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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer

The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ~20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

A Cognitive Systems Engineering Approach to Developing HMI Requirements for New Technologies

This document examines the challenges inherent in designing and regulating to support human-automation interaction for new technologies that will deployed into complex systems. A key question for new technologies, is how work will be accomplished by the human and machine agents. This question has traditionally been framed as how functions should be allocated between humans and machines. Such framing misses the coordination and synchronization that is needed for the different human and machine roles in the system to accomplish their goals. Coordination and synchronization demands are driven by the underlying human-automation architecture of the new technology, which are typically not specified explicitly by the designers. The human machine interface (HMI) which is intended to facilitate human-machine interaction and cooperation, however, typically is defined explicitly and therefore serves as a proxy for human-automation cooperation requirements with respect to technical standards for technologies. Unfortunately, mismatches between the HMI and the coordination and synchronization demands of the underlying human-automation architecture, can lead to system breakdowns. A methodology is needed that both designers and regulators can utilize to evaluate the expected performance of a new technology given potential human-automation architectures. Three experiments were conducted to inform the minimum HMI requirements a detect and avoid system for unmanned aircraft systems (UAS). The results of the experiments provided empirical input to specific minimum operational performance standards that UAS manufacturers will have to meet in order to operate UAS in the National Airspace System (NAS). These studies represent a success story for how to objectively and systematically evaluate prototype technologies as part of the process for developing regulatory requirements. They also provide an opportunity to reflect on the lessons learned from a recent research effort in order to improve the methodology for defining technology requirements for regulators in the future. The biggest shortcoming of the presented research program was the absence of the explicit definition, generation and analysis of potential human-automation architectures. Failure to execute this step in the research process resulted in less efficient evaluation of the candidate prototypes technologies in addition to the complete absence of different approaches to human-automation cooperation. For example, all of the prototype technologies that were evaluated in the research program assumed a human-automation architecture that relied on serial processing from the automation to the human. While this type of human-automation architecture is typical across many different technologies and in many different domains, it ignores different architectures where humans and automation work in parallel. Defining potential human-automation architectures a priori also allows regulators to develop scenarios that will stress the performance boundaries of the technology during the evaluation phase. The importance of adding this step of generating and evaluating candidate human-automation architectures prior to formal empirical evaluation is discussed.

human systems integration↗
NASA NTRS1984

Knowledge Based Systems: A Critical Survey of Major Concepts, Issues, and Techniques

This Working Paper Series entry presents a detailed survey of knowledge based systems. After being in a relatively dormant state for many years, only recently is Artificial Intelligence (AI) - that branch of computer science that attempts to have machines emulate intelligent behavior - accomplishing practical results. Most of these results can be attributed to the design and use of Knowledge-Based Systems, KBSs (or ecpert systems) - problem solving computer programs that can reach a level of performance comparable to that of a human expert in some specialized problem domain. These systems can act as a consultant for various requirements like medical diagnosis, military threat analysis, project risk assessment, etc. These systems possess knowledge to enable them to make intelligent desisions. They are, however, not meant to replace the human specialists in any particular domain. A critical survey of recent work in interactive KBSs is reported. A case study (MYCIN) of a KBS, a list of existing KBSs, and an introduction to the Japanese Fifth Generation Computer Project are provided as appendices. Finally, an extensive set of KBS-related references is provided at the end of the report.

Dominick, Wayne D.↗
DOE OSTI2021

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single–amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single– and multiple–amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1995

Adaptations of human skeletal muscle fibers to spaceflight

Human skeletal muscle fibers seem to share most of the same interrelationships among myosin ATPase activity, myosin heavy chain (MHC) phenotype, mitochondrial enzyme activities, glycolytic enzyme activities, and cross-sectional area (CSA) as found in rat, cat, and other species. One difference seems to be that fast fibers with high mitochrondrial content occur less frequently in humans than in the rat or cat. Recently, we have reported that the type of MHC expressed and the size of the muscle fibers in humans that have spent 11 days in space change significantly. Specifically, about 8% more fibers express fast MHCs and all phenotypes atrophy in the vastus lateralis (VL) post compared to preflight. In the present paper we examine the relationships among the population of myonuclei, MHC type, and CSA of single human muscle fibers before and after spaceflight. These are the first data that define the relationship among the types of MHC expressed, myonuclei number, and myonuclei domain of single fibers in human muscle. We then compare these data to similar measures in the cat. In addition, the maximal torque that can be generated by the knee extensors and their fatigability before and after spaceflight are examined. These data provide some indication of the potential physiologica consequences of the muscle adaptations that occur in humans in response to spaceflight.

M. Kathleen Day↗
DOE OSTI2026

Data for A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

AI/ML↗
DOE OSTI2026

Sim-to-real supervised domain adaptation for radioisotope identification

Machine learning has the potential to improve the speed and reliability of radioisotope identification using gamma spectroscopy. However, meticulously labeling an experimental dataset for training is often prohibitively expensive, while training models purely on synthetic data is risky due to the domain gap between simulated and experimental measurements. In this research, we demonstrate that supervised domain adaptation can substantially improve the performance of radioisotope identification models by transferring knowledge between synthetic and experimental data domains. We consider two domain adaptation scenarios: (1) a simulation-to-simulation adaptation, where we perform multi-label proportion estimation using simulated high-purity germanium detectors, and (2) a simulation-to-experimental adaptation, where we perform multi-class, single-label classification using measured spectra from handheld lanthanum bromide (LaBr) and sodium iodide (NaI) detectors. We begin by pretraining a spectral classifier on synthetic data using a custom transformer-based neural network. After subsequent fine-tuning on just 64 labeled experimental spectra, we achieve a test accuracy of 96% in the sim-to-real scenario with a LaBr detector, far surpassing a synthetic-only baseline model (75%) and a model trained from scratch (80%) on the same 64 spectra. Furthermore, we demonstrate that domain-adapted models learn more human-interpretable features than experiment-only baseline models. Overall, our results highlight the potential for supervised domain adaptation techniques to bridge the sim-to-real gap in radioisotope identification, enabling the development of accurate and explainable classifiers even in real-world scenarios where access to experimental data is limited.

Lalor, Peter W.↗
NASA NTRSDate not supplied

Identifying Human Errors and Error Mechanisms From Accident Reports Using Large Language Models

Emerging operational concepts for aviation hinge on novel paradigms for human machine interaction. Critical to their safe operation is early consideration of human error into the design process. Existing methods for consideration of human error require significant expert input, which is challenging both in early design and in novel systems for which there is little existing safety expertise. In this research, we propose a methodology for identifying human error, error producing factors, and mechanisms in early design from historical incident reports. Additionally, we hypothesize that cross-domain sharing of lessons learned can aid with early design human considerations in circumstances where data is not relevant or incomplete. This is addressed by identifying causes of human error in aviation and railway domains through applying state-of-the art natural language processing techniques to historical incident reports. Using this method, it is possible to extract extensive reports on human error from past incidents. Using the proposed approach, we identify nine human errors from railway reports and fourteen from aviation reports, with three errors common to both domains. There is at least one error producing conditions for each human error while a majority of the errors have more than one error mechanism. We also found that a majority of the human errors, error producing factors, and error mechanisms (even if they are not common between the domains) can be used to inform safe operations across domains as long as the errors are not domain specific and are interpreted and contextualized using engineering judgement.

Human Errors↗
DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Man-Machine Integration Design and Analysis System (MIDAS) v5: Augmentations, Motivations, and Directions for Aeronautics Applications

As automation and advanced technologies are introduced into transport systems ranging from the Next Generation Air Transportation System termed NextGen, to the advanced surface transportation systems as exemplified by the Intelligent Transportations Systems, to future systems designed for space exploration, there is an increased need to validly predict how the future systems will be vulnerable to error given the demands imposed by the assistive technologies. One formalized approach to study the impact of assistive technologies on the human operator in a safe and non-obtrusive manner is through the use of human performance models (HPMs). HPMs play an integral role when complex human-system designs are proposed, developed, and tested. One HPM tool termed the Man-machine Integration Design and Analysis System (MIDAS) is a NASA Ames Research Center HPM software tool that has been applied to predict human-system performance in various domains since 1986. MIDAS is a dynamic, integrated HPM and simulation environment that facilitates the design, visualization, and computational evaluation of complex man-machine system concepts in simulated operational environments. The paper will discuss a range of aviation specific applications including an approach used to model human error for NASA s Aviation Safety Program, and what-if analyses to evaluate flight deck technologies for NextGen operations. This chapter will culminate by raising two challenges for the field of predictive HPMs for complex human-system designs that evaluate assistive technologies: that of (1) model transparency and (2) model validation.

Gore, Brian F.↗
DOE OSTI2024

Beyond Human Vision: Exploring Materials with Machine Intelligence

Machine intelligence has the potential to revolutionize materials science, enabling autonomous synthesis, self-driving characterization, and accelerated modeling. However, despite the promise, successful implementation of these methods in day-to-day research remains a challenge. This talk will delve into the reasons behind this, exploring how truly intelligent experiments are hindered by opaque experiment control, a lack of domain-specific models, and human-centric design. Through a focus on the characterization of next-generation microelectronics and energy storage materials, I will share insights from both successful and failed attempts to implement machine intelligence. We will then explore the next steps necessary to unlock the full potential of machine intelligence in materials science, creating a future where intelligent systems work seamlessly alongside researchers to drive innovation and discovery.

artificial intelligence↗
NASA NTRS1987

Development of a semi-autonomous service robot with telerobotic capabilities

The importance to the United States of semi-autonomous systems for application to a large number of manufacturing and service processes is very clear. Two principal reasons emerge as the primary driving forces for development of such systems: enhanced national productivity and operation in environments whch are hazardous to humans. Completely autonomous systems may not currently be economically feasible. However, autonomous systems that operate in a limited operation domain or that are supervised by humans are within the technology capability of this decade and will likely provide reasonable return on investment. The two research and development efforts of autonomy and telerobotics are distinctly different, yet interconnected. The first addresses the communication of an intelligent electronic system with a robot while the second requires human communication and ergonomic consideration. Discussed here are work in robotic control, human/robot team implementation, expert system robot operation, and sensor development by the American Welding Institute, MTS Systems Corporation, and the Colorado School of Mines--Center for Welding Research.

Jones, J. E.↗
DOE OSTI2020

Genotype-Specific Neutralization of Norovirus Is Mediated by Antibodies Against the Protruding Domain of the Major Capsid Protein

Abstract Human noroviruses are the most common viral agents of acute gastroenteritis. Recently, human intestinal enteroids were shown to be permissive for norovirus infection. We tested their suitability as a system to study norovirus neutralization. Hyperimmune sera raised against virus-like particles (VLPs) representing different genotypes showed highly specific neutralization activity against GII.4 and GII.6 noroviruses. Carbohydrate blocking assays and neutralization exhibited similar patterns in antibody responses. Notably, sera produced against chimeric VLPs that presented swapped structural shell and protruding (P) domains, from different genotypes showed that neutralization is primarily mediated by antibodies mapping to the P domain of the norovirus capsid protein. This study provides empirical information on the antigenic differences among genotypes as measured by neutralization, which could guide vaccine design.

Ford-Siltz, Lauren A.↗
DOE OSTI2022

BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task

ABSTRACT Motivation Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model’s performance. Results We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets—BioASQ-7b, BioASQ-8b and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets. Availability and implementation BioADAPT-MRC is freely available as an open-source project at https://github.com/mmahbub/BioADAPT-MRC. Supplementary information Supplementary data are available at Bioinformatics online.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗