Lessons Learned in a Decade of Research Software Engineering GPU Applications
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ABSTRACT:
SUBMITTER: Krzhizhanovskaya V
PROVIDER: S-EPMC7304729 | biostudies-literature | 2020 May
REPOSITORIES: biostudies-literature
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Project description:Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to improve researchers' computing skills. This paper explains what we have learned along the way, the challenges we now face, and our plans for the future.
| S-EPMC3976103 | biostudies-literature
Project description:It has been 10 years since human metapneumovirus (HMPV) was identified as a causative agent of respiratory illness in humans. Since then, numerous studies have contributed to a substantial body of knowledge on many aspects of HMPV. This review summarizes our current knowledge on HMPV, HMPV disease pathogenesis, and disease intervention strategies and identifies a number of areas with key questions to be addressed in the future.
| S-EPMC3194831 | biostudies-literature
Project description:Candidate gene association studies, linkage studies and genome-wide association studies have highlighted the role of genetic factors in the development of ischemic stroke. This research started over a decade ago, and can be separated into three major periods of research. In the first wave classic susceptibility markers associated with other diseases (such as the Leiden mutation in Factor V and mutations in the prothrombin and 5,10-methylenetetrahydrofolate reductase (MTHFR) genes) were tested for their role in stroke. These first studies used just a couple of hundred samples or even less. The second and still ongoing period bridges the two other periods of research and has led to a rapid increase in the spectrum of functional variants of genes or genomic regions, discovered primarily in relation to other diseases, tested on larger stroke samples of clinically better stratified patients. Large numbers of these alleles were originally discovered by array-based genome-wide association studies. The third period of research involves the direct array screening of large samples; this approach represents significant progress for research in the field. Research into susceptibility genes for stroke has taught us that careful stratification of patients is critical, that susceptibility alleles are often shared between diseases, and that not all susceptibility factors that associate with clinical traits that are themselves risk factors for stroke (such as increase of triglycerides) necessarily represent susceptibility for stroke. Research so far has been mainly focused on large- and small-vessel associated stroke, and knowledge on other types of stroke, which represent much smaller population samples, is still very scarce. Although some susceptibility allele tests are on the palette of some direct-to-consumer companies, the clinical utility and clinical validity of these test results still do not support their use in clinical practice.
| S-EPMC3092115 | biostudies-literature
Project description:CrowdsourcingCrowdsourcing is the practice of obtaining needed ideas, services, or content by requesting contributions from a large group of people. Amazon Mechanical Turk is a web marketplace for crowdsourcing microtasks, such as answering surveys and image tagging. We explored the limits of crowdsourcing by using Mechanical Turk for a more complicated task: analysis and creation of wind simulations.Harnessing crowdworkers for engineeringOur investigation examined the feasibility of using crowdsourcing for complex, highly technical tasks. This was done to determine if the benefits of crowdsourcing could be harnessed to accurately and effectively contribute to solving complex real world engineering problems. Of course, untrained crowds cannot be used as a mere substitute for trained expertise. Rather, we sought to understand how crowd workers can be used as a large pool of labor for a preliminary analysis of complex data.Virtual wind tunnelWe compared the skill of the anonymous crowd workers from Amazon Mechanical Turk with that of civil engineering graduate students, making a first pass at analyzing wind simulation data. For the first phase, we posted analysis questions to Amazon crowd workers and to two groups of civil engineering graduate students. A second phase of our experiment instructed crowd workers and students to create simulations on our Virtual Wind Tunnel website to solve a more complex task.ConclusionsWith a sufficiently comprehensive tutorial and compensation similar to typical crowd-sourcing wages, we were able to enlist crowd workers to effectively complete longer, more complex tasks with competence comparable to that of graduate students with more comprehensive, expert-level knowledge. Furthermore, more complex tasks require increased communication with the workers. As tasks become more complex, the employment relationship begins to become more akin to outsourcing than crowdsourcing. Through this investigation, we were able to stretch and explore the limits of crowdsourcing as a tool for solving complex problems.
| S-EPMC4575153 | biostudies-literature
Project description:In this brief afterword, we discuss the challenges and lessons learned in the process of implementing a multisite, longitudinal study. Some of the lessons learned by the research team are shared regarding research design and analysis, strategies implemented to reduce threats to validity, and techniques used to promote teamwork and collaboration across sites.
| S-EPMC4704122 | biostudies-literature
Project description:Endometriosis is an incurable gynecological disease characterized by the abnormal growth of endometrium-like tissue, characteristic of the uterine lining, outside of the uterine cavity. Millions of people with endometriosis suffer from pelvic pain and infertility. This review aims to discuss whether nanomedicines that are promising therapeutic approaches for various diseases have the potential to create a paradigm shift in endometriosis management. For the first time, the available reports and achievements in the field of endometriosis nanomedicine are critically evaluated, and a summary of how nanoparticle-based systems can improve endometriosis treatment and diagnosis is provided. Parallels between cancer and endometriosis are also drawn to understand whether some fundamental principles of the well-established cancer nanomedicine field can be adopted for the development of novel nanoparticle-based strategies for endometriosis. This review provides the state of the art of endometriosis nanomedicine and perspective for researchers aiming to realize and exploit the full potential of nanoparticles for treatment and imaging of the disorder.
| S-EPMC7928207 | biostudies-literature
Project description:BackgroundMutual learning and shared decision-making are key elements of Participatory Action Research (PAR), highlighting the important role of the facilitator to support this. This study aims to illustrate how a facilitator can contribute to successful PAR sessions based on the reflection of three PAR projects.MethodsParticipatory sessions took place with adolescents for 3-4 school years. After each session (n = 252 sessions across three projects), facilitators filled in a reflection form that assessed the group process and their facilitating role. Facilitators independently coded a selection of 135 reflection forms partly deductive and partly inductive based on core PAR principles derived from a pragmatic literature search.ResultsA well-prepared session - for example, including active and creative participatory methods and a clearly stated goal - contributed to efficiency and the necessary flexibility. Making agreements, making sure everyone is heard and taking 'fun-time' appeared important for creating and maintaining a safe, functional and positive atmosphere. Finally, facilitators needed to encourage co-researchers to take the lead and adapt to the group dynamics, to ensure ownership and shared decision-making.ConclusionIn-depth qualitative analyses of a standardized reflection form used in three different PAR projects resulted in various lessons to support facilitators in collaborating with co-researchers in PAR projects.
| S-EPMC11342652 | biostudies-literature
Project description:In 2011, the Veterans Health Administration (VHA) implemented electronic consults (e-consults) as an alternative to in-person specialty visits to improve access and reduce travel for veterans. We conducted an evaluation to understand variation in the use of the new e-consult mechanism and the causes of variable implementation, guided by the Consolidated Framework for Implementation Research (CFIR).Qualitative case studies of 3 high- and 5 low-implementation e-consult pilot sites. Participants included e-consult site leaders, primary care providers, specialists, and support staff identified using a modified snowball sample.We used a 3-step approach, with a structured survey of e-consult site leaders to identify key constructs, based on the CFIR. We then conducted open-ended interviews, focused on key constructs, with all participants. Finally, we produced structured, site-level ratings of CFIR constructs and compared them between high- and low-implementation sites.Site leaders identified 14 initial constructs. We conducted 37 interviews, from which 4 CFIR constructs distinguished high implementation e-consult sites: compatibility, networks and communications, training, and access to knowledge and information. For example, illustrating compatibility, a specialist at a high-implementation site reported that the site changed the order of consult options so that all specialties listed e-consults first to maintain consistency. High-implementation sites also exhibited greater agreement on constructs.By using the CFIR to analyze results, we facilitate future synthesis with other findings, and we better identify common patterns of implementation determinants common across settings.
| S-EPMC4717483 | biostudies-literature
Project description:Dengue was first reported in Puerto Rico in 1899 and sporadically thereafter. Following outbreaks in 1963 and 1969, the Centers for Disease Control and Prevention has worked closely with the Puerto Rico Department of Health to monitor and reduce the public health burden of dengue. During that time, evolving epidemiologic scenarios have provided opportunities to establish, improve, and expand disease surveillance and interventional research projects. These initiatives have enriched the tools available to the global public health community to understand and combat dengue, including diagnostic tests, methods for disease and vector surveillance, and vector control techniques. Our review serves as a guide to organizations seeking to establish dengue surveillance and research programs by highlighting accomplishments, challenges, and lessons learned during more than a century of dengue surveillance and research conducted in Puerto Rico.
| S-EPMC6649339 | biostudies-literature
Project description:BackgroundGiven the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery.MethodsWe designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols.ResultsAnalysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3).ConclusionAn efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
| S-EPMC5361813 | biostudies-literature