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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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NASA NTRSDate not supplied

Transcriptomics Processing Pipelines for Space Biology: An Open Source and Consensus-Driven Approach

Transcriptomics holds significant value in elucidating the relationship between gene expression, experimental factors, biological factors, and various types of omics data. Enhancing our understanding of these connections is paramount for foundational biology, which plays a pivotal role in devising solutions for challenges pertinent to both space travel and terrestrial life. The NASA GeneLab project, part of the Open Science Data Repository (OSDR.nasa.gov), seeks to accelerate space biology research through cataloging and democratizing ‘omics data, including transcriptomics. Since raw omics data are largely inaccessible to non-bioinformaticians, GeneLab works with the scientific community via the Open Science Analysis Working Groups (AWGs) to develop standard processing pipelines to generate and publish processed data. Unlike raw data, processed data have greater immediate value to diverse users with varying technical backgrounds and computational capabilities. Standardizing processing workflows is essential to match the pace of raw data generation, ensure reproducibility, and enable standardized processed data for comparison across datasets. As of June 2023, transcriptomics studies comprise over half of GeneLab datasets hosted on the OSDR, including data from bulk RNA-seq and Affymetrix or Agilent 1-Channel DNA microarray assays. In collaboration with the AWGs, GeneLab developed consensus processing pipelines for these transcriptomics data types that includes quality control, background correction (microarray only), data normalization and quantification, culminating in the detection and annotation of differentially expressed genes. The work presented here describes Nextflow implementations of GeneLab’s consensus transcriptomics pipelines that automates and accelerates processing of these datasets. In addition to the core data processing, these workflows also include raw data staging and a robust verification and validation program to identify errors in real-time, stop additional downstream computation, and preserve computational resources. These workflows are used to generate GeneLab processed data hosted on the OSDR, and are publicly available as open source software for others to use at: https://github.com/nasa/GeneLab_Data_Processing.

Jonathan Oribello↗
DOE OSTI2025

Exploiting correlations in multi-coincidence Coulomb explosion patterns for differentiating molecular structures using machine learning

Coulomb explosion imaging (CEI) is a powerful technique for capturing the real-time motion of individual atoms during ultrafast photochemical reactions. CEI generates high-dimensional data with naturally embedded correlations that allow mapping the coordinated motion of nuclei in molecules. This enables reliable separation of competing reaction pathways and makes this approach uniquely suited for characterizing weak reaction channels. However, rich information contained in experimental CEI patterns remains largely underexploited due to challenges in visualizing correlations between multiple observables in multi-dimensional parameter space. Here we present a new approach to CEI of intermediate-sized polyatomic molecules, detecting up to eight ionic fragments in coincidence and leveraging machine-learning-based analysis to identify patterns and correlations in the resulting high-dimensional momentum-space data, enabling robust molecular structure identification and differentiation. Our approach provides high-dimensional background-free data encoding exceptionally rich structural information and establishes an automated, scalable framework for extracting insightful information from the data. As a demonstration, we apply this method to image and distinguish dichloroethylene isomers, showcasing its potential for broader applications in molecular imaging. Our results pave the way for channel-specific analysis of ultrafast structural dynamics in chemically relevant systems, particularly for disentangling mixed reaction pathways and detecting contributions from weak channels and minority species.

Chemical Physics (physics.chem-ph)↗
NASA NTRS1995

Starspot evolution, differential rotation, and magnetic cycles in the chromospherically active binaries lambda andromedae, sigma Geminorum, II Pegasi, and V711 Tauri

We have analyzed 15-19 yr of photoelectric photometry, obtained manually and with automated telescopes, of the chromospherically active binaries lambda And, sigma Gem, II Peg, and V711 Tau. These observations let us identify individual dark starspots on the stellar surfaces from periodic dimming of the starlight, follow the evolution of these spots, and search for long-term cyclic changes in the properties of these starspots that might reveal magnetic cycles analogous to the Sun's 11 yr sunspot cycle. We developed a computer code to fit a simple two-spot model to our observed light curves that allows us to extract the most easily determinable and most reliable spot parameters from the light curves, i.e., spot longitudes and radii. We then used these measured properties to identify individual spots and to chart their life histories by constructing migration and amplitude curves. We identified and followed 11 spots in lambda And, 16 in sigma Gem, 12 in II Peg, and 15 in V711 Tau. Lifetimes of individual spots ranged from a few months to longer than 6 yr. Differential rotation coefficients, estimated from the observed range of spot rotation periods for each star and defined by equation (2), were 0.04 for lambda And, 0.038 for sigma Gem, 0.005 for II Peg, and 0.006 for V711 Tau, versus 0.19 for the Sun. We searched for cyclic changes in mean brightness, B-V color index, and spot rotation period as evidence for long-term cycles. Of these, long-term variability in mean brightness appears to offer the best evidence for such cycles in these four stars. Cycles of 11.1 yr for lambda And, 8.5 yr for sigma Gem, 11 yr for II Peg, and 16 yr V711 Tau are implied by these mean brightness changes. Cyclic changes in spot rotation period were found in lambda And and possibly II Peg. Errors in B-V were too large for any long-term changes to be detectable.

Henry, Gregory W.↗
NASA NTRS1983

Tracking antenna arrays for near-millimeter waves

A two-dimensional monolithic array has been developed that gives the elevation and azimuth of point source targets. The array is an arrangement of rows and columns of antennas and bismuth bolometer detectors on a fused quartz substrate. Energy is focused onto the array through a lens placed on the back side of the substrate. At 1.38 mm with a 50 mm diameter objective lens, the array has demonstrated a positioning accuracy of 26 arcmin. In a differential mode this precision improves to 9 arcsec, limited by the mechanics of the rotating stage. This tracking could be automated to a fast two-step procedure where a source is first located to the nearest row and column, and then precisely located by scanning. With signal processing the array should be able to track multiple sources.

Tong, P. P.↗
NASA NTRS1994

Differential GPS and system integration of the Low Visibility Landing and Surface Operations (LVLASO) demonstration

The LVLASO Flight Demonstration of ASTA concepts (FDAC) integrates NASA-Langley's electronic moving map display and Transport Systems Research Vehicle (TSRV) (a modified Boeing 737 aircraft); ARINC's VHF data link, GPS ground station, and automated controller workstation; and Norden's surface radar/airport movement safety system. Aircraft location is shown on the electronic map display in the cockpit. An approved taxi route as well as other aircraft and surface traffic are also displayed. An Ashtech Z12 Global Positioning System (GPS) receiver on the TSRV estimates the aircraft's position. In Differential mode (DSPS), the Ashtech receiver accepts differential C/A code pseudorange corrections from a GPS ground station. The GPS ground station provides corrections up to ten satellites. The corrections are transmitted on a VHF data link at a 1 Hz. rate using the RTCM-104 format. DGPS position estimates will be within 5 meters of actual aircraft position. DGPS position estimates are blended with position, velocity, acceleration, and heading data from the TSRV Air Data/Inertial Reference System (ADIRS). The ADIRS data is accurate in the short-term, but drifts over time. The DGPS data is used to keep the ADIRS position accurate. Ownship position, velocity, heading, and turn rate are sent at a 20 Hz. rate to the electronic map display. Airport traffic is detected by the airport surface radar system. Aircraft and vehicles such as fuel trucks and baggage carts are detected. The traffic's location, velocity, and heading are sent to the TSRV. To prevent traffic symbology from jumping each second when a location update arrives, velocity and heading are used to predict a new traffic location for each display update. Possible runway incursions and collisions can be shown on the electronic map. Integrating the different systems used in the FDAC requires attention to the underlying coordinate systems. The airport diagram displayed on the electronic map is obtained from published navigational charts. The charts reference the North American Datum of 1927 (NAD27) or a local state-plane coordinate system. GPS uses the World Geodetic Standard of 1984 (WGS84). Both NAD27 and WGS84 model the Earth as an ellipsoid, however, they use a different origin and different size ellipsoids. Latitudes and longitudes given in these systems can be converted to a Cartesian system with the origin at the Earth's center. The surface radar detects traffic in a locally-level, rho-theta coordiante system. The electronic airport diagram is stored using a flat XY coordinate system. The map origin is at the tower and is referenced as True North up. All ownship and other traffic positions must be converted to the electronic map's frame of reference for display.

Rankin, James M.↗
DOE OSTI2025

Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases

Background Large language models (LLMs) are increasingly used medicine for diverse applications including differential diagnostic support. The training data used to create LLMs such as the Generative Pretrained Transformer (GPT) predominantly consist of English-language texts, but LLMs could be used across the globe to support diagnostics if language barriers could be overcome. Initial pilot studies on the utility of LLMs for differential diagnosis in languages other than English have shown promise, but a large-scale assessment on the relative performance of these models in a variety of European and non-European languages on a comprehensive corpus of challenging rare-disease cases is lacking. Methods We created 4917 clinical vignettes using structured data captured with Human Phenotype Ontology (HPO) terms with the Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema. These clinical vignettes span a total of 360 distinct genetic diseases with 2525 associated phenotypic features. We used translations of the Human Phenotype Ontology together with language-specific templates to generate prompts in English, Chinese, Czech, Dutch, French, German, Italian, Japanese, Spanish, and Turkish. We applied GPT-4o, version gpt-4o-2024-08-06, and the medically fine-tuned Meditron3-70B to the task of delivering a ranked differential diagnosis using a zero-shot prompt. An ontology-based approach with the Mondo disease ontology was used to map synonyms and to map disease subtypes to clinical diagnoses in order to automate evaluation of LLM responses. Findings For English, GPT-4o placed the correct diagnosis at the first rank 19.9% and within the top-3 ranks 27.0% of the time. In comparison, for the nine non-English languages tested here the correct diagnosis was placed at rank 1 between 16.9% and 20.6%, within top-3 between 25.4% and 28.6% of cases. The Meditron3 model placed the correct diagnosis within the first 3 ranks for 20.9% of cases in English and between 19.9% and 24.0% for the other nine languages. Interpretation The differential diagnostic performance of LLMs across a comprehensive corpus of rare-disease cases was largely consistent across the ten languages tested. This suggests that the utility of LLMs in clinical settings may extend to non-English clinical settings.

Artificial intelligence↗
NASA NTRS1997

Novel software for analysis of root gravitropism: comparative response patterns of Arabidopsis wild-type and axr1 seedlings

In an earlier study (Evans, Ishikawa & Estelle 1994, Planta 194, 215-222) we used a video digitizer system to compare the kinetics of auxin action on root elongation in wild-type seedlings and seedlings of auxin response mutants of Arabidopsis thaliana (L.) Heynh. We have since modified the system software to allow determination of elongation on opposite sides of vertical or gravistimulated roots and to allow continuous measurement of the angle of orientation of sequential subsections of the root during the response. We used this technology to compare the patterns of differential growth that generate curvature in roots of the Columbia ecotype and in the mutants axr1-3, axr1-12 and axr2, which show reduced gravitropic responsiveness and reduced sensitivity to inhibition by auxin. The pattern of differential growth during gravitropism differed in roots of wild-type and axr1 seedlings. In wild-type roots, initial curvature resulted from differential inhibition of elongation in the distal elongation zone (DEZ). This was followed by an acceleration of elongation along the top side of the DEZ. In roots of axr1-3, curvature resulted from differential stimulation of elongation whereas in roots of axr1-12 the response was variable. Roots of axr2 did not exhibit gravitropic curvature. The observation that the pattern of differential growth causing curvature is dramatically altered by a change in sensitivity to auxin is consistent with the classical Cholodny-Went theory of gravitropism which maintains that differential growth patterns induced by gravistimulation are mediated primarily by gravi-induced shifts in auxin distribution. The new technology introduced with this report allows automated determination of stimulus response patterns in the small but experimentally popular roots of Arabidopsis.

Non-NASA Center↗
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
NASA NTRS2000

Characterization of a 16-Bit Digitizer for Lidar Data Acquisition

A 6-MHz 16-bit waveform digitizer was evaluated for use in atmospheric differential absorption lidar (DIAL) measurements of ozone. The digitizer noise characteristics were evaluated, and actual ozone DIAL atmospheric returns were digitized. This digitizer could replace computer-automated measurement and control (CAMAC)-based commercial digitizers and improve voltage accuracy.

Williamson, Cynthia K.↗
DOE OSTI2024

Synchrophasor-Based Zonal Current Differential Protection for Secondary Low Voltage Networks

This report describes an approach to utilizing phasor measurement unit (PMU) data from multiple Intelligent Electronics Devices (IEDs) in a low-voltage network to produce a differential scheme for protecting the medium-voltage feeder and low-voltage network transformers. The proposed protection scheme is designed and prototyped on a real-time automation controller. Its performance is evaluated using real-time controller hardware-in-the-loop simulation. Lab testing results indicate that the proposed protection scheme allows significant distributed energy resources (DER) backfeed and enables selective and fast protection of medium voltage feeders.

42 ENGINEERING↗
DOE OSTI2026

Using PyBioNetFit to leverage qualitative and quantitative data in biological model parameterization and uncertainty quantification

Data generated in studies of cellular regulatory systems are often qualitative. For example, measurements of signaling readouts in the presence and absence of mutations may reveal a rank ordering of responses across conditions but not the precise extents of mutation-induced differences. Qualitative data are often ignored by mathematical modelers or are considered in an ad hoc manner, as in the study of Kocieniewski and Lipniacki (2013) [Phys Biol 10: 035006], which was focused on the roles of MEK isoforms in ERK activation. In this earlier study, model parameter values were tuned manually to obtain consistency with a combination of qualitative and quantitative data. This approach is not reproducible, nor does it provide insights into parametric or prediction uncertainties. Here, starting from the same data and the same ordinary differential equation (ODE) model structure, we generate formalized statements of qualitative observations, making these observations more reusable, and we improve the model parameterization procedure by applying a systematic and automated approach enabled by the software package PyBioNetFit. We also demonstrate uncertainty quantification (UQ), which was absent in the original study. Our results show that PyBioNetFit enables qualitative data to be leveraged, together with quantitative data, in parameterization of systems biology models and facilitates UQ. These capabilities are important for reliable estimation of model parameters and model analyses in studies of cellular regulatory systems and reproducibility.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2010

Isolation of Resistance-Bearing Microorganisms

To better exploit the principles of gas transport and mass transport during the processes of cell seeding of 3D scaffolds and in vitro culture of 3D tissue engineered constructs, the oscillatory cell culture bioreactor provides a flow of cell suspensions and culture media directly through a porous 3D scaffold (during cell seeding) and a 3D construct (during subsequent cultivation) within a highly gas-permeable closed-loop tube. This design is simple, modular, and flexible, and its component parts are easy to assemble and operate, and are inexpensive. Chamber volume can be very low, but can be easily scaled up. This innovation is well suited to work with different biological specimens, particularly with cells having high oxygen requirements and/or shear sensitivity, and different scaffold structures and dimensions. The closed-loop changer is highly gas permeable to allow efficient gas exchange during the cell seeding/culturing process. A porous scaffold, which may be seeded with cells, is fixed by means of a scaffold holder to the chamber wall with scaffold/construct orientation with respect to the chamber determined by the geometry of the scaffold holder. A fluid, with/without biological specimens, is added to the chamber such that all, or most, of the air is displaced (i.e., with or without an enclosed air bubble). Motion is applied to the chamber within a controlled environment (e.g., oscillatory motion within a humidified 37 C incubator). Movement of the chamber induces relative motion of the scaffold/construct with respect to the fluid. In case the fluid is a cell suspension, cells will come into contact with the scaffold and eventually adhere to it. Alternatively, cells can be seeded on scaffolds by gel entrapment prior to bioreactor cultivation. Subsequently, the oscillatory cell culture bioreactor will provide efficient gas exchange (i.e., of oxygen and carbon dioxide, as required for viability of metabolically active cells) and controlled levels of fluid dynamic shear (i.e., as required for viability of shear-sensitive cells) to the developing engineered tissue construct. This bioreactor was recently utilized to show independent and interactive effects of a growth factor (IGF-I) and slow bidirectional perfusion on the survival, differentiation, and contractile performance of 3D tissue engineering cardiac constructs. The main application of this system is within the tissue engineering industry. The ideal final application is within the automated mass production of tissue- engineered constructs. Target industries could be both life sciences companies as well as bioreactor device producing companies.

Venkateswaran, Kasthuri, J.↗
NASA NTRS2010

Oscillating Cell Culture Bioreactor

To better exploit the principles of gas transport and mass transport during the processes of cell seeding of 3D scaffolds and in vitro culture of 3D tissue engineered constructs, the oscillatory cell culture bioreactor provides a flow of cell suspensions and culture media directly through a porous 3D scaffold (during cell seeding) and a 3D construct (during subsequent cultivation) within a highly gas-permeable closed-loop tube. This design is simple, modular, and flexible, and its component parts are easy to assemble and operate, and are inexpensive. Chamber volume can be very low, but can be easily scaled up. This innovation is well suited to work with different biological specimens, particularly with cells having high oxygen requirements and/or shear sensitivity, and different scaffold structures and dimensions. The closed-loop changer is highly gas permeable to allow efficient gas exchange during the cell seeding/culturing process. A porous scaffold, which may be seeded with cells, is fixed by means of a scaffold holder to the chamber wall with scaffold/construct orientation with respect to the chamber determined by the geometry of the scaffold holder. A fluid, with/without biological specimens, is added to the chamber such that all, or most, of the air is displaced (i.e., with or without an enclosed air bubble). Motion is applied to the chamber within a controlled environment (e.g., oscillatory motion within a humidified 37 C incubator). Movement of the chamber induces relative motion of the scaffold/construct with respect to the fluid. In case the fluid is a cell suspension, cells will come into contact with the scaffold and eventually adhere to it. Alternatively, cells can be seeded on scaffolds by gel entrapment prior to bioreactor cultivation. Subsequently, the oscillatory cell culture bioreactor will provide efficient gas exchange (i.e., of oxygen and carbon dioxide, as required for viability of metabolically active cells) and controlled levels of fluid dynamic shear (i.e., as required for viability of shear-sensitive cells) to the developing engineered tissue construct. This bioreactor was recently utilized to show independent and interactive effects of a growth factor (IGF-I) and slow bidirectional perfusion on the survival, differentiation, and contractile performance of 3D tissue engineering cardiac constructs. The main application of this system is within the tissue engineering industry. The ideal final application is within the automated mass production of tissue- engineered constructs. Target industries could be both life sciences companies as well as bioreactor device producing companies.

Freed, Lisa E.↗
DOE OSTI2024

Lightning and Radar Measures of Mixed-Phase Updraft Variability in Tracked Storms during the TRACER Field Campaign in Houston, Texas

Properties of 7488 thunderstorms are summarized for June–September 2022 during the Tracking Aerosol Convection Interactions Experiment (TRACER) field campaign Houston, Texas, using polarimetric weather radar and VHF 3D Lightning Mapping Array data. Automated tracking of storms linked each instrument’s measurements to a data-defined, time-evolving storm footprint. Within each storm, the depth and magnitude of episodic columns of radar differential reflectivity and specific differential phase quantified the prevalence of updrafts that activated mixed-phase precipitation pathways. Lightning measurements further distinguished the degree of rimed precipitation formation: the fraction of tracks with lightning varied from day to day and cells with lightning had stronger polarimetric columns. Track-level correlation of the lightning flash rate with radar polarimetric measures had substantial spread, showing that lightning provides an additional signal of mixed-phase precipitation processes that can complement future studies of thermodynamic and aerosol controls on cloud microphysics in the Houston region.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1994

Eddy-Current Inspection Of Tab Seals On Beverage Cans

Eddy-current inspection system monitors tab seals on beverage cans. Device inspects all cans at usual production rate of 1,500 to 2,000 cans per minute. Automated inspection of all units replaces visual inspection by microscope aided by mass spectrometry. System detects defects in real time. Sealed cans on conveyor pass near one of two coils in differential eddy-current probe. Other coil in differential eddy-current probe positioned near stationary reference can on which tab seal is known to be of acceptable quality. Signal of certain magnitude at output of probe indicates defective can, automatically ejected from conveyor.

Bar-Cohen, Yoseph↗
NASA NTRS2024

Lightning and Radar Measures of Mixed Phase Updraft Variability in Tracked Storms During the TRACER Field Campaign in Houston, Texas

Properties of 7488 thunderstorms are summarized for June-September 2022 during the TRACER field campaign Houston, Texas using polarimetric weather radar and VHF 3D lightning mapping array data. Automated tracking of storms linked each instrument’s measurements to a data-defined, time-evolving storm footprint. Within each storm, the depth and magnitude of episodic columns of radar differential reflectivity and specific differential phase quantified the prevalence of updrafts that activated mixed-phase precipitation pathways. Lightning measurements further distinguished the degree of rimed precipitation formation: the fraction of tracks with lightning varied from day to day, and cells with lightning had stronger polarimetric columns. Track-level correlation of lightning flash rate with radar polarimetric measures had substantial spread, showing that lightning provides an additional signal of mixed-phase precipitation processes that can complement future studies of thermodynamic and aerosol controls on cloud microphysics in the Houston region.

TRACER field campaign↗
NASA NTRS1991

High performance computing system for flight simulation at NASA Langley

The computer architecture and components used in the NASA Langley Advanced Real-Time Simulation System (ARTSS) are briefly described and illustrated with diagrams and graphs. Particular attention is given to the advanced Convex C220 processing units, the UNIX-based operating system, the software interface to the fiber-optic-linked Computer Automated Measurement and Control system, configuration-management and real-time supervisor software, ARTSS hardware modifications, and the current implementation status. Simulation applications considered include the Transport Systems Research Vehicle, the Differential Maneuvering Simulator, the General Aviation Simulator, and the Visual Motion Simulator.

Cleveland, Jeff I., II↗
NASA NTRS2001

High-Speed Observer: Automated Streak Detection in SSME Plumes

A high frame rate digital video camera installed on test stands at Stennis Space Center has been used to capture images of Space Shuttle main engine plumes during test. These plume images are processed in real time to detect and differentiate anomalous plume events occurring during a time interval on the order of 5 msec. Such speed yields near instantaneous availability of information concerning the state of the hardware. This information can be monitored by the test conductor or by other computer systems, such as the integrated health monitoring system processors, for possible test shutdown before occurrence of a catastrophic engine failure.

Rieckoff, T. J.↗