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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

PWR ENDF/B-VII cross-section libraries for ORIGEN-ARP

New pressurized water reactor (PWR) cross-section libraries were generated for use with the ORIGEN-ARP depletion sequence in the SCALE nuclear analysis code system. These libraries are based on ENDF/B-VII nuclear data and were generated using the two-dimensional depletion sequence, TRITON/NEWT, in SCALE 6.1. The libraries contain multiple burnup-dependent cross-sections for seven PWR fuel designs, with enrichments ranging from 1.5 to 6 wt% {sup 235}U. The burnup range has been extended from the 72 GWd/MTU used in previous versions of the libraries to 90 GWd/MTU. Validation of the libraries using radiochemical assay measurements and decay heat measurements for PWR spent fuel showed good agreement between calculated and experimental data. Verification against detailed TRITON simulations for the considered assembly designs showed that depletion calculations performed in ORIGEN-ARP with the pre-generated libraries provide similar results as obtained with direct TRITON depletion, while greatly reducing the computation time. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
NASA NTRS2006

Leveraging Existing Mission Tools in a Re-Usable, Component-Based Software Environment

Emerging methods in component-based software development offer significant advantages but may seem incompatible with existing mission operations applications. In this paper we relate our positive experiences integrating existing mission applications into component-based tools we are delivering to three missions. In most operations environments, a number of software applications have been integrated together to form the mission operations software. In contrast, with component-based software development chunks of related functionality and data structures, referred to as components, can be individually delivered, integrated and re-used. With the advent of powerful tools for managing component-based development, complex software systems can potentially see significant benefits in ease of integration, testability and reusability from these techniques. These benefits motivate us to ask how component-based development techniques can be relevant in a mission operations environment, where there is significant investment in software tools that are not component-based and may not be written in languages for which component-based tools even exist. Trusted and complex software tools for sequencing, validation, navigation, and other vital functions cannot simply be re-written or abandoned in order to gain the advantages offered by emerging component-based software techniques. Thus some middle ground must be found. We have faced exactly this issue, and have found several solutions. Ensemble is an open platform for development, integration, and deployment of mission operations software that we are developing. Ensemble itself is an extension of an open source, component-based software development platform called Eclipse. Due to the advantages of component-based development, we have been able to vary rapidly develop mission operations tools for three surface missions by mixing and matching from a common set of mission operation components. We have also had to determine how to integrate existing mission applications for sequence development, sequence validation, and high level activity planning, and other functions into a component-based environment. For each of these, we used a somewhat different technique based upon the structure and usage of the existing application.

Greene, Kevin↗
DOE OSTI2014

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

STELLAR DIAMETERS AND TEMPERATURES. III. MAIN-SEQUENCE A, F, G, AND K STARS: ADDITIONAL HIGH-PRECISION MEASUREMENTS AND EMPIRICAL RELATIONS

Based on CHARA Array measurements, we present the angular diameters of 23 nearby, main-sequence stars, ranging from spectral types A7 to K0, 5 of which are exoplanet host stars. We derive linear radii, effective temperatures, and absolute luminosities of the stars using Hipparcos parallaxes and measured bolometric fluxes. The new data are combined with previously published values to create an Angular Diameter Anthology of measured angular diameters to main-sequence stars (luminosity classes V and IV). This compilation consists of 125 stars with diameter uncertainties of less than 5%, ranging in spectral types from A to M. The large quantity of empirical data is used to derive color-temperature relations to an assortment of color indices in the Johnson (BVR{sub J} I{sub J} JHK), Cousins (R{sub C} I{sub C}), Kron (R{sub K} I{sub K}), Sloan (griz), and WISE (W{sub 3} W{sub 4}) photometric systems. These relations have an average standard deviation of {approx}3% and are valid for stars with spectral types A0-M4. To derive even more accurate relations for Sun-like stars, we also determined these temperature relations omitting early-type stars (T{sub eff} > 6750 K) that may have biased luminosity estimates because of rapid rotation; for this subset the dispersion is only {approx}2.5%. We find effective temperatures in agreement within a couple of percent for the interferometrically characterized sample of main-sequence stars compared to those derived via the infrared flux method and spectroscopic analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

STRUCTURAL CONTROLS OF THE EMERSON PASS GEOTHERMAL SYSTEM, NORTHWESTERN NEVADA: CHARACTERIZATION OF A "BLIND" SYSTEM

The Pyramid Lake area is favorable for geothermal development due to the tectonic setting of the region. The Walker Lane belt, a dextral shear zone that accommodates ~20% relative motion between the Pacific and North American plates, terminates northwestward in northeast California. NW-directed dextral shear is transferred to WNW extension accommodated by N-to -NNE striking normal faults of the Basin and Range. As a consequence, enhanced dilation occurs on favorably oriented faults generating high geothermal potential in the northwestern Great Basin. The NW-striking right-lateral Pyramid Lake fault, a major structure of the northern Walker Lane, terminates at the southern end of Pyramid Lake and transfers strain to the NNE-striking down to the west Lake Range fault, resulting in high geothermal potential. Known geothermal systems in the area have not been developed due to cultural considerations of the Pyramid Lake Paiute Tribe. Therefore, exploration has been focused on discovering blind geothermal systems elsewhere on the reservation by identifying structurally favorable settings and indicators of past geothermal activity. One promising area is the northeast end of Pyramid Lake, where a broad left step between the west-dipping range-bounding faults of the Lake and Fox Ranges has led to the formation of a broad, faulted relay ramp. Furthermore, tufa mounds, mineralized veins, and altered Miocene rocks occur proximal to a thermal anomaly discovered by a 2-m shallow temperature survey at the north end of the step-over in Emerson Pass. Detailed geologic mapping has revealed a system of mainly NNE-striking down to the west normal faults. However, there are three notable exceptions to this generality, including 1) a prominent NW-striking apparent right-lateral fault, 2) a NW-striking down to the south fault which juxtaposes the base of the mid-Miocene Pyramid sequence against younger late Tertiary sedimentary rocks, and 3) a NNE-striking down to the east normal fault, which accommodates motion such that the Mesozoic Nightingale sequence is juxtaposed with late Tertiary sedimentary rocks. The NW dextral fault, the NNE-down to east fault, and several NNE-down to the west faults intersect roughly at the thermal anomaly in Emerson Pass. This suggests that fault intersections locally control upwelling of geothermal fluids within the step-over. Based on this assumption, it is proposed that the area near Buckbrush Springs be investigated further for geothermal potential. At this location, a NNE-down to the west normal fault, with >1 km of offset, intersects a NW-striking down to the south fault at a small left step in the NNE fault. Further studies will include collection of available kinematic indicators near the shallow thermal anomaly in Emerson Pass, geothermometry on Buckbrush Spring, and possibly drilling of temperature gradient wells in Emerson Pass and at Buckbrush Spring.

15 GEOTHERMAL ENERGY↗
NASA NTRS1996

Identification of the cAMP response element that controls transcriptional activation of the insulin-like growth factor-I gene by prostaglandin E2 in osteoblasts

Insulin-like growth factor-I (IGF-I), a multifunctional growth factor, plays a key role in skeletal growth and can enhance bone cell replication and differentiation. We previously showed that prostaglandin E2 (PGE2) and other agents that increase cAMP activated IGF-I gene transcription in primary rat osteoblast cultures through promoter 1 (P1), the major IGF-I promoter, and found that transcriptional induction was mediated by protein kinase A. We now have identified a short segment of P1 that is essential for full hormonal regulation and have characterized inducible DNA-protein interactions involving this site. Transient transfections of IGF-I P1 reporter genes into primary rat osteoblasts showed that the 328-base pair untranslated region of exon 1 was required for a full 5.3-fold response to PGE2; mutation in a previously footprinted site, HS3D (base pairs +193 to +215), reduced induction by 65%. PGE2 stimulated nuclear protein binding to HS3D. Binding, as determined by gel mobility shift assay, was not seen in nuclear extracts from untreated osteoblast cultures, was detected within 2 h of PGE2 treatment, and was maximal by 4 h. This DNA-protein interaction was not observed in cytoplasmic extracts from PGE2-treated cultures, indicating nuclear localization of the protein kinase A-activated factor(s). Activation of this factor was not blocked by cycloheximide (Chx), and Chx did not impair stimulation of IGF-I gene expression by PGE2. In contrast, binding to a consensus cAMP response element (CRE; 5'-TGACGTCA-3') from the rat somatostatin gene was not modulated by PGE2 or Chx. Competition gel mobility shift analysis using mutated DNA probes identified 5'-CGCAATCG-3' as the minimal sequence needed for inducible binding. All modified IGF-I P1 promoterreporter genes with mutations within this CRE sequence also showed a diminished functional response to PGE2. These results identify the CRE within the 5'-untranslated region of IGF-I exon 1 that is required for hormonal activation of IGF-I gene transcription by cAMP in osteoblasts.

NASA Discipline Musculoskeletal↗
DOE OSTI2013

Nature of Hα selected galaxies at z > 2. I. Main-sequence and dusty star-forming galaxies

We present the results from our narrow-band imaging surveys of Hα emitters (HAEs) at z = 2.2 and z = 2.5 in the Subaru/XMM-Newton Deep survey Field with near-infrared camera MOIRCS on the Subaru Telescope. We have constructed a clean sample of 63 star-forming galaxies at z = 2.2 and 46 at z = 2.5. For 12 (or ∼92%) out of 13 HAEs at z = 2.2, their Hα emission lines have been successfully detected by the spectroscopy. While about 42% of the red, massive HAEs with M {sub *} > 10{sup 10.8} M {sub ☉} contain active galactic nuclei (AGNs), most of the blue, less massive ones are likely to be star-forming galaxies. This suggests that the AGN may play an important role in galaxy evolution at the late stage of truncation. For the HAEs excluding possible AGNs, we estimate the gas-phase metallicities on the basis of [N II]/Hα ratios, and find that the metallicities of the Hα selected galaxies at z = 2.2 are lower than those of local star-forming galaxies at fixed stellar mass, as shown by previous studies. Moreover, we present and discuss the so-called main sequence of star-forming galaxies at z > 2 based on our unique sample of HAEs. By correlating the level of dust extinction with the location on the main sequence, we find that there are two kinds/modes of dusty star-forming galaxies: starbursting galaxies and metal-rich normal star-forming galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A Pattern Dictionary Method for Anomaly Detection

In this paper, we propose a compression-based anomaly detection method for time series and sequence data using a pattern dictionary. The proposed method is capable of learning complex patterns in a training data sequence, using these learned patterns to detect potentially anomalous patterns in a test data sequence. The proposed pattern dictionary method uses a measure of complexity of the test sequence as an anomaly score that can be used to perform stand-alone anomaly detection. We also show that when combined with a universal source coder, the proposed pattern dictionary yields a powerful atypicality detector that is equally applicable to anomaly detection. The pattern dictionary-based atypicality detector uses an anomaly score defined as the difference between the complexity of the test sequence data encoded by the trained pattern dictionary (typical) encoder and the universal (atypical) encoder, respectively. We consider two complexity measures: the number of parsed phrases in the sequence, and the length of the encoded sequence (codelength). Specializing to a particular type of universal encoder, the Tree-Structured Lempel–Ziv (LZ78), we obtain a novel non-asymptotic upper bound, in terms of the Lambert W function, on the number of distinct phrases resulting from the LZ78 parser. This non-asymptotic bound determines the range of anomaly score. As a concrete application, we illustrate the pattern dictionary framework for constructing a baseline of health against which anomalous deviations can be detected.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Nine-channel mid-power bipolar pulse generator based on a field programmable gate array

Many channel arbitrary pulse sequence generation is required for the electro-optic reconfiguration of optical waveguide networks in Lithium Niobate. Here we describe a scalable solution to the requirement for mid-power bipolar parallel outputs, based on pulse patterns generated by an externally clocked field programmable gate array. Positive and negative pulses can be generated at repetition rates up to 80 MHz with pulse width adjustable in increments of 1.6 ns across nine independent outputs. Each channel can provide 1.5 W of RF power and can be synchronised with the operation of other components in an optical network such as light sources and detectors through an external clock with adjustable delay.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes

Background: Pairing up primers to amplify desired targets and avoid undesired cross reactions can be a combinatorial challenge. Effective prediction of specificity and inclusivity from multiplexed primers and TaqMan®/ Luminex® probes is a critical step in PCR design. Results: Code is described to identify all primer and probe combinations from a list of unpaired, unordered candidates that should produce a product. It predicts and extracts all amplicon sequences in a large sequence database from a list of primers and probes, allowing degenerate bases and user-specified levels of primer-target mismatch tolerance. Amplicons hit by TaqMan®/Luminex® probes are indicated, and products may be annotated with gene information from NCBI. Fragment length distributions are calculated to predict electrophoretic gel banding patterns. Conclusions: Simulate_PCR is the only freely available software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. It requires no prior knowledge of how primers should be paired. Degenerate bases are allowed and entire amplicon sequences are extracted and annotated with gene information. Examples are provided for sets of TaqMan®/Luminex® PCR signatures predicted to amplify all HIV-1 genomes, all Coronaviridae genomes, and a group of antibiotic resistance genes. The software is a command line perl script freely available as open source.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

DIVA/DeviceEditor v6.1.2

DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.

Plahar, Hector [Lawrence Berkeley National Laborat↗
DOE OSTI2017

Optimal current profile control for enhanced repeatability of L-mode and H-mode discharges in DIII-D

In this work, model-based control techniques are used to obtain target current profiles in low-confinement-mode (L-mode) as well as high-confinement-mode (H-mode) DIII-D discharges. The control problem is formulated as a trajectory optimization problem to search for a feasible path from the expected initial condition to the desired target. The result comprises a sequence of feedforward (open-loop) control requests and a corresponding state evolution from the initial condition to the desired target. On top of this optimal feedforward control sequence a feedback (closed-loop) controller based on a linearized model and optimal control design techniques is added to track the desired state evolution. Furthermore, the effectiveness of the control approach is demonstrated with experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [ Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F 3:4 and F 4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. In addition, genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Analysis of simulated image sequences from sensors for restricted-visibility operations

A real time model of the visible output from a 94 GHz sensor, based on a radiometric simulation of the sensor, was developed. A sequence of images as seen from an aircraft as it approaches for landing was simulated using this model. Thirty frames from this sequence of 200 x 200 pixel images were analyzed to identify and track objects in the image using the Cantata image processing package within the visual programming environment provided by the Khoros software system. The image analysis operations are described.

Kasturi, Rangachar↗
DOE OSTI2020

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Here, the first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro , with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.

09 BIOMASS FUELS↗