the-loop end-to-end system that starts by processing article PDF files, performs image manipulation detection on the automatically extracted figures, and ends with image provenance graphs expressing the relationships between the images in question, to explain potential problems. To assess its efficacy, we introduce a dataset of scientific papers from around the globe containing annotated image manipulations and inadvertent reuse, which can serve as a benchmark for the problem at hand. Qualitative and quantitative results of the system are described using this dataset.
    DOI:  https://doi.org/10.1038/s41598-022-21535-3
  2. PLoS One. 2022 ;17(11): e0274441
      Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors' biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find evidence that authors do not consider quality, novelty or significance when posting or not posting research as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.
    DOI:  https://doi.org/10.1371/journal.pone.0274441
  3. World J Gastroenterol. 2022 Oct 07. 28(37): 5383-5394
      After three rounds of rigorous evaluation of core journals in gastroenterology and hepatology conducted by the Reference Citation Analysis (RCA) editorial team of Baishideng Publishing Group (Baishideng), the RCA database of Baishideng officially released the 2022 Journal Article Influence Index (2022 JAII) of 101 core journals in gastroenterology and hepatology, for the first time. The list of 101 core journals can be found at: https://www.referencecitationanalysis.com/SearchJournal. Among them, the highest 2022 JAII is 48.014 and the lowest is 3.900. This article highlights the top 20 journals, describes the calculation method for the 2022 JAII, the evaluation process, and the inclusion principles for journals in the RCA. These steps are the underpinning of the RCA's empirical journal academic evaluation service by which the digital platform addresses the needs of authors to select reliable journals for submission, readers to select high-quality literature for reading, and editors to track their own journal citation performance. As such, the RCA core journal list will serve as a useful Find-a-Journal tool. Any interested party is welcome to use this journal list and recommend it to their peers.
    Keywords:  Announcement; Find a journal; Gastroenterol-ogy and hepatology; Journal Article Influence Index; Journal list; Reference Citation Analysis
    DOI:  https://doi.org/10.3748/wjg.v28.i37.5383
  4. World J Orthop. 2022 Oct 18. 13(10): 891-902
      After three rounds of rigorous evaluation of core journals in orthopedics conducted by the Reference Citation Analysis (RCA) editorial team of Baishideng Publishing Group (Baishideng), the RCA database of Baishideng officially released the 2022 Journal Article Influence Index (2022 JAII) of 104 core journals and a list of high-quality academic journals in orthopedics, for the first time on August 9, 2022. The list of 104 core journals can be found at: https://www.referencecitationanalysis.com/SearchJournal. Among them, the highest 2022 JAII is 55.015 and the lowest is 3.076. This article introduces the 21 high-quality academic journals and describes the calculation method for the 2022 JAII, the evaluation process, and the inclusion principles for journals in the RCA. These steps are the underpinning of the RCA's empirical journal academic evaluation service by which the digital platform addresses the needs of authors to select reliable journals for submission, readers to select high-quality literature for reading, and editors to track their own journal citation performance. As such, the RCA core journal list will serve as a useful Find-a-Journal tool. Any interested party is welcome to use this journal list and recommend it to their peers.
    Keywords:  Announcement; Find a journal; Journal Article Influence Index; Journal list; Orthopedics; Reference Citation Analysis
    DOI:  https://doi.org/10.5312/wjo.v13.i10.891
  5. Ophthalmology. 2022 Nov 01. pii: S0161-6420(22)00860-0. [Epub ahead of print]
      OBJECTIVE: Evaluate the completeness of conflict of interest self-reporting by ophthalmology researchers and assess factors associated with self-reporting.DESIGN: Cross-sectional observational study PARTICIPANTS: We evaluated articles published between January and June 2017 in Ophthalmology, JAMA Ophthalmology, American Journal of Ophthalmology, and Investigative Ophthalmology & Visual Science. To more accurately assess the cases in which an author published multiple articles, we defined a unit of analysis, "authorship", where each author of each article is a unique data point. To enable comparison with the Open Payments Database (OPD), we only included authorships who were United States physicians.
    METHODS: For each authorship, we defined self-reported relationships as the companies listed in the article's conflict of interest disclosures. Based on journal policies, we defined OPD-reported relationships as the list of companies that reported payments to the author within 36 months before submission.
    MAIN OUTCOME MEASURES: For each authorship, we assessed the proportion of OPD-reported relationships that were self-reported. The primary measure was the proportion of authorships who reported none of their OPD-reported relationships.
    RESULTS: Of the 660 total authorships (486 unique authors), 413 authorships (63%) reported none of their OPD-reported relationships, 112 (17%) reported some, 9 (1%) reported all, and 126 (19%) had zero relationships. The proportion of authorships who self-reported none of their relationships was not significantly different between journals that require reporting of all relationships compared to journals that only require reporting of relevant relationships (adjusted percentage 61.4 vs 64.3%, p=0.46). Authorships who received more dollars during the reporting period had higher rates of self-reporting (p <.001).
    CONCLUSIONS: Even among journals that require complete reporting, self-reporting was low compared to an industry-maintained database of financial relationships. Deficiencies in reporting may undermine confidence in self-reporting and compromise the transparency that is needed to fairly interpret research results.
    Keywords:  Open Payments Database; conflict of interest; disclosures; ophthalmology
    DOI:  https://doi.org/10.1016/j.ophtha.2022.10.028
  6. Nature. 2022 11;611(7934): 33
      
    Keywords:  Ethics; Publishing; Research management
    DOI:  https://doi.org/10.1038/d41586-022-03516-8
  7. Nature. 2022 Nov;611(7934): 192-193
      
    Keywords:  Authorship; Communication; Computer science; Publishing
    DOI:  https://doi.org/10.1038/d41586-022-03479-w
  8. ATS Sch. 2022 Oct;3(3): 390-398
      Physicians in training are often taught how to conduct original research but may lack the skills necessary to write their results in a paper for the peer-reviewed medical literature. To help our critical care fellows increase their publication rates, we implemented an 8-hour scientific writing course that provides a structured approach to writing an academic research paper. We have demonstrated an increase in publication rate during fellowship from an average of 0.7 manuscripts per fellow just before course inception to 3.7 manuscripts per fellow in the current graduating class. We highlight strategies for developing a writing course aligned with adult learning theory within three key areas: planning, pedagogy, and implementation. Planning strategies center around creating a case for change, including multiple stakeholders with diverse backgrounds, including the research mentor, and ensuring accountability among stakeholders. Pedagogical strategies focus on harnessing the power of experiential learning, considering a flipped classroom approach, and peer teaching to leverage social and cognitive congruence. Implementation strategies include breaking down the writing process into manageable tasks, organizing the writing process according to learner needs, using peer review processes to drive learning, and celebrating the accomplishments of learners within the course. These strategies represent broad initiatives that can be tailored to local training needs and instituted across a wide variety of teaching platforms.
    Keywords:  authorship; curriculum; graduate medical education; research activities; teaching
    DOI:  https://doi.org/10.34197/ats-scholar.2022-0023PS
  9. ALTEX. 2022 Oct 31.
      Animal methods bias in scientific publishing is a newly defined type of publishing bias describing a preference for animal-based methods where they may not be necessary or where nonanimal-based methods may already be suitable, which impacts the likelihood or timeliness of a manuscript being accepted for publication. This article covers the output from a workshop between stakeholders in publishing, academia, industry, government, and non-governmental organizations. The intent of the workshop was to exchange perspectives on the prevalence, causes, and impact of animal methods bias in scientific publishing, as well as to explore mitigation strategies. Output from the workshop includes summaries of presentations, breakout group discussions, participant polling results, and a synthesis of recommendations for mitigation. Overall, participants felt that animal methods bias has a meaningful impact on scientific publishing, though more evidence is needed to demonstrate its prevalence. Significant consequences of this bias that were identified include the unnecessary use of animals in scientific procedures, the continued reliance on animals in research-even where suitable nonanimal methods exist, poor rates of clinical translation, delays in publication, and negative impacts on career trajectories in science. Workshop participants offered recommendations for journals, publishers, funders, governments, and other policy makers, as well as the scientific community at large, to reduce the prevalence and impacts of animal methods bias. The workshop resulted in the creation of working groups committed to addressing animal methods bias and activities are ongoing.
    Keywords:  ethics; nonanimal methods; translation; validation
    DOI:  https://doi.org/10.14573/altex.2210211
  10. Arch Dermatol Res. 2022 Nov 04.
      The degree of publication bias and impact of the Food and Drug Administration Amendments Act (FDAAA) of 2007, which aimed to improve clinical trial transparency, has yet to be examined for recent dermatologic drugs. The objective of our study was to estimate the degree of publication bias for clinical trials supporting FDA approval of new dermatologic drugs. This retrospective cohort study examined all phase II and III efficacy trials supporting approval of new dermatologic drugs from 2003 to 2018. FDA drug approval documents were reviewed for supportive clinical trial information, and publications were matched using PubMed and Google Scholar searches. Ratios of relative risks (RRR) comparing positive versus non-positive trials before and after FDAAA enactment served to estimate publication bias. We found that the likelihood of publishing positive versus non-positive drug trials in dermatology was unchanged before and after FDAAA enactment (RRR 0.87, 95% CI 0.37-2.08), as was the likelihood of publishing without misleading interpretation (RRR 1.51, 95% CI 0.22-10.50). There was no measurable publication bias for efficacy trials supporting new drug approvals in dermatology over the past 15 years. Fewer pre-FDAAA trials (n = 21) compared to post-FDAAA trials (n = 106) met inclusion criteria. Though not analyzed in this study, safety and secondary efficacy results are other potential sources for publication bias.
    Keywords:  Clinical trials; Dermatologic drugs; Negative reporting; Publication bias
    DOI:  https://doi.org/10.1007/s00403-022-02449-6
  11. Account Res. 2022 Nov 02.
      This letter to the editor furthers Dunleavy's commentary on Bolek et al. (2022). It needs to be pointed out that the peer review assessment format studied by Bolek et al. is rather unusual for a scientific journal, and Dunleavy's interpretation of a "commensuration bias" is more reflective of the unweighted scoring method.
    Keywords:  Commensuration bias; peer review; publication; research ethics
    DOI:  https://doi.org/10.1080/08989621.2022.2143267
  12. J Sleep Res. 2022 Oct 31. e13756
      The impact factor is used to rank the quality of scientific journals but has been criticised for a number of reasons. The aim of the study was to investigate sleep researchers' perceptions of sleep journals to determine whether subjective rankings of journals were in line with the journals' impact factors. Clarivate's Journal Citation Reports website was used to identify journals containing the words 'sleep' or 'dream' in the titles with an impact factor since 2018, resulting in 12 journals. A survey including questions about how the respondent would rank these journals (e.g., three most prestigious journals) was developed. A total of 122 sleep researchers completed the survey. Sleep, Sleep Medicine Reviews and Journal of Sleep Research were ranked as the three most prestigious sleep journals, in line with the impact factors of the journals. For the rest of the journals, the subjective rankings and impact factors did not correspond as much.
    Keywords:  impact factor; sleep journal; survey
    DOI:  https://doi.org/10.1111/jsr.13756
  13. Innov High Educ. 2022 Oct 28. 1-12
      Using five years of publishing data from the Journal of Higher Education, we describe the publication pipeline at the journal, explore trends with respect to topic, the geographic distribution of authors, and each paper's methodological approach. Following the presentation of these trends, we discuss implications for the field of higher education and those publishing within it.
    Keywords:  Journals; Publishing; Quantitative methods
    DOI:  https://doi.org/10.1007/s10755-022-09634-5
  14. BMJ Open Ophthalmol. 2022 10;pii: e001127. [Epub ahead of print]7(1):
      
    Keywords:  epidemiology
    DOI:  https://doi.org/10.1136/bmjophth-2022-001127