The case for open science: rare diseases
Ontology highlight
ABSTRACT:
SUBMITTER: Rubinstein Y
PROVIDER: S-EPMC7660964 | biostudies-literature | 2020 Sep
REPOSITORIES: biostudies-literature
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Project description:The Open Science Prize was established with the following objectives: first, to encourage the crowdsourcing of open data to make breakthroughs that are of biomedical significance; second, to illustrate that funders can indeed work together when scientific interests are aligned; and finally, to encourage international collaboration between investigators with the intent of achieving important innovations that would not be possible otherwise. The process for running the competition and the successes and challenges that arose are presented.
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Project description:Renal leiomyosarcomas (LMS) are extremely rare neoplasms with aggressive behaviour and poor survival prognosis. The most frequent somatic events in leiomyosarcomas are mutations in TP53, RB1, ATRX and PTEN genes, chromosomal instability and chromoanagenesis. By using chromosomal microarray analysis we identified monosomy of chromosomes 3 and 11, gain of Xp (ATRX) arm and three chromoanasynthesis regions (6q21-q27, 7p22.3-p12.1 and 12q13.11-q21.2), with MDM2 and CDK4 oncogenes copy number gains, whereas no CNVs or tumor specific SNVs in TP53, RB1 and PTEN genes were observed.
2020-06-04 | GSE151766 | GEO
Project description:ObjectivesThe aims of this paper is to search and explore publications in the field of pharmacovigilance for rare diseases and to visualize general information, research hotspots, frontiers and future trends in the field using the bibliometric tool CiteSpace to provide evidence-based evidence for scholars.MethodsWe searched the Web of Science Core Collection (WoSCC) for studies related to pharmacovigilance for rare diseases, spanning January 1, 1997-October 25, 2022. CiteSpace software was utilized to discuss countries/regions, institutions, authors, journals, and keywords.ResultsAfter screening, a total of 599 valid publications were included in this study, with a significant upward trend in the number of publications. These studies were from 68 countries/regions with the United States and the United Kingdom making the largest contributions to the field. 4,806 research scholars from 493 institutions conducted studies on pharmacovigilance for rare diseases. Harvard University and University of California were the top two productive institutions in the research field. He Dian of the Affiliated Hospital of Guizhou Medical University and Peter G.M. Mol of the University of Groningen, The Netherlands, were the two most prolific researchers. The Cochrane Database of Systematic Reviews and the New England Journal of Medicine were the journals with the highest number of articles and co-citation frequency respectively. Clinical trial, therapy and adverse event were the top three most cited keywords.ConclusionsBased on keywords co-occurrence analysis, four research topics were identified: orphan drug clinical trials, postmarketing ADR surveillance for orphan drugs, rare diseases and orphan drug management, and diagnosis and treatment of rare diseases. Immune-related adverse reactions and benefit-risk assessment of enzyme replacement therapy were at the forefront of research in this field. Treatment outcomes, early diagnosis and natural history studies of rare diseases may become hotspots for future research.
| S-EPMC10523788 | biostudies-literature
Project description:BackgroundThe open science movement is transforming scientific practice with the goal of enhancing the transparency, productivity, and reproducibility of research. Nevertheless, transparency is a complex concept, and efforts to promote some forms of transparency may do relatively little to advance other important forms of transparency.ObjectivesDrawing from the literature in history, philosophy, and sociology of science, we aim to distinguish between different forms of scientific transparency. Our goal is to identify strategies for achieving forms of transparency that are relevant not only to scientists but also to decision makers and members of the public.DiscussionWe draw a distinction between "scientifically relevant transparency" and "socially relevant transparency." Most of the prominent strategies associated with the open science movement (e.g., making data publicly available and registering studies) are designed primarily to promote scientifically relevant transparency. To achieve socially relevant transparency, which is particularly important in fields like environmental health, further steps are needed to provide scientific information in ways that are relevant to decision makers and members of the public.ConclusionsPromoting socially relevant transparency will require a range of activities by many different individuals and institutions. We propose an array of strategies that can be pursued by scientists and other scholars, journals, universities, funders, government agencies, and members of the public. https://doi.org/10.1289/EHP4808.
| S-EPMC6792383 | biostudies-literature
Project description:BackgroundDue to their low prevalence (< 5 in 10,000), rare diseases are an important area of research, with the active participation of those affected being a key factor. In the Citizen Science project "SelEe" (Researching rare diseases in a citizen science approach), citizens collaborate with researchers using a digital application, developed as part of the project together with those affected, to answer research questions on rare diseases. The aim of this study was to define the rare diseases to be considered, the project topics and the initial requirements for the implementation in a digital application.MethodsTo address our research questions, we took several steps to engage citizens, especially those affected by rare diseases. This approach included the following methods: pre- and post-survey (questionnaire), two workshops with focus group discussion and a requirements analysis workshop (with user stories).ResultsIn the pre-survey, citizens suggested 45 different rare diseases and many different disease groups to be considered in the project. Two main project topics (A) "Patient-guided documentation and data collection" (20 votes) and (B) "Exchange of experience and networking" (13 votes) were identified as priorities in the workshops and ranked in the post-survey. The requirements workshop resulted in ten user stories and six initial requirements to be implemented in the digital application.ConclusionQualitative, citizen science research can be used to collectively identify stakeholder needs, project topics and requirements for a digital application in specific areas, such as rare diseases.
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Project description:Norovirus (NoV) is the most commonly recognized cause of acute gastroenteritis, with over a million cases globally per year. While usually self-limiting, NoV poses a substantial economic burden because it is highly contagious and there are multiple transmission routes. Infection occurs through inhalation of vomitus; faecal-oral spread; and food, water and environmental contamination. While the incidence of the disease is predictably seasonal, much less is known about the relative contribution of the various exposure pathways in causing disease. Additionally, asymptomatic excretion and viral shedding make forecasting disease burden difficult. We develop a novel stochastic dynamic network model to investigate the contributions of different transmission pathways in multiple coupled social networks representing schools, hospitals, care-homes and family households in a community setting. We analyse how the networks impact on transmission. We used ward-level demographic data from Northumberland, UK to create a simulation cohort. We compared the results with extant data on NoV cases from the IID2 study. Connectivity across the simulated cohort was high. Cases of NoV showed marked seasonality, peaking in early winter and declining through the summer. For the first time, we show that fomites and food appear to be the most important exposure routes in determining the population burden of disease. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
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Project description:Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) - comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge - is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation.
| S-EPMC5852639 | biostudies-literature
Project description:Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.
| S-EPMC4973366 | biostudies-other
Project description:The way science and research is done is rapidly becoming more open and collaborative. The traditional way of publishing new findings in journals is becoming increasingly outdated and no longer serves the needs of much of science. Whilst preprints can bring significant benefits of removing delay and selection, they do not go far enough if simply implemented alongside the existing journal system. We propose that we need a new approach, an Open Science Platform, that takes the benefits of preprints but adds formal, invited, and transparent post-publication peer review. This bypasses the problems of the current journal system and, in doing so, moves the evaluation of research and researchers away from the journal-based Impact Factor and towards a fairer system of article-based qualitative and quantitative indicators. In the long term, it should be irrelevant where a researcher publishes their findings. What is important is that research is shared and made available without delay within a framework that encourages quality standards and requires all players in the research community to work as collaborators.
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Project description:Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global "maker" community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.
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