bims-skolko Biomed News
on Scholarly communication
Issue of 2020‒08‒02
twenty-six papers selected by
Thomas Krichel
Open Library Society


  1. Cancer Rep (Hoboken). 2019 Feb;2(1): e1150
    Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C.
      Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete description of how their study was designed and executed because they may not know how to accurately report the information or the mechanisms are not in place to facilitate transparent reporting. Here, we provide an overview of how authors can write manuscripts in a transparent and thorough manner. We introduce a set of reporting criteria that can be used for publishing, including recommendations on reporting the experimental design and statistical approaches. We also discuss how to accurately visualize the results and provide recommendations for peer reviewers to enhance rigor and transparency. Incorporating transparency practices into research manuscripts will significantly improve the reproducibility of the results by independent laboratories. SIGNIFICANCE: Failure to replicate research findings often arises from errors in the experimental design and statistical approaches. By providing a full account of the experimental design, procedures, and statistical approaches, researchers can address the reproducibility crisis and improve the sustainability of research outcomes. In this piece, we discuss the key issues leading to irreproducibility and provide general approaches to improving transparency and rigor in reporting, which could assist in making research more reproducible.
    Keywords:  Open Science; peer review; policy; publishing; scientific rigor; transparency
    DOI:  https://doi.org/10.1002/cnr2.1150
  2. Nucleic Acid Ther. 2020 Jul 27.
    Echevarría L, Malerba A, Arechavala-Gomeza V.
      Scientific advance is based on reproducibility, corroboration, and availability of research results. However, large numbers of experimental results that contradict previous work do not get published and many research results are not freely available as they are hidden behind paywalls. As part of COST Action "DARTER", a network of researchers in the field of RNA therapeutics, we have performed a small survey among our members and their colleagues to assess their opinion on the subject of publishing contradictory or ambiguous results and their attitude to open access (OA) publishing. Our survey indicates that, although researchers highly value publication of "negative" results, they often do not publish their own, citing lack of time and the perception that those results may not be as highly cited. OA, on the other hand, seems to be widely accepted, but in many cases not actively sought by researchers due to higher costs associated with it.
    Keywords:  Open Science; negative results; null hypothesis; open access; science policy
    DOI:  https://doi.org/10.1089/nat.2020.0865
  3. PeerJ. 2020 ;8 e9410
    Robinson-Garcia N, Costas R, van Leeuwen TN.
      The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices. This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities' output for 963 institutions. This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies.
    Keywords:  Open access; Open science; Research assessment; Research policy; Science of science; Scientometrics; Universities; Unpaywall
    DOI:  https://doi.org/10.7717/peerj.9410
  4. J Manag Care Spec Pharm. 2020 Aug;26(8): 956-960
    Happe LE.
      The preponderance of journals with dubious publishing practices has resulted in a new term in academic publishing: predatory journals. Although there is no standard definition, predatory journals generally subvert the traditional peer-reviewed system for financial gain. Common practices of predatory journals include publishing almost all submissions, a lack of transparency about publication fees, aggressive solicitation of contributors irrespective of relevant expertise and credentials, and even closely mimicking names of reputable journals-effectively acting as a decoy to attract authors and readers. Left unchecked, these journals have the potential to threaten the evidence base relied on by managed care pharmacists. Given the importance of peer-reviewed literature to managed care pharmacy practice, how is one to discern between a predatory journal and a reputable one? There are 5 key practices that distinguish reputable journals. First, reputable journals rely on peer reviewers who are experts in their respective fields to carefully review submitted manuscripts for suitability to publish. Second, reputable journals have a board of experts in relevant areas that serve in an advisory capacity to the editorial staff. Third, reputable journals follow recognized publishing standards to guide their policies, which range from determining authorship, to journal management, to handling allegations of misconduct. Fourth, reputable journals are transparent and fair about their levied fees, avoiding any real or perceived conflict of interest. Finally, reputable journals are indexed in searchable databases that have quality selection criteria for inclusion. These 5 criteria should be used by managed care authors and researchers when determining where to publish their papers and whether to serve as an editorial board member or peer reviewer when requested. Studies published in journals meeting these criteria can be deemed as reputable and suitable for review by managed care and health policymakers. It is essential that everyone involved in producing and using peer-reviewed literature is informed about the threat of predatory publishing and avoids engaging in any activities with these journals. DISCLOSURES: No funding was received for the writing of this article. The author is editor-in-chief of the Journal of Managed Care & Specialty Pharmacy and has nothing to disclose.
    DOI:  https://doi.org/10.18553/jmcp.2020.26.8.956
  5. Nat Ecol Evol. 2020 Aug;4(8): 995
      
    DOI:  https://doi.org/10.1038/s41559-020-1277-4
  6. Account Res. 2020 Jul 31.
    Norman MK, Mayowski CA, Fine MJ.
      Because peer review publication is essential for academic advancement across scientific fields, when authorship is wrongly attributed the consequences can be profound, particularly for junior researchers who are still establishing their professional norms and scientific reputations. Professional societies have published guidelines for authorship, yet authorship dilemmas frequently arise and have harmful consequences for scientific careers. Researchers have noted the complexities of authorship and called for new mechanisms to foster more ethical research cultures within institutions. To address this call, we organized a panel discussion at the Institute for Clinical Research Education at the University of Pittsburgh in which senior faculty members from diverse backgrounds and professional disciplines discussed their own authorship challenges (e.g., renegotiating author order, reconciling inter-professional authorship norms, managing co-author power differentials) and offered strategies to avoid and/or resolve them. Informed by growth mindset theory, our storytelling format facilitated an open exchange between senior and junior researchers, situated authorship dilemmas in specific contexts and career stages, and taught researchers how to address authorship challenges not adequately informed by guideline recommendations. Though not empirically assessed, we believe this approach represents a simple, low-cost, and replicable way to cultivate ethical and transparent authorship practices among researchers across scientific fields.
    Keywords:  Authorship; authorship ethics; conflict resolution; growth mindset; publication
    DOI:  https://doi.org/10.1080/08989621.2020.1804374
  7. Ugeskr Laeger. 2020 Jul 06. pii: V205034. [Epub ahead of print]182(28):
    Krag A, Pinborg A.
      
  8. Bull Math Biol. 2020 Jul 28. 82(8): 100
    Bendinskas KG, Caudill L, Melara LA.
      This note addresses the important role of undergraduate research journals in the undergraduate research experience. Peer review by professional researchers is identified as the most essential ingredient in establishing the relevance of these journals as venues for research dissemination. Included are examples of three such journals-Spora, SIAM Undergraduate Research Online, and the American Journal of Undergraduate Research-with demonstrated success in supporting the undergraduate research experience.
    Keywords:  E-Journal; Student research; Undergraduate education; Undergraduate research
    DOI:  https://doi.org/10.1007/s11538-020-00775-2
  9. SSRN. 2020 Feb 12. 3536663
    Majumder MS, Mandl KD.
      As of February 11, 2020, more than 43,000 cases of a novel coronavirus (2019-nCoV) have been reported worldwide. Using publicly available data regarding the transmissibility potential (i.e. basic reproduction number) of 2019-nCoV, we demonstrate that relevant preprint studies generated considerable search and news media interest prior to the publication of peer-reviewed studies in the same topic area. We then show that preprint estimate ranges for the basic reproduction number associated with 2019-nCoV overlap with those presented by peer-reviewed studies that were published at a later date. Taken together, we argue that preprints are capable of driving global discourse during public health crises; however, we recommend that a consensus-based approach - as we have employed here - be considered as a means of assessing the robustness of preprint findings prior to peer review.
    Keywords:  novel coronavirus; preprints; transmissibility
    DOI:  https://doi.org/10.2139/ssrn.3536663
  10. Elife. 2020 Jul 27. pii: e58496. [Epub ahead of print]9
    Abdill RJ, Adamowicz EM, Blekhman R.
      Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of 'contributor countries' (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.
    Keywords:  bibliometrics; bioRxiv; computational biology; meta-research; none; preprints; scientific publishing; systems biology
    DOI:  https://doi.org/10.7554/eLife.58496
  11. BMJ Evid Based Med. 2020 Jul 28. pii: bmjebm-2020-111487. [Epub ahead of print]
    Niriella MA, De Silva AP, de Silva HJ, Jayasinghe S.
      
    Keywords:  ethics; investigative techniques; policy; sociology, medical
    DOI:  https://doi.org/10.1136/bmjebm-2020-111487
  12. PLoS Biol. 2020 Jul;18(7): e3000763
    Culina A, van den Berg I, Evans S, Sánchez-Tójar A.
      Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies. Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology. Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors. We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation.
    DOI:  https://doi.org/10.1371/journal.pbio.3000763
  13. J Learn Disabil. 2020 Jul 31. 22219420945267
    van Dijk W, Schatschneider C, Hart SA.
      The Open Science movement has gained considerable traction in the last decade. The Open Science movement tries to increase trust in research results and open the access to all elements of a research project to the public. Central to these goals, Open Science has promoted five critical tenets: Open Data, Open Analysis, Open Materials, Preregistration, and Open Access. All Open Science elements can be thought of as extensions to the traditional way of achieving openness in science, which has been scientific publication of research outcomes in journals or books. Open Science in education sciences, however, has the potential to be much more than a safeguard against questionable research. Open Science in education science provides opportunities to (a) increase the transparency and therefore replicability of research and (b) develop and answer research questions about individuals with learning disabilities and learning difficulties that were previously impossible to answer due to complexities in data analysis methods. We will provide overviews of the main tenets of Open Science (i.e., Open Data, Open Analysis, Open Materials, Preregistration, and Open Access), show how they are in line with grant funding agencies' expectations for rigorous research processes, and present resources on best practices for each of the tenets.
    Keywords:  Open Science; learning disabilities; research practices
    DOI:  https://doi.org/10.1177/0022219420945267
  14. Nature. 2019 Aug 02.
    Alechine E.
      
    Keywords:  Authorship; Careers; Communication
    DOI:  https://doi.org/10.1038/d41586-019-02387-w
  15. Urology. 2020 Jul 23. pii: S0090-4295(20)30869-4. [Epub ahead of print]
    Cannon S, Ahn J, Shnorhavorian M, Kieran K, Merguerian P.
      OBJECTIVE: To evaluate the evolving role of gender in invited authorship and editorial positions in the Journal of Pediatric Urology.MATERIALS AND METHODS: We recorded editorial board members and first and senior authors for all editorials and invited commentaries for all issues of the Journal of Pediatric Urology from 2005 to August 2018. We also recorded first and senior authors for original research articles from selected years for comparison. Gender was confirmed for each individual by visiting institutional websites and performing internet searches. The same was done for the Societies for Pediatric Urology membership.
    RESULTS: A total of 143 editorials and 162 invited commentaries were identified within the study period, with numbers increasing each year. Overall, these publications had 448 first and senior authorships, of which 10% were female. Of the 898 editorial board positions over the study period, 7% were held by females. The proportion of female authorships increased over time (p = 0.04), while the proportion of female board members did not (p=0.9).
    CONCLUSIONS: Female invited authorship has increased over the past 13 years in the Journal of Pediatric Urology. However, editorial board membership has lagged, indicating an opportunity for improvement.
    Keywords:  Pediatric Urology; authorship; editorial boards; gender equality; workforce issues
    DOI:  https://doi.org/10.1016/j.urology.2020.05.097
  16. PeerJ. 2020 ;8 e9404
    Larios D, Brooks TM, Macfarlane NBW, Roy S.
      Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, "How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?" and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent's IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.
    Keywords:  Access to literature; Biodiversity conservation; Conservation organisations; Information seeking; Libraries; Open access
    DOI:  https://doi.org/10.7717/peerj.9404
  17. BMJ Open. 2020 Jul 28. 10(7): e038571
    Han MA, Guyatt G.
      INTRODUCTION: Sometimes, observational studies may provide important evidence that allow inferences of causality between exposure and outcome (although on most occasions only low certainty evidence). Authors, frequently and perhaps usually at the behest of the journals to which they are submitting, avoid using causal language when addressing evidence from observational studies. This is true even when the issue of interest is the causal effect of an intervention or exposure. Clarity of thinking and appropriateness of inferences may be enhanced through the use of language that reflects the issue under consideration. The objectives of this study are to systematically evaluate the extent and nature of causal language use in systematic reviews of observational studies and to relate that to the actual intent of the investigation.METHODS AND ANALYSIS: We will conduct a systematic survey of systematic reviews of observational studies addressing modifiable exposures and their possible impact on patient-important outcomes. We will randomly select 200 reviews published in 2019, stratified in a 1:1 ratio by use and non-use of the Grading of Recommendations Assessment, Development, and Evaluation (GRADE). Teams of two reviewers will independently assess study eligibility and extract data using a standardised data extraction forms, with resolution of disagreement by discussion and, if necessary, by third party adjudication. Through examining the inferences, they make in their papers' discussion, we will evaluate whether the authors' intent was to address causation or association. We will summarise the use of causal language in the study title, abstract, study question and results using descriptive statistics. Finally, we will assess whether the language used is consistent with the intention of the authors. We will determine whether results in reviews that did or did not use GRADE differ.
    ETHICS AND DISSEMINATION: Ethics approval for this study is not required. We will disseminate the results through publication in a peer-reviewed journals.
    REGISTRATION: Open Science Framework (osf.io/vh8yx).
    Keywords:  basic sciences; epidemiology; statistics & research methods
    DOI:  https://doi.org/10.1136/bmjopen-2020-038571
  18. F1000Res. 2020 ;9 210
    Schmidt L, Olorisade BK, McGuinness LA, Higgins JPT.
      Background: Researchers in evidence-based medicine cannot keep up with the amounts of both old and newly published primary research articles. Conducting and updating of systematic reviews is time-consuming. In practice, data extraction is one of the most complex tasks in this process. Exponential improvements in computational processing speed and data storage are fostering the development of data extraction models and algorithms. This, in combination with quicker pathways to publication, led to a large landscape of tools and methods for data extraction tasks. Objective: To review published methods and tools for data extraction to (semi)automate the systematic reviewing process. Methods: We propose to conduct a living review. With this methodology we aim to do monthly search updates, as well as bi-annual review updates if new evidence permits it. In a cross-sectional analysis we will extract methodological characteristics and assess the quality of reporting in our included papers. Conclusions: We aim to increase transparency in the reporting and assessment of machine learning technologies to the benefit of data scientists, systematic reviewers and funders of health research. This living review will help to reduce duplicate efforts by data scientists who develop data extraction methods. It will also serve to inform systematic reviewers about possibilities to support their data extraction.
    Keywords:  Data Extraction; Natural Language Processing; Reproducibility; Systematic reviews; Text mining
    DOI:  https://doi.org/10.12688/f1000research.22781.1
  19. Med J Malaysia. 2020 Jul;75(4): 323-324
    Rampal L, Liew BS, Oothuman P, Philip R, Mohd Sidik S, Hoe VC, Baharudin A.
      Proper understanding the 'Instructions to authors' for a particular journal is the key towards successful submission of a manuscript which will lead to it being published. Common errors that are frequently made by authors in their submission to the Malaysia Journal of Malaysia (MJM) that lead to rejection of their submission or requiring major revisions or minor revisions are listed and discussed in this article. Outright rejection prior to even a peer review process may be made for an article due to: it is poorly written or when there is suspicion on the authenticity of the submission, which contains elements that are suspected to be plagiarised, it is a duplicate submission or not in the format required by the MJM. The editor in charge of the issue makes a recommendation to the Editor in Chief for the final decision.
  20. Cureus. 2020 Jun 24. 12(6): e8802
    Hussain M, Rehman R, Baig M.
      Background With an upsurge in research in developing countries, researchers from allied sciences need to augment their skills for disseminating research work worldwide. Training workshop is one of the quick interventions which can enhance writing skills and ease research publication. Objective We designed this research to explore the perception of the faculty of different higher education institutes (HEIs) regarding manuscript writing and to assess the impact of these workshops in the improvement of cognitive capabilities of preliminary researchers in Pakistan. Methodology We conducted workshops in HEIs of Sindh, Pakistan. Contents of the workshop covered algorithm of writing manuscript and related descriptions, choice of quality journals, correspondence with the editor, and dealing with rejection. The knowledge of the participants was assessed by 15 items pre and post evaluation tests. McNamar's test assessed the significance of the change in knowledge. Kruskal Wallis test was performed to check the difference in the opinion of workshop quality among different institutes. Results A significant improvement was observed in participants' knowledge on the readers' prospects (P=0.001), the algorithm of writing (P<0.001), interpretations of results (P<0.001), and selection quality journal for publication (P <0.001). The agreement with the workshop's quality based on need, knowledge, and content was above average. Conclusion The participants' response regarding the effectiveness of manuscript writing for publication workshop was overwhelmingly positive, and there was a significant impact on the knowledge of the participants. There is a need for research training that will help for better capacity building in different HEIs of Pakistan.
    Keywords:  capacity building; cognitive abilities; interactive workshop; manuscript writing; pakistan; publications; research manuscript
    DOI:  https://doi.org/10.7759/cureus.8802
  21. Rev Chil Pediatr. 2020 Feb;pii: S0370-41062020000100139. [Epub ahead of print]91(1): 139-145
    Schonhaut Berman L, Millan Klüsse T, Zepeda Ortega AJ.
      Revista Chilena de Pediatría (RCHP) has been published uninterruptedly since its first edition in Ja nuary 1930, beyond political and economic fluctuations, technological innovation, and social trans formations. The objective of this article is to pay tribute to and thank the editors who participated so actively in the publication of the RCHP and to review the major milestones, which have led it to the position it has today as a mainstream magazine. Since its entry into the digital world two deca des ago, there has been a significant increase in the flow of manuscripts received, participation of foreign authors, citations received and promotion in international rankings. In 2014, the RCHP was incorporated into the National Library of Medicine (NLM) and, in 2017, into the Emerging Sources Citation Index (ESCI), while evaluating to receive an Impact Factor (IF) from the Journal Citation Report (JCR). As a representative magazine of a scientific society, it is essential to maintain a balance between scientific and economic sustainability, the promotion of national and international publica tion, the scientific impact need for continuing rising in international rankings, and the impact on our children>s care in the different corners of the country.
    DOI:  https://doi.org/10.32641/rchped.v91i1.1684