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DOE OSTI2022

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein

The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2' cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2021

Comparison of SAR and CYNSS surface water extent metrics over the Yucatan Lake wetland site

Wetlands have a major role in the carbon cycle, outgassing large quantities of carbon dioxide and methane through processes that are directly and strongly influenced by the duration and timing of inundation. Therefore, understanding the seasonal pattern of inundation can be a component for regional to global scale carbon models. Measurement of inundation extent also establishes a benchmark for the current status of wetland areas, useful in assessing the future impacts of climate change. The incorporation of frequent measurements of inundation extent into large-scale hydrological models would permit the evaluation of more detailed seasonal and longer-term floodplain dynamics and their associated management implications.The Cyclone GNSS (CYGNSS) constellation of satellites launched in 2016, and carries receivers capable of receiving data from L-band GNSS reflections. Delay Doppler maps (DDM) are generated on board and telemetered to the ground, along with a small number of raw data takes that can be used for special processing on the ground for evaluation purposes. It has been previously shown that these data can be sensitive to inundation.The NASA ISRO Synthetic Aperture Radar, currently planned for launch in January 2023, has both an L-band and S-band SAR for earth imaging. The L-band SAR, which will image the Earth's land mass twice every 12 days, has a requirement for measuring wetland inundation extent at the 1 ha scale. One of the sites that will be used to validate this requirement is Yucatan Lake, Louisiana. This oxbow lake and surrounding area located adjacent to the Mississippi river experiences periodic and extensive flooding in the surrounding forest areas.In 2019, NASA's UAVSAR fully polarimetric airborne L-band SAR conducted a flight campaign to image a dozen sites in the SE USA at approximately 12-day intervals and both in the morning and evening, to simulate the type of data NISAR will obtain. One site imaged during this campaign was the Yucatan Lake area, spanning water stages from low to high flood conditions.It has been demonstrated previously that GNSS reflectometry such as that measured by CYGNSS may be used to characterize surface inundation. It has also been known for decades that L-band SAR may be used to characterize not only the presence of open water, but also the presence of subcanopy inundation in forested areas. In this paper we will present results comparing data from these two types of instruments.

Lavalle, Marco↗

NASA NTRS1989

Doppler centroid estimation ambiguity for synthetic aperture radars

A technique for estimation of the Doppler centroid of an SAR in the presence of large uncertainty in antenna boresight pointing is described. Also investigated is the image degradation resulting from data processing that uses an ambiguous centroid. Two approaches for resolving ambiguities in Doppler centroid estimation (DCE) are presented: the range cross-correlation technique and the multiple-PRF (pulse repetition frequency) technique. Because other design factors control the PRF selection for SAR, a generalized algorithm is derived for PRFs not containing a common divisor. An example using the SIR-C parameters illustrates that this algorithm is capable of resolving the C-band DCE ambiguities for antenna pointing uncertainties of about 2-3 deg.

Chang, C. Y.↗

NASA NTRS1996

Polarimetric Radar Observations of Forest State for Determination of Ecosystem Processes

The objectives of this research are to test the hypotheses that ecologically significant forest state parameters may be estimated from SAR data. These include estimation of above ground biomass, plant water status, and near surface soil moisture under certain forest conditions. Test hypotheses in the northern hardwoods forest community, refine them if necessary, and establish techniques for retrieving this information from orbital SARs such as SIR-C/X-SAR. This report summarizes (1) recent progress, (2) significant results and (3) research plans concerning SIR-C/X-SAR research.

Ulaby, Fawwaz T.↗

NASA NTRS2011

Techniques and Tools for Estimating Ionospheric Effects in Interferometric and Polarimetric SAR Data

The InSAR Scientific Computing Environment (ISCE) is a flexible, extensible software tool designed for the end-to-end processing and analysis of synthetic aperture radar data. ISCE inherits the core of the ROI_PAC interferometric tool, but contains improvements at all levels of the radar processing chain, including a modular and extensible architecture, new focusing approach, better geocoding of the data, handling of multi-polarization data, radiometric calibration, and estimation and correction of ionospheric effects. In this paper we describe the characteristics of ISCE with emphasis on the ionospheric modules. To detect ionospheric anomalies, ISCE implements the Faraday rotation method using quadpolarimetric images, and the split-spectrum technique using interferometric single-, dual- and quad-polarimetric images. The ability to generate co-registered time series of quad-polarimetric images makes ISCE also an ideal tool to be used for polarimetric-interferometric radar applications.

Ionosphere↗

DOE OSTI2021

Lab Home Testing of Residential Isolation Space Control to Minimize Infectious Disease Transmission in Existing Single-Family Homes

Existing evidence strongly suggests that viral infectious diseases can be transmitted via an airborne route across distances in indoor environments. Accordingly, the risk of airborne transmission within homes should be managed. The public health emergency associated with SARS-CoV-2 makes controlling airborne transmission of respired viruses in indoor environments critical, especially in poorly ventilated indoor environments. The effectiveness of engineering interventions requiring minor efforts that create a negative-pressure isolation zone (IZ) for a contagious person has yet to be tested for existing residential homes. To mitigate the risk of airborne virus transmission and maximize health protection for the population in existing single-family homes, the relative effectiveness of several control strategies are investigated in this report. While very high-efficiency MERV filtration, high ventilation rates, and other controls can help be effective, most occupants are not likely to have the time or means for advanced measures found in hospitals. This project focused on testing relatively simple efforts that utilize existing or easy to acquire materials and simple processes.

30 DIRECT ENERGY CONVERSION↗

NASA NTRS1992

Polarimetric remote sensing of sea ice in the Beaufort Sea

Data were collected in March 1988 with the Jet Propulsion Laboratory (JPL) polarimetric airborne synthetic aperture radar (SAR). Full covariance matrices were obtained from the scattering data with proper consideration of the polarimetric calibration. Images were processed to form the sea ice scenes in the Beaufort sea. These scenes contain various ice types including thin ice, thick first-year ice, and multiyear ice. Sea ice was modeled as a layer random medium and the polarimetric backscattering coefficients were calculated under the distorted Born approximation with effective permittivities obtained from the strong fluctuation theory. Sea ice signatures remotely observed by the JPL SAR over the Beaufort sea ice scenes were interpreted by comparing their behavior at different incident angles with results obtained from the theoretical model.

Nghiem, S. V.↗

NASA NTRS1992

Registration of interferometric SAR images

Interferometric synthetic aperture radar (INSAR) is a new way of performing topography mapping. Among the factors critical to mapping accuracy is the registration of the complex SAR images from repeated orbits. A new algorithm for registering interferometric SAR images is presented. A new figure of merit, the average fluctuation function of the phase difference image, is proposed to evaluate the fringe pattern quality. The process of adjusting the registration parameters according to the fringe pattern quality is optimized through a downhill simplex minimization algorithm. The results of applying the proposed algorithm to register two pairs of Seasat SAR images with a short baseline (75 m) and a long baseline (500 m) are shown. It is found that the average fluctuation function is a very stable measure of fringe pattern quality allowing very accurate registration.

Lin, Qian↗

DOE OSTI2022

Soil moisture, physical and chemical properties coincident with airborne SAR data collections for 2017 and 2019, Seward Peninsula, Alaska

Soil samples were collected coincident with in-situ soil moisture and thaw depth measurements at NGEE Arctic study sites on the Seward Peninsula, Alaska in August 2017 and 2019 Field measurements and flights were conducted during both summers as a collaboration between the NASA ABoVE Project's Airborne SAR Campaign and the NGEE Arctic Project. Airborne overflights of L-band SAR instruments occurred during the soil sampling periods. Laboratory measurements of soil properties include bulk density, volumetric and gravimetric water content, carbon and nitrogen content, and particle size of mineral components. Soil samples processed and reported in this dataset were collected coincident with in situ measurements of soil moisture and thaw depth and airborne P-band and L-band SAR measurements as a collaboration between NGEE Arctic and NASA ABoVE. To learn more about how ABoVE protocols were applied for sampling site selection and making in situ measurements, see the following datasets: (2017: https://doi.org/10.5440/1423892 and 2019: https://doi.org/10.5440/1856042). Contained in this dataset are four .csv data files (including data dictionaries) and one zipped folder of *.pdf files.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort (with some overlap with Covid-19 pandemic) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1992

SAR backscatter from coniferous forest gaps

A study is in progress comparing Airborne Synthetic Aperture Radar (AIRSAR) backscatter from coniferous forest plots containing gaps to backscatter from adjacent gap-free plots. Issues discussed are how do gaps in the range of 400 to 1600 sq m (approximately 4-14 pixels at intermediate incidence angles) affect forest backscatter statistics and what incidence angles, wavelengths, and polarizations are most sensitive to forest gaps. In order to visualize the slant-range imaging of forest and gaps, a simple conceptual model is used. This strictly qualitative model has led us to hypothesize that forest radar returns at short wavelengths (eg., C-band) and large incidence angles (e.g., 50 deg) should be most affected by the presence of gaps, whereas returns at long wavelengths and small angles should be least affected. Preliminary analysis of 1989 AIRSAR data from forest near Mt. Shasta supports the hypothesis. Current forest backscatter models such as MIMICS and Santa Barbara Discontinuous Canopy Backscatter Model have in several cases correctly predicted backscatter from forest stands based on inputs of measured or estimated forest parameters. These models do not, however, predict within-stand SAR scene texture, or 'intrinsic scene variability' as Ulaby et al. has referred to it. For instance, the Santa Barbara model, which may be the most spatially coupled of the existing models, is not truly spatial. Tree locations within a simulated pixel are distributed according to a Poisson process, as they are in many natural forests, but tree size is unrelated to location, which is not the case in nature. Furthermore, since pixels of a simulated stand are generated independently in the Santa Barbara model, spatial processes larger than one pixel are not modeled. Using a different approach, Oliver modeled scene texture based on an hypothetical forest geometry. His simulated scenes do not agree well with SAR data, perhaps due to the simple geometric model used. Insofar as texture is the expression of biological forest processes, such as succession and disease, and physical ones, such as fire and wind-throw, it contains useful information about the forest, and has value in image interpretation and classification. Forest gaps are undoubtedly important contributors to scene variance. By studying the localized effects of gaps on forest backscatter, guided by our qualitative model, we hope to understand more clearly the manner in which spatial heterogeneities in forests produce variations in backscatter, which collectively give rise to scene texture.

Day, John L.↗

NASA NTRS1991

The role of the EOS SAR in Mission to Planet Earth

The Earth Observing System (EOS) synthetic aperture radar (SAR) is a multifrequency, multipolarization radar which will be capable of the global monitoring of key quantitative measurements of geophysical and biophysical parameters. Scheduled to fly on its own dedicated spacecraft, it is one of three platforms that will make up the space-based component to EOS. The role of the SAR in the EOS mission is discussed, wtih emphasis on the geophysical product variables which will be generated with the SAR and used in global hydrologic, biogeochemical and energy cycle models. The latest concepts for processing the data, including calibration and geophysical processing strategies, are presented.

Holt, Benjamin↗

NASA NTRS1996

SIR-C/X-SAR: Imaging Radar Analyses for Forest Ecosystem Modeling

Progress, significant results and future plans are discussed relating to the following objectives: (1) Ecosystem characterization using SIR-C/X-SAR and AirSAR data; (2) Improving radar backscatter models for forest canopies; and (3) Using SAR measurements and models with forest ecosystem models to improve inferences of ecosystem attributes and processes.

Ranson, K. Jon↗

NASA NTRS1994

Venus cartography

The entire surface of the planet Venus is being mapped at global and regional scales (1:50 million through 1:1.5 million) with synthetic aperture radar (SAR), radar altimeter, and radiometer measurements of physical properties from the Magellan spacecraft. The mapping includes SAR image mosaics, shaded relief maps, and topographic contour overlays made from altimetry data and by radargrammetric methods. Methods used include new techniques of radar image processing that became operational as a result of the Magellan mission. Special cartographic support products prepared by the USGS include: synthetic stereograms, color thematic maps of physical properties, digital shaded relief maps from opposite-look SAR, and topographic maps by radargrammetry. The area being mapped (at a resolution of 75 m/pixel) is roughly equivalent to that of Earth, including seafloors. The mapping is designed to support geologic and geophysical investigations.

Batson, R. M.↗

NASA NTRS1997

Active Microwave Remote Sensing Observations of Weddell Sea Ice

Since July 1991, the European Space Agency's ERS-1 and ERS-2 satellites have acquired radar data of the Weddell Sea, Antarctica. The Active Microwave Instrument on board ERS has two modes; SAR and Scatterometer. Two receiving stations enable direct downlink and recording of high bit-rate, high resolution SAR image data of this region. When not in an imaging mode, when direct SAR downlink is not possible, or when a receiving station is inoperable, the latter mode allows normalized radar cross-section data to be acquired. These low bit-rate ERS scatterometer data are tape recorded, downlinked and processed off-line. Recent advances in image generation from Scatterometer backscatter measurements enable complementary medium-scale resolution images to be made during periods when SAR images cannot be acquired. Together, these combined C-band microwave image data have for the first time enabled uninterrupted night and day coverage of the Weddell Sea region at both high (25 m) and medium-scale (-20 km) resolutions. C-band ERS-1 radar data are analyzed in conjunction with field data from two simultaneous field experiments in 1992. Satellite radar signature data are compared with shipborne radar data to extract a regional and seasonal signature database for recognition of ice types in the images. Performance of automated sea-ice tracking algorithms is tested on Antarctic data to evaluate their success. Examples demonstrate that both winter and summer ice can be effectively tracked. The kinematics of the main ice zones within the Weddell Sea are illustrated, together with the complementary time-dependencies in their radar signatures. Time-series of satellite images are used to illustrate the development of the Weddell Sea ice cover from its austral summer minimum (February) to its winter maximum (September). The combination of time-dependent microwave signatures and ice dynamics tracking enable various drift regimes to be defined which relate closely to the circulation of the sea ice in response to current and wind forcing and iceberg barriers. These are closely related to continental-shelf or central basin regimes, in which tidal forcing or barotropic circulation patterns appear to influence the sea-ice motion, respectively. These regimes provide valuable information about the regions of most prolific ice growth and influence of ice conditions upon air-sea-ice exchange processes in the Weddell Sea.

Drinkwater, Mark R.↗

NASA NTRS1984

SPECTRASAT: A concept for the collection of global directional wave spectra

The synthetic aperture radar (SAR) imagery from SEASAT revealed a rich tapestry of backscatter patterns from the surface of the ocean. Although still far from being fully understood, these patterns occurred on nearly all spatial scales accessible to the SAR, that is from its spatial resolution of 25 m to its full swath width of 100 km. Futhermore, the backscatter signature appear to reveal a large variety of atmospheric and oceanic processes that occur above, at, and below the ocean surface. Proper interpretation of these signatures of varying scales with respect to their underlying geophysical causes is a major objective of SAR ocean research. Even now, however, it is clear that SAR offers a unique means to monitor wind and waves over global scales. A properly designed, configured, and complimented orbiting SAR system should yield substantial improvements in operational forecasts vital to marine activities. Since wind and wave information is optimally extracted in the spectral domain, the name SPECTRASAT is proposed for this global collection scheme.

Beal, R. C.↗

NASA NTRS1982

The SIR-B science plan

The Shuttle Imaging Radar-B (SIR-B) will be the third in a series of spaceborne SAR experiments conducted by NASA which began with the 1978 launch of SEASAT and continued with the 1981 launch of SIR-A. Like SEASAT and SIR-A, SIR-B will operate at L-band and will be horizontally polarized. However, SIR-B will allow digitally processed imagery to be acquired at selectable incidence angles between 15 and 60 deg, thereby permitting, for the first time, parametric studies of the effect of illumination geometry on SAR image information extraction. This document presents a science plan for SIR-B and serves as a reference for the types of geoscientific, sensor, and processing experiments which are possible.

Source record↗

NASA NTRS1974

Vibrationally excited nitrogen in stable auroral red arcs and its effect on ionospheric recombination

The time-dependent continuity equations, including diffusion, were solved for the first six energy levels of molecular nitrogen for conditions in the thermosphere corresponding to stable auroral red (SAR) arcs. The results show that molecular nitrogen is excited vibrationally to the degree that the rate constant for the ionospheric loss process, O(+) + N2 yields NO(+) + N, is increased by as much as a factor of 7.6 at F2 region altitudes. It was found that deviations from the energetically equivalent Boltzmann distribution were large, causing the rate constant to be as much as 1.6 times the rate constant calculated for the Boltzmann distribution. These results indicate that SAR arc intensities as small as 58 R can produce noticeable increases in the ionosphere ion-atom interchange reaction rate and hence in the rate of loss of ionospheric electrons. It is suggested that the observed decrease of electron density in the F2 region in SAR arcs can probably be explained by enhanced reaction rates for ion-atom interchange between O(+) and N2 caused by vibrational excitation of molecular nitrogen by electron impact.

Newton, G. P.↗