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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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DOE OSTI2022

A modified Susceptible-Infected-Recovered model for observed under-reported incidence data

Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data when a fixed fraction of newly infected individuals are not observed. The parameters of the resulting system of differential equations are identifiable. Using these differential equations, we develop a stochastic model for the conditional distribution of current disease incidence given the entire past history of reported cases. We estimate the model parameters using Bayesian Markov Chain Monte-Carlo sampling of the posterior distribution. We use our model to estimate the transmission rate and fraction of asymptomatic individuals for the current Coronavirus 2019 outbreak in eight American Countries: the United States of America, Brazil, Mexico, Argentina, Chile, Colombia, Peru, and Panama, from January 2020 to May 2021. Our analysis reveals that the fraction of reported cases varies across all countries. For example, the reported incidence fraction for the United States of America varies from 0.3 to 0.6, while for Brazil it varies from 0.2 to 0.4.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

SARS-CoV-2 spike protein variant binding affinity to an angiotensin-converting enzyme 2 fusion glycoproteins

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (Covid-19) pandemic, continues to evolve and circulate globally. Current prophylactic and therapeutic countermeasures against Covid-19 infection include vaccines, small molecule drugs, and neutralizing monoclonal antibodies. SARS-CoV-2 infection is mainly mediated by the viral spike glycoprotein binding to angiotensin converting enzyme 2 (ACE2) on host cells for viral entry. As emerging mutations in the spike protein evade efficacy of spike-targeted countermeasures, a potential strategy to counter SARS-CoV-2 infection is to competitively block the spike protein from binding to the host ACE2 using a soluble recombinant fusion protein that contains a human ACE2 and an IgG1-Fc domain (ACE2-Fc). Here, we have established Chinese Hamster Ovary (CHO) cell lines that stably express ACE2-Fc proteins in which the ACE2 domain either has or has no catalytic activity. The fusion proteins were produced and purified to partially characterize physicochemical properties and spike protein binding. Our results demonstrate the ACE2-Fc fusion proteins are heavily N-glycosylated, sensitive to thermal stress, and actively bind to five spike protein variants (parental, alpha, beta, delta, and omicron) with different affinity. Our data demonstrates a proof-of-concept production strategy for ACE2-Fc fusion glycoproteins that can bind to different spike protein variants to support the manufacture of potential alternative countermeasures for emerging SARS-CoV-2 variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections

Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae , were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential cross-neutralizing epitopes on SARS-like viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we don’t yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift suggest low and time-varying establishment probabilities for new mutations, inform the parametrization of SARS-CoV-2 evolutionary models, and motivate future studies of the potential mechanisms for increased stochasticity in this system.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Chaos, Percolation and the Coronavirus Spread

The dynamics of the spreading of the COVID-19 virus has similar features to the turbulent flow, chaotic maps and other non-linear systems: a small seed grows exponentially and eventually saturates. Like in the percolation model, the virus is mostly dangerous if the probability of transmission (or the bond probability p in the percolation model) is high. This suggests a relation with the population density, ρ s , which must be higher than a certain value (ρ s > 1000 persons/km 2 ). A ‘seed’ implanted in such towns grows vigorously and affects nearby places at distance x. Thus, the spreading is governed by the ratio ρ = ρ s /x. Assuming a power law dependence τ of the number of positives to the virus N + from ρ, we find τ = 0.55, 0.75 and 0.96 for S.Korea, Italy and China respectively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave

Disease modelling has had considerable policy impact during the ongoing COVID-19 pandemic, and it is increasingly acknowledged that combining multiple models can improve the reliability of outputs. Here we report insights from ten weeks of collaborative short-term forecasting of COVID-19 in Germany and Poland (12 October–19 December 2020). The study period covers the onset of the second wave in both countries, with tightening non-pharmaceutical interventions (NPIs) and subsequently a decay (Poland) or plateau and renewed increase (Germany) in reported cases. Thirteen independent teams provided probabilistic real-time forecasts of COVID-19 cases and deaths. These were reported for lead times of one to four weeks, with evaluation focused on one- and two-week horizons, which are less affected by changing NPIs. Heterogeneity between forecasts was considerable both in terms of point predictions and forecast spread. Ensemble forecasts showed good relative performance, in particular in terms of coverage, but did not clearly dominate single-model predictions. The study was preregistered and will be followed up in future phases of the pandemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Publication and Impact of Preprints Included in the First 100 Editions of the CDC COVID-19 Science Update: Content Analysis

Preprints are publicly available manuscripts posted to various servers that have not been peer reviewed. Although preprints have existed since 1961, they have gained increased popularity during the COVID-19 pandemic due to the need for immediate, relevant information. The aim of this study is to evaluate the publication rate and impact of preprints included in the Centers for Disease Control and Prevention (CDC) COVID-19 Science Update and assess the performance of the COVID-19 Science Update team in selecting impactful preprints. All preprints in the first 100 editions (April 1, 2020, to July 30, 2021) of the Science Update were included in the study. Preprints that were not published were categorized as “unpublished preprints.” Preprints that were subsequently published exist in 2 versions (in a peer-reviewed journal and on the original preprint server), which were analyzed separately and referred to as “peer-reviewed preprint” and “original preprint,” respectively. Time to publish was the time interval between the date on which a preprint was first posted and the date on which it was first available as a peer-reviewed article. Impact was quantified by Altmetric Attention Score and citation count for all available manuscripts on August 6, 2021. Preprints were analyzed by publication status, publication rate, preprint server, and time to publication. Of the 275 preprints included in the CDC COVID-19 Science Update during the study period, most came from three servers: medRxiv (n=201, 73.1%), bioRxiv (n=41, 14.9%), and SSRN (n=25, 9.1%), with 8 (2.9%) coming from other sources. Additionally, 152 (55.3%) were eventually published. The median time to publish was 2.3 (IQR 1.4-3.7). When preprints posted in the last 2.3 months were excluded (to account for the time to publish), the publication rate was 67.8%. Moreover, 76 journals published at least one preprint from the CDC COVID-19 Science Update, and 18 journals published at least three. The median Altmetric Attention Score for unpublished preprints (n=123, 44.7%) was 146 (IQR 22-552) with a median citation count of 2 (IQR 0-8); for original preprints (n=152, 55.2%), these values were 212 (IQR 22-1164) and 14 (IQR 2-40), respectively; for peer-review preprints, these values were 265 (IQR 29-1896) and 19 (IQR 3-101), respectively. Prior studies of COVID-19 preprints found publication rates between 5.4% and 21.1%. Preprints included in the CDC COVID-19 Science Update were published at a higher rate than overall COVID-19 preprints, and those that were ultimately published were published within months and received higher attention scores than unpublished preprints. These findings indicate that the Science Update process for selecting preprints had a high fidelity in terms of their likelihood to be published and their impact. The incorporation of high-quality preprints into the CDC COVID-19 Science Update improves this activity’s capacity to inform meaningful public health decision-making.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

TDCOSMO - XVII. New time delays in 22 lensed quasars from optical monitoring with the ESO-VST 2.6m and MPG 2.2m telescopes

We present new time delays, the main ingredient of time delay cosmography, for 22 lensed quasars resulting from high-cadence r-band monitoring on the 2.6 m ESO VLT Survey Telescope and Max-Planck-Gesellschaft 2.2 m telescope. Each lensed quasar was typically monitored for one to four seasons, often shared between the two telescopes to mitigate the interruptions forced by the COVID-19 pandemic. The sample of targets consists of 19 quadruply and 3 doubly imaged quasars, which received a total of 1918 hours of on-sky time split into 21 581 wide-field frames, each 320 seconds long. In a given field, the 5-σ depth of the combined exposures typically reaches the 27th magnitude, while that of single visits is 24.5 mag – similar to the expected depth of the upcoming Vera-Rubin LSST. The fluxes of the different lensed images of the targets were reliably de-blended, providing not only light curves with photometric precision down to the photon noise limit, but also high-resolution models of the targets whose features and astrometry were systematically confirmed in Hubble Space Telescope imaging. This was made possible thanks to a new photometric pipeline, lightcurver, and the forward modelling method STARRED. Finally, the time delays between pairs of curves and their uncertainties were estimated, taking into account the degeneracy due to microlensing, and for the first time the full covariance matrices of the delay pairs are provided. Of note, this survey, with 13 square degrees, has applications beyond that of time delays, such as the study of the structure function of the multiple high-redshift quasars present in the footprint at a new high in terms of both depth and frequency. The reduced images will be available through the European Southern Observatory Science Portal.Key words: methods: data analysis / surveys / distance scale

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Aerosol transport pathways and source attribution in China during the COVID-19 outbreak

Abstract. Due to the coronavirus disease 2019 (COVID-19) pandemic, human activities and industrial productions were strictly restricted during January–March 2020 in China. Despite the fact that anthropogenic aerosol emissions largely decreased, haze events still occurred. Characterization of aerosol transport pathways and attribution of aerosol sources from specific regions are beneficial to air quality and pandemic control strategies. This study establishes source–receptor relationships in various regions covering all of China during the COVID-19 outbreak based on the Community Atmosphere Model version 5 with Explicit Aerosol Source Tagging (CAM5-EAST). Our analysis shows that PM2.5 burden over the North China Plain between 30 January and 19 February is mostly contributed by local emissions (40 %–66 %). For other regions in China, PM2.5 burden is largely contributed from nonlocal sources. During the most polluted days of the COVID-19 outbreak, local emissions within the North China Plain and eastern China contributed 66 % and 87 % to the increase in surface PM2.5 concentrations, respectively. This is associated with the anomalous mid-tropospheric high pressure at the location of the climatological East Asia trough and the consequently weakened winds in the lower troposphere, leading to the local aerosol accumulation. The emissions outside China, especially those from South Asia and Southeast Asia, contribute over 50 % to the increase in PM2.5 concentration in southwestern China through transboundary transport during the most polluted day. As the reduction in emissions in the near future is desirable, aerosols from long-range transport and unfavorable meteorological conditions are increasingly important to regional air quality and need to be taken into account in clean-air plans.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Excess deaths reveal unequal impact of COVID-19 in Ecuador

Latin America has struggled to control the transmission of COVID-19. Comparison of excess death (ED) rates during the pandemic reveals that Ecuador is among the highest impacted countries. In this analysis, we update our previous findings with the most complete all-cause mortality records available for 2020, disaggregated by sex, age, ethnicity and geography. Our study shows that in 2020, Ecuador had a 64% ED rate (95% CI 63% to 65%) or 64% more deaths than expected. Men had a higher ED rate, 75% (95% CI 73% to 76%), than women’s 51% (95% CI 49% to 52%), and this pattern of higher EDs for men than women held for most age groups. The only exception was the 20–29 age group, where women had 19% more deaths, compared to 10% more deaths for men, but that difference is not statistically significant. The analysis provides striking evidence of the lack of COVID-19 diagnostic testing in Ecuador: the confirmed COVID-19 deaths in 2020 accounted for only 21% of total EDs. Our significant finding is that indigenous populations, who typically account for about 5% of the deaths, show almost four times the ED rate of the majority mestizo group. Indigenous women in each age group have higher ED rates than the general population and, in ages between 20 and 49 years, they have higher ED rates than indigenous men. Indigenous women in the age group 20–29 years had an ED rate of 141%, which is commensurate to the ED rate of indigenous women older than 40 years.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Validation of pooling strategies of clinical COVID-19 samples for more efficient diagnostic testing

Pooling of COVID-19 clinical samples can offer significant reduction in reagents, time, and labor needed to test large numbers of clinical samples. Especially for testing asymptomatic and return-towork/ school cases, where the prevalence of COVID-19 may be relatively low, large groups of clinical samples can be classified as negative with a single test, with no need to test every sample individually. LANL has performed validation for two different pooling strategies to assess diagnostic assay sensitivity in pooled samples compared to the clinical positive sample alone. (1) Pooling study - Determine diagnostic assay sensitivity in pooled samples with ratios of 1:5, 1:10, 1:20, and 1:30 positive to negative clinical samples. (2) Reloading study - Determine diagnostic assay sensitivity in reloading of multiple clinical samples through a Qiagen column in 5x, 10, and 20x sample volumes (1 positive plus 4, 9, and 19 negative samples).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Preface to “From Coadsorption and Catalysis at Solid Surfaces to Liquid–Solid Interfaces in Theory and Experiment, Published in Honor of Professor Robert K. Grasselli, Irsee IX Symposium Kloster Irsee, Germany 16–19 June 2022 (Irsee IX)”

The 9th Irsee Symposium entitled “From Coadsorption and Catalysis at Solid Surfaces to Liquid–Solid Interfaces in Theory and Experiment”, sponsored by the Robert Karl Grasselli Foundation, took place at its traditional venue, the Schwäbisches Bildungszentrum in Irsee, Germany, on 16–19 June 2022. In the Irsee Symposium, selected experts gather every few years to discuss recent progress, challenges, new directions, and frontiers in catalysis. Furthermore, after the moratorium imposed on us by Covid-19, all the participants especially enjoyed the lively meeting and face-to-face interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

High-throughput virtual laboratory for drug discovery using massive datasets

Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit supercomputer, allowing an average molecular docking of 19,028 compounds per second. Over one billion compounds were docked to two SARS-CoV-2 protein structures with full optimization of ligand position and 20 poses per docking, each in under 24 hours. GPU acceleration and high-throughput optimizations of the docking program produced 350× mean speedup over the CPU version (50× speedup per node). GPU acceleration of both feature calculation for machine-learning based scoring and distributed database queries reduced processing of the 2.4 TB output by orders of magnitude. The resulting 50× speedup for the full pipeline reduces an initial 43 day runtime to 21 hours per protein for providing high-scoring compounds to experimental collaborators for validation assays.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The use of analgesics for intentional self-poisoning: Trends in U.S. poison center data

In the U.S., intentional self-poisonings with analgesics that are available without a prescription increased from 2000 to 2018. Given concerns regarding mental health outcomes during the COVID-19 pandemic, we examined and compared trends in pediatric and adult intentional self-poisoning with acetaminophen, aspirin, ibuprofen, and naproxen from 2016 to 2021 using the National Poison Data System (NPDS) to see if these trends have continued. We extracted annual case counts of all suspected suicide attempts from intentional poisoning, and of suspected suicide attempts resulting in major effects or death, from the NPDS for non-prescription single ingredient adult formulation acetaminophen, non-prescription single ingredient adult formulation aspirin, single ingredient formulation ibuprofen, and single ingredient formulation naproxen. We enumerated the cases by year, age, and gender. Most cases of intentional self-poisoning within the review period involved acetaminophen and ibuprofen and the 13–19-year-olds constituted the highest proportion of intentional self-poisoning cases across age groups for all four analgesics. Cases involving females predominated cases involving males by 3:1 or greater. Here, the 13–19-year-old age group also represented the largest proportion of cases that resulted in major clinical effects or deaths. An increasing trend in suicide poisoning cases with acetaminophen and ibuprofen was observed in the 6-19-years age group and this trend appeared to exacerbate from 2020 to 2021 corresponding with the start of the COVID-19 pandemic period.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Delivering Effective Virtual Energy-Focused Trainings: Successful Strategies and Lessons Learned from the Virtual Cohort In-Plant Training Pilot

While there are always barriers to energy efficiency efforts, few challenges have been as severe as the global COVID-19 pandemic. Many manufacturers throughout the United States and the world have been trying to determine how to safely open and operate their plants. To minimize the number of people working within facilities and maximize the physical distance between workers, only essential facility engineers are allowed into plants to ensure proper operations. The Department of Energy’s Better Plants Program created In-Plant Trainings (INPLTs) to help partners develop in-house expertise in energy efficiency. Delivering INPLTs in the traditional in-person fashion is infeasible under these circumstances. To continue providing INPLTs during this difficult time, the Better Plants Program piloted Virtual Cohort In-Plant Trainings (VINPLTs) on wastewater treatment and ammonia industrial refrigeration systems from October 27 to November 19, 2020. This paper provides an overview of the pilot, then discusses successful strategies and lessons learned from this pilot for delivering effective virtual energy-focused trainings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

An Extension Industrial Assessment Center in Eastern Great Lakes Region

The extension IAC at CWRU is funded for 3 years to conduct 10 assessments of small and medium-sized manufacturing facilities each year in Eastern Great Lakes region. Total 30 assessments was proposed in the SOPO but due to the Covid-19 pandemic, the IAC program was suspended for 1.5 years. A total of 20 assessments was contracted to the extension IAC at CWRU which have been successfully accomplished. In the proposal, we proposed to train 18 students in the extension IAC program, and actually we selected and trained 19 students even though the IAC project was suspended during half of its project period.

42 ENGINEERING↗