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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa

Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Back to functional hydrides: Effects of neutron-irradiated microstructure on hydrogen retention in yttrium hydride

Functional hydrides are promising candidates for advanced nuclear reactors, particularly in portable or transportable applications, due to their high hydrogen-retention capabilities, enabling efficient neutron moderation, and compact reactor design. However, hydrogen mobility in hydrides at elevated irradiation temperatures poses significant technological challenges, necessitating a comprehensive understanding of their irradiation behavior. Furthermore, this study investigated the microstructural and chemical stability of neutron-irradiated yttrium hydrides to assess their hydrogen-retention capacity. A targeted literature review was also conducted to contextualize neutron-irradiation effects on functional hydrides with regards to structural stability and hydrogen retention. Experimental characterizations revealed that, at high temperatures, irradiated hydrides retained their phase stability, which was likely enhanced by irradiation-induced microstructure evolution. Notably, an amorphous yttrium and oxygen -rich surface layer was present at the free surface of the hydride. Its thickness decreased while a continuous crystalline Y-O-rich layer was formed with increasing neutron damage. Additionally, the number density of dislocation loops and cavities generally increased as a function of neutron dose. First-principles calculations of hydrogen behavior within yttrium vacancy clusters in yttrium hydrides demonstrated vacancy-size-dependent hydrogen stability and configuration, highlighting the role of vacancy geometry in regulating hydrogen retention. Thus, the presence of irradiation-induced dislocation loops and cavities were hypothesized to improve hydrogen retention. Collectively, these findings advance the understanding of hydride behavior under neutron irradiation as well as their technological readiness for portable or transportable nuclear reactors.

Defect clusters↗
DOE OSTI2025

Structural Changes in Metal Chalcogenide Nanoclusters Associated with Single Heteroatom Incorporation

Atomically precise nanoclusters (NCs) are promising building blocks for designing materials and interfaces with unique properties. By incorporating heteroatoms into the core, the electronic and magnetic properties of NCs can be precisely tuned. To accurately predict these properties, density functional theory (DFT) is often employed, making the rigorous benchmarking of DFT results particularly important. In this study, we present a benchmarking approach based on metal chalcogenide NCs as a model system. We synthesized a series of bimetallic, iron-cobalt chalcogenide NCs [Co 6-x Fe x S 8 (PEt 3 ) 6 ] + (x = 0-6) (PEt = triethyl phosphine) and investigated the effect of heteroatoms in the octahedral metal chalcogenide core on their size and electronic properties. Using ion mobility-mass spectrometry (IM-MS), we observed a gradual increase in the collision cross section (CCS) with an increase in the number of Fe atoms in the core. DFT calculations combined with trajectory method CCS simulations successfully reproduced this trend, revealing that the increase in cluster size is primarily due to changes in metal-ligand bond lengths, while the electronic properties of the core remain largely unchanged. Moreover, this method allowed us to exclude certain multiplicity states of the NCs, as their CCS values were significantly different from those predicted for the lowest-energy structures. Here, this study demonstrates that gas-phase IM-MS is a powerful technique for detecting subtle size differences in atomically precise NCs, which are often challenging to observe using conventional NC characterization methods. Accurate CCS measurements are established as a benchmark for comparison with theoretical calculations. The excellent correspondence between experimental data and theoretical predictions establishes a robust foundation for investigating structural changes of transition metal NCs of interest to a broad range of applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A quantum eigenvalue solver based on tensor networks

Electronic ground states are of central importance in chemical simulations, but have remained beyond the reach of efficient classical algorithms except in cases of weak electron correlation or one-dimensional spatial geometry. We introduce a hybrid quantum-classical eigenvalue solver that constructs a wavefunction ansatz from a linear combination of matrix product states in rotated orbital bases, enabling the characterization of strongly correlated ground states with arbitrary spatial geometry. The energy is converged via a gradient-free generalized sweep algorithm based on quantum subspace diagonalization, with a potentially exponential speedup in the off-diagonal matrix element contractions upon translation into compact quantum circuits of linear depth in the number of qubits. Chemical accuracy is attained in numerical experiments for both a stretched water molecule and an octahedral arrangement of hydrogen atoms, achieving substantially better correlation energies compared to a unitary coupled-cluster benchmark, with orders of magnitude reductions in quantum resource estimates and a surprisingly high tolerance to shot noise. This proof-of-concept study suggests a promising new avenue for scaling up simulations of strongly correlated chemical systems on near-term quantum hardware.

chemistry↗
DOE OSTI2020

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis -element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Omics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunities

Plants produce a vast array of metabolites, the biosynthetic routes of which remain largely undetermined. Genome-scale enzyme and pathway annotations and omics technologies have revolutionized research to decrypt plant metabolism and produced a growing list of functionally characterized metabolic genes and pathways. However, what is known is still a tiny fraction of the metabolic capacity harbored by plants. Here, in this work, we review plant enzyme and pathway annotation resources and cutting-edge omics approaches to guide discovery and characterization of plant metabolic pathways. We also discuss strategies for improving enzyme function prediction by integrating protein 3D structure information and single cell omics. This review aims to serve as a primer for plant biologists to leverage omics datasets to facilitate understanding and engineering plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High-Temperature Pretreatment Effect on Co/SiO 2 Active Sites and Ethane Dehydrogenation

Here, we report the synthesis, optimization, and characterization of Co/SiO 2 for ethane nonoxidative dehydrogenation. Co/SiO 2 is synthesized via strong electrostatic adsorption using the widely available Co(NO 3 ) 2 as the precursor. We demonstrate that high-temperature pretreatment (900 °C) in an inert atmosphere can significantly enhance the initial activity of the Co/SiO 2 catalyst. X-ray absorption near-edge spectroscopy (XANES), temperature-programmed reduction (TPR), and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) suggest that highly dispersed Co(II) clusters are more active than Co 0 or CoO x nanoparticles. Fourier transform infrared (FTIR) and isopropanol (IPA) temperature-programmed desorption and density functional theory (DFT) calculations suggest that high-temperature treatment significantly increases the density of active Lewis acid sites, possibly via surface dehydroxylation of the catalyst.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Asynchronous quadratic control for constrained hidden markov jump linear systems with incomplete MTPM and MOCPM

Abstract This paper investigates the quadratic optimal control problem for constrained Markov jump linear systems with incomplete mode transition probability matrix (MTPM). Considering original system mode is not accessible, observed mode is utilized for asynchronous controller design where mode observation conditional probability matrix (MOCPM), which characterizes the emission between original modes and observed modes is assumed to be partially known. An LMI optimization problem is formulated for such constrained hidden Markov jump linear systems with incomplete MTPM and MOCPM. Based on this, a feasible state-feedback controller can be designed with the application of free-connection weighting matrix method. The desired controller, dependent on observed mode, is an asynchronous one which can minimize the upper bound of quadratic cost and satisfy restrictions on system states and control variables. Furthermore, clustering observation where observed modes recast into several clusters, is explored for simplifying the computational complexity. Numerical examples are provided to illustrate the validity.

Zhu, Jin↗
NASA NTRS2003

Premotor neurons encode torsional eye velocity during smooth-pursuit eye movements

Responses to horizontal and vertical ocular pursuit and head and body rotation in multiple planes were recorded in eye movement-sensitive neurons in the rostral vestibular nuclei (VN) of two rhesus monkeys. When tested during pursuit through primary eye position, the majority of the cells preferred either horizontal or vertical target motion. During pursuit of targets that moved horizontally at different vertical eccentricities or vertically at different horizontal eccentricities, eye angular velocity has been shown to include a torsional component the amplitude of which is proportional to half the gaze angle ("half-angle rule" of Listing's law). Approximately half of the neurons, the majority of which were characterized as "vertical" during pursuit through primary position, exhibited significant changes in their response gain and/or phase as a function of gaze eccentricity during pursuit, as if they were also sensitive to torsional eye velocity. Multiple linear regression analysis revealed a significant contribution of torsional eye movement sensitivity to the responsiveness of the cells. These findings suggest that many VN neurons encode three-dimensional angular velocity, rather than the two-dimensional derivative of eye position, during smooth-pursuit eye movements. Although no clear clustering of pursuit preferred-direction vectors along the semicircular canal axes was observed, the sensitivity of VN neurons to torsional eye movements might reflect a preservation of similar premotor coding of visual and vestibular-driven slow eye movements for both lateral-eyed and foveate species.

Non-NASA Center↗
NASA NTRSDate not supplied

Perturbations in Brain Functional Connectivity Patterns After Waking From Slow Wave Sleep Under Different Cognitive States

Sleep inertia refers to the state of transition between sleep and wake characterized by impaired alertness, confusion, and reduced cognitive and behavioral performance. While the behavioral symptoms of sleep inertia are well described, the neurological changes that lead to this state remain elusive. Here, to understand the state of sleep inertia and the reorganization that the brain undergoes, we took a graph theoretical approach and compared the EEG derived brain connectivity patterns before sleep and after waking up while participants (n = 10) performed multiple tasks that differed in cognitive complexities. We focused on how the degree and the clustering coefficient of brain regions (EEG sensors) change immediately after participants wake up from slow wave sleep. During a psychomotor vigilance task (PVT), designed to assess vigilant attention, we find that the brain regions with strong network connectivity (degree) before sleep show a reduction in connectivity after waking. In contrast, those with low connectivity before sleep have greater connectivity after waking. The regions that undergo these changes are specific to each participant and these findings are unique to the beta frequency range, which plays a key role in sensorimotor functioning and preserving the current state of the brain. Moreover, in tasks that required inhibitory control and arithmetic reasoning, we found that only regions with weak connectivity before sleep exhibited more connections after waking, but regions with high connectivity prior to sleeping remained unchanged, highlighting task specific effects. Furthermore, we find that during the PVT, the clustering coefficient within low frequency oscillations of the brain is reduced upon waking while it remains unchanged during other tasks. These results suggest that the connections between regions that are lost after abrupt awakening can be reallocated to other regions in order to renormalize the brain. However, this response may only be evident during specific cognitive states and may be more nuanced during complex task performance.

sleep inertia↗
DOE OSTI2021

Defect Characterization Using Positron Annihilation Spectroscopy on Laser-Ablated Surfaces

In recent years, short, pulsed laser ablation has been gaining popularity for machining small-scale test geometries from bulk samples and for efficient serial sectioning. These laser-based techniques are being added to the toolbox in material science, which makes it necessary to understand the changes in the material that occur from the laser–material interaction. Positron annihilation spectroscopy is a unique, nondestructive technique to investigate small defects in materials difficult to investigate by other tools. In this work, Doppler broadening and positron lifetime annihilation spectroscopy are utilized to help quantify the damage in materials treated with short, pulsed lasers. Using a femtosecond laser on single crystal silicon, this manuscript shows that clusters of vacancy-like defects and small voids increase systematically with laser power. Lastly, the damage induced by the laser can also reach to micrometer depths.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Microstructural evolution in doped high entropy alloys NiCoFeCr-3X (X=Pd/Al/Cu) under irradiation

Commonly studied equatomic single-phase FCC high entropy alloys based on 3d transition metals like NiCoFeCr do not provide adequate strength and radiation resistance at high doses for nuclear structural applications. In the current study, the major alloying effects like lattice distortion, ordering and clustering tendencies were investigated by adding low concentration of Pd, Al, or Cu respectively to study the doping effects on the ion irradiation response of NiCoFeCr alloy. The alloys were irradiated with 3 MeV Ni 2+ ions at 500 °C to a fluence of 1 × 10 17 /cm 2 at a beam flux of approximately 2.8 × 10 12 ions/cm 2 /s. The microstructural evolution upon irradiation i.e., formation of dislocation networks, radiation induced segregation and precipitation, and void formation were studied in detail. Further, post-irradiation characterization results showed that a Pd addition leads to a high void nucleation rate but controlled void growth, which may be attributed to increased lattice distortion. In Al added HEA, our microstructural analysis indicates that radiation induced ordered L1 2 precipitates do not affect void swelling significantly. Cu addition led to Cu precipitation that drastically suppressed dislocation density and void swelling of the alloy. Additionally, a model was developed to qualitatively describe the trend in void swelling of typical FCC alloys under ion irradiation. This model was able to qualitatively explain the suppression and reappearance of void swelling in ion irradiated alloys that generally occurs near the region with peak implanted ion concentration.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Irradiation-induced segregation at dislocation loops in CoCrFeMnNi high entropy alloy

To understand the redistribution of alloying elements in high entropy alloys under irradiation, we irradiated a CoCrFeMnNi alloy with 1 MeV Kr ions at room temperature and at 500°C, and characterized with atom probe tomography and transmission electron microscopy. At 500°C, Co and Ni were enriched around the interstitial, faulted and perfect, dislocation loops resulted from the ion irradiation. In contrast, no segregation was observed at room temperature. The inverse Kirkendall effect through vacancy flux, as opposed to the interstitial binding mechanism, was the primary underlying process attributing to the observed segregation. In addition, a ring-shaped segregation pattern was observed at the faulted dislocation loops, indicating a non-equilibrium nature of the defect clustering and solute segregation process in CoCrFeMnNi under irradiation at high temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Contribution of El Niño Southern Oscillation (ENSO) Diversity to Low‐Frequency Changes in ENSO Variance

Abstract El Niño Southern Oscillation (ENSO) diversity is characterized based on the longitudinal location of maximum sea surface temperature anomalies (SSTA) and amplitude in the tropical Pacific, as Central Pacific events are typically weaker than Eastern Pacific events. SSTA pattern and intensity undergo low‐frequency modulations, affecting ENSO prediction skill and remote impacts, and resulting in low‐frequency changes in ENSO variance. Yet, how different ENSO types contribute to these decadal variance changes remains unclear. Here, we decompose the low‐frequency changes of ENSO variance into contributions from ENSO diversity categories. We propose a fuzzy clustering of monthly SSTA to allow for non‐binary event category memberships, where each event can belong to different clusters. Our approach identifies two La Niña and three El Niño categories and shows that the major shift of ENSO variance in the mid‐1970s was associated with an increasing likelihood of strong La Niña and extreme El Niño events.

Geology↗
NASA NTRS2017

Structure in the 3D Galaxy Distribution: III. Fourier Transforming the Universe: Phase and Power Spectra

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform (FFT) of finely binned galaxy positions. In both cases deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multi-point hierarchy. We identify some threads of modern large scale inference methodology that will presumably yield detections in new wider and deeper surveys.

Galactic clusters↗
NASA NTRSDate not supplied

Optimizing Altitude Sampling and Sensitivity with the Goldstone Orbital Debris Radar

The NASA Orbital Debris Program Office (ODPO) has used the Goldstone Orbital Debris Radar (Goldstone) since 1993 to characterize orbital debris (OD) in low Earth orbit too small to be tracked by the U.S. Space Surveillance Network. Operated by NASA’s Jet Propulsion Laboratory, Goldstone can measure OD as small as 3 mm at 1000 km altitude and lower. Goldstone is a bistatic radar that for 25 years used Deep Space Station (DSS)-14 as a transmitter and DSS-15 as a receiver. In early 2018, DSS-15 was decommissioned and replaced with DSS-25 (and occasionally DSS-26) of the Deep Space Network Apollo Cluster. The increased baseline between DSS-14 and DSS-25 significantly reduced the instantaneous altitude coverage of the bistatic beam overlap. Initial measurements in 2018 were focused around 800 km, which has approximately the highest flux of sub-centimeter debris. In 2019, DSS-14 was offline for maintenance, and the ODPO designed an annual survey observation plan to efficiently sample altitudes from 700 km to 1000 km, since many NASA satellites fly in this range. This paper discusses the observation plan, including the development of the pointings, a refinement of the altitudes of interest, and an analysis of the effects of random pointing errors on beam overlap. Additionally, results from measurements taken in 2020 and 2021 are presented, showing that not only is the observation plan effective at sampling 700 km to 1000 km altitude, but it is also producing the most sensitive terrestrial radar measurements at these altitudes to date.

James Murray↗