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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 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The FEFF code

FEFF is a real-space multiple-scattering Green’s function code for simulating a variety of X-ray spectroscopies as well as ground-state and excited-state electronic structure. It is perhaps best known for its use in extended X-ray absorption fine-structure (EXAFS) calculations, particularly within various analysis codes such as DEMETER and LARCH. In addition to EXAFS, FEFF can also be used to calculate X-ray absorption near-edge structure (XANES), X-ray emission spectroscopy (XES), electron energy loss spectra (EELS) and many other spectroscopic quantities. Here, the basic approach used for the calculations is described, focusing on the most important approximations and aspects of the simulations. Here, the capabilities of the FEFF code, including those of the Java-based graphical user interface JFEFF, are also briefly described.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program ( PSSP ) [Pagola & Stephens (2010). J. Appl. Cryst. 43 , 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

XtalCAMP: a comprehensive program for the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data

XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.

36 MATERIALS SCIENCE↗
DOE OSTI2021

rmc-discord : reverse Monte Carlo refinement of diffuse scattering and correlated disorder from single crystals

A user-friendly program has been developed to analyze diffuse scattering from single crystals with the reverse Monte Carlo method. The approach allows for refinement of correlated disorder from atomistic supercells with magnetic or structural (occupational and/or displacive) disorder. The program is written in Python and optimized for performance and efficiency. Refinements of two user cases obtained with legacy neutron-scattering data demonstrate the effectiveness of the approach and the developed program. It is shown with bixbyite, a naturally occurring magnetic mineral, that the calculated three-dimensional spin-pair correlations are resolved with finer real-space resolution compared with the pair distribution function calculated directly from the reciprocal-space pattern. With the triangular lattice Ba 3 Co 2 O 6 (CO 3 ) 0.7 , refinements of occupational and displacive disorder are combined to extract the one-dimensional intra-chain correlations of carbonate molecules that move toward neighboring vacant sites to accommodate strain induced by electrostatic interactions. The program is packaged with a graphical user interface and extensible to serve the needs of single-crystal diffractometer instruments that collect diffuse-scattering data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

BioXTAS RAW 2 : new developments for a free open-source program for small-angle scattering data reduction and analysis

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting and D max finding algorithms; automated series ( e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares ( REGALS ); creation of electron-density reconstructions using electron density via solution scattering ( DENSS ); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A machine-learning-driven data labeling pipeline for scientific analysis in MLExchange

This study introduces a novel labeling pipeline to accelerate the labeling process of scientific data sets by using artificial intelligence (AI)-guided tagging techniques. This pipeline includes a set of interconnected web-based graphical user interfaces (GUIs), where Data Clinic and MLCoach enable the preparation of machine learning (ML) models for data reduction and classification, respectively, while Label Maker is used for label assignment. Throughout this pipeline, data can be accessed through a direct connection to a file system or through Tiled for access through Hypertext Transfer Protocol (HTTP). Our experimental results present three use cases where this labeling pipeline has been instrumental for the study of large X-ray scattering data sets in the area of pattern recognition, the remote analysis of resonant soft X-ray scattering data and the fine-tuning process of foundation models. These use cases highlight the labeling capabilities of this pipeline, including the ability to label large data sets in a short period of time, to perform remote data analysis while minimizing data movement and to enhance the fine-tuning process of complex ML models with human involvement.

Chavez, Tanny (ORCID:0000000193172896)↗
DOE OSTI2018

SciPhon : a data analysis software for nuclear resonant inelastic X-ray scattering with applications to Fe, Kr, Sn, Eu and Dy

We present the synchrotron radiation technique of nuclear resonant inelastic X-ray scattering (NRIXS), also known as nuclear resonance vibrational spectroscopy or nuclear inelastic scattering, provides a wealth of information on the vibrational properties of solids. It has found applications in studies of lattice dynamics and elasticity, superconductivity, heme biochemistry, seismology, isotope geochemistry and many other fields. It involves probing the vibrational modes of solids by using the nuclear resonance of Mössbauer isotopes such as 57 Fe, 83 Kr, 119 Sn, 151 Eu and 161 Dy. After data reduction, it provides the partial phonon density of states of the Mössbauer isotope that is investigated, as well as many other derived quantities such as the mean force constant of the chemical bonds and the Debye velocity. The data reduction is, however, not straightforward and involves removal of the elastic peak, normalization and Fourier–Log transformation. Furthermore, some of the quantities derived are highly sensitive to details in the baseline correction. A software package and several novel procedures to streamline and hopefully improve the reduction of the NRIXS data generated at sector 3ID of the Advanced Photon Source have been developed. The graphical user interface software is named SciPhon and runs as a Mathematica package. It is easily portable to other platforms and can be easily adapted for reducing data generated at other beamlines. Several tests and comparisons are presented that demonstrate the usefulness of this software, whose results have already been used in several publications. Here, the SciPhon software is used to reduce Kr, Sn, Eu and Dy NRIXS data, and potential implications for interpreting natural isotopic variations in those systems are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Solution scattering at the Life Science X-ray Scattering (LiX) beamline

This work reports the instrumentation and software implementation at the Life Science X-ray Scattering (LiX) beamline at NSLS-II in support of biomolecular solution scattering. For automated static measurements, samples are stored in PCR tubes and grouped in 18-position sample holders. Unattended operations are enabled using a six-axis robot that exchanges sample holders between a storage box and a sample handler, transporting samples from the PCR tubes to the X-ray beam for scattering measurements. The storage box has a capacity of 20 sample holders. At full capacity, the measurements on all samples last for ∼9 h. For in-line size-exclusion chromatography, the beamline-control software coordinates with a commercial high-performance liquid chromatography (HPLC) system to measure multiple samples in batch mode. The beamline can switch between static and HPLC measurements instantaneously. In all measurements, the scattering data span a wide q -range of typically 0.006–3.2 Å −1 . Functionalities in the Python package py4xs have been developed to support automated data processing, including azimuthal averaging, merging data from multiple detectors, buffer scattering subtraction, data storage in HDF5 format and exporting the final data in a three-column text format that is acceptable by most data analysis tools. These functionalities have been integrated into graphical user interfaces that run in Jupyter notebooks, with hooks for external data analysis software.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

pyXPCSviewer : an open-source interactive tool for X-ray photon correlation spectroscopy visualization and analysis

pyXPCSviewer , a Python-based graphical user interface that is deployed at beamline 8-ID-I of the Advanced Photon Source for interactive visualization of XPCS results, is introduced. pyXPCSviewer parses rich X-ray photon correlation spectroscopy (XPCS) results into independent PyQt widgets that are both interactive and easy to maintain. pyXPCSviewer is open-source and is open to customization by the XPCS community for ingestion of diversified data structures and inclusion of novel XPCS techniques, both of which are growing demands particularly with the dawn of near-diffraction-limited synchrotron sources and their dedicated XPCS beamlines.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Fixed-target serial crystallography at the Structural Biology Center

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

In situ chamber for studying battery failure using high-speed synchrotron radiography

The investigation of lithium-ion battery failures is a major challenge for personnel and equipment due to the associated hazards (thermal reaction, toxic gases and explosions). To perform such experiments safely, a battery abuse-test chamber has been developed and installed at the microtomography beamline ID19 of the European Synchrotron Radiation Facility (ESRF). The chamber provides the capability to robustly perform in situ abuse tests through the heat-resistant and gas-tight design for flexible battery geometries and configurations, including single-cell and multi-cell assemblies. High-speed X-ray imaging can be complemented by supplementary equipment, including additional probes (voltage, pressure and temperature) and thermal imaging. Together with the test chamber, a synchronization graphical user interface was developed, which allows an initial interpretation by time-synchronous visualization of the acquired data. Enabled by this setup, new meaningful insights can be gained into the internal processes of a thermal runaway of current and future energy-storage devices such as lithium-ion cells.

25 ENERGY STORAGE↗
DOE OSTI2019

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Thoreau: A fully-buried wireless underground sensor network in an urban environment

This paper describes the design and deployment of a functional Wireless Underground Sensor Network (WUSN) on a university campus. This is an unique system that is operational over a large area and over a long period of time, providing real time monitoring of the environment with the data being curated and displayed on an open website. The system details, including the architecture, node design, user interface, and deployment are provided. Initial measurement results are analyzed to show the functionality and performance of the system.

internet of things↗