Étiquette : biomedical research

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Tracking the popularity and outcomes of all bioRxiv preprints

Authors : Richard J. Abdill, Ran Blekhman

Researchers in the life sciences are posting their work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals.

Though the popularity and practical benefits of preprints are driving policy changes at journals and funding organizations, there is little bibliometric data available to measure trends in their usage.

Here, we collected and analyzed data on all 37,648 preprints that were uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find that preprints on bioRxiv are being read more than ever before (1.1 million downloads in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of more than 2,100 per month.

We also find that two-thirds of bioRxiv preprints posted in 2016 or earlier were later published in peer-reviewed journals, and that the majority of published preprints appeared in a journal less than six months after being posted.

We evaluate which journals have published the most preprints, and find that preprints with more downloads are likely to be published in journals with a higher impact factor. Lastly, we developed Rxivist.org, a website for downloading and interacting programmatically with indexed metadata on bioRxiv preprints.

URL : Tracking the popularity and outcomes of all bioRxiv preprints

Alternative location : https://www.biorxiv.org/content/early/2019/01/13/515643

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Open access medical journals: Benefits and challenges

Authors : Jenny Z.Wang, Aunna Pourang, Barbara Burrall

The world of medical science literature is ever increasingly accessible via the Internet. Open access online medical journals, in particular, offer access to a wide variety of useful information at no cost.

In addition, they provide avenues for publishing that are available to health care providers of all levels of training and practice. Whereas costs are less with the publishing of online open access journals, fewer resources for funding and technical support also exist.

A recent rise in predatory journals, which solicit authors but charge high fees per paper published and provide low oversight, pose other challenges to ensuring the credibility of accessible scientific literature.

Recognizing the value and efforts of legitimate open access online medical journals can help the reader navigate the over 11,000 open access journals that are available to date.

DOI : https://doi.org/10.1016/j.clindermatol.2018.09.010

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Biomedical authors’ awareness of publication ethics: an international survey

Authors : Sara Schroter, Jason Roberts, Elizabeth Loder, Donald B Penzien, Sarah Mahadeo, Timothy T Houle

Objective

The extent to which biomedical authors have received training in publication ethics, and their attitudes and opinions about the ethical aspects of specific behaviours, have been understudied. We sought to characterise the knowledge and attitudes of biomedical authors about common issues in publication ethics.

Design

Cross-sectional online survey.

Setting and participants

Corresponding authors of research submissions to 20 journals.

Main outcome measure(s)

Perceived level of unethical behaviour (rated 0 to 10) presented in five vignettes containing key variables that were experimentally manipulated on entry to the survey and perceived level of knowledge of seven ethical topics related to publishing (prior publication, author omission, self-plagiarism, honorary authorship, conflicts of interest, image manipulation and plagiarism).

Results

4043/10 582 (38%) researchers responded. Respondents worked in 100 countries and reported varying levels of publishing experience. 67% (n=2700) had received some publication ethics training from a mentor, 41% (n=1677) a partial course, 28% (n=1130) a full course and 55% (n=2206) an online course; only a small proportion rated training received as excellent.

There was a full range (0 to 10 points) in ratings of the extent of unethical behaviour within each vignette, illustrating a broad range of opinion about the ethical acceptability of the behaviours evaluated, but these opinions were little altered by the context in which it occurred.

Participants reported substantial variability in their perceived knowledge of seven publication ethics topics; one-third perceived their knowledge to be less than ‘some knowledge’ for the sum of the seven ethical topics and only 9% perceived ‘substantial knowledge’ of all topics.

Conclusions

We found a large degree of variability in espoused training and perceived knowledge, and variability in views about how ethical or unethical scenarios were. Ethical standards need to be better articulated and taught to improve consistency of training across institutions and countries.

URL : Biomedical authors’ awareness of publication ethics: an international survey

DOI : http://dx.doi.org/10.1136/bmjopen-2017-021282

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On the value of preprints: an early career researcher perspective

Authors : Sarvenaz Sarabipour​, Humberto J Debat, Edward Emmott, Steven Burgess, Benjamin Schwessinger, Zach Hensel

Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent, public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value.

The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision and resubmission causing redundant peer review.

This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. ECRs face changes in the academic landscape including the increased interdisciplinarity of life sciences research, expansion of the researcher population and consequent shifts in employer and funding demands.

The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal managed peer-review, can play a key role in addressing these ECR challenges.

Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback and facilitating collaborations. While there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted.

The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting needs to be addressed.

We provide a perspective from an interdisciplinary group of early career researchers on the value of preprints and advocate the wide adoption of preprints to advance knowledge and facilitate career development.

URL : On the value of preprints: an early career researcher perspective

DOI : https://doi.org/10.7287/peerj.preprints.27400v1

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Returning Individual Research Results to Participants

Authors : National Academies of Sciences, Engineering, and Medicine; Health and Medicine Division; Board on Health Sciences Policy; Committee on the Return of Individual-Specific Research Results Generated in Research Laboratories. Editors: Autumn S. Downey, Emily R. Busta, Michelle Mancher, and Jeffrey R. Botkin

When is it appropriate to return individual research results to participants? The immense interest in this question has been fostered by the growing movement toward greater transparency and participant engagement in the research enterprise.

Yet, the risks of returning individual research results—such as results with unknown validity—and the associated burdens on the research enterprise are competing considerations.

Returning Individual Research Results to Participants reviews the current evidence on the benefits, harms, and costs of returning individual research results, while also considering the ethical, social, operational, and regulatory aspects of the practice.

This report includes 12 recommendations directed to various stakeholders—investigators, sponsors, research institutions, institutional review boards (IRBs), regulators, and participants—and are designed to help (1) support decision making regarding the return of results on a study-by-study basis, (2) promote high-quality individual research results, (3) foster participant understanding of individual research results, and (4) revise and harmonize current regulations.

URL : https://www.ncbi.nlm.nih.gov/books/NBK513173/

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Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

Authors : Joshua D. Wallach, Kevin W. Boyack, John P. A. Ioannidis

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions.

Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks.

We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]).

Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]).

Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed.

Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

URL : Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

DOI : https://doi.org/10.1371/journal.pbio.2006930

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Sharing health research data – the role of funders in improving the impact

Authors : Robert F. Terry, Katherine Littler, Piero L. Olliaro

Recent public health emergencies with outbreaks of influenza, Ebola and Zika revealed that the mechanisms for sharing research data are neither being used, or adequate for the purpose, particularly where data needs to be shared rapidly.

A review of research papers, including completed clinical trials related to priority pathogens, found only 31% (98 out of 319 published papers, excluding case studies) provided access to all the data underlying the paper – 65% of these papers give no information on how to find or access the data.

Only two clinical trials out of 58 on interventions for WHO priority pathogens provided any link in their registry entry to the background data.

Interviews with researchers revealed a reluctance to share data included a lack of confidence in the utility of the data; an absence of academic-incentives for rapid dissemination that prevents subsequent publication and a disconnect between those who are collecting the data and those who wish to use it quickly.

The role of the funders of research needs to change to address this. Funders need to engage early with the researchers and related stakeholders to understand their concerns and work harder to define the more explicitly the benefits to all stakeholders.

Secondly, there needs to be a direct benefit to sharing data that is directly relevant to those people that collect and curate the data.

Thirdly more work needs to be done to realise the intent of making data sharing resources more equitable, ethical and efficient.

Finally, a checklist of the issues that need to be addressed when designing new or revising existing data sharing resources should be created. This checklist would highlight the technical, cultural and ethical issues that need to be considered and point to examples of emerging good practice that can be used to address them.

URL : Sharing health research data – the role of funders in improving the impact

DOI : http://dx.doi.org/10.12688/f1000research.16523.1