Archives des mots-clés : biomedical research

Rethinking the Journal Impact Factor and Publishing in the Digital Age

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Authors : Mark S. Nestor, Daniel Fischer, David Arnold, Brian Berman, James Q. Del Rosso

Clinical and experimental literature search has changed significantly over the past few decades, and with it, the way in which we value information. Today, our need for immediate access to relevant and specific literature, regardless of specialty, has led to a growing demand for open access to publications.

The Journal Impact Factor (JIF) has been a long-time standard for representing the quality or “prestige” of a journal, but it appears to be losing its relevance. Here, we define the JIF and deconstruct its validity as a modern measure of a journal’s quality, discuss the current models of academic publication, including their advantages and shortcomings, and discuss the benefits and shortcomings of a variety of open-access models, including costs to the author.

We have quantified a nonsubscribed physician’s access to full articles associated with dermatologic disease and aesthetics cited on PubMed. For some of the most common dermatology conditions, 23.1 percent of citations (ranging from 17.2% for melasma to 31.9% for malignant melanoma) were available as free full articles, and for aesthetic procedures, 18.9 percent of citations (ranging from 11.9% for laser hair removal to 27.9% for botulinum toxin) were available as free full articles.

Finally, we discuss existing alternative metrics for measuring journal impact and propose the adoption of a superior publishing model, one that satisfies modern day standards of scholarly knowledge pursuit and dissemination of scholarly publications for dermatology and all of medical science.

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028381/

Change in Format, Register and Narration Style in the Biomedical Literature: A 1948 Example

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Authors : Carlo Galli, Stefano Guizzardi

Scientific communication has evolved over time and the formats of scientific writing, including its stylistic modules, have changed accordingly.

Research articles from the past fit a research world that had not been taken over by the internet, electronic searches, the new media and even the science mass production of today and reflect a reality where scientific publications were designed to be read and appreciated by actual readers.

It is therefore useful to have a look back to what science looked like in the past and examine the biomedical literature from older archives because several features of those publications may actually harbor vital insights for today’s communication.

Maintaining a vivid awareness of the evolution of science language and modalities of communication may ensure a better and steadfast progression and ameliorate academic writing in the years to come.

With this goal in mind, the present commentary set out to review a 1948 scientific report by I.L. Bennett Jr, entitled “A study on the relationship between the fevers caused by bacterial pyrogens and by the intravenous injection of the sterile exudates of acute inflammation”, which appeared in the Journal of Experimental Medicine in September 1948.

URL : Change in Format, Register and Narration Style in the Biomedical Literature: A 1948 Example

DOI : https://doi.org/10.3390/publications8010010

Transparent, Reproducible, and Open Science Practices of Published Literature in Dermatology Journals: Cross-Sectional Analysis

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Authors : J Michael Anderson, Andrew Niemann, Austin L Johnson, Courtney Cook, Daniel Tritz, Matt Vassar

Background

Reproducible research is a foundational component for scientific advancements, yet little is known regarding the extent of reproducible research within the dermatology literature.

Objective

This study aimed to determine the quality and transparency of the literature in dermatology journals by evaluating for the presence of 8 indicators of reproducible and transparent research practices.

Methods

By implementing a cross-sectional study design, we conducted an advanced search of publications in dermatology journals from the National Library of Medicine catalog. Our search included articles published between January 1, 2014, and December 31, 2018.

After generating a list of eligible dermatology publications, we then searched for full text PDF versions by using Open Access Button, Google Scholar, and PubMed. Publications were analyzed for 8 indicators of reproducibility and transparency—availability of materials, data, analysis scripts, protocol, preregistration, conflict of interest statement, funding statement, and open access—using a pilot-tested Google Form.

Results

After exclusion, 127 studies with empirical data were included in our analysis. Certain indicators were more poorly reported than others. We found that most publications (113, 88.9%) did not provide unmodified, raw data used to make computations, 124 (97.6%) failed to make the complete protocol available, and 126 (99.2%) did not include step-by-step analysis scripts.

Conclusions

Our sample of studies published in dermatology journals do not appear to include sufficient detail to be accurately and successfully reproduced in their entirety. Solutions to increase the quality, reproducibility, and transparency of dermatology research are warranted.

More robust reporting of key methodological details, open data sharing, and stricter standards journals impose on authors regarding disclosure of study materials might help to better the climate of reproducible research in dermatology.

URL : Transparent, Reproducible, and Open Science Practices of Published Literature in Dermatology Journals: Cross-Sectional Analysis

DOI : https://doi.org/10.2196/16078

Determinants of Article Processing Charges for Medical Open Access Journals

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Author : Sumiko Asai

For-profit subscription journal publishers recently have extended their publishing range from subscription journals to numerous open access journals, thereby strengthening their presence in the open access journal market.

This study estimates the article processing charges for 509 medical open access journals using a sample selection model to examine the determinants of the charges.

The results show that publisher type tends to determine whether the journal charges an article processing charge as well as the level of the charge; and frequently cited journals generally set higher article processing charges. Moreover, large subscription journal publishers tend to set higher article processing charges for their open access journals after controlling for other factors.

Therefore, it is necessary to continue monitoring their activities from the viewpoint of competition policy.

DOI : http://dx.doi.org/10.3998/3336451.0022.103

bioRxiv: the preprint server for biology

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Authors : Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, John R. Inglis

The traditional publication process delays dissemination of new research, often by months, sometimes by years. Preprint servers decouple dissemination of research papers from their evaluation and certification by journals, allowing researchers to share work immediately, receive feedback from a much larger audience, and provide evidence of productivity long before formal publication.

Launched in 2013 as a non-profit community service, the bioRxiv server has brought preprint practice to the life sciences and recently posted its 64,000th manuscript.

The server now receives more than four million views per month and hosts papers spanning all areas of biology. Initially dominated by evolutionary biology, genetics/genomics and computational biology, bioRxiv has been increasingly populated by papers in neuroscience, cell and developmental biology, and many other fields.

Changes in journal and funder policies that encourage preprint posting have helped drive adoption, as has the development of bioRxiv technologies that allow authors to transfer papers easily between the server and journals.

A bioRxiv user survey found that 42% of authors post their preprints prior to journal submission whereas 37% post concurrently with journal submission. Authors are motivated by a desire to share work early; they value the feedback they receive, and very rarely experience any negative consequences of preprint posting.

Rapid dissemination via bioRxiv is also encouraging new initiatives that experiment with the peer review process and the development of novel approaches to literature filtering and assessment.

URL : bioRxiv: the preprint server for biology

DOI : https://doi.org/10.1101/833400

Worldwide inequality in access to full textscientific articles: the example ofophthalmology

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Authors : Christophe Boudry, Patricio Alvarez-Muñoz, Ricardo Arencibia-Jorge, Didier Ayena, Niels J. Brouwer, Zia Chaudhuri, Brenda Chawner, Emilienne Epee, Khalil Erraïs, Akbar Fotouhi, Almutez M. Gharaibeh, Dina H. Hassanein, Martina C. Herwig-Carl, Katherine Howard, Dieudonne Kaimbo Wa Kaimbo, Patricia-Ann Laughrea, Fernando A. Lopez, Juan D. Machin-Mastromatteo, Fernando K. Malerbi, Papa Amadou Ndiaye, Nina A. Noor, Josmel Pacheco-Mendoza, Vasilios P. Papastefanou, Mufarriq Shah, Carol L. Shields, Ya Xing Wang, Vasily Yartsev, Frederic Mouriaux

Background

The problem of access to medical information, particularly in low-income countries, has been under discussion for many years. Although a number of developments have occurred in the last decade (e.g., the open access (OA) movement and the website Sci-Hub), everyone agrees that these difficulties still persist very widely, mainly due to the fact that paywalls still limit access to approximately 75% of scholarly documents.

In this study, we compare the accessibility of recent full text articles in the field of ophthalmology in 27 established institutions located worldwide.

Methods

A total of 200 references from articles were retrieved using the PubMed database. Each article was individually checked for OA. Full texts of non-OA (i.e., “paywalled articles”) were examined to determine whether they were available using institutional and Hinari access in each institution studied, using “alternative ways” (i.e., PubMed Central, ResearchGate, Google Scholar, and Online Reprint Request), and using the website Sci-Hub.

Results

The number of full texts of “paywalled articles” available using institutional and Hinari access showed strong heterogeneity, scattered between 0% full texts to 94.8% (mean = 46.8%; SD = 31.5; median = 51.3%).

We found that complementary use of “alternative ways” and Sci-Hub leads to 95.5% of full text “paywalled articles,” and also divides by 14 the average extra costs needed to obtain all full texts on publishers’ websites using pay-per-view.

Conclusions

The scant number of available full text “paywalled articles” in most institutions studied encourages researchers in the field of ophthalmology to use Sci-Hub to search for scientific information.

The scientific community and decision-makers must unite and strengthen their efforts to find solutions to improve access to scientific literature worldwide and avoid an implosion of the scientific publishing model.

This study is not an endorsement for using Sci-Hub. The authors, their institutions, and publishers accept no responsibility on behalf of readers.

URL : Worldwide inequality in access to full textscientific articles: the example ofophthalmology

DOI : https://doi.org/10.7717/peerj.7850

Public Microbial Resource Centers: Key Hubs for Findable,Accessible, Interoperable, and Reusable (FAIR) Microorganismsand Genetic Materials

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Authors : P. Becker, M. Bosschaerts, P. Chaerle, H.-M. Daniel, A. Hellemans, A. Olbrechts, L. Rigouts, A. Wilmotte, M. Hendrickx

In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies.

These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues.

Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized.

This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers.

Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

URL : https://orbi.uliege.be/bitstream/2268/240381/1/Applied%20and%20Environmental%20Microbiology-2019-Becker-e01444-19.full-1.pdf