Category Archives: oa.medicine

Interventions in scholarly communication: Design lessons from public health | First Monday

Posted on by
Reply

Abstract:  Many argue that swift and fundamental interventions in the system of scholarly communication are needed. However, there are substantial disagreements over the short- and long-term benefits of most proposed approaches to changing the practice of science communication, and the lack of systematic, empirically based research in this area makes these controversies difficult to resolve. We argue that experience within public health can be usefully applied to scholarly communication. Starting with the history of DDT (Dichlorodiphenyltrichloroethane) application, we illustrate four ways complex human systems threaten reliable predictions and blunt ad-hoc interventions. We then show how these apply to interventions in scholarly publication – open access based on the article processing charge (APC), and preprints – to yield surprising results. Finally, we offer approaches to help guide the design of future interventions: identifying measures and outcomes, developing infrastructure, incorporating assessment, and contributing to theories of systemic change.

Health Policy and Planning’s transition to Open Access: moving into the future | Health Policy and Planning | Oxford Academic

Posted on by
Reply

“From 2024, Health Policy and Planning (HPP) will become a fully Open Access journal, in line with the overall trend in the publishing landscape.

A few decades ago, almost all journals were based on subscriptions, paid by libraries, universities and research institutes. More recently, we have seen strong growth in Open Access journals, where the cost of publishing is covered by authors, their funders or employing organizations.

At HPP, we have demonstrated our commitment to transitioning to a fully Open Access journal by gradually increasing our Open Access content in line with growth targets set by cOAlition S. This final step completes our transformative commitment to Open Access.

This change has no impact on the journal’s editorial policy, standards or processes.”

Analytical code sharing practices in biomedical research | bioRxiv

Posted on by
Reply

Abstract:  Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10?9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10?07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

 

[2308.07333] Computational reproducibility of Jupyter notebooks from biomedical publications

Posted on by
Reply

Abstract:  Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

BJA Open: a new open access journal for anaesthesiology, critical care, and pain medicine – BJA Open

Posted on by
Reply

“BJA Open is a new open access journal to complement British Journal of Anaesthesia. This editorial describes the rationale for the journal and the breadth of content it is seeking to attract. As with other BJA titles, BJA Open conforms to the highest standards of editorial and publication practice, and it aims to provide sector-leading author experience combined with reliable peer-reviewed content for the reader.”

 

Pandemia trouxe oportunidades para mais inclusão na ciência | RDBCI: Revista Digital de Biblioteconomia e Ciência da Informação

Posted on by
Reply

From Google’s English:  Abstract:  Introduction: The Covid-19 pandemic produced a large volume of scientific data and encouraged open science practices due to data sharing for the control of the Sars-CoV-2 virus. This scenario generated opportunities for the Open Science (AC) movement. Objective: The purpose of this article is to map the circulating narratives about AC practices during the pandemic – with emphasis on debates on public access to knowledge and practices and values ??characteristic of Equity, Diversity and Inclusion (EDI). Methodology:A documental and thematic analysis of 30 scientific articles, news in the press, blog posts and institutional materials published in Portuguese was carried out, obtained by searching for keywords in SciELO, Google and libraries of the Chamber and Senate. Results: It was observed that 36.6% (11) of the documents mentioned EDI values, while 70% (21) included discussions about public and universal access to knowledge. The texts could present both themes, being counted both in the EDI and public access categories. Of the sample, 23% (7) did not mention either of these two categories and 77% presented at least one of them. Conclusion:In general, the use of open science has been associated with the rapid production of responses to the pandemic, which raises questions about the continuity of open practices in periods when this urgency is not present. As for the debate on EDI, although still incipient, the pandemic presents opportunities for more inclusive knowledge co-production and practices — with real-time public debate experiences of building evidence.

The experiences of COVID-19 preprint authors: a survey of researchers about publishing and receiving feedback on their work during the pandemic [PeerJ]

Posted on by
Reply

Abstract:  The COVID-19 pandemic caused a rise in preprinting, triggered by the need for open and rapid dissemination of research outputs. We surveyed authors of COVID-19 preprints to learn about their experiences with preprinting their work and also with publishing their work in a peer-reviewed journal. Our research had the following objectives: 1. to learn about authors’ experiences with preprinting, their motivations, and future intentions; 2. to consider preprints in terms of their effectiveness in enabling authors to receive feedback on their work; 3. to compare the impact of feedback on preprints with the impact of comments of editors and reviewers on papers submitted to journals. In our survey, 78% of the new adopters of preprinting reported the intention to also preprint their future work. The boost in preprinting may therefore have a structural effect that will last after the pandemic, although future developments will also depend on other factors, including the broader growth in the adoption of open science practices. A total of 53% of the respondents reported that they had received feedback on their preprints. However, more than half of the feedback was received through “closed” channels–privately to the authors. This means that preprinting was a useful way to receive feedback on research, but the value of feedback could be increased further by facilitating and promoting “open” channels for preprint feedback. Almost a quarter of the feedback received by respondents consisted of detailed comments, showing the potential of preprint feedback to provide valuable comments on research. Respondents also reported that, compared to preprint feedback, journal peer review was more likely to lead to major changes to their work, suggesting that journal peer review provides significant added value compared to feedback received on preprints.

 

From biorepositories to data repositories: Open-access resources accelerate early R&D and validation of equitable diagnostic tools | PLOS Global Public Health

Posted on by
Reply

Abstract:  Diagnostics are critical tools that guide clinical decision-making for patient care and support disease surveillance. Despite its importance, developers and manufacturers often note that access to specimen panels and essential reagents is one of the key challenges in developing quality diagnostics, particularly in low-resource settings. A recent example, as the COVID-19 pandemic unfolded there was a need for clinical samples across the globe to support the rapid development of diagnostics. To address these challenges and gaps, PATH, a global nonprofit, along with its partners collaborated to create a COVID-19 biorepository to improve access to biological samples. Since then, the need for data resources to advance universal rapid diagnostic test (RDT) readers and noninvasive clinical measurement tools for screening children have also been identified and initiated. From biospecimens to data files, there are more similarities than differences in creating open-access repositories. And to ensure equitable technologies are developed, diverse sample panels and datasets are critical in the development process. Here we share one experience in creating open-access repositories as a case study to describe the steps taken, the key factors required to establish a biorepository, the ethical and legal frameworks that guided the initiative and the lessons learned. As diagnostic tools are evolving, more forms of data are critical to de-risk and accelerate early research and development (R&D) for products serving low resource settings. Creating physical and virtual repositories of freely available, well characterized, and high quality clinical and electronic data resources defray development costs to improve equitable access and test affordability.

 

Opening scientific knowledge to debunk myths and lies in human nutrition | SpringerLink

Posted on by
Reply

“However, if OA papers are free of charge and easily available online to everyone, their readability is overly complicated for a wider public due to the usage of both general scientific and technical jargon in writing academic studies [8, 9]. In recent years, following the so-called “Third Mission” (TM), universities and other institutions have started to disseminate scientific results in formats more suitable for the general public….”

What do eels teach about open access, medical education and professional ethics? The inception of Peripheral Nerve Stimulation in ancient Rome – Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation

Posted on by
Reply

“In conclusion, Largus offers a dual lesson for the 21st century. In an era when knowledge is often gated behind paywalls, Largus’s Compositiones underscore the importance of providing less privileged healthcare professionals with open access to evidence-based resources. Although the concept of open access is relatively new in medical scholarship and to our knowledge there is no concrete proof of a relevant discourse, the fact the he used colloquial language was already a breakthrough in this regard….”

Enter Preprint Servers: Is Peer Review Obsolete? – Structural Heart

Posted on by
Reply

“In aggregate, existing limitations coupled with the availability of alternate information sources has again raised the question of the value and relevance of medical journals. As any editor clearly knows, and as delineated above, medical journals have many imperfections. However, passing the crucible of peer review is the best assurance that new information is valid and may be actionable. So, like democracy, peer review journals may be imperfect, but they are the best alternative available. While providing some advantages, preprint servers and other sources for new investigative results all have significant limitations as well. They are perhaps most valuable in defining the areas in which current medical journals need to improve. In my view, the alternate sources of medical information will remain an important supplement to journals. However, they will never replace them. Since its initiation, peer review has survived for 360 years. It continues to be the most accurate and reliable method to assess new research findings, and surely will not become obsolete in the foreseeable future.”

 

Academicians’ awareness, attitude, and use of open access during the COVID-19 pandemic – Yigit Emrah Turgut, Alper Aslan, Nuran Varl? Denizalp, 2022

Posted on by
Reply

Abstract:  The aim of this research is to reveal academics’ awareness, attitude, and use of open access. In line with the research purpose, the survey research design is adopted. This research consists 151 academics from 12 basic research areas; eight of them being Professor Dr, 17 being Associate Professor Dr, 49 being Doctor Lecturer, and 77 being Research Assistant or Lecturer. A questionnaire consisting of 19 open access and five demographic information questions was used for the data collection tool. The research results show that 75% of the academics have open access awareness and that their awareness is generally created by information that they obtain through the Internet and their friends. In addition, most of the academics indicate that their awareness of open access has increased during the pandemic period. When considering the level of academics’ use of open access, it is found that 75% of the academics use articles in open access journals for their own research and 51% of the academics do not publish any articles in open access journals.

 

In pursuit of trusted information: the trials and tribulations of public access – Open Pharma – Innovations in medical publishing

Posted on by
Reply

“The concept of public, barrier-free access to research findings emerged at the turn of the century. At that time, the academic publishing landscape was dominated by subscription-based journals. Initially championed by researchers, the quest for public access (often referred to as ‘open access’) gained momentum over the past decade, buoyed by public access mandates from research funders and by the dawn of transformative agreements. Yet barriers to public access to research persist, among them maintaining the financial sustainability of current publishing models. A recent webinar from the Friends of the National Library of Medicine, which was titled Public access to health information: providing trusted information to all, brought together leading multidisciplinary experts in public access to discuss these challenges and the practicalities of ensuring public access for all….”

Medical advances typically begin with a study. Now, universities are struggling to afford them | CBC News

Posted on by
Reply

“Prices to access studies from peer-reviewed journals paid by universities — which are heavily subsidized by taxpayers — have risen more than 400 per cent over the past two decades, according to a study citing Statistics Canada data published in 2021. That’s the latest national information tracking cost increases over time, four specialists said.

Those rising costs have implications far beyond the ivory tower. Academic studies are a lifeblood of knowledge creation: from improved cancer treatments to debates about foreign policy or charting the advances of artificial intelligence, new information enters the public domain through peer-reviewed research….

The typical Canadian university library spends about 75 per cent of its acquisitions budget for new material on journal subscriptions, said Susan Haigh, executive director of the Canadian Association of Research Libraries (CARL), an umbrella group representing this country’s largest university libraries….

Van Raay and his colleague, Prof. Andreas Heyland, are part of a growing trend of researchers trying to wrest control over information from the big publishing firms. 

Their project, Peer Premier, is the first-ever professional peer review service intended to be independent of any journal or publisher, according to the University of Guelph….

To use the service, an author pays $1,100 to the organization, in contrast to more than $10,000 to publish in some top journals, Heyland said.

Of that money, $300 goes to each of the article’s three independent reviewers and the remaining $200 is used for project administration. Researchers who submit get fulsome comments from the reviewers and leave with an edited, peer-reviewed manuscript that can be submitted elseware for publication, he added….”

An Open Access Strategy for the Drug Repurposing Community – Drug Repurposing Central

Posted on by
Reply

Abstract:  To ensure the widest possible dissemination of research results to the academic community, pharmaceutical industry, patients and to the broader public, the EU-funded drug repurposing project REPO4EU is committed to an Open Science approach. Because Open Science can be interpreted widely, this document lays out the strategy of the project with regard to Open Access publishing, alternative metrics, intellectual property and FAIR data, in line with the goals of the European Commission. The Open Science Strategy forms the theoretical framework for the REPO4EU Open Science publishing portal that will develop into an open hub of research results and communication for the entire drug repurposing community.