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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

A systematic approach to the analysis of double faults within design basic accident methodology - 14501

Within the UK there is a general trend towards adopting Design Basis Accident (DBA) methodology for the assessment of radiological hazards, including criticality. DBA is a single fault methodology and comprises identifying the initiating event, its frequency and consequence. A fault with a very low initiating event frequency will not require further analysis. A fault sequence that terminates in a sub-critical configuration would also not require further analysis; although the identified passive features ensuring sub-criticality are subjected to engineering substantiation. Where faults do not pass this initial screening, two safety measures are generally required to ensure the fault does not progress to a criticality incident. This methodology provides a robust approach to single faults ensuring that an appropriate level and range of plant measures are identified and subjected to appropriate substantiation. However, a criticality is a cliff-edge effect and is dependent on multiple parameters. It is entirely possible under DBA to evaluate several single fault sequences and conclude that no measures are required because the single faults terminate in a sub-critical configuration. Importantly, for criticality safety, under DBA, there is no requirement to prevent important parameters from deviating from normal or upper bound 'safe' levels leaving the plant at greater risk in the event that further faults initiate. The combination of two faults could lead to a criticality incident but there is no current driver within DBA methodology to analyze these coincident or double faults. There is, therefore, potential to significantly under estimate the risk of criticality. This understanding is embodied within other methodologies such as the Double Contingency Principle. However, within the UK the DBA methodology has so significantly improved the analysis of single faults that, in some instances, consideration of double faults has taken a back seat. This is despite the UK regulator stating that 'criticality safety cases should employ the double contingency approach'. This paper presents a systematic approach to ensure that the potential for double faults or multiple parameter deviations to result in a criticality is effectively evaluated within the wider DBA methodology. The methodology determines which faults may be screened out from double fault analysis on the grounds of being 'unlikely' to initiate and being present for a 'short' duration. For those faults screened into double fault analysis, this guidance sets out the potential means of determining acceptable risk. These means include the specific evaluation of the risk of two criticality control parameters deviating simultaneously, the definition of additional safety measures and the definition of the boundary of safety for multiple parameters and the risk of exceeding this boundary. (authors)

42 ENGINEERING↗
DOE OSTI2016

A HIGH-RESOLUTION MULTIBAND SURVEY OF WESTERLUND 2 WITH THE HUBBLE SPACE TELESCOPE. II. MASS ACCRETION IN THE PRE-MAIN-SEQUENCE POPULATION

We present a detailed analysis of the pre-main-sequence (PMS) population of the young star cluster Westerlund 2 (Wd2), the central ionizing cluster of the H ii region RCW 49, using data from a high-resolution multiband survey with the Hubble Space Telescope. The data were acquired with the Advanced Camera for Surveys in the F555W, F814W, and F658N filters and with the Wide Field Camera 3 in the F125W, F160W, and F128N filters. We find a mean age of the region of 1.04 ± 0.72 Myr. The combination of dereddened F555W and F814W photometry in combination with F658N photometry allows us to study and identify stars with Hα excess emission. With a careful selection of 240 bona-fide PMS Hα excess emitters we were able to determine their Hα luminosity, which has a mean value L(Hα)=1.67×10{sup −31} erg s{sup −1}. Using the PARSEC 1.2S isochrones to obtain the stellar parameters of the PMS stars, we determined a mean mass accretion rate M-dot {sub acc}=4.43×10{sup −8} M{sub ⊙} yr{sup −1} per star. A careful analysis of the spatial dependence of the mass accretion rate suggests that this rate is ∼25% lower in the center of the two density peaks of Wd2 in close proximity to the luminous OB stars, compared to the Wd2 average. This rate is higher with increasing distance from the OB stars, indicating that the PMS accretion disks are being rapidly destroyed by the far-ultraviolet radiation emitted by the OB population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can’t directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Top-down analysis of protein samples by de novo sequencing techniques

MOTIVATION: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. RESULTS: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years

We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

MemGaze: Rapid and Effective Load-Level Memory Trace Analysis

A major challenge of memory analysis tools is combining high-resolution analysis and low overhead measurement. Currently, hardware/software-based analysis of load-level sequences incurs time slowdowns of O(100×). We present MemGaze, a tool for low-overhead, high-resolution memory analysis. MemGaze uses Intel’s Processor Tracing (PT) instruction ptwrite to collect sampled and compressed memory address traces for load-level, sequence-aware analysis of data reuse. We describe multi-resolution analysis for locations vs. operations, accesses vs. spatio-temporal reuse, and reuse (distance, rate, volume) vs. access patterns. Both trace size and resolution are controllable. We use MemGaze to elucidate the memory effects of different data structures and algorithms. For sampled traces that are ˜1% of a full one, analysis metrics have 1-25% MAPE for histograms of varying dynamic sequence lengths. With current suboptimal kernel support (PT runs continuously), MemGaze’s time overhead is typically 10–95%; 7× at worst. However, when PT runs only during samples, overhead is 10–35% on memory intensive regions and correlates with executed ptwrites.

Kilic, Ozgur O.↗
DOE OSTI2016

A survey of the sorghum transcriptome using single-molecule long reads

Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, these results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

RISK-INFORMED EXTERNAL HAZARDS ANALYSIS BY EEVE TOOLKIT

Introducing risk-informed safety analyses for external events can bring sensible benefits to the nuclear power industry easing the regulatory burden introduced in the aftermath of the Fukushima accident. In the framework of the US-DOE Light-Water Reactor Sustainability program, Risk-Informed Margin Characterization project (LWRS-RISMC), research activities were conducted at INL for developing and applying a toolkit for performing risk-informed external hazards analysis. The “EEVE” (External EVEnts) toolkit, a chain of INL and state-of-the-art codes, was set-up and applied for simulating earthquake-induced transients with internal flooding in a PWR. This was done using methodology set-up for evaluating new data and determining critical areas that would benefit most from advanced analysis methods. The methodology is agnostic and it can be applied to other external hazards than just seismic and flooding (e.g., high winds, intense precipitation, etc.). The first step was the deterministic calculations for evaluating the propagation of a set of earthquakes and for determining the effects on a fire suppression system in an auxiliary building. These deterministic calculations were performed using the LS-DYNA and the OPENSEE structural mechanics codes. Probability failures and event trees of a generic 3-loops Westinghouse PWR were derived from a generic SAPHIRE model. Seismically induced Loss of Offsite Power, Station Blackout, and fire suppression piping failure events were considered. SAPHIRE code allowed a pre-screening of all possible branches of the event tree and a selection of those with the largest Core Damage Frequency increase for further analysis using dynamic PRA methods. INL's EMRALD code performed dynamic PRA calculations of the identified sequences, integrating risk analysis with on-line deterministic safety analysis results (seismically-induced internal flooding calculations by NEUTRINO code and system analysis by RELAP5-3D code). RELAP5-3D Best-Estimate calculations coupled with RAVEN statistical code were used for deriving limit surfaces as function of relevant transient parameters. This data was used by EMRALD for determining the final core status (core damage/core safe). Finally, the coupling of seismic, flooding, system thermal-hydraulic, uncertainty quantification and probabilistic risk analysis for an advanced risk-informed external hazards analysis was demonstrated. Results showed the sensible decrease in the level of conservatism achieved using the developed risk-informed methodology, which allowed also improving the evaluation of the failure modes and failure probabilities of different components.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRSDate not supplied

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗
DOE OSTI2017

The metagenomic data life-cycle: standards and best practices

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is still needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS1995

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

NASA Discipline Neuroscience↗
NASA NTRS1988

Analysis of rotating flexible blades using MSC/NASTRAN

An overview is given of the use of MSC/NASTRAN in the analysis of rotating flexible blades. The geometrically nonlinear analysis using NASTRAN Solution Sequence 64 is discussed along with the determination of frequencies and mode shapes using Solution Sequence 63. Items unique to rotating blade analysis, such as setting angle, centrifugal softening effects, and hub flexibility, are emphasized.

Ernst, Michael A.↗
NASA NTRS2022

NASA Engineering and Safety Center Technical Bulletin No. 22-05: Launch Vehicle Flight Control Stability Margin Reduction Considerations

Launch vehicle ascent stability analyses typically rely on a combination of frequency and time domain analyses. Frequency domain analysis uses a sequence of high-fidelity linear models with constant parameters spanning the ascent trajectory. Complementary time domain analysis is performed using high-fidelity, nonlinear 6-DOF simulations. Analyses are typically dispersed to verify robustness to parameter variations by showing the vehicle meets frequency domain stability margin requirements and time domain performance metrics. This Technical Bulletin outlines standard stability margin best practices and provides recommendations for treatment of deviations from industry-standard launch vehicle stability margins due to vehicle flexibility, slosh dynamics, aerodynamics, other offending dynamics, or coupling thereof.

Launch Vehicle↗
DOE OSTI2024

Ensuring Solution Uniqueness in Three-Phase Power System State Estimation

This paper is concerned with the issue of potential non-unique solutions in three-phase state estimation. Theory of observability analysis for positive sequence power system state estimation is based on certain assumptions that avoid possibility of multiple solutions. Also, it is shown that observability of a positive sequence network remains independent of the network parameters or the operating state. When extending single-phase observability analysis directly to the three-phase case, this paper considers the possibility of converging to multiple solutions, i.e. solution non-uniqueness, even for cases where state estimator successfully converges. The study illustrates via numerical examples the likelihood of converging to entirely different solutions for certain network parameters. It also examines how the operating state, particularly under unbalanced loading, leads to solution non-uniqueness. The paper then describes an alternative approach to ensure a unique solution in three-phase state estimation. This method aims to accurately and uniquely estimate the state of any unbalanced three-phase system, irrespective of load imbalance, network configuration, existence of synchronous generators or transformers.

Power System State Estimation, Three-Phase, Distri↗
NASA NTRS1993

An investigation of the role of current and future remote sensing data systems in numerical meteorology

The goals of this research endeavor have been to develop a flexible and relatively complete framework for the investigation of current and future satellite data sources in numerical meteorology. In order to realistically model how satellite information might be used for these purposes, it is necessary that Observing System Simulation Experiments (OSSEs) be as complete as possible. It is therefore desirable that these experiments simulate in entirety the sequence of steps involved in bringing satellite information from the radiance level through product retrieval to a realistic analysis and forecast sequence. In this project we have worked to make this sequence realistic by synthesizing raw satellite data from surrogate atmospheres, deriving satellite products from these data and subsequently producing analyses and forecasts using the retrieved products. The accomplishments made in 1991 are presented. The emphasis was on examining atmospheric soundings and microphysical products which we expect to produce with the launch of the Advanced Microwave Sounding Unit (AMSU), slated for flight in mid 1994.

Diak, George R.↗
DOE OSTI2022

De novo transcriptome sequencing of Capsicum frutescens . L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU ‐9

Abstract Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth–promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress‐treated plants grown in a microorganism‐controlled environment. Our previous reports have selected Bacillus atrophaeus WU‐9 as PGPR significantly alleviating pepper ( Capsicum frutescens . L) salt stress. In this work, the RNA‐seq analysis of salt stress‐treated and untreated plants, grown with and without WU‐9 in a microorganism‐controlled environment, was used to reveal the plant salt stress alleviating mechanisms of WU‐9. Twelve sequencing libraries, prepared by treating with WU‐9 and salt (150 mM NaCl for 36 h), were constructed by RNA‐Seq technique. Non‐inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene‐activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU‐9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress‐responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens . L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR.

Wang, Wenfei↗
DOE OSTI2015

Structural effects of protein aging: Terminal marking by deamidation in human triosephosphate isomerase

Deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. Since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. Despite the importance of this process, there is a lack of detailed structural information explaining the effects of deamidation on the structure of proteins. Here, we studied the effects of deamidation on human triosephosphate isomerase (HsTIM), an enzyme for which deamidation of N15 and N71 has been long recognized as the signal for terminal marking of the protein. Deamidation was mimicked by site directed mutagenesis; thus, three mutants of HsTIM (N15D, N71D and N15D/N71D) were characterized. The results show that the N71D mutant resembles, structurally and functionally, the wild type enzyme. In contrast, the N15D mutant displays all the detrimental effects related to deamidation. The N15D/N71D mutant shows only minor additional effects when compared with the N15D mutation, supporting that deamidation of N71 induces negligible effects. The crystal structures show that, in contrast to the N71D mutant, where minimal alterations are observed, the N15D mutation forms new interactions that perturb the structure of loop 1 and loop 3, both critical components of the catalytic site and the interface of HsTIM. Based on a phylogenetic analysis of TIM sequences, we propose the conservation of this mechanism for mammalian TIMs.

59 BASIC BIOLOGICAL SCIENCES↗