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DOE OSTI2021

VariantStore: an index for large-scale genomic variant search

Abstract Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system. We show the scalability of VariantStore by indexing genomic variants from the TCGA project in 4 h and the 1000 Genomes project in 3 h. Querying for variants in a gene takes between 0.002 and 3 seconds using memory only 10% of the size of the full representation.

Pandey, Prashant↗

DOE OSTI2022

Manipulating the insulator–metal transition through tip-induced hydrogenation

Manipulating the insulator–metal transition in strongly correlated materials has attracted a broad range of research activity due to its promising applications in, for example, memories, electrochromic windows and optical modulators. Electric-field-controlled hydrogenation using ionic liquids and solid electrolytes is a useful strategy to obtain the insulator–metal transition with corresponding electron filling, but faces technical challenges for miniaturization due to the complicated device architecture. Here, in this work, we demonstrate reversible electric-field control of nanoscale hydrogenation into VO 2 with a tunable insulator–metal transition using a scanning probe. The Pt-coated probe serves as an efficient catalyst to split hydrogen molecules, while the positive-biased voltage accelerates hydrogen ions between the tip and sample surface to facilitate their incorporation, leading to non-volatile transformation from insulating VO 2 into conducting H x VO 2 . Remarkably, a negative-biased voltage triggers dehydrogenation to restore the insulating VO 2 . This work demonstrates a local and reversible electric-field-controlled insulator–metal transition through hydrogen evolution and presents a versatile pathway to exploit multiple functional devices at the nanoscale.

36 MATERIALS SCIENCE↗

NASA NTRS1992

Arcing in space structures in low Earth orbit

This report describes results of an experimental and theoretical program to investigate arcing of structures containing dielectric and conducting materials when they are biased negatively with respect to a plasma. An argon ion source generated Ar(+) ions of directed energy 20 to 40 eV and density approximately 10(exp 7) cm(exp -3) that impinged upon samples containing a dielectric material on top of a negatively biased Kovar plate. Arcing events were studied for bias voltages between -300 and -1000V with respect to the ion beam. The samples were Dow Corning 93-500 adhesive on Kovar, fused silica cover slips bonded on Kovar, and silicon solar cells mounted on Kovar. Measurements of discharge current, Kovar plate voltage, and radiation from the arc versus time were carried out. Microsecond duration exposure images and optical spectra in the 0.24 to 0.40 micron band were also acquired during arcing events. Arcing events were found to be associated with exposed adhesive and means were found to eliminate arcing altogether. The charging of a silica cover plate and the fields around the plate were calculated using a particle-in-cell code. Models were developed to explain the ignition of the arc and the physical processes occurring during the discharge.

Upschulte, B. L.↗

DOE OSTI2020

First Cosmology Results using Supernovae Ia from the Dark Energy Survey: Survey Overview, Performance, and Supernova Spectroscopy

We present details on the observing strategy, data-processing techniques, and spectroscopic targeting algorithms for the first three years of operation for the Dark Energy Survey Supernova Program (DES-SN). This five-year program using the Dark Energy Camera mounted on the 4 m Blanco telescope in Chile was designed to discover and follow supernovae (SNe) Ia over a wide redshift range (0.05 < z < 1.2) to measure the equation-of-state parameter of dark energy. We describe the SN program in full: strategy, observations, data reduction, spectroscopic follow-up observations, and classification. From three seasons of data, we have discovered 12,015 likely SNe, 308 of which have been spectroscopically confirmed, including 251 SNe Ia over a redshift range of 0.017 < z < 0.85. We determine the effective spectroscopic selection function for our sample and use it to investigate the redshift-dependent bias on the distance moduli of SNe Ia we have classified. The data presented here are used for the first cosmology analysis by DES-SN (“DES-SN3YR”), the results of which are given in Dark Energy Survey Collaboration et al. The 489 spectra that are used to define the DES-SN3YR sample are publicly available at https://des.ncsa.illinois.edu/releases/sn.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1985

Investigations of radiation-induced and carrier-enhanced conductivity

A steady-state carrier computer code, PECK (Parker Enhanced Carrier Kinetics), that predicts the radiation-induced conductivity (RIC) produced in a dielectric by an electron beam was developed. The model, which assumes instantly-trapped holes, was then applied to experimental measurements on thin Kapton samples penetrated by an electron beam. Measurements at high bias were matched in the model by an appropriate choice for the trap-modulated electron mobility. A fractional split between front and rear currents measured at zone bias is explained on the basis of beam-scattering. The effects of carrier-enhanced conductivity (CEC) on data obtained for thick, free-surface Kapton samples is described by using an analytical model that incorporates field injection of carriers from the RIC region. The computer code, LWPCHARGE, modified for carrier transport, is also used to predict partial penetration effects associated with CEC in the unirradiated region. Experimental currents and surface voltages, when incorporated in the appropriate models, provide a value for the trap modulated mobility that is in essential agreement with the RIC results.

Meulenberg, A., Jr.↗

DOE OSTI2023

Hyper Suprime-Cam Year 3 results: Cosmology from galaxy clustering and weak lensing with HSC and SDSS using the minimal bias model

Here, we present cosmological parameter constraints from a blind joint analysis of three two-point correlation functions measured from the Year 3 Hyper Suprime-Cam (HSC-Y3) imaging data, covering about 416 deg 2 , and the SDSS DR11 spectroscopic galaxies spanning the redshift range [0.15, 0.70]. We subdivide the SDSS galaxies into three luminosity-cut, and therefore nearly volume-limited samples separated in redshift, each of which acts as a large-scale structure tracer characterized by the measurement of the projected correlation function, w p ⁡(R). We also use the measurements of the galaxy-galaxy weak-lensing signal Δ⁢Σ⁡(R) for each of these SDSS samples which act as lenses for a secure sample of source galaxies selected from the HSC-Y3 shape catalog based on their photometric redshifts. We combine these measurements with the cosmic shear correlation functions, ξ ± ⁡($\vartheta$) measured for our HSC source sample. We model these observables with the minimal bias model of the galaxy clustering observables in the context of a flat Λ⁢CDM cosmology. We use conservative scale cuts, R >12 and 8⁢ℎ -1 Mpc for Δ⁢Σ and w p , respectively, where the minimal bias model is valid, in addition to conservative prior on the residual bias in the mean redshift of the HSC photometric source galaxies. We present various validation tests of our model as well as analysis methods. Our baseline analysis yields S 8 = $0.77⁢5^{+0.043}_{-0.038}$ (68% C.I.) for the Λ⁢CDM model, after marginalizing over uncertainties in other parameters. Our value of S 8 is consistent with that from the Planck 2018 data, but the credible interval of our result is still relatively large. We show that various internal consistency tests based on different splits of the data are passed. Our results are statistically consistent with those of a companion paper, which extends this analysis to smaller scales with an emulator-based halo model, using Δ⁢Σ⁡(R) and w p ⁡(R) down to R >3 and 2⁢ℎ -1 Mpc, respectively.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1995

Telescience operations with the solar array module plasma interaction experiment

The Solar Array Module Plasma Interactions Experiment (SAMPIE) is a flight experiment that flew on the Space Shuttle Columbia (STS-62) in March 1994, as part of the OAST-2 mission. The overall objective of SAMPIE was to determine the adverse environmental interactions within the space plasma of low earth orbit (LEO) on modern solar cells and space power system materials which are artificially biased to high positive and negative direct current (DC) voltages. The two environmental interactions of interest included high voltage arcing from the samples to the space plasma and parasitic current losses. High voltage arcing can cause physical damage to power system materials and shorten expected hardware life. parasitic current losses can reduce power system efficiency because electric currents generated in a power system drain into the surrounding plasma via parasitic resistance. The flight electronics included two programmable high voltage DC power supplies to bias the experiment samples, instruments to measure the surrounding plasma environment in the STS cargo bay, and the on-board data acquisition system (DAS). The DAS provided in-flight experiment control, data storage, and communications through the Goddard Space Flight Center (GSFC) Hitchhiker flight avionics to the GSFC Payload Operations Control Center (POCC). The DAS and the SAMPIE POCC computer systems were designed for telescience operations; this paper will focus on the experiences of the SAMPIE team regarding telescience development and operations from the GSFC POCC during STS-62. The SAMPIE conceptual development, hardware design, and system verification testing were accomplished at the NASA Lewis Research Center (LeRC). SAMPIE was developed under the In-Space Technology Experiment Program (IN-STEP), which sponsors NASA, industry, and university flight experiments designed to enable and enhance space flight technology. The IN-STEP Program is sponsored by the Office of Space Access and Technology (OSAT).

Wald, Lawrence W.↗

NASA NTRS2018

Uncertainty in Heart Rate Complexity Metrics Caused by R-Peak Perturbations

Heart rate complexity (HRC) is a proven metric for gaining insight into human stress and physiological deterioration. To calculate HRC, the detection of the exact instance of when the heart beats, the R-peak, is necessary. Electrocardiogram (ECG) signals can often be corrupted by environmental noise (e.g., from electromagnetic interference, movement artifacts), which can potentially alter the HRC measurement, producing erroneous inputs which feed into decision support models. Current literature has only investigated how HRC is affected by noise when R-peak detection errors occur (false positives and false negatives). However, the numerical methods used to calculate HRC are also sensitive to the specific location of the fiducial point of the R-peak. This raises many questions regarding how this fiducial point is altered by noise, the resulting impact on the measured HRC, and how we can account for noisy HRC measures as inputs into our decision models. This work uses Monte Carlo simulations to systematically add white and pink noise at different permutations of signal-to-noise ratios (SNRs), time segments, sampling rates, and HRC measurements to characterize the influence of noise on the HRC measure by altering the fiducial point of the R-peak. Using the generated information from these simulations provides improved decision processes for system design which address key concerns such as permutation entropy being a more precise, reliable, less biased, and more sensitive measurement for HRC than sample and approximate entropy.

Napoli, Nicholas J.↗

DOE OSTI2023

The stellar mass of the Gaia -Sausage/Enceladus accretion remnant

The Gaia-Sausage/Enceladus (GS/E) structure is an accretion remnant that comprises a large fraction of the Milky Way’s stellar halo. We study GS/E using high-purity samples of kinematically selected stars from APOGEE DR16 and Gaia. Employing a novel framework to account for kinematic selection biases using distribution functions, we fit density profiles to these GS/E samples and measure their masses. We find that GS/E has a shallow density profile in the inner Galaxy, with a break between 15 and 25 kpc beyond which the profile steepens. We also find that GS/E is triaxial, with axis ratios 1:0.55:0.45 (nearly prolate), and the major axis is oriented about 80° from the Sun–Galactic centre line and 16° above the plane. We measure a stellar mass for GS/E of $1.45\, ^{+0.92}_{-0.51}\, \mathrm{(stat.)}\, ^{+0.13}_{-0.37} \mathrm{(sys.)}\ \times 10^{8}$ M ⊙ . Our mass estimate is lower than others in the literature, a finding we attribute to the excellent purity of the samples we work with. We also fit a density profile to the entire Milky Way stellar halo, finding a mass in the range of 6.7–8.4 × 10 8 M ⊙ , and implying that GS/E could make up as little as 15–25 per cent of the mass of the Milky Way stellar halo. Our lower stellar mass combined with standard stellar mass-to-halo mass relations implies that GS/E constituted a minor 1:8 mass-ratio merger at the time of its accretion.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRSDate not supplied

Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

NASA’s GeneLab, part of the NASA Open Science Data Repository, is a space-related database that hosts a diverse range of transcriptomics, proteomics, epigenomics and genomics data. The NASA GeneLab Sample Processing Laboratory (SPL) generates omics data from biological experiments conducted aboard the International Space Station, Space Shuttle and space related ground experiments, this omics data then hosted on the GeneLab repository. Samples generated such experiments pose numerous technical challenges such as small experimental sample size, variance in dissection times, limited tissue preservation methods, prolonged storage time, and more. GeneLab SPL team had developed specialized expertise in nucleic acid extraction, library preparation and sequencing of such biological samples via extensive training and years of experience. In order to ensure data accuracy and consistency across experiments, SPL has developed standardized protocols for each species and tissue type. These protocols in conjunction with quality control metrics and data standards are crucial in generating of high-quality data. SPL protocols and standards have been developed in collaboration with the scientific community and had been made publicly available on the GeneLab portal, guaranteeing comparability of datasets across spaceflight experiments. To ensure reliability of data generation, SPL leverages cutting-edge innovations in laboratory automation for sample processing. By leveraging these state-of-the-art platforms, SPL achieves high levels of data reproducibility while significantly minimizing sources of bias and variability, especially across experiments with large numbers of samples. Over the past few years, the space biology investigator community has accessed SPL-generated data from the Open Science Data Repository for a myriad of data re-analysis and re-use studies. We observe a trend that in-house SPL-generated data consistently outperforms outsourced sequencing data in terms of technical standards, quality control metrics, timeliness of data delivery, and sequencing and reagent efficiency. Superior data generation has and will continue to enable discoveries in disease, diagnostic tools, and the biological effects of long duration spaceflight.

GeneLab↗

NASA NTRSDate not supplied

Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

GeneLab↗

NASA NTRS1985

Submillimeter wave absorption of n-type InSb at low temperatures

The absorption coefficient of two high-purity n-InSb samples is measured in the 10-40 per cm range using Fourier transform spectroscopy. The absorption coefficient spectrum is presented for both samples at 4.2 K. It is also shown for the lower resistance sample cooled to 2.2 K and heated by dc bias to elevated electron gas temperatures of 7.5 and 17.9 K. ac Drude theory gives rather poor agreement with experiment at 2.2 and 4.2 K but does much better when the sample electron gas is heated. In contrast, a simple quantum mechanical theory of absorption based on inverse Bremsstrahlung yields promising agreement at the lower temperatures although its applicability is questionable. The non-Drudian absorption is shown to have a favorable effect on the performance of InSb hot-electron bolometers.

Brown, E. R.↗

DOE OSTI2026

A spatiotemporally explicit and scalable indicator of intact lands across the conterminous United States, 1986–2023

Globally, ecologically intact areas are increasingly scarce. Agricultural expansion into previously uncultivated areas drives the loss of intact lands that might otherwise exhibit high levels of ecological integrity. Thus, the absence of cultivation can be an indicator of intact lands as measured from remote sensing data and thematic maps. Our objective for this study was to develop and compare tractable approaches based on remotely sensed satellite data to map spatial patterns of potentially intact lands across the conterminous U.S. (CONUS). Using annual cultivation probabilities derived from satellite observations, we classified and mapped potentially intact lands across CONUS from 1986 to 2023 at 30 m resolution. We created three maps, first by applying a constant cultivation probability threshold across CONUS, second by varying the threshold state-by-state to maximize state-level overall accuracies, and third by equalizing the state-level user's and producer's accuracies to minimize classification bias. Validation against 800,000+ independent ground samples resulted in CONUS-level overall accuracies ≥85% for the roughly 660 million ha of potentially intact land. Map accuracy varied with the proportion of potentially intact lands across regions, with the Pacific-Mountain and Great Plains regions exhibiting the highest accuracies, while Eastern CONUS exhibited a greater mix of potentially intact and non-intact lands and more moderate map accuracies. These novel maps and approaches can be adapted to different spatiotemporal extents to support conservation and production decisions ranging from species and ecosystems protection to reducing land conversion and climate mitigation.

agriculture↗

DOE OSTI2025

Deciphering the Scattering of Mechanically Driven Polymers Using Deep Learning

Here, we present a deep learning approach for analyzing two-dimensional scattering data of semiflexible polymers under external forces. In our framework, scattering functions are compressed into a three-dimensional latent space using a Variational Autoencoder (VAE), and two converter networks establish a bidirectional mapping between the polymer parameters (bending modulus, stretching force, and steady shear) and the scattering functions. The training data are generated using off-lattice Monte Carlo simulations to avoid the orientational bias inherent in lattice models, ensuring robust sampling of polymer conformations. The feasibility of this bidirectional mapping is demonstrated by the organized distribution of polymer parameters in the latent space. By integrating the converter networks with the VAE, we obtain a generator that produces scattering functions from given polymer parameters and an inferrer that directly extracts polymer parameters from scattering data. While the generator can be utilized in a traditional least-squares fitting procedure, the inferrer produces comparable results in a single pass and operates 3 orders of magnitude faster. This approach offers a scalable automated tool for polymer scattering analysis and provides a promising foundation for extending the method to other scattering models, experimental validation, and the study of time-dependent scattering data.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2025

Studying baryon acoustic oscillations using photometric redshifts from the DESI Legacy Imaging survey DR9

Context. The Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Survey DR9 (DR9 hereafter), with its extensive dataset of galaxy locations and photometric redshifts, presents an opportunity to study baryon acoustic oscillations (BAOs) in the region covered by the ongoing spectroscopic survey with DESI. Aims. We aim to investigate differences between different parts of the DR9 footprint. Furthermore, we want to measure the BAO scale for luminous red galaxies within them. Our selected redshift range of 0.6–0.8 corresponds to the bin in which a tension between DESI Y1 and eBOSS was found. Methods. We calculated the anisotropic two-point correlation function in a modified binning scheme to detect the BAOs in DR9 data. We then used template fits based on simulations to measure the BAO scale in the imaging data. Results. Our analysis reveals the expected correlation function shape in most of the footprint areas, showing a BAO scale consistent with Planck’s observations. Aside from identified mask-related data issues in the southern region of the South Galactic Cap, we find a notable variance between the different footprints. Conclusions. We find that this variance is consistent with the difference between the DESI Y1 and eBOSS data, and it supports the argument that that tension is caused by sample variance. Additionally, we also uncovered systematic biases not previously accounted for in photometric BAO studies. We emphasize the necessity of adjusting for the systematic shift in the BAO scale associated with typical photometric redshift uncertainties to ensure accurate measurements.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Seeing through noise in power laws

Despite widespread claims of power laws across the natural and social sciences, evidence in data is often equivocal. Modern data and statistical methods reject even classic power laws such as Pareto’s law of wealth and the Gutenberg–Richter law for earthquake magnitudes. We show that the maximum-likelihood estimators and Kolmogorov–Smirnov (K-S) statistics in widespread use are unexpectedly sensitive to ubiquitous errors in data such as measurement noise, quantization noise, heaping and censorship of small values. This sensitivity causes spurious rejection of power laws and biases parameter estimates even in arbitrarily large samples, which explains inconsistencies between theory and data. We show that logarithmic binning by powers of λ > 1 attenuates these errors in a manner analogous to noise averaging in normal statistics and that λ thereby tunes a trade-off between accuracy and precision in estimation. Binning also removes potentially misleading within-scale information while preserving information about the shape of a distribution over powers of λ, and we show that some amount of binning can improve sensitivity and specificity of K-S tests without any cost, while more extreme binning tunes a trade-off between sensitivity and specificity. We therefore advocate logarithmic binning as a simple essential step in power-law inference.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2026

Imaging systematics induced by galaxy subsample fluctuation: New systematics at second order

Imaging systematics refers to the inhomogeneous distribution of a galaxy sample caused by varying observing conditions and astrophysical foregrounds. Current mitigation methods correct the galaxy density fluctuations $n$ gal /$\bar{n}$ gal caused by imaging systematics assuming that all galaxies in a sample have the same $n$ gal /$\bar{n}$ gal . Under this assumption, the corrected sample cannot perfectly recover the true correlation function. Here, we name this effect subsample systematics. For a galaxy sample, even if its overall sample statistics [redshift distribution 𝑛⁡(𝑧), galaxy bias 𝑏⁡(𝑧)], are accurately measured, 𝑛⁡(𝑧), 𝑏⁡(𝑧) can still vary across the observed footprint. It makes the correlation function amplitude of galaxy clustering higher, while correlation functions for galaxy-galaxy lensing and cosmic shear do not have noticeable change. Such a combination could potentially degenerate with physical signals on small angular scales, such as the amplitude of galaxy clustering, the impact of neutrino mass on the matter power spectrum, etc. subsample systematics cannot be corrected using imaging systematics mitigation approaches that rely on the cross-correlation signal between imaging systematics maps and the observed galaxy density field. In this paper, we derive formulated expressions of subsample systematics, demonstrating its fundamental difference with other imaging systematics. We also provide several toy models to visualize this effect. Finally, we discuss a potential method to estimate and mitigate subsample systematics by forward modeling its behavior using synthetic source injection.

Kong, Hui [The Barcelona Institute of Science and ↗

DOE OSTI2022

A Systematic Review and Meta-Analysis of Tai Chi Training in Cardiorespiratory Fitness of Elderly People

Objectives. The purpose of this study was to investigate the influence of Tai Chi on cardiorespiratory fitness (CRF) in elderly people using meta-analysis. Methods. This study used seven electronic databases and data retrieved from randomized controlled trials (RCTs) investigating the role of Tai Chi on CRF in the elderly. All these 24 RCTs were screened and selected from 7 literature databases. The Stata 11.2 software (StataCorp, USA) was used for the meta-analysis, subgroup analysis, and bias test, while the Cochrane Collaboration’s tool was used for the assessment of the risk of bias (RoB). 4 researchers independently participated in sample selection, data extraction, and RoB assessment. Results. Following the inclusion criteria, 24 eligible studies were included in our analysis. The meta-analysis indicated that Tai Chi practice significantly increased the maximum rate of oxygen consumption (VO2 max) (weighted mean difference (WMD) = 3.76, 95% CI: 1.25 to 6.26, P < 0.1 ), leading to an overall reduction in the heart rate (HR) (WMD = −1.84, 95% CI: −2.04 to −1.63, P ≤ 0.001 ) and an increase in the O2 pulse (WMD = 0.94, 95% CI: 0.60 to 1.28, P ≤ 0.001 ) in individuals who practiced Tai Chi regularly compared with those who did not. The subgroup analysis suggested that overall in those who practiced Tai Chi, males (WMD = 1.48, 95% CI: 0.85 to 2.12, P ≤ 0.001 ) had higher O2 pulse than females (WMD = 0.73, 95% CI: 0.33 to 1.12, P ≤ 0.001 ). The subgroup analysis also showed an increase in the vital capacity (VC) (WMD = 316.05, 95% CI: 239.74 to 392.35, P ≤ 0.001 ) in individuals practicing Tai Chi. When the samples were further stratified by Tai Chi practicing time, the subgroup analysis suggested that individuals practicing Tai Chi over a period of 24 weeks showed no significant difference in VC (WMD = 82.95, 95% CI: -98.34 to 264.23, P = 0.370 ), while those practicing Tai Chi over a period of 48 weeks showed a significant increase (WMD = 416.62, 95% CI: 280.68 to 552.56, P ≤ 0.001 ). Furthermore, the subgroup analysis demonstrated that the increase in VC is significantly correlated with the Tai Chi practicing time (WMD = 344.97, 95% CI: 227.88 to 442.06, P ≤ 0.001 ). Conclusion. Regular Tai Chi practice could improve the CRF in the elderly, as indicated by significant improvement in indicators including VO2max, O2pulse, VC, and HR. However, gender and practice time might influence the overall beneficial outcomes.

Tan, Tianyang↗