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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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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Reagent-free Hyperspectral Diagnosis of SARS-CoV-2 Infection in Saliva Samples

Rapid, reagent-free pathogen-agnostic diagnostics that can be performed at the point of need are vital for preparedness against future outbreaks. Yet, many current strategies are pathogen-specific and require several reagents. We present hyperspectral sensing, using light to non-invasively measure the composition of several molecules to form a spectral signature, to overcome these barriers. To generate these spectral signatures, we present the ProSpectral TM V1, a novel, miniaturized hyperspectral platform with high spectral resolution with two mini-spectrometers. Furthermore, we developed state-of-the-art ML pipelines for near real-time analysis of spectral signatures in saliva samples. We found that we could accurately identify SARS-CoV-2 infection status in double-blinded saliva samples and demonstrate 100% accuracy on a hold out test dataset. To our knowledge, this establishes the fastest hyperspectral diagnostic platform and in a small form factor, and executable with liquid samples, without ligands or reagents, all while maintaining PCR level specificity and sensitivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tracking the SARS-CoV-2 Epidemic Using the Evolutionary Rate

This project aimed to track the developing COVID-19 epidemic through measuring the virus evolutionary rate. This may give us a way to estimate the impact of prevention campaigns and other changes in the epidemiology that we otherwise would have difficulty to estimate. Based on our previous knowledge of how viruses are affected by their environment, we investigated how spread and prevention measures may affect the virus evolutionary rate. We found that SARS-CoV-2, which causes the COVID-19 epidemic, evolves relatively slow as compared to other RNA viruses. Thus, this makes it hard to see rate changes and track the spread at a fine scale. This did in fact mislead several high-profile reports in the early phases of the epidemic. We published comments and editorials in leading journals on this. Because the COVID-19 epidemic is till ongoing, and much data is still incoming, it is likely that evolutionary-epidemiological analyses will reveal important facts later on.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Illumina Sequencing for SARS-CoV-2 Training [Slides]

This report compiles Wetlab training slides for DTRA sponsored training and has presentations titled: 1) Library Validation Step 2: Bioanalyzer DNA HS Assay, 2) Library Validation Step 3: qPCR, 3) Setting up a MiSeq Run, 4) Sample Prep & Initial QC, 5) Detailed Illumina MiSeq Sequencing, 6) AmpliSeq for Illumina: Best Practices, and 7) Sample/Data Management for SARS-CoV-2 Samples.

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

SAR Geolocation Using Range-Only Multilateration

Radar is by its basic nature a ranging instrument. If radar range measurements from multiple directions can be made and assembled, then multilateration allows locating a feature common to the set of Synthetic Aperture Radar (SAR) images to an accurate 3-D coordinate. The ability to employ effective multilateration algorithms is highly dependent on the geometry of the data collections, and the accuracy with which relative range measurements can be made. The problem can be cast as a least-squares exercise, and the concept of Dilution of Precision can describe the accuracy and precision with which a 3-D location can be made.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

SAR Geolocation Using Range-Doppler Multilateration

Radar is by its basic nature a ranging instrument. If radar range and range-rate measurements from multiple directions can be made and assembled, then multilateration allows locating a feature common to the set of Synthetic Aperture Radar (SAR) images to an accurate 3-D coordinate. The ability to employ effective multilateration algorithms is highly dependent on the geometry of the data collections, and the accuracy with which relative range measurements can be made. The problem can be cast as a least-squares exercise, and the concept of Dilution of Precision can describe the accuracy and precision with which a 3-D location can be made.

42 ENGINEERING↗
DOE OSTI2021

Optimizing Layered Control Strategies for Reducing Exposure to SARS-CoV-2

While there is growing understanding of the predominance of the airborne mode of transmission of the SARS-CoV-2 virus, there is a lack of guidance on how to build an effective system of controls to mitigate transmission in enclosed spaces. Such a system integrates multiple hazard-specific control measures to both eliminate or replace a hazard, and safeguard individuals against potential exposure and infection. Controls are defined by the US Occupational Safety and Health Association (OSHA) as the use of engineering methods to reduce the level of hazard inside a confined space. The Hierarchy of Controls provides a framework through which a system of controls can be examined; identifying those which directly remove or replace a hazard as the most effective, and individual behavioral measures (e.g., masking or shielding) as least effective. Use of such a framework to quantify control effectiveness might allow for the promotion of spaces as meeting a certain threshold of safety, likely adding to the confidence of space users resulting in increases in various metrics such as sales, visits, or likes.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Model for Interpreting Discordant SARS-CoV-2 Diagnostic Test Results

We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020–May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a 15.4% (95% CI 0.6%–56.7%) chance of being infected.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid–amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The Promise of Mutation Resistant Drugs for SARS-CoV-2 That Interdict in the Folding of the Spike Protein Receptor Binding Domain

In recent work, we proposed that effective therapeutic drugs aimed at treating the SARS-CoV-2 infection could be developed based on interdicting in the early steps of the folding pathway of key viral proteins, including the receptor binding domain (RBD) of the spike protein. In order to provide for a drug target on the protein, the earliest contact-formation event along the dominant folding pathway of the RBD spike protein was predicted employing the Sequential Collapse Model (SCM). The segments involved in the predicted earliest contact were suggested to provide optimal folding interdiction target regions (FITRs) for potential therapeutic drugs, with a focus on folding interdicting peptides (FIPs). In this paper, we extend our analysis to include 13 known single mutations of the RBD spike protein as well as the triple mutation B1.351 and the recent double mutation B1.617.2. The results show that the location of the FITR does not change in any of the 15 studied mutations, providing for a mutation-resistant drug design strategy for the RBD-spike protein.

Bergasa-Caceres, Fernando↗
DOE OSTI2022

Response to comment on ‘SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung’

Early in the SARS-CoV-2 pandemic, we compared transcriptome data from hospitalized COVID-19 patients and control patients without COVID-19. We found changes in procoagulant and fibrinolytic gene expression in the lungs of COVID-19 patients. These findings have been challenged based on issues with the samples. We have revisited our previous analyses in the light of this challenge and find that these new analyses support our original conclusions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Air Return Strategies and Airborne SARS-CoV-2

Dedicated ducted air return per zone for heating, ventilating, and air-conditioning (HVAC) systems is sometimes claimed to be a superior technique over plenum return strategy from the viewpoint of exposure reduction to airborne pathogens. While both the return strategies have advantages, there is limited evidence in the literature as to which strategy is superior merely from a standpoint of building vulnerability to airborne contaminants. We performed multizonal airborne contaminant dispersion modelling using CONTAM to simulate the overall building vulnerability to airborne SARS-CoV-2 aerosols when released in an office building and evaluated the two air return strategies. Results showed that for ducted returns, maintaining negative pressure in the release zone coupled with 100% outdoor air supply can greatly reduce overall building vulnerability. However, for a building maintained under a slight positive pressure and a recirculated air percentage as low as 31%, ducted returns do not necessarily outperform plenum returns in terms of overall building vulnerability to airborne pathogens. Building-specific details and factors that are not easily represented with multizone modelling are important, making general preferential statements for either strategy difficult to make. Insights from this study can guide new construction and retrofits of buildings both during and after the COVID-19 pandemic with the aim of safe re-occupancy of buildings while keeping the buildings resilient against potential future epidemics spread by airborne agents.

Shrestha, Prateek↗
DOE OSTI2022

Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.

Teixeira Prates, Erica↗