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At least 685 records · Page 38

Probabilistic Calibration of Expensive Models using Efficiently Trained Surrogates

Calibration of computational models in the presence of uncertainty is often cast as a Bayesian inference problem and solved via sampling methods, e.g., Markov chain Monte Carlo. When the computational model is expensive, this task becomes intractable due to the large number of samples required to accurately estimate the posterior distribution of the calibration parameters. A popular solution to this problem is to use machine learning to develop a faster-to-evaluate, lower-fidelity substitute for the original model to serve as a surrogate while solving the inference problem. Although considered an offline cost, generating training data to construct this surrogate model can still be an expensive task in practice. An active learning algorithm is presented that focuses training on improving surrogate accuracy specifically in and around the bulk of the posterior distribution, as this is where the model is exercised during calibration. Candidate samples are drawn from families of distributions related to an approximation of the posterior. The sample maximizing predictive variance is then selected for evaluation by the original computational model, yielding a label for the training point. Iterating this approach increases efficiency relative to space filling designs (e.g., Latin hypercube sampling) by avoiding low probability points. Practical considerations are discussed, including the benefits of using a sequential Monte Carlo sampling approach, convergence heuristics, and the importance of both exploration and exploitation given that the true posterior is unknown a priori.

uncertainty quantification↗

Data Report on Post-Irradiation Dimensional Change of AGC-1 Samples

This report documents the measured post irradiation dimensional change in the AGC-1 samples. The AGC-1 capsule is the first in six planned irradiation capsules comprising the Advanced Graphite Creep (AGC) test series. AGC-1 irradiation began September 5, 2009 in the Advanced Test Reactor (ATR) and was completed on January 8, 2011. The capsule was cooled for 3 months in the ATR Canal, and then shipped to MFC in April 2011 for disassembly and sample extraction. After extraction the samples were shipped to the INL Research Center (IRC) for initial post-irradiation examination (PIE) and storage in the irradiated graphite vault. The AGC-1 capsule design contained “matched pair” samples to ascertain the irradiation-induced dimensional changes and levels of creep experienced in different graphite types. The irradiation-induced dimensional changes and creep levels are determined by comparing the total dimensional change for stressed and unstressed samples of the same type of graphite exposed to the same dose levels and at similar temperatures. Under irradiation creep (i.e. permanent strain due to irradiation, stress, and temperature) the stressed samples should demonstrate more dimensional change than the unstressed samples. This additional dimensional change in the stressed samples is designated as “irradiation-induced creep” in graphite. The data are further presented using the parameters influencing dimensional change in graphite; levels of induced stress, temperature, graphite type, and dose. However, the AGC-1 post-irradiation examination is a significant endeavor and this data report serves to provide irradiation-induced dimensional change data for AGC capsule design refinement as well as a status on the progress of the PIE activities. The dimensional changes of both the samples and graphite body are very important to the design of the future AGC capsules (AGC-3 through AGC-6) and are provided as soon as the data are available in order to determine whether design changes to the next capsule are required. A complete evaluation of the irradiation-induced dimensional change data will be performed for a final AGC-1 PIE report that will include full analysis of pre- and post-irradiation data, with verified AGC-1 irradiation conditions of temperature and dose.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species

Here ecological understanding of disease risk, emergence, and dynamics and of the efficacy of control strategies relies heavily on efficient tools for microorganism identification and characterization. Misdetection, such as the misclassification of infected hosts as healthy, can strongly bias estimates of disease prevalence and lead to inaccurate conclusions. In natural plant ecosystems, interest in assessing microbial dynamics is increasing exponentially, but guidelines for detection of microorganisms in wild plants remain limited, particularly so for plant viruses. To address this gap, we explored issues and solutions associated with virus detection by serological and molecular methods in noncrop plant species as applied to the globally important Barley yellow dwarf virus PAV ( Luteoviridae ), which infects wild native plants as well as crops. With enzyme-linked immunosorbent assays (ELISA), we demonstrate how virus detection in a perennial wild plant species may be much greater in stems than in leaves, although leaves are most commonly sampled, and may also vary among tillers within an individual, thereby highlighting the importance of designing effective sampling strategies. With reverse transcription-PCR (RT-PCR), we demonstrate how inhibitors in tissues of perennial wild hosts can suppress virus detection but can be overcome with methods and products that improve isolation and amplification of nucleic acids. These examples demonstrate the paramount importance of testing and validating survey designs and virus detection methods for noncrop plant communities to ensure accurate ecological surveys and reliable assumptions about virus dynamics in wild hosts.

59 BASIC BIOLOGICAL SCIENCES↗

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗

Multiplexor and sensor system tradeoff study

The influence of certain sensor parameters on the accuracy of information extracted from satellite image data is studied, using a digital processing flow to simulate the effects of the sensor parameters. The method employed was to select representative images; scan and digitize them; process the digital data to simulate the effects of presampling filters, instantaneous field of view (IFOV) size and shape, sampling rates, noise, and word length; record the processed data on film; evaluate the film images; and draw conclusions from the evaluations. The study showed that presampling filters are not required to suppress aliasing, that the choice of square and circular IFOV shapes is not important, and that increased horizontal and vertical sampling rates produce an increase in apparent resolution. Work with low-contrast targets revealed a definite maximum in the tradeoff between IFOV size and SNR.

Ferneyhough, D. G., Jr.↗

Deciphering Martian climatic history using returned samples

By necessity, a Mars sample return mission must sample the upper few meters of the Martian surface. This material was subjected to a wide variety of physical processes. Presently, the most important processes are believed to be wind-driven erosion and deposition, and water ice accumulation at higher latitudes. A sample return mission represents an opportunity to better understand and quantify these important geological processes. By obtaining sample cores at key locations, it may be possible to interpret much of recent Martian climatic history.

Paige, D. A.↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II

X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation ( i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Finally, two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.

36 MATERIALS SCIENCE↗

Conodont survival and low iridium abundances across the Permian-Triassic boundary in south China

The Permian-Triassic sedimentary sequence of China includes one of the most complete and fossiliferous Paleozoic-Mesozoic boundaries known. Closely spaced sampling across the boundary, which is an important extinction event for most organisms, has produced good conodont faunas that show little diversity change. A drop in conodont abundance is the only apparent response to the extinction event. A low concentration of iridium in the boundary clay (0.002 part per billion + or - 20 percent), as well as in samples immediately below and above, that range from 0.004 to 0.034 part per billion do not support the proposal of an extraterrestrial impact event at this boundary in China.

Clark, D. L.↗

The Nature of Space Weathering in Samples From Asteroid (162173) Ryugu Revealed By Coordinated Analysis

Space weathering, driven primarily by micrometeorite bombardment and solar wind ion irradiation, alters the morphology, microstructure, and chemistry of the surface regolith on airless bodies. The accumulation of microstructural and chemical space weathering features, including melt deposits, amorphous rims, and nanophase iron-bearing particles (npFe), are associated with alterations of the spectral properties of the regolith. In particular, space weathering changes the spectral slope and reflectance of surface materials, and causes the attenuation of characteristic absorption bands in the visible to near-infrared wave-lengths, as well as a shift towards longer wavelengths of the Christiansen feature (CF)in thermal infrared spectra. Previous studies of space weathering characteristics have focused on siliceous bodies like the Moon and S-type asteroid Itokawa. However, observations of asteroid Ryugu by the JAXA Hayabusa2 spacecraft and subsequent analyses of returned samples revealed carbonaceous and hydrated materials. These samples provided our first opportunity to constrain the effects of space weathering processes on primitive, C-type asteroids. Analyses of returned samples to understand the space weathering of carbonaceous materials are important for accurately interpreting remote sensing observations of carbonaceous asteroids. In addition, the analysis of Hayabusa2 samples from Ryugu paved the way for the analysis of samples from the asteroid Bennu, re-turned by the NASA OSIRIS-REx mission. As space weathering impacts the microstructure, chemistry, and spectral characteristics of asteroidal surfaces, here we report the results of a coordinated analytical study of the micro-and nano-scale signatures of space weathering in samples returned from Ryugu.

L E Melendez↗

SAMPIE Measurements of the Space Station Plasma Current Analyzed

In March of 1994, STS-62 carried the NASA Lewis Research Center's Solar Array Module Plasma Interactions Experiment (SAMPIE) into orbit, where it investigated the plasma current collected and the arcs from solar arrays and other space power materials immersed in the low-Earth-orbit space plasma. One of the important experiments conducted was the plasma current collected by a four-cell coupon sample of solar array cells for the international space station. The importance of this experiment dates back to the 1990 and 1991 meetings of the Space Station Electrical Grounding Tiger Team. The Tiger Team determined that unless the electrical potentials on the space station structure were actively controlled via a plasma contactor, the space station structure would arc into the plasma at a rate that would destroy the thermal properties of its surface coatings in only a few years of operation. The space station plasma contactor will control its potentials by emitting electrons into the surrounding low-Earth-orbit plasma at the same rate that they are collected by the solar arrays. Thus, the level at which the space station solar arrays can collect current is very important in verifying that the plasma contactor design can do its job.

Source record↗

Mars Deep Drill - A Mission Concept for the Next Decade

In the not too distant future, NASA may consider sending a robotic mission to Mars to drill tens of meters below the surface to search for evidence of life. Mars science groups, including NASA's Mars Exploration Program Analysis Group (MEPAG), have repeatedly concluded that in situ scientific analyses of samples from significant depths below the surface are important for understanding Mars in general and for searching for evidence of past or present life in particular. Furthermore, there are several ongoing technology developments for relevant drills, the readiness of which seem promising for use by the second decade of this century. By accessing and analyzing material from tens of meters below the surface, in situ science investigations may help answer some important questions about Mars, in particular about whether life ever existed there. Drilling is a proven technique for terrestrial applications that appears viable for accessing Martian subsurface samples and bringing them to the surface for analysis by a variety of instruments. An end-to-end mission concept for a Deep Drill mission has been developed and appears feasible for launch in the next decade.

Mars↗

Effect of a Synchrotron X-ray Microtomography Imaging Experiment on the Amino Acid Content of a CM Chondrite

X-ray microcomputed tomography and synchrotron X-ray microcomputed tomography (μCT) are becoming popular tools for the reconnaissance imaging of chondrites. However, there are occasional concerns that the use of μCT may be detrimental to organic components of a chondrite. Soluble organic compounds represent ~2–10% of the total solvent extractable carbon in CI and CM carbonaceous chondrites and amino acids are among the most abundant compounds in the soluble organic fraction. We irradiated two samples of the Murchison CM2 carbonaceous chondrite under conditions slightly harsher (increased beam exposure time) than those typically used for x-ray μCT imaging experiments to determine if detectable changes in the amino acid abundance and distribution relative to a nonexposed control sample occurred. After subjecting two meteorite portions to ionizing radiation dosages of 1.1 kiloGray (kGy) and 1.2 kGy with 48.6 and 46.6 keV monochromatic X-rays, respectively, we analyzed the amino acid content of each sample. Within analytical errors, we found no differences in the amino acid abundances or enantiomeric ratios when comparing the control samples (nonexposed Murchison) and the irradiated samples. We show with calculations that any sample heating due to x-ray exposure is negligible. We conclude that a monochromatic synchrotron X-ray μCT experiment at beamline 13-BM-D of the Advanced Photon Source, which imparts ~1 kGy doses, has no detectable effect on the amino acid content of a carbonaceous chondrite. These results are important for the initial reconnaissance of returned samples from the OSIRIS-REx and Hayabusa 2 asteroid sample return missions.

Jon M. Friedrich↗

Large grain CBMM Nb ingot slices: An ideal test bed for exploring the microstructure-electromagnetic property relationships relevant to SRF

High purity (RRR > 200), large grain (> 5-10 cm) niobium ingot slices have been successfully used to fabricate radio frequency (RF) cavities for particle accelerators. They offer significantly reduced fabrication cost by eliminating processing steps and furthermore they provide the opportunity to study the influence of individual grain boundaries in SRF Nb. Here we summarize our measurements of grain boundary (GB) effects on the superconducting properties of large grain high purity niobium sheet manufactured by CBMM. We show by magneto-optical (MO) imaging that GBs allow premature flux penetration, but only when they are oriented close to the direction of the magnetic field. However, even low angle GBs produced by minor deformations commensurate with half-cell forming produce localized flux penetration. The transport properties of grain boundaries were investigated by direct transport across them and evidence for preferential vortex flow along the GBs of SRF Nb was observed for the first time. Using transmission electron microscopy (TEM) and micro crystallographic analysis with electron backscattered diffraction (EBSD), we were able to quantitatively characterize surface substructures that can lead to localized thermal breakdown of superconductivity. Important to these studies was the development of sample preparation techniques that made the cutout single, bi-crystal and tri-crystal Nb coupons as representative as possible of the surface properties of cavities manufactured by standard techniques.

36 MATERIALS SCIENCE↗

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM) thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB) to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, a 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.

36 MATERIALS SCIENCE↗

Connecting radio emission to AGN wind properties with broad absorption line quasars

ABSTRACT Broad absorption line quasars (BALQSOs) show strong signatures of powerful outflows, with the potential to alter the cosmic history of their host galaxies. These signatures are only seen in ∼10 per cent of optically selected quasars, although the fraction significantly increases in IR and radio selected samples. A proven physical explanation for this observed fraction has yet to be found, along with a determination of why this fraction increases at radio wavelengths. We present the largest sample of radio matched BALQSOs using the LOFAR Two-metre Sky Survey Data Release 2 and employ it to investigate radio properties of BALQSOs. Within the DR2 footprint, there are 3537 BALQSOs from Sloan Digital Sky Survey DR12 with continuum signal-to-noise ≥5. We find radio-detections for 1108 BALQSOs, with an important subpopulation of 120 LoBALs, an unprecedented sample size for radio matched BALQSOs given the sky coverage to date. BALQSOs are a radio-quiet population that show an increase of ×1.50 radio-detection fraction compared to non-BALQSOs. LoBALs show an increase of ×2.22 that of non-BALQSO quasars. We show that this detection fraction correlates with wind-strength, reddening, and C iv emission properties of BALQSOs and that these features may be connected, although no single property can fully explain the enhanced radio detection fraction. We create composite spectra for subclasses of BALQSOs based on wind strength and colour, finding differences in the absorption profiles of radio-detected and radio-undetected sources, particularly for LoBALs. Overall, we favour a wind-ISM interaction explanation for the increased radio-detection fraction of BALQSOs.

79 ASTRONOMY AND ASTROPHYSICS↗

Radiation attenuation by single-crystal diamond windows

As artificial diamond becomes more cost effective it is likely to see increasing use as a window for sample environment equipment used in diffraction experiments. Such windows are particularly useful as they exhibit exceptional mechanical properties in addition to being highly transparent to both X-ray and neutron radiation. A key application is in high-pressure studies, where diamond anvil cells (DACs) are used to access extreme sample conditions. However, despite their utility, an important consideration when using single-crystal diamond windows is their interaction with the incident beam. In particular, the Bragg condition will be satisfied for specific angles and wavelengths, leading to the appearance of diamond Bragg spots on the diffraction detectors but also, unavoidably, to loss of transmitted intensity of the beam that interacts with the sample. This effect can be particularly significant for energy-dispersive measurements, for example, in time-of-flight neutron diffraction work using DACs. Furthermore, this article presents a semi-empirical approach that can be used to correct for this effect, which is a prerequisite for the accurate determination of diffraction intensities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Global Retrieval of Aerosol Properties over Desert and Semi-Desert Regions from SeaWiFS and MODIS

Mineral aerosols (dust) play an important role in both climate forcing and oceanic productivity throughout the entire year. Due to the relatively short lifetime (a few hours to about a week), the distributions of these airborne dust particles vary extensively in both space and time. Consequently, satellite observations are needed over both source and sink regions for continuous temporal and spatial sampling of dust properties. However, despite their importance, the high spatial resolution satellite measurements of dust near its source have been lacking. In this paper, we will demonstrate the capability of a new satellite algorithm to retrieve aerosol optical thickness and single scattering albedo over bright-reflecting surfaces such as urban areas and deserts. Such retrievals have been difficult to perform using previously available algorithms that use wavelengths from the mid-visible to the near IR because they have trouble separating the aerosol signal from the contribution due to the bright surface reflectance. The new algorithm, called Deep Blue, utilizes blue-wavelength measurements from instruments such as SeaWiFS and MODIS to infer the properties of aerosols, sinre the stirfare reflectance nver land in the blue part of the spectrum is much lower than for longer wavelength channels. We have validated the satellite retrieved aerosol optical thickness with data from AERONET sunphotometers over desert and semi-desert regions. The comparisons show reasonable agreements between these two. These new satellite products will allow scientists to determine quantitatively the aerosol properties near sources using high spatial resolution measurements from SeaWiFS and MODIS-like instruments.

Hsu, Nai-Yung↗

Predicting the Mineral Composition of Dust Aerosols: Model Evaluation and Identification of Key Processes with Observations - Part 2

A global compilation of nearly sixty measurement studies is used to evaluate two methods of simulating the mineral composition of dust aerosols in an Earth system model. Both methods are based upon a Mean Mineralogical Table (MMT) that relates the soil mineral fractions to a global atlas of arid soil type. The Soil Mineral Fraction (SMF) method assumes that the aerosol mineral fractions match the fractions of the soil. The MMT is based upon soil measurements after wet sieving, a process that destroys aggregates of soil particles that would have been emitted from the original, undisturbed soil. The second method approximately reconstructs the emitted aggregates. This model is referred to as the Aerosol Mineral Fraction (AMF) method because the mineral fractions of the aerosols differ from those of the wet-sieved parent soil, partly due to reaggregation. The AMF method remedies some of the deficiencies of the SMF method in comparison to observations. Only the AMF method exhibits phyllosilicate mass at silt sizes, where they are abundant according to observations. In addition, the AMF quartz fraction of silt particles is in better agreement with measured values, in contrast to the overestimated SMF fraction. Measurements at distinct clay and silt particle sizes are shown to be more useful for evaluation of the models, in contrast to the sum over all particles sizes that is susceptible to compensating errors, as illustrated by the SMF experiment. Model errors suggest that allocation of the emitted silt fraction of each mineral into the corresponding transported size categories is an important remaining source of uncertainty. Evaluation of both models and the MMT is hindered by the limited number of size-resolved measurements of mineral content that sparsely sample aerosols from the major dust sources. The importance of climate processes dependent upon aerosol mineral composition shows the need for global and routine mineral measurements.

aerosols↗