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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA

Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention’s (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC’s probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

GenAI-Based Digital Twins Aided Data Augmentation Increases Accuracy in Real-Time Cokurtosis-Based Anomaly Detection of Wearable Data

Early detection of potential infectious disease outbreaks is crucial for developing effective interventions. In this study, we introduce advanced anomaly detection methods tailored for health datasets collected from wearables, offering insights at both individual and population levels. Leveraging real-world physiological data from wearables, including heart rate and activity, we developed a framework for the early detection of infection in individuals. Despite the availability of data from recent pandemics, substantial gaps remain in data collection, hindering method development. To bridge this gap, we utilized Wasserstein Generative Adversarial Networks (WGANs) to generate realistic synthetic wearable data, augmenting our dataset for training. Subsequently, we use these augmented datasets to implement a cokurtosis-based technique for anomaly detection in multivariate time-series data. Our approach includes a comprehensive assessment of uncertainties in synthetic data compared to the actual data upon which it was modeled, as well as the uncertainty associated with fine-tuning anomaly detection thresholds in physiological measurements. Through our work, we present an enhanced method for early anomaly detection in multivariate datasets, with promising applications in healthcare and beyond. This framework could revolutionize early detection strategies and significantly impact public health response efforts in future pandemics.

Data-Driven Digital Twins↗
DOE OSTI2020

The International Virus Bioinformatics Meeting 2020

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants

The emergence and availability of closely related clinical isolates of SARS-CoV-2 offers a unique opportunity to identify novel nonsynonymous mutations that may impact phenotype. Global sequencing efforts show that SARS-CoV-2 variants have emerged and then been replaced since the beginning of the pandemic, yet we have limited information regarding the breadth of variant-specific host responses. Using primary cell cultures and the K18-hACE2 mouse, we investigated the replication, innate immune response, and pathology of closely related, clinical variants circulating during the first wave of the pandemic. Mathematical modeling of the lung viral replication of four clinical isolates showed a dichotomy between two B.1. isolates with significantly faster and slower infected cell clearance rates, respectively. While isolates induced several common immune host responses to infection, one B.1 isolate was unique in the promotion of eosinophil-associated proteins IL-5 and CCL11. Moreover, its mortality rate was significantly slower. Lung microscopic histopathology suggested further phenotypic divergence among the five isolates showing three distinct sets of phenotypes: (i) consolidation, alveolar hemorrhage, and inflammation, (ii) interstitial inflammation/septal thickening and peribronchiolar/perivascular lymphoid cells, and (iii) consolidation, alveolar involvement, and endothelial hypertrophy/margination. Together these findings show divergence in the phenotypic outcomes of these clinical isolates and reveal the potential importance of nonsynonymous mutations in nsp2 and ORF8.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Interchangeability of the Assays Used to Assess the Activity of Anti-SARS-CoV-2 Monoclonal Antibodies

The recent global COVID-19 pandemic caused by SARS-CoV-2 lasted for over three years. A key measure in combatting this pandemic involved the measurement of the monoclonal antibody (mAb)-mediated inhibition of binding between the spike receptor-binding domain (RBD) and hACE2 receptor. Potency assessments of therapeutic anti-SARS-CoV-2 mAbs typically include binding or cell-based neutralization assays. We assessed the inhibitory activity of five anti-SARS-CoV-2 mAbs using ELISA, surface plasmon resonance (SPR), and four cell-based neutralization assays using different pseudovirus particles and 293T or A549 cells expressing hACE2 with or without TMPRSS2. We assessed the interchangeability between cell-based and binding assays by applying the Bland–Altman method under certain assumptions. Our data demonstrated that the IC50 [nM] values determined by eight neutralization assays are independent of the cell line, presence of TMPRSS2 enzyme on the cell surface, and pseudovirus backbone used. Moreover, the Bland–Altman analysis showed that the IC50 [nM] and KD [nM] values determined by neutralization/ELISA or by SPR are equivalent and that the anti-spike mAb activity can be attributed to one variable directly related to its tertiary conformational structure conformation, rate dissociation constant Koff. This parameter is independent from the concentrations of the components of the mAb:RBD:hACE2 complexes and can be used for a comparison between the activities of the different mAbs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The 2022 Outbreaks of African Swine Fever Virus Demonstrate the First Report of Genotype II in Ghana

African swine fever (ASF) is a lethal disease of domestic pigs that has been causing outbreaks for over a century in Africa ever since its first discovery in 1921. Since 1957, there have been sporadic outbreaks outside of Africa; however, no outbreak has been as devastating and as far-reaching as the current pandemic that originated from a 2007 outbreak in the Republic of Georgia. Derivatives with a high degree of similarity to the progenitor strain, ASFV-Georgia/2007, have been sequenced from various countries in Europe and Asia. However, the current strains circulating in Africa are largely unknown, and 24 different genotypes have been implicated in different outbreaks. In this study, ASF isolates were collected from samples from swine suspected of dying from ASF on farms in Ghana in early 2022. While previous studies determined that the circulating strains in Ghana were p72 Genotype I, we demonstrate here that the strains circulating in 2022 were derivatives of the p72 Genotype II pandemic strain. Therefore, this study demonstrates for the first time the emergence of Genotype II ASFV in Ghana.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

60 APPLIED LIFE SCIENCES↗
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↗
NASA NTRS2020

Current and future global climate impacts resulting from COVID-19

The global response to the COVID-19 pandemic has led to a sudden reduction of both GHG emissions and air pollutants. Here, using national mobility data, we estimate global emission reductions for ten species during the period February to June 2020. We estimate that global NOx emissions declined by as much as 30% in April, contributing a short-term cooling since the start of the year. This cooling trend is offset by ~20% reduction in global SO2 emissions that weakens the aerosol cooling effect, causing short-term warming. As a result, we estimate that the direct effect of the pandemic-driven response will be negligible, with a cooling of around 0.01 ± 0.005 °C by 2030 compared to a baseline scenario that follows current national policies. In contrast, with an economic recovery tilted towards green stimulus and reductions in fossil fuel investments, it is possible to avoid future warming of 0.3 °C by 2050.

Piers M. Forster↗
NASA NTRS2020

The Reinvention of Aviation: The Effects of Covid-19 on the Aviation Industry, and Actions Needed to Ensure its Future Success

This research project sought to develop short-term and long-term projections on the outlook of air transportation and to produce relevant recommendations for the direction of NASA aviation research as it adapts to the disrupted industry. We developed a model to estimate airline recovery trajectories, and researched the unique effects of the pandemic on various sectors of aviation. We found that the pandemic highlighted past flaws in the aviation system, creating widespread effects across the industry. As the industry looks towards recovery, we believe that it cannot simply return to 2019 operations, but instead perform a full reinvention to support long-term demand and prepare for future catastrophes. We recommend that NASA seize this opportunity to accelerate innovation through an increased focus on passenger satisfaction, meaningful steps towards sustainability, and significant collaboration with a diverse range of groups.

Andres Carranza↗
NASA NTRSDate not supplied

The Reinvention of Aviation: The Effects of Covid-19 on the Aviation Industry, and Actions Needed to Ensure its Future Success

This research project sought to develop short-term and long-term projections on the outlook of air transportation and to produce relevant recommendations for the direction of NASA aviation research as it adapts to the disrupted industry. We developed a model to estimate airline recovery trajectories, and researched the unique effects of the pandemic on various sectors of aviation. We found that the pandemic highlighted past flaws in the aviation system, creating widespread effects across the industry. As the industry looks towards recovery, we believe that it cannot simply return to 2019 operations, but instead perform a full reinvention to support long-term demand and prepare for future catastrophes. We recommend that NASA seize this opportunity to accelerate innovation through an increased focus on passenger satisfaction, meaningful steps towards sustainability, and significant collaboration with a diverse range of groups.

high school intern project↗
NASA NTRS2020

The Reinvention of Aviation: The Effects of Covid-19 on the Aviation Industry, and Actions Needed to Ensure its Future Success

This research project sought to develop short-term and long-term projections on the outlook of air transportation and to produce relevant recommendations for the direction of NASA aviation research as it adapts to the disrupted industry. We developed a model to estimate airline recovery trajectories, and researched the unique effects of the pandemic on various sectors of aviation. We found that the pandemic highlighted past flaws in the aviation system, creating widespread effects across the industry. As the industry looks towards recovery, we believe that it cannot simply return to 2019 operations, but instead perform a full reinvention to support long-term demand and prepare for future catastrophes. We recommend that NASA seize this opportunity to accelerate innovation through an increased focus on passenger satisfaction, meaningful steps towards sustainability, and significant collaboration with a diverse range of groups.

high school intern project↗
NASA NTRS2020

Electromagnetic Pain Relief/Blocking: Feasibility Assessment

Context/Background: Astronauts use pharmaceuticals during spaceflight to manage acute and chronic pain, but use of analgesics will have drawbacks for exploration-class missions because the shelf life of these medications is limited, resupply will be curtailed, astronauts may develop tolerance and/or addiction to these medications, and side effects can include impairment of cognitive abilities. Electromagnetic devices have been developed that treat pain terrestrially by affecting neuromodulation–dubbed “electroceuticals”, these devices have varied mechanisms of action that either stimulate or suppress neural activity in the central nervous system or peripheral nerves. Objective/Purpose: The available literature was reviewed and FDA-approved pain treatments (both pharmacological and non-pharmacological), as well as those currently under development, were assessed for their suitability for use in exploration class spaceflight missions. Data Sources: Due to the COVID-19 pandemic and the resulting closure of libraries, data sources were restricted to those available digitally. Online database searches included PubMed, U.S. Patent and Trademark Office, federal grant award databases (National Aeronautics and Space Administration (NASA), Department of Defense (DoD), National Institutes of Health (NIH)), and general internet searches. More than 1,600 records were reviewed in this effort. Study Selection/Eligibility Criteria: Targeted searches included different aspects of pain management. Priority was given to review studies, to cover as much of the available literature as possible in this limited effort. Study Appraisal and Synthesis Methods/Data Extraction and Data Synthesis: The titles of the studies and the awards that were obtained by searching online databases were reviewed and further information was sought for the relevant titles. Abstracts or award summaries were generally available online; for journal abstracts, full text articles were either available online or were requested via interlibrary loan. Results: An overwhelming majority of the literature focuses on the treatment of chronic rather than acute pain because it is assumed that acute pain only rarely fails to resolve and instead transitions into chronic pain when the central nervous system becomes hypersensitized. The available electromagnetic devices marketed for pain treatment have varying levels of invasiveness, use different mechanisms of action, and have demonstrated varying efficacy when evaluated scientifically. A truly noninvasive, highly efficient device is desired for use during spaceflight. One portable, self-contained, FDA-approved device was identified that, from preliminarily assessment, best met these criteria; the device noninvasively applies pulsed shortwave therapy (PSWT) to modify pain signals from peripheral nerves, however, the device has limited battery life and the effects are relatively non-selective in type of neural signal modified. Limitations: This current effort, although extensive, did not identify a comprehensive list of all alternatives for pain treatment. Once the pandemic limitations are lifted, a longer, more thorough effort may find additional options. Conclusions/Implications: The ideal electromagnetic pain treatment device for use on exploration-class spaceflight missions does not yet exist, but it may be available soon. It is not feasible for NASA to develop medical devices due to the schedule constraints for pending exploration-class missions, but adapting a promising device that is already FDA-approved might be an option. Monitoring research that is ongoing at other federal agencies is recommended, and further review of the candidate PSWT device identified in this current effort may be warranted.

Carol Mullenax↗
NASA NTRS2021

Towards Disentangling Lockdown-Driven Air Quality Changes in the Northeastern U.S.

In the absence of preventive therapies or effective treatment for most cases of coronavirus disease 2019 (COVID-19), governments worldwide have sought to minimize person-to-person severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through a variety of lock-down measures and social distancing policies. Extreme events like the COVID-19 pandemic present a tremendous opportunity to make quantitative connections between changes in anthropogenic forcing, social and economic activity, and the related Earth system response. In this comment, we examine air quality impacts associated with pandemic response measures in the Northeastern United States.

Air Quality↗
NASA NTRS2021

Interactions Between Two Existential Threats: COVID-19 and Climate Change

The COVID-19 pandemic and climate change are complex existential threats, unpredictable in many ways and unprecedented in modern times. There are parallels between the scale and scope of their impacts and responses. Understanding shared drivers, coupled vulnerabilities, and criteria for effective responses will help societies worldwide prepare for the simultaneous threats of climate change and future pandemics. We summarize some shared characteristics of COVID-19 and climate change impacts and interventions and discuss key policy implications and recommendations.

Climate change adaptation↗
NASA NTRSDate not supplied

Electromagnetic Pain Relief/Blocking: Feasibility Assessment

CONTEXT/BACKGROUND Astronauts use pharmaceuticals during spaceflight to manage acute and chronic pain, but use of analgesics will have drawbacks for exploration-class missions because the shelf life of these medications is limited, resupply will be curtailed, astronauts may develop tolerance and/or addiction to these medications, and side effects can include impairment of cognitive abilities. Electromagnetic devices have been developed that treat pain terrestrially by affecting neuromodulation–dubbed “electroceuticals”, these devices have varied mechanisms of action that either stimulate or suppress neural activity in the central nervous system or peripheral nerves. OBJECTIVE/PURPOSE The available literature was reviewed and FDA-approved pain treatments (both pharmacological and non-pharmacological), as well as those currently under development, were assessed for their suitability for use in exploration class spaceflight missions. DATA SOURCES Due to the COVID-19 pandemic and the resulting closure of libraries, data sources were restricted to those available digitally. Online database searches included PubMed, U.S. Patent and Trademark Office, federal grant award databases (National Aeronautics and Space Administration (NASA), Department of Defense (DoD), National Institutes of Health (NIH)), and general internet searches. More than 1,600 records were reviewed in this effort. STUDY SELECTION/ELIGIBILITY CRITERIA Targeted searches included different aspects of pain management. Priority was given to review studies, to cover as much of the available literature as possible in this limited effort. STUDY APPRAISAL AND SYNTHESIS METHODS/DATA EXTRACTION AND DATA SYNTHESIS The titles of the studies and the awards that were obtained by searching online databases were reviewed and further information was sought for the relevant titles. Abstracts or award summaries were generally available online; for journal abstracts, full text articles were either available online or were requested via interlibrary loan. RESULTS An overwhelming majority of the literature focuses on the treatment of chronic rather than acute pain because it is assumed that acute pain only rarely fails to resolve and instead transitions into chronic pain when the central nervous system becomes hypersensitized. The available electromagnetic devices marketed for pain treatment have varying levels of invasiveness, use different mechanisms of action, and have demonstrated varying efficacy when evaluated scientifically. A truly noninvasive, highly efficient device is desired for use during spaceflight. One portable, self-contained, FDA-approved device was identified that, from preliminarily assessment, best met these criteria; the device noninvasively applies pulsed shortwave therapy (PSWT) to modify pain signals from peripheral nerves, however, the device has limited battery life and the effects are relatively non-selective in type of neural signal modified. LIMITATIONS This current effort, although extensive, did not identify a comprehensive list of all alternatives for pain treatment. Once the pandemic limitations are lifted, a longer, more thorough effort may find additional options. CONCLUSIONS/IMPLICATIONS The ideal electromagnetic pain treatment device for use on exploration-class spaceflight missions does not yet exist, but it may be available soon. It is not feasible for NASA to develop medical devices due to the schedule constraints for pending exploration-class missions, but adapting a promising device that is already FDA-approved might be an option. Monitoring research that is ongoing at other federal agencies is recommended, and further review of the candidate PSWT device identified in this current effort may be warranted.

C A Mullenax↗
NASA NTRS2021

What Makes Hybrid Concurrent Engineering Teams Work and Not Work: A Theoretical Analysis

Aerospace concurrent engineering teams (CETs) have been around since 1995 and have evolved into various shapes and forms. Historically, CETs have been designed to function with all team members physically collocated. In order to continue operating during the coronavirus pandemic, these teams have had to become fully distributed in 2020. Previously, distributed CETs were predicted to be considerably less efficient than traditional CETs. However, at JPL studies are being successfully run at peak rate in a distributed mode. As nominal working conditions resume after the pandemic, a major question is whether these teams must go back to being fully collocated or if they can become successful hybrid teams, with half or more of the engineers working remotely. In order to address this question, it is important to understand the key characteristics that make a CET more likely to be successful in a remote mode. This paper revisits a framework for characterizing concurrent engineering teams, providing a means to describe and compare the behavior of concurrent engineering teams in various settings [1], and uses the framework to make recommendations for future hybrid teams.

Chattopadhyay, Debarati↗
NASA NTRSDate not supplied

A Remote, Human-in-the-Loop Evaluation of a Multiple-Drone Delivery Operation

Over time, advances in unmanned aircraft systems (UAS) have enabled a shift in the operational paradigm from one operator managing one aircraft to that of multiple operators working together to manage multiple aircraft. This shift has highlighted the need for effective human-autonomy teaming methods to maintain manageable workload levels for operators as well as high standards of system performance and safety. This paper presents a study aimed at evaluating whether automation can help operators manage workload during small UAS (sUAS) package delivery scenarios featuring contingency situations. These contingency situations, resulting from unplanned UAS Volume Reservations (UVRs), required flight path reroutes for multiple aircraft simultaneously. The study manipulated the number of aircraft affected by the UVRs and the level of automation support. The presence of terrain conflicts was also controlled within each scenario. Due to the COVID-19 pandemic, subjects were not able to gain direct access to the Ground Control System (GCS). Therefore, the study was conducted using a subject-surrogate paradigm that required subjects to relay commands through a verbal protocol from remote locations outside of the lab to a researcher surrogate who had direct control of the GCS interfaces at the lab location. Results show that the automated support condition was associated with faster reroute response times, more efficient reroute maneuvers, and significantly lower levels of perceived workload than the manual reroute condition. However, the automation support level did not significantly impact pilots’ ability to avoid the UVR successfully; pilots were overwhelmingly capable of avoiding the UVR in all conditions. The presence of terrain conflicts primarily impacted pilot performance by leading to multiple uploads per vehicle, which was not typically required when pilots only needed to maneuver laterally. Although subjects did not have direct control over the GCS, subjective ratings indicate that the displays under test provided them with sufficient information to manage their aircraft and promptly respond to the unplanned UVRs. Overall, the objective and subjective data strongly suggest that the verbal protocol and subject-surrogate paradigm were effective methods for collecting data remotely amid the COVID-19 pandemic.

multi-UAS↗