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DOE OSTI2021

Epidemiology, Clinical Features, and Outcomes of Coccidioidomycosis, Utah, 2006–2015

On the basis of a 1957 geographic Coccidioides seropositivity survey, 3 counties in southwestern Utah, USA, were considered coccidioidomycosis-endemic, but there has been a paucity of information on the disease burden in Utah since. We report findings from a recent clinical and epidemiologic study of coccidioidomycosis in Utah. To describe clinical characteristics, we identified all coccidioidomycosis cases in an integrated health system in the state during 2006–2015. For epidemiologic analysis, we used cases reported to the Utah Department of Health during 2009–2015. Mean state incidence was 1.83 cases/100,000 population/year. Washington County, in southwestern Utah, had the highest incidence, 17.2 cases/100,000 population/year. In a generalized linear model with time as a fixed effect, mean annual temperature, population, and new construction were associated with regional variations in incidence. Using these variables in a spatiotemporal model, we estimated the adjusted regional variation by county to predict areas where Coccidioides infections might increase.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

COVID-19 Data Curation Effort: An Initial Analysis of the Data

During the COVID-19 pandemic of 2020, major case reporting outlets quickly coalesced around two or three primary vendors. Johns Hopkins University and The New York Times were among the more prominent, and all were of great value to the nation, particularly during the uncertain early stages of the pandemic. They primarily focused on three major attributes: number of new cases, deaths, and recovery. Recognizing that many states were reporting very detailed data sets (e.g., hospital beds) at a county level or finer, the ORNL Pandemic Modeling team embarked on a major data curation effort from March to June 2020 for the purpose of capturing this wealth of detailed data. The challenge of curating this data was daunting. The number of attributes reported by the states grew on almost on a weekly basis. States were routinely shifting their web tool strategies away from easily parsable HTML-based formatting to new Tableau and ArcGIS content. This growth in the sheer number of attributes, combined with the unpredictable shifts in data format, meant an aggressive and agile combination of automated scripting and manual scraping was required to capture new daily streams. Further, the team had to scale up staff and widen its approach for capture and storage. As a result, the team collected more than 11 million data points. Following the close of this data collection effort on June 30 th , 2020, the team embarked on a major effort to appraise what had been collected, including an inventory list, spatial completeness, temporal completeness, scale and geographic characteristics, and a determination. A report on this matter was submitted on September 15 th , 2020, titled “DOE COVID-19 Data Curation Effort: Overview of Data Collection Coverage”. Over 2000 unique attributes had been netted over a wide range of spatial scales, including state, county, zip codes, health regions, and census blocks. Over 11 million individual data points were collected across these attributes, and spatial coverage (in total) included all 50 states and multiple territories. What became apparent in the process is that in the absence of any data standards, many states reported a wide variety of unique attributes that were not always compatible with attributes reported in other states. As time continued, states began adding new attributes and offering finer grain detail in some older attributes. This meant that not all data streams existed for the entire time period; in fact, the number tended to increase dramatically towards the end. Often, states would begin an attribute series and then stop altogether. These highly variable and uncertain conditions illuminated the need for harmonization approaches that would reconcile and conflate changing attribute names and detail over time. For example, grouping racial data reported as either Black or African American, depending on the state, into a single harmonized attribute. These choices would make a within-state analysis possible during the time period and lead to potential between-state analytics later on. This was almost entirely a manual decision process, requiring some subjective decision-making at times, to prevent a fragmented, short-lived collection of time series fragments that would offer few insights into trends, patterns, and correlates. This report imports harmonized data for state and county into the World Spatio-Temporal Analytics and Mapping Project (WSTAMP). WSTAMP is a major space-time analysis and visualization tool developed at ORNL for the National Geospatial-Intelligence Agency specifically for this kind of exploratory analysis. WSTAMP offers a rich analytical and graphical environment consisting of a wide range of analytics. These include time series plots, statistical summaries, data mining techniques, trend and pattern detection, and hypothesis generation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

5G Energy FRAME Report on 5G for Grid Use Case (Year 3 Final Report)

This report provides an extensive overview of the interrelationships among energy, communication, and computing—especially in the context of decarbonization goals, challenges, and opportunities. Technical examples enabled by 5G technologies and their performance are presented, discussed, based on the experiment performed at Pacific Northwest National Laboratory. This is the first use case focused on using 5G for the U.S. power grid and will be referred to as the 5G for Grid Use Case from here on. Specifically, this use case looks at the workflow, which integrates the performance data of a real-world 5G communication testbed and a grid transmission and distribution co-simulation platform. The cross-domain information flow and logic design are illustrated with a combination of power grid contingencies and events. Lastly, a summary of the project achievement and outcome is provided, along with a technology roadmap envisioned by the project team.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Google Health Trends performance reflecting dengue incidence for the Brazilian states

Abstract Background Dengue fever is a mosquito-borne infection transmitted by Aedes aegypti and mainly found in tropical and subtropical regions worldwide. Since its re-introduction in 1986, Brazil has become a hotspot for dengue and has experienced yearly epidemics. As a notifiable infectious disease, Brazil uses a passive epidemiological surveillance system to collect and report cases; however, dengue burden is underestimated. Thus, Internet data streams may complement surveillance activities by providing real-time information in the face of reporting lags. Methods We analyzed 19 terms related to dengue using Google Health Trends (GHT), a free-Internet data-source, and compared it with weekly dengue incidence between 2011 to 2016. We correlated GHT data with dengue incidence at the national and state-level for Brazil while using the adjusted R squared statistic as primary outcome measure (0/1). We used survey data on Internet access and variables from the official census of 2010 to identify where GHT could be useful in tracking dengue dynamics. Finally, we used a standardized volatility index on dengue incidence and developed models with different variables with the same objective. Results From the 19 terms explored with GHT, only seven were able to consistently track dengue. From the 27 states, only 12 reported an adjusted R squared higher than 0.8; these states were distributed mainly in the Northeast, Southeast, and South of Brazil. The usefulness of GHT was explained by the logarithm of the number of Internet users in the last 3 months, the total population per state, and the standardized volatility index. Conclusions The potential contribution of GHT in complementing traditional established surveillance strategies should be analyzed in the context of geographical resolutions smaller than countries. For Brazil, GHT implementation should be analyzed in a case-by-case basis. State variables including total population, Internet usage in the last 3 months, and the standardized volatility index could serve as indicators determining when GHT could complement dengue state level surveillance in other countries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

DOE COVID-19 Data Curation Effort: Overview of Initial Data Collection Coverage (March - June 2020)

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2020

Verification and Validation of MFiX-PIC

This work is aimed at verification and validation (V&V) of particle-in-cell (PIC) approach in the National Energy Technology Laboratory’s (NETL) Multiphase Flow with Interphase eXchanges (MFiX-PIC) which was officially released in April 2019. Under verification, the results from MFiX-PIC are compared with exact or analytical solutions, while experimental results are used for benchmarking under validation. The test suite consists of the following cases: Terminal velocity. Particle advection in time-varying flow field. Particle settling in a dense medium. Evaporation. Rayleigh-Taylor instability. Minimum fluidization. Mini-circulating fluidized bed. The cases reported in a format consistent with the existing Verification and Validation Manual (Musser et al., 2018) explore a wide range of flow velocities and concentration regimes. Only one case considered in this work verifies the implementation of heat and mass transfer routines in MFiX-PIC, while a few other studies are currently underway to further expand the validation space in reacting flows. This study highlights the need for a rigorous analysis to objectively quantify the effect of model parameters. In addition, there is a scarcity of high-quality experimental data in the literature suitable for validating PIC methodology. Future efforts would include performing experiments which provide results for a valuable database. While designing such experiments, particle count should be significant to have sufficient particles per parcel while maintaining an optimal parcel to cell volume ratio. Also, datasets should have objectively assessed experimental uncertainty whereby confidence interval in those measurements become more explicit.

42 ENGINEERING↗

DOE OSTI2022

Crystallization kinetics and nanoparticle ordering in semicrystalline polymer nanocomposites

There has been considerable interest in the nucleation and crystallization of polymers in the presence of nanoparticles (NPs, or nanofillers in general, NFs). Most of the extensive work in this area has focused on anisotropic, non-Brownian NFs (e.g., clay sheets, carbon nanotubes) whose spatial dispersion state in these nanocomposites is controlled by the process by which they are formed. Hence, NF spatial dispersion is generally limited and often remains poorly characterized. Thermodynamic handles that can be used to control NF dispersion state in the polymer melt include (a) favorable interactions between the polymer chains and the bare NP surfaces, or (b) the density and length of the chains, with the same chemistry as the matrix, grafted to the NP surface. These relatively large NFs merely act as stationary objects that affect the kinetics of nucleation by providing heterogeneous sites, and the crystallization rate by confining the polymer in the melt state. The dispersion state of the NFs can dramatically affect the nucleation and crystallization of the matrix, but in most cases reported, the NFs increase nucleation efficiency relative to the neat polymer. At higher NF loadings, the effect of polymer confinement by the NFs dominates, leading to a decrease in crystal growth rates. This review describes the most important lessons learned from these commonly studied systems and then extends to polymer composite systems containing small, mobile spherical NPs (typically smaller than 100 nm in size). The role of NP mobility, which provides for dynamic confinement of the polymer melt, on the kinetics of polymer crystallization (nucleation, growth, and overall crystallization) and how this behavior is mostly consistent with the case of immobile NF is a second important focus of this review. In addition to the role of NFs on crystallization kinetics, recently reported nanoparticle ordering phenomena such as the effect of matrix crystallization on the organization of small spherical NPs within the amorphous regions of the semicrystalline morphology are discussed. In conclusion, such phenomena are clearly not observed for large NFs and hence provide a point of departure from past works in this area.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2004

Gender and Decompression Sickness: A Critical Review and Analysis

The author addressed the following questions: are women at greater risk of decompression sickness and venous gas emboli at certain times in their reproductive cycle, is risk modified by the use of birth control pills (BCP), and is there a difference in overall risk between men and women under the same decompression dose? The summary considers information from the few abstracts and reports that were available. Except for the observation of more Type II DCS in women, particularly in women who fly after diving, there was no compelling evidence of a difference in DCS risk between men and women SCUBA divers. Many women that presented with DCS symptoms seemed to be in or near menses, with statistically fewer cases reported as time increased from menses. There was no compelling evidence that the use of BCP in SCUBA divers increases the risk of DCS. There were insufficient data about VGE from SCUBA diving to make any conclusion about the incidence of VGE and gender. In contrast, there were ample data about VGE from research in altitude chambers. Women produced less VGE and less Grade IV VGE compared to men under the same decompression dose, certainly when resting oxygen prebreathe (PB) was performed prior to ascent to altitude. Dual-cycle ergometry exercise during PB tends to reduce the differences in VGE between men and women. There was no compelling evidence that the risk of altitude DCS was different between men and women. However, a large number of DCS cases were associated with menses, and the use of BCP did seem to put women at a slightly greater risk than those that did not use BCP. There were substantial observations that women comprised a larger number of difficult cases that required complicated medical management.

Source record↗

DOE OSTI2022

SARS-CoV-2 Infection-Associated Aortic Thrombosis Treated with Oral Factor Xa Inhibition

Coronavirus disease 2019 (COVID-19) is an acute complex systemic disorder caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).While SARS-CoV-2 is known to cause significant pulmonary disease, various extrapulmonary manifestations of COVID-19 have also been reported. Growing evidence suggests that COVID-19 is associated with coagulopathy leading to micro and macrovascular complications. Although in patients with COVID-19, venous thromboembolic events are more frequent, arterial thrombosis also occurs at an increased rate. These often lead to acute life-threatening ischemia, which requires urgent diagnosis and treatment. We present case reports of two patients with an abnormal thrombus formation in the thoracic aorta who recently overcame COVID-19, which led to systemic embolism and splenic infarction. Ambulatory oral factor Xa inhibitor therapy led to aortic thrombosis resolution in both patients.

Strýčková, Alena↗

DOE OSTI2022

Integrating Public Health Surveillance and Environmental Data to Model Presence of Histoplasma in the United States

In the United States, the true geographic distribution of the environmental fungus Histoplasma capsulatum remains poorly understood but appears to have changed since it was first characterized. Histoplasmosis is caused by inhalation of the fungus and can range in severity from asymptomatic to life-threatening. Due to limited public health surveillance and under detection of infections, it is challenging to directly use reported case data to characterize spatial risk. Using monthly and yearly county-level public health surveillance data and various environmental and socioeconomic characteristics, we use a spatio-temporal occupancy model to estimate latent, or unobserved, presence of H. capsulatum , accounting for imperfect detection of histoplasmosis cases. We estimate areas with higher probabilities of the presence of H. capsulatum in the East North Central states around the Great Lakes, reflecting a shift of the endemic region to the north from previous estimates. The presence of H. capsulatum was strongly associated with higher soil nitrogen levels. In this investigation, we were able to mitigate challenges related to reporting and illustrate a shift in the endemic region from historical estimates. This work aims to help inform future surveillance needs, clinical awareness, and testing decisions for histoplasmosis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

Large language models (LLMs) show promise in supporting differential diagnosis, but their performance is challenging to evaluate due to the unstructured nature of their responses, and their accuracy compared to existing diagnostic tools is not well characterized. To assess the current capabilities of LLMs to diagnose genetic diseases, we benchmarked these models on 5213 previously published case reports using the Phenopacket Schema, the Human Phenotype Ontology and Mondo disease ontology. Prompts generated from each phenopacket were sent to seven LLMs, including four generalist models and three LLMs specialized for medical applications. The same phenopackets were used as input to a widely used diagnostic tool, Exomiser, in phenotype-only mode. The best LLM ranked the correct diagnosis first in 23.6% of cases, whereas Exomiser did so in 35.5% of cases. While the performance of LLMs for supporting differential diagnosis has been improving, it has not reached the level of commonly used traditional bioinformatics tools. Future research is needed to determine the best approach to incorporate LLMs into diagnostic pipelines.

Reese, Justin T. [Lawrence Berkeley National Labor↗

NASA NTRS1993

An Analytical Study of Dilution Jet Mixing in a Cylindrical Duct

The mixing performance in a mixing section of a rich burn/quick mix/lean burn (RQL) combustor was calculated using a 3-D numerical model in a non-reacting environment. The numerically calculated results were compared with the measured data reported by Hatch, Sowa, Samuelsen, and Holdeman, 1992. The numerical 3-D temperature fields qualitatively agree with the experimental data. Also, the development of the mixing flow and temperature non-uniformity trends throughout the mixing section for the numerically calculated results quantitatively agree with the measured data. The numerical model predicts less mixing and enhances the temperature gradients as compared to the measured data for the cases reported by Hatch et al. (1992) which include circular and slot orifice shapes (with different slant angles and aspect ratios). The predicted and measured results generally agree in the selection of the slanted slot orifice configuration yielding the best overall mixing performance (based on temperature uniformity) of all the configurations analyzed.

Oechsle, V. L.↗

NASA NTRS1993

An analytical study of dilution jet mixing in a cylindrical duct

Oechsle, V. L.↗

NASA NTRS2013

Parameter Estimation for Compact Binary Coalescence Signals with the First Generation Gravitational-Wave Detector Network

Compact binary systems with neutron stars or black holes are one of the most promising sources for ground-based gravitational-wave detectors. Gravitational radiation encodes rich information about source physics; thus parameter estimation and model selection are crucial analysis steps for any detection candidate events. Detailed models of the anticipated waveforms enable inference on several parameters, such as component masses, spins, sky location and distance, that are essential for new astrophysical studies of these sources. However, accurate measurements of these parameters and discrimination of models describing the underlying physics are complicated by artifacts in the data, uncertainties in the waveform models and in the calibration of the detectors. Here we report such measurements on a selection of simulated signals added either in hardware or software to the data collected by the two LIGO instruments and the Virgo detector during their most recent joint science run, including a blind injection where the signal was not initially revealed to the collaboration. We exemplify the ability to extract information about the source physics on signals that cover the neutron-star and black-hole binary parameter space over the component mass range 1M25M and the full range of spin parameters. The cases reported in this study provide a snapshot of the status of parameter estimation in preparation for the operation of advanced detectors.

Aasi, J.↗

NASA NTRS2024

Review of the Natural History of Renal Stones in U.S. Astronauts

BACKGROUND: The formation of renal stones in astronauts may pose a considerable threat to crew health and to the completion of mission objectives. Although a history of prior renal stones is an exclusion criterion for initial selection, there have been reported cases of renal stones that have developed after selection. This led to the establishment, nine years ago, of a standardized protocol to screen for the development of renal stones pre-and post-spaceflight in all active astronauts. OVERVIEW: Literature regarding stone makeup, size, location, time to passage, and outcomes were reviewed, as well as incidence of renal stones in astronaut analog populations such as military pilots and the general population. The Lifetime Surveillance of Astronaut Health (LSAH) database was queried and as of 2015 there have been 22 crew members who have reported 36 renal stone events from a population of 357 astronauts, with an incidence of 0.32 events per year. This compares favorably to the incidence of 0.37 to 0.46events per year in commercial pilots. DISCUSSION: The physiologic changes associated with spaceflight have been thought to present an increased risk for the development of stones, including hypercalciuria, decreased urine pH, and reduced urine volume. NASA’s screening program, based on a rigorous ultrasound method, has now provided nine years of clinical data used to reduce the risk of flying an astronaut with a renal stone that could threaten health and mission objectives. This work and data from the ultrasound screening program was used to update the clinical practice guideline for renal stone surveillance and treatment, and other NASA documents and programs that track this risk.

C McNerlin↗

DOE OSTI2023

Scanning Mobility Particle Sizer (SMPS)-Aerodynamic Particle Sizer (APS) Merged Size Distribution (mergedsmpsaps) Value-Added Product Report

Aerosol particles influence the Earth’s radiation balance directly by absorbing and scattering light and indirectly by influencing cloud formation, properties, and lifetimes. Measurements of aerosol particle optical properties, mass loading, size distributions, microphysical properties, cloud formation properties, and chemical composition are important for understanding the aerosol life cycle and for validating earth system models that predict these quantities. The Atmospheric Radiation Measurement (ARM) user facility’s Aerosol Observing System (AOS) is a highly instrumented platform designed to house instruments that measure many of these aerosol properties in situ. Currently, ARM operates at least four different instruments that measure a portion of the ambient aerosol size distribution. Most users are interested in the entire size distribution or a portion of the size distribution that extends across the measurement range of multiple instruments. However, merging these distributions is not trivial as the instruments employ different measurement principals and, in most cases, report data as a function of different representations of the aerosol diameter.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Challenges of COVID-19 Case Forecasting in the US, 2020–2021

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub ( https://covid19forecasthub.org ). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1–4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1979

A comparison of linear acoustic theory with experimental noise data for a small-scale hovering rotor

Linear acoustic calculations based on full aerodynamic data as input are presented and compared with measured cases reported by Boxwell et al. (1978). The full aerodynamic data are obtained using three programs giving radial loading, chordwise loading, and chordwise position of transition. It is shown that in the theoretical results the most significant noise source mechanism is due to blade thickness. Thus the conclusions of Boxwell et al. as to the importance of nonlinearities around the blades are upheld. These conclusions concern the width, shape and the level of the acoustic pressure calculated from linear acoustic theory. Some of the approximations involved in the application of acoustic analogy using quadrupole sources are discussed. It is necessary that the near- and far-field problems of rotating blades be treated together as shown for the case of an oscillating sphere.

Farassat, F.↗