bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒07‒24
eighteen papers selected by
Thomas Krichel
Open Library Society

  1. Heliyon. 2022 Mar;8(3): e09095
      Background: Environmental health and other researchers can benefit from automated or semi-automated summaries of data within published studies as summarizing study methods and results is time and resource intensive. Automated summaries can be designed to identify and extract details of interest pertaining to the study design, population, testing agent/intervention, or outcome (etc.). Much of the data reported across existing publications lack unified structure, standardization and machine-readable formats or may be presented in complex tables which serve as barriers that impede the development of automated data extraction methodologies.As full automation of data extraction seems unlikely soon, encouraging investigators to submit structured summaries of methods and results in standardized formats with meta-data tagging of content may be of value during the publication process. This would produce machine-readable content to facilitate automated data extraction, establish sharable data repositories, help make research data FAIR, and could improve reporting quality.Objectives: A pilot study was conducted to assess the feasibility of asking participants to summarize study methods and results using a structured, web-based data extraction model as a potential workflow that could be implemented during the manuscript submission process.
    Methods: Eight participants entered study details and data into the Health Assessment Workplace Collaborative (HAWC). Participants were surveyed after the extraction exercise to ascertain 1) whether this extraction exercise will impact their conducting and reporting of future research, 2) the ease of data extraction, including which fields were easiest and relatively more problematic to extract and 3) the amount of time taken to perform data extractions and other related tasks. Investigators then presented participants the potential benefits of providing structured data in the format they were extracting. After this, participants were surveyed about 1) their willingness to provide structured data during the publication process and 2) whether they felt the potential application of structured data entry approaches and their implementation during the journal submission process should continue to be further explored.
    Conclusions: Routine provision of structured data that summarizes key information from research studies could reduce the amount of effort required for reusing that data in the future, such as in systematic reviews or agency scientific assessments. Our pilot study suggests that directly asking authors to provide that data, via structured templates, may be a viable approach to achieving this: participants were willing to do so, and the overall process was not prohibitively arduous. We also found some support for the hypothesis that use of study templates may have halo benefits in improving the conduct and completeness of reporting of future research. While limitations in the generalizability of our findings mean that the conditions of success of templates cannot be assumed, further research into how such templates might be designed and implemented does seem to have enough chance of success that it ought to be undertaken.
    Keywords:  Author feedback; Author journal submission requirements; Author opinion; Author willingness; Automated data extraction; Data extraction; Data sharing; Data summary; Data templates; Manuscript submission; Natural language Processing (NLP); Science translation; Standardized data; Structured data; Study evaluation template; Systematic review
  2. Lancet. 2022 07 16. pii: S0140-6736(22)00921-7. [Epub ahead of print]400(10347): 159
  3. Lancet. 2022 07 16. pii: S0140-6736(22)01057-1. [Epub ahead of print]400(10347): 160
  4. Eur J Clin Invest. 2022 Jul 23. e13839
      Social media and new tools for engagement offer democratic platforms for enhancing constructive scientific criticism which had previously been limited. Constructive criticism can now be massive, timely, and open. However, new options have also enhanced obsessive criticism. Obsessive criticism tends to focus on one or a handful of individuals and their work, often includes ad hominem aspects, and the critics often lack field-specific skills and technical expertise. Typical behaviors include: repetitive and persistent comments (including sealioning), lengthy commentaries/tweetorials/responses often longer than the original work, strong degree of moralizing, distortion of the underlying work, argumentum ad populum, calls to suspend/censor/retract the work or the author, guilt by association, reputational tarnishing, large gains in followers specifically through attacks, finding and positing sensitive personal information, anonymity or pseudonymity, social media campaigning, and unusual ratio of criticism to pursuit of one's research agenda. These behaviors may last months or years. Prevention and treatment options may include awareness, identifying and working around aggravating factors, placing limits on the volume by editors, constructive pairing of commissioned editorials, incorporation of some hot debates from unregulated locations such as social media or PubPeer to the pages of scientific journals, preserving decency and focusing on evidence and arguments and avoiding personal statements, or (in some cases) ignoring. We need more research on the role of social media and obsessive criticism on an evolving cancel culture, the social media credibility, the use/misuse of anonymity and pseudonymity, and whether potential interventions from universities may improve or further weaponize scientific criticism.
    Keywords:  Twitter; cancel culture; criticism; peer review; social media
  5. Neurosurgery. 2022 Mar 01. 90(3): 262-269
      BACKGROUND: Statistically significant positive results are more likely to be published than negative or insignificant outcomes. This phenomenon, also termed publication bias, can skew the interpretation of meta-analyses. The widespread presence of publication bias in the biomedical literature has led to the development of various statistical approaches, such as the visual inspection of funnel plots, Begg test, and Egger test, to assess and account for it.OBJECTIVE: To determine how well publication bias is assessed for in meta-analyses of the neurosurgical literature.
    METHODS: A systematic search for meta-analyses from the top neurosurgery journals was conducted. Data relevant to the presence, assessment, and adjustments for publication bias were extracted.
    RESULTS: The search yielded 190 articles. Most of the articles (n = 108, 56.8%) were assessed for publication bias, of which 40 (37.0%) found evidence for publication bias whereas 61 (56.5%) did not. In the former case, only 11 (27.5%) made corrections for the bias using the trim-and-fill method, whereas 29 (72.5%) made no correction. Thus, 111 meta-analyses (58.4%) either did not assess for publication bias or, if assessed to be present, did not adjust for it.
    CONCLUSION: Taken together, these results indicate that publication bias remains largely unaccounted for in neurosurgical meta-analyses.
  6. Bone Jt Open. 2022 Aug;3(8): 582-588
      AIMS: Preprint servers allow authors to publish full-text manuscripts or interim findings prior to undergoing peer review. Several preprint servers have extended their services to biological sciences, clinical research, and medicine. The purpose of this study was to systematically identify and analyze all articles related to Trauma & Orthopaedic (T&O) surgery published in five medical preprint servers, and to investigate the factors that influence the subsequent rate of publication in a peer-reviewed journal.METHODS: All preprints covering T&O surgery were systematically searched in five medical preprint servers (medRxiv, OSF Preprints,, PeerJ, and Research Square) and subsequently identified after a minimum of 12 months by searching for the title, keywords, and corresponding author in Google Scholar, PubMed, Scopus, Embase, Cochrane, and the Web of Science. Subsequent publication of a work was defined as publication in a peer-reviewed indexed journal. The rate of publication and time to peer-reviewed publication were assessed. Differences in definitive publication rates of preprints according to geographical origin and level of evidence were analyzed.
    RESULTS: The number of preprints increased from 2014 to 2020 (p < 0.001). A total of 38.6% of the identified preprints (n = 331) were published in a peer-reviewed indexed journal after a mean time of 8.7 months (SD 5.4 (1 to 27)). The highest proportion of missing subsequent publications was in the preprints originating from Africa, Asia/Middle East, and South America, or in those that covered clinical research with a lower level of evidence (p < 0.001).
    CONCLUSION: Preprints are being published in increasing numbers in T&O surgery. Depending on the geographical origin and level of evidence, almost two-thirds of preprints are not subsequently published in a peer-reviewed indexed journal after one year. This raises major concerns regarding the dissemination and persistence of potentially wrong scientific work that bypasses peer review, and the orthopaedic community should discuss appropriate preventive measures.Cite this article: Bone Jt Open 2022;3(7):582-588.
    Keywords:  Digital health; Mann-Whitney U test; Orthopaedics; Preprints; Trauma; binomial test; biological sciences; chi-squared test; clinician; hip; orthopaedic surgery; randomized controlled trials; trauma surgery
  7. Int J Eat Disord. 2022 Jul 19.
      OBJECTIVE: Incorporating open science practices has become a priority for submission criteria in the International Journal of Eating Disorders (IJED). In this systematic review, we used the rigor and reproducibility framework developed by Hildebrandt and Prenoveau (2020) to examine the implementation of statistically sound open science principles in IJED, determining whether the cost and effort of incorporating these practices ultimately make research more likely to be cited.METHOD: For this systematic review, six trained coders examined 1145 articles published from January 2011 to May 2021, including the 5 years prior to the 2016 introduction of the Open Science Foundation article preregistration. We coded for the presence or absence of 10 specific open science elements and calculated citation metrics for each article.
    RESULTS: There was evidence of a significant positive relationship between time and total rigor and reproducibility (Total RR) criteria included in IJED articles following the implementation of preregistration in 2016. For every increase in year from 2011 to 2016, there was a .14 decrease in Total RR criteria. From 2016 to 2021, there was a .42 increase per volume in Total RR criteria. There was no statistically significant relationship between Total RR criteria and citation impact.
    DISCUSSION: Although findings indicate that statistical rigor and reproducibility in this field has increased, the lack of direct relationship between open science methods and article visibility for scientists suggests that there is a limited incentive for researchers to participate in reporting guidelines.
    PUBLIC SIGNIFICANCE: Statistical controversies within science threaten the rigor and reproducibility of published research. Open science practices, including the preregistration of study hypotheses, links to statistical code, and explicit data-sharing arguably generate reliable and valid inferences. This review illustrates the rigor and reproducibility of articles published in IJED between 2011 and 2021 and identifies whether open sciences practices have become increasingly prevalent in eating disorder research.
    Keywords:  authorship; eating disorders; open science; reproducibility; research; statistics
  8. J Clin Epidemiol. 2022 Jul 15. pii: S0895-4356(22)00179-2. [Epub ahead of print]
      OBJECTIVE: Fraudulent research exists but can be difficult to spot. Made-up studies and results can affect systematic reviews and clinical guidelines, causing harm through incorrect treatments and practices. Our aim was to explore indicators of research fraud that could be included in a screening tool to identify potentially problematic studies warranting closer scrutiny.STUDY DESIGN & SETTING: We conducted a qualitative international interview study, purposively recruiting participants with experience and/or expertise in: research integrity, systematic reviews, biomedical publishing, or whistle-blowing research fraud. We used thematic analysis to identify major concepts and ideas.
    RESULTS: We contacted 49 potential participants and interviewed 30 from 12 countries. Participants described research fraud as a growing concern, with a lack of widely accessible resources or education to assist in flagging problematic studies. They discussed early warning signs that could be contained in a screening tool for use either pre or post publication. We did not speak to participants from indexing services, information software/analytics companies, or the public. Our suggested screening tools are empirically derived but are preliminary and not validated.
    CONCLUSION: A practical tool of early warning signs for research fraud would be useful for peer reviewers, editors, publishers and systematic reviewers.
    Keywords:  esearch fraud; fraudulent data; publication ethics; qualitative research; research ethics; scientific misconduct
  9. Surg Endosc. 2022 Jul 18.
      INTRODUCTION: Accurate disclosure of conflicts of interest (COI) is critical to interpretation of study results, especially when industry interests are involved. We reviewed published manuscripts comparing robot-assisted cholecystectomy (RAC) and laparoscopic cholecystectomy (LC) to evaluate the relationship between COI disclosures and conclusions drawn on the procedure benefits and safety profile.METHODS: Searching Pubmed and Embase using key words "cholecystectomy", laparoscopic" and "robotic"/"robot-assisted" retrieved 345 publications. Manuscripts that compared benefits and safety of RAC over LC, had at least one US author and were published between 2014 and 2020 enabling verification of disclosures with reported industry payments in CMS's Open Payments database (OPD) (up to 1 calendar year prior to publication) were included in the analysis (n = 37).
    RESULTS: Overall, 26 (70%) manuscripts concluded that RAC was equivalent or better than LC (RAC +) and 11 (30%) concluded that RAC was inferior to LC (RAC-). Six manuscripts (5 RAC + and 1 RAC-) did not have clearly stated COI disclosures. Among those that had disclosure statements, authors' disclosures matched OPD records among 17 (81%) of RAC + and 9 (90%) RAC- papers. All 11 RAC- and 17 RAC + (65%) manuscripts were based on retrospective cohort studies. The remaining RAC + papers were based on case studies/series (n = 4), literature review (n = 4) and clinical trial (n = 1). A higher proportion of RAC + (85% vs 45% RAC-) manuscripts used data from a single institution. Authors on RAC + papers received higher amounts of industry payments on average compared to RAC- papers.
    CONCLUSIONS: It is imperative for authors to understand and accurately disclose their COI while disseminating scientific output. Journals have the responsibility to use a publicly available resource like the OPD to verify authors' disclosures prior to publication to protect the process of scientific authorship which is the foundation of modern surgical care.
    Keywords:  Cholecystectomy; Conflicts of interest; Disclosures; Laparoscopic; Open payments database; Robot-assisted
  10. Rural Remote Health. 2022 Jul;22(3): 7646
      The Indigenous Cultural Identity of Research Authors Standard (ICIRAS) is based on a gap in research publishing practice where Indigenous peoples' identity is not systematically and rigorously recognised in rural health research publications. There are widespread reforms, in different research areas, to counter the reputation of scientific research as a vehicle of racism and discrimination. Reflecting on these broader movements, the editorial teams of three rural health journals - Rural and Remote Health, the Australian Journal of Rural Health, and the Canadian Journal of Rural Medicine - adopted a policy of 'Nothing about Indigenous Peoples, without Indigenous Peoples'. This meant changing practices so that Indigenous Peoples' identity could be embedded in authorship credentials - such as in the byline. An environmental scan of literature about the inclusion of Indigenous Peoples in research revealed many ways in which editorial boards of journals could improve their process to signal to readers that Indigenous voices are included in rural health research publication governance. Improving the health and wellbeing of Indigenous peoples worldwide requires high-quality research evidence. This quality benchmark needs to explicitly signal the inclusion of Indigenous authors. The ICIRAS is a call to action for research journals and institutions to rigorously improve research governance and leadership to amplify the cultural identity of Indigenous peoples in rural health research.
    Keywords:   Indigenous Peoples; cultural identity; cultural provenance; cultural safety; author credentials
  11. Aust J Rural Health. 2022 Jul 20.
      AIM: We aim to promote discussion about an Indigenous Cultural Identity of Research Authors Standard (ICIRAS) for academic journal publications.CONTEXT: This is based on a gap in research publishing practice where Indigenous peoples' identity is not systematically and rigorously flagged in rural health research publications. There are widespread reforms, in different research areas, to counter the reputation of scientific research as a vehicle of racism and discrimination against the world's Indigenous peoples. Reflecting on these broader movements, the editorial teams of three rural health journals-the Australian Journal of Rural Health, the Canadian Journal of Rural Medicine, and Rural and Remote Health-recognised that Indigenous peoples' identity could be embedded in authorship details.
    APPROACH: An environmental scan (through a cultural safety lens where Indigenous cultural authority is respected, valued, and empowered) of literature was undertaken to detect the signs of inclusion of Indigenous peoples in research. This revealed many ways in which editorial boards of Journals could systematically improve their process so that there is 'nothing about Indigenous people, without Indigenous people' in rural health research publications.
    CONCLUSION: Improving the health and wellbeing of Indigenous peoples worldwide requires high quality research evidence. The philosophy of cultural safety supports the purposeful positioning of Indigenous peoples within the kaleidoscope of cultural knowledges as identified contributors and authors of research evidence. The ICIRAS is a call-to-action for research journals and institutions to rigorously improve publication governance that signals "Editing with IndigenUs and for IndigenUs".
    Keywords:  Indigenous peoples; author credentials; cultural identity; cultural provenance; cultural safety
  12. Clin Microbiol Infect. 2022 Jul 18. pii: S1198-743X(22)00367-6. [Epub ahead of print]