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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Correcting for reporting delay: an example using dengue fever data

One complication to infectious disease forecasting efforts is delay in reporting of cases, where real-time data often under-report the true disease burden. This pair of R scripts (1) provides example code demonstrating several strategies to account for the reporting delay and improve disease forecasts and (2) applies these methods using publicly-available data on dengue fever case reporting in Puerto Rico from 1990 to 2009.

Joann VanDervort, Lauren↗
DOE OSTI2021

Trade-offs between individual and ensemble forecasts of an emerging infectious disease

Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about human mobility, spatiotemporal variation in transmission potential, and the number of virus introductions. We found that which model assumptions had the most ensemble weight changed through time. We additionally identified a trade-off whereby some individual models outperformed ensemble models early in the epidemic, but on average the ensembles outperformed all individual models. Our results suggest that multiple models spanning uncertainty across alternative assumptions are necessary to obtain robust forecasts for emerging infectious diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Forecasting Zoonotic Infectious Disease Response to Climate Change: Mosquito Vectors and a Changing Environment

Infectious diseases are changing due to the environment and altered interactions among hosts, reservoirs, vectors, and pathogens. This is particularly true for zoonotic diseases that infect humans, agricultural animals, and wildlife. Within the subset of zoonoses, vector-borne pathogens are changing more rapidly with climate change, and have a complex epidemiology, which may allow them to take advantage of a changing environment. Most mosquito-borne infectious diseases are transmitted by mosquitoes in three genera: Aedes, Anopheles, and Culex, and the expansion of these genera is well documented. There is an urgent need to study vector-borne diseases in response to climate change and to produce a generalizable approach capable of generating risk maps and forecasting outbreaks. Here, we provide a strategy for coupling climate and epidemiological models for zoonotic infectious diseases. We discuss the complexity and challenges of data and model fusion, baseline requirements for data, and animal and human population movement. Disease forecasting needs significant investment to build the infrastructure necessary to collect data about the environment, vectors, and hosts at all spatial and temporal resolutions. These investments can contribute to building a modeling community around the globe to support public health officials so as to reduce disease burden through forecasts with quantified uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Disease Precognition [Slides]

How can we reduce the health and economic impacts future epidemics and pandemics? Global Real-Time Disease Forecasting is not just for weather anymore! Disease precognition technology is discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multiscale influenza forecasting

Abstract Influenza forecasting in the United States (US) is complex and challenging due to spatial and temporal variability, nested geographic scales of interest, and heterogeneous surveillance participation. Here we present Dante, a multiscale influenza forecasting model that learns rather than prescribes spatial, temporal, and surveillance data structure and generates coherent forecasts across state, regional, and national scales. We retrospectively compare Dante’s short-term and seasonal forecasts for previous flu seasons to the Dynamic Bayesian Model (DBM), a leading competitor. Dante outperformed DBM for nearly all spatial units, flu seasons, geographic scales, and forecasting targets. Dante’s sharper and more accurate forecasts also suggest greater public health utility. Dante placed 1st in the Centers for Disease Control and Prevention’s prospective 2018/19 FluSight challenge in both the national and regional competition and the state competition. The methodology underpinning Dante can be used in other seasonal disease forecasting contexts having nested geographic scales of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploring Climate-Disease Connections in Geopolitical Versus Ecological Regions: The Case of West Nile Virus in the United States

Many infectious disease forecasting models in the United States (US) are built with data partitioned into geopolitical regions centered on human activity as opposed to regions defined by natural ecosystems; although useful for data collection and intervention, this has the potential to mask biological relationships between the environment and disease. We explored this concept by analyzing the correlations between climate and West Nile virus (WNV) case data aggregated to geopolitical and ecological regions. We compared correlations between minimum, maximum, and mean annual temperature; precipitation; and annual WNV neuroinvasive disease (WNND) case data from 2005 to 2019 when partitioned into (a) climate regions defined by the National Oceanic and Atmospheric Administration (NOAA) and (b) Level I ecoregions defined by the Environmental Protection Agency (EPA). We found that correlations between climate and WNND in NOAA climate regions and EPA ecoregions were often contradictory in both direction and magnitude, with EPA ecoregions more often supporting previously established biological hypotheses and environmental dynamics underlying vector-borne disease transmission. Using ecological regions to examine the relationships between climate and disease cases can enhance the predictive power of forecasts at various scales, motivating a conceptual shift in large-scale analyses from geopolitical frameworks to more ecologically meaningful regions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗
DOE OSTI2021

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗
NASA NTRS2010

Namibian Flood Early Warning SensorWeb Pilot

The major goal of the Namibia SensorWeb Pilot Project is a scientifically sound, operational trans-boundary flood management decision support system for Southern African region to provide useful flood and waterborne disease forecasting tools for local decision makers. The Pilot Project established under the auspices of: Namibian Ministry of Agriculture Water and Forestry (MAWF), Department of Water Affairs; Committee on Earth Observing Satellites (CEOS), Working Group on Information Systems and Services (WGISS); and moderated by the United Nations Platform for Space-based Information for Disaster Management and Emergency Response (UN-SPIDER). The effort consists of identifying and prototyping technology which enables the rapid gathering and dissemination of both space-based and ground sensor data and data products for the purpose of flood disaster management and water-borne disease management.

Mandl, Daniel↗
NASA NTRS2004

Harnessing Systems Engineering Methodology in Using Earth Science Research Data for Real Applications

For the last three decades, Earth science remote sensing technologies have been providing an enormous amount of useful data and information serving to broaden our understanding of the home planet as a system. NASA's Earth science program has deployed about 18 complex satellites and is in the process of defining and launching multiple observing systems in this decade. At the same time, the European Community and many other countries such as Russia, France, India, Japan, and China have also significantly contributed to Earth science research. To date, the majority of such efforts have concentrated on expanding our scientific understanding of the multiple nonlinear and chaotic processes of Earth's behavior. In recent years, legislators and stakeholders have put serious pressure on the science community to devote more attention to making use of scientific results for societal benefit. For instance, there are a number of areas such as energy forecasting, aviation safety, agricultural efficiency, disaster management, air quality and public health that can directly take advantage of Earth science results to analyze and predict large scale problems and conditions. This is becoming even more important now that we live in a global economy interconnected via the internet and transportation systems; regional environmental conditions can have far reaching impact across continental boundaries. These factors dictate requirements for global data that can help us assess and control the devastating problems of famine, water resources, wildfires, human health and more. To do this requires a serious, organized, and systematic approach that transfers fundamental research products to the applied sciences domain. This paper presents a systems engineering and management process that can effectively make such transfer of data to the user community. Examples are presented on how the above decision making framework can help in solving critical problems such as the spread of vector borne diseases, forecasts of harmful algal blooms as well as forest fires and wildfires, and the intercontinental transport of dust storms and pollution.

Habib, Shahid↗
DOE OSTI2023

Scoping review of Culex mosquito life history trait heterogeneity in response to temperature

Abstract Background Mosquitoes in the genus Culex are primary vectors in the US for West Nile virus (WNV) and other arboviruses. Climatic drivers such as temperature have differential effects on species-specific changes in mosquito range, distribution, and abundance, posing challenges for population modeling, disease forecasting, and subsequent public health decisions. Understanding these differences in underlying biological dynamics is crucial in the face of climate change. Methods We collected empirical data on thermal response for immature development rate, egg viability, oviposition, survival to adulthood, and adult lifespan for Culex pipiens, Cx. quinquefasciatus, Cx. tarsalis , and Cx. restuans from existing literature according to the PRISMA scoping review guidelines. Results We observed linear relationships with temperature for development rate and lifespan, and nonlinear relationships for survival and egg viability, with underlying variation between species. Optimal ranges and critical minima and maxima also appeared varied. To illustrate how model output can change with experimental input data from individual Culex species, we applied a modified equation for temperature-dependent mosquito type reproduction number for endemic spread of WNV among mosquitoes and observed different effects. Conclusions Current models often input theoretical parameters estimated from a single vector species; we show the need to implement the real-world heterogeneity in thermal response between species and present a useful data resource for researchers working toward that goal. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines

Background: The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. Methods and findings: We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. Conclusions: These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Evaluation of an open forecasting challenge to assess skill of West Nile virus neuroinvasive disease prediction

Abstract Background West Nile virus (WNV) is the leading cause of mosquito-borne illness in the continental USA. WNV occurrence has high spatiotemporal variation, and current approaches to targeted control of the virus are limited, making forecasting a public health priority. However, little research has been done to compare strengths and weaknesses of WNV disease forecasting approaches on the national scale. We used forecasts submitted to the 2020 WNV Forecasting Challenge, an open challenge organized by the Centers for Disease Control and Prevention, to assess the status of WNV neuroinvasive disease (WNND) prediction and identify avenues for improvement. Methods We performed a multi-model comparative assessment of probabilistic forecasts submitted by 15 teams for annual WNND cases in US counties for 2020 and assessed forecast accuracy, calibration, and discriminatory power. In the evaluation, we included forecasts produced by comparison models of varying complexity as benchmarks of forecast performance. We also used regression analysis to identify modeling approaches and contextual factors that were associated with forecast skill. Results Simple models based on historical WNND cases generally scored better than more complex models and combined higher discriminatory power with better calibration of uncertainty. Forecast skill improved across updated forecast submissions submitted during the 2020 season. Among models using additional data, inclusion of climate or human demographic data was associated with higher skill, while inclusion of mosquito or land use data was associated with lower skill. We also identified population size, extreme minimum winter temperature, and interannual variation in WNND cases as county-level characteristics associated with variation in forecast skill. Conclusions Historical WNND cases were strong predictors of future cases with minimal increase in skill achieved by models that included other factors. Although opportunities might exist to specifically improve predictions for areas with large populations and low or high winter temperatures, areas with high case-count variability are intrinsically more difficult to predict. Also, the prediction of outbreaks, which are outliers relative to typical case numbers, remains difficult. Further improvements to prediction could be obtained with improved calibration of forecast uncertainty and access to real-time data streams (e.g. current weather and preliminary human cases). Graphical Abstract

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

EpiCast: Simulating Epidemics with Extreme Detail

In early 2020, COVID-19 swept the globe. Governments attempted to “flatten the curve” through business shutdowns and stay-at-home orders, but the United States was hit hard. By the end of March, mere months after the virus first emerged in humans 7,000 miles away, the U.S. had recorded 192,300 cases and 5,300 deaths. While this unprecedented disaster sent shockwaves through every level of society and clouded an uncertain future, state and local governments turned to computational and mathematical epidemiology researchers to help formulate intervention strategies to limit the spread of the disease. Traditional forecasting models provided a reasonable understanding of how the near future was likely to look, but local policy makers and public health communities still struggled to understand how potential mitigations ought to be implemented. Decision makers needed a way to measure the impact of their policy choices—they needed better technology. EpiCast answered the call, bringing urgently needed answers to policymakers grappling with how to adjust school and business schedules. EpiCast is modeling software that generates a synthetic, representative population to simulate infectious disease transmission in the United States with extreme detail and granularity. The software models human behavior combined with community-specific information to provide a fine-grained preview of the effect of potential mitigation strategies for decision makers.

60 APPLIED LIFE SCIENCES↗
NASA NTRSDate not supplied

Graph Representation Learning for Dengue Forecasting

In 2017, the largest recorded dengue outbreak in Sri Lanka’s history occurred. Since then, dengue has continued to threaten national health across Sri Lanka. The development of an effective Early Warning System (EWS) for dengue outbreaks is essential for Sri Lanka’s Ministry of Health to take preventative measures. We propose the use of Graph Neural Networks as EWS. Using earth observational data from NASAs global satellites and dengue incidence data from Sri Lanka s Ministry of Health, we developed a series of traditional and graph representation EWS to forecast Dengue cases across Sri Lanka’s 25 districts between 2013 and 2022. We demonstrate empirically that Graph Neural Networks which incorporate spatiotemporal relations significantly outperform traditional EWS such as Autoregressive Integrated Moving Average (ARIMA), Random Forest, and Long Short-Term Memory (LSTM). Our source code is available on GitHub and will be provided in the final submission.

Graph Neural Networks↗
DOE OSTI2025

Mapping Incidence and Prevalence Peak Data for SIR Modeling Applications

Infectious disease modeling and forecasting have played a key role in helping assess and respond to epidemics and pandemics. Recent work has leveraged data on disease peak infection and peak hospital incidence to fit compartmental models for the purpose of forecasting and describing the dynamics of a disease outbreak. Incorporating these data can greatly stabilize a compartmental model fit on early observations, where slight perturbations in the data may lead to model fits that forecast wildly unrealistic peak infection. We introduce a new method for incorporating historic data on the value and time of peak incidence of hospitalization into the fit for a Susceptible-Infectious-Recovered (SIR) model by formulating the relationship between an SIR model’s starting parameters and peak incidence as a system of two equations that can be solved computationally. We demonstrate how to calculate SIR parameter estimates – which describe disease dynamics such as transmission and recovery rates – using this method, and determine that there is a noticeable loss in accuracy whenever prevalence data is misspecified as incidence data. To exhibit the modeling potential, we update the Dirichlet-Beta State Space modeling framework to use hospital incidence data, as this framework was previously formulated to incorporate only data on total infections. This approach is assessed for practicality in terms of accuracy and speed of computation via simulation.

97 MATHEMATICS AND COMPUTING↗