Objective: The All of Us Evenings with Genetics (EwG) Research Program at Baylor College of Medicine (BCM), funded to engage research scholars to work with the All of Us data, developed a training curriculum for the Researcher Workbench, the platform to access and analyze All of Us data. All of Us EwG developed the curriculum so that it could teach scholars regardless of their skills and background in programming languages and cloud computing. All of Us EwG delivered this curriculum at the first annual All of Us EwG Faculty Summit in May 2022. The curriculum was evaluated both during and after the Faculty Summit so that it could be improved for future training.
Materials And Methods: Surveys were administered to assess scholars' familiarity with the programming languages and computational tools required to use the Researcher Workbench. The curriculum was developed using backward design and was informed by the survey results, a review of available resources for training users on the Researcher Workbench, and All of Us EwG members' collective experience training students. The curriculum was evaluated using feedback surveys during the Faculty Summit as well as virtual meetings and emails following the Faculty Summit.
Results: The evaluation results demonstrated the success of the curriculum and identified areas for improvement.
Discussion And Conclusion: The curriculum has been adapted and improved in response to evaluations and in response to changes to the All of Us data and infrastructure to train more researchers through this program and other scholarly programs.
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http://dx.doi.org/10.1093/jamia/ocae240 | DOI Listing |
Mol Biol Rep
January 2025
Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
Background: Sugarcane is cultivated globally and affected by more than 125 pathogens, which lead to various plant diseases. In recent years, high-throughput sequencing (HTS)-based genome analyses have been broadly adopted for the discovery of both characterized and un-characterized viruses from plant samples. In this study, the HTS data of sugarcane pooled sample retrieved from sequence read archive (SRA) were de novo re-assembled using CLC Genomic Workbench.
View Article and Find Full Text PDFmedRxiv
October 2024
National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, Maryland, USA.
Objective: The goal of this study was to investigate the association of perceived discrimination with health outcomes and disparities.
Materials And Methods: The study cohort consists of 60,180 participants from the four largest SIRE groups in the Research Program participant body: Asian (1,291), Black (4,726), Hispanic (5,336), and White (48,827). A perceived discrimination index (PDI) was derived from participant responses to the "Social Determinants of Health" survey, and the Researcher Workbench was used to analyze associations and mediation effects of PDI and self-identified race and ethnicity (SIRE) with 1,755 diseases.
medRxiv
October 2024
National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, Maryland, USA.
Socioeconomic deprivation - defined as a lack of social, economic and material resources - is associated with poor health outcomes and health disparities between population groups. The Research Program is a longitudinal cohort study of diverse participants from the United States, with demographic and social determinants of health data gleaned from participant surveys and health outcome data derived from electronic health records. We developed a composite index of socioeconomic deprivation (iSDI) using a cohort of 202,919 participants - based on education, employment, health insurance, housing, and income data - and we associated iSDI with health outcomes and disparities.
View Article and Find Full Text PDFCancers (Basel)
December 2024
Translational Oncology Research Center (TORC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar.
Background: Chemoresistance in triple-negative breast cancer (TNBC) presents a significant clinical hurdle, limiting the efficacy of treatments like doxorubicin. This study aimed to explore the molecular changes associated with doxorubicin resistance and identify potential therapeutic targets to overcome this resistance, thereby improving treatment outcomes for TNBC patients.
Methods: Doxorubicin-resistant (DoxR) TNBC models (MDA-MB-231 and BT-549) were generated by exposing cells to increasing concentrations of doxorubicin.
Mikrobiyol Bul
October 2024
The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, Netherlands.
As the number of coronavirus diseases-2019 (COVID-19) cases have decreased and measures have started to be implemented at an individual level rather than in the form of social restrictions, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) still maintains its importance and has already taken its place in the spectrum of agents investigated in multiplex molecular test panels for respiratory tract infections in routine diagnostic use. In this study, we aimed to present mutation analysis and clade distribution of whole genome sequences from randomly selected samples that tested positive with SARS-CoV-2 specific real-time reverse transcription polymerase chain reaction (rRT-PCR) test at different periods of the pandemic in our laboratory with a commercial easy-to-use kit designed for next-generation sequencing systems. A total of 84 nasopharyngeal/oropharyngeal swab samples of COVID-19 suspected patients which were sent for routine diagnosis to the medical microbiology laboratory and detected as SARSCoV-2 RNA positive with rRT-PCR were randomly selected from different periods for sequence analysis.
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