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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 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
NASA NTRS2013

RECOVIR Software for Identifying Viruses

Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

Chakravarty, Sugoto↗
DOE OSTI2014

Discovery of a thermally persistent h.c.p. solid-solution phase in the Ni-W system

Although the accepted Ni-W phase diagram does not reveal the existence of h.c.p.-based phases, h.c.p.-like stacking sequences were observed in magnetron-co-sputtered Ni-W thin films at W contents of 20 to 25 at. %, by using transmission electron microscopy and X-ray diffraction. The occurrence of this h.c.p.-like solid-solution phase could be rationalized by first-principles calculations, showing that the vicinity of the system's ground-state line is populated with metastable h.c.p.-based superstructures in the intermediate concentration range from 20 to 50 at. % W. The h.c.p.-like stacking in Ni-W films was observed to be thermally persistent, up to temperatures as high as at least 850 K, as evidenced by extensive X-ray diffraction analyses on specimens before and after annealing treatments. The tendency of Ni-W for excessive planar faulting is discussed in the light of these new findings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

An expectation–maximization framework for comprehensive prediction of isoform-specific functions

Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind. There is a need to understand the functional consequences of differential splicing, which could be supported by the generation of accurate and comprehensive isoform-specific gene ontology annotations. We present isoform interpretation, a method that uses expectation–maximization to infer isoform-specific functions based on the relationship between sequence and functional isoform similarity. We predicted isoform-specific functional annotations for 85 617 isoforms of 17 900 protein-coding human genes spanning a range of 17 430 distinct gene ontology terms. Comparison with a gold-standard corpus of manually annotated human isoform functions showed that isoform interpretation significantly outperforms state-of-the-art competing methods. We provide experimental evidence that functionally related isoforms predicted by isoform interpretation show a higher degree of domain sharing and expression correlation than functionally related genes. We also show that isoform sequence similarity correlates better with inferred isoform function than with gene-level function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Nearby Young, Active, Late-type Dwarfs in Gaia's First Data Release

The Galex Nearby Young Star Survey (GALNYSS) has yielded a sample of ∼2000 UV-selected objects that are candidate nearby (D≲150 pc), young (age ∼ 10–100 Myr), late-type stars. Here, we evaluate the distances and ages of the subsample of (19) GALNYSS stars with Gaia Data Release 1 (DR1) parallax distances D⩽120 pc. The overall youth of these 19 mid-K to early-M stars is readily apparent from their positions relative to the loci of main-sequence stars and giants in Gaia-based color-magnitude and color-color diagrams constructed for all stars detected by Galex and the Wide-field Infrared Space Explorer for which parallax measurements are included in DR1. The isochronal ages of all 19 stars lie in the range ∼10–100 Myr. Comparison with Li-based age estimates indicates a handful of these stars may be young main-sequence binaries rather than pre-main sequence stars. Nine of the 19 objects have not previously been considered as nearby, young stars, and all but one of these are found at declinations north of +30°. The Gaia DR1 results presented here indicate that the GALNYSS sample includes several hundred nearby, young stars, a substantial fraction of which have not been previously recognized as having ages ≲100 Myr.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1992

Pax: A permanent base for human habitation of Mars

The Advanced Design Program in Space Architecture at the University of Wisconsin-Milwaukee supported the synthesis report and two of its scenarios - 'Architecture 1' and 'Architecture 4' - and the Weaver ExPO report on near-term extraterrestrial explorations during the spring of 1992. The project investigated the implications of different mission scenarios, the Martian environment, supporting technologies, and especially human factors and environment-behavior considerations for the design of the first permanent Martian base. This paper presents the results of that investigation. The paper summarizes site selection, development of habitability design requirements based on environment-behavior research, construction sequencing, and a full concept design and design development for a first permanent Martian base and habitat. The proposed design is presented in terms of an integrative mission scenario and master plan phased through initial operational configuration, base site plan, and design development details of a complete Martian habitat for 18 crew members including all laboratory, mission control, and crew support spaces.

Moore, Gary T.↗
NASA NTRS2000

Cumulative Axial and Torsional Fatigue: An Investigation of Load-Type Sequencing Effects

Cumulative fatigue behavior of a wrought cobalt-base superalloy, Haynes 188 was investigated at 538 C under various single-step sequences of axial and torsional loading conditions. Initially, fully-reversed, axial and torsional fatigue tests were conducted under strain control at 538 C on thin-walled tubular specimens to establish baseline fatigue life relationships. Subsequently, four sequences (axial/axial, torsional/torsional, axial/torsional, and torsional/axial) of two load-level fatigue tests were conducted to characterize both the load-order (high/low) and load-type sequencing effects. For the two load-level tests, summations of life fractions and the remaining fatigue lives at the second load-level were computed by the Miner's Linear Damage Rule (LDR) and a nonlinear Damage Curve Approach (DCA). In general, for all four cases predictions by LDR were unconservative. Predictions by the DCA were within a factor of two of the experimentally observed fatigue lives for a majority of the cumulative axial and torsional fatigue tests.

Kalluri, Sreeramesh↗
DOE OSTI2019

De novo design of symmetric ferredoxins that shuttle electrons in vivo

A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from −405 to −515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli . These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

De novo design of symmetric ferredoxins that shuttle electrons in vivo

A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from −405 to −515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli. These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.

Andrew C. Mutter↗
DOE OSTI2023

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

ROSAT observations of the x ray binary HD 154791

We have been surveying the Taurus dark cloud for young stars using a variety of techniques. Two optical proper motion surveys identified 8 new pre-main sequence stars; an IRAS-based program discovered 6 new embedded sources and 4-6 new T Tauri stars. Finally, an optical objective prism survey found 12 new T Tauri stars. Our goal in this project is to examine and compare star formation in the dark clouds: Heiles cloud 2 (HCL2), L1537, L1538, and L1544. HCL2 is a very dense region actively forming young stars and contains 5-6 very young, deeply embedded sources; L1537 and L1538 have no known pre-main sequence stars; L1544 contains 7 optically visible T Tauri stars. These clouds appear roughly similar on optical sky survey plates. We would like to know why some of the clouds are active and why some are not. The first goal of the project is to survey the regions using IR photometry to identify very red pre-main sequence stars and X-ray imaging to identify solar-type young stars missed in the near-IR survey. We will follow up these observations with molecular line surveys to compare the conditions in various clouds with their star formation efficiencies.

Kenyon, Scott J.↗
DOE OSTI2020

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for Immediate Impacts of Soybean Cover Crop on Bacterial Community Composition and Diversity in Soil Under Long-Term Saccharum Monoculture

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Field Data↗
NASA NTRS2016

Analyzing Double Delays at Newark Liberty International Airport

When weather or congestion impacts the National Airspace System, multiple different Traffic Management Initiatives can be implemented, sometimes with unintended consequences. One particular inefficiency that is commonly identified is in the interaction between Ground Delay Programs (GDPs) and time based metering of internal departures, or TMA scheduling. Internal departures under TMA scheduling can take large GDP delays, followed by large TMA scheduling delays, because they cannot be easily fitted into the overhead stream. In this paper we examine the causes of these double delays through an analysis of arrival operations at Newark Liberty International Airport (EWR) from June to August 2010. Depending on how the double delay is defined between 0.3 percent and 0.8 percent of arrivals at EWR experienced double delays in this period. However, this represents between 21 percent and 62 percent of all internal departures in GDP and TMA scheduling. A deep dive into the data reveals that two causes of high internal departure scheduling delays are upstream flights making up time between their estimated departure clearance times (EDCTs) and entry into time based metering, which undermines the sequencing and spacing underlying the flight EDCTs, and high demand on TMA, when TMA airborne metering delays are high. Data mining methods (currently) including logistic regression, support vector machines and K-nearest neighbors are used to predict the occurrence of double delays and high internal departure scheduling delays with accuracies up to 0.68. So far, key indicators of double delay and high internal departure scheduling delay are TMA virtual runway queue size, and the degree to which estimated runway demand based on TMA estimated times of arrival has changed relative to the estimated runway demand based on EDCTs. However, more analysis is needed to confirm this.

traffic management advisor↗
DOE OSTI2018

Quantitative-qualitative assessments of environmental causal networks to support the DPSIR framework in the decision-making process

Highlights: • DSPIR framework is extended for supporting the decision-making process. • Environmental causal networks are used instead of unidirectional causalities. • Quantitative and qualitative data are combined to improve environmental assessments. • Decision-makers can choose management actions to reach favorable future scenarios. - Abstract: The DPSIR framework helps to identify and situate stressors, drivers and pressure variables within a dynamic environmental process composed of cause-effect relations. However, an important aspect related to its structural deficiency implies the use of unidirectional causalities between variables. In this work, we extend the capacities of the DPSIR framework by addressing three important points. Firstly, causal networks are built instead of unidirectional causalities, the former based on paths represented by sequences of cause-effect relations between involved variables. These paths are derived from the population growth as a driving force variable, along with CO{sub 2} emissions, waste, water and loss of vegetation cover as pressure variables. Trends of these paths are combined to determine and quantitatively assess a global environmental state trend whose impacts on the environment require corrective management actions as a response. Secondly, quantitative assessments of environmental trends are transformed into fuzzy-qualitative data to facilitate their interpretation. Thirdly, a method based on weighted environmental management actions is presented to decision-makers who aspire to change current path trends in order to approach desirable scenarios similar to those put forth by the OECD outlook towards 2030. The results obtained applying this framework to the State of Morelos, México, show that it can be a useful support tool in the selection and monitoring of management actions capable of reaching favorable environmental trends.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Adapting CLUTCH methodology to multigroup TSUNAMI-3D for eigenvalue sensitivity calculations

The sensitivity of the eigenvalue to uncertainties in nuclear data and its evaluation are important for nuclear criticality safety. TSUNAMI-3D sequences within the SCALE code system offer several options to the user community for calculating eigenvalue sensitivity coefficients with multigroup (MG) and continuous energy (CE) 3D transport capabilities. TSUNAMI-3D sequences implement the adjoint-based perturbation theory with MG KENO code, the Contributon Linked eigenvalue sensitivity/Uncertainty estimation via Track length importance CHaracterization (CLUTCH) method with CE KENO code, and the Iterated Fission Probability (IFP) method with CE KENO and Shift codes. Each method has benefits and limitations depending on the problem that is run. The work presented here aims to adapt the CLUTCH method, which enables the Contributon method's mesh-free, memory-efficient approach for calculating adjoint-weighted tallies for sensitivity calculations, to the MG TSUNAMI-3D sequence. This application would eliminate the explicit adjoint KENO calculation, as well as the memory-consuming mesh flux moment tallies required by the conventional MG TSUNAMI-3D. Smaller memory footprints in the CLUTCH methodology and relatively shorter runtimes in MG KENO transport can make MG TSUNAMI-3D a viable method for some complex problems. Moreover, this adaptation allows MG sensitivity calculations with Shift, ORNL's next-generation high-performance Monte Carlo transport code, which currently does not offer any sensitivity capabilities with MG particle transport simulations. Initial implementation of the new MG TSUNAMI-3D sequence and its preliminary results with a selected critical benchmark experiment in the Verified, Archived Library of Inputs and Data (VALID) are presented in this study.

KENO↗