bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒06‒05
23 papers selected by
Thomas Krichel
Open Library Society

  1. JAMA Netw Open. 2022 Jun 01. 5(6): e2215209
      Importance: Clinical trial data sharing holds promise for maximizing the value of clinical research. The International Committee of Medical Journal Editors (ICMJE) adopted a policy promoting data sharing in July 2018.Objective: To evaluate the association of the ICMJE data sharing policy with data availability and reproducibility of main conclusions among leading surgical journals.
    Design, Setting, and Participants: This cross-sectional study, conducted in October 2021, examined randomized clinical trials (RCTs) in 10 leading surgical journals before and after the implementation of the ICMJE data sharing policy in July 2018.
    Exposure: Implementation of the ICMJE data sharing policy.
    Main Outcomes and Measures: To demonstrate a pre-post increase in data availability from 5% to 25% (α = .05; β = 0.1), 65 RCTs published before and 65 RCTs published after the policy was issued were included, and their data were requested. The primary outcome was data availability (ie, the receipt of sufficient data to enable reanalysis of the primary outcome). When data sharing was available, the primary outcomes reported in the journal articles were reanalyzed to explore reproducibility. The reproducibility features of these studies were detailed.
    Results: Data were available for 2 of 65 RCTs (3.1%) published before the ICMJE policy and for 2 of 65 RCTs (3.1%) published after the policy was issued (odds ratio, 1.00; 95% CI, 0.07-14.19; P > .99). A data sharing statement was observed in 11 of 65 RCTs (16.9%) published after the policy vs none before the policy (risk ratio, 2.20; 95% CI, 1.81-2.68; P = .001). Data obtained for reanalysis (n = 4) were not from RCTs published with a data sharing statement. Of the 4 RCTs with available data, all of them had primary outcomes that were fully reproduced. However, discrepancies or inaccuracies that were not associated with study conclusions were identified in 3 RCTs. These concerned the number of patients included in 1 RCT, the management of missing values in another RCT, and discrepant timing for the principal outcome declared in the study registration and reported in the third RCT.
    Conclusions and Relevance: This cross-sectional study suggests that data sharing practices are rare in surgical journals despite the ICMJE policy and that most RCTs published in these journals lack transparency. The results of these studies may not be reproducible by external researchers.
  2. J Allied Health. 2022 ;51(2): 87
      As editor of the Journal of Allied Health, the current holder of that position maintains an ongoing interest in the editorials produced by individuals with similar responsibilities for other periodicals. One of many suitable areas to survey regularly is the vast portfolio of journals produced by the publishing company Nature. The March 2022 issue of the periodical Nature Human Behaviour offers a worthwhile illustration. The editor in that instance advanced the proposition that although peer review is far from perfect, it currently is the best tool to evaluate the robustness and validity of scientific research.
  3. PLoS One. 2022 ;17(6): e0268999
      As social issues like climate change become increasingly salient, digital traces left by scholarly documents can be used to assess their reach outside of academia. Our research examine who shared climate change research papers on Twitter by looking at the expressions used in profile descriptions. We categorized users in eight categories (academia, communication, political, professional, personal, organization, bots and publishers) associated to specific expressions. Results indicate how diverse publics may be represented in the communication of scholarly documents on Twitter. Supplementing our word detection analysis with qualitative assessments of the results, we highlight how the presence of unique or multiple categorizations in textual Twitter descriptions provides evidence of the publics of research in specific contexts. Our results show a more substantial communication by academics and organizations for papers published in 2016, whereas the general public comparatively participated more in 2015. Overall, there is significant participation of publics outside of academia in the communication of climate change research articles on Twitter, although the extent to which these publics participate varies between individual papers. This means that papers circulate in specific communities which need to be assessed to understand the reach of research on social media. Furthermore, the flexibility of our method provide means for research assessment that consider the contextuality and plurality of publics involved on Twitter.
  4. ATS Sch. 2022 Mar;3(1): 38-47
      Peer review is a necessary and important component of scholarly publication. When done well, it benefits both the reviewer and authors and improves the science itself. However, the skills of effective peer review are rarely taught. In the adolescent field of medical education research, peer review is especially important to advance the scientific rigor of the field. From our experience reviewing biomedical and medical education research, we have found that a thorough review takes multiple readings and multiple hours. The first reading provides a general overview of the aims and methods. Subsequent readings focus on the details of the methodology, results, and interpretation. The written review should provide firm but gentle feedback that the authors can use to improve their work, even if we have recommended rejection for this submission. We hope that this description of our process for reviewing a medical education research manuscript will assist others and thereby advance the quality of publications in our field.
    Keywords:  education; peer review; scholarship
  5. Comput Intell Neurosci. 2022 ;2022 3054668
      Scholars have been suffering from scams involving counterfeit academic journals for a long time, and there has been a relatively clear analysis of the causes of counterfeiting and the governance path for it in existing studies. However, the authors reexamined the counterfeiting and found the problem still prevails. Through the analysis of the multiple players involved in counterfeiting, the author points out that the current personnel evaluation mechanism and journal evaluation system are the root causes of counterfeiting and thus offer corresponding suggestions for further improvement.
  6. Account Res. 2022 May 30.
      Retracted clinical trials may be influential in citing systematic reviews and clinical guidelines.We assessed the influence of 27 retracted trials on systematic reviews and clinical guidelines (citing publications), then alerted authors to these retractions. Citing publications were randomized to up to three emails to contact author with/without up to two co-authors, with/without the editor. After one year we assessed corrective action.We included 88 citing publications; 51% (45/88) had findings likely to change if the retracted trials were removed, 87% (39/45) likely substantially.51% (44/86) of contacted citing publications replied. Including three authors rather than the contact author alone was more likely to elicit a reply (P=0.03), but including the editor did not increase replies (P=0.66). Whether findings were judged likely to change, and the size of the likely change, had no effect on response rate or action taken. One year after emails were sent only nine publications had published notifications.Email alerts to authors and editors are inadequate to correct the impact of retracted publications in citing systematic reviews and guidelines. Changes to bibliographic and referencing systems, and submission processes are needed. Citing publications with retracted citations should be marked until authors resolve concerns.
    Keywords:  Publication integrity; clinical guideline; impact; retraction; systematic review
  7. Curr Med Res Opin. 2022 May 30. 1-18
      Authorship criteria can be difficult to apply in complex situations, such as multicenter clinical trials, multidisciplinary research, or manuscripts reporting the results of several studies. Authors may need additional guidance to appropriately credit their colleagues even when using existing accepted author criteria and/or contributor taxonomies to guide their decisions. Definitions and explanations of authorship by various editorial groups such as International Committee of Medical Journal Editors, the Committee on Publication Ethics, the World Association of Medical Editors, and the Council of Science Editors emphasize intellectual input and accountability. Existing contributor taxonomies list additional activities that should be credited, but do not stand in for authorship criteria or confer authorship. The literature was searched for existing guidelines for authors that suggest how to apply accepted authorship criteria to activities listed in contributor taxonomies. No publication was identified that mapped specific authorship criteria to particular contributor taxonomies. Suggestions were developed to assist in differentiating activities that meet author criteria from other contributions outlined in two existing contributor taxonomies.
    Keywords:  CRediT; ICMJE; authorship attribution; authorship criteria; publication ethics
  8. Res Involv Engagem. 2022 Jun 02. 8(1): 23
      BACKGROUND: Peer-reviewed scientific publications and congress abstracts are typically written by scientists for specialist audiences; however, patients and other non-specialists are understandably interested in the potential implications of research and what they may mean for them. Plain language summaries (PLS)-summaries of scientific articles in easy-to-read language-are emerging as a valuable addition to traditional scientific publications. Co-creation of PLS with the intended audience is key to ensuring a successful outcome, but practical guidance on how to achieve this has been lacking.METHODS: Building on the Patient Engagement (PE) Quality Guidance previously developed by Patient Focused Medicines Development (PFMD), a multi-stakeholder working group (WG) of individuals with patient engagement experience and/or expertise in PLS was established to develop further activity-specific guidance. PLS guidance was developed through a stepwise approach that included several rounds of co-creation, public consultation (two rounds), internal review and a final external review. The iterative development process incorporated input from a wide variety of stakeholders (patient representatives, industry members, publishers, researchers, medical communications agencies, and public officials involved in research bodies). Feedback from each step was consolidated by the WG and used for refining the draft guidance. The final draft was then validated through external consultation.
    RESULTS: The WG comprised 14 stakeholders with relevant experience in PE and/or PLS. The WG developed a set of 15 ethical principles for PLS development. These include the necessity for objective reporting and the absence of any promotional intent, the need for balanced presentation, the importance of audience focus, the need to apply health literacy principles, and the importance of using inclusive and respectful language. The first public consultation yielded 29 responses comprising 478 comments or edits in the shared draft guidance. The second public consultation was an online survey of 14 questions which had 32 respondents. The final 'How-To' Guide reflects feedback received and provides a rational, stepwise breakdown of the development of PLS.
    CONCLUSIONS: The resulting 'How-To' Guide is a standalone, practical, ready-to-use tool to support multi-stakeholder co-creation of PLS.
    Keywords:  Patient engagement; Plain language summary; Scientific publication
  9. Hist Sci. 2022 Jun;60(2): 155-165
    Keywords:  Scientific publishing; history of the book; scientific authorship; scientific journal; scientific languages
  10. PLoS One. 2022 ;17(5): e0268993
      BACKGROUND: As part of the Open Science movement, this study aims to analyze the current state of open access and open data policies concerning the availability of articles and raw data of the journals belonging to the category "Medicine, General & Internal" of the Science Citation Index Expanded.METHODS: Journal data sharing policies were evaluated through the following variables: possibility of manuscript storage in repositories; reuse policy; publication on a website; and statement regarding complementary material. Subsequently, an analysis of the supplementary material associated with each article was performed through the PubMed Central repository. The study reported was assessed following the STROBE guidelines for observational studies.
    RESULTS: This study shows that only one-third of the journals included in the category "Medicine, General & Internal" allow the depositing of their documents in repositories and its reuse, while approximately half of the journals agree to publish the document on a website as well as to deposit supplementary material along with the publication. However, the reality about this last variable is that only 9.5% of the articles analyzed contained supplementary material being the main journals involved, BMJ Open, JAMA Network Open, New England Journal of Medicine, Lancet and Plos Medicine.
    CONCLUSIONS: The analysis of the opening policies of the journals concerning data availability in medical research reveals the unequal positioning of publishers towards the sharing of open data, the ambiguity regarding government policies about the obligation to deposit data and the need for ethical and standardization requirements in the typology/format of the data deposited without forgetting the important role that the researcher plays. Further studies based on journals indexed in medical databases other than Science Citation Index Expanded are needed.
  11. Account Res. 2022 Jun 01. 1-10
      Excessive publication pressure has been associated with detrimental aspects for individual researchers and scientific integrity but has not been well-studied in Eastern European countries. The aim of this study is to assess perceived publication pressure and its relationship with career stage, scientific field, and gender in Hungary. The survey included demographic questions, such as gender, age, scientific field, career stage, and the Revised Publication Pressure Questionnaire (PPQr). A total of 408 respondents completed the survey, 46% were female, and 54% were male. 45% are PhD students, 17% are postdocs or assistant professors, and 38% are associate or full professors. 31% are from the Biomedical Sciences, 39% from Natural Sciences, 18% from Social Sciences, and 12% from Humanities. Our results showed no significant disciplinary differences in perceived publication pressure. PhD students perceived a greater lack of resources than postdocs and professors. The same applied to postdocs and assistant professors when compared to associate professors. The findings also showed that female researchers perceive greater stress than male researchers. Our study highlights the need to improve mentoring during the development of early-career researchers. It also emphasizes the importance of organizational structures developing policies or strategies to address gender differences in academia.
    Keywords:  Publication pressure; gender differences; research bias; research integrity; responsible conduct of research; scientific misconduct
  12. Bioinformatics. 2022 May 27. pii: btac362. [Epub ahead of print]
      MOTIVATION: Technical advances have revolutionized the life sciences and researchers commonly face challenges associated with handling large amounts of heterogeneous digital data. The Findable, Accessible, Interoperable and Reusable (FAIR) principles provide a framework to support effective data management. However, implementing this framework is beyond the means of most researchers in terms of resources and expertise, requiring awareness of metadata, policies, community agreements, and other factors such as vocabularies and ontologies.RESULTS: We have developed the Globally Accessible Distributed Data Sharing (GADDS) platform to facilitate FAIR-like data-sharing in cross-disciplinary research collaborations. The platform consists of (i) a blockchain based metadata quality control system, (ii) a private cloud-like storage system and (iii) a version control system. GADDS is built with containerized technologies, providing minimal hardware standards and easing scalability, and offers decentralized trust via transparency of metadata, facilitating data exchange and collaboration. As a use case, we provide an example implementation in engineered living material technology within the Hybrid Technology Hub at the University of Oslo.
    AVAILABILITY: Demo version available at
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  13. J Dent Res. 2022 Jun 02. 220345221101321
      According to the FAIR principles, data produced by scientific research should be findable, accessible, interoperable, and reusable-for instance, to be used in machine learning algorithms. However, to date, there is no estimate of the quantity or quality of dental research data evaluated via the FAIR principles. We aimed to determine the availability of open data in dental research and to assess compliance with the FAIR principles (or FAIRness) of shared dental research data. We downloaded all available articles published in PubMed-indexed dental journals from 2016 to 2021 as open access from Europe PubMed Central. In addition, we took a random sample of 500 dental articles that were not open access through Europe PubMed Central. We assessed data sharing in the articles and compliance of shared data to the FAIR principles programmatically. Results showed that of 7,509 investigated articles, 112 (1.5%) shared data. The average (SD) level of compliance with the FAIR metrics was 32.6% (31.9%). The average for each metric was as follows: findability, 3.4 (2.7) of 7; accessibility, 1.0 (1.0) of 3; interoperability, 1.1 (1.2) of 4; and reusability, 2.4 (2.6) of 10. No considerable changes in data sharing or quality of shared data occurred over the years. Our findings indicated that dental researchers rarely shared data, and when they did share, the FAIR quality was suboptimal. Machine learning algorithms could understand 1% of available dental research data. These undermine the reproducibility of dental research and hinder gaining the knowledge that can be gleaned from machine learning algorithms and applications.
    Keywords:  deep learning, machine learning; dental informatics; electronic dental records; open data; outcomes research
  14. Nature. 2022 May 30.
    Keywords:  Government; Politics; Publishing; SARS-CoV-2
  15. Dev Cogn Neurosci. 2022 May 20. pii: S1878-9293(22)00058-5. [Epub ahead of print]55 101115
      As the largest longitudinal study of adolescent brain development and behavior to date, the Adolescent Brain Cognitive Development (ABCD) Study® has provided immense opportunities for researchers across disciplines since its first data release in 2018. The size and scope of the study also present a number of hurdles, which range from becoming familiar with the study design and data structure to employing rigorous and reproducible analyses. The current paper is intended as a guide for researchers and reviewers working with ABCD data, highlighting the features of the data (and the strengths and limitations therein) as well as relevant analytical and methodological considerations. Additionally, we explore justice, equity, diversity, and inclusion efforts as they pertain to the ABCD Study and other large-scale datasets. In doing so, we hope to increase both accessibility of the ABCD Study and transparency within the field of developmental cognitive neuroscience.
    Keywords:  Adolescent Brain Cognitive Development (ABCD) Study; Adolescent development; Longitudinal research; Open research; Practical guide
  16. J Clin Epidemiol. 2022 May 30. pii: S0895-4356(22)00138-X. [Epub ahead of print]
      OBJECTIVE: To evaluate the impact of co-publication on the citation of Cochrane evidence.STUDY DESIGN AND SETTING: This was a retrospective cohort study including Cochrane reviews published up to 31 December 2015 and their citing up to 11 July 2021, identified from the Web of Science Core Collection database.
    RESULTS: A total of 101 co-published and 202 non-co-published Cochrane reviews were included. The median for the total number of citations and the medians for the numbers of citations to the Cochrane review in the first, second, third and fifth years after publication in the co-published group were higher than those in the non-co-published group [71 (IQR: 37.5, 118.5) vs. 32.5 (13, 67); 1 (0, 3) vs. 0 (0, 1); 6 (3, 11.5) vs. 2 (1, 5); 8 (4, 15) vs. 3.5 (1, 8); 8 (4, 15) vs. 3 (1, 9), respectively, all p<0.001]. Co-publication of Cochrane reviews meant that 4 of 21 journals and 6 of 22 journals had a higher IF in the first and the second year after the co-publication than they would have had without the co-publication.
    CONCLUSION: Co-publication is associated with a higher citation frequency of Cochrane reviews and may increase the IF of the journal in which it is co-published. This facilitates broader application of Cochrane evidence and promotes its dissemination.
    Keywords:  Citation number; Co-publication; Cochrane reviews; Cohort study; Dissemination; Journal impact factor
  17. Anaesthesia. 2022 May 28.
    Keywords:  audit; quality assurance; quality improvement; quality science
  18. J Clin Epidemiol. 2022 May 30. pii: S0895-4356(22)00141-X. [Epub ahead of print]
      OBJECTIVES: To analyse researchers' compliance with their Data Availability Statement (DAS) from manuscripts published in open access journals with the mandatory DAS.STUDY DESIGN AND SETTING: We analyzed all articles from 333 open-access journals published during January 2019 by BioMed Central. We categorized types of DAS. We surveyed corresponding authors who wrote in DAS that they would share the data. A consent to participate in the study was sought for all included manuscripts. After accessing raw data sets, we checked whether data were available in a way that enabled re-analysis.
    RESULTS: Of 3556 analyzed articles, 3416 contained DAS. The most frequent DAS category (42%) indicated that the datasets are available on reasonable request. Among 1792 manuscripts in which DAS indicated that authors are willing to share their data, 1670 (93%) authors either did not respond or declined to share their data with us. Among 254 (14%) of 1792 authors who responded to our query for data sharing, only 122 (6.8%) provided the requested data.
    CONCLUSION: Even when authors indicate in their manuscript that they will share data upon request, the compliance rate is the same as for authors who do not provide DAS, suggesting that DAS may not be sufficient to ensure data sharing.
    Keywords:  Data availability statement; data sharing; non-compliance; open data
  19. PLoS One. 2022 ;17(6): e0269246
      There is broad recognition by practicing taxonomists that the field is going through a crisis, which has been dubbed the "taxonomic impediment". There are many aspects involved in said crisis, but publication practices in taxonomy are often neglected or relegated to the backseat. We provide an initial foray into this topic via a worldwide survey with taxonomists, spanning all botanical and zoological groups, and career stages. Demographically, most of the respondents identified themselves as males (70%), working in Europe or North America (68%), in universities (50%) or museums (27%). Over half of the respondents are established/late-career researchers (only about 25% of full professors were female), with a low number of early-career researchers and graduate students (i.e., taxonomists in training). Nearly 61% of the men acquired their highest title at least eleven years ago, while only 41% of the women did so. Nearly 92% of the respondents have published new species descriptions, while around 60% and 26% have synonymized, respectively, species-level or subspecies-level taxa. In general, respondents perceive the act of describing new species to be easier than synonymizing species (p = 0.05). Established/late-career researchers and male researchers, particularly in Oceania and North America, found it easier to publish nomenclatural acts such as new species descriptions, while early-career researchers had their acts contested more often. Our results reaffirm the low academic recognition of the field, the lack of funding for research and publishing charges especially in the Global South, and the difficulty in finding specialized outlets (and the low impact factor of those journals) as persistent issues in taxonomy. Other significant problems raised by respondents include ethical issues in the peer-review process, a bias against newcomers in the field coming either from established researchers or committees, and taxonomic vandalism.
  20. Eur Ann Otorhinolaryngol Head Neck Dis. 2022 May 27. pii: S1879-7296(22)00053-9. [Epub ahead of print]
      OBJECTIVE: To evaluate reviewing and editorial decision for articles submitted to the European Annals of Otorhinolaryngology Head & Neck Diseases.MATERIALS AND METHODS: A retrospective analysis was made of reviewers' comments on 1,133 scientific articles (700 original articles, 96 literature reviews, and 337 case reports), originating from 69 countries, consecutively submitted on-line between January 1st, 2020 and December 31st, 2021. The main objective was to document the acceptance rate and decision time. Accessory objectives were to synthesize the main comments and to screen for correlations between acceptance and the main characteristics of first authors, articles and reviewers' comments.
    RESULTS: In total, 4.1% of submitted articles were accepted. Median decision time differed significantly (P<0.0001), at 1 month in case of refusal and 4 months in case of acceptance. Reviewers mentioned failure to adhere to the journal's authors' guide, to use the appropriate EQUATOR guidelines and to adopt the recommended P<0.005 significance threshold in 94.8%, 54.2%, and 39.9% of cases, respectively. On multivariate analysis, 3 variables significantly impacted acceptance, which increased from 1.3% to 44.6% (P<0.0001) when an appropriate EQUATOR guideline was used and from 0.3% to 57.4% (P<0.0001) when the significance threshold was set at P<0.005, and decreased from 10.5% to 1.1% (P=0.0001) when the article did not originate from a French-speaking country (member of the Francophonie organization).
    CONCLUSION: Adhesion to modern scientific medical writing rules increased acceptance rates for articles in the European Annals of Otorhinolaryngology Head & Neck Diseases. Teaching modern scientific medical writing needs to be enhanced in otorhinolaryngology.
    Keywords:  Medical writing; Otorhinolaryngology; Scientific article