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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Early Cardiac Mitochondrial Molecular and Functional Responses to Acute Anthracycline Treatment in Wistar Rats

Abstract Doxorubicin (DOX) is an anticancer drug widely used to treat human and nonhuman tumors but the late and persistent cardio-toxicity reduces the therapeutic utility of the drug. The full mechanism(s) of DOX-induced acute, subchronic and delayed toxicity, which has a preponderant mitochondrial component, remains unclear; therefore, it is clinically relevant to identify early markers to identify patients who are predisposed to DOX-related cardiovascular toxicity. To address this, Wistar rats (16 weeks old) were treated with a single DOX dose (20 mg/kg, i.p.); then, mRNA, protein levels and functional analysis of mitochondrial endpoints were assessed 24 h later in the heart, liver, and kidney. Using an exploratory data analysis, we observed cardiac-specific alterations after DOX treatment for mitochondrial complexes III, IV, and preferentially for complex I. Conversely, the same analysis revealed complex II alterations are associated with DOX response in the liver and kidney. Interestingly, H2O2 production by the mitochondrial respiratory chain as well as loss of calcium-loading capacity, markers of subchronic toxicity, were not reliable indicators of acute DOX cardiotoxicity in this animal model. By using sequential principal component analysis and feature correlation analysis, we demonstrated for the first time alterations in sets of transcripts and proteins, but not functional measurements, that might serve as potential early acute markers of cardiac-specific mitochondrial toxicity, contributing to explain the trajectory of DOX cardiac toxicity and to develop novel interventions to minimize DOX cardiac liabilities.

Pereira, Gonçalo C.↗
DOE OSTI2020

K-space algorithmic reconstruction (KAREN): a robust statistical methodology to separate Bragg and diffuse scattering

Diffuse scattering occurring in the Bragg diffraction pattern of a long-range-ordered structure represents local deviation from the governing regular lattice. However, interpreting the real-space structure from the diffraction pattern presents a significant challenge because of the dramatic difference in intensity between the Bragg and diffuse components of the total scattering function. In contrast to the sharp Bragg diffraction, the diffuse signal has generally been considered to be a weak expansive or continuous background signal. In this paper, using 1D and 2D models, it is demonstrated that diffuse scattering in fact consists of a complex array of high-frequency features that must not be averaged into a low-frequency background signal. To evaluate the actual diffuse scattering effectively, an algorithm has been developed that uses robust statistics and traditional signal processing techniques to identify Bragg peaks as signal outliers which can be removed from the overall scattering data and then replaced by statistically valid fill values. This method, described as a 'K-space algorithmic reconstruction' (KAREN), can identify Bragg reflections independent of prior knowledge of a system's unit cell. KAREN does not alter any data other than that in the immediate vicinity of the Bragg reflections, and reconstructs the diffuse component surrounding the Bragg peaks without introducing discontinuities which induce Fourier ripples or artifacts from underfilling `punched' voids. The KAREN algorithm for reconstructing diffuse scattering provides demonstrably better resolution than can be obtained from previously described punch-and-fill methods. The superior structural resolution obtained using the KAREN method is demonstrated by evaluating the complex ordered diffuse scattering observed from the neutron diffraction of a single plastic crystal of CBr 4 using pair distribution function analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Isotopic Analysis using FRAM [Slides]

FRAM is an isotopic analysis code nominally designed for plutonium and uranium. It stands for Fixed-energy Response-function Analysis with Multiple efficiencies. It has self-calibration using several gamma-ray peaks and can analyze gamma ray data from 30keV to >1MeV of HPGe, CdTe, or LaBr3 detector. The key difference between the MGA family of codes (from LLNL) and FRAM is the use of user-editable analysis parameters in the latter.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Induction of mitochondrial biogenesis and respiration is associated with mTOR regulation in hepatocytes of rats treated with the pan-PPAR activator tetradecylthioacetic acid (TTA)

Highlights: Black-Right-Pointing-Pointer We investigated mechanisms of mitochondrial regulation in rat hepatocytes. Black-Right-Pointing-Pointer Tetradecylthioacetic acid (TTA) was employed to activate mitochondrial oxidation. Black-Right-Pointing-Pointer Mitochondrial biogenesis and respiration were induced. Black-Right-Pointing-Pointer It was confirmed that PPAR target genes were induced. Black-Right-Pointing-Pointer The mechanism involved activation mTOR. -- Abstract: The hypolipidemic effect of peroxisome proliferator-activated receptor (PPAR) activators has been explained by increasing mitochondrial fatty acid oxidation, as observed in livers of rats treated with the pan-PPAR activator tetradecylthioacetic acid (TTA). PPAR-activation does, however, not fully explain the metabolic adaptations observed in hepatocytes after treatment with TTA. We therefore characterized the mitochondrial effects, and linked this to signalling by the metabolic sensor, the mammalian target of rapamycin (mTOR). In hepatocytes isolated from TTA-treated rats, the changes in cellular content and morphology were consistent with hypertrophy. This was associated with induction of multiple mitochondrial biomarkers, including mitochondrial DNA, citrate synthase and mRNAs of mitochondrial proteins. Transcription analysis further confirmed activation of PPAR{alpha}-associated genes, in addition to genes related to mitochondrial biogenesis and function. Analysis of mitochondrial respiration revealed that the capacity of both electron transport and oxidative phosphorylation were increased. These effects coincided with activation of the stress related factor, ERK1/2, and mTOR. The protein level and phosphorylation of the downstream mTOR actors eIF4G and 4E-BP1 were induced. In summary, TTA increases mitochondrial respiration by inducing hypertrophy and mitochondrial biogenesis in rat hepatocytes, via adaptive regulation of PPARs as well as mTOR.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Cubic AgMnSbTe 3 Semiconductor with a High Thermoelectric Performance

The reaction of MnTe with AgSbTe 2 in an equimolar ratio (ATMS) provides a new semiconductor, AgMnSbTe 3 . AgMnSbTe 3 crystallizes in an average rock-salt NaCl structure with Ag, Mn, and Sb cations statistically occupying the Na sites. AgMnSbTe 3 is a p-type semiconductor with a narrow band gap of ~0.33 eV. A pair distribution function analysis indicates that local distortions are associated with the location of the Ag atoms in the lattice. Density functional theory calculations suggest a specific electronic band structure with multi-peak valence band maxima prone to energy convergence. In addition, Ag 2 Te nanograins precipitate at grain boundaries of AgMnSbTe 3 . Here, the energy offset of the valance band edge between AgMnSbTe 3 and Ag 2 Te is ~0.05 eV, which implies that Ag 2 Te precipitates exhibit a negligible effect on the hole transmission. As a result, ATMS exhibits a high power factor of ~12.2 μWcm -1 K -2 at 823 K, ultralow lattice thermal conductivity of ~0.34 Wm -1 K -1 (823 K), high peak ZT of ~1.46 at 823 K, and high average ZT of ~0.87 in the temperature range of 400–823 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Driving mode analysis—How uncertain functional inputs propagate to an output

Abstract Driving mode analysis elucidates how correlated features of uncertain functional inputs jointly propagate to produce uncertainty in the output of a computation. Uncertain input functions are decomposed into three terms: the mean functions, a zero‐mean driving mode, and zero‐mean residual. The random driving mode varies along a single direction, having fixed functional shape and random scale. It is uncorrelated with the residual, and under linear error propagation, it produces an output variance equal to that of the full input uncertainty. Finally, the driving mode best represents how input uncertainties propagate to the output because it minimizes expected squared Mahalanobis distance amongst competitors. These characteristics recommend interpretation of the driving mode as the single‐degree‐of‐freedom component of input uncertainty that drives output uncertainty. We derive the functional driving mode, show its superiority to other seemingly sensible definitions, and demonstrate the utility of driving mode analysis in an application. The application is the simulation of neutron transport in criticality experiments. The uncertain input functions are nuclear data that describe how Pu reacts to bombardment by neutrons. Visualization of the driving mode helps scientists understand what aspects of correlated functional uncertainty have effects that either reinforce or cancel one another in propagating to the output of the simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Direct processing of PbZr 0.53 Ti 0.47 O 3 films on glass and polymeric substrates

This work reports on direct crystallization of PbZr 0.53 Ti 0.47 O 3 (PZT) thin films on glass and polymeric substrates, using pulsed thermal processing (PTP). Specifically, xenon flash lamps deliver pulses of high intensity, short duration, broadband light to the surface of a chemical solution deposited thin film, resulting in the crystallization of the film. Structural analysis by X-ray diffraction (XRD) and transmission electron microscopy show the existence of perovskite structure in nano-sized grains (≤5 nm). Local functional analysis by band excitation piezoelectric spectroscopy and electrostatic force microscopy confirm the presence of a ferroelectric phase and retention of voltage-written polarization for multiple days. Based on structural and functional analyses, strategies are discussed for optimization of pulse voltage and duration for the realization of crystalline ferroelectric thin films. For ~200 nm-thick PZT films on glass substrates, 500 μs-long pulses were required for crystallization, starting with 100 pulses at 350 V, 10 or 25 pulses at 400 V and in general lower number of pulses at higher voltages (resulting in higher radiant energy). Overall power densities of >6.4 kW/cm 2 were needed for appearance of peaks corresponding to the perovskite phase in the XRD. Films on glass processed at 350–400 V had a higher degree of 111-oriented perovskite grains. Higher applied radiant energy (through increased pulse voltage or count) resulted in more random and/or partially 001-oriented films. For ~1 μm-thick PZT films on polymeric substrates, 10 to 25 250 μs-long pulses at voltages ranging between 200 to 250 V, corresponding to power densities of ~2.8 kW/cm 2 , were optimal for maximized perovskite phase crystallization, while avoiding substrate damage.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Jumping the gun: Smoking constituent BaP causes premature primordial follicle activation and impairs oocyte fusibility through oxidative stress

Benzo(a)pyrene (BaP) is an ovotoxic constituent of cigarette smoke associated with pre-mature ovarian failure and decreased rates of conception in IVF patients. Although the overall effect of BaP on female fertility has been documented, the exact molecular mechanisms behind its ovotoxicity remain elusive. In this study we examined the effects of BaP exposure on the ovarian transcriptome, and observed the effects of in vivo exposure on oocyte dysfunction. Microarray analysis of BaP cultured neonatal ovaries revealed a complex mechanism of ovotoxicity involving a small cohort of genes associated with follicular growth, cell cycle progression, and cell death. Histomorphological and immunohistochemical analysis supported these results, with BaP exposure causing increased primordial follicle activation and developing follicle atresia in vitro and in vivo. Functional analysis of oocytes obtained from adult Swiss mice treated neonatally revealed significantly increased levels of mitochondrial ROS/lipid peroxidation, and severely reduced sperm-egg binding and fusion in both low (1.5 mg/kg/daily) and high (3 mg/kg/daily) dose treatments. Our results reveal a complex mechanism of BaP induced ovotoxicity involving developing follicle atresia and accelerated primordial follicle activation, and suggest short term neonatal BaP exposure causes mitochondrial leakage resulting in reduced oolemma fluidity and impaired fertilisation in adulthood. This study highlights BaP as a key compound which may be partially responsible for the documented effects of cigarette smoke on follicular development and sub-fertility. -- Highlights: ► BaP exposure up-regulates canonical pathways linked with follicular growth/atresia. ► BaP causes primordial follicle activation and developing follicle atresia. ► BaP causes oocyte mitochondrial ROS and lipid peroxidation, impairing fertilisation. ► Short term neonatal BaP exposure compromises adult oocyte quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Nanopore facilitated monohydrocalcitic amorphous calcium carbonate precipitation

Predicting the precipitation of solids is important in both natural systems and subsurface energy applications. The factors controlling reaction mechanisms, phase selection and conversion between phases are particularly important. In this contribution the precipitation and growth of an amorphous calcium carbonate species from flowing aqueous solution in a nanoporous controlled pore glass is followed in situ with differential X-ray pair distribution function analysis. It is discovered that the local atomic structure of this phase indicates monohydrocalcite-like pair–pair correlations, yet is functionally amorphous because it lacks long-range structure. The unexpected occurrence of synthetic proto-monohydrocalcite amorphous calcium carbonate, precipitated from a solution undersaturated with respect to published solubilities, suggests that nanopore confinement facilitates formation of an amorphous phase at the expense of more favorable crystalline ones. Finally, this result illustrates that confinement and interface effects are physical factors exerting control on mineral nucleation behavior in natural and geological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis

Abstract Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.

Plant Sciences↗
DOE OSTI2024

Chemoproteogenomic stratification of the missense variant cysteinome

Abstract Cancer genomes are rife with genetic variants; one key outcome of this variation is widespread gain-of-cysteine mutations. These acquired cysteines can be both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain unidentified via chemoproteomics; identification is a critical step to enable functional analysis, including assessment of potential druggability and susceptibility to oxidation. Here, we pair cysteine chemoproteomics—a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues—with genomics to reveal the hidden landscape of cysteine genetic variation. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized two-stage false discovery rate (FDR) error controlled proteomic search, which is further enhanced with a user-friendly FragPipe interface. Chemoproteogenomics analysis reveals that cysteine acquisition is a ubiquitous feature of both healthy and cancer genomes that is further elevated in the context of decreased DNA repair. Reference cysteines proximal to missense variants are also found to be pervasive, supporting heretofore untapped opportunities for variant-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and is compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.

Desai, Heta (ORCID:0000000343621707)↗
DOE OSTI2018

Revealing the Role of Phase Structures of Bimetallic Nanocatalysts in the Oxygen Reduction Reaction

The ability to tune the atomic-level structure of alloy nanoparticles (NPs) is necessary for the design and preparation of active and stable catalysts for fuel cell reactions such as the oxygen reduction reaction (ORR), which is highly sensitive to the structure of the catalysts. We report here structurally tunable PdCu nanoparticle catalysts for the ORR obtained by varying the thermochemical treatment parameters. The phase type and the atomic structure of the nanoalloy catalysts strongly depend on the thermochemical treatment temperature and atmosphere, especially at low temperatures. While PdCu nanoalloys feature both body-centered cubic (bcc) and face-centered cubic (fcc) phase structures, a pure fcc structure, prepared by unusually low thermochemical treatment temperature, showed the highest catalytic activity for ORR. This was evidenced by a mass activity of eight times higher than that of commercial Pd catalyst. This activity enhancement was shown to be linked to the nanostructural tuning between fcc and bcc structures, as supported by systematic characterization using X-ray diffraction coupled with pair distribution function analysis. The impact of phase structure on the catalytic properties of the nanocatalyst is further substantiated by computational modeling based on density functional theory. Our results provide a fresh insight into the nanostructure-activity correlation at the atomic scale, which has significant implications for the design, synthesis, and processing of highly-active nanoalloy catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Report on proposed improvements to FRAM uncertainty

This report discusses uncertainty metrics pertaining to the FRAM (Fixed Energy, Response Function Analysis with Multiple Efficiencies) model with respect to several actinide nuclei, especially 241Am.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2011

Solution NMR and X-ray Crystal Structures of Membrane-associated Lipoprotein-17 Domain Reveal a Novel Fold

The conserved Lipoprotein-17 domain of membrane-associated protein Q9PRA0{_}UREPA from Ureaplasma parvum was selected for structure determination by the Northeast Structural Genomics Consortium, as part of the Protein Structure Initiative's program on structure-function analysis of protein domains from large domain sequence families lacking structural representatives. The 100-residue Lipoprotein-17 domain is a 'domain of unknown function' (DUF) that is a member of Pfam protein family PF04200, a large domain family for which no members have characterized biochemical functions. The three-dimensional structure of the Lipoprotein-17 domain of protein Q9PRA0{_}UREPA was determined by both solution NMR and by X-ray crystallography at 2.5 {angstrom}. The two structures are in good agreement with each other. The domain structure features three {alpha}-helices, {alpha}1 through {alpha}3, and five {beta}-strands. Strands {beta}1/{beta}2, {beta}3/{beta}4, {beta}4/{beta}5 are anti-parallel to each other. Strands {beta}1 and {beta}2 are orthogonal to strands {beta}3, {beta}4, {beta}5, while helix {alpha}3 is formed between the strands {beta}3 and {beta}4. One-turn helix {alpha}2 is formed between the strands {beta}1 and {beta}2, while helix {alpha}1 occurs in the N-terminal polypeptide segment. Searches of the Protein Data Bank do not identify any other protein with significant structural similarity to Lipoprotein-17 domain of Q9PRA0{_}UREPA, indicating that it is a novel protein fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The electrochemical storage mechanism in oxy-hydroxyfluorinated anatase for sodium-ion batteries

Replacing lithium ions with sodium ions as the charge carriers in rechargeable batteries can induce noticeable differences in the electrochemical storage mechanisms of electrode materials. Many material parameters, such as particle size, morphology, and the presence of defects, are known to further affect the storage mechanism. Here, we report an investigation of how the introduction of titanium vacancies into anatase TiO 2 affects the sodium storage mechanism. From pair distribution function analysis, we observe that sodium ions are inserted into titanium vacancies at the early stage of the discharge process. This is supported by density functional theory calculations, which predict that sodium insertion is more favourable at vacancies than at interstitial sites. Our calculations also show that the intercalation voltage is sensitive to the anion coordination environment of the vacancy. Sodiation to higher concentrations induces a phase transition toward a disordered rhombohedral structure, similar to that observed in defect-free TiO 2 . Finally, we find that the X-ray diffraction pattern of the rhombohedral phase drastically changes depending on the composition and degree of disorder, providing further comprehension on the sodium storage mechanism of anatase.

25 ENERGY STORAGE↗