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At least 1,351 records · Page 75

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DOE OSTI2021

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Redox-enabled electronic interrogation and feedback control of hierarchical and networked biological systems

Abstract Microelectronic devices can directly communicate with biology, as electronic information can be transmitted via redox reactions within biological systems. By engineering biology’s native redox networks, we enable electronic interrogation and control of biological systems at several hierarchical levels: proteins, cells, and cell consortia. First, electro-biofabrication facilitates on-device biological component assembly. Then, electrode-actuated redox data transmission and redox-linked synthetic biology allows programming of enzyme activity and closed-loop electrogenetic control of cellular function. Specifically, horseradish peroxidase is assembled onto interdigitated electrodes where electrode-generated hydrogen peroxide controls its activity. E. coli ’s stress response regulon, oxyRS , is rewired to enable algorithm-based feedback control of gene expression, including an eCRISPR module that switches cell-cell quorum sensing communication from one autoinducer to another—creating an electronically controlled ‘bilingual’ cell. Then, these disparate redox-guided devices are wirelessly connected, enabling real-time communication and user-based control. We suggest these methodologies will help us to better understand and develop sophisticated control for biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Gyrokinetic profile prediction and validation of a negative triangularity plasma in ASDEX Upgrade

In this work, gyrokinetic simulations are performed with the CGYRO code (Candy et al 2016 J. Comput. Phys. 324 73–93) for a negative triangularity H-mode plasma in ASDEX Upgrade, and compared with experimental measurements. The PORTALS framework (Rodriguez-Fernandez et al 2024 Nucl. Fusion 64 076034) is used to accelerate the prediction of kinetic profiles for this plasma, using surrogate modeling and Bayesian optimization. Ion heat flux, electron heat flux, and electron particle flux are simultaneously matched across the simulated radial regime of the plasma (normalized radius $r/a = 0.35-0.90$), and the resulting ion temperature, electron temperature, and electron density profiles match well with the experimental profile data within this radial range. A synthetic Correlation Electron Cyclotron Emission diagnostic is applied to find well-matched electron temperature fluctuation properties between simulation and experiment. The flux-matched profiles provide a basis for investigation of the turbulence nature across the plasma radius, revealing the dominance of Trapped Electron Mode turbulence at $r/a = 0.35$, the dominance of Ion Temperature Gradient turbulence at $r/a = 0.55$, 0.75, and 0.83, and an instability boundary at $r/a = 0.90$.

gyrokinetic simulation↗

DOE OSTI2024

Transformer-powered surrogates close the ICF simulation-experiment gap with extremely limited data

Abstract Recent advances in machine learning, specifically transformer architecture, have led to significant advancements in commercial domains. These powerful models have demonstrated superior capability to learn complex relationships and often generalize better to new data and problems. This paper presents a novel transformer-powered approach for enhancing prediction accuracy in multi-modal output scenarios, where sparse experimental data is supplemented with simulation data. The proposed approach integrates transformer-based architecture with a novel graph-based hyper-parameter optimization technique. The resulting system not only effectively reduces simulation bias, but also achieves superior prediction accuracy compared to the prior method. We demonstrate the efficacy of our approach on inertial confinement fusion experiments, where only 10 shots of real-world data are available, as well as synthetic versions of these experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

NovaDemux v39.07

This program is a sequence demultiplexer intended primarily for, but not limited to, Illumina sequencing machines. Typically, multiple experiments ("libraries") are pooled together and sequenced at once, with genetic molecules of these libraries tagged with a synthetic DNA "barcode". After sequencing, the data is demultiplexed into one file per library based on the barcode. However, errors in barcode reading cause misassignment and decrease yield. NovaDemux uses advanced statistical methods to maximize yield while minimizing misassignment compared to existing software.

Bushnell, Brian [Lawrence Berkeley National Labora↗

DOE OSTI2020

Radar Super Resolution using a Deep Convolutional Neural Network

Super-resolution involves synthetically increasing the resolution of gridded data beyond its native resolution. Typically, this is done using interpolation schemes, which estimate sub-grid scale values from neighboring data, and perform the same operation everywhere regardless of the large-scale context, or by requiring a network of radars with overlapping fields of view. Recently, significant progress has been made in single image super resolution using convolutional neural networks. Conceptually, a neural network may be able to learn relations between large scale precipitation features and the associated sub-pixel scale variability and outperform interpolation schemes. Here, we use a deep convolutional neural network to artificially enhance the resolution of NEXRAD PPI scans. The model is trained on 6-months of reflectivity observations from the Langley Hill WA (KLGX) radar, and we find that it substantially outperforms common interpolation schemes for x4 and x8 resolution increases based on several objective error and perceptual quality metrics.

radar, machine learning, super resolution, Remote ↗

DOE OSTI2023

Autoignition Delay Times of Hydrogen/Ammonia/Air Mixtures at Gas Turbine Relevant Conditions

This study reports the autoignition delay times of hydrogen/ammonia mixtures at conditions similar to turbine engine operating conditions (23 bar, 1100-1250 K). H2 was mixed with NH3 and shock-heated using synthetic air as the oxidizer. The data is compared against the current state-of-the-art NH3 chemical kinetic mechanisms found in the literature for undiluted fuel validation and refinement. Experiments were performed in a high-pressure shock tube and have shown detonation pressures reaching 200 bar. Lower temperature points have also exhibited non-ideal behavior, which calls for extensive chemical analysis to accurately report the IDTs. This work will aid in the design of air-breathing turbine engines using hydrogen and ammonia as fuel and develop a well-built NH3-based chemical kinetic mechanism.

Pierro, Michael↗

DOE OSTI2025

Frontal Slice Approaches for Tensor Linear Systems

Inspired by the row and column action methods for solving large-scale linear systems, in this work, we explore the use of frontal slices for solving tensor linear systems. In particular, this paper presents a novel approach for using frontal slices of a tensor $\mathcal{A}$ to solve tensor linear systems $\mathcal{A} ∗\mathcal{X} = \mathcal{B}$ where ∗ denotes the $t$-product. In addition, we consider variations of this method, including cyclic, block, and randomized approaches, each designed to optimize performance in different operational contexts. Our primary contribution lies in the development and convergence analysis of these methods. Experimental results on synthetically generated and real-world data, including applications such as image and video deblurring, demonstrate the efficacy of our proposed approaches and validate our theoretical findings.

Luo, Hengrui↗

DOE OSTI2022

Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET

Abstract. The ability to monitor, understand, and predict the dynamics of the terrestrial carbon cycle requires the capacity to robustly and coherently synthesize multiple streams of information that each provide partial information about different pools and fluxes. In this study, we introduce a new terrestrial carbon cycle data assimilation system, built on the PEcAn model–data eco-informatics system, and its application for the development of a proof-of-concept carbon “reanalysis” product that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. We first calibrated this system against plant trait and flux tower net ecosystem exchange (NEE) using a novel emulated hierarchical Bayesian approach. Next, we extended the Tobit–Wishart ensemble filter (TWEnF) state data assimilation (SDA) framework, a generalization of the common ensemble Kalman filter which accounts for censored data and provides a fully Bayesian estimate of model process error, to a regional-scale system with a calibrated localization. Combined with additional workflows for propagating parameter, initial condition, and driver uncertainty, this represents the most complete and robust uncertainty accounting available for terrestrial carbon models. Our initial reanalysis was run on an irregular grid of ∼ 500 points selected using a stratified sampling method to efficiently capture environmental heterogeneity. Remotely sensed observations of aboveground biomass (Landsat LandTrendr) and leaf area index (LAI) (MODIS MOD15) were sequentially assimilated into the SIPNET model. Reanalysis soil carbon, which was indirectly constrained based on modeled covariances, showed general agreement with SoilGrids, an independent soil carbon data product. Reanalysis NEE, which was constrained based on posterior ensemble weights, also showed good agreement with eddy flux tower NEE and reduced root mean square error (RMSE) compared to the calibrated forecast. Ultimately, PEcAn's new open-source regional data assimilation framework provides a scalable workflow for harmonizing multiple data constraints and providing a uniform synthetic platform for carbon monitoring, reporting, and verification (MRV) as well as accelerating terrestrial carbon cycle research.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1980

Coal conversion products industrial applications

Coal-based synthetic fuels complexes under development consideration by NASA/MSFC will produce large quantities of synthetic fuels, primarily medium BTU gas, which could be sold commercially to industries located in South Central Tennessee and Northern Alabama. The complexes would be modular in construction, and subsequent modules may produce liquid fuels or fuels for electric power production. Current and projected industries in the two states which have a propensity for utilizing coal-based synthetic fuels were identified, and a data base was compiled to support MFSC activities.

Dunkin, J. H.↗

NASA NTRS1985

Quenching Effects on Iron Site Partitioning in the Apollo 17 Orange Glass Composition

Mare petrogenesis and the structure of the lunar interior were studied. Analyses of the spectral signatures of glasses was useful to remote sensing applications in areas of the moon where glass is in significant proportions in the lunar soil. The studies provided information on Fe site occupancies in glasses, which are used to construe oxygen fugacities at the lunar surface. Data were obtained through work on synthetic analogues of lunar glasses. However, recent Mossbauer studies of an Apollo 15 green glass composition have shown that synthetic glasses are extremely sensitive to variations in quenching media. Glass structure and Fe(3+)/Fe(2+) ratios are strongly controlled by quenching conditions, which may mask the effects of the original glass' formation temperature or oxygen partial pressure. Synthetic glasses were often run at low fugacities on Pt wires. The effects of quench media on the Apollo 17 orange glass composition are considered.

Dyar, M. D.↗

NASA NTRS1989

Radar scattering from desert terrains, Pisgah/Lavic Region, California: Implications for Magellan

A major component of the 1988 Mojave Field Experiment involved the simultaneous acquisition of quad-polarization multifrequency airborne Synthetic Aperture Radar (SAR) imaging radar data and ground measurements thought to be relevant to the radar scattering behavior of a variety of desert surfaces. In preparation for the Magellan mission to Venus, the experiment was designed to explore the ability of SAR to distinguish types of geological surfaces, and the effects of varying incidence angles on the appearance of such surfaces. The airborne SAR system acquired images at approx. 10 m resolution, at 3 incidence angles (30, 40, 50 degs) and at 3 wavelengths (P:68 cm, L:24 cm, C:5.6 cm). The polarimetric capabilities of the instrument allow the simulation of any combination of transmit and receive polarizations during data reduction. Calibrated trihedral corner reflectors were deployed within each scene to permit absolute radiometric calibration of the image data. Initial analyses of this comprehensive radar data set is reported, with emphasis on implications for interpretation of Magellan data.

Plaut, J. J.↗

NASA NTRS1989

Alaska SAR Facility Mission planning software - An interactive mission planning system

The Alaska Synthetic Aperture Radar (SAR) Facility Mission Planning Subsystem is an interactive mission planning software system on the VAXStation 2000. This system has the capability to generate satellite ephemerides and mission parameters related to synthetic aperture radar missions. The mission data can be viewed as overlays on the world map in various projections and zooms. The system also provides schedule planning capabilities, using the INGRES DBMS to keep track of the various plans and schedules generated by the mission planner.

Lo, Martin W.↗

NASA NTRS1992

Surface processes on Venus

Magellan synthetic aperture radar (SAR) and altimetry data were analyzed to determine the nature and extent of surface modification for venusian plains in the Sedna Planitia, Alpha Regio, and western Ovda Regio areas. Specific cross sections derived from the SAR data were also compared to similar data for dry terrestrial basaltic lava flows (Lunar Crater and Cima volcanic fields) and playas (Lunar and Lavic Lakes) for which microtopographic profiles (i.e., quantitative roughness information) were available.

Arvidson, R. E.↗

NASA NTRS1993

Remote sensing for oceanography, hydrology and agriculture; Proceedings of Symposia A5, A3 and A9 of the COSPAR 29th Plenary Meeting, Washington, Aug. 28-Sept. 5, 1992

New results from satellite studies of the ocean and radar mapping of the earth are presented. Atttention is given to data from the ERS-1 satellite. Synthetic aperture radar mapping of land surface features and sea ice, radar backscatter measurements, and orbit altitude measurements are discussed. The use of remote sensing in hydrology, soil moisture determination, precipitation measurement, agricultural meteorology, and crop growth estimation is reviewed.

Gower, J. F. R.↗

NASA NTRS1993

Topographic mapping using radar interferometry - Processing techniques

In the summer of 1991 the NASA DC-8 airborne synthetic aperture radar (SAR) system acquired data with the radar configured in a C-band across-track interferometer mode. The data were processed to generate rectified topographic maps. A new processing scheme was developed featuring motion compensation, absolute phase retrieval, and three-dimensional 1ocation. The new processor has been tested using data which were acquired with extreme aircraft motion so that performance could be evaluated under adverse conditions. The topographic maps generated by the radar were compared to Digital Elevation Models (DEM's) derived using conventional optical stereo techniques. In one region we measured rms elevation deviations which were less than the specified DEM accuracy, and in the region covered by the more accurate DEM we found errors varying from 2.2 m rms in relatively flat terrain up to 5.0 m in mountainous areas. The rms difference between radar and DEM elevations over the 6.5 km by 22 km area covered by the more accurate DEM was 3.6 m.

Madsen, Soren N.↗

NASA NTRS1992

Hydrologic applications of SAR derived soil moisture

The MACHYDRO-90 was a multi-sensor aircraft campaign conducted to study drainage basin hydrology and the role of soil moisture in defining hydrologic characteristics and patterns. The results from the synthetic aperture radar (SAR) are presented. Data were collected over a period in which the soil conditions changed from dry to wet and then through a drying period which was close to ideal. Radar backscatter data are compared to detailed soil moisture samples taken to define soil moisture gradients within a watershed. The analysis also includes 40-MHz bandwidth SAR data, which provide very high spatial resolution. It is shown these data can be interpreted for hydrology and their application to hydrologic modeling is discussed.

Engman, Edwin T.↗

NASA NTRS1999

Review of Recent Results in Global MHD Modeling: ISTP Project Scientist for Theory and Ground-Based Observations

Global MHD (magnetohydrodynamic) simulations have shown a remarkable ability to describe the global dynamics of geospace. The limitations of the physical approximations underlying MHD would seem to limit the effectiveness of these codes, since kinetic and hybrid effects should manifest themselves by cross-scale coupling from microscales to mesoscales to global scales. However three effects appear to allow the codes to operate much more successfully than one would at first believe. They are:(l) the globally self-consistent nature of the codes with very well defined exterior boundary conditions (the solar wind) which allows the proper intercommunication between magnetospheric regions on MHD scales, (2) the control by global dynamics of the boundary layer locations where micro and meso scale processes operate, and (3) the critical role of numerical diffusion and with a sufficiently high resolution grid, the use of an empirical resistivity term, which if set at a level where the major magnetosphere boundaries properly calibrate against their observed locations, appear to well represent the effects of kinetic and hybrid processes on the global dynamics. The effectiveness of the global MHD codes, which have been developed under the ISTP mission, in describing Wind, Polar and Geotail observations, as well as ground-based observations are described. Particular emphasis is placed upon the Polar imaging data which when combined with ground-based data and global MHD-based synthetic aurora and convection patterns provide a powerful tool in understanding the final link in the solar-terrestrial chain: coupling into the atmosphere and ionosphere.

Curtis, Steven↗