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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Coronado Ecological Conservation: Assessing Vegetation Change Due to Border Wall Construction and Shifting Social Trails

Species monitoring is essential in mitigating the impacts of plant invasion, such as radical changes in an area’s ecosystem, degraded soil health, increased wildfire severity, landslides, and increased flooding. NASA DEVELOP partnered with the National Park Service (NPS) to investigate invasive species in disturbed lands: specifically, areas affected by off-trail walking and US-Mexico border construction activities. The team assessed how construction has impacted the distribution of Lehmann’s lovegrass and Russian thistle invasives throughout Coronado National Memorial, AZ from 1986 to 2022. Using data from Landsat 5 and 8, Sentinel-2, the National Agriculture Imagery Program, and PlanetScope, the team computed vegetation indices including the Normalized Difference Vegetation Index, Normalized Difference Moisture Index, Modified Soil Adjusted Vegetation Index 2, Enhanced Vegetation Index, and Tasseled Cap Wetness, Brightness, and Greenness transformations as vegetation health indicators to input into various machine learning algorithms. To minimize noise, the team conducted Principal Component Analysis on the vegetation indices and spectral bands before running k-means++ clustering and random forest classification algorithms. Between all datasets, we found the median area fully overtaken by invasive plants was 5.37% of the park’s total area in 2022. The NPS will use the end products to help increase restoration efforts in disturbed areas with high concentrations of invasive plants. The NPS’s collection of ground data for 2022–2023, in conjunction with future data collection, will notably improve the accuracy of classification models, leading to more precise monitoring of invasive spread over time.

Carson Schuetze↗
NASA NTRS2023

Optimizing Retrieval Spaces of Bio-Optical Models for Remote Sensing of Ocean Color

We investigated the optimal number of independent parameters required to accurately represent spectral remote sensing reflectances (𝑅 rs ) by performing principal component analysis on quality controlled in situ and synthetic 𝑅 rs data. We found that retrieval algorithms should be able to retrieve no more than four free parameters from 𝑅 rs spectra for most ocean waters. In addition, we evaluated the performance of five different bio-optical models with different numbers of free parameters for the direct inversion of in-water inherent optical properties (IOPs) from in situ and synthetic 𝑅 rs data. The multi-parameter models showed similar performances regardless of the number of parameters. Considering the computational cost associated with larger parameter spaces, we recommend bio-optical models with three free parameters for the use of IOP or joint retrieval algorithms.

Ocean Color↗
NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗
NASA NTRSDate not supplied

Batch Effect Correction Methods for NASA GeneLab Transcriptomic Datasets

RNA sequencing (RNA-seq) data from space biology experiments promise to yield invaluable insights into the effects of spaceflight on terrestrial biology. However, sample numbers from each study are low due to limited crew availability, hardware, and space. To increase statistical power, spaceflight RNA-seq datasets from different missions are often aggregated together. However, this can introduce technical variation or "batch effects", often due to differences in sample handling, sample processing, and sequencing platforms. Several computational methods have been developed to correct for technical batch effects, thereby reducing their impact on true biological signals. In this study, we combined 7 mouse liver RNA-seq datasets from NASA GeneLab (part of the NASA Open Science Data Repository) to evaluate several common batch effect correction methods (ComBat and ComBat-seq from the sva R package, and Median Polish, Empirical Bayes, and ANOVA from the MBatch R package). We quantitatively evaluated the ability of these methods to correct for technical batch variables in space biology RNA-seq data using the following criteria: BatchQC, principal component analysis, dispersion separability criterion, log fold change correlation, and differential gene expression analysis. Each batch variable / correction method combination was then assessed using a custom scoring approach to identify the optimal correction method for the combined dataset, by geometrically probing the space of all allowable scoring functions to yield an aggregate volume-based scoring measure. Finally, we describe the way in which the GeneLab multi-study analysis and visualization portal will allow users to examine the presence or absence of batch effects using multiple metrics. If the user chooses to perform batch effect correction, the scoring approach described here can be implemented to identify the optimal correction method to use for their specific combined dataset prior to analysis.

Lauren M. Sanders↗
NASA NTRSDate not supplied

Enabling Intelligent Data Downlink Prioritization of In-Situ Observations through Generalizable and Computationally Inexpensive Anomaly Detection

High-fidelity measurements of magnetic fields and other observed properties, such as energetic particle fluxes, are a necessary component to our understanding of the highly dynamic near-Earth space environment. As our desire to study smaller-scale phenomena such as shocks and dipolorizations has increased, we have been driven to take and telemeter measurements at higher cadences. Unfortunately, many missions are unable to downlink all their captured data due to the well-known data transmission bottleneck at the DSN. These missions must then prioritize their high-cadence data such that the most scientifically useful intervals are transmitted. One simple prioritization technique uses the spacecraft position to telemeter data from only the region of interest. Although easy to implement, this method does not leverage the available scientific data and can omit intervals of useful scientific data when they lie outside the region of interest. The Magnetospheric Multiscale Mission (MMS) uses mission-specific parameterization of several data products to automatically prioritize scientifically useful intervals. Then, MMS verifies the automatically selected intervals by having a domain expert manually select intervals for downlink. The overall complexity required by this technique make it prohibitive for deployment on low-cost platforms (i.e., CubeSats) or on future missions featuring large constellations of satellites such as the Geospace Dynamics Constellation (GDC). We present preliminary results for a simple, generic, and data-driven method of downlink prioritization for magnetic field (and other) measurements. Specifically, Principal Components Analysis (PCA) and One-Class Support Vector Machines (OC-SVMs) are used to detect intervals containing anomalous activity, which can then be prioritized for subsequent downlink. The computational simplicity of this algorithm makes it an excellent candidate for implementation on spaceflight hardware, as well as provide generalizability to a broad range of missions and data products. Initial analysis of this technique has been performed using magnetic field measurements from the Magnetospheric Multiscale Mission and CASSIOP, where it automatically identified scientifically interesting intervals containing Alfvén waves and EMIC activity.

Matthew G. Finley↗
NASA NTRSDate not supplied

Machine learning based noise reduction for satellite products: application to solar-induced fluorescence retrievals using simulated and real data

In the past two decades, global satellite measurements of terrestrial chlorophyll solar-induced fluorescence (SIF) have been used widely for a number of different applications related to physiology, phenology, and productivity of plants. However, SIF retrievals are inherently noisy due to the relatively small SIF spectral signature in comparison with observational noise. In this work, we examine how a spectral-based approach that employs principal component analysis along with a relatively shallow artificial neural network can be used to reduce noise and other artifacts in satellite level 2 (L2) products. We first apply the approach in a controlled environment in which radiance spectra are simulated with a full atmospheric and surface radiative transfer model for different scenarios including various SIF values that are known. Various levels of noise can be added to the simulated spectra. Resulting noisy and noise-reduced SIF retrievals are compared with the true values to assess performance. We then apply the noise reduction approach to real SIF derived from instruments flying on meteorological satellites. The results are evaluated by comparing SIF retrievals from different platforms with each other and with other independent data sets, showing enhanced capability to capture seasonal and interannual variability in SIF.

Chlorophyll fluorescence↗
NASA NTRSDate not supplied

Global SO 2 Data Record from OMPS Instruments on the JPSS Constellation

NASA’s Earth Observing System (EOS) SO 2 climate data record (CDR) started in 2004, with the launch of the Aura/Ozone Monitoring Instrument (OMI) and is now being continued with the SNPP/Ozone Mapping and Profiler Suite (OMPS) launched in 2011. Both OMI and SNPP/OMPS SO 2 CDRs are produced with the Goddard principal component analysis (PCA) spectral fitting algorithm. An advantage of the data-driven PCA retrieval technique is that it enables highly consistent retrievals from different instruments, by inherently accounting for various instrumental factors. To further extend the EOS SO 2 CDR, we are implementing the PCA SO 2 retrieval algorithm with the L1B measurements from OMPS instruments flying on the Joint Polar Satellite System (JPSS) constellation. In this presentation, we will provide an update on our progress in NOAA-20 (launched in 2017) and NOAA-21 (launched in 2022) PCA SO2 retrievals. We will focus on our new NOAA-20/OMPS PCA SO 2 EOS continuity product, to be publicly released in fall of 2023. We will present statistical analyses on the quality of NOAA-20 PCA SO 2 product, including retrieval noise, biases over background areas, and long-term stability. We will compare our PCA SO 2 retrievals from NOAA-20 with those from OMI, SNPP/OMPS, and S5P/TROPOMI (TROPOspheric Monitoring Instrument) for anthropogenic sources as well as large volcanic plumes. We will also discuss the application of a new machine learning technique that helps to further reduce the noise of NOAA-20 SO 2 retrievals. In addition, we will present preliminary PCA SO 2 retrievals from NOAA-21/OMPS, including those from direct readout implementation for aviation disaster avoidance. Finally, we will share some first results applying the PCA algorithm to NASA’s geostationary TEMPO (Tropospheric Emissions: Monitoring of Pollution) instrument to obtain hourly, high resolution SO 2 data over North America.

SO2↗
NASA NTRSDate not supplied

Continuing Long-term Global SO 2 Data Record with JPSS OMPS Instruments

NASA’s long-term Earth Observing System (EOS) SO 2 climate data record (CDR) started with Aura/Ozone Monitoring Instrument (OMI, launched in 2004) and is now being continued with the SNPP/Ozone Mapping and Profiler Suite (OMPS, launched in 2011). Both OMI and SNPP/OMPS SO 2 CDRs are produced with the Goddard principal component analysis (PCA) spectral fitting algorithm. By inherently accounting for various instrumental factors, the PCA technique enables highly consistent retrievals between different instruments. In this presentation, we will provide an overview on our effort to further extend the EOS SO 2 CDR, by implementing the PCA SO 2 algorithm with multiple OMPS instruments flying on the Joint Polar Satellite System (JPSS) constellation, including NOAA-20 (launched in 2017) and NOAA-21 (launched in 2022). We will present results analyzing our new NOAA-20/OMPS PCA SO 2 EOS continuity product, to be publicly released in fall of 2023. We will show statistical analyses on the quality of NOAA-20 PCA SO 2 product, such as retrieval noise, biases over background areas, and long-term stability. We will employ a previously established top-down method to estimate SO2 emissions from selected large point sources, using NOAA-20 SO 2 retrievals and assimilated wind fields as input. The SO 2 emission estimates derived from NOAA-20 retrievals will be compared with those from OMI, SNPP/OMPS, and S5P/TROPOMI (TROPOspheric Monitoring Instrument). We will also demonstrate the application of a new machine learning technique that further reduces the noise of NOAA-20 SO 2 retrievals. Finally, we will present preliminary PCA SO 2 retrievals from recently launched satellite sensors, including NOAA-21/OMPS and NASA’s geostationary TEMPO (Tropospheric Emissions: Monitoring of Pollution) instrument.

SO2↗
NASA NTRSDate not supplied

Enabling Intelligent Data Downlink Prioritization of In-Situ Observations through Generalizable and Computationally Inexpensive Anomaly Detection

High-fidelity measurements of magnetic fields and other observed properties, such as energetic particle fluxes, are a necessary component to our understanding of the highly dynamic near-Earth space environment. As our desire to study smaller-scale phenomena such as shocks and dipolorizations has increased, we have been driven to take and telemeter measurements at higher cadences. Unfortunately, many missions are unable to downlink all their captured data due to the well-known data transmission bottleneck at the DSN. These missions must then prioritize their high-cadence data such that the most scientifically useful intervals are transmitted. One simple prioritization technique uses the spacecraft position to telemeter data from only the region of interest. Although easy to implement, this method does not leverage the available scientific data and can omit intervals of useful scientific data when they lie outside the region of interest. The Magnetospheric Multiscale Mission (MMS) uses mission-specific parameterization of several data products to automatically prioritize scientifically useful intervals. Then, MMS verifies the automatically selected intervals by having a domain expert manually select intervals for downlink. The overall complexity required by this technique make it prohibitive for deployment on low-cost platforms (i.e., CubeSats) or on future missions featuring large constellations of satellites such as the Geospace Dynamics Constellation (GDC). We present preliminary results for a simple, generic, and data-driven method of downlink prioritization for magnetic field (and other) measurements. Specifically, Principal Components Analysis (PCA) and One-Class Support Vector Machines (OC-SVMs) are used to detect intervals containing anomalous activity, which can then be prioritized for subsequent downlink. The computational simplicity of this algorithm makes it an excellent candidate for implementation on spaceflight hardware, as well as provide generalizability to a broad range of missions and data products. Initial analysis of this technique has been performed using magnetic field measurements from the Magnetospheric Multiscale Mission and CASSIOP, where it automatically identified scientifically interesting intervals containing Alfvén waves and EMIC activity.

Matthew G. Finley↗
NASA NTRS2024

Cali Urban Development II: Investigating the Impacts of Land Use Change on Urban Heat and Social Vulnerability in Cali, Colombia

The surface urban heat island (SUHI) effect is an environmental phenomenon resulting in cities with higher temperatures than rural areas due to increased pavement and decreased cooling from vegetation. The city of Santiago de Cali in Colombia faces SUHI challenges exacerbated by land use change. The Cali municipal government agency, Departamento Administrativo de Gestión del Medio Ambiente, and the community organization Fundacion Dinamizadores Ambientales partnered with NASA DEVELOP to evaluate communities in Cali most vulnerable to urban heat. This project illustrated the utility of using NASA Earth observations to evaluate the relationship between land use, temperature, and social factors in Cali, Colombia between 2013 and 2023. The team used Landsat 7 Enhanced Thematic Mapper Plus (ETM+), Landsat 8 Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS), and Landsat 9 OLI-2/TIRS-2 to generate land surface temperature (LST) maps in Google Earth Engine through NASA DEVELOP’s Urban Heat Exposure Assessment Tempe 2.0 tool. Cloud cover limited the project feasibility, but it improved with Landsat 9 data. In ArcGIS Pro, the team found that LST was significantly higher in urban areas than in wetlands or forests. Using R Studio, the team ran a principal component analysis and found that health care and green space access were negatively correlated, and Afro-Colombian ethnicity was positively correlated with LST. With knowledge of the most impacted and vulnerable regions, the partner organizations can prioritize establishing healthcare facilities and green spaces in those areas to reduce the impacts of urban heat.

vegetation loss↗
NASA NTRSDate not supplied

Monitoring and Assessing Heat Vulnerability to Identify Locations for Heat Mitigation Efforts in Sarasota, Florida

Located in the coastal subtropical region, Florida’s Sarasota County receives plenty of sunlight for more than half of the year. However, the ongoing rise in summer temperatures attributed to climate change poses an increasing vulnerability to extreme heat for the residents. Moreover, the area's high relative humidity exacerbates the discomfort of high temperatures, thereby intensifying the severity of heat events and elevating the risks of heat-related illnesses. Our collaborations with Sarasota County Sustainability underscore shared concerns about the impact of urban heat island (UHI) on the community. We utilized Earth observation data from NASA Landsat 8 and Landsat 9’s Thermal Infrared Sensors (TIRS) and the International Space Station’s Ecosystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) to model UHI effects within the county during the summer from 2019 to 2023. By implementing the open-source Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) Urban Cooling software model, ArcGIS ModelBuilder, and principal component analysis, we identified the land surface temperature variance within the county and areas that are least capable of mitigating the effects of UHI. In addition, we use socioeconomic and demographic data as indicators to quantify vulnerability at the census tract level. The results revealed that heat intensity varies significantly across Sarasota County, with the highest temperatures being in the more developed western part of the region. We pinpointed that at least three vulnerable communities reside in high-heat regions: North Sarasota, Venice, and North Port. These areas demonstrate a confluence between socioeconomic sensitivity and environmental hazard, indicating a high priority in future heat mitigation efforts.

Theresia Phoa↗
DOE OSTI2014

Feasibility Study on the Use of On-line Multivariate Statistical Process Control for Safeguards Applications in Natural Uranium Conversion Plants

The objective of this work was to determine the feasibility of using on-line multivariate statistical process control (MSPC) for safeguards applications in natural uranium conversion plants. Multivariate statistical process control is commonly used throughout industry for the detection of faults. For safeguards applications in uranium conversion plants, faults could include the diversion of intermediate products such as uranium dioxide, uranium tetrafluoride, and uranium hexafluoride. This study was limited to a 100 metric ton of uranium (MTU) per year natural uranium conversion plant (NUCP) using the wet solvent extraction method for the purification of uranium ore concentrate. A key component in the multivariate statistical methodology is the Principal Component Analysis (PCA) approach for the analysis of data, development of the base case model, and evaluation of future operations. The PCA approach was implemented through the use of singular value decomposition of the data matrix where the data matrix represents normal operation of the plant. Component mole balances were used to model each of the process units in the NUCP. However, this approach could be applied to any data set. The monitoring framework developed in this research could be used to determine whether or not a diversion of material has occurred at an NUCP as part of an International Atomic Energy Agency (IAEA) safeguards system. This approach can be used to identify the key monitoring locations, as well as locations where monitoring is unimportant. Detection limits at the key monitoring locations can also be established using this technique. Several faulty scenarios were developed to test the monitoring framework after the base case or normal operating conditions of the PCA model were established. In all of the scenarios, the monitoring framework was able to detect the fault. Overall this study was successful at meeting the stated objective.

Ladd-Lively, Jennifer L↗
DOE OSTI2016

Construction of tolerance bounds for a multivariate response associated with a covariate: A case study

The purpose of this research is to describe and illustrate practical methods that can be used to construct tolerance bounds for a multivariate measurement associated with a covariate. These methods rely on principal components analysis and the parametric bootstap. The methods are illustrated with an example in which the vibration environment experienced by a test object being carried by an aircraft (known as captive carry) is characterized.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Extreme_SeaState_Contour_v1

This software generates environmental contours of extreme sea states using buoy observations of significant wave height and energy period or peak period. The code transforms these observations using principal component analysis (PCA) to create an uncorrelated representation of the data. The subsequent components are modeled using probability distributions and parameter fitting functions. The inverse first-order reliability method (I-FORM) is then applied to these models in order to generate an extreme event contour based on a given return period (i.e., 100 years).The subsequent contour is then transformed back into the original input space defined by the variables of interest in order to create an environmental contour of extreme sea states.

Source record↗
DOE OSTI2017

Using dynamic mode decomposition for real-time background/foreground separation in video

The technique of dynamic mode decomposition (DMD) is disclosed herein for the purpose of robustly separating video frames into background (low-rank) and foreground (sparse) components in real-time. Foreground/background separation is achieved at the computational cost of just one singular value decomposition (SVD) and one linear equation solve, thus producing results orders of magnitude faster than robust principal component analysis (RPCA). Additional techniques, including techniques for analyzing the video for multi-resolution time-scale components, and techniques for reusing computations to allow processing of streaming video in real time, are also described herein.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Gas hydrate characterization from a 3D seismic dataset in the deepwater eastern Gulf of Mexico

Seismic stratigraphic features are delineated using principal component analysis of the band limited data at potential gas hydrate sands, and compared and calibrated with spectral decomposition thickness to constrain thickness in the absence of well control. Layers in the abyssal fan sediments are thinner than can be resolved with 50 Hz seismic and thus comprise composite thin-bed reflections. Amplitude vs frequency analysis are used to indicate gas and gas hydrate reflections. Synthetic seismic wedge models show that with 50Hz seismic data, a 40% saturation of a Plio Pleistocene GoM sand in the hydrate stability zone with no subjacent gas can produce a phase change (negative to positive) with a strong correlation between amplitude and hydrate saturation. The synthetic seismic response is more complicated if the gas hydrate filled sediments overlie gassy sediments. Hydrate (or gas) saturation in thin beds enhances the amplitude response and can be used to estimate saturation. Gas hydrate saturation from rock physics, amplitude, and frequency analysis is compared to saturation derived from inversion at several interpreted gas hydrate accumulations in the eastern Gulf of Mexico.

gas hydrate↗
DOE OSTI2017

Gas hydrate characterization from a 3D seismic dataset in the deepwater eastern Gulf of Mexico

Principal component analysis of spectral decomposition results combined with amplitude and frequency seismic attributes derived from 3D seismic data are used for the identification and characterization of gas hydrate deposits in the deepwater eastern Gulf of Mexico. In the central deepwater Gulf of Mexico (GoM), logging while drilling LWD data provided insight to the amplitude response of gas hydrate saturation in sands, which could be used to characterize complex gas hydrate deposits in other sandy deposits. In this study, a large 3D seismic data set from equivalent and distal Plio Pleistocene sandy channel deposits in the deepwater eastern Gulf of Mexico is screened for direct hydrocarbon indicators for gas hydrate saturated sands.

gas hydrate↗