bims-skolko Biomed News
on Scholarly communication
Issue of 2020‒08‒30
twenty-five papers selected by
Thomas Krichel
Open Library Society


  1. J Card Fail. 2020 Aug;pii: S1071-9164(20)30878-2. [Epub ahead of print]26(8): 643-644
    Buttrick P.
      
    DOI:  https://doi.org/10.1016/j.cardfail.2020.07.007
  2. Br J Dermatol. 2020 Aug 28.
    Finlay AY.
      By reading an academic journal, you are already at high-risk of publishing addiction (PA). So read on and see if you have it. PA is proposed as a previously unreported behavioural addiction. Gambling, excessive smartphone use and unrestrained shopping are other behavioural "addictions".1,2 Although widespread, PA is masked by its normalisation within academia, as alcoholism may be accepted in a brewery. PA can greatly impact the lives of those in its grip.
    DOI:  https://doi.org/10.1111/bjd.19500
  3. BMC Med Res Methodol. 2020 Aug 25. 20(1): 213
    Tawfik GM, Giang HTN, Ghozy S, Altibi AM, Kandil H, Le HH, Eid PS, Radwan I, Makram OM, Hien TTT, Sherif M, Hossain AS, Thang TLL, Puljak L, Salem H, Numair T, Moji K, Huy NT.
      BACKGROUND: Although protocol registration of systematic reviews/meta-analysis (SR/MA) is still not mandatory, it is highly recommended that authors publish their SR/MA protocols prior to submitting their manuscripts for publication as recommended by the Cochrane guidelines for conducting SR/MAs. our aim was to assess the awareness, obstacles, and opinions of SR/MA authors about the protocol registration process.METHODS: A cross-sectional survey study included the authors who published SR/MAs during the period from 2010 to 2016, and they were contacted for participation in our survey study. They were identified through the literature search of SR/MAs in Scopus database. An online questionnaire was sent to each participant via e-mail after receiving their approval to join the study. We have sent 6650 emails and received 275 responses.
    RESULTS: A total of 270 authors responses were complete and included in the final analysis. Our results has shown that PROSPERO was the most common database used for protocol registration (71.3%). The registration-to-acceptance time interval in PROSPERO was less than 1 month (99.1%). Almost half of the authors (44.2%) did not register their protocols prior to publishing their SR/MAs and according to their opinion that the other authors lack knowledge of protocol importance and mandance to be registered, was the most commonly reported reason (44.9%). A significant percenatge of respondents (37.4%) believed that people would steal their ideas from protocol databases, while only 5.3% reported that their SR/MA had been stolen. However, the majority (72.9%) of participants have agreed that protocol registries play a role in preventing unnecessary duplication of reviews. Finally, 37.4% of participants agree that SR/MA protocol registration should be mandatory.
    CONCLUSION: About half of the participants believes that the main reason for not registering protocols, is that the other authors lack knowledge concerning obligation and importance to register the SR/MA protocols in advance. Therefore, tools should be available to mandate protocol registration of any SRs beforehand and increasing awareness about the benefits of protocol registration among researchers.
    Keywords:  Duplication; Idea theft; Meta-analysis; PROSPERO; Registration; Systematic review
    DOI:  https://doi.org/10.1186/s12874-020-01094-9
  4. Can J Ophthalmol. 2020 Aug 22. pii: S0008-4182(20)30684-0. [Epub ahead of print]
    Nyamai LA, Jin YP, Mathew DJ, Dharia RS, Trope GE, Buys YM.
      OBJECTIVE: To determine the proportion of indexed ophthalmology journals with article processing charges (APCs) and potential factors associated with APCs.DESIGN: Cross-sectional study.
    PARTICIPANTS: Web of Science-indexed Ophthalmology journals in 2019.
    METHODS: Indexed ophthalmology journal web sites were reviewed to obtain information on APCs, impact factor (IF), publication mode, publisher type, journal affiliation, waiver discount, and continent of origin. For data unavailable on the web site, the journal was contacted. Journal publication mode was categorized into subscription, fully open access, and hybrid (open access and subscription combined). Linear regression analysis was used to evaluate the association between APCs and the above variables.
    MAIN OUTCOME MEASURE: Proportion of ophthalmology journals with APCs.
    RESULTS: 59 indexed ophthalmology journals were identified; 3 (5.1%) subscription only, 10 (16.9%) open access, and 46 (78.0%) hybrid. Overall 52/59 (88.1%) journals had APCs; 10 of 59 journals (16.9%) required APCs for publication (7 fully open access and 3 hybrid journals), whereas 42/59 (71.2%, all hybrid journals) had optional APCs for open access. The 7/59 journals (11.9%) without APCs included 100% (3/3) of the subscription-only journals, 30% (3/10) of the open access, and 2% (1/46) of the hybrid journals. The mean cost for journals with APCs was US$2854 ± 708.9 (range US$490-5000). Higher IF, publication mode, and commercial publishers were associated with higher APCs.
    CONCLUSIONS: 16.9% of indexed ophthalmology journals in 2019 required APCs, and additional 71.2% hybrid journals had APCs for the option of open access. Independent predictors of APCs were IF and publication mode.
    DOI:  https://doi.org/10.1016/j.jcjo.2020.06.023
  5. Med Oncol. 2020 Aug 24. 37(10): 86
    Tanriverdi O, Ozcan M.
      The COVID-19 pandemic is a kind of global disaster caused by the new coronavirus-19, the SARS-CoV-2 virus. Since the first eruption of this pandemic, which adversely affected the world in many ways, a large number of publications have been presented to the world of science. In this article, possible publication ethical dilemmas related to scientific articles increasing in number during the COVID-19 pandemic were tried to be reminded through two examples of articles.
    Keywords:  COVID-19 pandemic; Publishing ethics; SARS-Cov-2; Scientific articles
    DOI:  https://doi.org/10.1007/s12032-020-01411-8
  6. Open Forum Infect Dis. 2020 Aug;7(8): ofaa304
    Spec A, Schwartz IS.
      Knowledge dissemination during COVID19 has been notable for the rise of pre-prints and publication by press release, favoring speed over accuracy. We stress the importance of journals in this landscape and highlight the value of editorial judgment and peer review.
    Keywords:  COVID-19; evidence-based medicine; methodology; peer-review; publishing
    DOI:  https://doi.org/10.1093/ofid/ofaa304
  7. J Bioeth Inq. 2020 Aug 25.
    Lipworth W, Gentgall M, Kerridge I, Stewart C.
      In response to the COVID-19 pandemic, there has been a rapid growth in research focused on developing vaccines and therapies. In this context, the need for speed is taken for granted, and the scientific process has adapted to accommodate this. On the surface, attempts to speed up the research enterprise appear to be a good thing. It is, however, important to consider what, if anything, might be lost when biomedical innovation is sped up. In this article we use the case of a study recently retracted from the Lancet to illustrate the potential risks and harms associated with speeding up science. We then argue that, with appropriate governance mechanisms in place (and adequately resourced), it should be quite possible to both speed up science and remain attentive to scientific quality and integrity.
    Keywords:  Biomedical publication; COVID-19; Pandemic; Research governance; Research integrity; Research quality
    DOI:  https://doi.org/10.1007/s11673-020-10013-y
  8. Scientometrics. 2020 Jul 01. 1-25
    Belli S, Mugnaini R, Baltà J, Abadal E.
      The COVID-19 pandemic is creating a global health emergency. Mapping this health emergency in scientific publications demands multiple approaches to obtain a picture as complete as possible. To progress in the knowledge of this pandemic and to control its effects, international collaborations between researchers are essentials, as well as having open and immediate access to scientific publications, what we called "coopetition". Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. We have analyzed 18,875 articles indexed in Web of Science. We performed the descriptive statistical analysis in order to explore the performance of the more prolific countries and organizations, as well as paying attention to the last 2 years. Registers have been analyzed separately via the VOSviewer software, drawing a network of links among countries and organizations to identify the starred countries and organizations, and the strongest links of the net. We have explored the capacity of researchers to generate scientific knowledge about a health crisis emergency, and their global capacity to collaborate among them in a global emergency. We consider that science is moving rapidly to find solutions to international health problems but access to this knowledge by society is not so quick due to several limitations (open access policies, corporate interests, etc.). We have observed that papers from China in the last 3 months (from January 2020 to March 2020) have a strong impact compared with papers published in years before. The United States and China are the major producers of documents of our sample, followed by all European countries, especially the United Kingdom, Germany, the Netherlands, and France. At the same time, the leading role of Saudi Arabia, Canada or South Korea should be noted, with a significant number of documents submitted but very different dynamics of international collaboration. The proportion of international collaboration is growing in all countries in 2019-2020, which contrasts with the situation of the last two decades. The organizations providing the most documents to the sample are mostly Chinese. The percentage of open access articles on coronavirus for the period 2001-2020 is 59.2% but if we focus in 2020 the figures increase up to 91.4%, due to the commitment of commercial publishers with the emergency.
    Keywords:  2019-nCoV; Bibliometric analysis; COVID-19; Coronavirus; Open access; SARS-CoV-2; Scientific collaborations
    DOI:  https://doi.org/10.1007/s11192-020-03590-7
  9. Scientometrics. 2020 Jul 24. 1-18
    Di Girolamo N, Meursinge Reynders R.
      The COVID-19 pandemic has been characterized by an unprecedented amount of published scientific articles. The aim of this study is to assess the type of articles published during the first 3 months of the COVID-19 pandemic and to compare them with articles published during 2009 H1N1 swine influenza pandemic. Two operators independently extracted and assessed all articles on COVID-19 and on H1N1 swine influenza that had an abstract and were indexed in PubMed during the first 3 months of these pandemics. Of the 2482 articles retrieved on COVID-19, 1165 were included. Over half of them were secondary articles (590, 50.6%). Common primary articles were: human medical research (340, 59.1%), in silico studies (182, 31.7%) and in vitro studies (26, 4.5%). Of the human medical research, the vast majority were observational studies and cases series, followed by single case reports and one randomized controlled trial. Secondary articles were mainly reviews, viewpoints and editorials (373, 63.2%). Limitations were reported in 42 out of 1165 abstracts (3.6%), with 10 abstracts reporting actual methodological limitations. In a similar timeframe, there were 223 articles published on the H1N1 pandemic in 2009. During the COVID-19 pandemic there was a higher prevalence of reviews and guidance articles and a lower prevalence of in vitro and animal research studies compared with the H1N1 pandemic. In conclusions, compared to the H1N1 pandemic, the majority of early publications on COVID-19 does not provide new information, possibly diluting the original data published on this disease and consequently slowing down the development of a valid knowledge base on this disease. Also, only a negligible number of published articles reports limitations in the abstracts, hindering a rapid interpretation of their shortcomings. Researchers, peer reviewers, and editors should take action to flatten the curve of secondary articles.
    Keywords:  Coronavirus; Covid-19; Healthcare policy; Research quality; SARS-nCoV-2; Study design
    DOI:  https://doi.org/10.1007/s11192-020-03632-0
  10. Scientometrics. 2020 Jun 25. 1-15
    Homolak J, Kodvanj I, Virag D.
      The Pandemic of COVID-19, an infectious disease caused by SARS-CoV-2 motivated the scientific community to work together in order to gather, organize, process and distribute data on the novel biomedical hazard. Here, we analyzed how the scientific community responded to this challenge by quantifying distribution and availability patterns of the academic information related to COVID-19. The aim of this study was to assess the quality of the information flow and scientific collaboration, two factors we believe to be critical for finding new solutions for the ongoing pandemic. The RISmed R package, and a custom Python script were used to fetch metadata on articles indexed in PubMed and published on Rxiv preprint server. Scopus was manually searched and the metadata was exported in BibTex file. Publication rate and publication status, affiliation and author count per article, and submission-to-publication time were analysed in R. Biblioshiny application was used to create a world collaboration map. Preliminary data suggest that COVID-19 pandemic resulted in generation of a large amount of scientific data, and demonstrates potential problems regarding the information velocity, availability, and scientific collaboration in the early stages of the pandemic. More specifically, the results indicate precarious overload of the standard publication systems, significant problems with data availability and apparent deficient collaboration. In conclusion, we believe the scientific community could have used the data more efficiently in order to create proper foundations for finding new solutions for the COVID-19 pandemic. Moreover, we believe we can learn from this on the go and adopt open science principles and a more mindful approach to COVID-19-related data to accelerate the discovery of more efficient solutions. We take this opportunity to invite our colleagues to contribute to this global scientific collaboration by publishing their findings with maximal transparency.
    Keywords:  Bibliometric; COVID-19; Data; Open science; Pandemic
    DOI:  https://doi.org/10.1007/s11192-020-03587-2
  11. Learn Publ. 2020 Jul 01.
    Helliwell JA, Bolton WS, Burke JR, Tiernan JP, Jayne DG, Chapman SJ.
      This study explores the response to COVID-19 from investigators, editors, and publishers and seeks to define challenges during the early stages of the pandemic. A cross-sectional bibliometric review of COVID-19 literature was undertaken between 1 November 2019 and 24 March 2020, along with a comparative review of Middle East respiratory syndrome (MERS) literature. Investigator responsiveness was assessed by measuring the volume and type of research published. Editorial responsiveness was assessed by measuring the submission-to-acceptance time and availability of original data. Publisher-responsiveness was assessed by measuring the acceptance-to-publication time and the provision of open access. Three hundred and ninety-eight of 2,835 COVID-19 and 55 of 1,513 MERS search results were eligible. Most COVID-19 studies were clinical reports (n = 242; 60.8%). The submission-to-acceptance [median: 5 days (IQR: 3-11) versus 71.5 days (38-106); P < .001] and acceptance-to-publication [median: 5 days (IQR: 2-8) versus 22.5 days (4-48·5-; P < .001] times were strikingly shorter for COVID-19. Almost all COVID-19 (n = 396; 99.5%) and MERS (n = 55; 100%) studies were open-access. Data sharing was infrequent, with original data available for 104 (26.1%) COVID-19 and 10 (18.2%) MERS studies (P = .203). The early academic response was characterized by investigators aiming to define the disease. Studies were made rapidly and openly available. Only one-in-four were published alongside original data, which is a key target for improvement.
    Keywords:  SARS‐CoV‐2; coronavirus; data sharing; dissemination; open‐access
    DOI:  https://doi.org/10.1002/leap.1317
  12. Med Humanit. 2020 Sep;46(3): 161
    Schillace B.
      
    Keywords:  medical humanities
    DOI:  https://doi.org/10.1136/medhum-2020-012026
  13. F1000Res. 2020;9:9 649
    Arrizabalaga O, Otaegui D, Vergara I, Arrizabalaga J, Méndez E.
      Background: The COVID-19 outbreak has made funders, researchers and publishers agree to have research publications, as well as other research outputs, such as data, become openly available. In this extraordinary research context of the SARS CoV-2 pandemic, publishers are announcing that their coronavirus-related articles will be made immediately accessible in appropriate open repositories, like PubMed Central, agreeing upon funders' and researchers' instigation. Methods: This work uses Unpaywall, OpenRefine and PubMed to analyse the level of openness of articles about COVID-19, published during the first quarter of 2020. It also analyses Open Access (OA) articles published about previous coronavirus (SARS CoV-1 and MERS CoV) as a means of comparison. Results: A total of 5,611 COVID-19-related articles were analysed from PubMed. This is a much higher amount for a period of 4 months compared to those found for SARS CoV-1 and MERS during the first year of their first outbreaks (335 and 116 articles, respectively).  Regarding the levels of openness, 88.8% of the SARS CoV-2 papers are freely available; similar rates were found for the other coronaviruses. Deeper analysis showed that (i) 67.4% of articles belong to an undefined Bronze category; (ii) 76.4% of all OA papers don't carry any license, followed by 10.4% which display restricted licensing. These patterns were found to be repeated in the three most frequent publishers: Elsevier, Springer and Wiley. Conclusions: Our results suggest that, although scientific production is much higher than during previous epidemics and is open, there is a caveat to this opening, characterized by the absence of fundamental elements and values ​​on which Open Science is based, such as licensing.
    Keywords:  COVID-19; OA analysis.; Open Access; Pandemic; PubMed; Publishing; Scholarly communication
    DOI:  https://doi.org/10.12688/f1000research.24136.1
  14. J Vasc Surg. 2020 Sep;pii: S0741-5214(20)31083-1. [Epub ahead of print]72(3): 775-776
    Gloviczki P, Lawrence PF.
      
    DOI:  https://doi.org/10.1016/j.jvs.2020.03.054
  15. Indian Dermatol Online J. 2020 Jul-Aug;11(4):11(4): 653-654
    Kumar R, Bhoil R, Bhoil R.
      
    DOI:  https://doi.org/10.4103/idoj.IDOJ_479_19
  16. Acta Neurochir (Wien). 2020 Aug 26.
    Deora H, Tripathi M, Chaurasia B, Grotenhuis JA.
      BACKGROUND: Scientific research can offer the joy of discovery. For many graduating neurosurgeons, often, a seminar, class, or instructional module is their first and only formal exposure to the world of conducting research responsibly, to write down and report the results of such research. The pressure to publish scientific research is high, but any young neurosurgeon who is unaware of how predatory publishers operate can get duped by it and can lose their valuable and hard-fought research. Hence, we have attempted to provide an overview of all potentially predatory neurosurgery publications and provide some "red flags" to recognize them.METHODS: A suspected list of predatory publications was collected via a thorough review of the Neurosurgery journals listed in 4 major so-called blacklists, i.e., Beall's list, Manca's list, Cabell's blacklist, and Strinzel blacklist and then cross-referenced with UGC CARE whitelist to remove any potential legitimate journals. All journals with a scope of the Neurosurgery publication were searched using terms in the search bar: "Neurosurgery", "Neuroanatomy", "Neuropathology", and "Neurological disorder/disease". Since all predatory journals claim to be open access, all possible types of open access journals on Scimago were also searched, and thus a comparison was possible in terms of publication cost and number of legitimate open access journals when compared with predatory ones. In addition, methodologies by which these journals penetrate legitimate indexes like PubMed was investigated.
    RESULTS: A total of 46 predatory journals were found and were enlisted along with their publishers and web addresses. Sixty of the 360 Neurosurgery journals listed on Scimago were open access and the fee for the predatory journals was substantially lower (< $150) when compared with legitimate journals ($900-$3000). Six types of open access types exist while a total of 26 red flags in 7 stages of publication can be found in predatory journals. These journals have penetrated indexes by having similar names to legitimate journals and by publishing articles with external funding which mandate their indexing.
    CONCLUSION: These 46 journals were defined as predatory by 4 major blacklists, and none of them was found in the UGC Care white list. They also fulfill the 26 red-flags that define a predatory journal. The blacklist detailed here may become redundant; hence "whenever in doubt" regarding a journal with "red-flags", the authors are advised to refer to whitelists to be on the safer side. Publishing in predatory journals leads to not only loss of valuable research but also discredits a researcher among his peers and can be hindrance in career progression. Some journals are even indexed on PubMed, and they have sophisticated webpages and high-quality online presentations.
    Keywords:  Academic neurosurgery; Neurosurgeon; Neurosurgery; Predatory journals
    DOI:  https://doi.org/10.1007/s00701-020-04546-9
  17. Int J Sports Physiol Perform. 2020 Sep 01. pii: ijspp.2020-0656. [Epub ahead of print]15(8): 1057-1058
    Buchheit M.
      
    DOI:  https://doi.org/10.1123/ijspp.2020-0656
  18. Surg Radiol Anat. 2020 Aug 26.
    Crampon F, Prum G, Trost O, Grignon B, Duparc F.
      INTRODUCTION: Our goal was to study the influence of the author's compliance with the Instructions for Authors for a submitted manuscript to a journal, on the final outcome of the submission.MATERIAL AND METHODS: 1200 consecutive submissions to the journal Surgical and Radiologic Anatomy have been evaluated and divided into four groups: A: Accepted, R: Rejected, I + : Instructions for Authors followed, I - : Instructions for Authors not followed. The quantity of manuscripts in the groups was measured and compared through statistical tests. We tried to determine if a specific category of authors was more likely to incorrectly follow the Instructions for Authors by verifying the lists of authors and the tables of contributions of co-authors. 322 (26.83%) manuscripts were accepted, 248 were I + , 74 were I - ; 878 (73.16%) were rejected, 526 were I + ; 352 were I - .
    RESULTS: The comparisons of the observed values and percentages showed significant differences between the groups. We could not identify a specific type of author associated with non-compliance with the Instructions for Authors.
    CONCLUSION: Most of the guidelines that have been published concern the preparation of the scientific contents of the manuscript (How to write), but the submission process (How to submit) has rarely been explained. We suggest including the rules of submitting a manuscript in graduate and post-graduate medical education.
    Keywords:  Guidelines for submitting; Instructions for authors; Medical education; Scientific publication
    DOI:  https://doi.org/10.1007/s00276-020-02561-0
  19. J Biomol Tech. 2020 Aug;31(Suppl): S40
    Searle B, Weintraub S.
      Most journals that publish proteomics data require raw data deposition. In addition to allowing reviewers and community members to validate findings in publications, knowledge captured in proteomics data resources can enable evidence synthesis across studies, speed assay development, and improve downstream bioinformatics tools. In this session we will present a variety of proteomics data resources and how to use them. We will show examples of proteomics data and open source code reuse for both new bioinformatics data interpretations and to guide future proteomics experiments. We will also present methods to build online lab notebooks that illustrate exploratory data analysis for proteomics experiments and take researchers from raw data and data tables to publishable figures.