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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗
DOE OSTI2025

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae

Introduction: Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. Methods: The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. Results: The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. Discussion: This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

09 BIOMASS FUELS↗
DOE OSTI2025

Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer’s Disease, Parkinson’s Disease, and Amyotrophic Lateral Sclerosis

Background: Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. Methods: Using untargeted mass spectrometry-based metabolomics and 16S sequencing of human stool, we investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs—amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson’s disease (PD)—and healthy controls (HC). Results: We discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and gut dysbiosis in NDDs. DHPS was downregulated in AD, ALS, and PD, while bacteria involved in DHPS metabolism, Eubacterium and Desulfovibrio, were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS, suggesting a potential role in DHPS metabolism. A catabolic product of DHPS is hydrogen sulfide, and when in excess, it is known to promote inflammation, oxidative stress, mitochondrial damage, and gut dysbiosis, known hallmarks of NDDs. Conclusions: These findings suggest that cryptic sulfur metabolism via DHPS is a potential missing link in our current understanding of gut dysbiosis associated with NDD onset and progression. As this was a hypothesis generating study, more work is needed to elucidate the role of DHPS in gut dysbiosis and neurodegenerative diseases.

Nutrition & Dietetics↗
NASA NTRS1971

Data compression system

A data compression system is described in which TV PCM data for each line scan is received in the form of a succession of multibit pixel words. All or selected bits of each word are compressed by providing difference values between successive pixel words and coding the difference values of a selected number of pixel words forming a block into a fundamental sequence (FS). The FS, based on its length and the number of words per block, is either transmitted as the compressed data or is used to generate a code FS or its complement is used to generate a code FS bar. When the code FS is generated, its length is compared with the original block PCM and only if the former is the shorter of the two is the code transmitted. Selected bits per pixel word may be compressed, while the remaining bits may be transmitted directly, or some of them may be omitted altogether.

Rice, R. F.↗
NASA NTRS1971

A class of orthogonal nonrecursive binomial filters.

The time- and frequency-domain properties of the orthogonal binomial sequences are presented. It is shown that these sequences, or digital filters based on them, can be generated using adders and delay elements only. The frequency-domain behavior of these nonrecursive binomial filters suggests a number of applications as low-pass Gaussian filters or as inexpensive bandpass filters.

Haddad, R. A.↗
NASA NTRS1973

Solution of quadratic matrix equations for free vibration analysis of structures.

An efficient digital computer procedure and the related numerical algorithm are presented herein for the solution of quadratic matrix equations associated with free vibration analysis of structures. Such a procedure enables accurate and economical analysis of natural frequencies and associated modes of discretized structures. The numerically stable algorithm is based on the Sturm sequence method, which fully exploits the banded form of associated stiffness and mass matrices. The related computer program written in FORTRAN V for the JPL UNIVAC 1108 computer proves to be substantially more accurate and economical than other existing procedures of such analysis. Numerical examples are presented for two structures - a cantilever beam and a semicircular arch.

Gupta, K. K.↗
NASA NTRS1973

Recent advances in numerical analysis of structural eigenvalue problems

A wide range of eigenvalue problems encountered in practical structural engineering analyses is defined, in which the structures are assumed to be discretized by any suitable technique such as the finite-element method. A review of the usual numerical procedures for the solution of such eigenvalue problems is presented and is followed by an extensive account of recently developed eigenproblem solution procedures. Particular emphasis is placed on the new numerical algorithms and associated computer programs based on the Sturm sequence method. Eigenvalue algorithms developed for efficient solution of natural frequency and buckling problems of structures are presented, as well as some eigenvalue procedures formulated in connection with the solution of quadratic matrix equations associated with free vibration analysis of structures. A new algorithm is described for natural frequency analysis of damped structural systems.

Gupta, K. K.↗
NASA NTRS1975

Alkyl substituted cyclic ethers in 2,300 M yr old Transvaal algal stromatolite

Two cyclic ethers have been identified for the first time from insoluble polymer-like kerogen in a Precambrian rock by ozonolysis, gas chromatography, and mass spectrometry. The ethers are 2-n-propyl-3-methyltetrahydrofuran and 2-n-propyltetrahydropyran. These compounds could prove to be the oldest indigenous biochemical fossils. The sample was obtained 750 m stratigraphically above the base of the Transvaal Sequence from an outcrop approximately 315 km north-east of Johannesburg, South Africa.

Zumberge, J. E.↗
NASA NTRS1986

Digital Pseudonoise Generator

Architecture developed for noise generator based on pseudorandom number sequence. Concept involves no additions or multiplications; outputs of set of feedback shift registers combined, bit-by-bit, in accordance with desired probability distribution. Digital, pseudorandom number output fed to digital-to-analog converter to generate pseudonoise signal suitable for testing broadband amplifiers.

Knoebel, A.↗
NASA NTRS1985

A retransmission protocol for the message service of a land mobile satellite experiment

The objectives of NASA's land mobile satellite experiments are discussed. The assigned multiple access protocol combined with a retransmission scheme is to provide reliable transmission of data messages from mobiles to base stations (BSs). The sequences for communication between mobiles and BSs, mobiles and the network management center (NMC), and BSs and NMC are examined, and an example of mobiles/BSs communication is provided. The performance of the retransmission protocol and data message reservation and message channels delays are analyzed. A bit error rate of 0.001 is observed for satellite channels in a mobile environment and the message error probability is between 0-0.1.

Yan, T.-Y.↗
NASA NTRS1987

Implications of isotopic signatures of noble gases for the origin and evolution of terrestrial atmospheres

It is contented that the initial quantities of noble gases present in planetesimals were controlled by the sizes and masses of the planets, and fit with a model of successive accretion. The successive accretion model proposed for the origin of terrestrial planets is based upon: (1) the sequence of zones of condensation of solar nebula, (2) the condensation sequence of minerals, iron and nickel in different P-T regimes of the solar nebula, and (3) the sequence in the nucleation of iron cores of the terrestrial planets.

Rao, A. S. P.↗
NASA NTRS1988

Future civil space program logistics

The NASA Shuttle-C unmanned launch vehicle and the Shuttle/Space Station-based Orbital Maneuver Vehicle will be used in support of NASA Space Station assembly and logistics operations, as well as for the orbital servicing of the Hubble Space Telescope (1989), the Advanced X-ray Astrophysical Facility (1996), and the Space Infrared Telescope Facility (1998). Accounts are presently given of these observatories' configurations, capabilities, and mission scenarios, as well as of the Shuttle-C-based Space Station assembly sequence.

Steincamp, James W.↗
NASA NTRS1991

The Kinematics of Turbulent Boundary Layer Structure

The long history of research into the internal structure of turbulent boundary layers has not provided a unified picture of the physics responsible for turbulence production and dissipation. The goals of the present research are to: (1) define the current state of boundary layer structure knowledge; and (2) utilize direct numerical simulation results to help close the unresolved issues identified in part A and to unify the fragmented knowledge of various coherent motions into a consistent kinematic model of boundary layer structure. The results of the current study show that all classes of coherent motion in the low Reynolds number turbulent boundary layer may be related to vortical structures, but that no single form of vortex is representative of the wide variety of vortical structures observed. In particular, ejection and sweep motions, as well as entrainment from the free-streem are shown to have strong spatial and temporal relationships with vortical structures. Disturbances of vortex size, location, and intensity show that quasi-streamwise vortices dominate the buffer region, while transverse vortices and vortical arches dominate the wake region. Both types of vortical structure are common in the log region. The interrelationships between the various structures and the population distributions of vortices are combined into a conceptual kinematic model for the boundary layer. Aspects of vortical structure dynamics are also postulated, based on time-sequence animations of the numerically simulated flow.

Robinson, Stephen Kern↗
NASA NTRS1991

Space architecture monograph series. Volume 4: Genesis 2: Advanced lunar outpost

This research and design study investigated advanced lunar habitats for astronauts and mission specialists on the Earth's moon. Design recommendations are based on environmental response to the lunar environment, human habitability (human factors and environmental behavior research), transportability (structural and materials system with least mass), constructability (minimizing extravehicular time), construction dependability and resilience, and suitability for NASA launch research missions in the 21st century. The recommended design uses lunar lava tubes, with construction being a combination of Space Station Freedom derived hard modules and light weight Kevlar laminate inflatable structures. The proposed habitat includes research labs and a biotron, crew quarters and crew support facility, mission control, health maintenance facility, maintenance work areas for psychological retreat, privacy, and comtemplation. Furniture, specialized equipment, and lighting are included in the analysis and design. Drawings include base master plans, construction sequencing, overall architectural configuration, detailed floor plans, sections and axonometrics, with interior perspectives.

Fieber, Joseph P.↗
NASA NTRS1992

Relative timing of substorm features in MHD simulations

An investigation of the temporal sequence of substorm phenomena based on three dimensional MHD (magnetohydrodynamic) simulations of magnetic reconnection and plasmoid formation is presented. The investigation utilizes a spatially localized resistivity model which leads to a significantly faster evolution than found in previous investigations. The analysis of the results concentrates on substorm features that have received considerable attention in the past. The formation of magnetic neutral lines, the occurrence of fast flows directed both earthward and tailward, and the magnetic field changes leading to the formation of the substorm current wedge, and to the depolarization of the magnetic field earthward of the reconnection region and its dependence on the spatial distribution of resistivity, are discussed. These phenomena are seen as an integral part of the nonlinear evolution of the three dimensional tearing instability.

Hesse, Michael↗
NASA NTRS1998

The Hadean, Through a Glass Telescopically: Observations of Young Solar Analogs

Investigations into the Earth's surface environment during the Hadean eon (prior to 3.8 Ga) are hampered by the paucity of the geological and geochemical record and the relative inaccessibility of better-preserved surfaces with possibly similar early histories (i.e., Mars). One approach is to observe nearby, young solar-mass stars as analogs to the Hadean Sun and its environment. A catalog of 38 G and early K stars within 25 pc was constructed based on main-sequence status, bolometric luminosity, lack of known stellar companions within 800 AU, and coronal X-ray luminosities commensurate with the higher activity of solar-mass stars <0.8 b.y. old. Spectroscopic data support the assignment of ages of 0.2 - 0.8 Ga for most of these stars. Observations of these objects will provide insight into external forces that influenced Hadean atmosphere, ocean, and surface evolution (and potential ecosystems), including solar luminosity evolution, the flux and spectrum of solar ultraviolet radiation, the intensity of the solar wind, and the intensity and duration of a late period of heavy bombardment. The standard model of solar evolution predicts a luminosity of 0.75 solar luminosity at the end of the Hadean, implying a terrestrial surface temperature inconsistent with the presence of liquid water and motivating atmospheric greenhouse models. An alternative model fo solar evolution that invokes mass loss, constructed to explain solar Li depletion, attenuates or reverses this luminosity evolution of the atmospheres of Earth and the other terrestrial planets. This model can be tested by Li abundance measurements. The continuum emission from stellar wind plasma during significant mass loss may be detectable at millimeter and radio wavelengths. The Earth (and Moon) experienced a period of intense bombardment prior to 3.8 Ga, long after accretion was completed in the inner solar system and possibly associated with the clearing of residual planetesimals in the outer solar system. Such a bombardment may have contributed volatiles and organics to the surface, but also have limited the appearacne of a biosphere. While planetary systems around solar systems cannot be detected directly with present technology, the thermal emission from the interplanetary dust generated during a similar heavy bombardment period can be. Midinfrared observations of a large uniform sample of solar analogs are used to constrain the frequency and duration of such events.

Gaidos, E. J.↗
NASA NTRS2002

Overview of the High Performance Antiproton (HiPAT) Experiment

The annihilation of matter with antimatter represents the highest energy density of any known reaction, producing 10(exp 8) MJ/g, approximately 10 orders of magnitude more energy per unit mass than chemical based combustion. To take the first step towards using this energy for propulsion applications the NASA MSFC Propulsion Research Center (PRC) has initiated a research activity examining the storage of low energy antiprotons. Storage was identified as a key enabling technology since it builds the experience base necessary to understand the handling of antiprotons for virtually all utilization and high-density storage concepts. To address this need, a device referred to as the High Performance Antiproton Trap (HiPAT) is under development at the NASA MSFC PRC. The HiPAT is an electromagnetic system (Penning-Malmberg design) consisting of a 4 Tesla superconductor, a high voltage confinement electrode system (operation up to 20 KV), and an ultra high vacuum test section (operating in the 10(exp -12) torr range). The system was designed to be portable with an ultimate goal of maintaining 10(exp 12) charged particles with a half-life of 18 days. Currently, this system is being experimentally evaluated using normal matter ions which are cheap to produce and relatively easy to handle. These normal ions provide a good indication of overall trap behavior, with the exception of assessing annihilation losses. The ions are produced external to HiPAT using two hydrogen ion sources, with adjustable beam energy and current. Ion are transported in a beam line and controlled through the use of electrostatic optics. These optics serve to both focus and gate the incoming ions, providing microsecond-timed pulses that are dynamically captured by cycling the HiPAT electric containment field like a 'trap door'. The layout of this system more closely simulates the operations expected at an actual antiproton production facility where 'packets' of antiprotons with pulse widths measured in 100's of nanoseconds could be provided. Initial dynamic capture experiments have been performed with both trap and ton source system functioning at approximately 10% of maximum levels, minimizing the potential for extraneous effects. Dynamic trapping techniques demonstrated the successful capture of millions of hydrogen ions with good agreement with the predicted loading based on the timing sequence, trap electric field, and ion beam current. These techniques will be expanded to examine multiple shot capture or 'stacking' to increase the total number of ions stored within HiPAT.

Martin, James J.↗
NASA NTRS2000

Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

NASA Discipline Exobiology↗