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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Decoding substance use disorder severity from clinical notes using a large language model

Substance use disorder (SUD) poses a major concern due to its detrimental effects on health and society. SUD identification and treatment depend on a variety of factors such as severity, co-determinants (e.g., withdrawal symptoms), and social determinants of health. Existing diagnostic coding systems used by insurance providers, like the International Classification of Diseases (ICD-10), lack granularity for certain diagnoses, but American clinicians will add this granularity (as that found within the Diagnostic and Statistical Manual of Mental Disorders classification or DSM-5) as supplemental unstructured text in clinical notes. Traditional natural language processing (NLP) methods face limitations in accurately parsing such diverse clinical language. Large language models (LLMs) offer promise in overcoming these challenges by adapting to diverse language patterns. This study investigates the application of LLMs for extracting severity-related information for various SUD diagnoses from clinical notes. We propose a workflow employing zero-shot learning of LLMs with carefully crafted prompts and post-processing techniques. Through experimentation with Flan-T5, an open-source LLM, we demonstrate its superior recall compared to the rule-based approach. Focusing on 11 categories of SUD diagnoses, we show the effectiveness of LLMs in extracting severity information, contributing to improved risk assessment and treatment planning for SUD patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Decoding NGC 7252 as a blue elliptical galaxy

Elliptical galaxies with blue optical colours and significant star formation are hypothesised to be major merger remnants of gas-rich spiral galaxies or normal elliptical galaxies with a sudden burst of star formation. We present here a scenario in which blue elliptical galaxies identified in shallow imaging surveys may fail to recover faint features that are indicative of past merger activity using a nearby major merger remnant. Based on deep optical imaging data of the post-merger galaxy, NGC 7252, we demonstrate that the galaxy can appear as an elliptical galaxy if it is observed at higher redshifts. The main body and the low surface brightness merger features found at the outskirts of the galaxy are blue in the optical g – r colour map. We argue that the higher-redshift blue elliptical galaxies discovered in surveys as shallow as the SDSS or DECaLS may be advanced mergers whose defining tidal features fall below the detection limits of the surveys. This should be taken into consideration during the morphological classification of these systems in future and ongoing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Decoding the formation of hammerhead ion populations observed by Parker Solar Probe

Context. In situ observations by the Parker Solar Probe (PSP) have revealed new properties of the proton velocity distributions (VDs), including hammerhead features that suggest a non-isotropic broadening of the beams. Aims. The present work proposes a very plausible explanation for the formation of hammerhead proton populations through the action of a proton firehose-like instability triggered by the proton beam. Methods. We investigated a self-generated firehose-like instability driven by the relative drift of ion populations using a simplified moment-based quasi-linear (QL) theory. While simpler and faster than advanced numerical simulations, this toy model provided rapid insights and concisely highlighted the role of plasma micro-instabilities in relaxing the observed anisotropies of particle VDs in the solar wind and space plasmas. Results. The QL theory proposed here shows that the resulting transverse waves are right-hand polarized and have two consequences on the protons: (i) They reduce the relative drift between the beam and the core, but above all, (ii) they induce a strong perpendicular temperature anisotropy specific to the observed hammerhead ion beam. Moreover, the long-run QL results suggest that these hammerhead distributions are rather transitory states that are still subject to relaxation mechanisms, in which instabilities such as the one discussed here are very likely involved. This foundational work motivates future detailed studies using advanced methods.

Shaaban, Shaaban M. (ORCID:000000030465598X)↗
DOE OSTI2020

Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

The aqueous proton is a common and long-studied species in chemistry, yet there is currently intense interest devoted to understanding its hydration structure and transport dynamics. Typically described in terms of two limiting structures observed in gas-phase clusters, the Zundel H 5 O 2 + and Eigen H 9 O 4 + ions, the aqueous structure is less clear due to the heterogeneity of hydrogen bonding environments and room-temperature structural fluctuations in water. The linear infrared (IR) spectrum, which reports on structural configurations, is challenging to interpret because it appears as a continuum of absorption, and the underlying vibrational modes are strongly anharmonically coupled to each other. Recent two-dimensional IR (2D IR) experiments presented strong evidence for asymmetric Zundel-like motifs in solution, but true structure–spectrum correlations are missing and complicated by the anharmonicity of the system. In this study, we employ high-level vibrational self-consistent field/virtual state configuration interaction calculations to demonstrate that the 2D IR spectrum reports on a broad distribution of geometric configurations of the aqueous proton. We find that the diagonal 2D IR spectrum around 1200 cm –1 is dominated by the proton stretch vibrations of Zundel-like and intermediate geometries, broadened by the heterogeneity of aqueous configurations. There is a wide distribution of multidimensional potential shapes for the proton stretching vibration with varying degrees of potential asymmetry and confinement. In conclusion, we find specific cross peak patterns due to aqueous Zundel-like species. These studies provide clarity on highly debated spectral assignments and stringent spectroscopic benchmarks for future simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Decoding diffraction and spectroscopy data with machine learning: A tutorial

This Tutorial provides a step-by-step guide on how to apply supervised machine-learning techniques to analyze diffraction and spectroscopy data. This Tutorial details four models—a reconstruction-focused model, a regression-focused model, a hybrid reconstruction/regression model, and a multimodal model—that use x-ray diffraction profiles and vibrational density of states spectra to predict various microstructural descriptors. In this Tutorial, we cover data pre-processing steps, constructions of the models via dimensionality reduction and regression, training, and analysis of these models. Comparisons of the model’s performance are provided, highlighting the strength and weakness of the various approaches utilized.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Decoding ultrafast polarization responses in lead halide perovskites by the two-dimensional optical Kerr effect

Significance Optoelectronic devices, such as photovoltaics or light-emitting diodes, are based on the interaction of light with charges in the active material. Lead halide perovskites (LHPs) have emerged as excellent materials for optoelectronics, but mysteries remain as to how these materials interact with light. Here, we develop a spectroscopic method to observe the nearly instantaneous responses of LHPs to propagating light fields. This method has allowed us to precisely trace a nonlinear material response resulting from the mixing of different light components overtaking each other during propagation. The resulting oscillatory signals could be easily confused with collective motions of ions or molecules, but are quantitatively accounted by strong nonlinear mixing and polarization-dressed light propagation in single-crystal LHPs.

14 SOLAR ENERGY↗
DOE OSTI2022

Viterbi decoding of CRES signals in Project 8

Abstract Cyclotron radiation emission spectroscopy (CRES) is a modern approach for determining charged particle energies via high-precision frequency measurements of the emitted cyclotron radiation. For CRES experiments with gas within the fiducial volume, signal and noise dynamics can be modelled by a hidden Markov model. We introduce a novel application of the Viterbi algorithm in order to derive informational limits on the optimal detection of cyclotron radiation signals in this class of gas-filled CRES experiments, thereby providing concrete limits from which future reconstruction algorithms, as well as detector designs, can be constrained. The validity of the resultant decision rules is confirmed using both Monte Carlo and Project 8 data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Decoding the shift-invariant data: applications for band-excitation scanning probe microscopy *

A shift-invariant variational autoencoder (shift-VAE) is developed as an unsupervised method for the analysis of spectral data in the presence of shifts along the parameter axis, disentangling the physically-relevant shifts from other latent variables. Using synthetic data sets, we show that the shift-VAE latent variables closely match the ground truth parameters. The shift VAE is extended towards the analysis of band-excitation piezoresponse force microscopy data, disentangling the resonance frequency shifts from the peak shape parameters in a model-free unsupervised manner. The extensions of this approach towards denoising of data and model-free dimensionality reduction in imaging and spectroscopic data are further demonstrated. This approach is universal and can also be extended to analysis of x-ray diffraction, photoluminescence, Raman spectra, and other data sets.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Active causal learning for decoding chemical complexities with targeted interventions

Abstract Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have become standard for predictions, but they face challenges when applied across different datasets due to reliance on correlations between molecular representation and target properties. These approaches typically depend on large datasets to capture the diversity within the chemical space, facilitating a more accurate approximation, interpolation, or extrapolation of the chemical behavior of molecules. In our research, we introduce an active learning approach that discerns underlying cause-effect relationships through strategic sampling with the use of a graph loss function. This method identifies the smallest subset of the dataset capable of encoding the most information representative of a much larger chemical space. The identified causal relations are then leveraged to conduct systematic interventions, optimizing the design task within a chemical space that the models have not encountered previously. While our implementation focused on the QM9 quantum-chemical dataset for a specific design task—finding molecules with a large dipole moment—our active causal learning approach, driven by intelligent sampling and interventions, holds potential for broader applications in molecular, materials design and discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Decoding crops one cell at a time: from cell atlases to single-cell genetics

Understanding the mechanisms underlying key agricultural traits remains a central challenge in crop research, but recent advances in technologies are providing powerful tools to address this issue. Among these, single-cell and spatial transcriptomics have revealed tissue heterogeneity and spatial organization, offering unique insights into cellular gene expression dynamics and the coordinated activity of multiple cell types. These approaches help uncover how specific cell types contribute to agricultural traits and refine candidate loci lists through integration with trait-associated loci. Additionally, single-cell and spatial transcriptomics have the potential to serve as cell-level readout platforms integrating cellular perturbations, enabling high-throughput discovery of causal relationships between genotype and gene expression at the cellular level in plants. Successful implementation will accelerate the identification of key genetic variants for crop improvement. Furthermore we review lessons learned from application of single-cell screening in mammalian cells, highlight major technical and biological barriers to its use in plants, and outline potential strategies to overcome these challenges. Together, the widespread application and integration of single-cell and spatial transcriptomics with other technologies enable not only the descriptive cataloging of cell states but also the causal interrogation of sequence functions and regulatory networks at cell type resolution, ultimately advancing gene function studies and accelerating crop improvement.

Cellular heterogeneity↗
DOE OSTI2022

Decoding the star forming properties of gas-rich galaxy pairs

Here we extend the analysis of Bok et al. (2020) in which the H i content of isolated galaxies from the AMIGA (Analysis of the interstellar Medium in Isolated GAlaxies) sample and selected paired galaxies from ALFALFA (Arecibo Legacy Fast ALFA) were examined as a potential driver of galaxy location on the WISE (Wide-field Infrared Survey Explorer) mid-infrared SFR–M * sequence. By further characterizing the isolated and pair galaxy samples, i.e. in terms of optical galaxy morphology, a more detailed and quantitative description of local galaxy environment by way of the local number density (η) and tidal strength (Q) parameters, star formation efficiency (SFE HI ), and H i integrated profile asymmetries, we present plausible pathways for the broadening of the pair sample H i deficiency distribution towards both high and low deficiencies compared to the narrower isolated galaxy sample distribution (i.e. σ PAIRS = 0.34 versus σ AMIGA = 0.28). We associate the gas-rich tail of the pair deficiency distribution with the highest Q values, large profile asymmetries, and low SFEs. From this, we infer that merger activity is enhancing gas supplies, as well as disrupting the efficiency of star formation, via strong gravitational torques. The gas-poor wing of the deficiency distribution appears to be populated with galaxies in denser environments (with larger η values on average), more akin to groups. Despite our gas-rich selection criterion, there is a small population of early-type galaxies in the pair sample, which primarily fall in the positive deficiency wing of the distribution. These results suggest that a combination of a denser galaxy environment, early-type morphology, and higher stellar mass is contributing to the broadening of the deficiency distribution towards larger deficiencies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Decoding the age–chemical structure of the Milky Way disc: an application of copulas and elicitable maps

In the Milky Way, the distribution of stars in the [α/Fe] versus [Fe/H] and [Fe/H] versus age planes holds essential information about the history of star formation, accretion, and dynamical evolution of the Galactic disc. We investigate these planes by applying novel statistical methods called copulas and elicitable maps to the ages and abundances of red giants in the Apache Point Observatory Galactic Evolution Experiment survey. We find that the high- and low-α disc stars have a clean separation in copula space and use this to provide an automated separation of the α sequences using a purely statistical approach. This separation reveals that the high-α disc ends at the same [α/Fe] and age at high [Fe/H] as the low-[Fe/H] start of the low-α disc, thus supporting a sequential formation scenario for the high- and low-α discs. We then combine copulas with elicitable maps to precisely obtain the correlation between stellar age τ and metallicity [Fe/H] conditional on Galactocentric radius R and height z in the range 0 < R < 20 kpc and |z| < 2 kpc. The resulting trends in the age–metallicity correlation with radius, height, and [α/Fe] demonstrate a ≈0 correlation wherever kinematically cold orbits dominate, while the naively expected negative correlation is present where kinematically hot orbits dominate. This is consistent with the effects of spiral-driven radial migration, which must be strong enough to completely flatten the age–metallicity structure of the low-α disc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Decoding ionic conductivity and reordering in cation-disordered pyrochlores

The ordered structure A 2 B 2 O 6 O’ in pyrochlores engenders twin rows of inequivalent anion sublattices each centred on alternating cations. While it is known that cation antisite disorder augments the ionic conductivity by several orders of magnitude, the local cation environment around the anions and the dynamic anion reordering during the cation disordering are not well-elucidated. Using atomistic simulations on Gd 2 Zr 2 O 7 , we first show that the anions engage in concerted hops to the neighbouring tetrahedral sites mostly along with the $\langle$1 0 0$\rangle$ direction while completely avoiding the octahedral sites. While the initially vacant 8 a sites start accommodating oxygen ions with increasing cation disorder, they show noticeable reluctance even at significant levels of disorder. We have also tracked both the distribution of available oxygen sites following random cation disorder, which is dependent only on cation disordering, and the probability of occupation of these sites. Interestingly, the available oxygen sites show a non-monotonic dependence on the number of B ions in the nearest neighbouring shell while the occupation probability of all the available oxygen sites increases monotonically. A tetrahedral oxygen site thus has a better probability of being occupied when it has a greater number of second neighbour B ions. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.

Science & Technology - Other Topics↗
DOE OSTI2024

Decoding the B → K ν ν excess at Belle II: Kinematics, operators, and masses

An excess in the branching fraction for B + → K + ν ν recently measured at Belle II may be a hint of new physics. We perform thorough likelihood analyses for different new physics scenarios such as B → K X with a new invisible particle X , or B → K χ χ through a scalar, vector, or tensor current with χ being a new invisible particle or a neutrino. We find that vector-current three-body decay with m X ≃ 0.6 GeV—which may be dark matter—is most favored, while two-body decay with m X ≃ 2 GeV is also competitive. The best-fit branching fractions for the scalar and tensor cases are a few times larger than for the two-body and vector cases. Past measurements provide further discrimination, although the best-fit parameters stay similar. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Decoding polymer self-dynamics using a two-step approach

The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. Here, we show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a “two-step” approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.

36 MATERIALS SCIENCE↗