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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 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Radioisotope Identification with List-Mode Gamma-Ray Data

This work explores the potential of utilizing temporal data from gamma-ray detectors, known as list-mode data, to enhance radioisotope identification. Traditional identification methods, which rely on full gamma-ray spectrum analysis, often require long dwell times and struggle with spectra containing similarly spaced spectral peaks. We hypothesize that by leveraging the probabilistic nature of nuclear decay and the time-encoded information from decay sequences and interactions with surrounding materials, we can improve classification accuracy over static spectral analysis. This research examines the temporal content of list-mode data through exploratory data analysis via correlation discovery and qualitative distribution analysis. Additionally, we propose a probabilistic classification model that can utilize spectral data, temporal data, or both to determine if the incorporation of temporal information improves radioisotope identification. Our findings suggest that the temporal information present in list-mode gamma-ray data has merit and should be further investigated to develop more robust and optimal methods for utilizing this temporal information in applications requiring radioisotope identification.

List-mode data↗
DOE OSTI2015

RADIAL VELOCITY OBSERVATIONS AND LIGHT CURVE NOISE MODELING CONFIRM THAT KEPLER-91b IS A GIANT PLANET ORBITING A GIANT STAR

Kepler-91b is a rare example of a transiting hot Jupiter around a red giant star, providing the possibility to study the formation and composition of hot Jupiters under different conditions compared to main-sequence stars. However, the planetary nature of Kepler-91b, which was confirmed using phase-curve variations by Lillo-Box et al., was recently called into question based on a re-analysis of Kepler data. We have obtained ground-based radial velocity observations from the Hobby-Eberly Telescope and unambiguously confirm the planetary nature of Kepler-91b by simultaneously modeling the Kepler and radial velocity data. The star exhibits temporally correlated noise due to stellar granulation which we model as a Gaussian Process. We hypothesize that it is this noise component that led previous studies to suspect Kepler-91b to be a false positive. Our work confirms the conclusions presented by Lillo-Box et al. that Kepler-91b is a 0.73 ± 0.13 M {sub Jup} planet orbiting a red giant star.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

IMG/M: integrated genome and metagenome comparative data analysis system

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Global stratigraphy of Venus: Analysis of a random sample of thirty-six test areas

The age relations between 36 impact craters with dark paraboloids and other geologic units and structures at these localities have been studied through photogeologic analysis of Magellan SAR images of the surface of Venus. Geologic settings in all 36 sites, about 1000 x 1000 km each, could be characterized using only 10 different terrain units and six types of structures. Mapping of such units and structures in 36 randomly distributed large regions shows evidence for a distinctive regional and global stratigraphic and geologic sequence. On the basis of this sequence we have developed a model that illustrates several major themes in the history of Venus. Most of the history of Venus (that of its first 80% or so) is not preserved in the surface geomorphological record. The major deformation associated with tessera formation in the period sometime between 0.5-1.0 b.y. ago (Ivanov and Basilevsky, 1993) is the earliest event detected. Our stratigraphic analyses suggest that following tessera formation, extensive volcanic flooding resurfaced at least 85% of the planet in the form of the presently-ridged and fractured plains. Several lines of evidence favor a high flux in the post-tessera period but we have no independent evidence for the absolute duration of ridged plains emplacement. During this time, the net state of stress in the lithosphere apparently changed from extensional to compressional, first in the form of extensive ridge belt development, followed by the formation of extensive wrinkle ridges on the flow units. Subsequently, there occurred local emplacement of smooth and lobate plains units which are presently essentially undeformed. The major events in the latest 10% of the presently preserved history of Venus are continued rifting and some associated volcanism, and the redistribution of eolian material largely derived from impact crater deposits. Detailed geologic mapping and stratigraphic synthesis are necessary to test this sequence and to address many of the outstanding problems raised by this analysis.

Basilevsky, Alexander T.↗
DOE OSTI2013

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

27-Hydroxycholesterol increases Myc protein stability via suppressing PP2A, SCP1 and FBW7 transcription in MCF-7 breast cancer cells

27-hydroxycholesterol (27-HC), the most abundant metabolite of cholesterol, is a risk factor for breast cancer. It can increase the proliferation of breast cancer cells and promote the metastasis of breast tumours in mouse models. Myc is a critical oncoprotein overexpressed in breast cancer. However, whether 27-HC affects Myc expression has not been reported. In the current study, we aimed to investigate the effects of 27-HC on Myc and the underlying mechanisms in MCF-7 breast cancer cells. Our data demonstrated that 27-HC activated Myc via increasing its protein stability. Three key negative modulators of Myc protein stability, PP2A, SCP1 and FBW7, were suppressed by 27-HC at the transcriptional level. We performed a data-mining analysis of the chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) data in the ChIPBase, and discovered that a number of putative transcription factors (TFs), including Myc itself, were involved in the transcriptional regulation of PP2A, SCP1 and FBW7. Our results provide a novel mechanistic insight into the activation of Myc by 27-HC via transcriptional repression of PP2A, SCP1 and FBW7 to increase Myc protein stability in breast cancer cells. - Highlights: • 27-Hydroxycholesterol (27-HC) activates Myc via increasing its protein stability. • 27-HC inhibits PP2A and SCP1 transcription to block pS62-Myc dephosphorylation. • 27-HC suppresses FBW7 transcription to prevent pT58-Myc degradation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

TOUGH-UDEC: A simulator for coupled multiphase fluid flows, heat transfers and discontinuous deformations in fractured porous media

A numerical simulator entitled TOUGH-UDEC is presented for the assessment of coupled thermal-hydraulic-mechanical processes in fractured porous media. Two existing well-established codes, TOUGH2 and UDEC, are coupled to model multiphase fluid flows, heat transfers, and discontinuous deformations in fractured porous media by means of discrete fracture representation. TOUGH2 is widely used for the modeling of heat transfers and multiphase multicomponent fluid flows, and UDEC is a well-known distinct element code for rock mechanics. The two codes are solved sequentially, with coupling parameters passed to each equation at specific intervals. After solving thermal-hydraulic equations within the TOUGH2 code, pressure and temperature information is imported into the UDEC model. Upon solving the mechanical equation within the UDEC code the calculated fracture apertures are converted to the equivalent permeability and porosity values for a TOUGH2 flow analysis. The solution is calculated by iteratively following an explicit sequence for numerical efficiency. Verifications are presented to demonstrate the capabilities of the coupled TOUGH-UDEC simulator. Three application examples of (1) shear dilation due to increased pore pressure, (2) thermal stress and (3) CO 2 injection, show that the new simulator can be an effective tool for geoengineering applications involving shear activation of fractures and faults.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence exhibit a complex and diffuse spatial distribution. The first-order complexity in aftershock distribution is clear and well beyond the influence of typical earthquake location uncertainty. The sequence included rupture of multiple fault segments, spatially separated. We use surface-wave based relative centroid locations to examine whether, at the small scale, the distribution of the aftershocks was influenced by location errors. Surface-wave based relative location has delineated precise oceanic transform fault earthquake locations in multiple regions. However, the relocated aftershocks off the coast of Sumatra seldom align along simple linear trends that are compatible with the corresponding fault strikes as estimated for the GCMT catalog. The relocation of roughly 60 moderate-earthquake epicentroids suggests that the faulting involved in the 2012 earthquake aftershock sequence included strain release along many short fault segments. Statistical analysis and temporal variations of aftershocks show a typical decay of the aftershocks but a relatively low number of aftershocks, as is common for intraplate oceanic earthquakes. Coulomb stress calculations indicate that most of the moderate-magnitude aftershocks are compatible with stress changes predicted by the large-event slip models. Furthermore the patterns in the aftershocks suggest that the formation of the boundary and eventual localization of deformation between the Indian and Australian plate is a complicated process.

2012 Sumatra Earthquake↗
DOE OSTI2023

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Robust predictions of specialized metabolism genes through machine learning

Plant specialized metabolism (SM) enzymes produce lineage-specific metabolites with important ecological, evolutionary, and biotechnological implications. Using Arabidopsis thaliana as a model, we identified distinguishing characteristics of SM and GM (general metabolism, traditionally referred to as primary metabolism) genes through a detailed study of features including duplication pattern, sequence conservation, transcription, protein domain content, and gene network properties. Analysis of multiple sets of benchmark genes revealed that SM genes tend to be tandemly duplicated, coexpressed with their paralogs, narrowly expressed at lower levels, less conserved, and less well connected in gene networks relative to GM genes. Although the values of each of these features significantly differed between SM and GM genes, any single feature was ineffective at predicting SM from GM genes. Using machine learning methods to integrate all features, a prediction model was established with a true positive rate of 87% and a true negative rate of 71%. In addition, 86% of known SM genes not used to create the machine learning model were predicted. We also demonstrated that the model could be further improved when we distinguished between SM, GM, and junction genes responsible for reactions shared by SM and GM pathways, indicating that topological considerations may further improve the SM prediction model. Application of the prediction model led to the identification of 1,220 A. thaliana genes with previously unknown functions, each assigned a confidence measure called an SM score, providing a global estimate of SM gene content in a plant genome.

data integration↗
DOE OSTI2012

NONLINEAR TIDES IN CLOSE BINARY SYSTEMS

We study the excitation and damping of tides in close binary systems, accounting for the leading-order nonlinear corrections to linear tidal theory. These nonlinear corrections include two distinct physical effects: three-mode nonlinear interactions, i.e., the redistribution of energy among stellar modes of oscillation, and nonlinear excitation of stellar normal modes by the time-varying gravitational potential of the companion. This paper, the first in a series, presents the formalism for studying nonlinear tides and studies the nonlinear stability of the linear tidal flow. Although the formalism we present is applicable to binaries containing stars, planets, and/or compact objects, we focus on non-rotating solar-type stars with stellar or planetary companions. Our primary results include the following: (1) The linear tidal solution almost universally used in studies of binary evolution is unstable over much of the parameter space in which it is employed. More specifically, resonantly excited internal gravity waves in solar-type stars are nonlinearly unstable to parametric resonance for companion masses M' {approx}> 10-100 M{sub Circled-Plus} at orbital periods P Almost-Equal-To 1-10 days. The nearly static 'equilibrium' tidal distortion is, however, stable to parametric resonance except for solar binaries with P {approx}< 2-5 days. (2) For companion masses larger than a few Jupiter masses, the dynamical tide causes short length scale waves to grow so rapidly that they must be treated as traveling waves, rather than standing waves. (3) We show that the global three-wave treatment of parametric instability typically used in the astrophysics literature does not yield the fastest-growing daughter modes or instability threshold in many cases. We find a form of parametric instability in which a single parent wave excites a very large number of daughter waves (N Almost-Equal-To 10{sup 3}[P/10 days] for a solar-type star) and drives them as a single coherent unit with growth rates that are a factor of Almost-Equal-To N faster than the standard three-wave parametric instability. These are local instabilities viewed through the lens of global analysis; the coherent global growth rate follows local rates in the regions where the shear is strongest. In solar-type stars, the dynamical tide is unstable to this collective version of the parametric instability for even sub-Jupiter companion masses with P {approx}< a month. (4) Independent of the parametric instability, the dynamical and equilibrium tides excite a wide range of stellar p-modes and g-modes by nonlinear inhomogeneous forcing; this coupling appears particularly efficient at draining energy out of the dynamical tide and may be more important than either wave breaking or parametric resonance at determining the nonlinear dissipation of the dynamical tide.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

CHARACTERIZATION OF A SPURIOUS ONE-YEAR SIGNAL IN HARPS DATA

The HARPS spectrograph is showing an extreme stability, close to the m s{sup −1} level, over more than 10 years of data. However, the radial velocities of some stars are contaminated by a spurious one-year signal with an amplitude that can be as high as a few m s{sup −1}. This signal is in opposition of phase with the revolution of Earth around the Sun and can be explained by the deformation of spectral lines crossing block stitchings of the CCD when the spectrum of an observed star is alternatively blueshifted and redshifted due to the motion of Earth around the Sun. This annual perturbation can be suppressed by either removing those affected spectral lines from the correlation mask used by the cross-correlation technique to derive precise radial velocities, or by simply fitting a yearly sinusoid to the radial velocity data. This is mandatory if we want to detect long-period low-amplitude signals in the HARPS radial velocities of quiet solar-type stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Hybrid deep learning architecture for general disruption prediction across tokamaks

In this paper, we present a new deep learning disruption prediction algorithm based on important findings from explorative data analysis which effectively allows knowledge transfer from existing devices to new ones, thereby predicting disruptions using very limited disruptive data from the new devices. Here, the explorative data analysis conducted via unsupervised clustering techniques confirms that time-sequence data are much better separators of disruptive and non-disruptive behavior than the instantaneous plasma state data with further advantageous implications for a sequence-based predictor. Based on such important findings, we have designed a new algorithm for multi-machine disruption prediction that achieves high predictive accuracy on the C-Mod (AUC=0.801), DIII-D (AUC=0.947) and EAST (AUC=0.973) tokamaks with limited hyperparameter tuning. Through numerical experiments, we show that boosted accuracy (AUC=0.959) is achieved on EAST predictions by including in the training only 20 disruptive discharges, thousands of non-disruptive discharges from EAST, and combining this with more than a thousand discharges from DIII-D and C-Mod. The improvement of predictive ability obtained by combining disruptive data from other devices is found to be true for all permutations of the three devices. Furthermore, by comparing the predictive performance of each individual numerical experiment, we find that non-disruptive data are machine-specific while disruptive data from multiple devices contain device-independent knowledge that can be used to inform predictions for disruptions occurring on a new device.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1562 scaffolds with 449.82 Mb, 80x of coverage and 22 952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

California Conservation Genomics Project—CCGP↗
DOE OSTI2024

Human Liver Epithelial Cells (HuH7) Response to HCoV-229E Infection Epigenomics (ATAC-Seq) (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-299E) infection alters chromatin accessibility in infected cells. Sample data was obtained from mock-infected cells, UV-inactivated virus treated cells, and replication competent HCoV-229E infected immortalized human liver cells (HuH7) at 24 hours post infection. Samples were processed using ATAC-seq methods for reported bar coded libraries. Sample data was acquired using an Illumina Hi-Seq 2500 sequencer system and further processed for ATAC-Seq expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SFA-VirOmics

PNNL's Soil Microbiome Science Focus Area (SFA) is focused on understanding the basic biology underpinning how interactions among various soil microbial community members, across trophic levels, lead to the emergence of community functions. Moisture, in particular, drives microbial interactions and influences everything from cell function to substrate fate within soils. The group predicts this results in repeatable, predictable phenotypes. The sum of these phenotypes comprises the “soil metaphenome”. Understanding how the soil metaphenome shifts in response to moisture will provide a basis for modeling and predicting these shifts in reaction network responses. Visit the PNNL Soil Microbiome Science Focus Area Program homepage for more information. PNNL’s Soil Microbiome SFA Virome Dataset Annotation page is an extension to the PNNL Soil Microbiome SFA repository on DataHub allows for exploring and downloading integrated experimental omics dataset annotations, associated experimental metadata, pre- and post-processed viral data files, and other associated materials directly related to experimental viral project data.

59 BASIC BIOLOGICAL SCIENCES↗

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