Converting Access Microbiology to an open research platform: community survey results
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SUBMITTER: Howat A
PROVIDER: S-EPMC8549388 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:IntroductionFuture digital health research hinges on methodologies to conduct remote clinical assessments and in-home monitoring. The Collaborative Aging Research Using Technology (CART) initiative was introduced to establish a digital technology research platform that could widely assess activity in the homes of diverse cohorts of older adults and detect meaningful change longitudinally. This paper reports on the built end-to-end design of the CART platform, its functionality, and the resulting research capabilities.MethodsCART platform development followed a principled design process aiming for scalability, use case flexibility, longevity, and data privacy protection while allowing sharability. The platform, comprising ambient technology, wearables, and other sensors, was deployed in participants' homes to provide continuous, long-term (months to years), and ecologically valid data. Data gathered from CART homes were sent securely to a research server for analysis and future data sharing.ResultsThe CART system was created, iteratively tested, and deployed to 232 homes representing four diverse cohorts (African American, Latinx, low-income, and predominantly rural-residing veterans) of older adults (n = 301) across the USA. Multiple measurements of wellness such as cognition (e.g., mean daily computer use time = 160-169 min), physical mobility (e.g., mean daily transitions between rooms = 96-155), sleep (e.g., mean nightly sleep duration = 6.3-7.4 h), and level of social engagement (e.g., reports of overnight visitors = 15-45%) were collected across cohorts.ConclusionThe CART initiative resulted in a minimally obtrusive digital health-enabled system that met the design principles while allowing for data capture over extended periods and can be widely used by the research community. The ability to monitor and manage health digitally within the homes of older adults is an important alternative to in-person assessments in many research contexts. Further advances will come with wider, shared use of the CART system in additional settings, within different disease contexts, and by diverse research teams.
| S-EPMC7768162 | biostudies-literature
Project description:The Navajo Nation placed a moratorium on genetic research studies in 2002, in part due to concerns about historical distrust, exploitation, limited expertise and resources, and the lack of a genetics policy. Navajo tribal leaders, scientists, and policy experts are exploring the possibility of lifting the moratorium, developing a genetic research policy, and discussing its potential health implications. This study aimed to identify the key concerns, needs, and desires of Navajo people regarding genetic research. We conducted a survey of Navajo individuals to assess knowledge of the moratorium and research, gauge interest in genetic research, and quantify appropriate genetic research topics to understand broad views and concerns. We performed descriptive statistics and tested associations between relevant categorical variables using Chi-square tests. We hypothesized that individuals with more knowledge about the moratorium and health research increased the likelihood of supporting and participating in genetic research. A total of 690 surveys from Navajo respondents were analyzed. Of these, 63% of respondents reported being unaware of the Navajo Nation's moratorium on genetic research. There were positive associations between those who knew about the moratorium and willingness to donate biospecimens for research under certain conditions, such as community involvement, review and approval by community leaders, research on diseases affecting the community, and support for lifting the moratorium (p-values < 0.001). We found no significant differences between age, gender, religious/spiritual beliefs, or agency affiliation with knowledge levels of genetics and related topics, participation in relation to beliefs, and donation of biospecimens. Interestingly, respondents who resided off the Navajo Nation were positively associated with having knowledge of the moratorium, having heard of discussions of genetics on the Navajo Nation, and the lawsuit filed by the Havasupai Tribe. Most respondents agreed that it was very important to develop a policy that incorporates cultural knowledge (56%), is beneficial (56%), and has data sharing protections (59%) before allowing genetic research on the Navajo Nation. Overall, a large proportion of respondents (46%) were unsure about lifting the moratorium and instead wanted more genetics education to assess its potential implications. The study results can inform the direction of future guidelines and policies.
| S-EPMC8675633 | biostudies-literature
Project description:Open-access mega-journals (OAMJs) are characterized by their large scale, wide scope, open-access (OA) business model, and "soundness-only" peer review. The last of these controversially discounts the novelty, significance, and relevance of submitted articles and assesses only their "soundness." This article reports the results of an international survey of authors (n = 11,883), comparing the responses of OAMJ authors with those of other OA and subscription journals, and drawing comparisons between different OAMJs. Strikingly, OAMJ authors showed a low understanding of soundness-only peer review: two-thirds believed OAMJs took into account novelty, significance, and relevance, although there were marked geographical variations. Author satisfaction with OAMJs, however, was high, with more than 80% of OAMJ authors saying they would publish again in the same journal, although there were variations by title, and levels were slightly lower than subscription journals (over 90%). Their reasons for choosing to publish in OAMJs included a wide variety of factors, not significantly different from reasons given by authors of other journals, with the most important including the quality of the journal and quality of peer review. About half of OAMJ articles had been submitted elsewhere before submission to the OAMJ with some evidence of a "cascade" of articles between journals from the same publisher.
| S-EPMC6853193 | biostudies-literature
Project description:SummaryThe affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers.AvailabilityThe SEQanswers community is freely accessible at http://SEQanswers.com/
| S-EPMC3338018 | biostudies-literature
Project description:The number of genome-wide association studies (GWAS) is growing rapidly leading to the discovery and replication of many new disease loci. Combining results from multiple GWAS datasets may potentially strengthen previous conclusions and suggest new disease loci, pathways or pleiotropic genes. However, no database or centralized resource currently exists that contains anywhere near the full scope of GWAS results.We collected available results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS.Using a genomic bin-based density analysis to search for highly associated regions of the genome, positive control loci (e.g., MHC loci) were detected with high sensitivity. Likewise, an analysis of highly repeated SNPs across GWAS identified replicated loci (e.g., APOE, LPL). At the same time we identified novel, highly suggestive loci for a variety of traits that did not meet genome-wide significant thresholds in prior analyses, in some cases with strong support from the primary medical genetics literature (SLC16A7, CSMD1, OAS1), suggesting these genes merit further study. Additional adjustment for linkage disequilibrium within most regions with a high density of GWAS associations did not materially alter our findings. Having a centralized database with standardized gene annotation also allowed us to examine the representation of functional gene categories (gene ontologies) containing one or more associations among top GWAS results. Genes relating to cell adhesion functions were highly over-represented among significant associations (p < 4.6 x 10(-14)), a finding which was not perturbed by a sensitivity analysis.We provide access to a full gene-annotated GWAS database which could be used for further querying, analyses or integration with other genomic information. We make a number of general observations. Of reported associated SNPs, 40% lie within the boundaries of a RefSeq gene and 68% are within 60 kb of one, indicating a bias toward gene-centricity in the findings. We found considerable heterogeneity in information available from GWAS suggesting the wider community could benefit from standardization and centralization of results reporting.
| S-EPMC2639349 | biostudies-literature
Project description:Scientific advance is based on reproducibility, corroboration, and availability of research results. However, large numbers of experimental results that contradict previous work do not get published and many research results are not freely available as they are hidden behind paywalls. As part of COST Action "DARTER", a network of researchers in the field of RNA therapeutics, we have performed a small survey among our members and their colleagues to assess their opinion on the subject of publishing contradictory or ambiguous results and their attitude to open access (OA) publishing. Our survey indicates that, although researchers highly value publication of "negative" results, they often do not publish their own, citing lack of time and the perception that those results may not be as highly cited. OA, on the other hand, seems to be widely accepted, but in many cases not actively sought by researchers due to higher costs associated with it.
| S-EPMC8215407 | biostudies-literature
Project description:The proportion of research outputs published in open access journals or made available on other freely-accessible platforms has increased over the past two decades, driven largely by funder mandates, institutional policies, grass-roots advocacy, and changing attitudes in the research community. However, the relative effectiveness of these different interventions has remained largely unexplored. Here we present a robust, transparent and updateable method for analysing how these interventions affect the open access performance of individual institutes. We studied 1,207 institutions from across the world, and found that, in 2017, the top-performing universities published around 80-90% of their research open access. The analysis also showed that publisher-mediated (gold) open access was popular in Latin American and African universities, whereas the growth of open access in Europe and North America has mostly been driven by repositories.
| S-EPMC7536542 | biostudies-literature
Project description:Dissemination of results is a fundamental aspect of the scientific process and requires an avenue for publication that is specifically designed to suit the nature of the research being communicated. Undergraduate research journals provide a unique forum for students to report scientific findings and ideas while learning about the complete scientific process. We have developed a peer-reviewed, open-access, international undergraduate research journal that is linked to a course-based undergraduate research experience. We reflect on lessons learned and recommend effective approaches for the implementation and operation of a successful undergraduate research journal.
| S-EPMC7452719 | biostudies-literature
Project description:Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.
| S-EPMC5954204 | biostudies-literature
Project description:Science is changing: the volume and complexity of data are increasing, the number of studies is growing and the goal of achieving reproducible results requires new solutions for scientific data management. In the field of neuroscience, the German National Research Data Infrastructure (NFDI-Neuro) initiative aims to develop sustainable solutions for research data management (RDM). To obtain an understanding of the present RDM situation in the neuroscience community, NFDI-Neuro conducted a comprehensive survey among the neuroscience community. Here, we report and analyze the results of the survey. We focused the survey and our analysis on current needs, challenges, and opinions about RDM. The German neuroscience community perceives barriers with respect to RDM and data sharing mainly linked to (1) lack of data and metadata standards, (2) lack of community adopted provenance tracking methods, (3) lack of secure and privacy preserving research infrastructure for sensitive data, (4) lack of RDM literacy, and (5) lack of resources (time, personnel, money) for proper RDM. However, an overwhelming majority of community members (91%) indicated that they would be willing to share their data with other researchers and are interested to increase their RDM skills. Taking advantage of this willingness and overcoming the existing barriers requires the systematic development of standards, tools, and infrastructure, the provision of training, education, and support, as well as additional resources for RDM to the research community and a constant dialogue with relevant stakeholders including policy makers to leverage of a culture change through adapted incentivization and regulation.
| S-EPMC9933933 | biostudies-literature