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

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.

 

Science Has a Reproducibility Problem. Can Sample Sharing Help?

“The two of us — a materials science researcher with the Czech Academy of Sciences and a trained evolutionary biologist who’s now active in science education and outreach — believe open science can go a step further: Scientists should make a more concerted effort to share their physical samples. Doing so would improve reproducibility, spur innovation, and help level the playing field in a pursuit where funding and resources are unevenly distributed.

To see the importance of sample sharing, one need look no further than the Covid-19 pandemic. Although China publicly shared the genetic sequence data of the novel coronavirus, SARS-CoV-2, about two weeks after the first cluster of cases was reported in late 2019, the world had to wait another two and a half weeks to get access to physical samples of the virus, from researchers in Australia. While synthetic biology has made it possible to reconstruct viruses from genetic data, actual viral isolates can still be needed to recover infectious viral particles for developing diagnostic tests, antivirals, and vaccine testing….”

G7 Science and Technology Ministers’ Communique

“We share a growing concern that some actors may attempt to unfairly exploit or distort the open research environment and misappropriate research results for economic, strategic, geopolitical, or military purposes. This undermines the principles and values that underpin open, transparent, reciprocal, and accountable international research cooperation and the integrity of research and may pose security risks….

The G7 will collaborate in expanding open science with equitable dissemination of scientific knowledge and publicly funded research outputs including research data and scholarly publications in line with the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. This is so that researchers and people throughout the world can benefit from them as well as contribute to the creation of new knowledge, stimulation of innovation, democratization of access to knowledge by society and the development of solutions for global challenges. This will also help to build more reproducible and trusted research results.

We recognize openness, freedom, and inclusiveness should be enhanced globally for the sound development of scientific research. When making decisions about openness, the respect for universal human rights and the protection of national security are essential, and principles and rules related to academic freedom, research integrity, privacy, and protection of intellectual property rights should be applied and upheld.

We acknowledge that open science platforms can allow the rapid sharing of pathogen samples and pathogen genetic sequence data on a global scale. They should also enable early development and more rapid, effective, and equitable access to MCMs for the prevention and control of emerging and re-emerging infectious diseases. Robust multilateral data sharing is needed to ensure continued societal resilience to the global issues of today and the future….

The G7 also supports immediate open and public access to government-funded scholarly publications and scientific data, and supports the endeavors of the scientific community to address challenges in scholarly publishing for broader sharing of appropriate scientific outputs. To this end, we support the efforts of the G7 Open Science Working Group in promoting the interoperability and sustainability of infrastructure for research outputs, supporting research assessment approaches that incentivize and reward open science practices, and encouraging “research on research”, aimed at helping to shape a more effective evidence-based research policy…. ”

Attitudes Toward Providing Open Access for Use of Biospecimens and Health Records: A Cross-Sectional Study from Jordan

Abstract:  Purpose: Biospecimen repositories and big data generated from clinical research are critically important in advancing patient-centered healthcare. However, ethical considerations arising from reusing clinical samples and health records for subsequent research pose a hurdle for big-data health research. This study aims to assess the public’s opinions in Jordan toward providing blanket consent for using biospecimens and health records in research.

Participants and Methods: A cross-sectional study utilizing a self-reported questionnaire was carried out in different cities in Jordan, targeting adult participants. Outcome variables included awareness of clinical research, participation in clinical research, and opinions toward providing open access to clinical samples and records for research purposes. Descriptive analysis was utilized for reporting the outcome as frequency (percentages) out of the total responses. Univariate and multivariate logistic regression were used to investigate the association between independent variables and the outcome of interest.

Results: A total of 1033 eligible participants completed the questionnaire. Although the majority (90%) were aware of clinical research, only 24% have ever participated in this type of research. About half (51%) agreed on providing blanket consent for the use of clinical samples, while a lower percentage (43%) agreed on providing open access to their health records. Privacy concerns and lack of trust in the researcher were cited as major barriers to providing blanket consent. Participation in clinical research and having health insurance were predictors for providing open access to clinical samples and records.

Conclusion: The lack of public trust in Jordan toward data privacy is evident from this study. Therefore, a governance framework is needed to raise and maintain the public’s trust in big-data research that warrants the future reuse of clinical samples and records. As such, the current study provides valuable insights that will inform the design of effective consent protocols required in data-intensive health research.

A global approach for natural history museum collections | Science

Abstract:  Over the past three centuries, people have collected objects and specimens and placed them in natural history museums throughout the world. Taken as a whole, this global collection is the physical basis for our understanding of the natural world and our place in it, an unparalleled source of information that is directly relevant to issues as diverse as wildlife conservation, climate change, pandemic preparedness, food security, invasive species, rare minerals, and the bioeconomy (1). Strategic coordination and use of the global collection has the potential to focus future collecting and guide decisions that are relevant to the future of humanity and biodiversity. To begin to map the aggregate holdings of the global collection, we describe here a simple and fast method to assess the contents of any natural history museum, and report results based on our assessment of 73 of the world’s largest natural history museums and herbaria from 28 countries.

From the body of the article:

“Natural history museums have generally operated independently, and no interoperable data structure exists to provide open access to their collective holdings. Because most natural history museum data are not digitally discoverable, the networks of data aggregators have not been able to access these “dark data” …”

 

The Netherlands Heart Tissue Bank : Strengthening the cardiovascular research infrastructure with an open access Cardiac Tissue Repository – PubMed

Abstract:  Aim: Cardiac diseases remain a leading cause of cardiovascular disease (CVD) related hospitalisation and mortality. That is why research to improve our understanding of pathophysiological processes underlying cardiac diseases is of great importance. There is a strong need for healthy and diseased human cardiac tissue and related clinical data to accomplish this, since currently used animal and in vitro disease models do not fully grasp the pathophysiological processes observed in humans. This design paper describes the initiative of the Netherlands Heart Tissue Bank (NHTB) that aims to boost CVD-related research by providing an open-access biobank.

Methods: The NHTB, founded in June 2020, is a non-profit biobank that collects and stores biomaterial (including but not limited to myocardial tissue and blood samples) and clinical data of individuals with and without previously known cardiac diseases. All individuals aged ? 18 years living in the Netherlands are eligible for inclusion as a potential future donor. The stored samples and clinical data will be available upon request for cardiovascular researchers.

Conclusion: To improve the availability of cardiac tissue for cardiovascular research, the NHTB will include extensive (cardiac) biosamples, medical images, and clinical data of donors with and without a previously known cardiac disease. As such, the NHTB will function as a translational bridge to boost a wide range of cardiac disease-related fundamental and translational studies.

decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature? | GigaScience | Oxford Academic

Abstract:  Research resource identifiers (RRIDs) are persistent unique identifiers for scientific resources used to conduct studies such as reagents and tools. Inclusion of these identifiers into the scientific literature has been demonstrated to improve the reproducibility of papers because resources, like antibodies, are easier to find, making methods easier to reproduce. RRIDs also dramatically reduce the use of problematic resources, such as contaminated cell lines. The addition of RRIDs into a manuscript means that authors have to look up information that they may have previously omitted or confront information about problems that may have been reported about their resources. The use of RRIDs is primarily driven by champion journals, such as GigaScience and others. Although still nascent, this practice lays important groundwork for citation types that can cover non-traditional scholarly output, such as software tools and key reagents; giving authors of various types of tools scholarly credit for their contributions.

 

The Pandemic Response Box?Accelerating Drug Discovery Efforts after Disease Outbreaks | ACS Infectious Diseases

Abstract:  The current Covid-19 pandemic has underlined the need for a more coordinated and forward-looking investment in the search for new medicines targeting emerging health care threats. Repositioning currently approved drugs is a popular approach to any new emerging disease, but it represents a first wave of response. Behind this would be a second wave of more specifically designed therapies based on activities against specific molecular targets or in phenotypic assays. Following the successful deployment and uptake of previous open access compound collections, we assembled the Pandemic Response Box, a collection of 400 compounds to facilitate drug discovery in emerging infectious disease. These are based on public domain information on chemotypes currently in discovery and early development which have been shown to have useful activities and were prioritized by medicinal chemistry experts. They are freely available to the community as a pharmacological test set with the understanding that data will be shared rapidly in the public domain.

Biodiversity Community Integrated Knowledge Library (BiCIKL)

Abstract:  BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use.

 

NIH-Wide Strategic Plan: Fiscal Years 2021-2025

“NIH is committed to making findings from the research that it funds accessible and available in a timely manner, while also providing safeguards for privacy, intellectual property, security, and data management. For instance, NIH-funded investigators are expected to make the results and accomplishments of their activities freely available within 12 months of publication. NIH also encourages investigators to share results prior to peer review, such as through preprints, to speed the dissemination of their findings and enhance the rigor of their work through informal peer review. A robust culture of data sharing is critical to continued progress in science, maximizing NIH’s investment in research, and assurance of the highest levels of transparency and rigor. To this end, NIH will continue to promote opportunities for data management and sharing while allowing flexibility for various data types, sharing platforms, and strategies. Additionally, NIH is implementing a policy requiring that all applications include data sharing and management plans that consider input from stakeholders….”

VACANCY: SENIOR GLOBAL HEALTH ADVOCATE ON ACCESS TO MEDICINES

“As global health advocate at Wemos you will be part of the Access to Medicines team to realise the operational and policy aims of our Access to Medicines programme. You will build and strengthen coalitions on Access to Medicines, gather relevant knowledge and work to implement an effective advocacy strategy towards (inter)national stakeholders. Your objective? To advocate that everyone, everywhere, has access to high-quality, affordable medicines and other medical products that meet their medical needs….

Health is a human right and commodities like vaccines should be considered a global public good, especially considering the high amount of public money invested in the R&D of the vaccines. We are concerned about the lack of 1) transparency of pricing and R&D costs, 2) conditions for public funding, 3) fair regulations, and 4) cooperation between countries….”

Actives from MMV Open Access Boxes? A suggested way forward

Abstract:  It is estimated that more than 1 billion people across the world are affected by a neglected tropical disease (NTD) that requires medical intervention. These diseases tend to afflict people in areas with high rates of poverty and cost economies billions of dollars every year. Collaborative drug discovery efforts are required to reduce the burden of these diseases in endemic regions. The release of “Open Access Boxes” is an initiative launched by Medicines for Malaria Venture (MMV) in collaboration with its partners to catalyze new drug discovery in neglected diseases. These boxes are mainly requested by biology researchers across the globe who may not otherwise have access to compounds to screen nor knowledge of the workflow that needs to be followed after identification of actives from their screening campaigns. Here, we present guidelines on how to move such actives beyond the hit identification stage, to help in capacity strengthening and enable a greater impact of the initiative.

 

 

Principles of open, transparent and reproducible science in author guidelines of sleep research and chronobiology journals

Abstract:  Background: “Open science” is an umbrella term describing various aspects of transparent and open science practices. The adoption of practices at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but their uptake differs from discipline to discipline. Here, we asked to what extent journals in the field of sleep research and chronobiology encourage or even require following transparent and open science principles in their author guidelines.

Methods: We scored the author guidelines of a comprehensive set of 27 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor. The TOP Factor is a quantitative summary of the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges.

Results: Across the 27 journals, we find low values on the TOP Factor (median [25 th, 75 th percentile] 3 [1, 3], min. 0, max. 9, out of a total possible score of 29) in sleep research and chronobiology journals.

Conclusions: Our findings suggest an opportunity for sleep research and chronobiology journals to further support recent developments in transparent and open science by implementing transparency and openness principles in their author guidelines.