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At least 487 records · Page 27

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗

Impact of LANDSAT MSS Sensor Differences on Change Detection Analysis

Change detection techniques were used to pinpoint differences in the multispectral band scanners on LANDSAT 2, 3, and 4 satellites. The method of analysis was to co-register 512 by 512 pixel subwindows for all data pairs followed by scattergram generation and analysis. In all cases, the LANDSAT-4 data were used as the base to which other images were registered. There appear to be no major problems preventing use of LANDSAT-4 MSS with previous MSS sensors for charge detection, provided the interference noise can be removed or minimized. This noise may result in detection of spurious changes, as well as affect other uses of the data, including image classification. Analysis of dark (water and forests), rather than light features will be most impacted because the noise will form a higher percentage of the total response at low DN values. Any data normalizations for change detection should be based upon the data, rather than solely upon calibration information. While the observed relative radiometric transfer function between LANDSAT 3 and 4 was approximately as predicted, there were still significant deviations. Normalizing based upon data content also can have the advantage of allowing simultaneous normalization of the atmosphere as well as the radiometry.

Likens, W. C.↗

A case study demonstration of the soil temperature extrema recovery rates after precipitation cooling at 10-cm soil depth

Since the invention of maximum and minimum thermometers in the 18th century, diurnal temperature extrema have been taken for air worldwide. At some stations, these extrema temperatures were collected at various soil depths also, and the behavior of these temperatures at a 10-cm depth at the Tifton Experimental Station in Georgia is presented. After a precipitation cooling event, the diurnal temperature maxima drop to a minimum value and then start a recovery to higher values (similar to thermal inertia). This recovery represents a measure of response to heating as a function of soil moisture and soil property. Eight different curves were fitted to a wide variety of data sets for different stations and years, and both power and exponential curves were fitted to a wide variety of data sets for different stations and years. Both power and exponential curve fits were consistently found to be statistically accurate least-square fit representations of the raw data recovery values. The predictive procedures used here were multivariate regression analyses, which are applicable to soils at a variety of depths besides the 10-cm depth presented.

Welker, Jean Edward↗

PlasmoData.jl — A Julia framework for modeling and analyzing complex data as graphs

Datasets encountered in scientific and engineering applications appear in complex formats (e.g., images, multivariate time series, molecules, video, text strings, networks). Graph theory provides a unifying framework to model such datasets and enables the use of powerful tools that can help analyze, visualize, and extract value from data. In this work, we present PlasmoData.jl, an open-source, Julia framework that uses concepts of graph theory to facilitate the modeling and analysis of complex datasets. The core of our framework is a general data modeling abstraction, which we call a DataGraph. We show how the abstraction and software implementation can be used to represent diverse data objects as graphs and to enable the use of tools from topology, graph theory, and machine learning (e.g., graph neural networks) to conduct a variety of tasks. We illustrate the versatility of the framework by using real datasets: (i) an image classification problem using topological data analysis to extract features from the graph model to train machine learning models; (ii) a disease outbreak problem where we model multivariate time series as graphs to detect abnormal events; and (iii) a technology pathway analysis problem where we highlight how we can use graphs to navigate connectivity. Further, our discussion also highlights how PlasmoData.jl leverages native Julia capabilities to enable compact syntax, scalable computations, and interfaces with diverse packages. Overall, we show that the DataGraph abstraction and PlasmoData.jl Julia package are able to model data within graphs and enable useful analysis.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Application of digital terrain data to quantify and reduce the topographic effect on LANDSAT data

Integration of LANDSAT multispectral scanner (MSS) data with 30 m U.S. Geological Survey (USGS) digital terrain data was undertaken to quantify and reduce the topographic effect on imagery of a forested mountain ridge test site in central Pennsylvania. High Sun angle imagery revealed variation of as much as 21 pixel values in data for slopes of different angles and aspects with uniform surface cover. Large topographic effects were apparent in MSS 4 and 5 was due to a combination of high absorption by the forest cover and the MSS quantization. Four methods for reducing the topographic effect were compared. Band ratioing of MSS 6/5 and MSS 7/5 did not eliminate the topographic effect because of the lack of variation in MSS 4 and 5 radiances. The three radiance models examined to reduce the topographic effect required integration of the digital terrain data. Two Lambertian models increased the variation in the LANDSAT radiances. The nonLambertian model considerably reduced (86 per cent) the topographic effect in the LANDSAT data. The study demonstrates that high quality digital terrain data, as provided by the USGS digital elevation model data, can be used to enhance the utility of multispectral satellite data.

Justice, C. O.↗

Resolving Ice Cloud Optical Thickness Biases Between CALIOP and MODIS Using Infrared Retrievals

Despite its importance as one of the key radiative properties that determines the impact of upper tropospheric clouds on the radiation balance, ice cloud optical thickness (IOT) has proven to be one of the more challenging properties to retrieve from space-based remote sensing measurements. In particular, optically thin upper tropospheric ice clouds (cirrus) have been especially challenging due to their tenuous nature, extensive spatial scales, and complex particle shapes and light scattering characteristics. The lack of independent validation motivates the investigation presented in this paper, wherein systematic biases between MODIS Collection 5 (C5) and CALIOP Version 3 (V3) unconstrained retrievals of tenuous IOT (< 3) are examined using a month of collocated A-Train observations. An initial comparison revealed a factor of two bias between the MODIS and CALIOP IOT retrievals. This bias is investigated using an infrared (IR) radiative closure approach that compares both products with MODIS IR cirrus retrievals developed for this assessment. The analysis finds that both the MODIS C5 and the unconstrained CALIOP V3 retrievals are biased (high and low, respectively) relative to the IR IOT retrievals. Based on this finding, the MODIS and CALIOP algorithms are investigated with the goal of explaining and minimizing the biases relative to the IR. For MODIS we find that the assumed ice single scattering properties used for the C5 retrievals are not consistent with the mean IR COT distribution. The C5 ice scattering database results in the asymmetry parameter (g) varying as a function of effective radius with mean values that are too large. The MODIS retrievals have been brought into agreement with the IR by adopting a new ice scattering model for Collection 6 (C6) consisting of a modified gamma distribution comprised of a single habit (severely roughened aggregated columns); the C6 ice cloud optical property models have a constant g approx. = 0.75 in the mid-visible spectrum, 5-15% smaller than C5. For CALIOP, the assumed lidar ratio for unconstrained retrievals is fixed at 25 sr for the V3 data products.This value is found to be inconsistent with the constrained (predominantly nighttime) CALIOP retrievals. An experimental data set was produced using a modified lidar ratio of 32 sr for the unconstrained retrievals (an increase of 28%), selected to provide consistency with the constrained V3 results. These modifications greatly improve the agreement with the IR and provide consistency between the MODIS and CALIOP products. Based on these results the recently released MODIS C6 optical products use the single habit distribution given above, while the upcoming CALIOP V4 unconstrained algorithm will use higher lidar ratios for unconstrained retrievals.

Cloud↗

Characterization of Particle Size Standard NIST 1019b with SynchrotronX-ray Microtomography and Digital Data Extraction

We show that synchrotron x-ray microtomography ({mu}CT) followed by digital data extraction can be used to examine the size distribution and particle morphologies of the polydisperse (750 to 2450 {micro}m diameter) particle size standard NIST 1019b. Our size distribution results are within errors of certified values with data collected at 19.5 {micro}m/voxel. One of the advantages of using {mu}CT to investigate the particles examined here is that the morphology of the glass beads can be directly examined. We use the shape metrics aspect ratio and sphericity to examine of individual standard beads morphologies as a function of spherical equivalent diameters. We find that the majority of standard beads possess near-spherical aspect ratios and sphericities, but deviations are present at the lower end of the size range. The majority (> 98%) of particles also possess an equant form when examined using a common measure of equidimensionality. Although the NIST 1019b standard consists of loose particles, we point out that an advantage of {mu}CT is that coherent materials comprised of particles can be examined without disaggregation.

36 MATERIALS SCIENCE↗

Overview of SPRITE: Saturn Probe Interior and aTmosphere Explorer Concept

The Saturn PRobe Interior and aTmosphere Explorer (SPRITE) mission concept targets high-priority Planetary Science Decadal Survey science objectives. This mission concept would deliver the SPRITE entry probe into the Saturn atmosphere to obtain in situ measurements of elemental abundances and isotopic ratios, which would help distinguish the role Saturn played in the solar system formation and co-evolution of other planets. An Atmospheric Structure Investigation sensor package on the entry probe would provide in situ measurements of the pressure/temperature and wind structure below the cloud-tops, and a Quadrupole Mass Spectrometer and Tunable Laser Spectrometer suite would determine the composition of Saturn’s atmosphere. The SPRITE mission concept described in this paper uses a solar-powered carrier-relay spacecraft to deliver the battery-powered entry probe to Saturn after a 10-year Venus-Earth-Earth gravity-assist trajectory, and then relays the probe data back to Earth during the carrier-relay spacecraft Saturn flyby. A high-heritage design approach is implemented for the flight elements to minimize technical risk and enable successful return of this high-value science data.

Cuddy, Cavan↗

Utilization of ERTS-1 data in the Houston area

The author has identified the following significant results. Using clustering techniques, several large lakes in Texas have been accurately delineated in computer printout graymaps. It was also found that small bodies of water (one to two acres in size) could be detected by searching for small reflectance values in the infrared data. A graymap printout of a lake described a shore outline that was not consistent with available maps. Field examination revealed that the actual level of the lake was below that for which the map was drawn. The current lake configuration agrees in shape and relative size with the ERTS-1 data printout. Water turbidity causes reflectance changes which are detectable in ERTS-1 band 7 data. A comparison has been made of the Monterey Bay, California area using 1971 aerial color infrared photography and a 1972 ERTS-1 band 7 infrared image. This comparison revealed that some event has occurred to impound a significant amount of water in the area since the infrared photography was taken. Data values in the ERTS-1 infrared image exhibit detectable changes in brightness at inflow points, where high turbidity would be present. Researchers had not expected to detect water turbidity patterns in band 7 (800 to 1100 nanometers).

Erb, R. B.↗

ASCENDS: Advanced Data SCiENce Toolkit for Non-Data Scientists

Data science capabilities are becoming important more and more. Even though there exist many data science and machine learning tools, they are not intuitive for many traditional scientists who are not familiar with programming. ASCENDS provides easy and intuitive interfaces (command-line interface, graphical user interface) to users so they can use data science capabilities without having to understand programming language. ASCENDS performs data visualization, machine learning model training, storing and prediction (regression problem), automatic hyperparameter tuning, and supports various machine learning models including random forest, kernel ridge, nearest neighbor, neural network, etc. Users can use standard CSV (comma separated values) format data set and investigate the feature columns that are highly correlated to a target column; further, they can learn ML models, then store and use them for predictions. The tool is supposed to be generically applicable so that it can be used for many different applications.

Sangkeun, MattLee↗

Scientific Uses and Directions of SPDF Data Services

From a science user's perspective, the multi-mission data and orbit services of NASA's Space Physics Data Facility (SPDF) project perform as a working and highly functional heliophysics virtual observatory. CDAWeb enables plots, listings and file downloads for current data across the boundaries of missions and instrument types (and now including data from THEMIS and STEREO), VSPO access to a wide range of distributed data sources. SSCWeb, Helioweb and our 3D Animated Orbit Viewer (TIPSOD) provide position data and query logic for most missions currently-important to heliophysics science. OMNIWeb with its new extension to 1- and 5- minute resolution provides interplanetary parameters at the Earth's bow shock as a unique value-added data product. To enable easier integrated use of our capabilities by developers and by the emerging heliophysics VxOs, our data and services are available through webservices-based APls as well as through our direct user interfaces. SPDF has also now developed draft descriptions of its holdings in SPASE-compliant XML In addition to showcasing recent enhancements to SPDF capabilities, we will use these systems and our experience in developing them: to demonstrate a few typical science use cases; to discuss key scope and design issues among users, service providers and end data providers; and to identify key areas where existing capabilities and effective interface design are still inadequate to meet community needs.

Fung, Shing↗

Design, performance, and calculated error of a Faraday cup for absolute beam current measurements of 600-MeV protons

A mobile self-contained Faraday cup system for beam current measurments of nominal 600 MeV protons was designed, constructed, and used at the NASA Space Radiation Effects Laboratory. The cup is of reentrant design with a length of 106.7 cm and an outside diameter of 20.32 cm. The inner diameter is 15.24 cm and the base thickness is 30.48 cm. The primary absorber is commercially available lead hermetically sealed in a 0.32-cm-thick copper jacket. Several possible systematic errors in using the cup are evaluated. The largest source of error arises from high-energy electrons which are ejected from the entrance window and enter the cup. A total systematic error of -0.83 percent is calculated to be the decrease from the true current value. From data obtained in calibrating helium-filled ion chambers with the Faraday cup, the mean energy required to produce one ion pair in helium is found to be 30.76 + or - 0.95 eV for nominal 600 MeV protons. This value agrees well, within experimental error, with reported values of 29.9 eV and 30.2 eV.

Beck, S. M.↗

A Revised Trajectory Algorithm to Support En Route and Terminal Area Self-Spacing Concepts

This document describes an algorithm for the generation of a four dimensional trajectory. Input data for this algorithm are similar to an augmented Standard Terminal Arrival (STAR) with the augmentation in the form of altitude or speed crossing restrictions at waypoints on the route. This version of the algorithm accommodates descent Mach values that are different from the cruise Mach values. Wind data at each waypoint are also inputs into this algorithm. The algorithm calculates the altitude, speed, along path distance, and along path time for each waypoint.

Aircraft operations↗

Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values

Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R 2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control.

COVID19↗

Cubesat Constellation Design for Air Traffic Monitoring

Suitably equipped global and local air traffic can be tracked. The tracking information may then be used for control from ground-based stations by receiving the Automatic Dependent Surveillance-Broadcast (ADS-B) signal. The ADS-B signal, emitted from the aircraft's Mode-S transponder, is currently tracked by terrestrial based receivers but not over remote oceans or sparsely populated regions such as Alaska or the Pacific Ocean. Lack of real-time aircraft time/location information in remote areas significantly hinders optimal planning and control because bigger "safety bubbles" (lateral and vertical separation) are required around the aircraft until they reach radar-controlled airspace. Moreover, it presents a search-and-rescue bottleneck. Aircraft in distress, e.g. Air France AF449 that crashed in 2009, take days to be located or cannot be located at all, e.g. Malaysia Airlines MH370 in 2014. In this paper, we describe a tool for designing a constellation of small satellites which demonstrates, through high-fidelity modeling based on simulated air traffic data, the value of space-based ADS-B monitoring and provides recommendations for cost-efficient deployment of a constellation of small satellites to increase safety and situational awareness in the currently poorly-served surveillance area of Alaska. Air traffic data has been obtained from the Future ATM Concepts Evaluation Tool (FACET), developed at NASA Ames Research Center, simulated over the Alaskan airspace over a period of one day. The simulation is driven by MATLAB with satellites propagated and coverage calculated using AGI's Satellite ToolKit(STK10).

cubesats↗

Excited Vibrational Level Rotational Constants for SiC2: A Sensitive Molecular Diagnostic for Astrophysical Conditions

Silacyclopropynylidene, SiC2, is a known and highly abundant circumstellar molecule. Its spectrum has been established as a major component of lines observed toward the carbon-rich star IRC +10216 (CW Leonis). It has been detected in its low-lying v(sub 3) = 1 and 2 vibrational states as well as in various isotopic compositions. Increasing sensitivity and spatial resolution will enable many more emission or absorption lines to be detected. In order to detect new molecular species, unassigned lines of known species must be identified. This work uses established ab initio quartic force fields to produce data necessary for this classification of lines related to SiC2. Agreement between the theoretical vibrational frequencies and known rotational and spectroscopic constants is quite good, as good as 5 cm(exp -1) and 3 MHz, respectively in some cases. Additionally, experimentally unknown vibrational frequencies and rotational constants are provided for the first overtones and combination bands in addition to 3(sub v3), the second overtone of the low-lying antisymmetric stretch/carbide rotation mode. Frequencies of v(sub 3) = 3 low-J rotational transitions of the main isotopic species are also estimated from published data for v(sub 3) ≤ 2. Further, we determine rotational and centrifugal distortion parameters for which in most cases vibrational effects due to the v(sub 3) mode were reduced to first, and in several cases also to second order. These values may approximate equilibrium values better than the ground state values. The data produced herein will aid in the experimental and observational characterization of this known astromolecule in order to identify some of the unassigned lines for a known entity.

Astrochemistry↗

Assessment of Computer-based Geologic Mapping of Rock Units in the LANDSAT-4 Scene of Northern Death Valley, California

Results from a series of geologic classifications conducted on a thematic mapper subscene of the northern Death Valley, California are reported. Measurements of accuracy are made through comparison with the 1977 edition of the Death Valley geologic sheet. This employs a simplified map version which is registered by computer to the image data base, allowing a pixel by pixel match with the classified scene. The results show accuracy ranges from 36 to 79% depending on the type of classifier used and the statistical adjustments made to the data. Accuracy values in identifying geologic units were 2 to 3 times higher for those in the relatively flat valleys than for units in the rugged mountainous terrain. Improvements in accuracy will be sought by correcting for slope/aspect variations in mountainous terrain using topographic data recorded in Defense Mapping Agency (DMA) tapes. The above classification results will also be compared with ratio and principal component image classifications made from the same scene.

Short, N. M.↗

Human performance and physiological function during a 24-hr exposure to 1% bromotrifluoromethane (Halon 1301)

Performance and physiological measurements were obtained from four pairs of men exposed for 24 hr to 1% (10,000 ppm) Halon 1301 (bromotrifluoromethane, CBrF3) and to air with order counterbalanced using a double-blind protocol. Cognitive and motor performance was assessed before, during, and after the exposures using seven scales of the Automated Portable Testing System, which produced 13 measures of performance. Halon inhalation induced decrements in 2 of the 13 measures, but actual and estimated magnitudes of the decrements were no greater than 5% of baseline values. Physiological data were obtained before, during, and after the exposures from clinical chemistry analyses of blood and urine samples, pulmonary function tests, and monitoring of vital signs. Significant change during Halon inhalation was observed for 6 of the 52 variables assessed; however, all physiological values remained within clinically acceptable limits. No cardiovascular effects were noted. This study demonstrated that exposure to 1% Halon 1301 for 24 hr can produce minor disturbance of central nervous system function as assessed by cognitive tasks.

Randomized Controlled Trial↗