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At least 487 records · Page 27

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Terahertz time-domain spectroscopy imaging of pancreatic ductal adenocarcinoma tissues

Pancreatic ductal adenocarcinoma (PDAC) ranks among the malignancies with the highest fatality and morbidity rates. This is predominantly attributable to an absence of understanding the intricate and diverse microenvironment of the tumor. We use terahertz time-domain spectroscopy (THz-TDS) imaging in transmission geometry to probe ex-vivo the heterogenous microenvironment of the genetically modified murine PDAC tissue that closely resembles the PDAC heterogeneity in human malignancy. We introduced a maximum a-posteriori probability estimation algorithm to objectively the tumor’s heterogenous microenvironment using the average values of refractive index and absorption coefficient within the useable terahertz bandwidth as imaging markers. Furthermore, direct comparison of stained histopathologic images and the refractive index and the absorption coefficient high-resolution, two dimensional maps of the same PDAC samples confirms the high potential of the THz-TDS method for tumor tissue characterization.

absorption↗

DOE OSTI2020

Structural basis for autophagy inhibition by the human Rubicon–Rab7 complex

Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7–GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7–GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab–effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Automated piezoresponse force microscopy domain tracking during fast thermally stimulated phase transition in CuInP 2 S 6

Real-time tracking of dynamic nanoscale processes such as phase transitions by scanning probe microscopy is a challenging task, typically requiring extensive and laborious human supervision. Smart strategies to track specific regions of interest (ROI) in the system during such transformations in a fast and automated manner are necessary to study the evolution of the microscopic changes in such dynamic systems. In this work, we realize automated ROI tracking in piezoresponse force microscopy during a fast (≈0.8 °C s –1 ) thermally stimulated ferroelectric-to-paraelectric phase transition in CuInP 2 S 6 . We use a combination of fast (1 frame per second) sparse scanning with compressed sensing image reconstruction and real-time offset correction via phase cross correlation. The applied methodology enables in situ fast and automated functional nanoscale characterization of a certain ROI during external stimulation that generates sample drift and changes local functionality.

36 MATERIALS SCIENCE↗

NASA NTRS2024

Cognitive Performance in ISS Astronauts on 6-Month Low Earth Orbit Missions

Introduction: Current and future astronauts will endure prolonged exposure to spaceflight hazards and environmental stressors that could compromise cognitive functioning, yet cognitive performance in current missions to the International Space Station remains critically under-characterized. We systematically assessed cognitive performance across 10 cognitive domains in astronauts on 6-month missions to the ISS. Methods: Twenty-five professional astronauts were administered the Cognition Battery as part of National Aeronautics and Space Administration (NASA) Human Research Program Standard Measures Cross-Cutting Project. Cognitive performance data were collected at five mission phases: pre-flight, early flight, late flight, early post-flight, and late post-flight. We calculated speed and accuracy scores, corrected for practice effects, and derived z-scores to represent deviations in cognitive performance across mission phases from the sample’s mean baseline (i.e., pre-flight) performance. Linear mixed models with random subject intercepts and pairwise comparisons examined the relationships between mission phase and cognitive performance. Results: Cognitive performance was generally stable over time with some differences observed across mission phases for specific subtests. There was slowed performance observed in early flight on tasks of processing speed, visual working memory, and sustained attention. We observed a decrease in risk-taking propensity during late flight and post-flight mission phases. Beyond examining group differences, we inspected scores that represented a significant shift from the sample’s mean baseline score, revealing that 11.8% of all flight and post-flight scores were at or below 1.5 standard deviations below the sample’s baseline mean. Finally, exploratory analyses yielded no clear pattern of associations between cognitive performance and either sleep or ratings of alertness. Conclusions: There was no evidence for a systematic decline in cognitive performance for astronauts on a 6-month missions to the ISS. Some differences were observed for specific subtests at specific mission phases, suggesting that processing speed, visual working memory, sustained attention, and risk-taking propensity may be the cognitive domains most susceptible to change in Low Earth Orbit for high performing, professional astronauts. We provide descriptive statistics of pre-flight cognitive performance from 25 astronauts, the largest published preliminary normative database of its kind to date, to help identify significant performance decrements in future samples.

Data curation↗

DOE OSTI2024

Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties

KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a’s thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably,KRAS4aexhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approachingKRAS4bin the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.

Science & Technology - Other Topics↗

DOE OSTI2024

Effects of N -glycans on the structure of human IgA2

The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and structural characterization of recombinant monomeric human IgA2, which varies in the amount/locations of attached glycans. Monomeric IgA2 antibodies were produced by removing the N-linked glycans in the CH1 and CH2 domains. The impact of glycans on oligomer formation, thermal stability, and receptor binding was evaluated. In addition, we performed a structural analysis of recombinant IgA2 in solution using Small Angle X-Ray Scattering (SAXS) to examine the effect of glycans on protein structure and flexibility. Our results indicate that the absence of glycans in the Fc tail region leads to higher-order aggregates. SAXS, combined with atomistic modeling, showed that the lack of glycans in the CH2 domain results in increased flexibility between the Fab and Fc domains and a different distribution of open and closed conformations in solution. When binding with the Fcα-receptor, the dissociation constant remains unaltered in the absence of glycans in the CH1 or CH2 domain, compared to the fully glycosylated protein. These results provide insights into N-glycans’ function on IgA2, which could have important implications for developing more effective IgA-based therapeutics in the future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid–Amino Acid Bond Pair Concept

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.

Biochemistry & Molecular Biology↗

NASA NTRS1987

A human performance modelling approach to intelligent decision support systems

Manned space operations require that the many automated subsystems of a space platform be controllable by a limited number of personnel. To minimize the interaction required of these operators, artificial intelligence techniques may be applied to embed a human performance model within the automated, or semi-automated, systems, thereby allowing the derivation of operator intent. A similar application has previously been proposed in the domain of fighter piloting, where the demand for pilot intent derivation is primarily a function of limited time and high workload rather than limited operators. The derivation and propagation of pilot intent is presented as it might be applied to some programs.

Mccoy, Michael S.↗

NASA NTRS2002

RIACS FY2002 Annual Report

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. Operated by the Universities Space Research Association (a non-profit university consortium), RIACS is located at the NASA Ames Research Center, Moffett Field, California. It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in September 2003. Ames has been designated NASA's Center of Excellence in Information Technology. In this capacity, Ames is charged with the responsibility to build an Information Technology (IT) Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA Ames and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1) Automated Reasoning for Autonomous Systems; 2) Human-Centered Computing; and 3) High Performance Computing and Networking. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains including aerospace technology, earth science, life sciences, and astrobiology. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

Leiner, Barry M.↗

NASA NTRS2006

Generalized Separation of an Object Jettisoned from the ISS

The International Space Station (ISS) Program faces unprecedented logistics challenges in both upmass and downmass. Some items employed on the ISS exterior present significant technical issues for a controlled de-orbit on either the shuttle or an expendable supply vehicle. Such manifest problems arise due to structural degradation, insufficient containment of hazardous pressures or contents, excessive size, or some combination of all of these factors. In addition, the mounting hardware and other flight service equipment to manifest the returned equipment must itself be launched, competing with other upmass. EVA techniques and equipment to successfully contain and secure such problematic equipment result in numerous significant risks to the spacewalking crews and cost and schedule risks to the program. The ISS Program office has therefore developed a policy that advises the jettison of the most problematic objects. Such jettisoned items join a small family of nearly co-planar orbital debris objects that threaten the ISS on several timescales, besides threatening all satellites with perigee below the ISS orbit and the general human population on Earth. This analysis addresses the governing physics and the ensuing risks when an object is jettisoned. It is shown that there are four time domains which must be considered, each with its own inherent problems, and that a ballistic solution is usually possible that satsfies all constraints in all domains.

Bacon, Jack↗

NASA NTRS2016

The Trick Simulation Toolkit: A NASA/Opensource Framework for Running Time Based Physics Models

The Trick Simulation Toolkit is a simulation development environment used to create high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. Its purpose is to generate a simulation executable from a collection of user-supplied models and a simulation definition file. For each Trick-based simulation, Trick automatically provides job scheduling, numerical integration, the ability to write and restore human readable checkpoints, data recording, interactive variable manipulation, a run-time interpreter, and many other commonly needed capabilities. This allows simulation developers to concentrate on their domain expertise and the algorithms and equations of their models. Also included in Trick are tools for plotting recorded data and various other supporting utilities and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX computer operating systems. This paper describes Trick's design and use at NASA Johnson Space Center.

Penn, John M.↗

DOE OSTI2022

OpenPATH and Itinerum Integration: A Case Study of Merging Open-Source Projects: Preprint

Throughout the transportation sector, multiple mobility tracking platforms have been developed independently, in parallel, with similar use cases and infrastructure. Maintaining such platforms on an individual level can result in duplicated effort. Innovation within the field could be slowed by the limited resource of people working on extremely similar projects. We provide a case study in how such platforms can be combined with low effort and provide an example in the mobility domain of what the resulting integration points, modules and ownership may look like. OpenPATH (formerly e-mission) and Itinerum are two examples of similar independently developed human mobility tracking platforms that extend beyond standard traffic data collection. Due to the open source nature of the projects, members from both teams decided to merge the functionality, thereby only hosting a single data collection process and limiting maintenance of separate intake platforms. On the front-end, specific questionnaire functionality from Itinerum, mainly the ability to display and return questions and results focused on sociodemographic attributes, was integrated into the OpenPATH user interface. On the back-end, an export pipeline stage was created to transport collected data back to the Itinerum database. Upon completion, the OpenPATH application retained its original functionality while adding the ability to export data for future data sharing and creating an avenue to incorporate Itinerum hosted questions and answers. Itinerum benefits from the rich feature set and infrastructure of OpenPATH without losing needed elements such as the questionnaire component. This case study, within the transportation sector, illustrates the various configurations in which open source software can be developed, maintained and deployed.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

In Silico Human Mobility Data Science: Leveraging Massive Simulated Mobility Data (Vision Paper)

Human mobility data science using trajectories or check-ins of individuals has many applications. Recently, we have seen a plethora of research efforts that tackle these applications. However, research progress in this field is limited by a lack of large and representative datasets. The largest and most commonly used dataset of individual human trajectories captures fewer than 200 individuals, while datasets of individual human check-ins capture fewer than 100 check-ins per city per day. Thus, it is not clear if findings from the human mobility data science community would generalize to large populations. Since obtaining massive, representative, and individual-level human mobility data is hard to come by due to privacy considerations, the vision of this work is to embrace the use of data generated by large-scale socially realistic microsimulations. Informed by both real data and leveraging social and behavioral theories, massive spatially explicit microsimulations may allow us to simulate entire megacities at the person level. The simulated worlds, which do not capture any identifiable personal information, allow us to perform “in silico” experiments using the simulated world as a sandbox in which we have perfect information and perfect control without jeopardizing the privacy of any actual individual. In silico experiments have become commonplace in other scientific domains such as chemistry and biology, permitting experiments that foster the understanding of concepts without any harm to individuals. This work describes challenges and opportunities for leveraging massive and realistic simulated alternate worlds for in silico human mobility data science.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Structural basis for Clostridium perfringens enterotoxin targeting of claudins at tight junctions in mammalian gut

The bacterium Clostridium perfringens causes severe, sometimes lethal gastrointestinal disorders in humans, including enteritis and enterotoxemia. Type F strains produce an enterotoxin (CpE) that causes the third most common foodborne illness in the United States. CpE induces gut breakdown by disrupting barriers at cell–cell contacts called tight junctions (TJs), which are formed and maintained by claudins. Targeted binding of CpE to specific claudins, encoded by its C-terminal domain (cCpE), loosens TJ barriers to trigger molecular leaks between cells. Cytotoxicity results from claudin-bound CpE complexes forming pores in cell membranes. In mammalian tissues, ~24 claudins govern TJ barriers—but the basis for CpE’s selective targeting of claudins in the gut was undetermined. We report the structure of human claudin-4 in complex with cCpE, which reveals that enterotoxin targets a motif conserved in receptive claudins and how the motif imparts high-affinity CpE binding to these but not other subtypes. The structural basis of CpE targeting is supported by binding affinities, kinetics, and half-lives of claudin–enterotoxin complexes and by the cytotoxic effects of CpE on claudin-expressing cells. By correlating the binding residence times of claudin–CpE complexes we determined to claudin expression patterns in the gut, we uncover that the primary CpE receptors differ in mice and humans due to sequence changes in the target motif. These findings provide the molecular and structural element CpE employs for subtype-specific targeting of claudins during pathogenicity of C. perfringens in the gut and a framework for new strategies to treat CpE-based illnesses in domesticated mammals and humans.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2015

NASA Galactic Cosmic Radiation Environment Model: Badhwar-O'Neill (2014)

The Badhwar‐O'Neill (BON) Galactic Cosmic Ray (GCR) flux model is used by NASA to certify microelectronic systems and in the analysis of radiation health risks for human space flight missions. Of special interest to NASA is the kinetic energy region below 4.0 GeV/n due to the fact that exposure from GCR behind shielding (e.g., inside a space vehicle) is heavily influenced by the GCR particles from this energy domain. The BON model numerically solves the Fokker‐Planck differential equation to account for particle transport in the heliosphere due to diffusion, convection, and adiabatic deceleration under the assumption of a spherically symmetric heliosphere. The model utilizes a GCR measurements database from various particle detectors to determine the boundary conditions. By using an updated GCR database and improved model fit parameters, the new BON model (BON14) is significantly improved over the previous BON models for describing the GCR radiation environment of interest to human space flight.

O'Neill, P. M.↗

DOE OSTI2024

Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides

The bacterial cyclic oligonucleotide-based antiphage signaling system (CBASS) is similar to the cGAS–STING system in humans, containing an enzyme that synthesizes a cyclic nucleotide on viral infection and an effector that senses the second messenger for the antiviral response. Cap5, containing a SAVED domain coupled to an HNH DNA endonuclease domain, is the most abundant CBASS effector, yet the mechanism by which it becomes activated for cell killing remains unknown. We present here high-resolution structures of full-length Cap5 from Pseudomonas syringae (Ps) with second messengers. Here, the key to PsCap5 activation is a dimer-to-tetramer transition, whereby the binding of second messenger to dimer triggers an open-to-closed transformation of the SAVED domains, furnishing a surface for assembly of the tetramer. This movement propagates to the HNH domains, juxtaposing and converting two HNH domains into states for DNA destruction. These results show how Cap5 effects bacterial cell suicide and we provide proof-in-principle data that the CBASS can be extrinsically activated to limit bacterial infections.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Spread spectrum time domain reflectometry (SSTDR) and frequency domain reflectometry (FDR) cable inspection using machine learning

Cables are initially qualified for nuclear power plant use for 40 years. As plants extend their operating license to 60 and 80 years, justification for continued cable use must shift to a condition-based approach since it is cost prohibitive to completely replace cables that are likely still capable of performing their design function. The Pacific Northwest National Laboratory (PNNL) Accelerated and Real Time Experimental Nodal Analysis (ARENA) cable motor test bed was used to test the response of a commercial spread spectrum time domain reflectometry (SSTDR) system, a laboratory instrument software-controlled SSTDR, and a vector network analyzer-based frequency domain reflectometry (FDR) system to various cable anomalies. The three instrument systems were able to interrogate cables over a range of frequency bandwidths that can be helpful for human data analysis. Data were subjected to supervised and unsupervised machine learning (ML) analyses to distinguish normal undamaged cable responses from anomalous cable responses. Both supervised and unsupervised ML approaches produced encouraging results with an undamaged/anomalous prediction accuracy from 0.69% to 0.87%. Recommendations for further development and field implementation include increased and more balanced sample sets particularly including more training data.

SSTDR, FDR, Reflectometry, Machine Learning, ARENA↗

NASA NTRS1990

Applications of ISES for coastal zone studies

In contrast to the discipline- and process-oriented topics addressed, coastal zone studies are defined geographically by the special circumstances inherent in the interface between land and water. The characteristics of coastal zones which make them worthy of separate consideration are: (1) the dynamic nature of natural and anthropogenic processes taking place; (2) the relatively restricted spatial domain of the narrow land/water interface; and (3) the large proportion of the Earth's population living within coastal zones, and the resulting extreme pressure on natural and human resources. These characteristics place special constraints and priorities on remote sensing applications, even though the applications themselves bear close relation to those addressed by other elements of this report (e.g., oceans, ice, vegetation/land use). The discussion which follows first describes the suite of remote sensing activities relevant to coastal zone studies. Potential Information Sciences Experiment System (ISES) experiments will then be addressed within two general categories: applications of real-time data transmission and applications of onboard data acquisition and processing.

Bartlett, D. S.↗