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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Strain-Level Differences in Porphyrin Production and Regulation in Propionibacterium acnes Elucidate Disease Associations

Propionibacterium acnes is an important skin commensal, but it is also considered a pathogenic factor in several diseases including acne vulgaris, the most common skin disease. While previous studies have revealed P. acnes strain-level differences in health and disease associations, the underlying molecular mechanisms remain unknown. Recently, we demonstrated that vitamin B 12 supplementation increases P. acnes production of porphyrins, a group of proinflammatory metabolites important in acne development (D. Kang, B. Shi, M. C. Erfe, N. Craft, and H. Li, Sci. Transl. Med. 7:293ra103, 2015, doi:10.1126/scitranslmed.aab2009). In this study, we compared the porphyrin production and regulation of multiple P. acnes strains. We revealed that acne-associated type IA-2 strains inherently produced significantly higher levels of porphyrins, which were further enhanced by vitamin B 12 supplementation. On the other hand, health-associated type II strains produced low levels of porphyrins and did not respond to vitamin B 12 . Using a small-molecule substrate and inhibitor, we demonstrated that porphyrin biosynthesis was modulated at the metabolic level. We identified a repressor gene (deoR) of porphyrin biosynthesis that was carried in all health-associated type II strains, but not in acne-associated type IA-2 strains. The expression of deoR suggests additional regulation of porphyrin production at the transcriptional level in health-associated strains. Our findings provide one potential molecular mechanism for the different contributions of P. acnes strains to skin health and disease and support the role of vitamin B 12 in acne pathogenesis. Our study emphasizes the importance of understanding the role of the commensal microbial community in health and disease at the strain level and suggests potential utility of health-associated P. acnes strains in acne treatment.

5-aminolevulinic acid↗
DOE OSTI2013

Kinetics of generation, relaxation, and accumulation of electronic excitations under two-photon interband picosecond absorption in tungstate and molibdate crystals

Under two-photon 523.5 nm interband picosecond laser excitation, we measured the kinetics of induced absorption in PbWO{sub 4}, ZnWO{sub 4}, and PbMoO{sub 4} crystals with 532 to 633 nm continuous probe radiation. We obtained real-time information about the dynamics of the generation, relaxation, and accumulations of electronic excitations over a wide time range (from picoseconds to hundreds of seconds) and the 77-300 K temperature range. For the studied crystals, exponential temperature-independent growth of the induced absorption (IA) with 60 ns rise time reflects the dynamics of the generation of electronic excitation. The kinetics of the IA exponential growth with temperature-dependent 3.5-11 {mu}s time constants reflect the dynamics of energy migration between neighboring tungstate (molibdate) ions to traps for the studied crystals. The multiexponential relaxation absorption kinetics strongly depend on temperature, and the relaxation decay time of induced absorption increased from tens to hundreds of milliseconds to seconds under crystal cooling from 300 to 77 K. We found that the increase in the laser pump repetition rate (0-10 Hz) leads to the accumulation of electronic excitations. Control of the repetition rate and the number of excitations allowed us to change the relaxation time of the induced absorption by more than two orders of magnitude. Due to accumulation of excitations at 77 K, the absorption relaxation time can exceed 100 s for PbWO{sub 4} and PbMoO{sub 4} crystals. In the initially transparent crystals, two-photon interband absorption (2PA) leads to crystals opacity at the 523 and 633 nm wavelengths. (An inverse optical transmission of the crystals exceeds 50-55 at a 50-100 GW/cm{sup 2} pump intensity.) Measured at {approx}1 mW probe radiation of 532 and 633 nm wavelengths, the induced absorption values are comparable with those obtained under two-photon absorption at {approx}5 kW pump power. An optical 2PA shutter for the visible spectral range is proposed with a variable shutting time from hundreds of microseconds to tens of seconds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Nonlinear ion modes in a strongly coupled plasma in the presence of nonthermal ion fluids and polarization force

The nonlinear propagation of ion-acoustic (IA) waves in a strongly coupled plasma system containing Maxwellian electrons and nonthermal ions has been theoretically and numerically investigated. The well-known reductive perturbation technique is used to derive both the Burgers and Korteweg−de Vries (KdV) equations. Their shock and solitary wave solutions have also been numerically analyzed in understanding localized electrostatic disturbances. It has been observed that the basic features (viz. polarity, amplitude, width, etc.) of IA waves are significantly modified by the effect of polarization force and other plasma parameters (e.g., the electron-to-ion number density ratio and ion-to-electron temperature ratio). This is a unique finding among all theoretical investigations made before, whose probable implications are discussed in this investigation. The implications of the results obtained from this investigation may be useful in understanding the wave propagation in both space and laboratory plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Bioscience COVID Rapid Response Report

The COVID-19 disease outbreak and its impact on global health and economies have highlighted the national security threat posed by pathogens with pandemic potential and the need for rapid development of effective diagnostics and medical countermeasures. The Bioscience IA selected for funding rapid COVID LDRD project proposals that addressed critical R&D gaps in pandemic response that could be accomplished in 1-3 months with the requested funding. In total, the Bioscience IA funded nine rapid projects that addressed 1) rapid and accurate methods for SARS-CoV-2 RNA detection, 2) modeling tools to help prioritize populations for diagnostic testing, 3) bioinformatic tools to track SARS-CoV-2 genomic sequence changes over time, 4) molecular inhibitors of SARS-CoV-2 cellular infection, and 5) method for rapid staging of COVID19 disease to enable administration of more effective treatments. In addition, LDRD funded one larger project to be completed in FY21 that leverages Sandia capabilities to address the need for platform diagnostics and therapeutics that can be rapidly tailored against emerging pathogen targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Iso-VIG14.1.0

Soil samples were collected in triplicate in the Fall of 2017 across the three grassland locations having differences in historical annual precipitation (WA-TmG.1.0, KS-TmG.1.0, and IA-TmG.1.0). For each location, one deeply sequenced composite metagenome (> 1 terabase) were screened for viruses,In addition, each of the three field soil samples were individually sequenced to provide three replicate metagenomes (WA-TmG.2.0, KS-TmG.2.0, and IA-TmG.2.0) for statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling PAH Mixture Interactions in a Human In Vitro Organotypic Respiratory Model

One of the most significant challenges in human health risk assessment is to evaluate hazards from exposure to environmental chemical mixtures. Polycyclic aromatic hydrocarbons (PAHs) are a class of ubiquitous contaminants typically found as mixtures in gaseous and particulate phases in ambient air pollution associated with petrochemicals from Superfund sites and the burning of fossil fuels. However, little is understood about how PAHs in mixtures contribute to toxicity in lung cells. To investigate mixture interactions and component additivity from environmentally relevant PAHs, two synthetic mixtures were created from PAHs identified in passive air samplers at a legacy creosote site impacted by wildfires. The primary human bronchial epithelial cells differentiated at the air–liquid interface were treated with PAH mixtures at environmentally relevant proportions and evaluated for the differential expression of transcriptional biomarkers related to xenobiotic metabolism, oxidative stress response, barrier integrity, and DNA damage response. Component additivity was evaluated across all endpoints using two independent action (IA) models with and without the scaling of components by toxic equivalence factors. Both IA models exhibited trends that were unlike the observed mixture response and generally underestimated the toxicity across dose suggesting the potential for non-additive interactions of components. Overall, this study provides an example of the usefulness of mixture toxicity assessment with the currently available methods while demonstrating the need for more complex yet interpretable mixture response evaluation methods for environmental samples.

3D in vitro models↗
DOE OSTI2016

ASSESSMENT OF SYSTEMATIC CHROMATIC ERRORS THAT IMPACT SUB-1% PHOTOMETRIC PRECISION IN LARGE-AREA SKY SURVEYS

Meeting the science goals for many current and future ground-based optical large-area sky surveys requires that the calibrated broadband photometry is both stable in time and uniform over the sky to 1% precision or better. Past and current surveys have achieved photometric precision of 1%–2% by calibrating the survey’s stellar photometry with repeated measurements of a large number of stars observed in multiple epochs. The calibration techniques employed by these surveys only consider the relative frame-by-frame photometric zeropoint offset and the focal plane position-dependent illumination corrections, which are independent of the source color. However, variations in the wavelength dependence of the atmospheric transmission and the instrumental throughput induce source color-dependent systematic errors. These systematic errors must also be considered to achieve the most precise photometric measurements. In this paper, we examine such systematic chromatic errors (SCEs) using photometry from the Dark Energy Survey (DES) as an example. We first define a natural magnitude system for DES and calculate the systematic errors on stellar magnitudes when the atmospheric transmission and instrumental throughput deviate from the natural system. We conclude that the SCEs caused by the change of airmass in each exposure, the change of the precipitable water vapor and aerosol in the atmosphere over time, and the non-uniformity of instrumental throughput over the focal plane can be up to 2% in some bandpasses. We then compare the calculated SCEs with the observed DES data. For the test sample data, we correct these errors using measurements of the atmospheric transmission and instrumental throughput from auxiliary calibration systems. The residual after correction is less than 0.3%. Moreover, we calculate such SCEs for Type Ia supernovae and elliptical galaxies and find that the chromatic errors for non-stellar objects are redshift-dependent and can be larger than those for stars at certain redshifts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

LOW MACH NUMBER MODELING OF CONVECTION IN HELIUM SHELLS ON SUB-CHANDRASEKHAR WHITE DWARFS. II. BULK PROPERTIES OF SIMPLE MODELS

The dynamics of helium shell convection driven by nuclear burning establish the conditions for runaway in the sub-Chandrasekhar-mass, double-detonation model for SNe Ia, as well as for a variety of other explosive phenomena. We explore these convection dynamics for a range of white dwarf core and helium shell masses in three dimensions using the low Mach number hydrodynamics code MAESTRO. We present calculations of the bulk properties of this evolution, including time-series evolution of global diagnostics, lateral averages of the 3D state, and the global 3D state. We find a variety of outcomes, including quasi-equilibrium, localized runaway, and convective runaway. Our results suggest that the double-detonation progenitor model is promising and that 3D dynamic convection plays a key role.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

CONSTRAINTS ON NON-FLAT COSMOLOGIES WITH MASSIVE NEUTRINOS AFTER PLANCK 2015

We investigate two dark energy cosmological models (i.e., the ΛCDM and ϕ CDM models) with massive neutrinos assuming two different neutrino mass hierarchies in both the spatially flat and non-flat scenarios, where in the ϕ CDM model the scalar field possesses an inverse power-law potential, V ( ϕ ) ∝ ϕ {sup −} {sup α} ( α > 0). Cosmic microwave background data from Planck 2015, baryon acoustic oscillation data from 6dFGS, SDSS-MGS, BOSS-LOWZ and BOSS CMASS-DR11, the joint light-curve analysis compilation of SNe Ia apparent magnitude observations, and the Hubble Space Telescope H {sub 0} prior, are jointly employed to constrain the model parameters. We first determine constraints assuming three species of degenerate massive neutrinos. In the spatially flat (non-flat) ΛCDM model, the sum of neutrino masses is bounded as Σ m {sub ν} < 0.165(0.299) eV at 95% confidence level (CL). Correspondingly, in the flat (non-flat) ϕ CDM model, we find Σ m {sub ν} < 0.164(0.301) eV at 95% CL. The inclusion of spatial curvature as a free parameter results in a significant broadening of confidence regions for Σ m {sub ν} and other parameters. In the scenario where the total neutrino mass is dominated by the heaviest neutrino mass eigenstate, we obtain similar conclusions to those obtained in the degenerate neutrino mass scenario. In addition, the results show that the bounds on Σ m {sub ν} based on two different neutrino mass hierarchies have insignificant differences in the spatially flat case for both the ΛCDM and ϕ CDM models; however, the corresponding differences are larger in the non-flat case.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

BAYESIAN ESTIMATION OF THERMONUCLEAR REACTION RATES

The problem of estimating non-resonant astrophysical S -factors and thermonuclear reaction rates, based on measured nuclear cross sections, is of major interest for nuclear energy generation, neutrino physics, and element synthesis. Many different methods have been applied to this problem in the past, almost all of them based on traditional statistics. Bayesian methods, on the other hand, are now in widespread use in the physical sciences. In astronomy, for example, Bayesian statistics is applied to the observation of extrasolar planets, gravitational waves, and Type Ia supernovae. However, nuclear physics, in particular, has been slow to adopt Bayesian methods. We present astrophysical S -factors and reaction rates based on Bayesian statistics. We develop a framework that incorporates robust parameter estimation, systematic effects, and non-Gaussian uncertainties in a consistent manner. The method is applied to the reactions d(p, γ ){sup 3}He, {sup 3}He({sup 3}He,2p){sup 4}He, and {sup 3}He( α , γ ){sup 7}Be, important for deuterium burning, solar neutrinos, and Big Bang nucleosynthesis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

SN2002es-like supernovae from different viewing angles

In this article, we compare optical light curves of two SN2002es-like Type Ia supernovae (SNe), iPTF14atg and iPTF14dpk, from the intermediate Palomar Transient Factory. Although the two light curves resemble each other around and after maximum, they show distinct early-phase rise behavior in the r-band. On the one hand, iPTF14atg revealed a slow and steady rise that lasted for 22 days with a mean rise rate of 0.2–0.3 mag day{sup –1}, before it reached the R-band peak (−18.05 mag). On the other hand, iPTF14dpk rose rapidly to −17 mag within a day of discovery with a rise rate >1.8 mag day{sup −1}, and then rose slowly to its peak (−18.19 mag) with a rise rate similar to iPTF14atg. The apparent total rise time of iPTF14dpk is therefore only 16 days. We show that emission from iPTF14atg before −17 days with respect to its maximum can be entirely attributed to radiation produced by collision between the SN and its companion star. Such emission is absent from iPTF14dpk probably because of an unfavored viewing angle, provided that SN2002es-like events arise from the same progenitor channel. We further show that an SN2002es-like SN may experience a dark phase after the explosion but before its radioactively powered light curve becomes visible. This dark phase may be lit by radiation from supernova–companion interaction.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Stellar Variability at the Main-sequence Turnoff of the Intermediate-age LMC Cluster NGC 1846

Intermediate-age (IA) star clusters in the Large Magellanic Cloud (LMC) present extended main-sequence turn-offs (MSTO) that have been attributed to either multiple stellar populations or an effect of stellar rotation. Recently it has been proposed that these extended main sequences can also be produced by ill-characterized stellar variability. Here we present Gemini-S/Gemini Multi-Object Spectrometer (GMOS) time series observations of the IA cluster NGC 1846. Using differential image analysis, we identified 73 new variable stars, with 55 of those being of the Delta Scuti type, that is, pulsating variables close the MSTO for the cluster age. Considering completeness and background contamination effects, we estimate the number of δ Sct belonging to the cluster between 40 and 60 members, although this number is based on the detection of a single δ Sct within the cluster half-light radius. This amount of variable stars at the MSTO level will not produce significant broadening of the MSTO, albeit higher-resolution imaging will be needed to rule out variable stars as a major contributor to the extended MSTO phenomenon. Though modest, this amount of δ Sct makes NGC 1846 the star cluster with the highest number of these variables ever discovered. Lastly, our results present a cautionary tale about the adequacy of shallow variability surveys in the LMC (like OGLE) to derive properties of its δ Sct population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Photometric Classification of Early-time Supernova Light Curves with SCONE

Abstract In this work, we present classification results on early supernova light curves from SCONE, a photometric classifier that uses convolutional neural networks to categorize supernovae (SNe) by type using light-curve data. SCONE is able to identify SN types from light curves at any stage, from the night of initial alert to the end of their lifetimes. Simulated LSST SNe light curves were truncated at 0, 5, 15, 25, and 50 days after the trigger date and used to train Gaussian processes in wavelength and time space to produce wavelength–time heatmaps. SCONE uses these heatmaps to perform six-way classification between SN types Ia, II, Ibc, Ia-91bg, Iax, and SLSN-I. SCONE is able to perform classification with or without redshift, but we show that incorporating redshift information improves performance at each epoch. SCONE achieved 75% overall accuracy at the date of trigger (60% without redshift), and 89% accuracy 50 days after trigger (82% without redshift). SCONE was also tested on bright subsets of SNe ( r < 20 mag) and produced 91% accuracy at the date of trigger (83% without redshift) and 95% five days after trigger (94.7% without redshift). SCONE is the first application of convolutional neural networks to the early-time photometric transient classification problem. All of the data processing and model code developed for this paper can be found in the SCONE software package 1 1 github.com/helenqu/scone located at github.com/helenqu/scone (Qu 2021).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

The origin of the iron-rich knot in tycho's supernova remnant

X-ray observations of supernova remnants (SNRs) allow us to investigate the chemical inhomogeneity of ejecta, offering unique insight into the nucleosynthesis in supernova explosions. Here we present detailed imaging and spectroscopic studies of the “Fe knot” located along the eastern rim of the Type Ia SNR Tycho (SN 1572) using Suzaku and Chandra long-exposure data. Surprisingly, the Suzaku spectrum of this knot shows no emission from Cr, Mn, or Ni, which is unusual for the Fe-rich regions in this SNR. Within the framework of the canonical delayed-detonation models for SN Ia, the observed mass ratios M{sub Cr}/M{sub Fe}<0.023, M{sub Mn}/M{sub Fe}<0.012, and M{sub Ni}/M{sub Fe}<0.029 (at 90% confidence) can only be achieved for a peak temperature of (5.3–5.7) × 10{sup 9} K and a neutron excess of ≲2.0×10{sup −3}. These constraints rule out the deep, dense core of a Chandrasekhar-mass white dwarf as the origin of the Fe knot and favor either incomplete Si burning or an α-rich freeze-out regime, probably close to the boundary. An explosive He burning regime is a possible alternative, although this hypothesis is in conflict with the main properties of this SNR.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Uniform Contribution of Supernova Explosions to the Chemical Enrichment of Abell 3112 out to R{sub 200}

The spatial distribution of the metals residing in the intra-cluster medium (ICM) of galaxy clusters records all the information on a cluster’s nucleosynthesis and chemical enrichment history. We present measurements from a total of 1.2 Ms Suzaku XIS and 72 ks Chandra observations of the cool-core galaxy cluster Abell 3112 out to its virial radius (∼1470 kpc). We find that the ratio of the observed supernova type Ia explosions to the total supernova explosions has a uniform distribution at a level of 12%–16% out to the cluster’s virial radius. The observed fraction of type Ia supernova explosions is in agreement with the corresponding fraction found in our Galaxy and the chemical enrichment of our Galaxy. The non-varying supernova enrichment suggests that the ICM in cluster outskirts was enriched by metals at an early stage before the cluster itself was formed during a period of intense star formation activity. Additionally, we find that the 2D delayed detonation model CDDT produce significantly worse fits to the X-ray spectra compared to simple 1D W7 models. This is due to the relative overestimate of Si, and the underestimate of Mg in these models with respect to the measured abundances.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Two New Calcium-rich Gap Transients in Group and Cluster Environments

We present the Palomar Transient Factory discoveries and the photometric and spectroscopic observations of PTF11kmb and PTF12bho. We show that both transients have properties consistent with the class of calcium-rich gap transients, specifically lower peak luminosities and rapid evolution compared to ordinary supernovae, and a nebular spectrum dominated by [Ca ii] emission. A striking feature of both transients is their host environments: PTF12bho is an intracluster transient in the Coma Cluster, while PTF11kmb is located in a loose galaxy group, at a physical offset ∼150 kpc from the most likely host galaxy. Deep Subaru imaging of PTF12bho rules out an underlying host system to a limit of M{sub R}>−8.0 mag, while Hubble Space Telescope imaging of PTF11kmb reveals a marginal counterpart that, if real, could be either a background galaxy or a globular cluster. We show that the offset distribution of Ca-rich gap transients is significantly more extreme than that seen for SNe Ia or even short-hard gamma-ray bursts (sGRBs). Thus, if the offsets are caused by a kick, they require higher kick velocities and/or longer merger times than sGRBs. We also show that almost all Ca-rich transients found to date are in group and cluster environments with elliptical host galaxies, indicating a very old progenitor population; the remote locations could partially be explained by these environments having the largest fraction of stars in the intragroup/intracluster light following galaxy–galaxy interactions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Gas Removal in the Ursa Minor Galaxy: Linking Hydrodynamics and Chemical Evolution Models

We present results from a non-cosmological, three-dimensional hydrodynamical simulation of the gas in the dwarf spheroidal galaxy Ursa Minor. Assuming an initial baryonic-to-dark-matter ratio derived from the cosmic microwave background radiation, we evolved the galactic gas distribution over 3 Gyr, taking into account the effects of the types Ia and II supernovae. For the first time, we used in our simulation the instantaneous supernovae rates derived from a chemical evolution model applied to spectroscopic observational data of Ursa Minor. We show that the amount of gas that is lost in this process is variable with time and radius, being the highest rates observed during the initial 600 Myr in our simulation. Our results indicate that types Ia and II supernovae must be essential drivers of the gas loss in Ursa Minor galaxy (and probably in other similar dwarf galaxies), but it is ultimately the combination of galactic winds powered by these supernovae and environmental effects (e.g., ram-pressure stripping) that results in the complete removal of the gas content.

79 ASTRONOMY AND ASTROPHYSICS↗