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At least 901 records · Page 50

Learning high-dimensional parametric maps via reduced basis adaptive residual networks

We propose a scalable framework for the learning of high-dimensional parametric maps via adaptively constructed residual network (ResNet) maps between reduced bases of the inputs and outputs. When just few training data are available, it is beneficial to have a compact parametrization in order to ameliorate the ill-posedness of the neural network training problem. By linearly restricting high-dimensional maps to informed reduced bases of the inputs, one can compress high-dimensional maps in a constructive way that can be used to detect appropriate basis ranks, equipped with rigorous error estimates. A scalable neural network learning framework is thus to learn the nonlinear compressed reduced basis mapping. Unlike the reduced basis construction, however, neural network constructions are not guaranteed to reduce errors by adding representation power, making it difficult to achieve good practical performance. Inspired by recent approximation theory that connects ResNets to sequential minimizing flows, we present an adaptive ResNet construction algorithm. This algorithm allows for depth-wise enrichment of the neural network approximation, in a manner that can achieve good practical performance by first training a shallow network and then adapting. We prove universal approximation of the associated neural network class for $L^2_v$ functions on compact sets. Our overall framework allows for constructive means to detect appropriate breadth and depth, and related compact parametrizations of neural networks, significantly reducing the need for architectural hyperparameter tuning. Numerical experiments for parametric PDE problems and a 3D CFD wing design optimization parametric map demonstrate that the proposed methodology can achieve remarkably high accuracy for limited training data, and outperformed other neural network strategies we compared against.

42 ENGINEERING↗

Data for Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production, a Process Model for Lipid-Producing Energy Crops

Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 °C and 180 °C for 10 minutes) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.

Conversion↗

Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense )

The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.

59 BASIC BIOLOGICAL SCIENCES↗

Cylindricity Sensitivity Thermal Model of the AGR-5/6/7 Experiment in the Advanced Test Reactor

The AGR-5/6/7 experiment is currently being irradiated in the Advanced Test Reactor (ATR) at the Idaho National Laboratory and is approximately 70% complete. Several fuel and material irradiation experiments have been planned for the U.S. Department of Energy Advanced Gas Reactor Fuel Development and Qualification Program, which supports the development and qualification of tristructural isotropic (TRISO) coated particle fuel for use in high-temperature gas-cooled reactors. The goals of these experiments are to provide irradiation performance data to support fuel process development, qualify fuel for normal operating conditions, support development of fuel performance models and codes, and provide irradiated fuel and materials for post-irradiation examination and safety testing. Originally planned and named as separate fuel experiments, but subsequently combined into a single test train, AGR-5/6/7 is testing low-enriched uranium oxycarbide TRISO fuel. The AGR-5/6/7 test train has 5 capsules with thermocouples and independent gas control mixtures. Unique to this paper is a sensitivity study concerning the cylindricity of the graphite holders containing the fuel compacts and their eccentricity in relation to the stainless-steel capsule walls. Each capsule has small nubs on the outside used for centering the graphite holder inside the stainless-steel capsule with a small gas gap used to control temperature. Due to machining tolerances of these nubs and vibration wearing the nubs down when the experiment is running in the reactor, the possibility exists that the holder may move around radially. Each capsule is equipped with several thermocouples placed at various radii and depths within each graphite holder. This paper will show the sensitivity of offsetting the graphite holder for various radii in 45-degree increments around the circle with the objective of minimizing the difference between the measured thermocouples and the modeled thermocouple temperatures. Separate gas mixtures of helium/neon are introduced into this gas gap between the holder and capsule wall and changed as necessary to maintain the desired thermocouple temperatures to keep the fuel compacts at constant temperature as the nuclear reactor conditions change. The goal of the sensitivity study is to find a radius and an angle to offset the holder from perfectly centered for each of the five capsules separately. The complex thermal model includes fission heating, gamma heating, radiation heat transfer, and heat transfer via conduction and radiation across the control gaps. Subroutines linked to the thermal model offer an easy method to offset the graphite holder from the capsule walls without remeshing the entire model.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Soil Components in Heterogeneous Impact Glass in Martian Meteorite EETA79001

Martian soil composition can illuminate past and ongoing near-surface processes such as impact gardening [2] and hydrothermal and volcanic activity [3,4]. Though the Mars Exploration Rovers (MER) have analyzed the major-element composition of Martian soils, no soil samples have been returned to Earth for detailed chemical analysis. Rao et al. [1] suggested that Martian meteorite EETA79001 contains melted Martian soil in its impact glass (Lithology C) based on sulfur enrichment of Lithology C relative to the meteorite s basaltic lithologies (A and B) [1,2]. If true, it may be possible to extract detailed soil chemical analyses using this meteoritic sample. We conducted high-resolution (~0.3 m/pixel) element mapping of Lithology C in thin section EETA79001,18 by energy dispersive spectrometry (EDS). We use these data for principal component analysis (PCA).

Schrader, C. M.↗

Design of Mini-Plate-1 Irradiation Test for Qualification of High-Density, Low-Enriched U-10Mo Monolithic Fuel

The United States High Performance Research Reactor project is tasked with fuel development and qualification leading to conversion of higher power research and test reactors in the US from high-enriched uranium (HEU) to low-enriched uranium (LEU) fuels. Here, this manuscript identifies the functional and operational design requirements of the first miniature test plate (mini-plate [MP]) irradiation campaign (MP-1) of commercially fabricated LEU U-10Mo monolithic plate-type fuel and is the precursor to a large parametric mini-plate test (MP-2) aimed at producing the data to support regulatory qualification of the LEU U-10Mo monolithic fuel. The manuscript (1) provides a general description of the selected U-10Mo LEU fuel and (2) defines the overall experiment design and functional requirements to accomplish the specific test objective of MP-1, which is to confirm that the commercially manufactured LEU U-10Mo monolithic fuel meets the established requirements of geometric stability, mechanical integrity and stable and predictable behavior. The fuel testing parameters are established by the need to bound performance behavior within the operational envelope of the reactors being converted.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Regulation of β-cell death by ADP-ribosylhydrolase ARH3 via lipid signaling in insulitis

Lipids are regulators of insulitis and β-cell death in type 1 diabetes development, but the underlying mechanisms are poorly understood. Here, we investigated how the islet lipid composition and downstream signaling regulate β-cell death. We performed lipidomics using three models of insulitis: human islets and EndoC-βH1 β cells treated with the pro-inflammatory cytokines interlukine-1β and interferon-γ, and islets from pre-diabetic non-obese mice. We also performed mass spectrometry and fluorescence imaging to determine the localization of lipids and enzyme in islets. RNAi, apoptotic assay, and qPCR were performed to determine the role of a specific factor in lipid-mediated cytokine signaling. Across all three models, lipidomic analyses showed a consistent increase of lysophosphatidylcholine species and phosphatidylcholines with polyunsaturated fatty acids and a reduction of triacylglycerol species. Imaging assays showed that phosphatidylcholines with polyunsaturated fatty acids and their hydrolyzing enzyme phospholipase PLA2G6 are enriched in islets. In downstream signaling, omega-3 fatty acids reduce cytokine-induced β-cell death by improving the expression of ADP-ribosylhydrolase ARH3. The mechanism involves omega-3 fatty acid-mediated reduction of the histone methylation polycomb complex PRC2 component Suz12, upregulating the expression of Arh3, which in turn decreases cell apoptosis. Our data provide insights into the change of lipidomics landscape in β cells during insulitis and identify a protective mechanism by omega-3 fatty acids.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

Preliminary neutronic analysis of a cavity test reactor

A reference configuration was calculated for a cavity test reactor to be used for testing the gascore nuclear rocket concept. A thermal flux of 4.1 x 10 to the 14th power neutrons per square centimeter per second in the cavity was provided by a driver fuel loading of 6.4 kg of enriched uranium in MTR fuel elements. The reactor was moderated and cooled by heavy water and reflected with 25.4 cm of beryllium. Power generation of 41.3 MW in the driver fuel is rejected to a heat sink. Design effort was directed toward minimization of driver power while maintaining 2.7 MW in the cavity during a test run. Ancillary data on material reactivity worths, reactivity coefficients, flux spectra, and power distributions are reported.

Whitmarsh, C. L., Jr.↗

Trends of Sr and Nd isotopes through time near the Japan Sea in northeastern Japan

Nd and Sr isotopic analyses were performed on selected volcanic rocks of 27-6 Ma age in the Green Tuff region of northeastern Japan, in adjacent areas, and in two ultramafic inclusions from Ichinomegata. The isotopic data plot generally along the region of the mantle array, and the volcanic rocks vary in epsilon(Nd) from -0.9 to 5.7, and in epsilon(Sr) from 14.1 to -16.3. It is found that the volcanic rocks are part of an evolutionary pattern over a time period of 27 Ma, and that the pattern goes from an initially enriched source to that of a very depleted source. A greater-than-15-Ma preopening stage, characterized by an enriched isotopic signature, and a less-than-15-Ma postopening stage, characterized by a depleted signature, are identified. It is suggested that the degree of continental crust involvement is high during the preopening stages of a back-arc basin when it is associated with a rifted continental mass.

Nohda, S.↗

Oxygen Fugacity of the Upper Mantle of Mars. Evidence from the Partitioning Behavior of Vanadium in Y980459 (Y98) and other Olivine-Phyric Shergottites

Using partitioning behavior of V between olivine and basaltic liquid precisely calibrated for martian basalts, we determined the redox state of primitive (olivine-rich, high Mg#) martian basalts near their liquidus. The combination of oxidation state and incompatible element characteristics determined from early olivine indicates that correlations between fO2 and other geochemical characteristics observed in many martian basalts is also a fundamental characteristic of these primitive magmas. However, our data does not exhibit the range of fO2 observed in these previous studies.. We conclude that the fO2 for the martian upper mantle is approximately IW+1 and is incompatible-element depleted. It seems most likely (although clearly open to interpretation) that these mantle-derived magmas assimilated a more oxidizing (>IW+3), incompatible-element enriched, lower crustal component as they ponded at the base of the martian crust.

Shearer, C. K.↗

MassIVE MSV000094084 - Data files for manuscript - Selected ion monitoring for orbitrap-based metabolomics: Please open README-data-for-SIM-paper-20240210.doc for details.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage. Please open README-data-for-SIM-paper-20240210.doc for details. [doi:10.25345/C5JH3DD3K] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Rabinowitz, Joshua↗

A Plan to Qualify New Fuel for the High Flux Isotope Reactor for Material Minimization

The High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) is one of five high power research reactors the Office of Material Management and Minimization (M3) Program, Office of Conversion is working to convert from using highly enriched uranium (HEU) fuel to using low-enriched uranium (LEU) fuel. This effort stems from the primary objective within the U.S. Department of Energy (DOE) National Nuclear Security Administration (NNSA) to achieve permanent threat reduction by minimizing, and when possible, eliminating weapon-usable nuclear material around the world. Under M3’s Office of Conversion, the U.S. High Performance Research Reactor (USHPRR) Project is pursuing fuel qualification and licensing of LEU fuels to support the high-performance reactors. All high-performance reactors except HFIR will be converted to LEU monolithic uranium-molybdenum alloy fuel. HFIR will be evaluated for conversion to LEU using a uranium silicide fuel, namely, U3Si2-Al dispersion fuel. The mission of the USHPRR Project is to develop the technology needed to reduce, and eventually eliminate, worldwide use of HEU in civilian applications. The goal is to develop the technical means needed to use low enriched uranium (LEU) instead of HEU fuel in research and test reactors without significant penalties in performance, economics, or safety of the reactors. The USHPRR Project has four major elements, called Pillars: Fuel Qualification (FQ) managed at Idaho National Laboratory (INL), Fuel Fabrication (FF) managed at Pacific Northwest National Laboratory (PNNL), Reactor Conversion (RC) managed at Argonne National Laboratory (Argonne), and Cross-Cutting (CC) managed at Savannah River National Laboratory (SRNL). FQ is responsible for the qualification of the fuel type. RC is responsible for supporting reactor conversion analysis and overseeing licensing submittals leading to conversions of domestic reactors to LEU fuel. For the FQ effort, FQ (INL) worked in collaboration with RC (Argonne) and ORNL to develop the plan for the uranium silicide fuel qualification for HFIR. The resulting HFIR Fuel Qualification Plan provides the general approach for the USHPRR team to move the selected uranium silicide fuel design for HFIR conversion through qualification. Authorization and use in HFIR will be approved through the DOE’s Office of Science. Uranium silicide fuel was previously qualified in NUREG-1313 at an approximate maximum heat flux of 1.4 MW/m2 and a maximum fuel section temperature of about 130°C. In addition to the different regulator process utilized by DOE, these upper limits will be exceeded in HFIR; therefore, further testing will be necessary to ensure the fuel can meet HFIR qualification requirements. The HFIR fuel loading may exceed 4.8 gU/cm3 which was determined in the NUREG-1313 safety evaluation to be acceptable for use in non-power NRC-licensed reactors provided there exist no other safety considerations. In addition, the uranium silicide fuel will need to be qualified in a HFIR-specific design. This plan includes the currently available information from the USHPRR Project Functions and Requirements document and expands these requirements to ensure that planned tests have traceable results providing evidence that the requirements have been met. Data collection methods are discussed as well as the process to show that the requirements have been met. This document is designed to provide a pathway for researchers to obtain data necessary and at the appropriate quality level for HFIR fuel qualification

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Modification of cell wall polysaccharide guides cell division in Streptococcus mutans

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits

Subclinical doses of LPS (SD-LPS) are known to cause low-grade inflammatory activation of monocytes, which could lead to inflammatory diseases including atherosclerosis and metabolic syndrome. Sodium 4-phenylbutyrate is a potential therapeutic compound which can reduce the inflammation caused by SD-LPS. To understand the gene regulatory networks of these processes, we have generated scRNA-seq data from mouse monocytes treated with these compounds and identified 11 novel cell clusters. We have developed a machine learning method to integrate scRNA-seq, ATAC-seq, and binding motifs to characterize gene regulatory networks underlying these cell clusters. Using guided regularized random forest and feature selection, our method achieved high performance and outperformed a traditional enrichment-based method in selecting candidate regulatory genes. Our method is particularly efficient in selecting a few candidate genes to explain observed expression pattern. In particular, among 531 candidate TFs, our method achieves an auROC of 0.961 with only 10 motifs. Finally, we found two novel subpopulations of monocyte cells in response to SD-LPS and we confirmed our analysis using independent flow cytometry experiments. Our results suggest that our new machine learning method can select candidate regulatory genes as potential targets for developing new therapeutics against low grade inflammation.

60 APPLIED LIFE SCIENCES↗

Energy spectrum of sputtered uranium

The fission track technique for detecting uranium 235 was used in conjunction with a mechanical time-of-flight spectrometer to measure the energy spectrum in the region 1 eV to 1 keV of material sputtered from a 93% enriched U-235 foil by 80 keV Ar-40(+) ions. The spectrum was found to exhibit a peak in the region 2-4 eV and to decrease approximately as E to the -1.77 power for E is approximately greater than 100 eV. The design, construction and resolution of the mechanical spectrometer are discussed and comparisons are made between the data and the predictions of the ramdom collision cascade model of sputtering.

Weller, R. A.↗

Sulfur abundances in the solar wind measured by SWICS on Ulysses

One of the nine experiments on Ulysses (launched October, 1990), the Solar Wind Ion Composition Spectrometer, utilizes an energy per charge deflection system along with time of flight technology to uniquely determine the mass and mass per charge of solar wind particles. Thus the composition of various solar wind types can be analyzed. Using the SWICS data accumulated during the in-ecliptic phase of the mission, we have determined the sulfur abundance, relative to silicon, in two different types of solar wind: transient and coronal hole associated flows. Sulfur is of extreme interest because it is one of the few elements that lies in the transitional region of the FIP-dependent relative abundance enrichment function, observed for solar energetic particles and some types of solar wind flows.

Shafer, C. M.↗