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DOE OSTI2024

Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution

Tumor deconvolution is a reliable way to disentangle the diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor samples, and the gold standard datasets used to assess the algorithms are geared toward the analysis of gene expression (e.g., RNA-seq) rather than protein levels in tumor cells. While gene expression is less expensive to measure, protein levels provide a more accurate view of immune markers. To facilitate the development as well as improve the reproducibility and reusability of multi-omic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages containerization to compare tumor deconvolution algorithms across multiomic data sets. Decomprolute incorporates the large-scale multiomic data sets produced by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomic data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteogenomic tumor deconvolution benchmarking platform. The platform consists of modular architecture and it comes with well-defined input and output formats at each module. As a result, it is robust and extendable easily with additional algorithms or analyses. The platform is available for access and use at http://pnnl-compbio.github.io/decomprolute.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2001

In Interactive, Web-Based Approach to Metadata Authoring

NASA's Global Change Master Directory (GCMD) serves a growing number of users by assisting the scientific community in the discovery of and linkage to Earth science data sets and related services. The GCMD holds over 8000 data set descriptions in Directory Interchange Format (DIF) and 200 data service descriptions in Service Entry Resource Format (SERF), encompassing the disciplines of geology, hydrology, oceanography, meteorology, and ecology. Data descriptions also contain geographic coverage information, thus allowing researchers to discover data pertaining to a particular geographic location, as well as subject of interest. The GCMD strives to be the preeminent data locator for world-wide directory level metadata. In this vein, scientists and data providers must have access to intuitive and efficient metadata authoring tools. Existing GCMD tools are not currently attracting. widespread usage. With usage being the prime indicator of utility, it has become apparent that current tools must be improved. As a result, the GCMD has released a new suite of web-based authoring tools that enable a user to create new data and service entries, as well as modify existing data entries. With these tools, a more interactive approach to metadata authoring is taken, as they feature a visual "checklist" of data/service fields that automatically update when a field is completed. In this way, the user can quickly gauge which of the required and optional fields have not been populated. With the release of these tools, the Earth science community will be further assisted in efficiently creating quality data and services metadata. Keywords: metadata, Earth science, metadata authoring tools

Pollack, Janine↗

NASA NTRS2016

Incorporating the TRMM Dataset into the GPM Mission Data Suite

In June 2015 the TRMM satellite came to its end. The 17 plus year of mission data that it provided has proven a valuable asset to a variety of science communities. This 17plus year data set does not, however, stagnate with the end of the mission itself. NASA/JAXA intend to integrate the TRMM data set into the data suite of the GPM mission. This will ensure the creation of a consistent, intercalibrated, accurate dataset within GPM that extends back to November of 1998. This paper describes the plans for incorporating the TRMM 17plus year data into the GPM data suite. These plans call for using GPM algorithms for both radiometer and radar to reprocess TRMM data as well as intercalibrating partner radiometers using GPM intercalibration techniques. This reprocessing will mean changes in content, logical format and physical format as well as improved geolocation, sensor corrections and retrieval techniques.

TRMM↗

NASA NTRS2000

On the Long-Term Calibration of the TOMS Total Ozone Record

Comparison of Total Ozone Mapping Spectrometer (TOMS) data to the network of ground-based Dobson/Brewer measurements reveals difference in the time dependence of the calibration of the two systems. We have been searching for a method to determine the time dependence of the TOMS calibrations that is independent of the Dobson/Brewer network. In a separate paper by DeLand et al., calibrations of the Solar Backscatter UV Spectrometer (SBUV) instruments have been rederived using the D-pair (306/313 nm wavelengths) data at the equator. These calibrations have been applied to the data from the Nimbus 7 SBUV and the NOAA 9 and 11 SBUV/2 data to derive a new version 7 data set for each instrument. We have used these data to do a detailed comparison to the Nimbus 7 and Earth Probe TOMS data. Assuming that the D-pair establishes the correct calibration, these comparisons reveal some small calibration drifts (approximately 1%) in the TOMS data. They also reveal an offset in the D-pair calibration with respect to the Dobson network of approximately 8 Dobson units with the Dobson being lower than the D-pair. The D-pair calibration offsets have been used to create a merged ozone data set from TOMS with a calibration that has been determined independent of the Dobson/Brewer network. Trend analyses of these data will be presented and compared to trend analyses using the ground-based data.

Stolarski, Richard S.↗

NASA NTRS2006

Analyzing Electric Field Morphology Through Data-Model Comparisons of the GEM IM/S Assessment Challenge Events

The storm-time inner magnetospheric electric field morphology and dynamics are assessed by comparing numerical modeling results of the plasmasphere and ring current with many in situ and remote sensing data sets. Two magnetic storms are analyzed, April 22,2001 and October 21-23,2001, which are the events selected for the Geospace Environment Modeling (GEM) Inner Magnetosphere/Storms (IM/S) Assessment Challenge (IMSAC). The IMSAC seeks to quantify the accuracy of inner magnetospheric models as well as synthesize our understanding of this region. For each storm, the ring current-atmosphere interaction model (RAM) and the dynamic global core plasma model (DGCPM) were run together with various settings for the large-scale convection electric field and the nightside ionospheric conductance. DGCPM plasmaspheric parameters were compared with IMAGE-EUV plasmapause extractions and LANL-MPA plume locations and velocities. RAM parameters were compared with Dst*, LANL-MPA fluxes and moments, IMAGE-MENA images, and IMAGE-HENA images. Both qualitative and quantitative comparisons were made to determine the electric field morphology that allows the model results to best fit the plasma data at various times during these events. The simulations with self-consistent electric fields were, in general, better than those with prescribed field choices. This indicates that the time-dependent modulation of the inner magnetospheric electric fields by the nightside ionosphere is quite significant for accurate determination of these fields (and their effects). It was determined that a shielded Volland-Stern field description driven by the 3-hour Kp index yields accurate results much of the time, but can be quite inconsistent. The modified Mcllwain field description clearly lagged in overall accuracy compared to the other fields, but matched some data sets (like Dst*) quite well. The rankings between the simulations varied depending on the storm and the individual data sets, indicating that each field description did well for some place, time, and energy range during the events, as well as doing less well in other places, times, and energies. Several unresolved issues regarding the storm-time inner magnetospheric electric field are discussed.

Liemohn, Michael W.↗

NASA NTRS1986

Global duricrust on Mars - Analysis of remote-sensing data

A study is conducted of the infrared thermal emission, radio thermal emission, and radar reflection data sets with the objective to obtain a simple and self-consistent model for the Mars surface. The results are compared with in situ observations at the Viking Lander sites. Attention is given to thermal inertia values, the abundance of surface rocks, radar/thermal correlations, diurnal temperature deviations, and radio emission data. It is suggested that all of the global remote-sensing data sets considered can be reconciled on the basis of variations in the degree of formation of a case-hardened crust or duricrust. On the other hand, no other model which has been proposed in conjunction with any individual data set can satisfy all of the constraints discussed.

Jakosky, B. M.↗

DOE OSTI2022

Network Anomaly Detection Using Federated Learning

The internet is turning out to be an integral part of every-one's lives as more and more devices are being connected to serve societal needs. Our work is motivated by two ma-jor observations. Firstly, one drawback of connecting to the network is the threat of network attacks that can compromise users' private information, leading to data loss and adversely affecting productivity. There are several traditional security mechanisms to defend against these attacks, such as firewalls, virtual private networks (VPNs), demilitarized zones (DMZs), and vulnerability scanners. One way to prevent these attacks is early detection and prevention. However, these kinds of architecture do not scale very well because of their centralized nature. Secondly, we observe from heuristics and data set distributions that the majority of the requests made to a server are innocuous. Therefore, almost all server request data sets are highly imbalanced, weighted highly towards the harmless requests.

Marfo, William↗

DOE OSTI2020

Efficient 3-D velocity model building using joint inline and crossline plane-wave wave-equation migration velocity analyses

SUMMARY Wave-equation migration velocity analysis (WEMVA) is an image-domain inversion method for velocity model building. Automatic plane-wave WEMVA (PWEMVA) calculates the moveouts of plane-wave common-image gathers (CIGs) by searching a best-fitting parabola with semblance analysis and backprojects residual CIG moveouts into wavefield wave paths with a reflection tomographic kernel. However, 3-D PWEMVA is very computationally expensive because 3-D reflection tomographic inversion requires at least five 3-D reverse-time migrations per iteration and stores two types of source wavefields at model boundaries. We develop a joint inline and crossline PWEMVA method for efficient 3-D velocity model building. We alternatively implement the inline and crossline PWEMVAs with a constraint for each other, in which we iteratively construct the 3-D velocity model update through 1-D spline interpolation of 2-D gradients. The inline and crossline joint inversion is practical since PWEMVA only inverts for low-wavenumber velocity perturbations along wave paths, and the method can take less than 1 per cent of the computational cost of full 3-D PWEMVA. To construct unaliased plane waves for our joint inline and crossline PWEMVA, we develop a 3-D data interpolation method in the frequency–wavenumber (FK) domain to recover regularly and randomly missing traces. The method minimizes the misfit on sufficiently localized data subsets with iterative optimal step lengths and a gradient preconditioner that iteratively selects dominant dips along different azimuths. In numerical experiments, we use a 3-D synthetic seismic data set and a land 3-D field seismic data set acquired at the Farnsworth CO2-EOR (enhanced oil recovery) field to demonstrate the efficacy of our velocity model building and data interpolation methods.

Liu, Xuejian↗

NASA NTRS2014

Detection of Unexpected High Correlations between Balance Calibration Loads and Load Residuals

An algorithm was developed for the assessment of strain-gage balance calibration data that makes it possible to systematically investigate potential sources of unexpected high correlations between calibration load residuals and applied calibration loads. The algorithm investigates correlations on a load series by load series basis. The linear correlation coefficient is used to quantify the correlations. It is computed for all possible pairs of calibration load residuals and applied calibration loads that can be constructed for the given balance calibration data set. An unexpected high correlation between a load residual and a load is detected if three conditions are met: (i) the absolute value of the correlation coefficient of a residual/load pair exceeds 0.95; (ii) the maximum of the absolute values of the residuals of a load series exceeds 0.25 % of the load capacity; (iii) the load component of the load series is intentionally applied. Data from a baseline calibration of a six-component force balance is used to illustrate the application of the detection algorithm to a real-world data set. This analysis also showed that the detection algorithm can identify load alignment errors as long as repeat load series are contained in the balance calibration data set that do not suffer from load alignment problems.

strain-gage balance↗

NASA NTRS1996

Parallelization and Visual Analysis of Multidimensional Fields: Application to Ozone Production, Destruction, and Transport in Three Dimensions

The three-dimensional, spectral transport model used in the current project was first successfully integrated over climatological time scales by Dr. Guang Ping Lou for the simulation of atmospheric N2O using the United Kingdom Meteorological Office (UKMO) 4-dimensional, assimilated wind and temperature data set. A non-parallel, FORTRAN version of this integration using a fairly simple N2O chemistry package containing only photo-chemical reactions was used to verify our initial parallel model results. The integrations reproduced the gross features of the observed stratospheric climatological N2O distributions but also simulated the structure of the stratospheric Antarctic vortex and its evolution. Subsequently, Dr. Thomas Kindler, who produced much of the parallel version of our model, enlarged the N2O model chemistry package to include N2O reactions involving O(D-1) and also introduced assimilated wind data from NASA as well as UKMO. Initially, transport calculations without chemistry were run using Carbon-14 as a non-reactive tracer gas with the result that large differences in the transport properties of the two assimilated wind data sets were apparent from the resultant Carbon-14 distributions. Subsequent calculations for N2O, including its chemistry, with the two input winds data sets with verification from UARS satellite observations have refined the transport differences between the two such that the model's steering capabilities could be used to infer the correct climatological vertical velocity fields required to support the N2O observations. During this process, it was also discovered that both the NASA and the UKMO data contained spurious values in some of the higher frequency wave components, leading to incorrect local transport calculations and ultimately affecting the large scale properties of the model's N2O distributions, particularly at tropical latitudes. Subsequent model runs with wind data that had been filtered to remove some of the high frequency components produced much more realistic N2O distributions. During the past few months, the UKMO wind data base for a complete two-year period was processed into spectral form for model use. This new version of the input transport data base now includes complete temperature fields as well as the necessary wind data. This was done to facilitate advanced chemical calculations in the parallel model which often depend upon temperature. Additional UKMO data is being added as it becomes available.

Schwan, Karsten↗

NASA NTRS2020

Modeling the Uncertainties of Solar System Ephemerides for Robust Gravitational-wave Searches with Pular-timing Arrays

The regularity of pulsar emissions becomes apparent once we reference the pulses’ times of arrivals to the inertial rest frame of the solar system. It follows that errors in the determination of Earthʼs position with respect to the solar system barycenter can appear as a time-correlated bias in pulsar-timing residual time series, affecting the searches for low-frequency gravitational waves performed with pulsar-timing arrays. Indeed, recent array data sets yield different gravitational-wave background upper limits and detection statistics when analyzed with different solar system ephemerides. Crucially, the ephemerides do not generally provide usable error representations. In this article, we describe the motivation, construction, and application of a physical model of solar system ephemeris uncertainties, which focuses on the degrees of freedom (Jupiterʼs orbital elements) most relevant to gravitational-wave searches with pulsar-timing arrays. This model, BAYESEPHEM, was used to derive ephemeris-robust results in NANOGravʼs 11 yr stochastic-background search, and it provides a foundation for future searches by NANOGrav and other consortia. The analysis and simulations reported here suggest that ephemeris modeling reduces the gravitational-wave sensitivity of the 11 yr data set and that this degeneracy will vanish with improved ephemerides and with pulsar-timing data sets that extend well beyond a single Jovian orbital period.

M Vallisneri↗

NASA NTRS2013

Common Practice Lightning Strike Protection Characterization Technique to Quantify Damage Mechanisms on Composite Substrates

To support FAA certification airworthiness standards, composite substrates are subjected to lightning direct-effect electrical waveforms to determine performance characteristics of the lightning strike protection (LSP) conductive layers used to protect composite substrates. Test results collected from independent LSP studies are often incomparable due to variability in test procedures & applied practices at different organizations, which impairs performance correlations between different LSP data sets. Under a NASA supported contract, The Boeing Company developed technical procedures and documentation as guidance in order to facilitate a test method for conducting universal common practice lightning strike protection test procedures. The procedures obtain conformity in future lightning strike protection evaluations to allow meaningful performance correlations across data sets. This universal common practice guidance provides the manufacturing specifications to fabricate carbon fiber reinforced plastic (CFRP) test panels, including finish, grounding configuration, and acceptable methods for pretest nondestructive inspection (NDI) and posttest destructive inspection. The test operations guidance elaborates on the provisions contained in SAE ARP5416 to address inconsistencies in the generation of damage protection performance data, so as to provide for maximum achievable correlation across capable lab facilities. In addition, the guidance details a direct effects test bed design to aid in quantification of the multi-physical phenomena surrounding a lightning direct attachment supporting validation data requirements for the development of predictive computational modeling. The lightning test bed is designed to accommodate a repeatable installation procedure to secure the test panel and eliminate test installation uncertainty. It also facilitates a means to capture the electrical waveform parameters in 2 dimensions, along with the mechanical displacement and thermal heating parameters which occur during lightning attachment. Following guidance defined in the universal common practice LSP test documents, protected and unprotected CFRP panels were evaluated at 20, 40 and 100KAmps. This report presents analyzed data demonstrating the scientific usefulness of the common practice approach. Descriptions of the common practice CFRP test articles, LSP test bed fixture, and monitoring techniques to capture the electrical, mechanical and thermal parameters during lightning attachment are presented here. Two methods of measuring the electrical currents were evaluated, inductive current probes and a newly developed fiberoptic sensor. Two mechanical displacement methods were also examined, optical laser measurement sensors and a digital imaging correlation camera system. Recommendations are provided to help users implement the common practice test approach and obtain LSP test characterizations comparable across data sets.

Szatkowski, George N.↗

NASA NTRS2000

BOREAS RSS-3 Reflectance Measured from a Helicopter-Mounted SE-590

The BOREAS RSS-3 team collected multiple remotely sensed data sets from the NASA UH-1 helicopter. This data set includes helicopter-based radiometric measurements of forested sites acquired during BOREAS made with an SE-590 processed to reflectance factors. The data used in this analysis were collected in 1994 during the three BOREAS IFCs at numerous tower and auxiliary sites in both the NSA and the SSA. The 15-degree FOV of the SE-590 yielded a ground resolution of approximately 79 m at the 300-m nominal altitude. The data are provided in tabular ASCII files.

Hall, Forrest G.↗

NASA NTRS1983

SEASAT synthetic-aperture radar data user's manual

The SEASAT Synthetic-Aperture Radar (SAR) system, the data processors, the extent of the image data set, and the means by which a user obtains this data are described and the data quality is evaluated. The user is alerted to some potential problems with the existing volume of SEASAT SAR image data, and allows him to modify his use of that data accordingly. Secondly, the manual focuses on the ultimate focuses on the ultimate capabilities of the raw data set and evaluates the potential of this data for processing into accurately located, amplitude-calibrated imagery of high resolution. This allows the user to decide whether his needs require special-purpose data processing of the SAR raw data.

Pravdo, S. H.↗

NASA NTRS1993

How diverse is the asteroid belt?

For approximately twenty years, many different asteroid taxonomies, which used many different observational data sets, have been developed to try to group asteroids into classes that contain members with similar spectral characteristics. However, to understand the structure of the asteroid belt, the resulting classes are only useful if they are grouping together asteroids with somewhat similar mineralogies and thermal histories. Until recently, these taxonomies have focused on spectral reflectance data from 0.3 to 1.1 microns and visual albedo. But in the last five years, observational data sets (e.g., 0.8 to 2.5 microns spectra, CCD spectra, 3 microns spectra, and radar albedos) for a small number of asteroids were compiled that can give a better mineralogical interpretation, but whose use in asteroid taxonomy was relatively limited. Analyses of these 'supplementary' data sets show that most asteroid classes contain members with different compositions and/or thermal histories. To understand the diversity of the asteroid belt, the number of objects with these observations must be expanded and used in the next generation of taxonomies.

Burbine, Thomas H.↗

NASA NTRS2004

Visual data mining for quantized spatial data

In previous papers we've shown how a well known data compression algorithm called Entropy-constrained Vector Quantization ( can be modified to reduce the size and complexity of very large, satellite data sets. In this paper, we descuss how to visualize and understand the content of such reduced data sets.

cluster analysis↗

DOE OSTI2024

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

ABSTRACT Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. IMPORTANCE Ecosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Biotechnology & Applied Microbiology↗

NASA NTRS1994

(abstract) Mount Rainier: New Remote Sensing Observations of a Decade Volcano

Mount Rainier was selected as a Decade Volcano by the International Association of Volcanology and Chemistry of the Earth's Interior. The purpose of this selection is to focus scientific and public attention on Mount Rainier during the current decade, the United Nations-designated International Decade of Natural Hazard Reduction. The Mount Rainier science plan calls for remote sensing surveys to monitor the volcano. To date, we have conducted airborne surveys with visible and near-infrared, thermal infrared, and interferometric radar instruments. Our preliminary analysis of some night-time time-series thermal infrared survey data sets of the summit suggests that, aside from seasonal variations in snow cover, there have been no qualitative changes in the size or pattern of the summit hot spots. Day-time airborne surveys were done to record the current surface appearance of the volcano and map hydrothermal alteration in the summit region. An interferometric radar survey yielded a high-resolution digital elevation model (DEM) which serves as a base for the registration of the other remote sensing data sets. More importantly, the DEM documents the current topography of glaciers and valleys. Planned biannual radar survey of mount rainier will produce a data set from which seasonal changes in glacier and valley topography can be characterized. Such characterization is essential if we are to recognize geothermally induced changes in snow and ice cover.

infrared radar interferometry glaciers seasonal va↗