An interactive web application for the dissemination of human systems immunology data.

BACKGROUND: Systems immunology approaches have proven invaluable in translational research settings. The current rate at which large-scale datasets are generated presents unique challenges and opportunities. Mining aggregates of these datasets could accelerate the pace of discovery, but new solutions are needed to integrate the heterogeneous data types with the contextual information that is necessary for interpretation. In addition, enabling tools and technologies facilitating investigators' interaction with large-scale datasets must be developed in order to promote insight and foster knowledge discovery. METHODS: State of the art application programming was employed to develop an interactive web application for browsing and visualizing large and complex datasets. A collection of human immune transcriptome datasets were loaded alongside contextual information about the samples. RESULTS: We provide a resource enabling interactive query and navigation of transcriptome datasets relevant to human immunology research. Detailed information about studies and samples are displayed dynamically; if desired the associated data can be downloaded. Custom interactive visualizations of the data can be shared via email or social media. This application can be used to browse context-rich systems-scale data within and across systems immunology studies. This resource is publicly available online at [Gene Expression Browser Landing Page ( https://gxb.benaroyaresearch.org/dm3/landing.gsp )]. The source code is also available openly [Gene Expression Browser Source Code ( https://github.com/BenaroyaResearch/gxbrowser )]. CONCLUSIONS: We have developed a data browsing and visualization application capable of navigating increasingly large and complex datasets generated in the context of immunological studies. This intuitive tool ensures that, whether taken individually or as a whole, such datasets generated at great effort and expense remain interpretable and a ready source of insight for years to come.

Prospective Case-control Study of Contact Tracing Speed for Emergency Department-based Contact Tracers.

INTRODUCTION: In Snohomish County, WA, the time from obtaining a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test and initiating contact tracing is 4-6 days. We tested whether emergency department (ED)-based contact tracing reduces time to initiation and completion of contact tracing investigations. METHODS: All eligible coronavirus disease 2019 (COVID-19)-positive patients were offered enrollment in this prospective case-control study. Contact tracers were present in the ED from 7 AM to 2 AM for 60 consecutive days. Tracers conducted interviews using the Washington State Department of Health's extended COVID-19 reporting form, which is also used by the Snohomish Health District (SHD). RESULTS: Eighty-one eligible SARS-CoV-2 positive patients were identified and 71 (88%) consented for the study. The mean time between positive COVID-19 test result and initiation of contact tracing investigation was 111 minutes with a median of 32 minutes (range: 1-1,203 minutes). The mean time from positive test result and completion of ED-based contact tracing investigation was 244 minutes with a median of 132 minutes (range: 23-1,233 minutes). In 100% of the enrolled cases, contact tracing was completed within 24 hours of a positive COVID-19 test result. For comparison, during this same period, SHD was able to complete contact tracing in 64% of positive cases within 24 hours of notification of a positive test result (P < 0.001). In the ED, each case identified a mean of 2.8 contacts as compared to 1.4 contacts identified by SHD-interviewed cases. There was no statistically significant difference between the percentage of contacts reached through ED contact tracing (82%) when compared to the usual practice (78%) (P = 0.16). CONCLUSION: When contact tracing investigations occur at the point of diagnoses, the time to initiation and completion are reduced, there is higher enrollment, and more contacts are identified.