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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A temperature profile diagnostic for radiation waves on OMEGA-60

Predicting and matching radiation wave propagation with computational models has proven difficult. Information provided by experiments studying radiation flow has been limited when only radiation breakout is measured. We have developed the COAX (co-axial) diagnostic platform to provide spatial temperature profiles of a radiation wave through low density foams as a more detailed constraint for simulations. COAX uses a standard, laser-driven OMEGA-60 halfraum to drive radiation down a titanium-laden silicon oxide foam. Point-projection X-ray absorption spectroscopy perpendicular to the radiation flow measures the spatial profile of titanium ionization. The spectroscopic measurement utilizes a broadband capsule backlighter. Imaging and streak spectroscopy are used to characterize the size and spectrum of this source. Radiography provides an additional constraint by capturing the developing shock as the radiation flow becomes subsonic. The DANTE diagnostic is used to measure the halfraum temperature. Here, we provide a spectroscopic analysis of COAX data to determine temperature, and we describe experimental sources of uncertainty. The temperature is obtained by comparison to multi-temperature synthetic spectra post-processed from radiation-hydrodynamics simulations. Quantitative comparison between data and synthetic spectra generated from temperature profiles at relevant simulation times enable determination of a peak temperature of 114 ± 8 eV at 265 ± 22.4 μm from the halfraum. This represents an improvement over the temperature uncertainties of previous radiation flow experiments. Further refinements to the spectroscopic analysis could achieve ±4 eV. The combination between space-resolved spectroscopy and radiography enables us to determine the distance from the halfraum of both the radiation front and the shock front at the time of measurement. For the example shown in this paper the radiation front position is 600–630 μm at 3.43 ± 0.16 ns and the shock front position is 633 μm at 3.3 ± 0.24 ns.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Recovery Profiles of T-Cell Subsets Following Low-Dose Total Body Irradiation and Improvement With Cinnamon

Purpose: Inefficient T-cell reconstitution from x-ray–induced immune damage reduces antitumor response. To understand the profile of T-cell reconstitution after irradiation will overcome the barrier of antitumor immunity. This study aimed to identify the recovery profile of T-cell subsets following x-ray irradiation and to highlight the role of cinnamon on efficient T-cell restoration postexposure in the antitumor response. Methods and Materials: CD3{sup +}, CD8{sup +}, and CD4{sup +} T cells and Th1, Th2, Th17, and regulatory T (Treg) cells were evaluated at different time points after single low-dose total body irradiation (SLTBI) with or without cinnamon treatments. T-bet, GATA3, RORγt, and Foxp3 signaling specific for Th1, Th2, Th17, and Treg were also analyzed by RT-PCR assay. The effects of cinnamon on efficient T-cell subset reconstitution was confirmed in a lung melanoma model in irradiated mice. Results: Reconstitution of CD4{sup +} T cells was delayed more than that of CD8{sup +} T cells in T-cell restoration after SLTBI. The production of IFNγ by Th1 or Tc1 cells was sharply decreased and was accompanied by reduced T-bet mRNA, even when total T-cell numbers had recovered; the frequencies of Th17 and Treg cells and their specific transcription factors (RORγt and Foxp3, respectively) were obviously increased. Irradiation-induced inefficient T-cell reconstitution impaired the antitumor capacities in the lung melanoma model. Pretreatment with cinnamon in irradiated mice accelerated the generation of Th1 and reduced the differentiation of Treg cells by activating T-bet and limiting transcriptions of Foxp3. Improvement resulting from cinnamon pretreatment on the efficient T-cell recovery profile from SLTBI promoted antitumor immunity in the lung melanoma model. Conclusions: T-cell reconstitution from SLTBI was characterized by impaired Th1 and elevated Th17 and Treg cells. Cinnamon effectively improved the imbalance of T-cell subsets by promoting the proliferation of Th1 and by suppressing expansions of Th17 and Tregs. The role of cinnamon in efficient T-cell reconstitution from SLTBI is effective in antitumor immunity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

D retention and depth profile behavior for single crystal tungsten with high temperature neutron irradiation

Single crystalline W (tungsten) samples irradiated at 633, 963 and 1073 K by neutrons to a damage level of 0.1 dpa were exposed to a high-flux D (deuterium) plasma at 673, 873 and 973 K, respectively, in TPE (Tritium Plasma Experiment) at INL (Idaho National Laboratory). Deuterium desorption was analyzed by TDS (Thermal Desorption Spectroscopy), and D depth profiles were determined by NRA (Nuclear Reaction Analysis) at SNL (Sandia National Laboratories). HIDT (Hydrogen Isotope Diffusion and Trapping) simulation code was applied to evaluate D behavior for neutron-damaged W at higher temperature. The D retention at depths up to 3 f.tm for the neutron-damaged sample at 673 K was two orders of magnitude larger than that for undamaged tungsten, and its D desorption spectrum had a single broad stage at around 900 K. As the neutron irradiation/plasma exposure temperature increased, D retention was largely reduced, and the desorption temperature was increased to higher temperatures above 1100 K. The D depth profiles by NRA also showed D migration toward bulk by higher temperature irradiation, compared to undamaged W. The HIDT simulation indicated that the major binding energy of D was changed from 1.43 eV to 2.07 eV at higher neutron irradiation and plasma exposure temperatures, suggesting that some vacancies and small vacancy clusters would aggregate to form larger voids, or depopulation of weak traps at high D plasma exposure temperatures. It can be said that more stable trapping sites played dominant roles in the D retention at higher neutron irradiation and plasma exposure temperature. The binding energy by HIDT simulation was almost consistent with the reported value by TMAP, but the consideration of not only total D retention measured by TDS but also D depth profile by NRA led to the more accurate D behavior in neutron-damaged W.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Application of the Hartmann–Tran profile to precise experimental data sets of 12 C 2 H 2

Self- and nitrogen-broadened line shape data for the P e (11) line of the ν₁ + ν₃ band of acetylene, recorded using a frequency comb-stabilized laser spectrometer, have been analyzed using the Hartmann–Tran profile (HTP) line shape model in a multispectrum fitting. In total, the data included measurements recorded at temperatures between 125 K and 296 K and at pressures between 4 and 760 Torr. New, sub-Doppler, frequency comb-referenced measurements of the positions of multiple underlying hot band lines have also been made. These underlying lines significantly affect the P e (11) line profile at temperatures above 240 K and poorly known frequencies previously introduced errors into the line shape analyses. Thus, the behavior of the HTP model was compared to the quadratic speed dependent Voigt profile (QSDVP) expressed in the frequency and time domains. A parameter uncertainty analysis was carried out using a Monte Carlo method based on the estimated pressure, transmittance and frequency measurement errors. From the analyses, the P e (11) line strength was estimated to be 1.2014(50) × 10 -20 in cm.molecules⁻¹ units at 296 K with the standard deviation in parenthesis. For analyzing these data, we found that a reduced form of the HTP, equivalent to the QSDVP, was most appropriate because the additional parameters included in the full HTP were not well determined. As a supplement to this work, expressions for analytic derivatives and a lineshape fitting code written in Matlab for the HTP are available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Background of SAM atom-fraction profiles

Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which is validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Design and Prototyping of an Ionization Profile Monitor for the SNS Accumulator Ring

An ionization profile monitor (IPM) has been designed for the Spallation Neutron Source (SNS) accumulator ring. Utilizing ionized electrons produced by beam-gas ionization, the SNS IPM uses a 120 kV bias potential to overcome beam space charge and accelerate electrons towards a movable particle detector. A 300 G magnetic field is used to confine the transverse electron motion, resulting in profile errors at the estimated 7% level. With a system bandwidth of 17.5 MHz. The SNS IPM is capable of measuring turn-by-turn beam profiles for a fully accumulated beam. This paper presents a description of the system and design.

Bartkoski, Dirk A↗
DOE OSTI2020

Space-charge effects in ionization beam profile monitors

Ionization profile monitors (IPMs) are widely used in accelerators for non-destructive and fast diagnostics of high energy particle beams. At high beam intensities, the space-charge forces make the measured IPM profiles significantly different from those of the beams. We analyze dynamics of the secondaries in IPMs and develop an effective algorithm to reconstruct the beam sizes from the measured IPM profiles. Efficiency of the developed theory is illustrated in application to the Fermilab 8 GeV proton Booster IPMs.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

Analysis of the pebble burnup profile in a pebble-bed nuclear reactor

It is known that in a pebble bed nuclear reactor, each fuel pebble draining through the core experiences a different amount of burnup depending on the precise trajectory that it follows. Understanding the burnup profile of pebbles is essential for reactor safety, as well as for fuel economy. Here, we introduce a method for constructing the burnup profile based on performing a discrete element simulation of the pebble drainage, followed by a burnup calculation in each individual pebble. This method is more accurate than previous approaches, and in particular it captures the extremal cases of pebble burnup. We demonstrate the method using the geometry, neutron flux data, and thermal characteristics from the HTR-10 reactor being developed at Tsinghua University. We examine pebble burnup during a single drainage cycle, and over multiple drainage cycles characteristic of normal reactor operation. Our results show that the presence of slow-moving boundary layers of pebbles near the reactor wall strongly influences the burnup profile. We perform a systematic study where the pebble–pebble and pebble–wall friction coefficients are independently varied, and we show that the strength of the boundary layers is a complex interplay of these two parameters.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Active microbial biomass decreases, but microbial growth potential remains similar across soil depth profiles under deeply-vs. shallow-rooted plants

Climate-smart land management practices that replace shallow-rooted annual crop systems with deeply-rooted perennial plants can contribute to soil carbon sequestration. However, deep soil carbon accrual may be influenced by active microbial biomass and their capacity to assimilate fresh carbon at depth. Incorporating active microbial biomass, dormancy, and growth in microbially-explicit models can improve our ability to predict soil's capacity to store carbon. But, so far, the microbial parameters that are needed for such modeling are poorly constrained, especially in deep soil layers. Here, we used a lab incubation experiment and growth kinetics model to estimate how microbial parameters vary along 240 cm of soil depth in profiles under shallow- (soy) and deeply-rooted (switchgrass) plants 11 years after plant cover conversion. We also assessed resource origin and availability (total organic carbon, 14 C, extractable organic carbon, specific UV absorbance of K 2 SO 4 extractable organic C, total nitrogen, total dissolved nitrogen) along the soil profiles to examine associations between soil chemical and biological parameters. Even though root biomass was greater and rooting depth was deeper under switchgrass than soy, resource availability and microbial growth parameters were generally similar between vegetation types. Instead, depth significantly influenced soil chemical and biological parameters. For example, resource availability and total and relative active microbial biomass decreased with soil depth. Decreases in the relative active microbial biomass coincided with increased lag time (response time to external carbon inputs) along the soil profiles. Even at a depth of 210–240 cm, microbial communities were activated to grow by added resources within a day. Maximum specific growth rate decreased to a depth of 90 cm and then remained consistent in deeper layers. Our findings show that >10 years of vegetation and rooting depth changes may not be long enough to alter microbial growth parameters, and suggest that at least a portion of the microbial community in deep soils can grow rapidly in response to added resources. Our study determined microbial growth parameters that can be used in microbially-explicit models to simulate carbon dynamics in deep soil layers.

14C↗
DOE OSTI2016

Global gene expression profiles in brain regions reflecting abnormal neuronal and glial functions targeting myelin sheaths after 28-day exposure to cuprizone in rats

Both developmental and postpubertal cuprizone (CPZ) exposure impairs hippocampal neurogenesis in rats. We previously found that developmental CPZ exposure alters the expression of genes related to neurogenesis, myelination, and synaptic transmission in specific brain regions of offspring. Here, we examined neuronal and glial toxicity profiles in response to postpubertal CPZ exposure by using expression microarray analysis in the hippocampal dentate gyrus, corpus callosum, cerebral cortex, and cerebellar vermis of 5-week-old male rats exposed to 0, 120, and 600 mg/kg CPZ for 28 days. Genes showing transcript upregulation were subjected to immunohistochemical analysis. We found transcript expression alterations at 600 mg/kg for genes related to synaptic transmission, Ache and Prima1, and cell cycle regulation, Tfap4 and Cdkn1a, in the dentate gyrus, which showed aberrant neurogenesis in the subgranular zone. This dose downregulated myelination-related genes in multiple brain regions, whereas KLOTHO{sup +} oligodendrocyte density was decreased only in the corpus callosum. The corpus callosum showed an increase in transcript levels for inflammatory response-related genes and in the number of CD68{sup +} microglia, MT{sup +} astrocytes, and TUNEL{sup +} apoptotic cells. These results suggest that postpubertal CPZ exposure targets synaptic transmission and cell cycle regulation to affect neurogenesis in the dentate gyrus. CPZ suppressed myelination in multiple brain regions and KLOTHO-mediated oligodendrocyte maturation only in the corpus callosum. The increased number of CD68{sup +} microglia, MT{sup +} astrocytes, and TUNEL{sup +} apoptotic cells in the corpus callosum may be involved in the induction of KLOTHO{sup +} oligodendrocyte death and be a protective mechanism against myelin damage following CPZ exposure. - Highlights: • Target gene expression profiles were examined in rats after 28-day CPZ exposure. • Multiple brain region-specific global gene expression profiling was performed. • CPZ affected synaptic function and cell cycling in the hippocampal dentate gyrus. • CPZ suppressed KLOTHO-mediated oligodendrocyte maturation in the corpus callosum. • CPZ increased metallothionein-mediated protective mechanism against myelin damage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Ultrasonic radiation from wedges of cubic profile: Experimental results

This work presents experimental results demonstrating the increase in ultrasonic radiation obtained from a wedge of cubic profile relative to a plate of uniform thickness. The wedge of cubic profile provides high efficiency sound radiation matching layer from a mounted piezoelectric transducer into the surrounding air. Previous research on structures with indentations of power-law profile has focused on vibration mitigation using the so called “acoustic black-hole” effect, whereas here such structures are used to enhance ultrasonic radiation. The work provides experimental verification of the numerical results of Remillieux et al. (2014).

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2016

Changes in global gene expression profiles induced by HPV 16 E6 oncoprotein variants in cervical carcinoma C33-A cells

We analyzed the effects of the expression of HPV 16 E6 oncoprotein variants (AA-a, AA-c, E-A176/G350, E-C188/G350, E-G350), and the E-Prototype in global gene expression profiles in an in vitro model. E6 gene was cloned into an expression vector fused to GFP and was transfected in C33-A cells. Affymetrix GeneChip Human Transcriptome Array 2.0 platform was used to analyze the expression of over 245,000 coding transcripts. We found that HPV16 E6 variants altered the expression of 387 different genes in comparison with E-Prototype. The altered genes are involved in cellular processes related to the development of cervical carcinoma, such as adhesion, angiogenesis, apoptosis, differentiation, cell cycle, proliferation, transcription and protein translation. Our results show that polymorphic changes in HPV16 E6 natural variants are sufficient to alter the overall gene expression profile in C33-A cells, explaining in part the observed differences in oncogenic potential of HPV16 variants. - Highlights: • Amino acid changes in HPV16 E6 variants modulate the transciption of specific genes. • This is the first comparison of global gene expression profile of HPV 16 E6 variants. • Each HPV 16 E6 variant appears to have its own molecular signature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometry data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.

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

nmRanalysis: An Open-Source Web Application for Semi-automated NMR Metabolite Profiling

Though data acquisition and initial signal pre-processing of nuclear magnetic resonance (NMR) spectra have achieved high degrees of automation, downstream processing - specifically the profiling of spectra - has bottlenecked the overall NMR analysis workflow. Several efforts have been made to mitigate this bottleneck, but these solutions often trade an increase in automation for limitations elsewhere. Here, in this technical note, we introduce nmRanalysis, a user-friendly web-application that integrates the strengths of existing profiling tools for a more automated profiling workflow. nmRa-nalysis additionally incorporates novel features, including a machine-learning-driven recommender system for me-tabolite identification, further increasing the utility of nmRanalysis over the individual tools that it incorporates.

Flores, Javier E. [Pacific Northwest National Labo↗
DOE OSTI2020

Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network

Advancements in molecular separations coupled with mass spectrometry have enabled large-scale metabolome analyses for clinical cohorts. A population of interest for metabolome profiling are patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic bases, as well as mechanistic drivers of the disease and possible treatment options. We undertook the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Un-diagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN pa-tients took place over three years. We describe the study design to adjust for measurements collected over a long time-scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case-studies of interest that demonstrate the utility of metabolome profiling for rare diseases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

Recent advances in sample preparation enable label-free MS-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 µL to sub-µL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by broad proteomics research community. Here we report a facile one-pot nanoproteomics method termed SOPs-MS (Surfactant-assisted One-Pot sample processing at the standard volume coupled with MS) for convenient proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOP-MS for label-free single-cell proteomics at low µL volume (Commun Bio 2021, 4, 265), we have systematically evaluated its processing volume at 10-200 µL using 100 human cells for robust reproducible nanoproteomic analysis. The processing volume of 50 µL which is in the range of volume for standard proteomics sample preparation, has been selected for easy sample handling with benchtop micropipette. Using the commonly accessible LC-MS platform, SOPs-MS allows for reliable label-free quantification of ~1200-2700 protein groups from 50-1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS can reveal distinct protein signatures between any two subpopulation cells with identification of ~1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells as well as low-input samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Relative Activities of the β-Ketoacyl-CoA and Acyl-CoA Reductases Influence the Product Profile and Flux in a Reversed β-Oxidation Pathway

The β-oxidation pathway, normally involved in the catabolism of fatty acids, can be functionally made to act as a fermentative, iterative, elongation pathway when driven by the activity of a trans-enoyl-CoA reductase (TER). Here, the terminal acyl-CoA reduction to alcohol can occur on substrates with varied chain lengths, leading to a broad distribution of fermentation products in vivo. Tight control of the average chain length and product profile is desirable, as the chain length greatly influences the molecular properties and the commercial value. Lacking a termination enzyme with a narrow chain length preference, we sought alternative factors that could influence the product profile and pathway flux in the iterative pathway. In this study, we reconstituted the reversed β-oxidation (R-βox) pathway in vitro with a purified tri-functional complex (FadBA) responsible for the thiolase, enoyl-CoA hydratase, and hydroxyacyl-CoA dehydrogenase activities, a TER, and an acyl-CoA reductase. Using this system, we determined the rate-limiting step of the elongation cycle and demonstrated that by controlling the ratio of these three enzymes and the ratio of NADH and NADPH, we can influence the average chain length of the alcohol product profile.

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

Climatology of the Vertical Profiles of Polarimetric Radar Variables and Retrieved Microphysical Parameters in Continental/Tropical MCSs and Landfalling Hurricanes

Most existing cloud models tend to overestimate the size of cloud ice particles and underestimate their concentration. This emphasizes the need to provide a reliable observational reference to optimize cloud model performance, particularly in areas of high concentration of ice at high altitudes. The dual-polarization radars give the community a unique opportunity to quantify cloud ice with a good accuracy using polarimetric radar retrievals. Here, in this study, we utilize the network of operational WSR-88D radars to build a climatology of the vertical profiles of radar variables, such as radar reflectivity Z, differential reflectivity Z DR , and specific differential phase K DP as well as the radar-retrieved vertical profiles of ice water content (IWC) above the melting layer and liquid water content below it, mean volume diameter D m , and total number concentration N t of ice and liquid particles. Such climatology was created for continental/marine mesoscale convective systems (MCSs) and tropical cyclones including hurricanes. The dataset includes 13 continental MCSs, 10 marine MCSs, and 11 tropical cyclones. Separate statistics of the “background” vertical profiles and the ones associated with high IWC aloft have been obtained in the course of this study. It is shown that continental MCSs exhibit larger size of ice in lower concentration aloft compared to the marine MCSs and especially tropical cyclones/hurricanes. A combination of high KDP and low Z aloft signifies lower D m , higher N t , and often substantial IWC.

54 ENVIRONMENTAL SCIENCES↗