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At least 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A fully contained sample holder capable of electron-yield detection at soft X-ray energies

A holder has been developed that enables electron yield-detected soft X-ray spectroscopy of fully contained samples at low temperature. Crucially, this design uses elements of the sample containment to collect ejected electrons, removing the need to expose samples directly to the vacuum environment of the spectrometer. The design is modular and should be adaptable to a number of different endstation configurations, enabling spectroscopy of air-sensitive, radioactive and vacuum-sensitive (biological) samples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Sampling on NISQ Devices: "Who’s the Fairest One of All?"

Modern NISQ devices are subject to a variety of biases and sources of noise that degrade the solution quality of computations carried out on these devices. A natural question that arises in the NISQ era, is how fairly do these devices sample ground state solutions. To this end, we run five fair sampling problems (each with at least three ground state solutions) that are based both on quantum annealing and, on the Grover Mixer, -QAOA algorithm for gate-based NISQ hardware. In particular, we use seven IBM Q devices, the Aspen-9 Rigetti device, the IonQ device, and three D-Wave quantum annealers. For each of the fair sampling problems, we measure the ground state probability, the relative fairness of the frequency of each ground state solution with respect to the other ground state solutions, and the aggregate error as given by each hardware provider. Overall, our results show that NISQ devices do not achieve fair sampling yet. Furthermore, we also observe differences in the software stack with a particular focus on compilation techniques that illustrate what work will still need to be done to achieve a seamless integration of frontend (i.e., quantum circuit description) and backend compilation.

Computer Science↗
DOE OSTI2024

Sampling in Long-Screened Wells: Issues, Misconceptions, and Solutions

The issues associated with long-screened wells (LSWs) (and open boreholes) at contaminated sites are well documented in the groundwater literature but are still not fully appreciated in practice. As established in seminal and review papers going back over three decades, the interpretation of sampling results from LSWs is challenging in the presence of vertical hydraulic gradients and borehole flow; furthermore, LSWs allow for vertical redistribution of contamination between aquifer layers. Acknowledgment of these issues has led to the development of new technologies and well designs to enable discrete-zone monitoring (DZM), yet LSWs remain common for many reasons, for example, as multipurpose wells, for geophysical logging, and (or) as legacy installations. Despite the literature on LSWs and despite the adoption of DZM at many sites, the use of LSWs persists and the challenges of interpreting sampling results from LSWs remain. In this issue paper, we provide a conceptual overview of the problems posed by LSWs and review existing literature and past work to improve the interpretation of sampling in LSWs. We draw on experience from previous studies at the Hanford Site in eastern WA, USA, and use synthetic examples to illustrate key concepts and challenges for interpretation. A recently published analytical modeling framework is used to develop illustrative synthetic examples and demonstrate a workflow for building scientific intuition to understand issues around interpreting samples from LSWs, which is critical to effective characterization and groundwater remediation at sites with LSWs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The iron oxidation state of Ryugu samples

The Hayabusa2 mission sampled Ryugu, an asteroid that did not suffer extensive thermal metamorphism, and returned rocks to the Earth with no significant air exposure. It therefore offers a unique opportunity to study the redox state of carbonaceous Cb-type asteroids and evaluate the overall redox state of the most primitive rocks of the solar system. An analytical framework was developed to investigate the iron mineralogy and valence state in extraterrestrial material at the micron scale by combining x-ray diffraction, conventional Mössbauer (MS), and nuclear forward scattering (NFS) spectroscopies. An array of standard minerals was analyzed and cross-calibrated between MS and NFS. Then, MS and NFS spectra on three Ryugu grains were collected at the bulk and the micron scales. In Ryugu samples, iron is essentially accommodated in magnetite, clay minerals (serpentine–smectite), and sulfides. Only a single set of Mössbauer parameters was necessary to account for the entire variability observed in MS and NFS spectra, at all spatial scales investigated. These parameters therefore make up a fully consistent iron mineralogical model for the Ryugu samples. As far as MS and NFS spectroscopies are concerned, Ryugu grains are overall similar to each other and share most of their mineralogical features with CI-type chondrites. In detail however, no ferrihydrite is found in Ryugu particles even at the very sensitive scale of Mössbauer spectroscopy. The typical Fe 3+ /Fe tot of clay minerals is much lower than typical redox ratios measured in CI chondrites (Fe 3+ /Fe tot = 85%–90%). Furthermore, magnetite from Ryugu is stoichiometric with no significant maghemite component, whereas up to 12% of maghemite was previously identified in the Orgueil's so-called magnetite. These differences suggest that most CI meteorites suffered terrestrial alteration and that the preterrestrial composition of these carbon-rich samples was less oxidized than previously measured. However, it is not clear yet whether or not the parent bodies of CI chondrites were as reduced as Ryugu. Finally, the high spatial resolution of NFS allows to disentangle the redox state and the crystal chemistry of iron accommodated in serpentine and smectite. The most likely polytype of serpentine is lizardite, containing <35% of Fe 3+ , a fraction of which being tetrahedrally coordinated. Smectite is more oxidized (Fe 3+ /Fe tot > 65%) and mainly contains octahedral ferric iron. In conclusion, this finding implies that these clays formed from highly alkaline fluids and the spatial variability highlighted here may suggest a temporal evolution or a spatial variability of the nature of this fluid.

58 GEOSCIENCES↗
DOE OSTI2018

Simple effective conservative treatment of uncertainty from sparse samples of random functions

This paper examines the variability of predicted responses when multiple stress-strain curves (reflecting variability from replicate material tests) are propagated through a finite element model of a ductile steel can being slowly crushed. Over 140 response quantities of interest (including displacements, stresses, strains, and calculated measures of material damage) are tracked in the simulations. Each response quantity’s behavior varies according to the particular stress-strain curves used for the materials in the model. We desire to estimate response variability when only a few stress-strain curve samples are available from material testing. Propagation of just a few samples will usually result in significantly underestimated response uncertainty relative to propagation of a much larger population that adequately samples the presiding random-function source. A simple classical statistical method, Tolerance Intervals, is tested for effectively treating sparse stress-strain curve data. The method is found to perform well on the highly nonlinear input-to-output response mappings and non-standard response distributions in the can-crush problem. The results and discussion in this paper support a proposition that the method will apply similarly well for other sparsely sampled random variable or function data, whether from experiments or models. Finally, the simple Tolerance Interval method is also demonstrated to be very economical.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Image-derived and arterial blood sampled input functions for quantitative PET imaging of the angiotensin II subtype 1 receptor in the kidney

Purpose: The radioligand {sup 11}C-KR31173 has been introduced for positron emission tomography (PET) imaging of the angiotensin II subtype 1 receptor in the kidney in vivo. To study the biokinetics of {sup 11}C-KR31173 with a compartmental model, the input function is needed. Collection and analysis of arterial blood samples are the established approach to obtain the input function but they are not feasible in patients with renal diseases. The goal of this study was to develop a quantitative technique that can provide an accurate image-derived input function (ID-IF) to replace the conventional invasive arterial sampling and test the method in pigs with the goal of translation into human studies. Methods: The experimental animals were injected with [{sup 11}C]KR31173 and scanned up to 90 min with dynamic PET. Arterial blood samples were collected for the artery derived input function (AD-IF) and used as a gold standard for ID-IF. Before PET, magnetic resonance angiography of the kidneys was obtained to provide the anatomical information required for derivation of the recovery coefficients in the abdominal aorta, a requirement for partial volume correction of the ID-IF. Different image reconstruction methods, filtered back projection (FBP) and ordered subset expectation maximization (OS-EM), were investigated for the best trade-off between bias and variance of the ID-IF. The effects of kidney uptakes on the quantitative accuracy of ID-IF were also studied. Biological variables such as red blood cell binding and radioligand metabolism were also taken into consideration. A single blood sample was used for calibration in the later phase of the input function. Results: In the first 2 min after injection, the OS-EM based ID-IF was found to be biased, and the bias was found to be induced by the kidney uptake. No such bias was found with the FBP based image reconstruction method. However, the OS-EM based image reconstruction was found to reduce variance in the subsequent phase of the ID-IF. The combined use of FBP and OS-EM resulted in reduced bias and noise. After performing all the necessary corrections, the areas under the curves (AUCs) of the AD-IF were close to that of the AD-IF (average AUC ratio =1 ± 0.08) during the early phase. When applied in a two-tissue-compartmental kinetic model, the average difference between the estimated model parameters from ID-IF and AD-IF was 10% which was within the error of the estimation method. Conclusions: The bias of radioligand concentration in the aorta from the OS-EM image reconstruction is significantly affected by radioligand uptake in the adjacent kidney and cannot be neglected for quantitative evaluation. With careful calibrations and corrections, the ID-IF derived from quantitative dynamic PET images can be used as the input function of the compartmental model to quantify the renal kinetics of {sup 11}C-KR31173 in experimental animals and the authors intend to evaluate this method in future human studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

The Spectrum of Thermally Stimulated Surface Plasmon Polaritons of a Linear Sample

An analytical model of the spectrum of thermally stimulated surface plasmon polaritons (TSSPPs) coming to the edge of a linear conducting sample has been developed. It has been found that the spectrum of such TSSPPs obeys neither the Wien law nor the Stefan–Boltzmann law for thermal radiation. The maximum of this spectrum is shifted to the low-frequency region with respect to the spectrum of the absolutely black body, and the magnitude of the shift is proportional to the sample length. The plasmon nature of the intensity increment of thermal radiation from the edge of a plane face of a duralumin sample has been verified experimentally. It has been shown that the intensity and spectrum of this increment can be controlled both by the sample temperature and by the extension of the face.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Experimental Determination of the Radial Displacement Field in the Neck of Samples after a Tensile Test

This Letter presents the results of a study of the radial displacement fields arising upon stretching of cylindrical samples before their disintegration. The object of study was sv-07Kh16N6 stainless steel wire containing filiform defects oriented along the sample axis. Using X-ray tomography of the sample necks, the coordinates of the defect points in the sample are determined and the displacement field is recovered from them. The resulting dependence is represented by an approximate formula.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Efficient sampling of constrained high-dimensional theoretical spaces with machine learning

Abstract Models of physics beyond the Standard Model often contain a large number of parameters. These form a high-dimensional space that is computationally intractable to fully explore. Experimental results project onto a subspace of parameters that are consistent with those observations, but mapping these constraints to the underlying parameters is also typically intractable. Instead, physicists often resort to scanning small subsets of the full parameter space and testing for experimental consistency. We propose an alternative approach that uses generative models to significantly improve the computational efficiency of sampling high-dimensional parameter spaces. To demonstrate this, we sample the constrained and phenomenological Minimal Supersymmetric Standard Models subject to the requirement that the sampled points are consistent with the measured Higgs boson mass. Our method achieves orders of magnitude improvements in sampling efficiency compared to a brute force search.

Hollingsworth, Jacob↗
DOE OSTI2018

Elemental and topographical imaging of microscopic variations in deposition on NSTX-U and DIII-D samples

Tokamak plasma facing components have surface roughness that can cause microscopic spatial variations in erosion and deposition and hence influence material migration, erosion lifetime, dust and tritium accumulation, and plasma contamination. However high spatial resolution measurements of deposition on the scale of the surface roughness have been lacking to date. We will present elemental images of graphite samples from NSTX-U and DIII-D DiMES experiments performed with a Scanning Auger Microprobe at sub-micron resolution that show strong microscopic variations in deposition and correlate this with 3D topographical maps of surface irregularities. The NSTX-U samples were boronized and exposed to deuterium plasmas and the DiMES samples had localized Al and W films and were exposed to dedicated helium plasmas. Topographical maps of the samples were performed with a 3D confocal optical microscope and compared to the elemental deposition pattern. The results revealed localized deposition concentrated in areas shadowed from the ion flux, incident in a direction calculated (for the DiMES case) by taking account of the magnetic pre-sheath.

Surface analysis↗
DOE OSTI2015

Does size matter? Separations on guard columns for fast sample analysis applied to bioenergy research

Increasing sample throughput is needed when large numbers of samples have to be processed. In chromatography, one strategy is to reduce column length for decreased analysis time. Therefore, the feasibility of analyzing samples simply on a guard column was explored using refractive index and ultraviolet detection. Results from the guard columns were compared to the analyses using the standard 300 mm Aminex HPX-87H column which is widely applied to the analysis of samples from many biotechnology- and bioenergy-related experiments such as biomass conversions or fermentations.

Biotechnology & Applied Microbiology↗
DOE OSTI2023

Standard experimental paradigm designs and data exclusion practices in cognitive psychology can inadvertently introduce systematic “shadow” biases in participant samples

Abstract Standard cognitive psychology research practices can introduce inadvertent sampling biases that reduce the reliability and generalizability of the findings. Researchers commonly acknowledge and understand that any given study sample is not perfectly generalizable, especially when implementing typical experimental constraints (e.g., limiting recruitment to specific age ranges or to individuals with normal color vision). However, less obvious systematic sampling constraints, referred to here as “shadow” biases, can be unintentionally introduced and can easily go unnoticed. For example, many standard cognitive psychology study designs involve lengthy and tedious experiments with simple, repetitive stimuli. Such testing environments may 1) be aversive to some would-be participants (e.g., those high in certain neurodivergent symptoms) who may self-select not to enroll in such studies, or 2) contribute to participant attrition, both of which reduce the sample’s representativeness. Likewise, standard performance-based data exclusion efforts (e.g., minimum accuracy or response time) or attention checks can systematically remove data from participants from subsets of the population (e.g., those low in conscientiousness). This commentary focuses on the theoretical and practical issues behind these non-obvious and often unacknowledged “shadow” biases, offers a simple illustration with real data as a proof of concept of how applying attention checks can systematically skew latent/hidden variables in the included population, and then discusses the broader implications with suggestions for how to manage and reduce, or at a minimum acknowledge, the problem.

Siritzky, Emma M.↗
DOE OSTI2015

Neutron-Irradiated Samples as Test Materials for MPEX

Plasma Material Interaction (PMI) is a major concern in fusion reactor design and analysis. The Material-Plasma Exposure eXperiment (MPEX) will explore PMI under fusion reactor plasma conditions. Samples with accumulated displacements per atom (DPA) damage produced by fast neutron irradiations in the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) will be studied in the MPEX facility. This paper presents assessments of the calculated induced radioactivity and resulting radiation dose rates of a variety of potential fusion reactor plasma-facing materials (such as tungsten). The scientific code packages MCNP and SCALE were used to simulate irradiation of the samples in HFIR including the generation and depletion of nuclides in the material and the subsequent composition, activity levels, gamma radiation fields, and resultant dose rates as a function of cooling time. A challenge of the MPEX project is to minimize the radioactive inventory in the preparation of the samples and the sample dose rates for inclusion in the MPEX facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

A novel analysis method for paired-sample microbial ecology experiments

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). Finally, when analyzing empirical data (wholegenome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Untargeted, tandem mass spectrometry (LC/MS-MS) metaproteomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of Lawrence Berkeley National Laboratory (LBNL) Terrestrial Ecosystem Science (TES) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization. This package contains soil metaproteomics data in the context of site specific metagenomes from soil depth profiles in three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. These metaproteomes were collected in 2018 after 4.5 years of warming from five depth intervals (0-10 cm, 10-30 cm, 30-45 cm, 45-60 cm, 60-80 cm). For protein identification, the collected spectra were searched following a target-decoy search strategy against a database of metagenome predicted proteins (covering 96 samples from 2014 to 2021) representing the complete sequence diversity at the site. Data was searched with mass spectrometry database search tool (MS-GF+) using Pacific Northwest National Laboratory (PNNL)'s Data Management System (DMS) Processing pipeline. The metagenomes are published as part of another data package. Raw metaproteomic data and the data products from MS-GF+ are deposited in the Mass Spectrometry Interactive Virtual Environment (MassIVE) database under accession no. MSV000097826. Here we present a dataset that includes spectral counts for the detected proteins across samples (EMSL50964_BrodieAllMAGs_Globals_SC.txt), the sequences of the detected proteins, and sample metadata file that contains site information for the soil metaproteome samples.

Belowground Biogeochemistry Science Focus Area↗
DOE OSTI2024

A Provably Accurate Randomized Sampling Algorithm for Logistic Regression

In statistics and machine learning, logistic regression is a widely-used supervised learning technique primarily employed for binary classification tasks. When the number of observations greatly exceeds the number of predictor variables, we present a simple, randomized sampling-based algorithm for logistic regression problem that guarantees high-quality approximations to both the estimated probabilities and the overall discrepancy of the model. Our analysis builds upon two simple structural conditions that boil down to randomized matrix multiplication, a fundamental and well-understood primitive of randomized numerical linear algebra. We analyze the properties of estimated probabilities of logistic regression when leverage scores are used to sample observations, and prove that accurate approximations can be achieved with a sample whose size is much smaller than the total number of observations. To further validate our theoretical findings, we conduct comprehensive empirical evaluations. Overall, our work sheds light on the potential of using randomized sampling approaches to efficiently approximate the estimated probabilities in logistic regression, offering a practical and computationally efficient solution for large-scale datasets.

Chowdhury, Agniva↗
DOE OSTI2015

Solvent hold tank sample results for MCU-14-913 and MCU-14-986/987: October 2014 monthly

SRNL received two sets of SHT samples (MCU-14-913, pulled 10/7/2014 and MCU-14-986/987, pulled on 10/27/2014) for analysis. The samples were analyzed for composition. Analysis of sample MCU-14- 913 indicated low concentrations of the suppressor (TiDG) and of the modifier (CS-7SB) in the solvent. The addition of suppressor and modifier to the solvent on October 26, 2014 restored the concentration of these components to nominal levels as confirmed with the analysis of sample MCU-14-986/987. The laboratory will continue to monitor the quality of the solvent in particular for any new impurity or degradation of the solvent components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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