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All sourcesNASA NTRSDOE OSTI
NASA NTRS2019

Bringing Analysis Closer to Data: Developing a Visualization Tool for L2 Earth Science Satellite Data

Earth Science satellite missions provide a unique opportunity for scientists to visualize complex and multifaceted observations projected geospatially across maps of the Earth. While visualization tools can help scientists comprehend, analyze, and share data, visualizing Level-2 Earth Sciences data poses its own specific set of challenges. Since the geospatial information in Level-2 data files is stored as independent variables, the plotting process involves matching dimensional information from latitude and longitude with a desired variable. Variables are stored in different ways across various Earth Science data file formats, which complicates the process of extracting data and plotting variables from a given file without requiring extensive user input and prerequisite familiarity with the file type variable structure. In coordination with NASA’s Goddard Earth Sciences Data Information Services Center (GES DISC), the team developed a Level-2 Earth Science data visualization tool that aims to address some of the complexities associated with plotting Level-2 data. This tool offers command-line and user interface support for file and variable selection to accommodate varying use cases and degrees of user familiarity with the structure of a given file. The visualization tool is written in Python 3 and utilizes a modular approach to facilitate continued expansion and reuse. In addressing some common complications involved in plotting Level-2 Earth Sciences data, the tool aims to help to link the process of analysis more directly with data acquisition and visualization, bringing analysis closer to data across levels of processing.

Li, Angela W.↗
DOE OSTI2018

Stepwise approach to SNP-set analysis illustrated with the Metabochip and colorectal cancer in Japanese Americans of the Multiethnic Cohort

Background: Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome scans. Because of low frequency (low statistical power), less-common variants are best analyzed using SNP-set methods such as gene-set or pathway-based analyses. However, there is as yet no clear consensus regarding how to focus in on potential risk variants following set-based analyses. We used a stepwise, telescoping approach to analyze commonand rare-variant data from the Illumina Metabochip array to assess genomic association with colorectal cancer (CRC) in the Japanese sub-population of the Multiethnic Cohort (676 cases, 7180 controls). We started with pathway analysis of SNPs that are in genes and pathways having known mechanistic roles in colorectal cancer, then focused on genes within the pathways that evidenced association with CRC, and finally assessed individual SNPs within the genes that evidenced association. Pathway SNPs downloaded from the dbSNP database were cross-matched with Metabochip SNPs and analyzed using the logistic kernel machine regression approach (logistic SNP-set kernel-machine association test, or sequence kernel association test; SKAT) and related methods. Results: The TGF-β and WNT pathways were associated with all CRC, and the WNT pathway was associated with colon cancer. Individual genes demonstrating the strongest associations were TGFBR2 in the TGF-β pathway and SMAD7 (which is involved in both the TGF-β and WNT pathways). As partial validation of our approach, a known CRC risk variant in SMAD7 (in both the TGF-β and WNT pathways: rs11874392) was associated with CRC risk in our data. We also detected two novel candidate CRC risk variants (rs13075948 and rs17025857) in TGFBR2, a gene known to be associated with CRC risk. Conclusions: A stepwise, telescoping approach identified some potentially novel risk variants associated with colorectal cancer, so it may be a useful method for following up on results of set-based SNP analyses. Further work is required to assess the statistical characteristics of the approach, and additional applications should aid in better clarifying its utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Including Chi-Nu 235 U PFNS Experimental Data into an ENDF/B-VIII.1 Release Candidate Evaluation

This report documents an evaluation of 235 U prompt fission neutron spectra (PFNS) that is a release candidate for the upcoming U.S. nuclear data library, ENDF/B-VIII.1. This evaluation differs from its predecessor, ENDF/B-VIII.0, mainly by the inclusion of 235 U PFNS measured by the Chi-Nu team of LANL and LLNL. This data set is the first one that covers the 235 U PFNS for continuous incident-neutron energies of 1⁻20 MeV and outgoing-neutron energies from 10 keV⁻10 MeV with high precision. Previous data sets were either measured in a limited energy range or with less precision. Hence, these new Chi-Nu data provide decisive information for the evaluation. The resulting evaluated data correspond well to the new experimental PFNS. The evaluated PFNS also produce average mean energies and 239 Pu/ 235 U PFNS in agreement with associated Chi-Nu data. If one uses the new evaluated data to predict the neutron multiplication factor, k eff , of selected ICSBEP critical assemblies, the differences of simulated values compared to those using ENDF/B-VIII.0 is modest (less than 55 pcm). This difference in k eff can be easily accommodated by changes in the 235 U average prompt fission neutron multiplicity that is currently being re-evaluated. In addition to that, the new PFNS predict on average 235 U LLNL pulsed-sphere neutron-leakage spectra better than ENDF/B-VIIII.0 PFNS.

235U↗
DOE OSTI2019

Dynamic Mode Decomposition for Compressive System Identification

Dynamic mode decomposition has emerged as a leading technique to identify spatiotemporal coherent structures from high-dimensional data, benefiting from a strong connection to nonlinear dynamical systems via the Koopman operator. In this work, we integrate and unify two recent innovations that extend DMD to systems with actuation [Proctor et al., 2016] and systems with heavily subsampled measurements [Brunton et al., 2015]. When combined, these methods yield a novel framework for compressive system identification [code is publicly available at: https://github.com/zhbai/cDMDc]. It is possible to identify a low-order model from limited input-output data and reconstruct the associated full-state dynamic modes with compressed sensing, adding interpretability to the state of the reduced-order model. Moreover, when full-state data is available, it is possible to dramatically accelerate downstream computations by first compressing the data. We demonstrate this unified framework on two model systems, investigating the effects of sensor noise, different types of measurements (e.g., point sensors, Gaussian random projections, etc.), compression ratios, and different choices of actuation (e.g., localized, broadband, etc.). In the first example, we explore this architecture on a test system with known low-rank dynamics and an artificially inflated state dimension. The second example consists of a real-world engineering application given by the fluid flow past a pitching airfoil at low Reynolds number. This example provides a challenging and realistic test-case for the proposed method, and results demonstrate that the dominant coherent structures are well characterized despite actuation and heavily subsampled data.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1999

Condition Monitoring of Large-Scale Facilities

This document provides a summary of the research conducted for the NASA Ames Research Center under grant NAG2-1182 (Condition-Based Monitoring of Large-Scale Facilities). The information includes copies of view graphs presented at NASA Ames in the final Workshop (held during December of 1998), as well as a copy of a technical report provided to the COTR (Dr. Anne Patterson-Hine) subsequent to the workshop. The material describes the experimental design, collection of data, and analysis results associated with monitoring the health of large-scale facilities. In addition to this material, a copy of the Pennsylvania State University Applied Research Laboratory data fusion visual programming tool kit was also provided to NASA Ames researchers.

Hall, David L.↗
NASA NTRS2002

Cell prestress. I. Stiffness and prestress are closely associated in adherent contractile cells

The tensegrity hypothesis holds that the cytoskeleton is a structure whose shape is stabilized predominantly by the tensile stresses borne by filamentous structures. Accordingly, cell stiffness must increase in proportion with the level of the tensile stress, which is called the prestress. Here we have tested that prediction in adherent human airway smooth muscle (HASM) cells. Traction microscopy was used to measure the distribution of contractile stresses arising at the interface between each cell and its substrate; this distribution is called the traction field. Because the traction field must be balanced by tensile stresses within the cell body, the prestress could be computed. Cell stiffness (G) was measured by oscillatory magnetic twisting cytometry. As the contractile state of the cell was modulated with graded concentrations of relaxing or contracting agonists (isoproterenol or histamine, respectively), the mean prestress ((t)) ranged from 350 to 1,900 Pa. Over that range, cell stiffness increased linearly with the prestress: G (Pa) = 0.18(t) + 92. While this association does not necessarily preclude other interpretations, it is the hallmark of systems that secure shape stability mainly through the prestress. Regardless of mechanism, these data establish a strong association between stiffness of HASM cells and the level of tensile stress within the cytoskeleton.

NASA Discipline Cell Biology↗
DOE OSTI2015

Search for production of an $\Upsilon$(1S) meson in association with a W or Z boson using the full 1.96 TeV $p\bar{p}$ collision data set at CDF

Production of the Υ(1S) meson in association with a vector boson is a rare process in the standard model with a cross section predicted to be below the sensitivity of the Tevatron. Observation of this process could signify contributions not described by the standard model or reveal limitations with the current nonrelativistic quantum-chromodynamic models used to calculate the cross section. We perform a search for this process using the full Run II data set collected by the CDF II detector corresponding to an integrated luminosity of 9.4 fb -1 . Our search considers the Υ→μμ decay and the decay of the W and Z bosons into muons and electrons. Furthermore, in these purely leptonic decay channels, we observe one ΥW candidate with an expected background of 1.2±0.5 events, and one ΥZcandidate with an expected background of 0.1±0.1 events. Both observations are consistent with the predicted background contributions. The resulting upper limits on the cross section for Υ+W/Zproduction are the most sensitive reported from a single experiment and place restrictions on potential contributions from non-standard-model physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Cosmic shear power spectra in practice

Cosmic shear is one of the most powerful probes of Dark Energy, targeted by several current and future galaxy surveys. Lensing shear, however, is only sampled at the positions of galaxies with measured shapes in the catalog, making its associated sky window function one of the most complicated amongst all projected cosmological probes of inhomogeneities, as well as giving rise to inhomogeneous noise. Partly for this reason, cosmic shear analyses have been mostly carried out in real-space, making use of correlation functions, as opposed to Fourier-space power spectra. Since the use of power spectra can yield complementary information and has numerical advantages over real-space pipelines, it is important to develop a complete formalism describing the standard unbiased power spectrum estimators as well as their associated uncertainties. Building on previous work, this paper contains a study of the main complications associated with estimating and interpreting shear power spectra, and presents fast and accurate methods to estimate two key quantities needed for their practical usage: the noise bias and the Gaussian covariance matrix, fully accounting for survey geometry, with some of these results also applicable to other cosmological probes. Here, we demonstrate the performance of these methods by applying them to the latest public data releases of the Hyper Suprime-Cam and the Dark Energy Survey collaborations, quantifying the presence of systematics in our measurements and the validity of the covariance matrix estimate. We make the resulting power spectra, covariance matrices, null tests and all associated data necessary for a full cosmological analysis publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1998

The Design and Evaluation of the Lighting Imaging Sensor Data Applications Display (LISDAD)

The design and evaluation of the Lightning Imaging Sensor Data Applications Display (LISDAD). The ultimate goal of the LISDAD system is to quantify the utility of total lightning information in short-term, severe-weather forecasting operations. To this end, scientists from NASA, NWS, and MIT organized an effort to study the relationship of lightning and severe-weather on a storm-by-storm, and even cell-by-cell basis for as many storms as possible near Melbourne, Florida. Melbourne was chosen as it offers a unique combination of high probability of severe weather and proximity to major relevant sensors - specifically: NASA's total lightning mapping system at Kennedy Space Center (the LDAR system at KSC); a NWS/NEXRAD radar (at Melbourne); and a prototype Integrated Terminal Weather System (ITWS, at Orlando), which obtains cloud-to-ground lightning Information from the National Lightning Detection Network (NLDN), and also uses NSSL's Severe Storm Algorithm (NSSL/SSAP) to obtain information about various storm-cell parameters. To assist in realizing this project's goal, an interactive, real-time data processing system (the LISDAD system) has been developed that supports both operational short-term weather forecasting and post facto severe-storm research. Suggestions have been drawn from the operational users (NWS/Melbourne) in the design of the data display and its salient behavior. The initial concept for the users Graphical Situation Display (GSD) was simply to overlay radar data with lightning data, but as the association between rapid upward trends in the total lightning rate and severe weather became evident, the display was significantly redesigned. The focus changed to support the display of time series of storm-parameter data and the automatic recognition of cells that display rapid changes in the total-lightning flash rate. The latter is calculated by grouping discrete LDAR radiation sources into lightning flashes using a time-space association algorithm. Specifically, the GSD presents the user with the Composite Maximum Reflectivity obtained from the NWS/NEXRAD. Superimposed upon this background image are placed small black circles indicating the locations of storm cells identified by the NSSL/SSA. The circles become cyan if lightning is detected within the storm-cell; if the cell has lightning rates indicative of a severe-storm, the circle turns red. This paper will: (1) review the design of LISDAD system; (2) present some examples of its data display; and shown results of the lightning based severe-weather prediction algorithm.

Boldi, B.↗
DOE OSTI2016

Improved limits on dark matter annihilation in the Sun with the 79-string IceCube detector and implications for supersymmetry

We present an improved event-level likelihood formalism for including neutrino telescope data in global fits to new physics. We derive limits on spin-dependent dark matter-proton scattering by employing the new formalism in a re-analysis of data from the 79-string IceCube search for dark matter annihilation in the Sun, including explicit energy information for each event. The new analysis excludes a number of models in the weak-scale minimal supersymmetric standard model (MSSM) for the first time. This work is accompanied by the public release of the 79-string IceCube data, as well as an associated computer code for applying the new likelihood to arbitrary dark matter models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance

In recent years, biosurveillance has become the buzzword under which a diverse set of ideas and activities regarding detecting and mitigating biological threats are incorporated depending on context and perspective. Increasingly, biosurveillance practice has become global and interdisciplinary, requiring information and resources across public health, One Health, and biothreat domains. Even within the scope of infectious disease surveillance, multiple systems, data sources, and tools are used with varying and often unknown effectiveness. Evaluating the impact and utility of state-of-the-art biosurveillance is, in part, confounded by the complexity of the systems and the information derived from them. We present a novel approach conceptualizing biosurveillance from the perspective of the fundamental data streams that have been or could be used for biosurveillance and to systematically structure a framework that can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities. Moreover, the Biosurveillance Data Stream Framework and associated definitions are proposed as a starting point to facilitate the development of a standardized lexicon for biosurveillance and characterization of currently used and newly emerging data streams. Criteria for building the data stream framework were developed from an examination of the literature, analysis of information on operational infectious disease biosurveillance systems, and consultation with experts in the area of biosurveillance. To demonstrate utility, the framework and definitions were used as the basis for a schema of a relational database for biosurveillance resources and in the development and use of a decision support tool for data stream evaluation.

47 OTHER INSTRUMENTATION↗
NASA NTRS1986

A design for a new catalog manager and associated file management for the Land Analysis System (LAS)

Due to the larger number of different types of files used in an image processing system, a mechanism for file management beyond the bounds of typical operating systems is necessary. The Transportable Applications Executive (TAE) Catalog Manager was written to meet this need. Land Analysis System (LAS) users at the EROS Data Center (EDC) encountered some problems in using the TAE catalog manager, including catalog corruption, networking difficulties, and lack of a reliable tape storage and retrieval capability. These problems, coupled with the complexity of the TAE catalog manager, led to the decision to design a new file management system for LAS, tailored to the needs of the EDC user community. This design effort, which addressed catalog management, label services, associated data management, and enhancements to LAS applications, is described. The new file management design will provide many benefits including improved system integration, increased flexibility, enhanced reliability, enhanced portability, improved performance, and improved maintainability.

Greenhagen, Cheryl↗
DOE OSTI2021

A Data-Driven Framework for Automated Detection of Aircraft-Generated Signals in Seismic Array Data Using Machine Learning

Abstract Ground motions associated with aircraft overflights can cover a significant portion of the seismic data collected by shallowly emplaced seismometers, such as new nodal and Distributed Acoustic Sensing systems. This article describes the first published framework for automated detection of aircraft on single channel and multichannel seismic data. The seismic data are converted to spectrograms in a sliding time window and classified as aircraft or nonaircraft in each window using a deep convolutional neural network trained with analyst-labeled data. A majority voting scheme is used to convert the output from the sequence of sliding time windows onto a decision time sequence for each channel and to combine the binary classifications on the decision time sequences across multiple channels. Precision, recall, and F-score are used to quantify the detection performance of the algorithm on nodal data using fourfold time-series cross validation. By applying our framework to data from the Sage Brush Flats nodal array in Southern California, we provide a benchmark performance and demonstrate the advantage of using an array of sensors.

Geochemistry & Geophysics↗
NASA NTRS2003

Predicting protein functions from redundancies in large-scale protein interaction networks

Interpreting data from large-scale protein interaction experiments has been a challenging task because of the widespread presence of random false positives. Here, we present a network-based statistical algorithm that overcomes this difficulty and allows us to derive functions of unannotated proteins from large-scale interaction data. Our algorithm uses the insight that if two proteins share significantly larger number of common interaction partners than random, they have close functional associations. Analysis of publicly available data from Saccharomyces cerevisiae reveals >2,800 reliable functional associations, 29% of which involve at least one unannotated protein. By further analyzing these associations, we derive tentative functions for 81 unannotated proteins with high certainty. Our method is not overly sensitive to the false positives present in the data. Even after adding 50% randomly generated interactions to the measured data set, we are able to recover almost all (approximately 89%) of the original associations.

Proteins/chemistry/metabolism↗
DOE OSTI2014

Association between arsenic exposure from drinking water and hematuria: Results from the Health Effects of Arsenic Longitudinal Study

Arsenic (As) exposure has been associated with both urologic malignancy and renal dysfunction; however, its association with hematuria is unknown. We evaluated the association between drinking water As exposure and hematuria in 7843 men enrolled in the Health Effects of Arsenic Longitudinal Study (HEALS). Cross-sectional analysis of baseline data was conducted with As exposure assessed in both well water and urinary As measurements, while hematuria was measured using urine dipstick. Prospective analyses with Cox proportional regression models were based on urinary As and dipstick measurements obtained biannually since baseline up to six years. At baseline, urinary As was significantly related to prevalence of hematuria (P-trend < 0.01), with increasing quintiles of exposure corresponding with respective prevalence odds ratios of 1.00 (reference), 1.29 (95% CI: 1.04–1.59), 1.41 (95% CI: 1.15–1.74), 1.46 (95% CI: 1.19–1.79), and 1.56 (95% CI: 1.27–1.91). Compared to those with relatively little absolute urinary As change during follow-up (− 10.40 to 41.17 μg/l), hazard ratios for hematuria were 0.99 (95% CI: 0.80–1.22) and 0.80 (95% CI: 0.65–0.99) for those whose urinary As decreased by > 47.49 μg/l and 10.87 to 47.49 μg/l since last visit, respectively, and 1.17 (95% CI: 0.94–1.45) and 1.36 (95% CI: 1.10–1.66) for those with between-visit increases of 10.40 to 41.17 μg/l and > 41.17 μg/l, respectively. These data indicate a positive association of As exposure with both prevalence and incidence of dipstick hematuria. This exposure effect appears modifiable by relatively short-term changes in drinking water As. - Highlights: • Hematuria is the most common symptom of urinary tract disease. • Arsenic exposure is associated with renal dysfunction and urologic malignancy. • Water arsenic was positively associated with prevalence and incidence of hematuria. • Reduction in exposure lowered hematuria risk especially in low-to-moderate exposed. • Arsenic-related hematuria may represent nonmalignant or premalignant condition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

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↗
DOE OSTI2019

An Assessment of Hydropower Environmental Mitigation Costs

This report provides an assessment of environmental mitigation costs for hydropower projects across the United States (U.S.) based on data extracted from Environmental Assessments (EA) submitted to the Federal Energy Regulatory Commission (FERC). EAs are required by the Federal Power Act (FPA) for hydropower license and relicense applications to weigh the “power” and “non-power” (i.e. environmental) benefits of their development and operation. For this analysis, we collected data from 184 EA documents reviewed by FERC between 1996 and 2018, and created a database of environmental protection, mitigation, and enhancement (PM&E) measures with their associated economic information. The data cover two hydropower relicense categories—103 Relicensed Conventional Hydropower Dams (RCHD) and 6 Relicensed Pumped Storage Hydropower (RPSH) projects—and three new development categories—57 hydropower retrofits at Non-Powered Dams (NPD), 11 New Stream-Reach Development (NSD) projects and 6 Pumped Storage Hydropower (NPSH) projects. For the analysis, we classify the PM&E measures into 11 Tier 1 categories. We evaluated capital and operations & maintenance (O&M) costs of PM&E measures on a $\$$/kW basis by project type and mitigation category, as well as their share in the total project levelized cost of energy (LCOE).

13 HYDRO ENERGY↗
NASA NTRS2010

Community-Based Services that Facilitate Interoperability and Intercomparison of Precipitation Datasets from Multiple Sources

Over the past 12 years, large volumes of precipitation data have been generated from space-based observatories (e.g., TRMM), merging of data products (e.g., gridded 3B42), models (e.g., GMAO), climatologies (e.g., Chang SSM/I derived rain indices), field campaigns, and ground-based measuring stations. The science research, applications, and education communities have greatly benefited from the unrestricted availability of these data from the Goddard Earth Sciences Data and Information Services Center (GES DISC) and, in particular, the services tailored toward precipitation data access and usability. In addition, tools and services that are responsive to the expressed evolving needs of the precipitation data user communities have been developed at the Precipitation Data and Information Services Center (PDISC) (http://disc.gsfc.nasa.gov/precipitation or google NASA PDISC), located at the GES DISC, to provide users with quick data exploration and access capabilities. In recent years, data management and access services have become increasingly sophisticated, such that they now afford researchers, particularly those interested in multi-data set science analysis and/or data validation, the ability to homogenize data sets, in order to apply multi-variant, comparison, and evaluation functions. Included in these services is the ability to capture data quality and data provenance. These interoperability services can be directly applied to future data sets, such as those from the Global Precipitation Measurement (GPM) mission. This presentation describes the data sets and services at the PDISC that are currently used by precipitation science and applications researchers, and which will be enhanced in preparation for GPM and associated multi-sensor data research. Specifically, the GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) will be illustrated. Giovanni enables scientific exploration of Earth science data without researchers having to perform the complicated data access and match-up processes. In addition, PDISC tool and service capabilities being adapted for GPM data will be described, including the Google-like Mirador data search and access engine; semantic technology to help manage large amounts of multi-sensor data and their relationships; data access through various Web services (e.g., OPeNDAP, GDS, WMS, WCS); conversion to various formats (e.g., netCDF, HDF, KML (for Google Earth)); visualization and analysis of Level 2 data profiles and maps; parameter and spatial subsetting; time and temporal aggregation; regridding; data version control and provenance; continuous archive verification; and expertise in data-related standards and interoperability. The goal of providing these services is to further the progress towards a common framework by which data analysis/validation can be more easily accomplished.

Liu, Zhong↗