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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes ( i.e ., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg .

Lui, Lauren↗
DOE OSTI2025

LaBr 3 : Ce self-activation analysis for measuring fast neutron fields

Measurement of the fast neutron production rate in deuterium–tritium (D–T) fusion reactions is important for applications such as active interrogation, fusion diagnostics, and borehole logging. Such measurements are typically performed by neutron activation analysis of metal foils, especially copper. Copper foil activation analysis requires efficiency and energy calibrations of the detector used to measure the foil, and it relies on the detection of 511 keV gamma rays, which are prominent in the active background when neutrons are being produced. Alternatives, such as 79m Br produced by inelastic neutron scattering on 79 Br, are limited by short half-life, low-energy gamma emission, and inability to selectively measure D–T neutrons. This work describes a novel alternative approach to measure ≳10 MeV neutron fields based on self-activation analysis of a LaBr 3 :Ce detector. The activity of 78 Br, the activation product of the 79 Br(n,2n) 78 Br reaction, is used to determine the neutron flux and infer the neutron production rate. We experimentally demonstrate the method with a cylindrical LaBr 3 :Ce crystal with a diameter and height of 3.81 cm that was placed at an ~18 cm distance from the neutron production point, at a 90° angle with respect to the deuteron beam in a D–T neutron generator. Operating voltage and current of the generator were adjusted to evaluate the technique’s performance over a nominal generator output range of approximately (1 - 9) x 10 7 n/s. The neutron output obtained from LaBr 3 :Ce activation agrees to within three standard deviations of the output obtained using copper activation. The self-activation technique can be conveniently employed in a variety of applications to simplify measurements of fast neutrons produced in D–T fusion reactions.

Active interrogationLaBr3↗
DOE OSTI2022

An ontology-based fault generation and fault propagation analysis approach for safety-critical computer systems at the design stage

Abstract Fault propagation analysis is a process used to determine the consequences of faults residing in a computer system. A typical computer system consists of diverse components (e.g., electronic and software components), thus, the faults contained in these components tend to possess diverse characteristics. How to describe and model such diverse faults, and further determine fault propagation through different components are challenging problems to be addressed in the fault propagation analysis. This paper proposes an ontology-based approach, which is an integrated method allowing for the generation, injection, and propagation through inference of diverse faults at an early stage of the design of a computer system. The results generated by the proposed framework can verify system robustness and identify safety and reliability risks with limited design level information. In this paper, we propose an ontological framework and its application to analyze an example safety-critical computer system. The analysis result shows that the proposed framework is capable of inferring fault propagation paths through software and hardware components and is effective in predicting the impact of faults.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Estimating Soil Thermal Inertia Profiles From the Passive Equilibration of a Temperature Probe

Knowledge of the distribution of soil thermal properties is important for understanding subsurface hydrological and biogeochemical processes. This study describes and evaluates quick thermal profiling (QTP), a new measurement technique aimed at providing rapid, depth-resolved measurements of soil thermal inertia at numerous locations across the landscape. A cylindrical probe with temperature sensors at multiple depths is quickly inserted into the ground, and soil thermal inertia is estimated from how quickly the probe temperature equilibrates with the soil. To this end, a finite volume heat transfer model is used to generate temperature equilibration time series across combinations of controlling factors, and a gridded search inversion approach is applied to infer soil thermal inertia. Field tests in the Arctic indicate that QTP measurements have a minimum uncertainty of 0.14 J m −2 K −1 s −1/2 and covary with dual-probe heat pulse thermal analyzer measurements (concordance correlation coefficient = 0.56) with a root-mean-square error of 0.40 J m −2 K −1 s −1/2 . Besides demonstrating the value of QTP for estimating thermal inertia, this study identifies various sources of measurement uncertainty, particularly probe-soil contact resistance and frictional heating. Further, analysis of soil samples indicates that thermal inertia can be used to estimate thermal conductivity and dry bulk density in the studied area, although such inferences are highly site-specific. Overall, the QTP method holds promise to generate thermal inertia data products and to complement other characterization approaches for advancing understanding of soil properties across far more locations than is currently possible.

Lamb, J. R. [Lawrence Berkeley National Laboratory↗
DOE OSTI2023

Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa

In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2–7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya’s Brucellosis Control Policy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Detectable ship tracks account for just 5% of aerosol indirect forcing from ship emissions

Ship emissions are a major source of aerosols over oceans, affecting both air quality and energy balance of the climate. However, estimates of their climate forcing diverge between studies relying on visible ship-tracks and those based on models. Here we show that forcing due to visible ship-tracks accounts for just 5% of the total forcing over the southeast Atlantic shipping-lane. Most forcing from ship emissions comes from aerosols that do not form detectable ship-tracks. They are only tips of the iceberg. We make three forcing calculations, one bottom-up based on visible ship-tracks, one top-down based on spatial relationships, and a hybrid approach that combines top-down or model estimated cloud droplet number concentration changes and cloud adjustments. Although the forcing based on machine learning detected ship tracks is an order of magnitude greater than prior results using manually detected ship-tracks, it remains only 5% of that inferred by top-down or cloud adjustment based methods for pre-2020 shipping. The top-down and the combined cloud adjustments methods show similar forcing for the post-2020 reduction in ships’ sulfur emission, although the methods have important regional differences in cloud adjustments that need further investigation. Our results reconcile a long-standing discrepancy in the literature and have important implications for aerosol indirect forcing and marine cloud brightening.

Yuan, Tianle [NASA Goddard Space Flight Center (GS↗
DOE OSTI2017

Complete fold annotation of the human proteome using a novel structural feature space

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Inferring dark matter substructure with astrometric lensing beyond the power spectrum

Abstract Astrometry—the precise measurement of positions and motions of celestial objects—has emerged as a promising avenue for characterizing the dark matter population in our Galaxy. By leveraging recent advances in simulation-based inference and neural network architectures, we introduce a novel method to search for global dark matter-induced gravitational lensing signatures in astrometric datasets. Our method based on neural likelihood-ratio estimation shows significantly enhanced sensitivity to a cold dark matter population and more favorable scaling with measurement noise compared to existing approaches based on two-point correlation statistics. We demonstrate the real-world viability of our method by showing it to be robust to non-trivial modeled as well as unmodeled noise features expected in astrometric measurements. This establishes machine learning as a powerful tool for characterizing dark matter using astrometric data.

convolutional neural networks (1938)↗
DOE OSTI2024

The hyperplane of early-type galaxies: using stellar population properties to increase the precision and accuracy of the fundamental plane as a distance indicator

ABSTRACT We use deep spectroscopy from the SAMI (Sydney-AAO Multi-object Integral) Galaxy Survey to explore the precision of the fundamental plane (FP) of early-type galaxies as a distance indicator for future single-fibre spectroscopy surveys. We study the optimal trade-off between sample size and signal-to-noise ratio (SNR), and investigate which additional observables can be used to construct hyperplanes with smaller intrinsic scatter than the FP. We add increasing levels of random noise (parametrized as effective exposure time) to the SAMI spectra to study the effect of increasing measurement uncertainties on the FP- and hyperplane-inferred distances. We find that, using direct-fit methods, the values of the FP and hyperplane best-fitting coefficients depend on the spectral SNR, and reach asymptotic values for a mean $\langle \mathrm{ SNR} \rangle =40\, \mathrm{\mathring{\rm A}}^{-1}$. As additional variables for the FP we consider three stellar-population observables: light-weighted age, stellar mass-to-light ratio, and a novel combination of Lick indices ($I_\mathrm{age}$). For an $\langle \mathrm{ SNR} \rangle =45~\mathrm{\mathring{\rm A}}^{-1}$ (equivalent to 1-h exposure on a 4-m telescope), all three hyperplanes outperform the FP as distance indicators. Being an empirical spectral index, $I_\mathrm{age}$ avoids the model-dependent uncertainties and bias underlying age and mass-to-light ratio measurements, yet yields a 10 per cent reduction of the median distance uncertainty compared to the FP. We also find that, as a by-product, the $I_\mathrm{age}$ hyperplane removes most of the reported environment bias of the FP. After accounting for the different SNR, these conclusions also apply to a 50 times larger sample from SDSS-III (Sloan Digital Sky Survey). However, in this case, only $\mathrm{ age}$ removes the environment bias.

D’Eugenio, Francesco (ORCID:0000000323888172)↗
DOE OSTI2024

Feature-agnostic metabolomics for determining effective subcytotoxic doses of common pesticides in human cells

Although classical molecular biology assays can provide a measure of cellular response to chemical challenges, they rely on a single biological phenomenon to infer a broader measure of cellular metabolic response. These methods do not always afford the necessary sensitivity to answer questions of subcytotoxic effects, nor do they work for all cell types. Likewise, boutique assays such as cardiomyocyte beat rate may indirectly measure cellular metabolic response, but they too, are limited to measuring a specific biological phenomenon and are often limited to a single cell type. For these reasons, toxicological researchers need new approaches to determine metabolic changes across various doses in differing cell types, especially within the low-dose regime. Here, the data collected herein demonstrate that LC-MS/MS-based untargeted metabolomics with a feature-agnostic view of the data, combined with a suite of statistical methods including an adapted environmental threshold analysis, provides a versatile, robust, and holistic approach to directly monitoring the overall cellular metabolomic response to pesticides. When employing this method in investigating two different cell types, human cardiomyocytes and neurons, this approach revealed separate subcytotoxic metabolomic responses at doses of 0.1 and 1 µM of chlorpyrifos and carbaryl. These findings suggest that this agnostic approach to untargeted metabolomics can provide a new tool for determining effective dose by metabolomics of chemical challenges, such as pesticides, in a direct measurement of metabolomic response that is not cell type-specific or observable using traditional assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Magnetic dipole γ-ray strength functions in the crossover from spherical to deformed neodymium isotopes

We calculate the magnetic dipole $\gamma$-ray strength functions in a chain of even-mass neodymium isotopes $^{144-152}$Nd in the framework of the configuration-interaction (CI) shell model. We infer the strength function by applying the maximum entropy method (MEM) to the exact imaginary-time response function calculated with the shell-model Monte Carlo (SMMC) method. The success of the MEM depends on the choice of a good strength function as a prior distribution. We investigate two choices for the prior strength function: the static path approximation (SPA) and the quasiparticle random-phase approximation (QRPA). We find that the QRPA is a better approximation at low temperatures (i.e., near the ground state), while the SPA is a better choice at finite temperatures. We identify a low-energy enhancement (LEE) in the MEM deexcitation $M1$ strength functions of the even-mass neodymium isotopes and compare with recent experimental results for the total deexcitation $\gamma$-ray strength functions. The LEE is already seen in the SPA strength function but not in the QRPA strength function, indicating the importance of large-amplitude static fluctuations around the mean field in reproducing the LEE. Our method is currently the only one which can reproduce LEE in heavy open-shell nuclei where conventional CI shell model calculations are prohibited. With the onset of deformation as number of neutrons increases along the chain of neodymium isotopes, we observe that some of the LEE strength transfers to a low-energy excitation, which we interpret as a finite-temperature ``scissors'' mode. Here, we also observe a finite-temperature spin-flip mode.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

A comparison of histopathology imaging comprehension algorithms based on multiple instance learning

Whole slide imaging (WSI), also called digital virtual microscopy, is a new imaging modality. It allows for the application of AI and machine learning methods to cancer pathology to help establish a means for the automatic diagnosis of cancer cases. However, designing machine-learning models for WSI is computationally challenging due to its required ultra-high resolution. The current state-of-the-art models use multiple instance learning (MIL). MIL is a weakly-supervised learning method in which the model uses an array of inferences from many smaller instances to make a final classification about the entire set. In the context of WSI, researchers divide the ultra-high-resolution image into many patches. The model then classifies the slide based on an array of inferences from the patches. Among several ways of making the final classification, attention-based mechanisms have resulted in superb accuracy scores. The Transformer, one attention-based algorithm, has reported substantial improvements for WSI comprehension tasks. In this project, we studied and compared several WSI comprehension algorithms. We used the following three datasets: CAMELYON16+17, TCGALung, and TCGA-Kidney. We found that attention-based MIL algorithms performed better than standard MIL algorithms for classifying WSI images, achieving a higher mean accuracy and AUC. However, none of the attention-based algorithms performed significantly better than the others, reporting accuracy scores that varied widely. Presumably, it is due to the limited availability of training samples in the data corpus. Since it is not easy to increase the samples from human subjects, some machine learning techniques like transfer learning could help mitigate this issue.

Saunders, Adam↗
DOE OSTI2019

Toward a Better Understanding of Species Interactions through Network Biology

Within the last decade, there has been an explosion of multi-omics data generated for several microbial systems. At the same time, new methods of analysis have emerged that are based on inferring networks that link features both within and between species based on correlation in abundance. These developments prompt two important questions. What can be done with network approaches to better understand microbial species interactions? What challenges remain in applying network approaches to query the more complex systems of natural settings? Here, I briefly describe what has been done and what questions still need to be answered. Over the next 5 to 10 years, we will be in a strong position to infer networks that contain multiple kinds of omic data and describe systems with multiple species. These applications will open the door for a better understanding and use of microbiomes across a variety of fields.

Microbiology↗
DOE OSTI2021

The Attraction Indian Buffet Distribution

We propose the attraction Indian buffet distribution (AIBD), a distribution for binary feature matrices influenced by pairwise similarity information. Binary feature matrices are used in Bayesian models to uncover latent variables (i.e., features) that explain observed data. The Indian buffet process (IBP) is a popular exchangeable prior distribution for latent feature matrices. In the presence of additional information, however, the exchangeability assumption is not reasonable or desirable. The AIBD can incorporate pairwise similarity information, yet it preserves many properties of the IBP, including the distribution of the total number of features. Thus, much of the interpretation and intuition that one has for the IBP directly carries over to the AIBD. A temperature parameter controls the degree to which the similarity information affects feature-sharing between observations. Unlike other nonexchangeable distributions for feature allocations, the probability mass function of the AIBD has a tractable normalizing constant, making posterior inference on hyperparameters straight-forward using standard MCMC methods. A novel posterior sampling algorithm is proposed for the IBP and the AIBD. We demonstrate the feasibility of the AIBD as a prior distribution in feature allocation models and compare the performance of competing methods in simulations and an application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

ExtremeMETA: High-speed Lightweight Image Segmentation Model by Remodeling Multi-channel Metamaterial Imagers

Deep neural networks (DNNs) have heavily relied on traditional computational units, such as CPUs and GPUs. However, this conventional approach brings significant computational burden, latency issues, and high power consumption, limiting their effectiveness. This has sparked the need for lightweight networks such as ExtremeC3Net. Meanwhile, there have been notable advancements in optical computational units, particularly with metamaterials, offering the exciting prospect of energy-efficient neural networks operating at the speed of light. Yet, the digital design of metamaterial neural networks (MNNs) faces precision, noise, and bandwidth challenges, limiting their application to intuitive tasks and low-resolution images. In this study, we proposed a large kernel lightweight segmentation model, ExtremeMETA. Based on ExtremeC3Net, our proposed model, ExtremeMETA maximized the ability of the first convolution layer by exploring a larger convolution kernel and multiple processing paths. With the large kernel convolution model, we extended the optic neural network application boundary to the segmentation task. To further lighten the computation burden of the digital processing part, a set of model compression methods was applied to improve model efficiency in the inference stage. The experimental results on three publicly available datasets demonstrated that the optimized efficient design improved segmentation performance from 92.45 to 95.97 on mIoU while reducing computational FLOPs from 461.07 MMacs to 166.03 MMacs. The large kernel lightweight model ExtremeMETA showcased the hybrid design’s ability on complex tasks.

large convolution kernel↗
DOE OSTI2017

Non-negative Matrix Factorization for Self-calibration of Photometric Redshift Scatter in Weak-lensing Surveys

Photo- z error is one of the major sources of systematics degrading the accuracy of weak-lensing cosmological inferences. Zhang et al. proposed a self-calibration method combining galaxy–galaxy correlations and galaxy–shear correlations between different photo- z bins. Fisher matrix analysis shows that it can determine the rate of photo- z outliers at a level of 0.01%–1% merely using photometric data and do not rely on any prior knowledge. In this paper, we develop a new algorithm to implement this method by solving a constrained nonlinear optimization problem arising in the self-calibration process. Based on the techniques of fixed-point iteration and non-negative matrix factorization, the proposed algorithm can efficiently and robustly reconstruct the scattering probabilities between the true- z and photo- z bins. The algorithm has been tested extensively by applying it to mock data from simulated stage IV weak-lensing projects. We find that the algorithm provides a successful recovery of the scatter rates at the level of 0.01%–1%, and the true mean redshifts of photo- z bins at the level of 0.001, which may satisfy the requirements in future lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

COol Companions ON Ultrawide orbiTS (COCONUTS). I. A High-gravity T4 Benchmark around an Old White Dwarf and a Re-examination of the Surface-gravity Dependence of the L/T Transition

We present the first discovery from the COol Companions ON Ultrawide orbiTS (COCONUTS) program, a large-scale survey for wide-orbit planetary and substellar companions. We have discovered a comoving system COCONUTS-1, composed of a hydrogen-dominated white dwarf (PSO J058.9855+45.4184; d = 31.5 pc) and a T4 companion (PSO J058.9869+45.4296) at a 40farcs6 (1280 au) projected separation. We derive physical properties for COCONUTS-1B from (1) its near-infrared spectrum using cloudless Sonora atmospheric models, and (2) its luminosity and the white dwarf's age (${7.3}_{-1.6}^{+2.8}$ Gyr) using Sonora evolutionary models. The two methods give consistent temperatures and radii, but atmospheric models infer a lower surface gravity and therefore an unphysically young age. Assuming evolutionary model parameters (${T}_{\mathrm{eff}}={1255}_{-8}^{+6}$ K, $\mathrm{log}\,g={5.44}_{-0.03}^{+0.02}$ dex, $R={0.789}_{-0.005}^{+0.011}$ ${R}_{\mathrm{Jup}}$), we find that cloudless model atmospheres have brighter Y- and J-band fluxes than the data, suggesting that condensate clouds have not fully dispersed around 1300 K. The W2 flux (4.6 μm) of COCONUTS-1B is fainter than models, suggesting non-equilibrium mixing of CO. To investigate the gravity dependence of the L/T transition, we compile all 60 known L6-T6 benchmarks and derive a homogeneous set of temperatures, surface gravities, and masses. As is well known, young, low-gravity late-L dwarfs have significantly fainter, redder near-infrared photometry and ≈200–300 K cooler temperatures than old, high-gravity objects. Our sample now reveals such gravity dependence becomes weaker for T dwarfs, with young objects having comparable near-infrared photometry and ≈100 K cooler temperatures compared to old objects. Finally, we find that young objects have a larger amplitude J-band brightening than old objects, and also brighten at H band as they cross the L/T transition.

79 ASTRONOMY AND ASTROPHYSICS↗