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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Adaptive elasticity policies for staging-based in situ visualization

In situ processing aims to alleviate the growing gap between computation and I/O capabilities by performing data processing close to the data source. In situ processing is widely used to process data generated by multiple data sources, including observation data from edge devices or scientific observational facilities and the simulation data generated by scientific computation on a high-performance computing (HPC) platform. For a scientific workflow that is run on an HPC platform and composed of a simulation program and an in situ data analytics or visualization (abbreviated as ana/vis) task, there is an implicit assumption that the computing resources assigned to the workflow keep static during the workflow execution. However, with the converging trend between the HPC and cloud computing platform, running the in situ ana/vis task in an elastic way is promising to decrease its overhead and improve its resource utilization rate. Resource elasticity represents the ability to change resource configurations such as the number of computing nodes/processes during workflow execution. An elastic job may dynamically adjust resource configurations; it may use a few resources at the beginning and more resources toward the end of the job when interesting data appear. However, it is hard to predict a priori how many computing nodes/processes need to be added/removed during the workflow execution to adapt to changing workflow needs. How to efficiently guide elasticity operations, such as growing or shrinking the number of processes used for in situ analysis during workflow execution, is an open-ended research question. In this article, we present adaptive elasticity policies that adopt workflow runtime information collected during workflow execution to predict how to trigger the addition/removal of processes in order to minimize in situ processing overhead. Taking in situ visualization tasks as an example, we integrate the presented elasticity policies into a staging-based elastic workflow and evaluate its efficiency in multiple elasticity scenarios. Compared with the situation without elasticity or with a static elasticity policy that uses a fixed number of processes for each rescaling operation, the adaptive elasticity policy can save overhead in finding a proper resource configuration and improve resource utilization efficiency. Furthermore, one experiment illustrates that the adaptive elasticity policy saves 41% of core-hours compared with the situation without the resource elasticity.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Three-dimensional quadratic modeling and quantitative evaluation of the diaphragm on a volumetric CT scan in patients with chronic obstructive pulmonary disease

Purpose: In patients with chronic obstructive pulmonary disease (COPD), diaphragm function may deteriorate due to reduced muscle fiber length. Quantitative analysis of the morphology of the diaphragm is therefore important. In the authors current study, they propose a diaphragm segmentation method for COPD patients that uses volumetric chest computed tomography (CT) data, and they provide a quantitative analysis of the diaphragmatic dimensions. Methods: Volumetric CT data were obtained from 30 COPD patients and 10 normal control patients using a 16-row multidetector CT scanner (Siemens Sensation 16) with 0.75-mm collimation. Diaphragm segmentation using 3D ray projections on the lower surface of the lungs was performed to identify the draft diaphragmatic lung surface, which was modeled using quadratic 3D surface fitting and robust regression in order to minimize the effects of segmentation error and parameterize diaphragm morphology. This result was visually evaluated by an expert thoracic radiologist. To take into consideration the shape features of the diaphragm, several quantification parameters—including the shape index on the apex (SIA) (which was computed using gradient set to 0), principal curvatures on the apex on the fitted diaphragm surface (CA), the height between the apex and the base plane (H), the diaphragm lengths along the x-, y-, and z-axes (XL, YL, ZL), quadratic-fitted diaphragm lengths on the z-axis (FZL), average curvature (C), and surface area (SA)—were measured using in-house software and compared with the pulmonary function test (PFT) results. Results: The overall accuracy of the combined segmentation method was 97.22% ± 4.44% while the visual accuracy of the models for the segmented diaphragms was 95.28% ± 2.52% (mean ± SD). The quantitative parameters, including SIA, CA, H, XL, YL, ZL, FZL, C, and SA were 0.85 ± 0.05 (mm{sup −1}), 0.01 ± 0.00 (mm{sup −1}), 17.93 ± 10.78 (mm), 129.80 ± 11.66 (mm), 163.19 ± 13.45 (mm), 71.27 ± 17.52 (mm), 61.59 ± 16.98 (mm), 0.01 ± 0.00 (mm{sup −1}), and 34 380.75 ± 6680.06 (mm{sup 2}), respectively. Several parameters were correlated with the PFT parameters. Conclusions: The authors propose an automatic method for quantitatively evaluating the morphological parameters of the diaphragm on volumetric chest CT in COPD patients. By measuring not only the conventional length and surface area but also the shape features of the diaphragm using quadratic 3D surface modeling, the proposed method is especially useful for quantifying diaphragm characteristics. Their method may be useful for assessing morphological diaphragmatic changes in COPD patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Regional surname affinity: A spatial network approach

Abstract Objective We investigate surname affinities among areas of modern‐day China, by constructing a spatial network, and making community detection. It reports a geographical genealogy of the Chinese population that is result of population origins, historical migrations, and societal evolutions. Materials and methods We acquire data from the census records supplied by China's National Citizen Identity Information System, including the surname and regional information of 1.28 billion registered Chinese citizens. We propose a multilayer minimum spanning tree (MMST) to construct a spatial network based on the matrix of isonymic distances, which is often used to characterize the dissimilarity of surname structure among areas. We use the fast unfolding algorithm to detect network communities. Results We obtain a 10‐layer MMST network of 362 prefecture nodes and 3,610 edges derived from the matrix of the Euclidean distances among these areas. These prefectures are divided into eight groups in the spatial network via community detection. We measure the partition by comparing the inter‐distances and intra‐distances of the communities and obtain meaningful regional ethnicity classification. Discussion The visualization of the resulting communities on the map indicates that the prefectures in the same community are usually geographically adjacent. The formation of this partition is influenced by geographical factors, historic migrations, trade and economic factors, as well as isolation of culture and language. The MMST algorithm proves to be effective in geo‐genealogy and ethnicity classification for it retains essential information about surname affinity and highlights the geographical consanguinity of the population.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

36 MATERIALS SCIENCE↗

DOE OSTI2016

Evaluation of Functional Marrow Irradiation Based on Skeletal Marrow Composition Obtained Using Dual-Energy Computed Tomography

Purpose: To develop an imaging method to characterize and map marrow composition in the entire skeletal system, and to simulate differential targeted marrow irradiation based on marrow composition. Methods and Materials: Whole-body dual energy computed tomography (DECT) images of cadavers and leukemia patients were acquired, segmented to separate bone marrow components, namely, bone, red marrow (RM), and yellow marrow (YM). DECT-derived marrow fat fraction was validated using histology of lumbar vertebrae obtained from cadavers. The fractions of RM (RMF = RM/total marrow) and YMF were calculated in each skeletal region to assess the correlation of marrow composition with sites and ages. Treatment planning was simulated to target irradiation differentially at a higher dose (18 Gy) to either RM or YM and a lower dose (12 Gy) to the rest of the skeleton. Results: A significant correlation between fat fractions obtained from DECT and cadaver histology samples was observed (r=0.861, P<.0001, Pearson). The RMF decreased in the head, neck, and chest was significantly inversely correlated with age but did not show any significant age-related changes in the abdomen and pelvis regions. Conformity of radiation to targets (RM, YM) was significantly dependent on skeletal sites. The radiation exposure was significantly reduced (P<.05, t test) to organs at risk (OARs) in RM and YM irradiation compared with standard total marrow irradiation (TMI). Conclusions: Whole-body DECT offers a new imaging technique to visualize and measure skeletal-wide marrow composition. The DECT-based treatment planning offers volumetric and site-specific precise radiation dosimetry of RM and YM, which varies with aging. Our proposed method could be used as a functional compartment of TMI for further targeted radiation to specific bone marrow environment, dose escalation, reduction of doses to OARs, or a combination of these factors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Ambient Aerosol Is Physically Larger on Cloudy Days in Bondville, Illinois

Particle chemical composition affects aerosol optical and physical properties in ways important for the fate, transport, and impact of atmospheric particulate matter. For example, hygroscopic constituents take up water to increase the physical size of a particle, which can alter the extinction properties and atmospheric lifetime. At the collocated AERosol RObotic NETwork (AERONET) and Interagency Monitoring of PROtected Visual Environments (IMPROVE) network monitoring stations in rural Bondville, Illinois, we employ a novel cloudiness determination method to compare measured aerosol physicochemical properties on predominantly cloudy and clear sky days from 2010 to 2019. On cloudy days, aerosol optical depth (AOD) is significantly higher than on clear sky days in all seasons. Measured angstrom ngstro''m exponents are significantly smaller on cloudy days, indicating physically larger average particle size for the sampled populations in all seasons except winter. Mass concentrations of fine particulate matter that include estimates of aerosol liquid water (ALW) are higher on cloudy days in all seasons but winter. More ALW on cloudy days is consistent with larger particle sizes inferred from angstrom ngstro''m exponent measurements. Aerosol chemical composition that affects hygroscopicity plays a determining impact on cloudy versus clear sky differences in AOD, angstrom ngstro''m exponents, and ALW. This work highlights the need for simultaneous collocated, high-time-resolution measurements of both aerosol chemical and physical properties, in particular at cloudy times when quantitative understanding of tropospheric composition is most uncertain.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Interfacial analysis of a PEM electrolyzer using X-ray computed tomography

Explore the source record for details and available documents.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Towards Feature-Preserving 2D and 3D Vector Field Compression

The objective of this work is to develop error-bounded lossy compression methods to preserve topological features in 2D and 3D vector fields. Specifically, we explore the preservation of critical points in piecewise linear vector fields. We define the preservation of critical points as, without any false positive, false negative, or false type change in the decompressed data, (1) keeping each critical point in its original cell and (2) retaining the type of each critical point (e.g., saddle and attracting node). The key to our method is to adapt a vertex-wise error bound for each grid point and to compress input data together with the error bound field using a modified lossy compressor. Our compression algorithm can be also embarrassingly parallelized for large data handling and in situ processing. We benchmark our method by comparing it with existing lossy compressors in terms of false positive/negative/type rates, compression ratio, and various vector field visualizations with several scientific applications.

critical points↗

DOE OSTI2014

SU-C-18A-05: Registration Accuracy of MR-Based Images to On-Board Megavoltage Cone-Beam CT for Brain Patient Setup

Purpose: To quantify the difference in isocenter shifts when co-registering MR and MR-based pseudo CTs (pCT) with on-board megavoltage conebeam CT (CBCT) images. Methods: Fast Spoiled Gradient Echo MRs were used to generate pCTs (research version of Advantage Sim MD™, GE Healthcare) for ten patients who had prior brain radiotherapy. The planning CT (rCT) for each was co-registered with the MR, and the plan isocenter and two other reference points were transferred to the MR and pCT. CBCT images (with the machine isocenter) from a single treatment day were coregistered with the 3 test images (MR, pCT and rCT), by two observers and by an automated registration algorithm. The reference points were used to calculate patient shifts and rotations from the registrations. The shifts calculated from the test image registrations were compared to each other and to the shifts performed by the therapists who treated the patients on that day. Results: The average difference in absolute value between the isocenter shifts from the MR-, pCT- and rCT-CBCT registrations, and the therapist shifts, were 2.02, 3.01 and 0.89 mm (craniocaudal), 1.14, 1.34 and 0.46 mm (lateral), and 1.37, 3.43 and 1.43 mm (vertical), respectively. The MR- and pCT-CBCT registrations differed by 1.99, and 2.53 mm (craniocaudal), 1.36, and 1.37 mm (lateral), and 0.74 and 2.34 mm (vertical), respectively, from the average rCT-CBCT shifts. On average, differences of 2.39 (craniocaudal), 1.28 (lateral) and 2.84 mm (vertical) were seen between the MR and pCT shifts. Rotations relative to the CBCT coordinate system were on average <2° for the MR and rCT, and <6° for the pCT. Conclusion: In this study, FSPGR MR-CBCT registrations were more precise compared to the pCT-CBCT registrations. For improved accuracy, MR sequences that are optimal for bony anatomy visualization are necessary. GE healthcare has provided a research version of Advantage Sim MD to UCSF. No financial support was provided.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

RELAP5-3D developmental assessment: Comparison of version 4.2.1i on Linux and Windows

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.2i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2014

RELAP5-3D Developmental Assessment: Comparison of Versions 4.2.1i and 4.1.3i

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code using versions 4.2.1i and 4.1.3i. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions changed between these two code versions and can be used to identify cases in which the assessment judgment may need to be changed in Volume III of the code manual. Changes to the assessment judgments made after reviewing all of the assessment cases are also provided.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Validation of the HyRAM+ physics models for use with propane

The Hydrogen Risk Assessment Model Plus (HyRAM+) toolkit combines quantitative risk assessment with simulations of unignited dispersion, ignited turbulent diffusion flames, and indoor accumulation with delayed ignition of fuels. HyRAM+ is differentiated from HyRAM in that it includes models and leak data for other alternate fuels. The models of the physical phenomena need to be validated for each of the fuels in the toolkit. This report shows the validation for propane which is being used as a surrogate for autogas, which is a mixture of propane and butane and used in internal combustion engines in vehicles. For flame length comparisons, five previously published experiments from peer reviewed journals were used to validate our models. The validation looked at flame lengths and flame widths with respect to different leak diameters, mass flow rates, and source pressures. Most of the sources included more than one set of experimental data, which were collected using different methods (CCD cameras, IR visualization etc.). In general, HyRAM+ overpredicts the flame lengths by around 65%. For heat and radiation models, we compared the heat flux and radiation data reported from two different sources to the values calculated by HyRAM+. For higher mass flow rates, the HyRAM+ calculated flame length results gave a better estimate of what is found in the experiments (65% error), but a higher error (85%) is observed between the HyRAM+ calculated lengths and the experimental flame lengthsfor lower mass flows. Some differences can be attributed to outdoor environmental effects (i.e. wind speed) and uncertainties in jet flame shapes. The propane flame trajectory is predicted for a high Reynolds number case with Re = 12,500 and a low Reynolds number case where Re = 2,000. The Re=12,500 case which is momentum dominated matches well with the experimental flame trajectory, but the agreement for the bouancy driven low Reynolds number case is not as good. Dispersion modeling for unignited propane was also analyzed. We compared the mole fraction, mixture fraction, mean velocity, concentration half width, and inverse mass concentration over an axial distance from different credible journals to the values calculated by HyRAM+. The results display good agreement but generally, HyRAM+ predicts a wider profile for mole fraction and mixture fraction experiments. Overall, HyRAM+’s results are reasonable for predicting the flame length, heat flux, flame trajectory, and dispersion for propane and can be used in risk analyses

08 HYDROGEN↗

DOE OSTI2017

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Evaluating the Efficacy of Wavelet Configurations on Turbulent-Flow Data

I/O is increasingly becoming a significant constraint for simulation codes and visualization tools on modern supercomputers. Data compression is an attractive workaround, and, in particular, wavelets provide a promising solution. However, wavelets can be applied in multiple configurations, and the variations in configuration impact accuracy, storage cost, and execution time. While the variation in these factors over wavelet configurations have been explored in image processing, they are not well understood for visualization and analysis of scientific data. To illuminate this issue, we evaluate multiple wavelet configurations on turbulent-flow data. Our approach is to repeat established analysis routines on uncompressed and lossy-compressed versions of a data set, and then quantitatively compare their outcomes. Our findings show that accuracy varies greatly based on wavelet configuration, while storage cost and execution time vary less. Overall, our study provides new insights for simulation analysts and visualization experts, who need to make tradeoffs between accuracy, storage cost, and execution time.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Breaking the barrier of human-annotated training data for machine learning-aided plant research using aerial imagery

Machine learning (ML) can accelerate biological research. However, the adoption of such tools to facilitate phenotyping based on sensor data has been limited by (i) the need for a large amount of human-annotated training data for each context in which the tool is used and (ii) phenotypes varying across contexts defined in terms of genetics and environment. This is a major bottleneck because acquiring training data is generally costly and time-consuming. This study demonstrates how a ML approach can address these challenges by minimizing the amount of human supervision needed for tool building. A case study was performed to compare ML approaches that examine images collected by an uncrewed aerial vehicle to determine the presence/absence of panicles (i.e. “heading”) across thousands of field plots containing genetically diverse breeding populations of 2 Miscanthus species. Automated analysis of aerial imagery enabled the identification of heading approximately 9 times faster than in-field visual inspection by humans. Leveraging an Efficiently Supervised Generative Adversarial Network (ESGAN) learning strategy reduced the requirement for human-annotated data by 1 to 2 orders of magnitude compared to traditional, fully supervised learning approaches. The ESGAN model learned the salient features of the data set by using thousands of unlabeled images to inform the discriminative ability of a classifier so that it required minimal human-labeled training data. This method can accelerate the phenotyping of heading date as a measure of flowering time in Miscanthus across diverse contexts (e.g. in multistate trials) and opens avenues to promote the broad adoption of ML tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

pixelvar79/ESGAN-Flowering-Detection-paper

Varela, Sebastian↗

DOE OSTI2018

Franklin expedition lead exposure: New insights from high resolution confocal x-ray fluorescence imaging of skeletal microstructure

In the summer of 1845, under the command of Sir John Franklin, 128 officers and men aboard Royal Navy ships HMS Erebus and HMS Terror sailed into Lancaster Sound and entered the waters of Arctic North America. The goal of this expedition was to complete the discovery of a northwest passage by navigating the uncharted area between Barrow Strait and Simpson Strait. Franklin and his crew spent the first winter at Beechey Island, where three crewmen died and were buried. In September 1846, the ships became stranded in ice off the northwest coast of King William Island, where they remained until April 1848. At that time, the crew, reduced to 105, deserted the ships and retreated south along the island’s western and southern shores in a desperate attempt to reach the mainland and via the Back River, to obtain aid at a Hudson’s Bay Company Post. Sadly, not one individual survived. Previous analyses of bone, hair, and soft tissue samples from expedition remains found that crewmembers’ tissues contained elevated lead (Pb) levels, suggesting that Pb poisoning may have contributed to their demise; however, questions remain regarding the timing and degree of exposure and, ultimately, the extent to which the crewmembers may have been impacted. To address this historical question, we investigated three hypotheses. First, if elevated Pb exposure was experienced by the crew during the expedition, we hypothesized that those sailors who survived longer (King William Island vs. Beechey Island) would exhibit more extensive uptake of Pb in their bones and vice versa. Second, we hypothesized that Pb would be elevated in bone microstructural features forming at or near the time of death compared with older tissue. Finally, if Pb exposure played a significant role in the failure of the expedition we hypothesized that bone samples would exhibit evidence of higher and more sustained uptake of Pb than that of a contemporary comparator naval population from the 19 th century. To test these hypotheses, we analyzed bone and dental remains of crew members and compared them against samples derived from the Royal Navy cemetery in Antigua. Synchrotron-based high resolution confocal X-ray fluorescence imaging was employed to visualize Pb distribution within bone and tooth microstructures at the micro scale. The data did not support our first hypothesis as Pb distribution within the samples from the two different sites was similar. Evidence of Pb within skeletal microstructural features formed near the time of death lent support to our second hypothesis but consistent evidence of a marked elevation in Pb levels was lacking. Finally, the comparative analysis with the Antigua samples did not support the hypothesis that the Franklin sailors were exposed to an unusually high level of Pb for the time period. Taken all together our skeletal microstructural results do not support the conclusion that Pb played a pivotal role in the loss of Franklin and his crew.

59 BASIC BIOLOGICAL SCIENCES↗