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All sources NASA NTRS DOE OSTI

DOE OSTI2025

LinkML: an open data modeling framework

Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.

AI-ready data↗

DOE OSTI2015

Average Structure Evolution of δ-phase Pu-Ga Alloys

[Full Text] Plutonium metal is a highly unusual element, exhibiting six allotropes at ambient pressure, from room temperature to its melting point. Many phases of plutonium metal are unstable with temperature, pressure, chemical additions, and time. This strongly affects structure and properties, and becomes of high importance, particularly when considering effects on structural integrity over long time periods. The fcc δ-phase deserves additional attention, not only in the context of understanding the electronic structure of Pu, but also as one of the few high-symmetry actinide phases that can be stabilized down to ambient pressure and room temperature by alloying it with trivalent elements. We will present results on recent work on aging of Pu-2at.%Ga and Pu-7at.%Ga alloys

36 MATERIALS SCIENCE↗

NASA NTRS1988

Explanation production by expert planners

Although the explanation capability of expert systems is usually listed as one of the distinguishing characteristics of these systems, the explanation facilities of most existing systems are quite primitive. Computer generated explanations are typically produced from canned text or by direct translation of the knowledge structures. Explanations produced in this manner bear little resemblance to those produced by humans for similar tasks. The focus of our research in explanation is the production of justifications for decisions by expert planning systems. An analysis of justifications written by people for planning tasks has been taken as the starting point. The purpose of this analysis is two-fold. First, analysis of the information content of the justifications will provide a basis for deciding what knowledge must be represented if human-like justifications are to be produced. Second, an analysis of the textual organization of the justifications will be used in the development of a mechanism for selecting and organizing the knowledge to be included in a computer-produced explanation. This paper describes a preliminary analysis done of justifications written by people for a planning task. It is clear that these justifications differ significantly from those that would be produced by an expert system by tracing the firing of production rules. The results from the text analysis have been used to develop an augmented phrase structured grammar (APSG) describing the organization of the justifications. The grammar was designed to provide a computationally feasible method for determining textual organization that will allow the necessary information to be communicated in a cohesive manner.

Bridges, Susan↗

DOE OSTI2021

Fully quantum calculations of O 2 –N 2 scattering using a new potential energy surface: Collisional perturbations of the oxygen 118 GHz fine structure line

A proper description of the collisional perturbation of the shapes of molecular resonances is important for remote spectroscopic studies of the terrestrial atmosphere. Of particular relevance are the collisions between the $\text{O}_2$ and $\text{N}_2$ molecules—the two most abundant atmospheric species. In this work, we report a new highly accurate $\text{O}_2(\text{X}^3Σ^–_g)–\text{N}_2(\text{X}^1Σ^+_g)$ potential energy surface and use it for performing the first quantum scattering calculations addressing line shapes for this system. We use it to model the shape of the 118 GHz fine structure line in $\text{O}_2$ perturbed by collisions with $\text{N}_2$ molecules, a benchmark system for testing our methodology in the case of an active molecule in a spin triplet state. The calculated collisional broadening of the line agrees well with the available experimental data over a wide temperature range relevant for the terrestrial atmosphere. This work constitutes a step toward populating the spectroscopic databases with ab initio line shape parameters for atmospherically relevant systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

PDF Entity Annotation Tool (PEAT)

While different text mining approaches – including the use of Artificial Intelligence (AI) and other machine based methods - continue to expand at a rapid pace, the tools used by researchers to create the labeled datasets required for training, modeling, and evaluation remain rudimentary. Labeled datasets contain the target attributes the machine is going to learn; for example, training an algorithm to delineate between images of a car or truck would generally require a set of images with a quantitative description of the underlying features of each vehicle type. Development of labeled textual data that can be used to build natural language machine learning models for scientific literature is not currently integrated into existing manual workflows used by domain experts. Published literature is rich with important information, such as different types of embedded text, plots, and tables that can all be used as inputs to train ML/natural language processing (NLP) models, when extracted and prepared in machine readable formats. Currently, both normalized data extraction of use to domain experts and extraction to support development of ML/NLP models are labor intensive and cumbersome manual processes. Automatic extraction of data and information from formats such as PDFs that are optimized for layout and human readability, not machine readability. The PDF (Portable Document Format) Entity Annotation Tool (PEAT) was developed with the goal of allowing users to annotate publications within their current print format, while also allowing those annotations to be captured in a machine-readable format. One of the main issues with traditional annotation tools is that they require transforming the PDF into plain text to facilitate the annotation process. While doing so lessens the technical challenges of annotating data, the user loses all structure and provenance that was inherent in the underlying PDF. Also, textual data extraction from PDFs can be an error prone process. Challenges include identifying sequential blocks of text and a multitude of document formats (multiple columns, font encodings, etc.). As a result of these challenges, using existing tools for development of NLP/ML models directly from PDFs is difficult because the generated outputs are not interoperable. We created a system that allows annotations to be completed on the original PDF document structure, with no plain text extraction. The result is an application that allows for easier and more accurate annotations. In addition, by including a feature that grants the user the ability to easily create a schema, we have developed a system that can be used to annotate text for different domain-centric schemas of relevance to subject matter experts. Different knowledge domains require distinct schemas and annotation tags to support machine learning.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Cation Disorder of ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ in Super‐Earth Mantles

Understanding the mineralogy of exoplanets is essential for unraveling their interior structures, dynamics, and evolution. For large super-Earths, the post-post spinel ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$, one of the major mantle phases, may undergo the order-disorder transition (ODT) at high temperatures. However, the ODT phase boundary of ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ has not been rigorously constrained. Additionally, fundamental thermodynamic properties of the disordered ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ remain poorly investigated. Here, we develop a unified machine learning potential (MLP) for ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ of ab initio accuracy under super-Earth mantle conditions. With the efficient MLP, we extensively calculate the free energy of post-post spinel ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ via the thermodynamic integration method. The results are used to constrain the ODT phase boundary. Furthermore, we report the P-V-T equation of state and Grüneisen parameters for post-post spinel ${\text{Mg}}_{\mathbf{2}}{\text{SiO}}_{\mathbf{4}}$ across various degrees of disorder. These thermodynamic properties are further applied to update the adiabatic thermal profiles and the mass-radius relation of super-Earths.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Leveraging BERT and Network-Based Attention Analysis for Identifying Treatment Milestones in EHRs

This study introduces a sophisticated data-driven framework for analyzing Electronic Health Records (EHRs) using transformer-based models to identify and disentangle overlapping treatment contexts. The framework leverages a preprocessing pipeline that transforms structured procedural codes into semantically enriched descriptive text, enabling the use of attention mechanisms to cluster medical events into treatment milestones—cohesive and distinct components of care processes. The methodology is rigorously validated using synthetic datasets derived from the MIMIC-III database, designed to simulate the heterogeneity and overlapping procedural contexts characteristic of real-world EHR scenarios. Quantitative evaluation highlights the framework’s robustness in disentangling concurrent care pathways, with attention metrics and unsupervised clustering approaches demonstrating the ability to preserve intra-context relationships while distinguishing inter-context dependencies. By addressing challenges inherent in data heterogeneity, this approach provides a foundation for uncovering complex treatment patterns, advancing clinical decision-making, and optimizing resource allocation in diverse healthcare environments.

Kim, Minsu [ORNL] (ORCID:0000000224185535)↗

NASA NTRS2020

Characterization of International Space Station Crew Members' Workload Contributing to Fatigue, Sleep Disruption and Circadian De-synchronization

The focus of this paper is to characterize how the International Space Station (ISS) crewmembers’ workload may be contributing to sleep loss, circadian misalignment and fatigue. Both sleep quantity and subjective sleep quality are reduced in ISS crewmembers (Barger, Flynn-Evans, Kubey, Walsh, Ronda, Wang, Wright, & Czeisler, 2014). Evidence indicates that the use of hypnotic drugs does not appear to promote extended sleep duration. Because sleep is often driven by psychosocial as well as somatic attributes, traditional therapies may only partially moderate the problem for some individuals. Accordingly, searching for additional abatement tactics is a sensible plan. Scientific studies have shown that sleep can be disrupted from work-related stressors. On the ISS, to optimize their time, the crewmembers follow prescribed, ambitious and rigorous schedules with shared deadlines. Here it will be argued that these human capital leveraging techniques may be undermining the astronaut’s sleep, which could negatively impact performance. Along with half of the Earth-bound working population (Paoli & Merllié, 2001), ISS crewmembers may not be adequately recovering from their workload. This paper begins with a characterization of the working conditions of ISS crewmembers, describes the development of rigorous schedules and portrays a typical workday. Terrestrially-based research is compiled to describe how full and partial sleep deprivation affect physical and cognitive performance and how ISS work characteristics may disrupt sleep and subsequent performance. The literature points toward potential solutions to astronaut fatigue that is related to their workload. Finally, throughout the text, evidence is provided from semi-structured interviews, biographies and textual databases to support the argument that astronaut workload is contributing to their sleep loss and fatigue and that research, development and mitigation strategies should focus on enhancing the restorative process.

fatigue↗

DOE OSTI2020

Thermodynamics and magnetism in the two-dimensional to three-dimensional crossover of the Hubbard model

The realization of antiferromagnetic (AF) correlations in ultracold fermionic atoms on an optical lattice is a significant achievement. Experiments have been carried out in one, two, and three dimensions, and have also studied anisotropic configurations with stronger tunneling in some lattice directions. Such anisotropy is relevant to the physics of cuprate superconductors and other strongly correlated materials. Moreover, this anisotropy might be harnessed to enhance AF order. Here we numerically investigate, using the determinant quantum Monte Carlo method, a simple realization of anisotropy in the three-dimensional (3D) Hubbard model in which the tunneling between planes, $t_⊥$, is unequal to the intraplane tunneling $\textit{t}$. This model interpolates between the three-dimensional isotropic ($t_⊥ = t$) and two-dimensional (2D;$t_⊥$ = 0) systems. In this work, we show that at fixed interaction strength to tunneling ratio ($\textit{U/t}$), anisotropy can enhance the magnetic structure factor relative to both 2D and 3D results. However, this enhancement occurs at interaction strengths below those for which the Néel temperature $T_{\text{Néel}}$ is largest, in such a way that the structure factor cannot be made to exceed its value in isotropic 3D systems at the optimal $\textit{U/t}$. We characterize the 2D-3D crossover in terms of the magnetic structure factor, real space spin correlations, number of doubly occupied sites, and thermodynamic observables. An interesting implication of our results stems from the entropy's dependence on anisotropy. As the system evolves from 3D to 2D, the entropy at a fixed temperature increases. Correspondingly, at fixed entropy, the temperature will decrease going from 3D to 2D. This suggests a cooling protocol in which the dimensionality is adiabatically changed from 3D to 2D.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2016

Ab Initio Structure Determination and Photoluminescent Properties of an Efficient, Thermally Stable Blue Phosphor, Ba 2 Y 5 B 5 O 17 :Ce 3+

Here, the crystal structure of a novel barium yttrium borate, Ba 2 Y 5 B 5 O 17 , was determined using a combination of ab initio global optimization algorithms and density functional theory calculations along with Rietveld refinement of high-resolution synchrotron X-ray powder diffraction data. Synthesized using a high-temperature solid-state route, the structure consists of edge- and corner-sharing Y- and Ba-centered polyhedra along with BO 3 trigonal planes. Ba and Y occupy four crystallographically independent sites with two fully occupied by Y and two having a statistical mixture of Y and Ba. Substituting Ce 3+ into the structure for Y 3+ yields blue photoluminescence ($λ_{\text{em}}$ = 443 nm) upon excitation with UV ($λ_{\text{em}}$ = 365 nm) light. The emission of this new compound is efficient with an external quantum yield of 70% and is stable as a function of temperature with a quenching temperature of ≈400 K.

36 MATERIALS SCIENCE↗

DOE OSTI2011

Toward Parallel Document Clustering

A key challenge to automated clustering of documents in large text corpora is the high cost of comparing documents in a multimillion dimensional document space. The Anchors Hierarchy is a fast data structure and algorithm for localizing data based on a triangle inequality obeying distance metric, the algorithm strives to minimize the number of distance calculations needed to cluster the documents into “anchors” around reference documents called “pivots”. We extend the original algorithm to increase the amount of available parallelism and consider two implementations: a complex data structure which affords efficient searching, and a simple data structure which requires repeated sorting. The sorting implementation is integrated with a text corpora “Bag of Words” program and initial performance results of end-to-end a document processing workflow are reported.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

Molecular beam homoepitaxy of N-polar AlN on bulk AlN substrates

N-polar AlN epilayers were grown on the N-face of single-crystal bulk AlN substrates by plasma-assisted molecular beam epitaxy. A combination of in situ thermal deoxidation and Al-assisted thermal desorption at high temperature aided in removing native surface oxides and impurities from the N-polar surface of the substrate enabling successful homoepitaxy. Subsequent epitaxial growth of the AlN layer on the in situ cleaned substrates, grown in a sufficiently high Al droplet regime, exhibited smooth surface morphologies with clean and wide atomic steps. KOH etch studies confirmed the N-polarity of the homoepitaxial films. Secondary ion mass spectrometry profiles show Si and H impurity concentrations below the noise levels, whereas O and C impurity concentrations of [Formula: see text] and [Formula: see text] atoms/cm 3 are observed, respectively. Although the structural defect densities are low, they interestingly appear as inversion domains of different dimensionalities.

Singhal, Jashan↗

NASA NTRS1998

Structure and Dynamics of Coronal Plasma

Brief summaries of the four published papers produced within the present performance period of NASA Grant NAGW-4081 are presented. The full text of the papers are appended to the report. The first paper titled "Coronal Structures Observed in X-rays and H-alpa Structures" was published in the Kofu Symposium proceedings. The study analyzes cool and hot behavior of two x-ray events, a small flare and a surge. It was found that a large H-alpha surge appears in x-rays as a very weak event, while a weak H-alpha feature corresponds to the brightest x-ray emission on the disk at the time of the observation. Calculations of the heating necessary to produce these signatures, and implications for the driving and heating mechanisms of flares vs. surges are presented. The second paper "Differential Magnetic Field Shear in an Active Region" has been published in The Astrophysical Journal. The study compared the three dimensional extrapolation of magnetic fields with the observed coronal structure in an active region. Based on the fit between observed coronal structure throughout the volume of the region and the calculated magnetic field configurations, the authors propose a differential magnetic field shear model for this active region. The decreasing field shear in the outer portions of the AR may indicate a continual relaxation of the magnetic field with time, corresponding to a net transport of helicity outward. The third paper "Difficulties in Observing Coronal Structure" has been published in the journal Solar Physics. This paper discusses the evidence that the temperature and density structure of the corona are far more complicated than had previously been thought. The discussion is based on five studies carried out by the group on coronal plasma properties, showing that any one x-ray instrument does see all of the plasma present in the corona, that hot and cool material may appear to be co-spatial at a given location in the corona, and that simple magnetic field extrapolations provide only a poor fit to the observed structure. The fourth paper "Analysis and Comparison of Loop Structures Imaged with NIXT and Yohkoh/SXT" has been published in Astronomy and Astrophysics. This paper analyzes and compares a variety of coronal loops, deriving loop pressure and emission measure from loop models. They are able to determine the volume filling factor in the corona, which is found to be in the range 0.001 to 0.01 for compact loops, and of order 1 for large structures. The small values suggest highly filamented structures, especially at lower temperatures.

Golub, Leon↗

DOE OSTI2022

Exploring 2 + 2 answers to 3 + 1 questions

We explore potential uses of physics formulated in Kleinian (i.e. 2 + 2) signature spacetimes as a tool for understanding properties of physics in Lorentzian (i.e. 3 + 1) signature. Much as Euclidean (i.e. 4 + 0) signature quantities can be used to formally construct the ground state wavefunction of a Lorentzian signature quantum field theory, a similar analytic continuation to Kleinian signature constructs a state of low particle flux in the direction of analytic continuation. There is also a natural supersymmetry algebra available in 2 + 2 signature, which serves to constrain the structure of correlation functions. Spontaneous breaking of Lorentz symmetry can produce various [Formula: see text] supersymmetry algebras that in 3 + 1 signature correspond to nonsupersymmetric systems. We speculate on the possible role of these structures in addressing the cosmological constant problem.

Physics↗

DOE OSTI2020

Evidence for pseudo–Jahn-Teller distortions in the charge density wave phase of 1$\textit{T}-\text{TiSe}_2$

Here, the charge density wave (CDW) instability in 1$\textit{T}-\text{TiSe}_2$ is revisited to investigate its electronic and structural origins using angle resolved photoemission spectroscopy (ARPES), neutron diffraction, and density functional theory (DFT) calculations. The evidence for Jahn-Teller (JT)-like distortions in the CDW state is provided from the local structure analysis that shows splitting of the Ti-Se bonds into short and long. The magnitude of the split is inconsistent with the commonly accepted Di Salvo model for the structural distortions in the CDW phase. From the APRES data, it is deduced that a nontrivial temperature-dependent energy shift of the Se $4\textit{p}$ valence bands occurs, but is absent for the Ti $3\textit{d}$ conduction bands. Collectively, these observations suggest that a JT-like mechanism is most likely central to the CDW instability in 1$\textit{T}-\text{TiSe}_2$.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Standardized report template for indeterminate renal masses at CT and MRI: a collaborative product of the SAR Disease-Focused Panel on Renal Cell Carcinoma

Purpose: To create a succinct yet comprehensive evidence-based structured report template for indeterminate renal masses characterized at CT and MRI. Methods: This IRB-exempt, iterative, multi-institutional quality improvement project was informed by published data derived from a multi-institutional survey and a multi-institutional review of CT and MRI radiology reports. A two-stage blinded Delphi process by the 16-member 12-institution Society of Abdominal Radiology Disease-Focused Panel on Renal Cell Carcinoma was conducted to create a structured report template for indeterminate renal masses evaluated at CT and MRI. Individual reporting characteristics were scored by members as ‘core,’ ‘optional,’ or ‘exclude.’ Threshold for inclusion was ≥ 80% support. If < 80% members considered a characteristic a ‘core’ feature, but ≥ 80% considered it either ‘core’ or ‘optional,’ it was considered an ‘optional’ feature. If neither was the case, the characteristic was excluded. Free-text comments were permitted. Characteristics considered ‘core’ by 50–99% of respondents in Round 1 (i.e., nonunanimous support) and uninvestigated free-text comments were assessed in Round 2. Core and optional structured reporting templates were derived. Results: The response rate was 100% in Round 1 (16/16) and Round 2 (16/16). In Round 1, 5 characteristics had unanimous support as ‘core’ features. Following Round 2, 13 characteristics had ≥ 80% support as ‘core’ features, and 10 characteristics had ≥ 80% support as ‘optional’ features. Structured report templates were derived. Discussion: Structured ‘core’ and ‘optional’ templates for indeterminate renal masses at CT and MRI were derived, which may improve compliance with reporting preferred and essential imaging characteristics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2017

Graph Learning in Knowledge Bases

The amount of text data has been growing exponentially in recent years, giving rise to automatic information extraction methods that store text annotations in a database. The current state-of-theart structured prediction methods, however, are likely to contain errors and it’s important to be able to manage the overall uncertainty of the database. On the other hand, the advent of crowdsourcing has enabled humans to aid machine algorithms at scale. As part of this project we introduced pi-CASTLE , a system that optimizes and integrates human and machine computing as applied to a complex structured prediction problem involving conditional random fields (CRFs). We proposed strategies grounded in information theory to select a token subset, formulate questions for the crowd to label, and integrate these labelings back into the database using a method of constrained inference. On both a text segmentation task over academic citations and a named entity recognition task over tweets we showed an order of magnitude improvement in accuracy gain over baseline methods.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1975

Key elements in building a successful photocomposition applications program

TEXTCOMP, a photocomposition applications program developed by the Technical Information and Documentation Division of the Jet Propulsion Laboratory using the Comp-2 language of Alphanumeric Publication Systems, is described. In Comp-2, each unique block of information such as a paragraph, centered heading, or side heading is termed a 'record'. All commands required for typesetting a record are grouped and identified by a record ID. Once the basic ground rules for typesetting are put into effect by a record ID, changes can be made in texts by means of in-text codes designed to access special characters or perform special operations. The approach used in the design of record ID's and in-text codes for TEXTCOMP to produce a code set structured for maximum usability by non-computer oriented personnel is discussed.

Korbuly, D. K.↗