A modeling pipeline to relate municipal wastewater surveillance and regional public health data.

As COVID-19 becomes endemic, public health departments benefit from improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging due to the high noise typical of environmental samples. We have developed a generalized pipeline using in- and out-of-sample model selection to test the ability of different correction models to reduce the variance in wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but the pipeline should be used to reevaluate any new data set as the sources of variance may change across locations, lab methods, and disease states. Using our best-fit model, we investigated the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We did this in a rolling manner for corrected wastewater data and for other prevalence indicators and statistically compared the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We found that wastewater trends often lead other COVID-19 indicators in predicting new surges.

Making Sense of Sensor Data: How Local Environmental Conditions Add Value to Social Science Research.

Recent advances in computing technologies have enabled the development of low-cost, compact weather and air quality monitors. The U.S. federally funded Array of Things (AoT) project has deployed more than 140 such sensor nodes throughout the City of Chicago. This paper combines a year's worth of AoT sensor data with household data collected from 450 elderly Chicagoans in order to explore the feasibility of using previously unavailable data on local environmental conditions to improve traditional neighborhood research. Specifically, we pilot the use of AoT sensor data to overcome limitations in research linking air pollution to poor physical and mental health and find support for recent findings that exposure to pollutants contributes to both respiratory and dementia-related diseases. We expect that this support will become even stronger as sensing technologies continue to improve and more AoT nodes come online, enabling additional applications to social science research where environmental context matters.

An integrated cyberGIS and machine learning framework for fine-scale prediction of Urban Heat Island using satellite remote sensing and urban sensor network data.

Due to climate change and rapid urbanization, Urban Heat Island (UHI), featuring significantly higher temperature in metropolitan areas than surrounding areas, has caused negative impacts on urban communities. Temporal granularity is often limited in UHI studies based on satellite remote sensing data that typically has multi-day frequency coverage of a particular urban area. This low temporal frequency has restricted the development of models for predicting UHI. To resolve this limitation, this study has developed a cyber-based geographic information science and systems (cyberGIS) framework encompassing multiple machine learning models for predicting UHI with high-frequency urban sensor network data combined with remote sensing data focused on Chicago, Illinois, from 2018 to 2020. Enabled by rapid advances in urban sensor network technologies and high-performance computing, this framework is designed to predict UHI in Chicago with fine spatiotemporal granularity based on environmental data collected with the Array of Things (AoT) urban sensor network and Landsat-8 remote sensing imagery. Our computational experiments revealed that a random forest regression (RFR) model outperforms other models with the prediction accuracy of 0.45 degree Celsius in 2020 and 0.8 degree Celsius in 2018 and 2019 with mean absolute error as the evaluation metric. Humidity, distance to geographic center, and PM2.5 concentration are identified as important factors contributing to the model performance. Furthermore, we estimate UHI in Chicago with 10-min temporal frequency and 1-km spatial resolution on the hottest day in 2018. It is demonstrated that the RFR model can accurately predict UHI at fine spatiotemporal scales with high-frequency urban sensor network data integrated with satellite remote sensing data.

Conceptualizing a Genomics Software Institute (GSI).

Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).