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At least 397 records · Page 22

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Most transcriptomic studies of SARS-CoV-2 infection have focused on differentially expressed genes, which do not necessarily reveal the genes mediating the transcriptomic changes. In contrast, exploiting curated biological network, our PathExt tool identifies central genes from the differentially active paths mediating global transcriptomic response. Here we apply PathExt to multiple cell line infection models of SARS-CoV-2 and other viruses, as well as to COVID-19 patient-derived PBMCs. The central genes mediating SARS-CoV-2 response in cell lines were uniquely enriched for ATP metabolic process, G1/S transition, leukocyte activation and migration. In contrast, PBMC response reveals dysregulated cell-cycle processes. In PBMC, the most frequently central genes are associated with COVID-19 severity. Importantly, relative to differential genes, PathExt-identified genes show greater concordance with several benchmark anti-COVID-19 target gene sets. We propose six novel anti-SARS-CoV-2 targets ADCY2, ADSL, OCRL, TIAM1, PBK, and BUB1, and potential drugs targeting these genes, such as Bemcentinib, Phthalocyanine, and Conivaptan.

59 BASIC BIOLOGICAL SCIENCES↗

Amplitude calibration of spaceborne synthetic aperture radars

Problems encountered during attempts to calibrate SAR imagery, recent successful experiments conducted with SEASAT SAR data, and a proposed program for the calibration and validation of the radar imagery from the forthcoming SIR-B SAR are discussed. The SEASAT SAR data for 10 passes over Death valley, California, were processed with a modified digital correlator. The procedure included a preliminary screening of the data to check for raw data saturation, compensation of waveforms and estimation of the amplitude of the pilot tone. All data was normalized to this pilot tone signal to reduce the effects of variable gains in the data links and ground receivers. The digital correlation algorithm generated image data. Evaluation of 6 passes results in a maximum pass to pass gain variation of only 1.1 dB and a standard deviation amongst the passes of 0.35 dB.

Held, D. N.↗

Amplitude calibration of spaceborne synthetic aperture radars

Problems encountered during attempts to calibrate SAR imagery, recent successful experiments conducted with SEASAT SAR data, and a proposed program for the calibration and validation of the radar imagery from the forthcoming SIR-B SAR are discussed. The SEASAT SAR data for 10 passes over Death Valley, California, were processed with a modified digital correlator. The procedure included a preliminary screening of the data to check for raw data saturation, compensation of waveforms and estimation of the amplitude of the pilot tone. All data was normalized to this pilot tone signal to reduce the effects of variable gains in the data links and ground receivers. The digital correlation algorithm generated image data. Evaluation of 6 passes results in a maximum pass to pass gain variation of only 1.1 dB and a standard deviation amongst the passes of 0.35 dB. previously announced in STAR as N83-26215

Held, D. N.↗

The RADARSAT Geophysical Processor System

The RADARSAT Geophysical Processor System (RGPS) is a processing system dedicated to the analysis of Synthetic Aperture Radar (SAR) data of sea ice collected by the Canadian RADARSAT satellite (Raney et al., 1991).

radarsat ice sea ice polar ice arctic ocean sar sy↗

Onboard Data Processor for Change-Detection Radar Imaging

A computer system denoted a change-detection onboard processor (CDOP) is being developed as a means of processing the digitized output of a synthetic-aperture radar (SAR) apparatus aboard an aircraft or spacecraft to generate images showing changes that have occurred in the terrain below between repeat passes of the aircraft or spacecraft over the terrain. When fully developed, the CDOP is intended to be capable of generating SAR images and/or SAR differential interferograms in nearly real time. The CDOP is expected to be especially useful for understanding some large-scale natural phenomena and/or mitigating natural hazards: For example, it could be used for near-real-time observation of surface changes caused by floods, landslides, forest fires, volcanic eruptions, earthquakes, glaciers, and sea ice movements. It could also be used to observe such longer-term surface changes as those associated with growth of vegetation (relevant to estimation of wildfire fuel loads). The CDOP is, essentially, an interferometric SAR processor designed to operate aboard a radar platform.

Lou, Yunling↗

Collaborative, Rapid Mapping of Water Extents During Hurricane Harvey Using Optical and Radar Satellite Sensors

On August 25, 2017, Hurricane Harvey made landfall between Port Aransas and Port O'Connor, Texas, bringing with it unprecedented amounts of rainfall and record flooding. In times of natural disasters of this nature, emergency responders require timely and accurate information about the hazard in order to assess and plan for disaster response. Due to the extreme flooding impacts associated with Hurricane Harvey, delineations of water extent were crucial to inform resource deployment. Through the USGS's Hazards Data Distribution System, government and commercial vendors were able to acquire and distribute various satellite imagery to analysts to create value-added products that can be used by these emergency responders. Rapid-response water extent maps were created through a collaborative multi-organization and multi-sensor approach. One team of researchers created Synthetic Aperture Radar (SAR) water extent maps using modified Copernicus Sentinel data (2017), processed by ESA. This group used backscatter images, pre-processed by the Alaska Satellite Facility's Hybrid Pluggable Processing Pipeline (HyP3), to identify and apply a threshold to identify water in the image. Quality control was conducted by manually examining the image and correcting for potential errors. Another group of researchers and graduate student volunteers derived water masks from high resolution DigitalGlobe and SPOT images. Through a system of standardized image processing, quality control measures, and communication channels the team provided timely and fairly accurate water extent maps to support a larger NASA Disasters Program response. The optical imagery was processed through a combination of various band thresholds and by using Normalized Difference Water Index (NDWI), Modified Normalized Water Index (MNDWI), Normalized Difference Vegetation Index (NDVI), and cloud masking. Several aspects of the pre-processing and image access were run on internal servers to expedite the provision of images to analysts who could focus on manipulating thresholds and quality control checks for maximum accuracy within the time constraints. The combined results of the radar- and optical-derived value-added products through the coordination of multiple organizations provided timely information for emergency response and recovery efforts.

SERVIR↗

Kinematics of Strong Discontinuities

Synthetic Aperture Radar (SAR) provides a detailed view of the Arctic ice cover. When processed with the RADARSAT Geophysical Processor System (RGPS), it provides estimates of sea ice motion and deformation over large regions of the Arctic for extended periods of time. The deformation is dominated by the appearance of linear kinematic features that have been associated with the presence of leads. The RGPS deformation products are based on the assumption that the displacement and velocity are smooth functions of the spatial coordinates. However, if the dominant deformation of multiyear ice results from the opening, closing and shearing of leads, then the displacement and velocity can be discontinuous. This presentation discusses the kinematics associated with strong discontinuities that describe possible jumps in displacement or velocity. Ice motion from SAR data are analyzed using this framework. It is assumed that RGPS cells deform due to the presence of a lead. The lead orientation is calculated to optimally account for the observed deformation. It is shown that almost all observed deformation can be represented by lead opening and shearing. The procedure used to reprocess motion data to account for leads will be described and applied to regions of the Beaufort Sea. The procedure not only provides a new view of ice deformation, it can be used to obtain information about the presence of leads for initialization and/or validation of numerical simulations.

Peterson, K.↗

Supercomputing Pipelines Search for Therapeutics Against COVID-19

The urgent search for drugs to combat SARS-CoV-2 has included the use of supercomputers. The use of general-purpose graphical processing units (GPUs), massive parallelism, and new software for high-performance computing (HPC) has allowed researchers to search the vast chemical space of potential drugs faster than ever before. We developed a new drug discovery pipeline using the Summit supercomputer at Oak Ridge National Laboratory to help pioneer this effort, with new platforms that incorporate GPU-accelerated simulation and allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins. Here, this effort will accelerate the process of developing drugs to combat the current COVID-19 pandemic and other diseases.

60 APPLIED LIFE SCIENCES↗

Multi-frequency SAR, SSM/I and AVHRR derived geophysical information of the marginal ice zone

A description is given of the fusion of synthetic aperture radar (SAR), special sensor microwave imager (SSM/I), and NOAA Advanced Very High Resolution Radiometer (AVHRR) data to study arctic processes. These data were collected during the SIZEX/CEAREX experiments that occurred in the Greenland Sea in March of 1989. Detailed comparisons between the SAR, AVHRR, and SSM/I indicated: (1) The ice edge position was in agreement to within 25 km, (2) The SSM/I SAR total ice concentration compared favorably, however, the SSM/I significantly underpredicted the multiyear fraction, (3) Combining high resolution SAR with SSM/I can potentially map open water and new ice features in the marginal ice zone (MIZ) which cannot be mapped by the single sensors, and (4) The combination of all three sensors provides accurate ice information as well as sea surface temperature and wind speeds.

Shuchman, R. A.↗

Multifrequency observations

Analyses of synthetic aperture radar (SAR) image data were performed at DLR to classify various kinds of vegetation and different terrain types. The data were collected both with the DLR experimental synthetic aperture radar (E-SAR) in X-band, C-band, and L-band and with the NASA/JPL DC-8 SAR in C-band, L-band, and P-band. E-SAR is a single frequency and single polarization system (both parameters can be selected) but several flights were used to collect multifrequency/multipolarization data which were geometrically matched after processing. Classification of different crop types was based on comparison of the backscatter coefficients of calibrated SAR data in different frequency bands and polarizations. The DC-8 STAR collects polarimetric data in different bands simultaneously. Data acquired with the NASA/JPL DC-8 STAR are qualified for scientific investigations by reducing the cross-talk and channel imbalance to a tolerable extent. The data are absolutely calibrated by using reference targets with known backscattering cross-sections. The signatures and polarimetric features of terrain types, such as grassland, concrete, sea, forest (coniferous; deciduous) and urban areas, are extracted and discussed with respect to frequency and incidence angle dependence. A multifrequency polarimetric feature vector was applied for classification. The results of this new approach for separating and classifying different object classes are presented.

Glitz, R.↗

DESDynI Quad First Stage Processor - A Four Channel Digitizer and Digital Beam Forming Processor

The proposed Deformation, Eco-Systems, and Dynamics of Ice Radar (DESDynI-R) L-band SAR instrument employs multiple digital channels to optimize resolution while keeping a large swath on a single pass. High-speed digitization with very fine synchronization and digital beam forming are necessary in order to facilitate this new technique. The Quad First Stage Processor (qFSP) was developed to achieve both the processing performance as well as the digitizing fidelity in order to accomplish this sweeping SAR technique. The qFSP utilizes high precision and high-speed analog to digital converters (ADCs), each with a finely adjustable clock distribution network to digitize the channels at the fidelity necessary to allow for digital beam forming. The Xilinx produced FX130T Virtex 5 part handles the processing to digitally calibrate each channel as well as filter and beam form the receive signals. Demonstrating the digital processing required for digital beam forming and digital calibration is instrumental to the viability of the proposed DESDynI instrument. The qFSP development brings this implementation to Technology Readiness Level (TRL) 6. This paper will detail the design and development of the prototype qFSP as well as the preliminary results from hardware tests.

Chuang, Chung-Lun↗

The contribution of ion-cyclotron waves to electron heating and SAR-arc excitation near the storm-time plasmapause

The potential role of ion-cyclotron waves in the electron heating process has been studied, using the HOTRAY code. It is demonstrated that ion-cyclotron waves can play an important role in both the energy transfer to plasmaspheric electrons and the subsequent downward heat conduction to SAR arc altitudes. In particular, such waves can experience enhanced path integrated amplification along the steep plasmapause density gradient. The latter tends to keep the wave normal angle small on several successive bounces across the equator, thus allowing cyclotron-resonant amplification leading to a total gain of up to 20 e-foldings. When the wave propagation vector becomes highly oblique, absorption occurs during Landau resonance with thermal plasmaspheric electrons, increasing the electron temperature in the direction parallel to the ambient field and leading directly to heat conduction into ionosphere.

Thorne, Richard M.↗

Polymer, Additives, and Processing Effects on N95 Filter Performance

The current severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic has highlighted the need for personal protective equipment, specifically filtering facepiece respirators like N95 masks. While it is common knowledge that polypropylene (PP) is the industry standard material for filtration media, trial and error is often required to identify suitable commercial precursors for filtration media production. This work aims to identify differences between several commercial grades of PP and demonstrate the development of N95 filtration media with the intent that the industry partners can pivot and help address N95 shortages. Three commercial grades of high melt flow index PP were melt blown at Oak Ridge National Laboratory and broadly characterized by several methods including differential scanning calorimetry (DSC), X-ray diffraction (XRD), and neutron scattering. Despite the apparent similarities (high melt flow and isotacticity) between PP feedstocks, the application of corona charging and charge enhancing additives improve each material to widely varying degrees. From the analysis performed here, the most differentiating factor appears to be related to crystallization of the polymer and the resulting electret formation. Materials with higher crystallization onset temperatures, slower crystallization rates, and larger number of crystallites form a stronger electret and are more effective at filtration.

36 MATERIALS SCIENCE↗

Decoherence-protected quantum gates for a hybrid solid-state spin register

Protecting the dynamics of coupled quantum systems from decoherence by the environment is a key challenge for solid-state quantum information processing. An idle quantum bit (qubit) can be efficiently insulated from the outside world by dynamical decoupling, as has recently been demonstrated for individual solid-state qubits. However, protecting qubit coherence during a multi-qubit gate is a non-trivial problem in general, the decoupling disrupts the interqubit dynamics and hence conflicts with gate operation. This problem is particularly salient for hybrid systems, in which different types of qubit evolve and decohere at very different rates. Here we present the integration of dynamical decoupling into quantum gates for a standard hybrid system, the electron-nuclear spin register. Our design harnesses the internal resonance in the coupled-spin system to resolve the conflict between gate operation and decoupling. We experimentally demonstrate these gates using a two-qubit register in diamond operating at room temperature. Quantum tomography reveals that the qubits involved in the gate operation are protected as accurately as idle qubits. We also perform Grover's quantum search algorithm, and achieve fidelities of more than 90% even though the algorithm run-time exceeds the electron spin dephasing time by two orders of magnitude. Our results directly allow decoherence-protected interface gates between different types of solid-state qubit. Ultimately, quantum gates with integrated decoupling may reach the accuracy threshold for fault-tolerant quantum information processing with solid-state devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Concerning the feasibility of a real time SAR digital processor for VOIR low resolution imaging modes

The feasibility of real time digital processing of synthetic aperture radar data for Venus orbiting imaging radar low resolution modes was investigated. First, it is shown that range migration is not a problem for these modes. Then, under the assumption of no range migration, fast Fourier transform implementations for accomplishing both range and azimuth correlation in real time are shown to be feasible with current technology.

Truong, T. K.↗

A comparative study of SAR data compression schemes

The amount of data collected from spaceborne remote sensing has substantially increased in the last years. During same time period, the ability to store or transmit data has not increased as quickly. At this time, there is a growing interest in developing compression schemes that could provide both higher compression ratios and lower encoding/decoding errors. In the case of the spaceborne Synthetic Aperture Radar (SAR) earth observation system developed by the French Space Agency (CNES), the volume of data to be processed will exceed both the on-board storage capacities and the telecommunication link. The objective of this paper is twofold: to present various compression schemes adapted to SAR data; and to define a set of evaluation criteria and compare the algorithms on SAR data. In this paper, we review two classical methods of SAR data compression and propose novel approaches based on Fourier Transforms and spectrum coding.

Lambert-Nebout, C.↗

A secure measurement unit for an inspection system used in nuclear arms-control verification

Verification of arms control treaties may require information barriers to protect sensitive data acquired during the verification process. These information barriers are commonly implemented in software, but must store and operate on data that are vulnerable to attack and tampering. Here, we present a new Secure Measurement Unit based on a modified pipeline SAR ADC architecture. The idea is to move the information barrier back into the digitization process so that prohibited data is never created. A prototype 65nm CMOS Secure Measurement Unit (SMU) was tested using U-235, U-238, Co-60, Cs-137 and Am-241 sources. Here, the prototype accurately digitized allowable signals while being immune to side-channel attacks on signals within preset forbidden regions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗