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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 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora↗
DOE OSTI2020

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays

Abstract Summary Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. Availability and implementation The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

CONSTAX2: improved taxonomic classification of environmental DNA markers

Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

comparative genomics↗
DOE OSTI2021

Discovery of a new extragalactic circular radio source with ASKAP: ORC J0102–2450

ABSTRACT We present the discovery of another odd radio circle (ORC) with the Australian Square Kilometre Array Pathfinder (ASKAP) at 944 MHz. The observed radio ring, ORC J0102–2450, has a diameter of ∼70 arcsec or 300 kpc, if associated with the central elliptical galaxy DES J010224.33–245039.5 (z ∼ 0.27). Considering the overall radio morphology (circular ring and core) and lack of ring emission at non-radio wavelengths, we investigate if ORC J0102–2450 could be the relic lobe of a giant radio galaxy seen end on or the result of a giant blast wave. We also explore possible interaction scenarios, for example, with the companion galaxy, DES J010226.15–245104.9, located in or projected on to the south-eastern part of the ring. We encourage the search for further ORCs in radio surveys to study their properties and origin.

Koribalski, Bärbel S. (ORCID:000000034351993X)↗
DOE OSTI2020

CoreCruncher : Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Abstract Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial genomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e. its int-attP region) is cohesive. The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing

Abstract Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.

Araújo, Pedro M. M.↗
DOE OSTI2020

Charge conservation and higher moments of charge fluctuations

Higher moments of distributions of net charge and baryon number in heavy-ion collisions have been proposed as signals of fundamental QCD phase transitions. In order to better understand background processes for these observables, models are presented which enable one to gauge the effects of local charge conservation, decays of resonances and clusters, Bose symmetrization, and volume fluctuations. Monte Carlo methods for generating samplings of particles consistent with local charge conservation are presented and are followed by a review of simple analytic models involving a single type of charge with a constant experimental efficiency. The main model consists of thermal emission superimposed onto a simple parametrization of collective flow, known as a blast wave, with emission being consistent with individual canonical ensembles. The spatial extent of local charge conservation is parameterized by the size and extent over which charge is conserved. Here, the sensitivity of third- and fourth-order moments, skewness and kurtosis, to these parameters, and to beam energy and baryon density is explored. Comparisons with STAR data show that a significant part of the observed non-Poissonian fluctuations in net-proton fluctuations are explained by charge and baryon-number conservation, but that measurements of the STAR collaboration for fluctuations of net electric charge significantly differ from expectations of the models presented here.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Onset of radial flow in p + p collisions

It has been debated for decades whether hadrons emerging from p+p collisions exhibit collective expansion. The signal of the collective motion in p+p collisions is not as clear as in heavy-ion collisions because of the low multiplicity and large fluctuation in p+p collisions. Tsallis Blast-Wave (TBW) model is a thermodynamic approach, introduced to handle the overwhelming correlation and fluctuation in the hadronic processes. We have systematically studied the identified particle spectra in p+p collisions from RHIC to LHC using TBW and found no appreciable radial flow in p+p collisions below √s = 900 GeV. At LHC higher energy of 7 TeV in p+p collisions, the radial flow velocity achieves an average of (β) = 0.320 ± 0.005. This flow velocity is comparable to that in peripheral (40-60%) Au+Au collisions at RHIC. In addition, breaking of the identified particle spectra m T scaling was also observed at LHC from a model independent test.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Measurements of dielectron production in Au + Au collisions at s N N = 200 GeV from the STAR experiment

We report on measurements of dielectron (e⁺e⁻) production in Au+Au collisions at a center-of-mass energy of 200 GeV per nucleon-nucleon pair using the STAR detector at RHIC. Systematic measurements of the dielectron yield as a function of transverse momentum (p T ) and collision centrality show an enhancement compared to a cocktail simulation of hadronic sources in the low invariant-mass region (M ee < 1GeV/c 2 ). This enhancement cannot be reproduced by the ρ-meson vacuum spectral function. In minimum-bias collisions, in the invariant-mass range of 0.30 – 0.76GeV/c², integrated over the full p T acceptance, the enhancement factor is 1.76±0.06(stat.)±0.26(sys.)±0.29(cocktail). The enhancement factor exhibits weak centrality and p T dependence in STAR's accessible kinematic regions, while the excess yield in this invariant-mass region as a function of the number of participating nucleons follows a power-law shape with a power of 1.44±0.10. Models that assume an in-medium broadening of the ρ-meson spectral function consistently describe the observed excess in these measurements. In addition, we report on measurements of ω- and Φ-meson production through their e⁺e⁻ decay channel. These measurements show good agreement with Tsallis blast-wave model predictions, as well as, in the case of the Φ meson, results through its K⁺K⁻ decay channel. In the intermediate invariant-mass region (1.1 < M ee < 3GeV/c²), we investigate the spectral shapes from different collision centralities. Physics implications for possible in-medium modification of charmed hadron production and other physics sources are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Centrality dependence of identified particle elliptic flow in relativistic heavy ion collisions at s N N = 7.7 – 62.4 GeV

Here, elliptic flow (v 2 ) values for identified particles at midrapidity in Au + Au collisions measured by the STAR experiment in the Beam Energy Scan at the Relativistic Heavy Ion Collider at √s NN = 7.7–62.4 GeV are presented for three centrality classes. The centrality dependence and the data at √s NN = 14.5 GeV are new. Except at the lowest beam energies, we observe a similar relative v 2 baryon-meson splitting for all centrality classes which is in agreement within 15% with the number-of-constituent quark scaling. The larger v 2 for most particles relative to antiparticles, already observed for minimum bias collisions, shows a clear centrality dependence, with the largest difference for the most central collisions. Also, the results are compared with a multiphase transport (AMPT) model and fit with a blast wave model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Measurement of the higher-order anisotropic flow coefficients for identified hadrons in Au + Au collisions at s N N = 200 GeV

In this paper, measurements of the anisotropic flow coefficients v 2 {Ψ 2 }, v 3 {Ψ 3 }, v 4 {Ψ 4 }, and v 4 {Ψ 2 } for identified particles (π ± , K ± , and p + ¯p) at midrapidity, obtained relative to the event planes Ψ m at forward rapidities in Au + Au collisions at s N N = 200 GeV , are presented as a function of collision centrality and particle transverse momenta p T . The v n coefficients show characteristic patterns consistent with hydrodynamical expansion of the matter produced in the collisions. For each harmonic n, a modified valence quark-number N q scaling [plotting v n {Ψ m }/(N q ) n/2 versus transverse kinetic energies (KE T )/N q ] is observed to yield a single curve for all the measured particle species for a broad range of KE T . A simultaneous blast-wave model fit to the observed v n {Ψ m }(p T ) coefficients and published particle spectra identifies radial flow anisotropies ρ n {Ψ m } and spatial eccentricities s n {Ψ m } at freeze-out. Finally, these are generally smaller than the initial-state participant-plane geometric eccentricities ε n {Ψ PP m } as also observed in the final eccentricity from quantum interferometry measurements with respect to the event plane.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Measurement of elliptic flow of light nuclei at s N N = 200 , 62.4, 39, 27, 19.6, 11.5, and 7.7 GeV at the BNL Relativistic Heavy Ion Collider

Here we present measurements of second-order azimuthal anisotropy ( v 2 ) at midrapidity ( |y| < 1.0 ) for light nuclei d , t , 3 He (for $\sqrt{s}$$_{NN}$ = 200 , 62.4, 39, 27, 19.6, 11.5, and 7.7 GeV) and antinuclei$\bar{d}$ ( $\sqrt{s}$$_{NN}$ = 200 , 62.4, 39, 27, and 19.6 GeV) and 3 ¯¯¯¯¯ He ( $\sqrt{s}$$_{NN}$ = 200 GeV) in the STAR (Solenoidal Tracker at RHIC) experiment. The v 2 for these light nuclei produced in heavy-ion collisions is compared with those for p and $\bar{p}$. We observe mass ordering in nuclei v 2 ( p T ) at low transverse momenta ( p T < 2.0 GeV/c). We also find a centrality dependence of v 2 for d and $\bar{d}$ . The magnitude of v 2 for t and 3 He agree within statistical errors. Light-nuclei v 2 are compared with predictions from a blast-wave model. Atomic mass number ( A ) scaling of light-nuclei v 2 (p T ) seems to hold for p T / A < 1.5 GeV/c . Results on light-nuclei v 2 from a transport-plus-coalescence model are consistent with the experimental measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Phenomenological models of two-particle correlation distributions on transverse momentum in relativistic heavy-ion collisions

Two-particle, pair-number correlation distributions on two-dimensional transverse momentum (p t1 , p t2 ) constructed from the particle production in relativistic heavy-ion collisions allow access to dynamical processes in these systems beyond what can be studied with angular correlations alone. Only a few measurements of this type have been reported in the literature, and phenomenological models, which facilitate physical interpretation of the correlation structures, are nonexistent. Ongoing efforts at the Relativistic Heavy-Ion Collider (RHIC) will provide a significant volume of these correlation measurements in the future. In anticipation of these new data, two phenomenological models are developed which describe two-dimensional (2D) correlation distributions on transverse momentum. One model is based on a collision event-by-event fluctuating blast wave. The other is based on event-by-event fluctuations in fragmenting color-flux tubes and in jets. Both models are shown to be capable of accurately describing the measured single-particle p t distributions for minimum-bias Au+Au collisions at √s NN = 200 GeV. Both models are then applied to preliminary, charged-particle correlation measurements on 2D transverse momentum. Here, the capabilities of the two models for describing the overall structure of these correlations, the stability of the fitting results with respect to collision centrality, and the resulting trends of the dynamical fluctuations are evaluated. In general, both phenomenological models are capable of qualitatively describing the major correlation structures on transverse momentum and can be used to establish the required magnitudes and centrality trends of the fluctuations. Both models will be useful for interpreting the forthcoming correlation data from the RHIC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Centrality and transverse momentum dependence of D 0 -meson production at mid-rapidity in Au + Au collisions at s NN = 200 GeV

Here, we report a new measurement of D 0 -meson production at mid-rapidity (| y | < 1) in Au + Au collisions at $\sqrt{s}$$_ {NN}$ = 200 GeV utilizing the heavy flavor tracker, a high resolution silicon detector at the STAR experiment. Invariant yields of D 0 mesons with transverse momentum p T ≲ 9 GeV / c are reported in various centrality bins (0–10%, 10–20%, 20–40%, 40–60%, and 60–80%). Blast-wave thermal models are used to fit the D 0 -meson p T spectra to study D 0 hadron kinetic freeze-out properties. The average radial flow velocity extracted from the fit is considerably smaller than that of light hadrons (π, K, and p), but comparable to that of hadrons containing multiple strange quarks (Φ, Ξ - ) , indicating that D 0 mesons kinetically decouple from the system earlier than light hadrons. The calculated D 0 nuclear modification factors reaffirm that charm quarks suffer a large amount of energy loss in the medium, similar to those of light quarks for p T > 4 GeV/c in central 0–10% Au + Au collisions. At low p T , the nuclear modification factors show a characteristic structure qualitatively consistent with the expectation from model predictions that charm quarks gain sizable collective motion during the medium evolution. The improved measurements are expected to offer new constraints to model calculations and help gain further insights into the hot and dense medium created in these collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗