bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒09‒18
23 papers selected by
Thomas Krichel
Open Library Society


  1. Nat Ecol Evol. 2022 Sep 15.
      Using a database of open data policies for 199 journals in ecology and evolution, we found no detectable link between data sharing requirements and article retractions or corrections. Despite the potential for open data to facilitate error detection, poorly archived datasets, the absence of open code and the stigma associated with correcting or retracting articles probably stymie error correction. Requiring code alongside data and destigmatizing error correction among authors and journal editors could increase the effectiveness of open data policies at helping science self-correct.
    DOI:  https://doi.org/10.1038/s41559-022-01879-9
  2. PLoS One. 2022 ;17(9): e0273783
      The question of whether it is appropriate to attribute authorship to deceased individuals of original studies in the biomedical literature is contentious. Authorship guidelines utilized by journals do not provide a clear consensus framework that is binding on those in the field. To guide and inform the implementation of authorship frameworks it would be useful to understand the extent of the practice in the scientific literature, but studies that have systematically quantified the prevalence of this phenomenon in the biomedical literature have not been performed to date. To address this issue, we quantified the prevalence of publications by deceased authors in the biomedical literature from the period 1990-2020. We screened 2,601,457 peer-reviewed papers from the full text Europe PubMed Central database. We applied natural language processing, stringent filtering and manual curation to identify a final set of 1,439 deceased authors. We then determined these authors published a total of 38,907 papers over their careers with 5,477 published after death. The number of deceased publications has been growing rapidly, a 146-fold increase since the year 2000. This rate of increase was still significant when accounting for the growing total number of publications and pool of authors. We found that more than 50% of deceased author papers were first submitted after the death of the author and that over 60% of these papers failed to acknowledge the deceased authors status. Most deceased authors published less than 10 papers after death but a small pool of 30 authors published significantly more. A pool of 266 authors published more than 90% of their total publications after death. Our analysis indicates that the attribution of deceased authorship in the literature is not an occasional occurrence but a burgeoning trend. A consensus framework to address authorship by deceased scientists is warranted.
    DOI:  https://doi.org/10.1371/journal.pone.0273783
  3. Science. 2022 Sep 16. 377(6612): 1251
      "Matthew effect" is powerful, unusually large study finds.
    DOI:  https://doi.org/10.1126/science.ade8714
  4. Nature. 2022 09;609(7927): 441
      
    Keywords:  Authorship; Publishing; Research data; Research management
    DOI:  https://doi.org/10.1038/d41586-022-02915-1
  5. Wilderness Environ Med. 2022 Sep;pii: S1080-6032(22)00137-5. [Epub ahead of print]33(3): 265-266
      
    DOI:  https://doi.org/10.1016/j.wem.2022.07.006
  6. Cell Rep. 2022 Sep 13. pii: S2211-1247(22)01181-0. [Epub ahead of print]40(11): 111353
      In this Q&A, Cell Press Community Review Product Manager Matt Pavlovich talks to George Burslem, Dan Larson, Susanne Lens, and Victor Greiff about their experience reviewing manuscripts submitted to Community Review. These scientists share their thoughts on Community Review and other emerging peer review paradigms.
    DOI:  https://doi.org/10.1016/j.celrep.2022.111353
  7. eNeuro. 2022 Sep-Oct;9(5):pii: ENEURO.0318-22.2022. [Epub ahead of print]9(5):
      Limited reproducibility and validity are major sources of concern in biology and other fields of science. Their origins have been extensively described and include material variability, incomplete materials and methods report, results selection, defective experimental design, lack of power, inappropriate statistics, overinterpretation, and reluctance to publish negative results. Promoting complete and accurate communication of positive and negative results is a major objective. Multiple steps in this direction are taken, but they are not sufficient and the general construction of articles has not been questioned. I propose here a simple change with a potentially strong positive impact. First, when they complete a substantial coherent set of experiments, scientists deposit their positive or negative results in a database ["deposited results," (DRs)], including detailed materials, methods, raw data, analysis, and processed results. The DRs are technically reviewed and validated as "validated DRs" (vDRs) or rejected until satisfactory. vDR databases are open (after an embargo period if requested by the authors) and can later be updated by them or others with replications or replication failures, providing a comprehensive active log of scientific data. Articles, in this proposal, are then built as they currently are, except they only include vDRs as strong and open building blocks. I argue that this approach would increase the transparency, reproducibility, and reliability of scientific publications and have additional advantages including accurate author credit, better material for evaluation, exhaustive scientific archiving, and increased openness of life science material.
    DOI:  https://doi.org/10.1523/ENEURO.0318-22.2022
  8. J Clin Epidemiol. 2022 Sep 13. pii: S0895-4356(22)00225-6. [Epub ahead of print]
      OBJECTIVE: To examine the prevalence of presumed predatory publications in Cochrane reviews, which are considered the gold standard.STUDY DESIGN AND SETTING: We selected two Cochrane Networks with broad scope: the Musculoskeletal, Oral, Skin and Sensory (MOSS) Network and the Public Health and Health Systems Network. From reviews produced by all Review Groups in those Networks in 2018 and 2019, we extracted included study citations published after 2000. For each citation, we assessed the journal and publisher using an algorithmic process based on characteristics known to be common among predatory publishers. Knowing that predatory status can be fluid and subjective, we scored citations on a spectrum from "reputable" to "presumed predatory" based on publication characteristics available at the time of assessment.
    RESULTS: We extracted 6965 citations from 321 reviews. Of these citations, 5734 were published by entities widely accepted as reputable, leaving 1591 for further assessment. We flagged 55 citations as concerning.
    DISCUSSION: Cochrane reviews across diverse topic areas included studies from flagged publishers, although this number is small. Because of this, there is potential for studies from predatory journals to influence the conclusions of systematic reviews. Researchers should stay aware of this potential threat to the quality of reviews.
    Keywords:  predatory publications; research integrity; systematic reviews as topic
    DOI:  https://doi.org/10.1016/j.jclinepi.2022.09.004
  9. PLoS Biol. 2022 Sep 12. 20(9): e3001783
      Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader's ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template.
    DOI:  https://doi.org/10.1371/journal.pbio.3001783
  10. Front Cardiovasc Med. 2022 ;9 932138
      Scientific fraud represents, to varying degrees, an increasingly important part of medical literature and is estimated to make up nearly 20% of this literature. The increase in the number of articles accessible in preprint without peer review during the COVID-19 pandemic has led to an increase in the accessibility of fraudulent articles. In recent years, the viral increase in the number of predatory journals has contributed to polluting the scientific literature with articles whose content is unverifiable. Given the international nature of biomedical research, there is an urgent need to define unequivocally what is considered scientific fraud. In order to counter scientific misconduct, national and supranational procedures should be implemented to inform researchers at the beginning of their medical and biomedical training. Ethics commissions should implement local procedures for monitoring ongoing research. Finally, the fight against predatory journals requires information for researchers and the availability of tools to identify these journals.
    Keywords:  biomedical research; fraud; plagiarism; predatory journals; scientific misconduct
    DOI:  https://doi.org/10.3389/fcvm.2022.932138
  11. Health Sci Rep. 2022 Sep;5(5): e831
      Background: Pakistan being a low- and middle-income country, its institutes are substantially deficient in scientific and technological aspects and share limited research contributions to the world repositories. Therefore, there is a rising concern to reflect on the history and status of publishing attitudes among medical students in Pakistan and to highlight and address the barriers that they are facing.Methods: A study was conducted aiming to determine the experience, motivation, and attitude of medical students in regarding publishing practices throughout Pakistan in several medical colleges. A multivariable logistic regression model was used to find the independent predictors of students publishing a research article. Forward selection was used to arrive at the final stepwise logistic regression. Odds ratio (OR) and 95% confidence interval (CI) were calculated. p < 0.05 was considered significant for all statistical tests.
    Results: From a sample size of 1225 participants, only 6.6% of students had published an article in our study. Of these, 59% were males and 31.3% were in final year. Males were more likely to publish articles than females (OR = 2.69, 95% CI: 1.37-5.26) and final-year students were more likely to publish articles than first-year students (OR = 7.48, 95% CI: 1.34-41.81). Students that had the knowledge that performing research is the way through which they will be judged for jobs had significantly higher odds of getting an article published (OR = 16.21, 95% CI: 3.65-71.88). Additionally, students who had been taught how to write a paper and those who knew the process of submitting an article were more likely to get published than the others.
    Conclusion: Our study has successfully highlighted the status of publishing among medical students in Pakistan. Our findings serve as an eye opener and call to action for authorities to address the grievances of students in terms of barriers, lack of mentorship, and lack of research teaching. We hope our findings can guide a strong policy change to facilitate the next generation of passionate researchers.
    Keywords:  Pakistan; medical students; publishing practices and barriers
    DOI:  https://doi.org/10.1002/hsr2.831
  12. Biochem Res Int. 2022 ;2022 1492058
      Writing an effective manuscript is one of the pivotal steps in the successful closure of the research project, and getting it published in a peer-reviewed and indexed journal adds to the academic profile of a researcher. Writing and publishing a scientific paper is a tough task that researchers and academicians must endure in staying relevant in the field. Success in translating the benchworks into the scientific content, which is effectively communicated within the scientific field, is used in evaluating the researcher in the current academic world. Writing is a highly time-consuming and skill-oriented process that requires familiarity with the numerous publishing steps, formatting rules, and ethical guidelines currently in vogue in the publishing industry. In this review, we have attempted to include the essential information that novice authors in their early careers need to possess, to be able to write a decent first scientific manuscript ready for submission in the journal of choice. This review is unique in providing essential guidance in a simple point-wise manner in conjunction with easy-to-understand illustrations to familiarize novice researchers with the anatomy of a basic scientific manuscript.
    DOI:  https://doi.org/10.1155/2022/1492058
  13. Cir Esp (Engl Ed). 2022 Sep 10. pii: S2173-5077(22)00361-1. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1016/j.cireng.2022.02.016
  14. Nanoscale Horiz. 2022 Sep 15.
      Nanoscale Horizons is proud to announce our new Emerging Investigator Series that will highlight exceptional work by early-career nanoscience and nanotechnology researchers, selected by our Editorial Board.
    DOI:  https://doi.org/10.1039/d2nh90040h