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DOE OSTI2019

Improving Ligand Geometry in Protein Data Bank Structures Computationally

Information about the three‐dimensional structures of complex biological molecules is an indispensable research tool for many fields of study, including biology, chemistry, pharmacology, and computer science. The Protein Data Bank (PDB) is an public digital archive providing access to structures of nucleic acids, proteins, and large macromolecular machines determined experimentally by X‐ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and 3‐dimensional electron microscopy (3DEM). PDB structures undergo validation for structural plausibility upon their deposition into the PDB using the program Mogul, which cross references each deposited structure against similar data in the Cambridge Structural Database (CSD). Ligands associated with PDB structures are a common source of structural inaccuracy. In this study, a programmatic pipeline was developed to determine if ligand geometric accuracy could be improved using known computational tools. Ligands with dubious geometry were identified through a Python mining code. A sample set of the identified structures was remodeled into minimum energy conformations using the molecular dynamics program AMBER and then fit to the original experimental density maps using the molecular modeling program Coot. The refined models were compared to the original models in the PDB as well as to similar structures in the CSD using the deposition statistical validation server. Preliminary results suggest that the pipeline effectively identifies and improves ligand structures that possess inaccurate geometry. This method can be used to evaluate and improve the accuracy of specific ligands in structures both archived and pending deposition. Support or Funding Information This work was supported by an NSF REU and the RCSB PDB [NSF (DBI‐1338415), NIH, and DOE.] This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Miller, Beck↗

NASA NTRS1997

Mapping Surface Cover Parameters Using Aggregation Rules and Remotely Sensed Cover Classes

A coupled model, which combines the Biosphere-Atmosphere Transfer Scheme (BATS) with an advanced atmospheric boundary-layer model, was used to validate hypothetical aggregation rules for BATS-specific surface cover parameters. The model was initialized and tested with observations from the Anglo-Brazilian Amazonian Climate Observational Study and used to simulate surface fluxes for rain forest and pasture mixes at a site near Manaus in Brazil. The aggregation rules are shown to estimate parameters which give area-average surface fluxes similar to those calculated with explicit representation of forest and pasture patches for a range of meteorological and surface conditions relevant to this site, but the agreement deteriorates somewhat when there are large patch-to-patch differences in soil moisture. The aggregation rules, validated as above, were then applied to remotely sensed 1 km land cover data set to obtain grid-average values of BATS vegetation parameters for 2.8 deg x 2.8 deg and 1 deg x 1 deg grids within the conterminous United States. There are significant differences in key vegetation parameters (aerodynamic roughness length, albedo, leaf area index, and stomatal resistance) when aggregate parameters are compared to parameters for the single, dominant cover within the grid. However, the surface energy fluxes calculated by stand-alone BATS with the 2-year forcing, data from the International Satellite Land Surface Climatology Project (ISLSCP) CDROM were reasonably similar using aggregate-vegetation parameters and dominant-cover parameters, but there were some significant differences, particularly in the western USA.

Arain, Altaf M.↗

NASA NTRS2015

The Role of the NASA Global Hawk Link Module as an Information Nexus For Atmospheric Mapping Missions

The Link Module described in this paper was developed for the NASA Uninhabited Aerial System (UAS) Global Hawk Pacific Mission (GloPAC) Airborne Science Campaign; four flights of 30 hour duration, supporting the Aura Validation Experiment (AVE). It was used again during the Genesis and Rapid Intensification Processes (GRIP) experiment, a NASA Earth Science field experiment to better understand how tropical storms form and develop into major hurricanes. In these missions, the Link Module negotiated all communication over the high bandwidth Ku satellite link, archived all the science data from onboard experiments in a spatially enabled database, routed command and control of the instruments from the Global Hawk Operations Center, and re-transmitted select data sets directly to experimenters control and analysis systems. The availability of aggregated information from collections of sensors, and remote control capabilities, in real-time, is revolutionizing the way Airborne Science is being conducted. The Link Module NG now being flown in support of the NASA Earth Venture missions, the Hurricane and Severe Storm Sentinel (HS3) mission, and Airborne Tropical Tropopause Experiment (A TTREX) mission, has advanced data fusion technologies that are further advancing the Scientific productivity, flexibility and robustness of these systems. On-the-fly traffic shaping has been developed to allow the high definition video, used for critical flight control segments, to dynamically allocate variable bandwidth on demand. Historically, the Link Module evolved from the instrument and communication interface controller used by NASA's Pathfinder and Pathfinder plus solar powered UAS's in the late 1990' s. It later was expanded for use in the AIRDAS four channel scanner flown on the NASA Altus UAS, and then again to a module in the AMS twelve channel multispectral scanner flying on the NASA (Predator-b) Ikhana UAS. The current system is the answer to the challenges imposed by extremely long duration UASs, with on-board multi-instrument (>= 12) Sensor Webs.

Hurricanes↗

NASA NTRS2002

A Lightning Channel Retrieval Algorithm for the North Alabama Lightning Mapping Array (LMA)

A new multi-station VHF time-of-arrival (TOA) antenna network is, at the time of this writing, coming on-line in Northern Alabama. The network, called the Lightning Mapping Array (LMA), employs GPS timing and detects VHF radiation from discrete segments (effectively point emitters) that comprise the channel of lightning strokes within cloud and ground flashes. The network will support on-going ground validation activities of the low Earth orbiting Lightning Imaging Sensor (LIS) satellite developed at NASA Marshall Space Flight Center (MSFC) in Huntsville, Alabama. It will also provide for many interesting and detailed studies of the distribution and evolution of thunderstorms and lightning in the Tennessee Valley, and will offer many interesting comparisons with other meteorological/geophysical wets associated with lightning and thunderstorms. In order to take full advantage of these benefits, it is essential that the LMA channel mapping accuracy (in both space and time) be fully characterized and optimized. In this study, a new revised channel mapping retrieval algorithm is introduced. The algorithm is an extension of earlier work provided in Koshak and Solakiewicz (1996) in the analysis of the NASA Kennedy Space Center (KSC) Lightning Detection and Ranging (LDAR) system. As in the 1996 study, direct algebraic solutions are obtained by inverting a simple linear system of equations, thereby making computer searches through a multi-dimensional parameter domain of a Chi-Squared function unnecessary. However, the new algorithm is developed completely in spherical Earth-centered coordinates (longitude, latitude, altitude), rather than in the (x, y, z) cartesian coordinates employed in the 1996 study. Hence, no mathematical transformations from (x, y, z) into spherical coordinates are required (such transformations involve more numerical error propagation, more computer program coding, and slightly more CPU computing time). The new algorithm also has a more realistic definition of source altitude that accounts for Earth oblateness (this can become important for sources that are hundreds of kilometers away from the network). In addition, the new algorithm is being applied to analyze computer simulated LMA datasets in order to obtain detailed location/time retrieval error maps for sources in and around the LMA network. These maps will provide a more comprehensive analysis of retrieval errors for LMA than the 1996 study did of LDAR retrieval errors. Finally, we note that the new algorithm can be applied to LDAR, and essentially any other multi-station TWA network that depends on direct line-of-site antenna excitation.

Koshak, William↗

DOE OSTI2023

Mapping foliar photosynthetic capacity in sub-tropical and tropical forests with UAS-based imaging spectroscopy: Scaling from leaf to canopy

Accurate understanding of the variability in foliar physiological traits across landscapes is critical to improve parameterization and evaluation of terrestrial biosphere models (TBMs) that seek to represent the response of terrestrial ecosystems to a changing climate. Numerous studies suggest imaging spectroscopy can characterize foliar biochemical and morphological traits at the canopy scale, but there is only limited evidence for retrieving canopy photosynthetic capacity (e.g., maximum carboxylation rate, V c,max and maximum electron transport rate, J max ). Moreover, the effect of canopy structure within forest communities on scaling up spectra-trait relationships from leaf to canopy level is not well known. To advance the spectra-trait approach and enable the estimation of key traits using remote sensing, we collected imaging spectroscopy data from an Unoccupied Aerial System (UAS) platform over two forest sites in China (a subtropical forest in Mt. Dinghu and a tropical rainforest in Xishuangbanna). At these sites, we also collected ground measurements of leaf spectra and traits, including biochemical (leaf nitrogen, phosphorus, chlorophyll, and water content), morphological (leaf mass per area, LMA) and physiological (V c,max25 and J max25 ) traits (n=135 tree-crowns from 42 species across two sites). Using a partial least-squares regression (PLSR) approach, we built and tested spectra-trait models with repeated cross-validation. The spectral models developed with leaf spectra were directly transferred to canopy spectra to evaluate the effect of canopy structure. Here we further applied canopy spectral models to map these traits at individual tree-crown scale. The results demonstrate that (1) UAS-based canopy spectra can be used to estimate V c,max (R 2 =0.55, nRMSE=11.79%), Jmax (R 2 =0.54, nRMSE=12.34%), and five additional foliar traits (R 2 =0.38-0.60, nRMSE=10.11-13.56%) at the tree-crown scale with demonstrated generalizability across two sites; (2) canopy structure strongly affects the spectratrait relationships from leaf to canopy level, but the effects vary considerably across foliar traits and cannot be well captured by the 4SAIL canopy radiative transfer model. UAS-based imaging spectroscopy maps large variability in all foliar traits (including physiological traits) with spatially explicit information, reproducing the field-observed inter- and intra-specific variations. These results demonstrate the capability of using UAS-based imaging spectroscopy for characterizing the variability of foliar physiological traits at individual tree-crown scale over forest landscapes and highlight the similar generalizability but different biophysical mechanisms underlying spectra-trait relationships at leaf and canopy levels.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2021

Exploring Sentinel-1 and Sentinel-2 diversity for Flood inundation mapping using deep learning

Identification of flood water extent from satellite images has historically relied on either synthetic aperture radar (SAR) or multi-spectral (MS) imagery. MS sensors are limited to cloud free conditions, whereas SAR imagery is plagued by noise-like speckle. Prior studies that use combinations of MS and SAR data to overcome individual limitations of these sensors have not fully examined sensitivity of flood mapping performance to different combinations of SAR and MS derived spectral indices or band transformations in color space. This study explores the use of diverse bands of Sentinel 2 (S2) through well-established water indices and Sentinel 1 (S1) derived SAR imagery along with their combinations to assess their capability for generating accurate flood inundation maps. The robustness in performance of S-1 and S-2 band combinations was evaluated using 446 hand labeled flood inundation images spanning across 11 flood events from Sen1Floods11 dataset which are highly diverse in terms of land cover as well as location. A modified K-fold cross validation approach is used to evaluate the performance of 32 combinations of S1 and S2 bands using a fully connected deep convolutional neural network known as U-Net. Our results indicated that usage of elevation information has improved the capability of S1 imagery to produce more accurate flood inundation maps. Compared to a median F1 score of 0.62 when using only S1 bands, the combined use of S1 and elevation information led to an improved median F1 score of 0.73. Water extraction indices based on S2 bands have a statistically significant superior performance in comparison to S1. Among all the band combinations, HSV (Hue, Saturation, Value) transformation of S2 bands provides a median F1 score of 0.9, outperforming the commonly used water spectral indices owing to HSV’s transformation’s superior contrast distinguishing abilities. Additionally, U-Net algorithm was able to learn the relationship between raw S2 based water extraction indices and their corresponding raw S2 bands, but not of HSV owing to relatively complex computation involved in the latter. Results of the paper establishes important benchmarks for the extension of S1 and S2 data-based flood inundation mapping efforts over large spatial extents.

Goutam Konapala↗

DOE OSTI2014

SU-F-BRF-10: Deformable MRI to CT Validation Employing Same Day Planning MRI for Surrogate Analysis

Purpose: To compare rigid and deformable registrations of the prostate in the multi-modality setting (diagnostic-MRI to planning-CT) by utilizing a planning-MRI as a surrogate. The surrogate allows for the direct quantitative analysis which can be difficult in the multi-modality domain where intensity mapping differs. Methods: For ten subjects, T2 fast-spin-echo images were acquired at two different time points, the first several weeks prior to planning (diagnostic-MRI) and the second on the same day in which the planning CT was collected (planning-MRI). Significant effort in patient positioning and bowel/bladder preparation was undertaken to minimize distortion of the prostate in all datasets. The diagnostic-MRI was deformed to the planning-CT utilizing a commercially available deformable registration algorithm synthesized from local registrations. The deformed MRI was then rigidly aligned to the planning MRI which was used as the surrogate for the planning-CT. Agreement between the two MRI datasets was scored using intensity based metrics including Pearson correlation and normalized mutual information, NMI. A local analysis was performed by looking only within the prostate, proximal seminal vesicles, penile bulb and combined areas. A similar method was used to assess a rigid registration between the diagnostic-MRI and planning-CT. Results: Utilizing the NMI, the deformable registrations were superior to the rigid registrations in 9 of 10 cases demonstrating a 15.94% improvement (p-value < 0.001) within the combined area. The Pearson correlation showed similar results with the deformable registration superior in the same number of cases and demonstrating a 6.97% improvement (p-value <0.011). Conclusion: Validating deformable multi-modality registrations using spatial intensity based metrics is difficult due to the inherent differences in intensity mapping. This population provides an ideal testing ground for MRI to CT deformable registrations by obviating the need for multi-modality comparisons which are inherently more challenging. Deformable registrations generated in this work significantly outperformed rigid alignments. Research reported in this abstract was supported by the NIH National Cancer Institute R21CA153826 “MRI-Guided Radiotherapy and Biomarkers for Prostate Cancer” and Bankhead-Coley Cancer Research Program 10BT-03 “MRI-Guided Radiotherapy and Biomarkers for Prostate Cancer”.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1999

Spaceflight Validation of Hzetrn Code

HZETRN is being developed as a fast deterministic radiation transport code applicable to neutrons, protons, and multiply charged ions in the space environment. It was recently applied to 50 hours of IMP8 data measured during the August 4, 1972 solar event to map the hourly exposures within the human body under several shield configurations. This calculation required only 18 hours on a VAX 4000 machine. A similar calculation using the Monte Carlo method would have required two years of dedicated computer time. The code has been benchmarked against well documented and tested Monte Carlo proton transport codes with good success. The code will allow important trade studies to be made with relative ease due to the computational speed and will be useful in assessing design alternatives in an integrated system software environment. Since there are no well tested Monte Carlo codes for HZE particles, we have been engaged in flight validation of the HZETRN results. To date we have made comparison with TEPC, CR-39, charge particle telescopes, and Bonner spheres. This broad range of detectors allows us to test a number of functions related to differing physical processes which add to the complicated radiation fields within a spacecraft or the human body, which functions can be calculated by the HZETRN code system. In the present report we will review these results.

Wilson, J. W.↗

NASA NTRS2016

Drought Impacts on Agricultural Production and Land Fallowing in California's Central Valley in 2015

The ongoing drought in California substantially reduced surface water supplies for millions of acres of irrigated farmland in California's Central Valley. Rapid assessment of drought impacts on agricultural production can aid water managers in assessing mitigation options, and guide decision making with respect to mitigation of drought impacts. Satellite remote sensing offers an efficient way to provide quantitative assessments of drought impacts on agricultural production and increases in fallow acreage associated with reductions in water supply. A key advantage of satellite-based assessments is that they can provide a measure of land fallowing that is consistent across both space and time. We describe an approach for monthly and seasonal mapping of uncultivated agricultural acreage developed as part of a joint effort by USGS, USDA, NASA, and the California Department of Water Resources to provide timely assessments of land fallowing during drought events. This effort has used the Central Valley of California as a pilot region for development and testing of an operational approach. To provide quantitative measures of uncultivated agricultural acreage from satellite data early in the season, we developed a decision tree algorithm and applied it to time-series data from Landsat TM (Thematic Mapper), ETM+ (Enhanced Thematic Mapper Plus), OLI (Operational Land Imager), and MODIS (Moderate Resolution Imaging Spectroradiometer). Our effort has been focused on development of indicators of drought impacts in the March-August timeframe based on measures of crop development patterns relative to a reference period with average or above average rainfall. To assess the accuracy of the algorithms, monthly ground validation surveys were conducted across 650 fields from March-September in 2014 and 2015. We present the algorithm along with updated results from the accuracy assessment, and data and maps of land fallowing in the Central Valley in 2015.

Valleys↗

DOE OSTI2024

Transient anisotropic kernel for probabilistic learning on manifolds

PLoM (Probabilistic Learning on Manifolds) is a method introduced in 2016 for handling small training datasets by projecting an Itô equation from a stochastic dissipative Hamiltonian dynamical system, acting as the MCMC generator, for which the KDE-estimated probability measure with the training dataset is the invariant measure. PLoM performs a projection on a reduced-order vector basis related to the training dataset, using the diffusion maps (DMAPS) basis constructed with a time-independent isotropic kernel. In this paper, we propose a new ISDE projection vector basis built from a transient anisotropic kernel, providing an alternative to the DMAPS basis to improve statistical surrogates for stochastic manifolds with heterogeneous data. The construction ensures that for times near the initial time, the DMAPS basis coincides with the transient basis. For larger times, the differences between the two bases are characterized by the angle of their spanned vector subspaces. The optimal instant yielding the optimal transient basis is determined using an estimation of mutual information from Information Theory, which is normalized by the entropy estimation to account for the effects of the number of realizations used in the estimations. Consequently, this new vector basis better represents statistical dependencies in the learned probability measure for any dimension. Three applications with varying levels of statistical complexity and data heterogeneity validate the proposed theory, showing that the transient anisotropic kernel improves the learned probability measure.

Diffusion maps↗

DOE OSTI2025

Autonomous Nanoparticle Synthesis Guided by In Situ Multiscale Structural Characterization

Autonomous synthesis platforms promise rapid exploration of vast parameter spaces; yet, integrating in situ structural characterization in closed-loop synthesis optimization remains challenging. We demonstrate a realization of such a closed-loop platform coupled with a droplet-flow microreactor, in situ X-ray scattering methods (SAXS/WAXS), and Gaussian process optimization to synthesize citrate-reduced Au nanoparticles with targeted characteristics. The system efficiently explored ∼19,000 synthesis recipes through 365 experiments, achieving precise control over size (4–60 nm) and polydispersity (σ < 0.11) across large citrate/gold ratios, exceeding traditional synthesis boundaries (1–10). Beyond confirming classical Turkevich–Frens trends, partial-dependence analysis revealed strong nonlinear coupling among precursor, citrate, and pH effects. Combining quantitative SAXS/WAXS analysis with electron microscopy characterization, we uncovered that crystallite size (d c ) and particle size (d) follow d c = 0.18d + β, where synthesis chemistry controls the intercept β while maintaining a universal slope. This parallel-band structure enables independent tuning of crystallite domain size at fixed particle diameter through a combination of chloride, gold precursor, citrate, and pH contributions (cross-validated Spearman ρ = 0.7 ± 0.1). High-resolution electron microscopy shows multiple lattice-fringe orientations within single particles, directly confirming polycrystalline domains and the ability to tune d c at the fixed d. The platform’s validation includes indistinguishable static versus flowing measurements, stable droplet transport at 100 °C, and <5% run-to-run variation, establishing a robust framework for mapping and controlling multiscale nanoparticle structure across expansive chemical spaces. In conclusion, the developed closed-loop platform can be applied to a borad range of nanosyntheis processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2019

Group-invariant solutions for one dimensional, inviscid hydrodynamics

In this paper, the results of the Lie group method carried out by Ovsiannikov are utilized to study the one-dimensional hydrodynamic equations governing compressible, inviscid fluid flow in the absence of heat conduction. One-parameter subgroups of the admissible R-parameter Lie group of point transformations of the system are applied to reduce the first-order, non-linear system of partial differential equations (PDE)s to a first-order system of ordinary differential equations (ODE)s. Closed-form solutions to the reduced ODE systems are subsequently determined using a linear velocity profile ansatz. These solutions are valid in one-dimensional (1D) planar, cylindrical and spherical geometries and are connected to solutions of the governing system of PDEs through an inverse map. The linear velocity type solutions were first considered by Sedov in 1953 and constitute a subclass of all possible similarity solutions of the compressible hydrodynamics equations. They further serve as illustrative examples of using solutions obtained for the reduced ODEs to find solutions of the associated system of PDEs. Consequently, the reduced systems of ODEs are provided in their entirety inviting additional solutions to be determined via alternative explicit or numerical solution techniques.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination

In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019) Proc Natl Acad Sci USA , 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The Simons Observatory: Combining cross-spectral foreground cleaning with multitracer B -mode delensing for improved constraints on inflation

The Simons Observatory (SO), due to start full science operations in early 2025, aims to set tight constraints on inflationary physics by inferring the tensor-to-scalar ratio r from measurements of cosmic microwave background (CMB) polarization B-modes. Its nominal design including three small-aperture telescopes (SATs) targets a precision σ⁡(r = 0) ≤ 0.003 without delensing. Achieving this goal and further reducing uncertainties requires a thorough understanding and mitigation of other large-scale B-mode sources such as Galactic foregrounds and weak gravitational lensing. We present an analysis pipeline aiming to estimate r by including delensing within a cross-spectral likelihood, and demonstrate it for the first time on SO-like simulations accounting for various levels of foreground complexity, inhomogeneous noise and partial sky coverage. As introduced in an earlier SO delensing paper, lensing B-modes are synthesized using internal CMB lensing reconstructions as well as Planck-like cosmic infrared background maps and LSST-like galaxy density maps. We then extend SO’s power-spectrum-based foreground-cleaning algorithm to include all auto- and cross-spectra between the lensing template and the SAT B-modes in the likelihood function. This allows us to constrain r and the parameters of our foreground model simultaneously. Within this framework, we demonstrate the equivalence of map-based and cross-spectral delensing and use it to motivate an optimized pixel-weighting scheme for power spectrum estimation. We start by validating our pipeline in the simplistic case of uniform foreground spectral energy distributions. In the absence of primordial B-modes, we find that the 1⁢σ statistical uncertainty on r, σ⁡(r), decreases by 37% as a result of delensing. Tensor modes at the level of r = 0.01 are successfully detected by our pipeline. Even when using more realistic foreground models including spatial variations in the dust and synchrotron spectral properties, we obtain unbiased estimates of r both with and without delensing by employing the moment-expansion method. In this case, uncertainties are increased due to the higher number of model parameters, and delensing-related improvements range between 27% and 31%. These results constitute the first realistic assessment of the delensing performance at SO’s nominal sensitivity level.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Aboveground Biomass Estimation Using NISAR Simulated ALOS-2 Time Series Data

Aboveground biomass (AGB) is a critical parameter to better understand the global carbon cycle and to develop sustainable forest management. However, a large uncertainty prevails. L-band SAR data have demonstrated strong potential to accurately retrieve AGB over low-biomass regions (<100 Mg ha-1). The upcoming NASA-ISRO Synthetic Aperture Radar mission will collect data at L- and S-band over earth’s landmass with a repeat period of 12 days, allowing us to have ample data for monitoring biomass and its dynamics. One of the key science requirements of the mission is to produce annual AGB maps at 1-ha resolution with RMS accuracy of 20 Mg/ha for 80 percentage of area over low-biomass regions in Calibration/Validation sites. The NISAR biomass algorithm will generate AGB maps based on the parameterization of semi-empirical model along with NISAR time-series dual pol data (HH and HV). To calibrate and validate the model for mission requirements, the mission will use reference estimates of AGB produced from ground inventory plots and airborne LiDAR data collected over selected sites distributed across different global ecoregions. This paper presents the initial results of the calibration/validation of the NISAR AGB retrieval algorithm over the Lenoir Landing (LENO), Alabama, USA site using NISAR simulated ALOS-2 time series data. Five multi-temporal dual-pol HH and HV NISAR Simulated ALOS 2 data collections were used as input to assess the performance of the model. The model AGB retrieval results shows that the NISAR model was able to achieve RMS accuracy within 20 Mg/ha.

Ramachandran, Naveen [Jet Propulsion Laboratory, C↗

DOE OSTI2019

Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis

Abstract Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M . × giganteus (M×g) ‘1993–1780', in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus , this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis . Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F 1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47 . The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 ( CEX13 ), WRKY2 transcription factor, and cold shock domain ( CSDP1 ). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

TH-CD-201-01: BEST IN PHYSICS (THERAPY): Assessment of Thin-Film CdTe as An Effective Detector for Microdosimety at Gold-Tissue Interface

Purpose: Presence of interfaces between high and low atomic number materials, often encountered in diagnostic imaging and radiation therapy, leads to radiation dose perturbation. This phenomenon is characterized by a very narrow region of sharp dose enhancement at the interface. The rapid fall-off of the dose enhancement over a very short distance from the interface makes the experimental dosimetry nontrivial. We use an in-house-built inexpensive thin-film Cadmium Telluride (CdTe) photodetector to study this effect at the gold-tissue interface and verify our experimental results with Monte Carlo (MC) modeling. Methods: Three micron thick CdTe photodetectors were fabricated in our lab. One, ten or one hundred micron thick gold foils placed in a tissue-equivalent-phantom were irradiated with a clinical Ir-192 high dose rate source and current measured with a CdTe detector in each case was compared against the current measured for all uniform tissue-equivalent phantom. Percentage signal enhancement (PSE) due to each gold foil was compared against MC modeled percentage dose enhancement (PDE), obtained from the geometry mimicking the experimental setup. Results: The experiment based PSEs due to 1, 10, and 100 micron thick gold foils at the closest measured distance of measurement (12.5 micron) from the interface were 42.6 ± 10.8, 137.0 ± 11.9 and 203.0 ± 15.4 respectively. The corresponding MC modeled PDEs were 38.1 ± 1, 164 ± 1 and 249 ± 1 respectively. The experimental and MC modeled values showed a closer agreement at the larger distances from the interface. Conclusion: The dose enhancement near the gold-tissue interface was measured using an in-house-built high-resolution CdTe-based photodetector and validated with MC simulations. A close agreement of the experimental results with the corresponding MC modeled results shows that CdTe detector can be utilized for mapping interface dose distribution encountered in the application of ionizing radiation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Data from Winter Hardiness of Miscanthus (III): Genome‐Wide Association and Genomic Prediction for Overwintering Ability in Miscanthus sinensis

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780′, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus , this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis . Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47 . The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

Biomass Analytics↗