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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Improvement of eukaryotic protein predictions from soil metagenomes

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗
DOE OSTI2021

Diagenetic formation of uranium-silica polymers in lake sediments over 3,300 years

Significance Understanding the long-term fate of widespread noncrystalline uranium (U) species is critical to improving our knowledge of U biogeochemistry and U-contaminated environments. We use naturally U-enriched lake sediments that have been deposited for thousands of years as an analogue for the progressive evolution of contaminated environments, in order to uncover if noncrystalline species may evolve into more resistant crystalline phases. We combine multidisciplinary tools including U isotope ratio and speciation techniques to describe a mineralogical transformation where organic-bound U evolves into polymeric and nanocrystalline uranium-silica phases that are still easily remobilized even 3,300 y after their deposition. These findings bring an interpretation that illuminates an active debate on uranium mobility in the environment.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2025

The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors

H5Nx viruses continue to wreak havoc in avian and mammalian species worldwide. The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of hosts in diverse climatic environments. Fortunately, transmission to and between humans is scarce. Yet, if such an event were to occur, it could spark a pandemic as humans are immunologically naïve to H5 viruses. A significant determinant of transmission to and between humans is the ability of the influenza A virus hemagglutinin (HA) protein to shift from an avian-type to a human-type receptor specificity. Here, we demonstrate that a 2016 2.3.4.4e virus HA can convert to human-type receptor binding via a single Q226L mutation, in contrast to a cleavage-modified 2016 2.3.4.4b virus HA. Using glycan arrays, X-ray structural analyses, tissue- and direct glycan binding, we show that L133a Δ and 227Q are vital for this phenotype. Thus, whereas the 2.3.4.4e virus HA only needs a single amino acid mutation, the modified 2016 2.3.4.4b HA was not easily converted to human-type receptor specificity.

Science & Technology - Other Topics↗
DOE OSTI2020

Stellar splashback: the edge of the intracluster light

We examine the outskirts of galaxy clusters in the C-EAGLE simulations to quantify the ‘edges’ of the stellar and dark matter distribution. The radius of the steepest slope in the dark matter, commonly used as a proxy for the splashback radius, is located at $\sim \, r_{200 \rm m}$; the strength and location of this feature depends on the recent mass accretion rate, in good agreement with previous work. Interestingly, the stellar distribution (or intracluster light, ICL) also has a well-defined edge, which is directly related to the splashback radius of the halo. Thus, detecting the edge of the ICL can provide an independent measure of the physical boundary of the halo, and the recent mass accretion rate. We show that these caustics can also be seen in the projected density profiles, but care must be taken to account for the influence of substructures and other non-diffuse material, which can bias and/or weaken the signal of the steepest slope. This is particularly important for the stellar material, which has a higher fraction bound in subhaloes than the dark matter. Finally, we show that the ‘stellar splashback’ feature is located beyond current observational constraints on the ICL, but these large projected distances (>> 1 Mpc) and low surface brightnesses (μ>>32 mag arcsec -2 ) can be reached with upcoming observational facilities such as the Vera C. Rubin Observatory, the Nancy Grace Roman Space Telescope, and Euclid.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A new step forward in realistic cluster lens mass modelling: analysis of Hubble Frontier Field Cluster Abell S1063 from joint lensing, X-ray, and galaxy kinematics data

We present a new method to simultaneously and self-consistently model the mass distribution of galaxy clusters that combines constraints from strong lensing features, X-ray emission, and galaxy kinematics measurements. We are able to successfully decompose clusters into their collisionless and collisional mass components thanks to the X-ray surface brightness, as well as use the dynamics of cluster members, to obtain more accurate masses exploiting the fundamental plane of elliptical galaxies. Knowledge from all observables is included through a consistent Bayesian approach in the likelihood or in physically motivated priors. We apply this method to the galaxy cluster Abell S1063 and produce a mass model that we publicly release with this paper. The resulting mass distribution presents different ellipticities for the intra-cluster gas and the other large-scale mass components as well as deviation from elliptical symmetry in the main halo. We assess the ability of our method to recover the masses of the different elements of the cluster using a mock cluster based on a simplified version of our Abell S1063 model. Thanks to the wealth of mutliwavelength information provided by the mass model and the detected X-ray emission, we also found evidence for an ongoing merger event with gas sloshing from a smaller infalling structure into the main cluster. In agreement with previous findings, the total mass, gas profile, and gas mass fraction are all consistent with small deviations from the hydrostatic equilibrium. This new mass model for Abell S1063 is publicly available, as the lenstool extension used to construct it.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Cosmological constraints from density-split clustering in the BOSS CMASS galaxy sample

We present a clustering analysis of the BOSS DR12 CMASS galaxy sample, combining measurements of the galaxy two-point correlation function and density-split clustering down to a scale of $1 \, h^{-1}\, \text{Mpc}$. Our theoretical framework is based on emulators trained on high-fidelity mock galaxy catalogues that forward model the cosmological dependence of the clustering statistics within an extended-ΛCDM framework, including redshift-space and Alcock–Paczynski distortions. Our base-ΛCDM analysis finds ω cdm = 0.1201 ± 0.0022, σ 8 = 0.792 ± 0.034, and n s = 0.970 ± 0.018, corresponding to fσ 8 = 0.462 ± 0.020 at z ≈ 0.525, which is in agreement with Planck 2018 predictions and various clustering studies in the literature. We test single-parameter extensions to base-ΛCDM, varying the running of the spectral index, the dark energy equation of state, and the density of mass-less relic neutrinos, finding no compelling evidence for deviations from the base model. We model the galaxy–halo connection using a halo occupation distribution framework, finding signatures of environment-based assembly bias in the data. We validate our pipeline against mock catalogues that match the clustering and selection properties of CMASS, showing that we can recover unbiased cosmological constraints even with a volume 84 times larger than the one used in this study.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

SUNBIRD : a simulation-based model for full-shape density-split clustering

Combining galaxy clustering information from regions of different environmental densities can help break cosmological parameter degeneracies and access non-Gaussian information from the density field that is not readily captured by the standard two-point correlation function (2PCF) analyses. However, modelling these density-dependent statistics down to the non-linear regime has so far remained challenging. We present a simulation-based model that is able to capture the cosmological dependence of the full shape of the density-split clustering (DSC) statistics down to intra-halo scales. Our models are based on neural-network emulators that are trained on high-fidelity mock galaxy catalogues within an extended-ΛCDM framework, incorporating the effects of redshift-space, Alcock–Paczynski distortions, and models of the halo–galaxy connection. Our models reach sub-percent level accuracy down to $1 \, h^{-1}\text{Mpc}$ and are robust against different choices of galaxy–halo connection modelling. When combined with the galaxy 2PCF, DSC can tighten the constraints on ω cdm , σ 8 , and n s by factors of 2.9, 1.9, and 2.1, respectively, compared to a 2PCF-only analysis. DSC additionally puts strong constraints on environment-based assembly bias parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Amino acid substrate specificities and tissue expression profiles of the nine CYP79A encoding genes in Sorghum bicolor

Cytochrome P450s of the CYP79 family catalyze two N-hydroxylation reactions, converting a selected number of amino acids into the corresponding oximes. The sorghum genome (Sorghum bicolor) harbours nine CYP79A encoding genes, and here sequence comparisons of the CYP79As along with their substrate recognition sites (SRSs) are provided. The substrate specificity of previously uncharacterized CYP79As was investigated by transient expression in Nicotiana benthamiana and subsequent transformation of the oximes formed into the corresponding stable oxime glucosides catalyzed by endogenous UDPG-glucosyltransferases (UGTs). CYP79A61 uses phenylalanine as a substrate, whereas CYP79A91, CYP79A93, and CYP79A95 use valine and isoleucine as substrates, with CYP79A93 showing the ability also to use phenylalanine. CYP79A94 uses isoleucine as a substrate. Analysis of 249 sorghum transcriptomes from two different sorghum cultivars showed the expression levels and tissue-specific expression of the CYP79As. CYP79A1 is the committed gene in dhurrin formation and was the highest expressed gene in most tissues/organs. CYP79A61 was primarily expressed in fully developed leaf blades and leaf sheaths. CYP79A91 and CYP79A92 were expressed mainly in roots >200 cm below ground, while CYP79A93 and CYP79A94 were most highly expressed in the leaf collar and leaf sheath, respectively. Here, the possible signalling effects of the oximes and their metabolites produced in different sorghum tissues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Constraints on the Hubble constant from supernova Refsdal’s reappearance

The Hubble constant measures the expansion rate of the Universe, but different methods give inconsistent values. Kelly et al. studied a supernova that had its light split into multiple images by the gravitational lensing of a foreground galaxy cluster. They combined measurements of the time delay between the multiple images with predictions made by multiple lensing models of the cluster. Furthermore, this approach allowed the authors to make a blinded measurement of the Hubble constant, finding a value that is more consistent with that derived from the cosmic microwave background than with the cosmic distance ladder.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Activating a Natural Fault Zone in the Swiss Alps

One major hurdle for understanding earthquake mechanics are observational limitations. Important phenomena like strain localisation, fault dilation, and fault healing are readily studied in rock mechanical laboratory experiments and with numerical models. At the scale of natural earthquakes, however, these phenomena are often unresolvable, even by state-of-the-art observatories. To overcome this limitation, we are currently building the Earthquake Physics Testbed at the Bedretto Underground Laboratory for Geosciences and Geoenergies (BedrettoLab), an experimental testbed where we can activate an extensively instrumented natural fault zone via hydraulic stimulation. The goal of the Fault Activation and Earthquake Rupture (FEAR) project is to induce earthquakes of up to Mw~1.0 on this exceptionally well characterised and instrumented fault zone. Here we summarize the main scientific goals and current FEAR project status, and present first results from conducted experiments. We discuss how this large-scale experimental approach may allow us to tackle both fundamental science as well as practical questions on earthquake physics, induced seismicity and seismic hazard.

Meier, Men-Andrin↗
DOE OSTI2023

Mixed-Linkage Glucan Is the Main Carbohydrate Source and Starch Is an Alternative Source during Brachypodium Grain Germination

Seeds of the model grass Brachypodium distachyon are unusual because they contain very little starch and high levels of mixed-linkage glucan (MLG) accumulated in thick cell walls. It was suggested that MLG might supplement starch as a storage carbohydrate and may be mobilised during germination. In this work, we observed massive degradation of MLG during germination in both endosperm and nucellar epidermis. The enzymes responsible for the MLG degradation were identified in germinated grains and characterized using heterologous expression. By using mutants targeting MLG biosynthesis genes, we showed that the expression level of genes coding for MLG and starch-degrading enzymes was modified in the germinated grains of knocked-out cslf6 mutants depleted in MLG but with higher starch content. Our results suggest a substrate-dependent regulation of the storage sugars during germination. These overall results demonstrated the function of MLG as the main carbohydrate source during germination of Brachypodium grain. More astonishingly, cslf6 Brachypodium mutants are able to adapt their metabolism to the lack of MLG by modifying the energy source for germination and the expression of genes dedicated for its use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

ARES. II. Characterizing the Hot Jupiters WASP-127 b, WASP-79 b, and WASP-62b with the Hubble Space Telescope

This paper presents the atmospheric characterization of three large, gaseous planets: WASP-127 b, WASP-79 b, and WASP-62 b. We analyzed spectroscopic data obtained with the G141 grism (1.088–1.68 μm) of the Wide Field Camera 3 on board the Hubble Space Telescope using the Iraclis pipeline and the TauREx3 retrieval code, both of which are publicly available. For WASP-127 b, which is the least dense planet discovered so far and is located in the short-period Neptune desert, our retrieval results found strong water absorption corresponding to an abundance of log(H{sub 2}O) = −2.71{sub −1.05}{sup +0.78} and absorption compatible with an iron hydride abundance of log(FeH) = −5.25{sub −1.10}{sup +0.88}, with an extended cloudy atmosphere. We also detected water vapor in the atmospheres of WASP-79 b and WASP-62 b, with best-fit models indicating the presence of iron hydride, too. We used the Atmospheric Detectability Index as well as Bayesian log evidence to quantify the strength of the detection and compared our results to the hot Jupiter population study by Tsiaras et al. While all the planets studied here are suitable targets for characterization with upcoming facilities such as the James Webb Space Telescope and Ariel, WASP-127 b is of particular interest due to its low density, and a thorough atmospheric study would develop our understanding of planet formation and migration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

ARES. V. No Evidence For Molecular Absorption in the HST WFC3 Spectrum of GJ 1132 b

We present a study on the spatially scanned spectroscopic observations of the transit of GJ 1132 b, a warm (∼500 K) super-Earth (1.13 R {sub ⊕}) that was obtained with the G141 grism (1.125–1.650 μm) of the Wide Field Camera 3 (WFC3) on board the Hubble Space Telescope. We used the publicly available Iraclis pipeline to extract the planetary transmission spectra from the five visits and produced a precise transmission spectrum. We analyzed the spectrum using the TauREx3 atmospheric retrieval code, with which we show that the measurements do not contain molecular signatures in the investigated wavelength range and are best fit with a flat-line model. Our results suggest that the planet does not have a clear primordial, hydrogen-dominated atmosphere. Instead, GJ 1132 b could have a cloudy hydrogen-dominated atmosphere, have a very enriched secondary atmosphere, be airless, or have a tenuous atmosphere that has not been detected. Due to the narrow wavelength coverage of WFC3, these scenarios cannot be distinguished yet, but the James Webb Space Telescope may be capable of detecting atmospheric features, although several observations may be required to provide useful constraints.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

The Magnificent Five Images of Supernova Refsdal: Time Delay and Magnification Measurements

In late 2014, four images of supernova (SN) "Refsdal," the first known example of a strongly lensed SN with multiple resolved images, were detected in the MACS J1149 galaxy-cluster field. Following the images' discovery, the SN was predicted to reappear within hundreds of days at a new position ~8'' away in the field. The observed reappearance in late 2015 makes it possible to carry out Refsdal's original proposal to use a multiply imaged SN to measure the Hubble constant H0, since the time delay between appearances should vary inversely with H0. Moreover, the position, brightness, and timing of the reappearance enable a novel test of the blind predictions of galaxy-cluster models, which are typically constrained only by the positions of multiply imaged galaxies. We have developed a new photometry pipeline that uses DOLPHOT to measure the fluxes of the five images of SN Refsdal from difference images. We apply four separate techniques to perform a blind measurement of the relative time delays and magnification ratios between the last image SX and the earlier images S1–S4. We measure the relative time delay of SX–S1 to be 376.0$^{+5.6}_{–5.5}$ days and the relative magnification to be 0.30$^{+0.5}_{–0.3}$. This corresponds to a 1.5% precision on the time delay and 17% precision for the magnification ratios and includes uncertainties due to millilensing and microlensing. In an accompanying paper, we place initial and blind constraints on the value of the Hubble constant.

79 ASTRONOMY AND ASTROPHYSICS↗