What Sepsis Researchers Can Learn from COVID-19.
Ontology highlight
ABSTRACT:
SUBMITTER: Schinkel M
PROVIDER: S-EPMC7781118 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Although some studies reported the comprehensive mRNA expression analysis of coronavirus disease 2019 (COVID-19) using blood samples to understand its pathogenesis, the characteristics of RNA expression in COVID-19 and sepsis have not been compared. We compared the transcriptome expression of whole blood samples from patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patients with sepsis caused by other bacteria who entered the intensive care unit to clarify the COVID-19-specific RNA expression and understand its pathogenesis. Transcriptomes related to mitochondria were upregulated in COVID-19, whereas those related to neutrophils were upregulated in sepsis. However, the transcriptomes related to neutrophils were upregulated in both COVID-19 and sepsis compared to in healthy controls, whereas the mitochondrial transcriptomes were upregulated in COVID-19 and downregulated in sepsis compared to in healthy controls. Moreover, sepsis showed sub-optimal intrinsic apoptotic features compared with COVID-19. The transcriptome expression of COVID-19 has been examined in vitro but has not been widely validated using human specimens. This study improves the understanding of the pathogenesis of COVID-19 and can contribute to the development of treatments.
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2023-03-24 | GSE222393 | GEO
Project description:There is emerging literature on the disruptive effects of the COVID-19 pandemic on college students, but little is known about the impacts on undergraduate researchers (UGRs). On the basis of survey data collected in Summer 2020, this paper examines how less competent mentorship and COVID-19-related difficulties shaped UGRs' graduate school intentions. Results suggest that the pandemic strengthened UGRs' graduate school intentions when UGRs experienced fewer COVID-19-related difficulties. The pandemic weakened URG's graduate school intentions when they had a less competent faculty mentor. Having a more competent postgraduate mentor had a positive effect on UGRs' graduate school intentions in response to the pandemic. Those findings indicate that higher quality postgraduate mentorship may serve as an effective surrogate for lower quality faculty mentorship. Findings suggest that immediate strategies are needed to bolster graduate school aspirations among specific groups of UGRs in response to the pandemic. UGRs of particular concern include those who were highly impacted by COVID-19 with less competent mentors, were first-generation college students, had less prior research experience, had their Summer 2020 research experiences canceled, and were social/behavioral sciences majors.
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Project description:Objective:As computer programming becomes increasingly important in the biomedical sciences and more libraries offer programming classes, it is crucial for librarians to understand how researchers use programming in their work. The goal of this study was to understand why biomedical researchers who enrolled in a library-sponsored workshop wanted to learn to program in R and Python. Methods:Semi-structured in-depth interviews were performed with fourteen researchers registered for beginning R and Python programming workshops at the University of California, San Francisco Library. A thematic analysis approach was used to extract the top reasons that researchers learned to program. Results:Four major themes emerged from the interviews. Researchers wanted to learn R and Python programming in order to perform their data analysis independently, to be an informed collaborator, to engage with new forms of big data research, and to have more flexibility in the tools that they used for their research. Conclusions:Librarians designing programming workshops should remember that most researchers are hoping to apply their new skills to a specific research task such as data cleaning, data analysis, and statistics and that language preferences can vary based on research community as well as personal preferences. Understanding the programming goals of researchers will make it easier for librarians to partner effectively and offer services that are critically needed in the biomedical community.
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Project description:Severely-afflicted COVID-19 patients can exhibit disease manifestations representative of sepsis, including acute respiratory distress syndrome and multiple organ failure. We hypothesized that diagnostic tools used in managing all-cause sepsis, such as clinical criteria, biomarkers, and gene expression signatures, should extend to COVID-19 patients. Here we analyzed the whole blood transcriptome of 124 early (1-5 days post-hospital admission) and late (6-20 days post-admission) sampled patients with confirmed COVID-19 infections from hospitals in Quebec, Canada. Mechanisms associated with COVID-19 severity were identified between severity groups (ranging from mild disease to the requirement for mechanical ventilation and mortality), and established sepsis signatures were assessed for dysregulation. Specifically, gene expression signatures representing pathophysiological events, namely cellular reprogramming, organ dysfunction, and mortality, were significantly enriched and predictive of severity and lethality in COVID-19 patients. Mechanistic endotypes reflective of distinct sepsis aetiologies and therapeutic opportunities were also identified in subsets of patients, enabling prediction of potentially-effective repurposed drugs. The expression of sepsis gene expression signatures in severely-afflicted COVID-19 patients indicates that these patients should be classified as having severe sepsis. Accordingly, in severe COVID-19 patients, these signatures should be strongly considered for the mechanistic characterization, diagnosis, and guidance of treatment using repurposed drugs.
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