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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 OSTI2017

A Randomized Phase 2 Trial of Prophylactic Manuka Honey for the Reduction of Chemoradiation Therapy–Induced Esophagitis During the Treatment of Lung Cancer: Results of NRG Oncology RTOG 1012

Purpose: Randomized trials have shown that honey is effective for the prevention of radiation-induced mucositis in head and neck cancer patients. Because there is no efficacious preventative for radiation esophagitis in lung cancer patients, this trial compared liquid honey, honey lozenges, and standard supportive care for radiation esophagitis. Methods: The patients were stratified by percentage of esophagus receiving specific radiation dose (V60 Gy esophagus <30% or ≥30%) and were then randomized between supportive care, 10 mL of liquid manuka honey 4 times a day, and 2 lozenges (10 mL of dehydrated manuka honey) 4 times a day during concurrent chemotherapy and radiation therapy. The primary endpoint was patient-reported pain on swallowing, with the use of an 11-point (0-10) scale at 4 weeks (Numerical Rating Pain Scale, NRPS). The study was designed to detect a 15% relative reduction of change in NRPS score. The secondary endpoints were trend of pain over time, opioid use, clinically graded and patient-reported adverse events, weight loss, dysphagia, nutritional status, and quality of life. Results: 53 patients were randomized to supportive care, 54 were randomized to liquid honey, and 56 were randomized to lozenge honey. There was no significant difference in the primary endpoint of change in the NRPS at 4 weeks between arms. There were no differences in any of the secondary endpoints except for opioid use at 4 weeks during treatment between the supportive care and liquid honey arms, which was found to be significant (P=.03), with more patients on the supportive care arm taking opioids. Conclusion: Honey as prescribed within this protocol was not superior to best supportive care in preventing radiation esophagitis. Further testing of other types of honey and research into the mechanisms of action are needed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Theoretical Study of High Harmonic Generation in Monolayer NbSe 2

High harmonic generation (HHG) is a powerful probe of electron dynamics on attosecond to femtosecond time scales and has been successfully used to detect electronic and structural changes in solid-state quantum materials, including transition-metal dichalcogenides (TMDs). Among TMDs, bulk NbSe 2 exhibits charge density wave (CDW) order below 33 K and becomes superconducting below 7.3 K. Monolayer NbSe 2 also has superconducting and CDW behavior and is therefore interesting as a material whose different structural and electronic properties could be probed via HHG. Here, we predict the HHG response of the pristine 2H and CDW phases of monolayer NbSe 2 using real-time time-dependent density functional theory under the application of a simulated laser pulse excitation. We find that due to the lack of inversion symmetry in both monolayer phases, it is possible to excite even harmonics and that the even harmonics appear as the transverse components of the current response under excitations polarized along the zigzag direction of the monolayer, while odd harmonics arise from the longitudinal current response in all excitation directions. This suggests that the even and odd harmonic responses can be controlled via the polarization of the probing field, opening an avenue for potentially useful applications in optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Plasmonic Terahertz Devices and Sensors Based on Carbon Electronics

Tunable terahertz (THz) photonic devices are imperative in a wide range of applications ranging from THz signal modulation to molecular sensing. One of the currently prevailing methods is based on arrays of metallic or dielectric resonators integrated with functional materials in response to an external stimulus, in which for the purpose of sensing the external stimuli may introduce inadvertent undesirable effects into the target samples to be measured. Here we developed an alternative approach by postprocessing nanothickness macro-assembled graphene (nMAG) films with widely tunable THz conductivity, enabling versatile solid-state THz devices and sensors, showing multifunctional nMAG-based applications. The THz conductivities of free-standing nMAGs showed a broad range from 1.2 x 10 3 S/m in reduced graphene oxide before annealing to 4.0 x 10 6 S/m in a nMAG film annealed at 2800 °C. We fabricated nMAG/dielectric/metal and nMAG/dielectric/nMAG THz Salisbury absorbers with broad reflectance ranging from 0% to 80%. The highly conductive nMAG films enabled THz metasurfaces for sensing applications. Taking advantage of the resonant field enhancement arising from the plasmonic metasurface structures and the strong interactions between analyte molecules and nMAG films, we have successfully detected diphenylamine with a limit of detection of 4.2 pg. Those wafer-scale nMAG films present promising potential in high-performance THz electronics, photonics, and sensors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Seeing the Disturbed Forest for the Trees: Remote Sensing Is Underutilized to Quantify Critical Zone Response to Unprecedented Disturbance

Understanding the severity and extent of near surface critical zone (CZ) disturbances and their ecosystem response is a pressing concern in the face of increasing human and natural disturbances. Predicting disturbance severity and recovery in a changing climate requires comprehensive understanding of ecosystem feedbacks among vegetation and the surrounding environment, including climate, hydrology, geomorphology, and biogeochemistry. Field surveys and satellite remote sensing have limited ability to effectively capture the spatial and temporal variability of disturbance and CZ properties. Technological advances in remote sensing using new sensors and new platforms have improved observations of changes in vegetation canopy structure and productivity; however, integrating measures of forest disturbance from various sensing platforms is complex. By connecting the potential for remote sensing technologies to observe different CZ disturbance vectors, we show that lower severity disturbance and slower vegetation recovery are more difficult to quantify. Case studies in montane forests from the western United States highlight new opportunities, including evaluating post-disturbance forest recovery at multiple scales, shedding light on understory vegetation regrowth, detecting specific physiological responses, and refining ecohydrological modeling. Learning from regional CZ disturbance case studies, we propose future directions to synthesize fragmented findings with (a) new data analysis using new or existing sensors, (b) data fusion across multiple sensors and platforms, (c) increasing the value of ground-based observations, (d) disturbance modeling, and (e) synthesis to improve understanding of disturbance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Automatic detection of methane emissions in multispectral satellite imagery using a vision transformer

Curbing methane emissions is among the most effective actions that can be taken to slow down global warming. However, monitoring emissions remains challenging, as detection methods have a limited quantification completeness due to trade-offs that have to be made between coverage, resolution and detection accuracy. Here we show that deep learning can overcome the trade-off in terms of spectral resolution that comes with multi-spectral satellite data, resulting in a methane detection tool with global coverage and high temporal and spatial resolution. We compare our detections with airborne methane measurement campaigns, which suggests that our method can detect methane point sources in Sentinel-2 data down to plumes of 0.01 km 2 , corresponding to 200 to 300 kg CH 4 /h -1 sources. Our model shows an order of magnitude improvement over the state-of-the-art, providing a significant step towards the automated, high resolution detection of methane emissions at a global scale, every few days.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bringing weak transitions to light

Abstract Weak transitions between quantum states are of fundamental importance for a broad range of phenomena from analytical biochemistry to precision physics, but generally challenge experimental detection. Due to their small cross sections scaling with the absolute square of their transition matrix elements, spectroscopic measurements often fail in particular in the presence of competing background processes. Here we introduce a general concept to break this scaling law and enhance the transition probability by exploiting a stronger laser-coupled pathway to the same excited state. We demonstrate the concept experimentally by attosecond transient absorption spectroscopy in helium atoms. The quasi-forbidden transitions from the ground state 1s 2 to the weakly coupled doubly excited 2p3dandsp 2,4− states are boosted by an order of magnitude. Enhancing single-photon-suppressed transitions can find widespread applicability, from spectral diagnostics of complex molecules in life and chemical sciences to precision spectroscopy of weak transitions in metastable atomic nuclei in the search for new physics.

Science & Technology - Other Topics↗
DOE OSTI2018

An Algorithm for Enhancing the Image Contrast of Electron Tomography

Abstract Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1–3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

Planck 2015 results: XVIII. Background geometry and topology of the Universe

We report that maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χ rec ), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio ΔlnL > -5 relative to a simply-connected flat Planck best-fit model) are: R i > 0.97 χ rec for the T3 cubic torus; and R i > 0.56 χ rec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R i > 0.97 χ rec at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. In the physically motivated setting, where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 7.6 × 10 -10 (95% CL).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Mapping the Perseus galaxy cluster with XRISM: Gas kinematic features and their implications for turbulence

We present extended gas kinematic maps of the Perseus cluster based on a combination of five new XRISM/Resolve pointings observed in 2025 with four performance verification datasets from 2024, totaling a net exposure of 745 ks. To date, Perseus remains the only cluster that has been extensively mapped out to ≃0.7 r 2500 by XRISM/Resolve, while simultaneously offering sufficient spatial resolution to resolve gaseous substructures driven by mergers and active galactic nucleus (AGN) feedback. Our observations cover multiple radial directions and a broad range of dynamical scales, enabling us to characterize the kinematic properties of the intracluster medium up to a scale of ∼500 kpc. In the measurements, we detected high-velocity dispersions (≃300km s −1 ) in the eastern region of the cluster that are spatially coincident with the extended X-ray surface brightness excess and correspond to a nonthermal pressure fraction of ≃7 − 13%. The velocity field outside the AGN-dominant region can be effectively described by a single, large-scale kinematic driver based on the velocity structure function, which statistically favors an energy injection scale of at least a few hundred kpc. The estimated turbulent dissipation energy is comparable to the gravitational potential energy released by a recent merger, implying a significant role of turbulent cascade in the merger energy conversion. In the bulk velocity field, we observed a dipole-like pattern along the east-west direction with an amplitude of ≃ ± 200 − 300 km s −1 , indicating rotational motions induced by the recent merger event. This feature constrains the viewing direction to ≃30° −50° relative to the normal of the merger plane. Our hydrodynamic simulations suggest that Perseus has experienced at least two energetic mergers since redshift z ∼ 1, the most recent of which is associated with the radio galaxy IC310, in agreement with recent SRG/eROSITA findings. This study showcases exciting scientific opportunities for future missions with high-resolution spectroscopic capabilities (e.g., HUBS, LEM, and NewAthena).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Tailoring the surface density of silicon nanocrystals embedded in SiO{sub x} single layers

In this article, we explore the possibility of modifying the silicon nanocrystal areal density in SiO{sub x} single layers, while keeping constant their size. For this purpose, a set of SiO{sub x} monolayers with controlled thickness between two thick SiO{sub 2} layers has been fabricated, for four different compositions (x = 1, 1.25, 1.5, or 1.75). The structural properties of the SiO{sub x} single layers have been analyzed by transmission electron microscopy (TEM) in planar view geometry. Energy-filtered TEM images revealed an almost constant Si-cluster size and a slight increase in the cluster areal density as the silicon content increases in the layers, while high resolution TEM images show that the size of the Si crystalline precipitates largely decreases as the SiO{sub x} stoichiometry approaches that of SiO{sub 2}. The crystalline fraction was evaluated by combining the results from both techniques, finding a crystallinity reduction from 75% to 40%, for x = 1 and 1.75, respectively. Complementary photoluminescence measurements corroborate the precipitation of Si-nanocrystals with excellent emission properties for layers with the largest amount of excess silicon. The integrated emission from the nanoaggregates perfectly scales with their crystalline state, with no detectable emission for crystalline fractions below 40%. The combination of the structural and luminescence observations suggests that small Si precipitates are submitted to a higher compressive local stress applied by the SiO{sub 2} matrix that could inhibit the phase separation and, in turn, promotes the creation of nonradiative paths.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Monte Carlo simulation of an x-ray luminescence optical tomography scanner prototype

In this work we report the calculation of the deposited energy distribution produced by an x-ray luminescence optical tomography (XLOT) system in a phantom containing different concentrations of Gd{sub 2}O{sub 2}S:Eu nanoparticles. The calculations were performed via Monte Carlo simulation considering spectra from a W target x-ray tube operating between 30 and 90 kVp, with 1.0 mm Al added filtration. CT and XLOT tomographic images were reconstructed from the same data. The results show that XLOT has better detectability than CT alone, that the dose scales linearly with kVp for a fixed concentration of Gd{sub 2}O{sub 2}S:Eu and air-kerma rate, the scattered radiation contribution to the total dose and signal is about 20% and that the dose ratio for a 3 mm diameter insert containing 10 mg/ml Gd{sub 2}O{sub 2}S embedded in a 30 mm diameter water phantom is 6:1. This ratio drops to less than 2:1 for a 1 mg/ml concentration. Finally we show that the method of conjugate images can be used to correct for artifacts due to attenuation effects in XLOT images.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

A FLUX ROPE NETWORK AND PARTICLE ACCELERATION IN THREE-DIMENSIONAL RELATIVISTIC MAGNETIC RECONNECTION

We investigate magnetic reconnection and particle acceleration in relativistic pair plasmas with three-dimensional particle-in-cell simulations of a kinetic-scale current sheet in a periodic geometry. We include a guide field that introduces an inclination between the reconnecting field lines and explore outside-of-the-current sheet magnetizations that are significantly below those considered by other authors carrying out similar calculations. Thus, our simulations probe the transitional regime in which the magnetic and plasma pressures are of the same order of magnitude. The tearing instability is the dominant mode in the current sheet for all guide field strengths, while the linear kink mode is less important even without the guide field, except in the lower magnetization case. Oblique modes seem to be suppressed entirely. In its nonlinear evolution, the reconnection layer develops a network of interconnected and interacting magnetic flux ropes. As smaller flux ropes merge into larger ones, the reconnection layer evolves toward a three-dimensional, disordered state in which the resulting flux rope segments contain magnetic substructure on plasma skin depth scales. Embedded in the flux ropes, we detect spatially and temporally intermittent sites of dissipation reflected in peaks in the parallel electric field. Magnetic dissipation and particle acceleration persist until the end of the simulations, with simulations with higher magnetization and lower guide field strength exhibiting greater and faster energy conversion and particle energization. At the end of our largest simulation, the particle energy spectrum attains a tail extending to high Lorentz factors that is best modeled with a combination of two additional thermal components. We confirm that the primary energization mechanism is acceleration by the electric field in the X-line region. The highest-energy positrons (electrons) are moderately beamed with median angles {approx}30 Degree-Sign -40 Degree-Sign relative to (the opposite of) the direction of the initial current density, but we speculate that reconnection in more highly magnetized plasmas would give rise to stronger beaming. Finally, we discuss the implications of our results for macroscopic reconnection sites, and which of our results may be expected to hold in systems with higher magnetizations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Confronting simulations of optically thick gas in massive halos with observations at z = 2-3

Cosmological hydrodynamic simulations predict the physical state of baryons in the circumgalactic medium (CGM), which can be directly tested via quasar absorption line observations. We use high-resolution 'zoom-in' simulations of 21 galaxies to characterize the distribution of neutral hydrogen around halos in the mass range M {sub vir} ∼ 2 × 10{sup 11} to 4 × 10{sup 12} M {sub ☉} at z ∼ 2. We find that both the mass fraction of cool (T ≤ 3 × 10{sup 4} K) gas and the covering fraction of optically thick Lyman limit systems (LLSs) depend only weakly on halo mass, even around the critical value for the formation of stable virial shocks. The covering fraction of LLSs interior to the virial radius varies between f {sub c} ∼ 0.05-0.2, with significant scatter among halos. Our simulations of massive halos (M {sub vir} ≥ 10{sup 12} M {sub ☉}) underpredict the covering fraction of optically thick gas observed in the quasar CGM by a large factor. The reason for this discrepancy is unclear, but several possibilities are discussed. In the lower mass halos (M {sub vir} ≥ 5 × 10{sup 11} M {sub ☉}) hosting star-forming galaxies, the predicted covering factor agrees with observations; however, current samples of quasar-galaxy pairs are too small for a conclusive comparison. To overcome this limitation, we propose a new observable: the small-scale autocorrelation function of optically thick absorbers detected in the foreground of close quasar pairs. We show that this new observable can constrain the underlying dark halos hosting LLSs at z ∼ 2-3, as well as the characteristic size and covering factor of the CGM.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Observational requirements for Lyα forest tomographic mapping of large-scale structure at z ∼ 2

The z ≳ 2 Lyα forest traces the underlying dark matter distribution on large scales and, given sufficient sightlines, can be used to create three-dimensional (3D) maps of large-scale structures. We examine the observational requirements to construct such maps and estimate the signal-to-noise as a function of exposure time and sightline density. Sightline densities at z = 2.25 are n {sub los} ≈ [360, 1200, 3300] deg{sup –2} at limiting magnitudes of g = [24.0, 24.5, 25.0], resulting in transverse sightline separations of (d ) ≈ [3.6, 1.9, 1.2] h {sup –1} Mpc, which roughly sets the reconstruction scale. We simulate these reconstructions using mock spectra with realistic noise properties and find that spectra with S/N ≈ 4 per angstrom can be used to generate maps that clearly trace the underlying dark matter at overdensities of ρ/(ρ) ∼ 1. For the VLT/VIMOS spectrograph, exposure times t {sub exp} = [4, 6, 10] hr are sufficient for maps with spatial resolution ε{sub 3D} = [5.0, 3.2, 2.3] h {sup –1} Mpc. Assuming ∼250 h {sup –1} Mpc is probed along the line of sight, 1 deg{sup 2} of survey area would cover a comoving volume of ≈10{sup 6} h {sup –3} Mpc{sup 3} at (z) ∼ 2.3, enabling the efficient mapping of large volumes with 8-10 m telescopes. These maps could be used to study galaxy environments, the topology of large-scale structures at high z, and to detect proto-clusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Massive young stellar object W42-MME: The discovery of an infrared jet using VLT/NACO near-infrared images

We report on the discovery of an infrared jet from a deeply embedded infrared counterpart of the 6.7 GHz methanol maser emission (MME) in W42 (i.e., W42-MME). We show that W42-MME drives a parsec-scale H{sub 2} outflow, with the detection of a bow shock feature at ∼0.52 pc to the north. The inner ∼0.4 pc part of the H{sub 2} outflow has a position angle of ∼18° and the position angle of ∼40° is found farther away on either side of the outflow from W42-MME. W42-MME is detected at wavelengths longer than 2.2 μm and is a massive young stellar object with an estimated stellar mass of 19 ± 4 M{sub ⊙}. We map the inner circumstellar environment of W42-MME using Very Large Telescope (VLT)/NACO adaptive optics K{sub s} and L′ observations at resolutions of ∼0.″ 2 and ∼0.″1, respectively. We discover a collimated jet in the inner 4500 AU using the L′ band, which contains prominent Brα line emission. The jet is located inside an envelope/cavity (extent ∼10,640 AU) that is tapered at both ends and is oriented along the north–south direction. Such observed morphology of the outflow cavity around the massive star is scarcely known and is very crucial for understanding the jet-outflow formation process in massive star formation. Along the flow axis, which is parallel to the previously known magnetic field, two blobs are found in both the NACO images at distances of ∼11800 AU, located symmetrically from W42-MME. The observed W42-MME jet-outflow configuration can be used to constrain the jet launching and jet collimation models in massive star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

The next generation Virgo Cluster Survey. IX. Estimating the efficiency of galaxy formation on the lowest-mass scales

The Next Generation Virgo Cluster Survey has recently determined the luminosity function of galaxies in the core of the Virgo cluster down to unprecedented magnitude and surface brightness limits. Comparing simulations of cluster formation to the derived central stellar mass function, we attempt to estimate the stellar-to-halo-mass ratio (SHMR) for dwarf galaxies, as it would have been before they fell into the cluster. This approach ignores several details and complications, e.g., the contribution of ongoing star formation to the present-day stellar mass of cluster members, and the effects of adiabatic contraction and/or violent feedback on the subhalo and cluster potentials. The final results are startlingly simple, however; we find that the trends in the SHMR determined previously for bright galaxies appear to extend down in a scale-invariant way to the faintest objects detected in the survey. These results extend measurements of the formation efficiency of field galaxies by two decades in halo mass or five decades in stellar mass, down to some of the least massive dwarf galaxies known, with stellar masses of ∼10{sup 5} M{sub ⊙}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Limits on the fluctuating part of y-type distortion monopole from Planck and SPT results

We use the published Planck and SPT cluster catalogs [1,2] and recently published y-distortion maps [3] to put strong observational limits on the contribution of the fluctuating part of the y-type distortions to the y-distortion monopole. Our bounds are 5.4× 10{sup −8} < ( y) < 2.2× 10{sup −6}. Our upper bound is a factor of 6.8 stronger than the currently best upper 95% confidence limit from COBE-FIRAS of ( y) <15× 10{sup −6}. In the standard cosmology, large scale structure is the only source of such distortions and our limits therefore constrain the baryonic physics involved in the formation of the large scale structure. Our lower limit, from the detected clusters in the Planck and SPT catalogs, also implies that a Pixie-like experiment should detect the y-distortion monopole at >27-σ. The biggest sources of uncertainty in our upper limit are the monopole offsets between different HFI channel maps that we estimate to be <10{sup −6}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testisspecific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

59 BASIC BIOLOGICAL SCIENCES↗