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At least 379 records · Page 21

Priority research directions for in situ data management: Enabling scientific discovery from diverse data sources

In January 2019, the US Department of Energy, Office of Science program in Advanced Scientific Computing Research, convened a workshop to identify priority research directions (PRDs) for in situ data management (ISDM). A fundamental finding of this workshop is that the methodologies used to manage data among a variety of tasks in situ can be used to facilitate scientific discovery from many different data sources—simulation, experiment, and sensors, for example—and that being able to do so at numerous computing scales will benefit real-time decision-making, design optimization, and data-driven scientific discovery. This article describes six PRDs identified by the workshop, which highlight the components and capabilities needed for ISDM to be successful for a wide variety of applications—making ISDM capabilities more pervasive, controllable, composable, and transparent, with a focus on greater coordination with the software stack and a diversity of fundamentally new data algorithms.

97 MATHEMATICS AND COMPUTING↗

Space station protective coating development

A generic list of Space Station surfaces and candidate material types is provided. Environmental exposures and performance requirements for the different Space Station surfaces are listed. Coating materials and the processing required to produce a viable system, and appropriate environmental simulation test facilities are being developed. Mass loss data from the original version of the atomic oxygen test chamber and the improved facility; additional environmental exposures performed on candidate materials; and materials properties measurements on candidate coatings to determine the effects of the exposures are discussed. Methodologies of production, and coating materials, used to produce the large scale demonstration articles are described. The electronic data base developed for the contract is also described. The test chamber to be used for exposure of materials to atomic oxygen was built.

Pippin, H. G.↗

Quantifying the Benefit of a Pathologic Complete Response After Neoadjuvant Chemoradiotherapy in the Treatment of Esophageal Cancer

Purpose: To better define the benefit of a pathologic complete response (pCR) after neoadjuvant chemoradiotherapy in the treatment of esophageal and gastroesophageal cancer, we undertook a comprehensive review of the literature to derive a pooled analysis of crude survival data and quantify the survival benefit of pCR vs. residual disease at esophagectomy. Methods and Materials: In all, 22 articles were reviewed. Crude overall survival data, stratified by patients with pCR vs. those with residual disease at esophagectomy, were collected and analyzed using a chi-square analysis. The relative and absolute survival benefit of achieving a pCR were calculated and analyzed. Finally, stratified median survival times were also analyzed. Results: Overall survival for patients with pCR was 93.1%, 75.0%, and 50.0% at 2, 3, and 5 years, respectively, whereas it was 36.8%, 29.0%, and 22.6% for patients with residual tumor (p < 0.025). The mean relative survival benefit of pCR at 2, 3, and 5 years was 2.05, 2.35, and 2.84, respectively. The mean absolute survival benefit of pCR was 35.66%, 33.79%, and 33.20%, respectively. Median survival times for patients with pCR were significantly longer than for those with residual tumor (p = 0.011). Conclusion: In esophageal and gastroesophageal cancers, pCR seems to significantly increase overall survival in patients undergoing neoadjuvant chemoradiotherapy. Specifically, the data suggest that patients with pCR are two to three times more likely to survive than are those with residual tumor at esophagectomy. Moreover, these data suggest that 33-36% more patients survive when pCR is achieved than when it is not.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Data management and processing workflow for the Materials Physics and Engineering group beamlines at the Advanced Photon Source

The ability to store, organize, process and distribute experimental data effectively, efficiently and securely is particularly important for large user facilities like the Advanced Photon Source. In this article, the deployment of the APS Data Management System (DM) at the 1-ID and 6-BM beamlines of the APS is described. These two beamlines support a wide range of experimental techniques and generate data at relatively high rates, making them ideal candidates to illustrate the deployment and customization of the DM system and its tools. Using several usage examples at these beamlines, various capabilities of the DM system are described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Bayesian tomography and integrated data analysis in fusion diagnostics

In this article, a Bayesian tomography method using non-stationary Gaussian process for a prior has been introduced. The Bayesian formalism allows quantities which bear uncertainty to be expressed in the probabilistic form so that the uncertainty of a final solution can be fully resolved from the confidence interval of a posterior probability. Moreover, a consistency check of that solution can be performed by checking whether the misfits between predicted and measured data are reasonably within an assumed data error. In particular, the accuracy of reconstructions is significantly improved by using the non-stationary Gaussian process that can adapt to the varying smoothness of emission distribution. The implementation of this method to a soft X-ray diagnostics on HL-2A has been used to explore relevant physics in equilibrium and MHD instability modes. This project is carried out within a large size inference framework, aiming at an integrated analysis of heterogeneous diagnostics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Distributed Detection of Malicious Attacks on Consensus Algorithms with Applications in Power Networks

Consensus-based distributed algorithms are well suited for coordination among agents in a cyber-physical system. These distributed schemes, however, suffer from their vulnerability to cyber attacks that are aimed at manipulating data and control ow. In this article, we present a novel distributed method for detecting the presence of such intrusions for a distributed multi-agent system following ratio consensus. We employ a Max-Min protocol to develop low cost, easy to implement detection strategies where each participating node detects the intrusion independently, eliminating the need for a trusted certifying agent in the network. The effectiveness of the detection method is demonstrated by numerical simulations on a 1000 node network to demonstrate the efficacy and simplicity of implementation.

27 ARPA - Advanced Research Projects Agency-Energy↗

AMPR/SSMI data comparisons

The AMPR was flown during CAPE and STORMFEST, during which some good data were gathered. Significant instrument noise problems were encountered in both deployments which appear to be temperature related. These are being fixed before the TOGA COARE deployment. New calibration loads have also been manufactured for the TOGA COARE configuration. Eric Smith at FSU had been analyzing the AMPR data and has written a journal article to be submitted early this summer. The emphasis of his work is on the interpretation of low resolution microwave data from space, based upon what we have learned from the high-resolution AMPR signatures.

Spencer, Roy W.↗

Finding, Organizing, and Preserving Legacy Nuclear Test Monitoring Data—Examples from the Livermore Nevada Network

A challenge for geophysical research is the relatively short time for which continuous digital data have been available. There are many events of research interest where much of the data were collected by analog or temporary digital means. These legacy data require special efforts to find, organize, and preserve for future research. Here, we focus on one type of legacy data, nuclear explosions, and associated events (e.g., collapses, aftershocks) of high interest for nuclear monitoring research and development. For nuclear tests conducted in Nevada, the Lawrence Livermore Nevada Network recorded valuable data on a variety of formats. In this article, we briefly review this network, and describe one set of data that previously was available via CD-ROM by request, and since 2018 has become available through Incorporated Research Institutions for Seismology as assembled dataset 18-001.

58 GEOSCIENCES↗

Accelerating Asymptotically Exact MCMC for Computationally Intensive Models via Local Approximations

We construct a new framework for accelerating Markov chain Monte Carlo in posterior sampling problems where standard methods are limited by the computational cost of the likelihood, or of numerical models embedded therein. Our approach introduces local approximations of these models into the Metropolis–Hastings kernel, borrowing ideas from deterministic approximation theory, optimization, and experimental design. Previous efforts at integrating approximate models into inference typically sacrifice either the sampler’s exactness or efficiency; our work seeks to address these limitations by exploiting useful convergence characteristics of local approximations. We prove the ergodicity of our approximate Markov chain, showing that it samples asymptotically from the exact posterior distribution of interest. We describe variations of the algorithm that employ either local polynomial approximations or local Gaussian process regressors. Our theoretical results reinforce the key observation underlying this article: when the likelihood has some local regularity, the number of model evaluations per Markov chain Monte Carlo (MCMC) step can be greatly reduced without biasing the Monte Carlo average. Numerical experiments demonstrate multiple order-of-magnitude reductions in the number of forward model evaluations used in representative ordinary differential equation (ODE) and partial differential equation (PDE) inference problems, with both synthetic and real data. Supplementary materials for this article are available online.

97 MATHEMATICS AND COMPUTING↗

The future low-temperature geochemical data-scape as envisioned by the U.S. geochemical community

Data sharing benefits the researcher, the scientific community, and the public by allowing the impact of data to be generalized beyond one project and by making science more transparent. However, many scientific communities have not developed protocols or standards for publishing, citing, and versioning datasets. One community that lags in data management is that of low-temperature geochemistry (LTG). This paper resulted from an initiative from 2018 through 2020 to convene LTG and data scientists in the U.S. to strategize future management of LTG data. Through webinars, a workshop, a preprint, a townhall, and a community survey, the group of U.S. scientists discussed the landscape of data management for LTG – the data-scape. Currently this data-scape includes a “street bazaar” of data repositories. This was deemed appropriate in the same way that LTG scientists publish articles in many journals. The variety of data repositories and journals reflect that LTG scientists target many different scientific questions, produce data with extremely different structures and volumes, and utilize copious and complex metadata. Nonetheless, the group agreed that publication of LTG science must be accompanied by sharing of data in publicly accessible repositories, and, for sample-based data, registration of samples with globally unique persistent identifiers. LTG scientists should use certified data repositories that are either highly structured databases designed for specialized types of data, or unstructured generalized data systems. Recognizing the need for tools to enable search and cross-referencing across the proliferating data repositories, the group proposed that the overall data informatics paradigm in LTG should shift from “build data repository, data will come” to “publish data online, cybertools will find”. Funding agencies could also provide portals for LTG scientists to register funded projects and datasets, and forge approaches that cross national boundaries. Finally, the needed transformation of the LTG data culture requires emphasis in student education on science and management of data.

58 GEOSCIENCES↗

Processing AIRS Scientific Data Through Level 3

The Atmospheric Infra-Red Sounder (AIRS) Science Processing System (SPS) is a collection of computer programs, known as product generation executives (PGEs). The AIRS SPS PGEs are used for processing measurements received from the AIRS suite of infrared and microwave instruments orbiting the Earth onboard NASA's Aqua spacecraft. Early stages of the AIRS SPS development were described in a prior NASA Tech Briefs article: Initial Processing of Infrared Spectral Data (NPO-35243), Vol. 28, No. 11 (November 2004), page 39. In summary: Starting from Level 0 (representing raw AIRS data), the AIRS SPS PGEs and the data products they produce are identified by alphanumeric labels (1A, 1B, 2, and 3) representing successive stages or levels of processing. The previous NASA Tech Briefs article described processing through Level 2, the output of which comprises geo-located atmospheric data products such as temperature and humidity profiles among others. The AIRS Level 3 PGE samples selected information from the Level 2 standard products to produce a single global gridded product. One Level 3 product is generated for each day s collection of Level 2 data. In addition, daily Level 3 products are aggregated into two multiday products: an eight-day (half the orbital repeat cycle) product and monthly (calendar month) product.

Granger, Stephanie↗

CoREC: Scalable and Resilient In-memory Data Staging for In-situ Workflows

The dramatic increase in the scale of current and planned high-end HPC systems is leading new challenges, such as the growing costs of data movement and IO, and the reduced mean time between failures (MTBF) of system components. In-situ workflows, i.e., executing the entire application workflows on the HPC system, have emerged as an attractive approach to address data-related challenges by moving computations closer to the data, and staging-based frameworks have been effectively used to support in-situ workflows at scale. However, the resilience of these staging-based solutions has not been addressed, and they remain susceptible to expensive data failures. Furthermore, naive use of data resilience techniques such as n-way replication and erasure codes can impact latency and/or result in significant storage overheads. In this article, we present CoREC, a scalable and resilient in-memory data staging runtime for large-scale in-situ workflows. CoREC uses a novel hybrid approach that combines dynamic replication with erasure coding based on data access patterns. It also leverages multiple levels of replications and erasure coding to support diverse data resiliency requirements. Furthermore, the article presents optimizations for load balancing and conflict-avoiding encoding, and a low overhead, lazy data recovery scheme. We have implemented the CoREC runtime and have deployed with the DataSpaces staging service on leadership class computing machines and present an experimental evaluation in the article. Here, the experiments demonstrate that CoREC can tolerate in-memory data failures while maintaining low latency and sustaining high overall storage efficiency at large scales.

97 MATHEMATICS AND COMPUTING↗

Rotational and reflectional equivariant convolutional neural network for data-limited applications: Multiphase flow demonstration

This article deals with approximating steady-state particle-resolved fluid flow around a fixed particle of interest under the influence of randomly distributed stationary particles in a dispersed multiphase setup using convolutional neural network (CNN). The considered problem involves rotational symmetry about the mean velocity (streamwise) direction. Thus, this work enforces this symmetry using SE(3)-equivariant, special Euclidean group of dimension 3, CNN architecture, which is translation and three-dimensional rotation equivariant. This study mainly explores the generalization capabilities and benefits of a SE(3)-equivariant network. Accurate synthetic flow fields for Reynolds number and particle volume fraction combinations spanning over a range of [86.22, 172.96] and [0.11, 0.45], respectively, are produced with careful application of symmetry-aware data-driven approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

FERMI-LAT OBSERVATIONS OF HIGH- AND INTERMEDIATE-VELOCITY CLOUDS: TRACING COSMIC RAYS IN THE HALO OF THE MILKY WAY

It is widely accepted that cosmic rays (CRs) up to at least PeV energies are Galactic in origin. Accelerated particles are injected into the interstellar medium where they propagate to the farthest reaches of the Milky Way, including a surrounding halo. The composition of CRs coming to the solar system can be measured directly and has been used to infer the details of CR propagation that are extrapolated to the whole Galaxy. In contrast, indirect methods, such as observations of γ-ray emission from CR interactions with interstellar gas, have been employed to directly probe the CR densities in distant locations throughout the Galactic plane. In this article we use 73 months of data from the Fermi Large Area Telescope in the energy range between 300 MeV and 10 GeV to search for γ-ray emission produced by CR interactions in several high- and intermediate-velocity clouds (IVCs) located at up to ∼7 kpc above the Galactic plane. We achieve the first detection of IVCs in γ rays and set upper limits on the emission from the remaining targets, thereby tracing the distribution of CR nuclei in the halo for the first time. We find that the γ-ray emissivity per H atom decreases with increasing distance from the plane at 97.5% confidence level. This corroborates the notion that CRs at the relevant energies originate in the Galactic disk. The emissivity of the upper intermediate-velocity Arch hints at a 50% decline of CR densities within 2 kpc from the plane. We compare our results to predictions of CR propagation models.

79 ASTRONOMY AND ASTROPHYSICS↗

Generating Uncertainty Distributions for Seismic Signal Onset Times

Signal arrival-time estimation plays a critical role in a variety of downstream seismic analyses, including location estimation and source characterization. Any arrival-time errors propagate through subsequent data-processing results. In this article, we detail a general framework for refining estimated seismic signal arrival times along with full estimation of their associated uncertainty. Using the standard short-term average/long-term average threshold algorithm to identify a search window, we demonstrate how to refine the pick estimate through two different approaches. In both cases, new waveform realizations are generated through bootstrap algorithms to produce full a posteriori estimates of uncertainty of onset arrival time of the seismic signal. The onset arrival uncertainty estimates provide additional data-derived information from the signal and have the potential to influence seismic analysis along several fronts.

58 GEOSCIENCES↗

Implementation of data citations and persistent identifiers at the ORNL DAAC

A requirement of data archives is that data holdings can be easily discovered, accessed, and used. One approach to improving data discovery and access is through data citations coupled with Digital Object Identifiers (DOI). The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) since 1998 has issued data citations that have been accepted and used in peer-reviewed journals. Citation elements established by the ORNL DAAC are similar to those used for journal articles (authors, year, product title, and information to locate), and beginning in 2007 included a DOI that is persistent, actionable, specific, and complete. The approach used at the ORNL DAAC also allows for referring to subsets of the data, by including within the citation the temporal and spatial extent, and parameters used. Data citations allow readers to find data and reproduce the results of the research article, and also use those data to test new hypotheses, design new sample collections, or construct or evaluate models. The ORNL DAAC uses a manual method to compile data citations and has developed a database that links research articles and their use of specific ORNL DAAC data products. Automation of the data citation compilation process, as is the case for articles, will enable data citations to become a more common practice. In addition to enhancing discovery and access of the data used in a research article, the citation gives credit to data generators, data centers and their funders, and, through citation indices, determine the scientific impact of a data set.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Mammalian Chromosome Analysis and Sorting by Flow Cytometry

The analysis of chromosomes by flow cytometry is termed flow cytogenetics, and it involves the analysis and sorting of single mitotic chromosomes in suspension. The study of flow karyograms provides insight into chromosome number and structure to provide information on chromosomal DNA content and can enable the detection of deletions, translocations, or any forms of aneuploidy. Beyond its clinical applications, flow cytogenetics greatly contributed to the Human Genome Project through the ability to sort pure populations of chromosomes for gene mapping, cloning, and the construction of DNA libraries. Maximizing the potential of these important applications of flow cytogenetics relies on precise instrument setup and optimal sample processing, both of which impact the accuracy and quality of the data that are generated. This article is a compilation of the existing protocols that describe the stepwise methodology of accumulating, isolating, and staining metaphase chromosomes to prepare single-chromosome suspensions for flow cytometric analysis and sorting. Although the chromosome preparation protocols have remained largely unchanged, cytometer technology has advanced dramatically since these protocols were originally developed. Advances in cytometry technologies offer new and exciting approaches for understanding and monitoring chromosomal aberrations, but the hallmark of these protocols remains their simplicity in methodologies and reagent requirements and the accuracy of data resolvable to every chromosome of the cell.

59 BASIC BIOLOGICAL SCIENCES↗

Acceptance criteria for in situ surveillance of MSR materials based on thermally-loaded mechanical test articles

This report describes practices and acceptance test procedures for designing, running, and maintaining a material surveillance program in a future operating molten salt reactor. The programs described here rely on test data from passively actuated mechanical test articles inserted into critical regions of the reactor and periodically removed for out-of-reactor testing. The report defines definite acceptance procedures, based on the results of these tests, to determine whether a component can continue to operate accounting for the accumulation of environmentally-assisted mechanical damage in the component materials to date, and extrapolated out through the next inspection period. Additionally, the report describes work on a software tool implementing many of the surveillance methods and procedures described here and progress on simplified methods for inferring damage accumulation in the test articles, based on out-of-reactor thermal cycling, that do not rely on sophisticated numerical analysis.

36 MATERIALS SCIENCE↗