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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.

dirigent protein↗
DOE OSTI2021

Formin nanoclustering-mediated actin assembly during plant flagellin and DSF signaling

Plants respond to bacterial infection acutely with actin remodeling during plant immune responses. The mechanisms by which bacterial virulence factors (VFs) modulate plant actin polymerization remain enigmatic. Here, we show that plant-type-I formin serves as the molecular sensor for actin remodeling in response to two bacterial VFs: Xanthomonas campestris pv. campestris (Xcc) diffusible signal factor (DSF), and pathogen-associated molecular pattern (PAMP) flagellin in pattern-triggered immunity (PTI). Both VFs regulate actin assembly by tuning the clustering and nucleation activity of formin on the plasma membrane (PM) at the nano-sized scale. By being integrated within the cell-wall-PM-actin cytoskeleton (CW-PM-AC) continuum, the dynamic behavior and function of formins are highly dependent on each scaffold layer’s composition within the CW-PM-AC continuum during both DSF and PTI signaling. Our results reveal a central mechanism for rapid actin remodeling during plant-bacteria interactions, in which bacterial signaling molecules fine tune plant formin nanoclustering in a host mechanical-structure-dependent manner.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Identification of tau leptons using a convolutional neural network with domain adaptation

A tau lepton identification algorithm,DeepTau, based on convolutional neural network techniques, has been developed in the CMS experiment to discriminate reconstructed hadronic decays of tau leptons (τ h ) from quark or gluon jets and electrons and muons that are misreconstructed as τ h candidates. The latest version of this algorithm, v2.5, includes domain adaptation by backpropagation, a technique that reduces discrepancies between collision data and simulation in the region with the highest purity of genuine τh candidates. Additionally, a refined training workflow improves classification performance with respect to the previous version of the algorithm, with a reduction of 30–50% in the probability for quark and gluon jets to be misidentified as τ h candidates for given reconstruction and identification efficiencies. This paper presents the novel improvements introduced in theDeepTau algorithm and evaluates its performance in LHC proton-proton collision data at √(s) = 13 and 13.6 TeV collected in 2018 and 2022 with integrated luminosities of 60 and 35 fb -1 , respectively. Techniques to calibrate the performance of the τ h identification algorithm in simulation with respect to its measured performance in real data are presented, together with a subset of results among those measured for use in CMS physics analyses.

Large detector-systems performance↗
DOE OSTI2021

Active matter commensuration and frustration effects on periodic substrates

In this report we show that self-driven particles coupled to a periodic obstacle array exhibit active matter commensuration effects that are absent in the Brownian limit. As the obstacle size is varied for sufficiently large activity, a series of commensuration effects appear in which the motility induced phase separation produces commensurate crystalline states, while for other obstacle sizes we find frustrated or amorphous states. The commensuration effects are associated with peaks in the amount of sixfold ordering and the maximum cluster size. When a drift force is added to the system, the mobility contains peaks and dips similar to those found in transport studies for commensuration effects in superconducting vortices and colloidal particles.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Parallel Optical Flow Processing of 4D Cardiac CT Data on Multicore Clusters, In: 2014 IEEE 17th International Conference on Computational Science and Engineering

Optical flow is the distribution of apparent velocities of movement of brightness patterns in a sequence of images. For large 3D image sequences, optical flow applications are time consuming and memory-bound. To cope with these problems, in this paper, we present parallel optical flow processing of 4D cardiac CT data on multicore cluster systems to significantly shorten the time for computing velocity fields of the heart in order to aid cardiologists in diagnosing heart disease such as myocardial infarction and cardiac dysrhythmia in time. First, we modify and extend two traditional 2D optical flow methods Horn-Schunck and Lucas-Kanade to three-dimensional cases to process the 4D cardiac CT data. Second, we extend Mat lab MPI to support parallel computing with Mat lab and Octave on these cluster systems. Then we develop the parallel Mat lab/Octave optical flow applications for the 4D cardiac CT data in detail. Our experimental results show that these parallel optical flow applications have good scalability with close to linear speedup, and are able to shorten the image processing time significantly from more than 5 hours on 4 cores to 1.5 minutes on 1024 cores.

Engineering↗
DOE OSTI2016

Machine learning based job status prediction in scientific clusters

Large high-performance computing systems are built with increasing number of components with more CPU cores, more memory, and more storage space. At the same time, scientific applications have been growing in complexity. Together, they are leading to more frequent unsuccessful job statuses on HPC systems. From measured job statuses, 23.4% of CPU time was spent to the unsuccessful jobs. Here, we set out to study whether these unsuccessful job statuses could be anticipated from known job characteristics. To explore this possibility, we have developed a job status prediction method for the execution of jobs on scientific clusters. The Random Forests algorithm was applied to extract and characterize the patterns of unsuccessful job statuses. Experimental results show that our method can predict the unsuccessful job statuses from the monitored ongoing job executions in 99.8% the cases with 83.6% recall and 94.8% precision. Lastly, this prediction accuracy can be sufficiently high that it can be used to mitigation procedures of predicted failures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisticated, integrative methods have been described, but commonly suffer from limited accessibility to the resulting predictions and reduced biological interpretability. Here we present the Limb-Enhancer Genie (LEG), a collection of highly accurate, genome-wide predictions of enhancers in the developing limb, available through a user-friendly online interface. We predict limb enhancers using a combination of > 50 published limb-specific datasets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage of the patterns observed at previously in vivo validated elements. By combining different statistical models, our approach outperforms current state-of-the-art methods and provides interpretable measures of feature importance. Our results indicate that including a previously unappreciated score that quantifies tissue-specific nuclease accessibility significantly improves prediction performance. We demonstrate the utility of our approach through in vivo validation of newly predicted elements. Moreover, we describe general features that can guide the type of datasets to include when predicting tissue-specific enhancers genome-wide, while providing an accessible resource to the general biological community and facilitating the functional interpretation of genetic studies of limb malformations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Life Cycle Analysis of Kidney Gene Expression in Male F344 Rats

Age is a predisposing condition for susceptibility to chronic kidney disease and progression as well as acute kidney injury that may arise due to the adverse effects of some drugs. Age-related differences in kidney biology, therefore, are a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of genes expressed in the kidney at various life cycle stages will impact susceptibility to adverse drug reactions. Therefore, establishing changes in baseline expression data between these life stages is the first and necessary step in evaluating this hypothesis. Untreated male F344 rats were sacrificed at 2, 5, 6, 8, 15, 21, 78, and 104 weeks of age. Kidneys were collected for histology and gene expression analysis. Agilent whole-genome rat microarrays were used to query global expression profiles. An ANOVA (p,0.01) coupled with a fold-change.1.5 in relative mRNA expression, was used to identify 3,724 unique differentially expressed genes (DEGs). Principal component analyses of these DEGs revealed three major divisions in life-cycle renal gene expression. K-means cluster analysis identified several groups of genes that shared age-specific patterns of expression. Pathway analysis of these gene groups revealed age-specific gene networks and functions related to renal function and aging, including extracellular matrix turnover, immune cell response, and renal tubular injury. Large age-related changes in expression were also demonstrated for the genes that code for qualified renal injury biomarkers KIM-1, Clu, and Tff3. These results suggest specific groups of genes that may underlie age-specific susceptibilities to adverse drug reactions and disease. This analysis of the basal gene expression patterns of renal genes throughout the life cycle of the rat will improve the use of current and future renal biomarkers and inform our assessments of kidney injury and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation

Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Star Formation, Supernovae, Iron, and α: Consistent Cosmic and Galactic Histories

Recent versions of the observed cosmic star formation history (SFH) have resolved an inconsistency with the stellar mass density history. We show that the revised SFH also scales up the delay-time distribution (DTD) of Type Ia supernovae (SNe Ia), as determined from the observed volumetric SN Ia rate history, aligning it with other field-galaxy SN Ia DTD measurements. The revised-SFH-based DTD has a t{sup −1.1±0.1} form and a Hubble-time-integrated production efficiency of N/M{sub ⋆}=1.3±0.1 SNe Ia per 1000 M{sub ⊙} of formed stellar mass. Using these revised histories and updated empirical iron yields of the various SN types, we re-derive the cosmic iron accumulation history. Core-collapse SNe and SNe Ia have contributed about equally to the total mass of iron in the universe today. We find the track of the average cosmic gas element in the [α/Fe] versus [Fe/H] abundance-ratio plane. The track is broadly similar to the observed main locus of Galactic stars in this plane, indicating a Milky Way (MW) SFH similar in form to the cosmic one. We easily find a simple MW SFH that makes the track closely match this stellar locus. Galaxy clusters appear to have a higher-normalization DTD. This cluster DTD, combined with a short-burst MW SFH peaked at z = 3, produces a track that matches remarkably well the observed “high-α” locus of MW stars, suggesting the halo/thick-disk population has had a galaxy-cluster-like formation mode. Thus, a simple two-component SFH, combined with empirical DTDs and SN iron yields, suffices to closely reproduce the MW’s stellar abundance patterns.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Hierarchical Cluster Analysis of Service Usage and Geographic Variation in Medicare Spending

Per capita Medicare spending varies considerably throughout the Unites States, even after taking into account factors such as cost of living and pre-existing conditions of the Medicare populations. Additionally, per capita spending may vary up to four times as much under Medicare as it does under private insurance. Several studies have explored the Medicare-costs differences between regions with respect to how Medicare services are used. The recent public release of a large, relatively fine-grained set of Medicare data over four annual periods (2007–2010) by the Centers for Medicare and Medicaid Services (CMS), allowed us to perform a broad-scale exploratory analysis of Medicare service-usage patterns. The CMS data set contains data on the Health Care Referral Region level, which subsets the United States into 306 distinct regions. To identify potential trends in service usage over these regions, we used hierarchical agglomerative cluster analysis (HACA) to group regions into clusters based on similarity of service-usage patterns. Much previous work on the subject of cost variation starts with analysis of cost. By beginning with service-usage data, HACA effectively uncoupled patterns of service-usage from overall patterns of cost. We found that while some Medicare services were used in a fairly consistent manner over all clusters, other services varied considerably. Variation in how frequently services are used may provide insight into practices that are particularly expensive or particularly cost effective. It also may be possible to develop recommendations for more cost-efficient high-quality medical care by taking such information into account. In addition, the variance among the frequencies with which some services are used may point to inconsistent standards of medical practice that are not necessarily directly reflected in total cost, or to more deeply underlying geographic or demographic factors that are not necessarily reflected directly in total cost.

Vacha, Linnet↗
DOE OSTI2015

The Hubble space telescope UV legacy survey of galactic globular clusters. I. Overview of the project and detection of multiple stellar populations

In this paper we describe a new UV-initiative Hubble Space Telescope project (GO-13297) that will complement the existing F606W and F814W database of the Advanced Camera for Surveys Globular Cluster (GC) Treasury by imaging most of its clusters through UV/blue WFC3/UVIS filters F275W, F336W, and F438W. This “magic trio” of filters has shown an uncanny ability to disentangle and characterize multiple population (MP) patterns in GCs in a way that is exquisitely sensitive to C, N, and O abundance variations. Combination of these passbands with those in the optical also gives the best leverage for measuring helium enrichment. The dozen clusters that had previously been observed in these bands exhibit a bewildering variety of MP patterns, and the new survey will map the full variance of the phenomenon. The ubiquity of multiple stellar generations in GCs has made the formation of these cornerstone objects more intriguing than ever; GC formation and the origin of their MPs have now become one and the same problem. In this paper we will describe the database and our data reduction strategy, as well as the uses we intend to make of the final photometry, astrometry, and PMs. We will also present preliminary color–magnitude diagrams from the data so far collected. These diagrams also draw on data from GO-12605 and GO-12311, which served as a pilot project for the present GO-13297.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

THE INTRACLUSTER PLASMA: A UNIVERSAL PRESSURE PROFILE?

The pressure profiles of the intracluster plasma in galaxy clusters show a wide variance when observed in X-rays at low redshifts, z {approx}< 0.2. We find the profiles to follow two main patterns, featuring either a steep or a shallow shape throughout both core and outskirts. We trace these shapes back to a physical dichotomy of clusters into two classes, marked by either low entropy (LE) or high entropy (HE) throughout. From X-ray observations and Sunyaev-Zel'dovich (SZ) stacked data at higher redshifts 0.2 {approx}< z {approx}< 0.4, we obtain evidence of an increasing abundance of HEs relative to LEs. We propose this to constitute a systematic trend toward high z; specifically, we predict the pressure profiles to converge into a truly universal HE-like template for z {approx}> 0.5. We submit our physical templates and converging trend for further observational tests, in view of current and upcoming measurements of individual, stacked, and integrated SZ signals.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A weather pattern responsible for increasing wildfires in the western United States

Abstract The western United States (U.S.) has been experiencing more severe wildfires, in part due to climate change, but the underlying synoptic patterns and their modulation in driving fire weather is unclear. Here we investigated the relationship between weather regimes (WRs) and fire weather indices, specifically vapor pressure deficit (VPD) and the Canadian Forest Fire Weather Index. By identifying five singular WRs using k-means clustering, we found that a particular regime (WR-2), one characterized by a distinct tripolar wave train pattern over the continental U.S., has exhibited an increased frequency since 1980. The ascribed WR-2 regime was found to be mainly responsible for rising trends in the fire weather indices, especially VPD. Further, the average fire indices of the WR-2 regime played a more important role than the frequency in shaping the rising trends in the fire weather indices. The increased frequency of the WR-2 WR was mainly attributed to anthropogenic forcing and, the year-to-year variation of the frequency was associated with sea surface temperature anomalies over the subtropical eastern Pacific. Human-induced climate change might have furthered the exacerbation of wildfire danger in the western U.S. by modulating the behaviors of WRs and fire weather indices.

Zhang, Wei (ORCID:0000000221698749)↗
DOE OSTI2023

Extension of Large Fire Emissions From Summer to Autumn and Its Drivers in the Western US

Abstract Burned areas in the western US have increased ten‐fold since 1980s, which are attributable to multiple factors, including increasing heat, changing precipitation patterns, and extended drought. To better understand how these factors contribute to large fire emissions (gridded monthly fire emissions >95th percentile of all the fire emissions in the western US; 0.009 Gg/month), we build a machine learning model to predict fire emissions (PM 2.5 ) over the western US at 0.25° resolution, interpreted using explainable artificial intelligence (XAI). From the predictor contributions derived from XAI, we conduct k‐means clustering analysis to identify four clusters of predictor variables representing different drivers of large fire emissions. The four clusters feature the contributions of fuel load (Cluster 1) and different levels of dryness (Cluster 2–4), controlled by fuel moisture, drought condition, and fire‐favorable large‐scale meteorological patterns featuring high temperature, high pressure, and low relative humidity. In the past two decades, large fire emissions peak in summer. However, large fire emissions increased significantly in September and October in 2010–2020 relative to 2000–2009, extending the peak large fire emissions from summer to autumn. The larger enhancements of large fire emissions during autumn compared to summer are contributed by decreased fuel moisture, along with more frequent concurrent fire‐favorable large‐scale meteorological patterns and drought. These results highlight fuel drying as a common driver supported by multiple drivers, such as warmer temperature and more frequent synoptic patterns favorable for fires, in increasing the autumn risk of large fire emissions across the western US.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Two-component vector solitons in defocusing Kerr-type media with spatially modulated nonlinearity

We present a class of exact solutions to the coupled (2+1)-dimensional nonlinear Schrödinger equation with spatially modulated nonlinearity and a special external potential, which describe the evolution of two-component vector solitons in defocusing Kerr-type media. We find a robust soliton solution, constructed with the help of Whittaker functions. For specific choices of the topological charge, the radial mode number and the modulation depth, the solitons may exist in various forms, such as the half-moon, necklace-ring, and sawtooth vortex-ring patterns. Our results show that the profile of such solitons can be effectively controlled by the topological charge, the radial mode number, and the modulation depth. - Highlights: • Two-component vector soliton clusters in defocusing Kerr-type media are reported. • These soliton clusters are constructed with the help of Whittaker functions. • The half-moon, necklace-ring and vortex-ring patterns are found. • The profile of these solitons can be effectively controlled by three soliton parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Signatures of large-scale cold fronts in the optically-selected merging cluster HSC J085024+001536

Abstract We represent a joint X-ray, weak-lensing, and optical analysis of the optically-selected merging cluster, HSC J085024+001536, from the Subaru HSC-SSP survey. Both the member galaxy density and the weak-lensing mass map show that the cluster is composed of south-east and north-west components. The two-dimensional weak-lensing analysis shows that the south-east component is the main cluster, and the sub-cluster and main cluster mass ratio is $0.32^{+0.75}_{-0.23}$. The north-west sub-cluster is offset by ∼700 kpc from the main cluster center, and their relative line-of-sight velocity is ∼1300 km s−1 from spectroscopic redshifts of member galaxies. The X-ray emission is concentrated around the main cluster, while the gas mass fraction within a sphere of 1′ radius of the sub-cluster is only $f_{\mathrm{gas}}=4.0^{+2.3}_{-3.3}\%$, indicating that the sub-cluster gas was stripped by ram pressure. An X-ray residual image shows three arc-like excess patterns, of which two are symmetrically located at ∼550 kpc from the X-ray morphological center, and the other is close to the X-ray core. The excess close to the sub-cluster has a cold-front feature where dense-cold gas and thin-hot gas contact. The two outer excesses are tangentially elongated about ∼450–650 kpc, suggesting that the cluster is merged with a non-zero impact parameter. Overall features revealed by the multi-wavelength datasets indicate that the cluster is at the second impact or later. Since the optically-defined merger catalog is unbiased for merger boost of the intracluster medium, X-ray follow-up observations will pave the way to understand merger physics at various phases.

Tanaka, Keigo↗