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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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Human Primary Airway Epithelium +/- Macrophages Response to HCoV-229E Infection Transcriptomics (ACS-DP3)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-299E) infection. Sample data was obtained for mock and infected (MOI 3) primary human airway epithelial cells with and without macrophages and grown in air-liquid interface conditions. Sample data was acquired using an Illumina Hi-Seq 4000 sequencer system and further processed for RNA sequencing (RNA-Seq) expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Human Liver Epithelium Response to HCoV-229E Infection Epigenomics (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-229E) infection alters chromatin accessibility in infected cells only. Sample data was obtained for mock and infected (standard and UV-inactivated) immortalized human liver cells (HuH-7) and collected 24 hrs. post infection. Samples were processed using assay for transposase-accessible chromatin using high-throughput sequencing (ATAC-Seq) and generated bar coded library samples were evaluated for RNA sequencing (RNA-Seq) expression analysis. Processed ATAC-Seq datasets are openly accessible from the download button and contain secondary processed RNA-Seq results files and supporting metadata materials. Data download includes a sample naming key, infection titer metadata, normalized counts, and relevant computational source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, they present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Primer and platform effects on 16S rRNA tag sequencing

Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data produced with different protocols can be meaningfully compared, is often unknown. Here we compare results obtained using three different amplification primer sets (targeting V4, V6–V8, and V7–V8) and two sequencing technologies (454 pyrosequencing and Illumina MiSeq) using DNA from a mock community containing a known number of species as well as complex environmental samples whose PCR-independent profiles were estimated using shotgun sequencing. We find that paired-end MiSeq reads produce higher quality data and enabled the use of more aggressive quality control parameters over 454, resulting in a higher retention rate of high quality reads for downstream data analysis. While primer choice considerably influences quantitative abundance estimations, sequencing platform has relatively minor effects when matched primers are used. In conclusion, beta diversity metrics are surprisingly robust to both primer and sequencing platform biases.

16S rRNA gene sequencing↗
DOE OSTI2023

Comparative transcriptome analysis of rainbow trout gonadal cells (RTG-2) infected with U and J genogroup infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV) is the causative pathogen of infectious hematopoietic necrosis, outbreaks of which are responsible for significant losses in rainbow trout aquaculture. Strains of IHNV isolated worldwide have been classified into five major genogroups, J, E, L, M, and U. To date, comparative transcriptomic analysis has only been conducted individually for the J and M genogroups. In this study, we compared the transcriptome profiles in U genogroup and J genogroup IHNV-infected RTG-2 cells with mock-infected RTG-2 cells. The RNA-seq results revealed 17,064 new genes, of which 7,390 genes were functionally annotated. Differentially expressed gene (DEG) analysis between U and J IHNV-infected cells revealed 2,238 DEGs, including 1,011 downregulated genes and 1,227 upregulated genes. Among the 2,238 DEGs, 345 new genes were discovered. The DEGs related to immune responses, cellular signal transduction, and viral diseases were further analyzed. RT-qPCR validation confirmed that the changes in expression of the immune response-related genes trpm2 , sting , itgb7 , ripk2 , and irf1 , cellular signal transduction-related genes irl , cacnb2 , bmp2l , gadd45α , and plk2 , and viral disease-related genes mlf1, mtor, armc5 , pik3r1 , and c-myc were consistent with the results of transcriptome analysis. Taken together, our findings provide a comprehensive transcriptional analysis of the differential virulence of the U and J genogroups of IHNV, and shed new light on the pathogenic mechanisms of IHNV strains.

Zhao, Jing-Zhuang↗
DOE OSTI2023

Inhibition of ethylene involved in resistance to E. turcicum in an exotic-derived double haploid maize population

Northern corn leaf blight (NCLB) is an economically important disease of maize. While the genetic architecture of NCLB has been well characterized, the pathogen is known to overcome currently deployed resistance genes, and the role of hormones in resistance to NCLB is an area of active research. The objectives of the study were (i) to identify significant markers associated with resistance to NCLB, (ii) to identify metabolic pathways associated with NCLB resistance, and (iii) to examine role of ethylene in resistance to NCLB. We screened 252 lines from the exotic-derived double haploid BGEM maize population for resistance to NCLB in both field and greenhouse environments. We used a genome wide association study (GWAS) and stepwise regression to identify four markers associated with resistance, followed by a pathway association study tool (PAST) to identify important metabolic pathways associated with disease severity and incubation period. The ethylene synthesis pathway was significant for disease severity and incubation period. We conducted a greenhouse assay in which we inhibited ethylene to examine the role of ethylene in resistance to NCLB. We observed a significant increase in incubation period and a significant decrease in disease severity between plants treated with the ethylene inhibitor and mock-treated plants. Our study confirms the potential of the BGEM population as a source of novel alleles for resistance. We also confirm the role of ethylene in resistance to NCLB and contribute to the growing body of literature on ethylene and disease resistance in monocots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Nanoindentation of HMX and Idoxuridine to Determine Mechanical Similarity

Assessing the mechanical behavior (elastic properties, plastic properties, and fracture phenomena) of molecular crystals is often complicated by the difficulty in preparing samples. Pharmaceuticals and energetic materials in particular are often used in composite structures or tablets, where the individual grains can strongly impact the solid behavior. Nanoindentation is a convenient method to experimentally assess these properties, and it is used here to demonstrate the similarity in the mechanical properties of two distinct systems: individual crystals of the explosive cyclotetramethylene tetranitramine (HMX) and the pharmaceutical idoxuridine were tested in their as-precipitated state, and the effective average modulus and hardness (which can be orientation dependent) were determined. Both exhibit a hardness of 1.0 GPa, with an effective reduced modulus of 25 and 23 GPa for the HMX and idoxuridine, respectively. They also exhibit similar yield point behavior. This indicates idoxuridine may be a suitable mechanical surrogate (or “mock”) for HMX. While the methodology to assess elastic and plastic properties was relatively insensitive to specific crystal orientation (i.e., a uniform distribution in properties was observed for all random crystals tested), the indentation-induced fracture properties appear to be much more sensitive to tip-crystal orientation, and an unloading slope analysis is used to demonstrate the need for further refinement in relating toughness to orientation in these materials with relatively complex slip systems and crystal structures. View Full-Text

36 MATERIALS SCIENCE↗
DOE OSTI2024

A ‘Nuclear Bomb’ or Just ‘a Joke’? Groundwater Models May Help Communicate Nuanced Risks to the Great Salt Lake

The Great Salt Lake entered the zeitgeist of environmental concern in 2022 when a coalition of scientists and activists warned in a highly publicized report that the lake might be just five years away from complete desiccation, a possibility one state official warned was tantamount to an “environmental nuclear bomb”. Shortly thereafter, an unpredicted and unprecedented pluvial winter resulted in an increase in inflow, temporarily halting the lake’s decline and prompting Utah’s governor to mock the dire prediction as “a joke”, an outcome that speaks to the tension between agenda-setting and trust-building that researchers face when sharing worst-case warnings, particularly those based on short-term variability. Here, we describe a robust relationship between the lake and groundwater in the surrounding region and demonstrate how coupled models can thus be used to improve lake elevation predictions, suggesting that while the situation may not be as dire as some have warned, the lake remains at long-term risk as a result of climate warming. We further suggest that efforts to communicate the risk of future desiccation should be informed by stochastic variability and guided by long-term fluctuations in the total water storage of the endorheic lake’s watershed.

Environmental Sciences & Ecology↗
DOE OSTI2016

PROBABILISTIC CROSS-IDENTIFICATION IN CROWDED FIELDS AS AN ASSIGNMENT PROBLEM

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

MERGER SIGNATURES IN THE DYNAMICS OF STAR-FORMING GAS

The recent advent of integral field spectrographs and millimeter interferometers has revealed the internal dynamics of many hundreds of star-forming galaxies. Spatially resolved kinematics have been used to determine the dynamical status of star-forming galaxies with ambiguous morphologies, and constrain the importance of galaxy interactions during the assembly of galaxies. However, measuring the importance of interactions or galaxy merger rates requires knowledge of the systematics in kinematic diagnostics and the visible time with merger indicators. We analyze the dynamics of star-forming gas in a set of binary merger hydrodynamic simulations with stellar mass ratios of 1:1 and 1:4. We find that the evolution of kinematic asymmetries traced by star-forming gas mirrors morphological asymmetries derived from mock optical images, in which both merger indicators show the largest deviation from isolated disks during strong interaction phases. Based on a series of simulations with various initial disk orientations, orbital parameters, gas fractions, and mass ratios, we find that the merger signatures are visible for ∼0.2–0.4 Gyr with kinematic merger indicators but can be approximately twice as long for equal-mass mergers of massive gas-rich disk galaxies designed to be analogs of z ∼ 2–3 submillimeter galaxies. Merger signatures are most apparent after the second passage and before the black holes coalescence, but in some cases they persist up to several hundred Myr after coalescence. About 20%–60% of the simulated galaxies are not identified as mergers during the strong interaction phase, implying that galaxies undergoing violent merging process do not necessarily exhibit highly asymmetric kinematics in their star-forming gas. The lack of identifiable merger signatures in this population can lead to an underestimation of merger abundances in star-forming galaxies, and including them in samples of star-forming disks may bias the measurements of disk properties such as intrinsic velocity dispersion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

INFERRING THE GALACTIC POTENTIAL WITH GAIA AND FRIENDS: SYNERGIES WITH OTHER SURVEYS

In the coming decade, the Gaia satellite will precisely measure the positions and velocities of millions of stars in the Galactic halo, including stars in many tidal streams. These streams, the products of hierarchical accretion of satellite galaxies by the Milky Way (MW), can be used to infer the Galactic gravitational potential thanks to their initial compactness in phase space. Plans for observations to extend Gaia’s radial velocity (RV) measurements to faint stars, and to determine precise distances to RR Lyrae in streams, would further extend the power of Gaia’s kinematic catalog to characterize the MW’s potential at large Galactocentric distances. In this work I explore the impact of these extra data on the ability to fit the potential using the method of action clustering, which statistically maximizes the information content (clumpiness) of the action space of tidal streams, eliminating the need to determine stream membership for individual stars. Using a mock halo in a toy spherical potential, updated post-launch error models for Gaia, and estimates for RV and distance errors for the tracers to be followed up, I show that combining either form of additional information with the Gaia catalog greatly reduces the bias in determining the scale radius and total mass of the Galaxy compared to the use of Gaia data alone.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Cosmic evolution of long gamma-ray burst luminosity

The cosmic evolution of gamma-ray burst (GRB) luminosity is essential for revealing the GRB physics and for using GRBs as cosmological probes. We investigate the luminosity evolution of long GRBs with a large sample of 258 Swift/BAT GRBs. By describing the peak luminosity evolution of individual GRBs as L{sub p}∝(1+z){sup k}, we get k=1.49±0.19 using the nonparametric τ statistics method without considering observational biases of GRB trigger and redshift measurement. By modeling these biases with the observed peak flux and characterizing the peak luminosity function of long GRBs as a smoothly broken power law with a break that evolves as L{sub b}∝(1+z){sup k{sub b}}, we obtain k{sub b}=1.14{sub −0.47}{sup +0.99} through simulations based on the assumption that the long GRB rate follows the star formation rate incorporating the cosmic metallicity history. The derived k and k{sub b} values are systematically smaller than those reported in previous papers. By removing the observational biases of the GRB trigger and redshift measurement based on our simulation analysis, we generate mock complete samples of 258 and 1000 GRBs to examine how these biases affect the τ statistics method. We get k=0.94±0.14 and k=0.80±0.09 for the two samples, indicating that these observational biases may lead to overestimating the k value. With the large uncertainty of k{sub b} derived from our simulation analysis, one cannot even convincingly argue for a robust evolution feature of the GRB luminosity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

PRECISE MEASUREMENT OF THE REIONIZATION OPTICAL DEPTH FROM THE GLOBAL 21 cm SIGNAL ACCOUNTING FOR COSMIC HEATING

As a result of our limited data on reionization, the total optical depth for electron scattering, τ, limits precision measurements of cosmological parameters from the Cosmic Microwave Background (CMB). It was recently shown that the predicted 21 cm signal of neutral hydrogen contains enough information to reconstruct τ with sub-percent accuracy, assuming that the neutral gas was much hotter than the CMB throughout the entire epoch of reionization (EoR). Here we relax this assumption and use the global 21 cm signal alone to extract τ for realistic X-ray heating scenarios. We test our model-independent approach using mock data for a wide range of ionization and heating histories and show that an accurate measurement of the reionization optical depth at a sub-percent level is possible in most of the considered scenarios even when heating is not saturated during the EoR, assuming that the foregrounds are mitigated. However, we find that in cases where heating sources had hard X-ray spectra and their luminosity was close to or lower than what is predicted based on low-redshift observations, the global 21 cm signal alone is not a good tracer of the reionization history.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

RADIO SYNCHROTRON FLUCTUATION STATISTICS AS A PROBE OF MAGNETIZED INTERSTELLAR TURBULENCE

We investigate how observations of synchrotron intensity fluctuations can be used to probe the sonic and Alfvénic Mach numbers of interstellar turbulence, based on mock observations performed on simulations of magnetohydrodynamic turbulence. We find that the structure function slope and a diagnostic of anisotropy that we call the integrated quadrupole ratio modulus both depend on the Alfvénic Mach number. However, these statistics also depend on the orientation of the mean magnetic field in the synchrotron emitting region relative to our line of sight, and this creates a degeneracy that cannot be broken by observations of synchrotron intensity alone. We conclude that the polarization of synchrotron emission could be analyzed to break this degeneracy, and suggest that this will be possible with the Square Kilometre Array.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

SPENDING TOO MUCH TIME AT THE GALACTIC BAR: CHAOTIC FANNING OF THE OPHIUCHUS STREAM

The Ophiuchus stellar stream is peculiar: (1) its length is short given the age of its constituent stars, and (2) several probable member stars have dispersions in sky position and velocity that far exceed those seen within the stream. The stream’s proximity to the Galactic center suggests that its dynamical history is significantly influenced by the Galactic bar. We explore this hypothesis with models of stream formation along orbits consistent with Ophiuchus’ properties in a Milky Way potential model that includes a rotating bar. In all choices for the rotation parameters of the bar, orbits fit to the stream are strongly chaotic. Mock streams generated along these orbits qualitatively match the observed properties of the stream: because of chaos, stars stripped early generally form low-density, high-dispersion “fans” leaving only the most recently disrupted material detectable as a strong over-density. Our models predict that there should be a significant amount of low-surface-brightness tidal debris around the stream with a complex phase-space morphology. The existence of or lack of these features could provide interesting constraints on the Milky Way bar and would rule out formation scenarios for the stream. This is the first time that chaos has been used to explain the properties of a stellar stream and is the first demonstration of the dynamical importance of chaos in the Galactic halo. The existence of long, thin streams around the Milky Way, presumably formed along non- or weakly chaotic orbits, may represent only a subset of the total population of disrupted satellites.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Garrotxa cosmological simulations of milky way-sized galaxies: general properties, hot-gas distribution, and missing baryons

We introduce a new set of simulations of Milky Way (MW)-sized galaxies using the AMR code ART + hydrodynamics in a Λ cold dark matter cosmogony. The simulation series is called GARROTXA and it follows the formation of a halo/galaxy from z = 60 to z = 0. The final virial mass of the system is ∼7.4 × 10{sup 11} M {sub ⊙}. Our results are as follows. (a) Contrary to many previous studies, the circular velocity curve shows no central peak and overall agrees with recent MW observations. (b) Other quantities, such as M-∗(6 × 10{sup 10} M {sub ⊙}) and R {sub d} (2.56 kpc), fall well inside the observational MW range. (c) We measure the disk-to-total ratio kinematically and find that D/T = 0.42. (d) The cold-gas fraction and star formation rate at z = 0, on the other hand, fall short of the values estimated for the MW. As a first scientific exploitation of the simulation series, we study the spatial distribution of hot X-ray luminous gas. We have found that most of this X-ray emitting gas is in a halo-like distribution accounting for an important fraction but not all of the missing baryons. An important amount of hot gas is also present in filaments. In all our models there is not a massive disk-like hot-gas distribution dominating the column density. Our analysis of hot-gas mock observations reveals that the homogeneity assumption leads to an overestimation of the total mass by factors of 3–5 or to an underestimation by factors of 0.7–0.1, depending on the used observational method. Finally, we confirm a clear correlation between the total hot-gas mass and the dark matter halo mass of galactic systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Can we detect the color-density relation with photometric redshifts?

A variety of methods have been proposed to define and to quantify galaxy environments. While these techniques work well in general with spectroscopic redshift samples, their application to photometric redshift surveys remains uncertain. To investigate whether galaxy environments can be robustly measured with photo-z samples, we quantify how the density measured with the nearest-neighbor approach is affected by photo-z uncertainties by using the Durham mock galaxy catalogs in which the 3D real-space environments and the properties of galaxies are known exactly. Furthermore, we present an optimization scheme in the choice of parameters used in the 2D projected measurements that yield the tightest correlation with respect to the 3D real-space environments. By adopting the optimized parameters in the density measurements, we show that the correlation between the 2D projected optimized density and the real-space density can still be revealed, and the color–density relation is also visible out to z ∼ 0.8 even for a photo-z uncertainty (σ{sub Δ{sub z/(1+z)}}) up to 0.06. We find that at redshifts 0.3 < z < 0.5 a deep (i ∼ 25) photometric redshift survey with σ{sub Δ{sub z/(1+z)}} = 0.02 yields a performance in small-scale density measurement that is comparable to a shallower i ∼ 22.5 spectroscopic sample with ∼10% sampling rate. Finally, we discuss the application of the local density measurements to the Pan-STARRS1 Medium Deep Survey (PS-MDS), one of the largest deep optical imaging surveys. Using data from ∼5 square degrees of survey area, our results show that it is possible to measure local density and to probe the color–density relation with 3σ confidence level out to z ∼ 0.8 in the PS-MDS. The color–density relation, however, quickly degrades for data covering smaller areas.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

ACCELERATED FITTING OF STELLAR SPECTRA

Stellar spectra are often modeled and fitted by interpolating within a rectilinear grid of synthetic spectra to derive the stars’ labels: stellar parameters and elemental abundances. However, the number of synthetic spectra needed for a rectilinear grid grows exponentially with the label space dimensions, precluding the simultaneous and self-consistent fitting of more than a few elemental abundances. Shortcuts such as fitting subsets of labels separately can introduce unknown systematics and do not produce correct error covariances in the derived labels. In this paper we present a new approach—Convex Hull Adaptive Tessellation (chat)—which includes several new ideas for inexpensively generating a sufficient stellar synthetic library, using linear algebra and the concept of an adaptive, data-driven grid. A convex hull approximates the region where the data lie in the label space. A variety of tests with mock data sets demonstrate that chat can reduce the number of required synthetic model calculations by three orders of magnitude in an eight-dimensional label space. The reduction will be even larger for higher dimensional label spaces. In chat the computational effort increases only linearly with the number of labels that are fit simultaneously. Around each of these grid points in the label space an approximate synthetic spectrum can be generated through linear expansion using a set of “gradient spectra” that represent flux derivatives at every wavelength point with respect to all labels. These techniques provide new opportunities to fit the full stellar spectra from large surveys with 15–30 labels simultaneously.

79 ASTRONOMY AND ASTROPHYSICS↗