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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

SU-E-T-42: A Method to Determine the Optimal Proton Scanned Beam Angle to Ensure Robust Treatment Planning

Purpose: The ability of pencil beam scanning (PBS) to deliver highly conformal dose distributions may be affected by patient- and physics-related uncertainties. In clinical practice, selection of proton beam angles is determined qualitatively. This study investigates whether an optimal proton PBS beam angle could be quantitatively determined to ensure robust planning for pelvic targets. Methods: PBS beam angles were optimized based on two independent criteria; shortest and most homogeneous path from the patient surface to the distal edge of the target. The beam angle optimization criteria for gantry angles between 90°-270° were quantified in 10° increments for each ray, calculated as the straight line distance from the surface of the skin to the CTV’s distal edge. The goal was to minimize the path length of a proton PBS beam from the patient surface to the distal edge of the CTV, relative to the entry point, while minimizing HU inhomogeneity along the ray. HU homogeneity (i.e. HU variation) was quantitatively defined as the standard deviation of the average intra-ray HU intensity distribution of the rays comprising a single beam. This method was validated relative to inter-fraction changes on ten consecutive, locally advanced, rectal cancer patients, who underwent an average 4 verification CTs. The displacement of the 95–98% isodose lines was determined from forward calculated dose distributions on verification CTs. Results: The posterior beam (180°) had the average shortest path length, 132.7±17.2mm, and the most homogenous path, 31.9±4.3HU. The 95–98% isodose lines from all plans verified our path length to within 2.3±1.2% and HU homogeneity to within 1.2±0.5%. Conclusion: The proposed optimization algorithm determined the posterior beam dose distribution as the most robust relative to inter-fraction variation for large pelvic targets treated with PBS and was validated via verification CT for our patient cohort. Future work will focus on further algorithm development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-201-10: Experimental Determination of Modified TG-43 Dosimetry Parameters for the Xoft Axxent® Electronic Brachytherapy Source

Purpose: The establishment of an air kerma rate standard at NIST for the Xoft Axxent{sup ®} electronic brachytherapy source (Axxent{sup ®} source) motivated the establishment of a modified TG-43 dosimetry formalism. This work measures the modified dosimetry parameters for the Axxent{sup ®} source in the absence of a treatment applicator for implementation in Xoft’s treatment planning system. Methods: The dose-rate conversion coefficient (DRCC), radial dose function (RDF) values, and polar anisotropy (PA) were measured using TLD-100 microcubes with NIST-calibrated sources. The DRCC and RDF measurements were performed in liquid water using an annulus of Virtual Water™ designed to align the TLDs at the height of the anode at fixed radii from the source. The PA was measured at several distances from the source in a PMMA phantom. MCNP-determined absorbed dose energy dependence correction factors were used to convert from dose to TLD to dose to liquid water for the DRCC, RDF, and PA measurements. The intrinsic energy dependence correction factor from the work of Pike was used. The AKR was determined using a NIST-calibrated HDR1000 Plus well-type ionization chamber. Results: The DRCC was determined to be 8.6 (cGy/hr)/(µGy/min). The radial dose values were determined to be 1.00 (1cm), 0.60 (2cm), 0.42 (3cm), and 0.32 (4cm), with agreement ranging from (5.7% to 10.9%) from the work of Hiatt et al. 2015 and agreement from (2.8% to 6.8%) with internal MCNP simulations. Conclusion: This work presents a complete dataset of modified TG-43 dosimetry parameters for the Axxent{sup ®} source in the absence of an applicator. Prior to this study a DRCC had not been measured for the Axxent{sup ®} source. This data will be used for calculating dose distributions for patients receiving treatment with the Axxent{sup ®} source in Xoft’s breast balloon and vaginal applicators, and for intraoperative radiotherapy. Sources and partial funding for this work were provided by Xoft Inc. (a subsidiary of iCAD). This work was also supported by the Radiological Sciences T32 Training Grant through the University of Wisconsin-Madison Medical Physics department (5T32CA009206-37).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Application of Microwave Plasma Atomic Emission Spectrometry and Hydride Generation for Determination of Arsenic and Selenium in Mineral Water

The ability to determine arsenic and selenium at their maximum acceptable concentrations (MAC) in drinking water via microwave plasma atomic emission spectrometry (MP-AES) and hydride generation is shown in this study. The determination of these elements is possible even in samples with a high degree of mineralization (up to 12 g/L). To provide the required sensitivity of determination of both elements, certain operating modes of the spray chamber for hydride generation are chosen. The conditions for the determination of these elements in mineral and medical-table waters are proposed.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Determination of optical constants of a biaxially anisotropic film by standard multiangle monochromatic ellipsometry

Possibilities of standard multiangle monochromatic ellipsometry in the determination of parameters of a uniform biaxially anisotropic layer are studied for the case of an arbitrary orientation of the two principal axes in the plane of incidence of the light beam and perpendicularity of the third axis to the plane of incidence. Using numerical simulation, it has been found that the measurement accuracy that is necessary in the determination of all the three principal components of the dielectric permittivity tensor ε and tilt angle of the axes using only angular dependences of ellipsometric parameters must be no worse than 0.0001°, which is far beyond the accuracy limits provided by present-day ellipsometers. If the tilt angle is known, standard multiangle monochromatic ellipsometry provides the determination of thickness and all three principal components of the dielectric permittivity tensor. This method allows one to determine the layer thickness and tensor component for the axis perpendicular to the plane of incidence, as well as the average value of components for the axes lying in the plane of incidence without involving the data about the tilt angle of the axes. This is demonstrated by an example of experimental data for biaxially anisotropic SiO{sub x} films obtained by oblique deposition of silicon monoxide SiO evaporated in vacuum.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Determination of the top quark mass circa 2013: methods, subtleties, perspectives

We present an up-to-date overview of the problem of top quark mass determination. We assess the need for precision in the top mass extraction in the LHC era together with the main theoretical and experimental issues arising in precision top mass determination. We collect and document existing results on top mass determination at hadron colliders and map the prospects for future precision top mass determination at e(+)e(-) colliders. We present a collection of estimates for the ultimate precision of various methods for top quark mass extraction at the LHC

Juste, Aurelio↗
DOE OSTI2021

Comparison of Spectroscopic Techniques for Determining the Peroxide Value of 19 Classes of Naturally Aged, Plant-Based Edible Oils

The peroxide value of edible oils is a measure of the degree of oxidation, which directly relates to the freshness of the oil sample. Several studies previously reported in the literature have paired various spectroscopic techniques with multivariate analyses to rapidly determine peroxide values using field portable and process instrumentation; those efforts presented “best-case scenarios” with oils from narrowly defined training and test sets. The purpose of this paper is to evaluate the use of near- and mid-infrared absorption and Raman scattering spectroscopies on oil samples from different oil classes, including seasonal and vendor variations, to determine which measurement technique or combination thereof is best for predicting peroxide values. Following peroxide value assays of each oil class using an established titration-based method, global and global-subset calibration models were constructed from spectroscopic data collected on the 19 oil classes used in this study. Spectra from each optical technique were used to create partial least squares regression calibration models to predict the peroxide value of unknown oil samples. A global peroxide value model based on near-infrared (8 mm optical path length) oil measurements produced the lowest RMSEP (4.9), followed by 24 mm optical path length near infrared (5.1), Raman (6.9) and 50 µm optical path length mid-infrared (7.3). However, it was determined that the Raman RMSEP resulted from chance correlations. Global peroxide value models based on low-level fusion of the NIR (8 and 24 mm optical path length) data and all infrared data produced the same RMSEP of 5.1. Global subset models, based on any of the spectroscopies and olive oil training sets from any class (pure, extra light, extra virgin), all failed to extrapolate to the non-olive oils. However, the near-infrared global subset model built on extra virgin olive oil could extrapolate to test samples from other olive oil classes. This work demonstrates the difficulty of developing a truly global method for determining peroxide value of oils.

36 MATERIALS SCIENCE↗
DOE OSTI2019

RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical in a chassis organism is computationally intractable. Many current methods provide a single solution to this problem, but fail to provide all optimal pathways, optional sub-optimal solutions or hybrid biological/non-biological solutions. Here we present RetSynth, software with a novel algorithm for determining all optimal biological pathways given a starting biological chassis and target chemical. By dynamically selecting constraints, the number of potential pathways scales by the number of fully independent pathways and not by the number of overall reactions or size of the metabolic network. This feature allows all optimal pathways to be determined for a large number of chemicals and for a large corpus of potential chassis organisms. Additionally, this software contains other features including the ability to collect data from metabolic repositories, perform flux balance analysis, and to view optimal pathways identified by our algorithm using a built-in visualization module. This software also identifies sub-optimal pathways and allows incorporation of non-biological chemical reactions, which may be performed after metabolic production of precursor molecules. The novel algorithm designed for RetSynth streamlines an arduous and complex process in metabolic engineering. Our stand-alone software allows the identification of candidate optimal and additional sub-optimal pathways, and provides the user with necessary ranking criteria such as target yield to decide which route to select for target production. Furthermore, the ability to incorporate non-biological reactions into the final steps allows determination of pathways to production for targets that cannot be solely produced biologically. With this comprehensive suite of features RetSynth exceeds any open-source software or webservice currently available for identifying optimal pathways for target production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass

Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.

09 BIOMASS FUELS↗
DOE OSTI2012

Determination of the impact of glycolate on arp and mcu operations

Savannah River Remediation (SRR) is evaluating an alternate flowsheet for the Defense Waste Processing Facility (DWPF) using glycolic acid as a reductant. An important aspect of the development of the glycolic acid flowsheet is determining if glycolate has any detrimental downstream impacts. Testing was performed to determine if there is any impact to the strontium and actinide sorption by monosodium titanate (MST) and modified monosodium titanate (mMST) or if there is an impact to the cesium removal at the Modular Caustic-Side Solvent Extraction Processing Unit (MCU). Sorption testing was performed using both MST and modified MST (mMST) in the presence of 5,000 and 10,000 ppm (mass basis) glycolate. 10,000 ppm is the estimated bounding concentration expected in the DWPF recycle stream based on DWPF melter flammable gas model results. The presence of glycolate was found to slow the removal of Sr and Pu by MST, while increasing the removal rate of Np. Results indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. There was no measurable effect on U removal at either glycolate concentration. The slower removal rates for Sr and Pu at 5,000 and 10,000 ppm glycolate could result in lower DF values for these sorbates in ARP based on the current (12 hours) and proposed (8 hours) contact times. For the highest glycolate concentration used in this study, the percentage of Sr removed at 6 hours of contact decreased by 1% and the percentage of Pu removed decreased by nearly 7%. The impact may prove insignificant if the concentration of glycolate that is returned to the tank farm is well below the concentrations tested in this study. The presence of glycolate also decreased the removal rates for all three sorbates (Sr, Pu, and Np) by mMST. Similarly to MST, the results for mMST indicate that the impact is a kinetic effect, and the overall capacity of the material is not affected. The presence of glycolate did not change the lack of affinity of mMST for U. Pre-contacting the MST or mMST with glycolate did not have a significant effect on the performance of the materials when compared to tests having the same concentration of glycolate present in the simulant. These findings suggest that the glycolate is likely influencing removal by sorbate complexation and not by depositing onto or forming a film on the surface of the MST solids. Since the DF values are salt batch dependent, it is not possible to a priori quantify the impacts of glycolate on future processing campaigns. However, we recommend that the impacts of glycolate be evaluated during each salt batch qualification when a final processing concentration is defined, and recommendations can then be made on how to mitigate negative impacts, if needed. Impacts to the performance of the MST or mMST could be mitigated by increasing contact time or increasing sorbent concentrations. In addition to the MST and mMST testing, testing was performed to determine if there is an impact to the cesium removal at Modular Caustic-Side Solvent Extraction Processing Unit (MCU). An Extraction-Scrub-Strip (ESS) test routine was used to simulate cesium removal at the MCU. For this, SRNL performed three ESS tests, using the same basic aqueous waste simulant and solvent. For one test, SRNL added 5,000 ppm (mass basis) of glycolate and added 10,000 ppm of glycolate to a second test. A control test contained no glycolate. The results of all three tests were virtually identical for all the extraction, scrub and strip tests. (A single data point in the 5,000 ppm test is physically impossible and SRNL is currently resolving this obvious error.) At this time, SRNL concludes that the presence of up to 10,000 ppm of glycolate does not affect cesium removal by the current solvent system used in the MCU. Although not tested, the impact of glycolate for the Next Generation Solvent - that replaces BOBCalixC6 with MaxCalix - is expected to be very similar to that for the baseline solvent. Testing is needed to confirm. Additional testing is recommended to both further examine the nature of the interaction of glycolate with MST and mMST and also to help address some postulated risks on ARP/MCU operations with implementation of the glycolate flowsheet. The additional testing includes FTIR and Raman spectroscopy to examine the surface of the MST and mMST particles, iodometric titrations to determine the peroxide content in the mMST before and after exposure to glycolate, particle size measurements of the MST and mMST from the experiments performed with glycolate, and measurements of soluble Ti in the supernate from these glycolate experiments. With regards to MCU impacts, the following tests are also recommended based on the premortem risk assessment.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

In-situ Neutron Scattering Determination of 3D Phase-Morphology Correlations in Fullerene Block Copolymer Systems

High efficiency solar energy devices can potentially meet all global energy requirements by efficiently harvesting energy from the solar spectrum. However, for solar technologies to be ubiquitous and meet the global power requirements, innovative and revolutionary approaches to trap solar energy are needed. In this regard, organic photovoltaics (OPVs) have drawn much attention, largely due to the ease with which OPVs can be manufactured at much lower costs compared to conventional inorganic PVs. Currently the most efficient OPV devices (at ~10%) are still below a technologically useful efficiency (~15%). It can be argued that to date most of the development of the OPVs has been driven by their electronic properties, without much consideration or understanding of the structure and morphology of the organic components and in particular how these affect the performance of the solar cell devices. It is only in the last few years that the latter has begun to be addressed. Arguably, without a complete understanding of the effect of morphology and structure on device performance, the theoretical maximum efficiency of these devices is unlikely to ever be realized. A thorough understanding of the structure and morphology of the polymers and how this affects device efficiency is vital to achieve the full potential of OPVs. If OPV devices with 15% efficiency can be achieved, coupled with the predicted low cost of processing, such devices would create an enabling technology, making these types of solar cells significant power generators and thereby reduce the dependency on conventional energy sources. This would fulfill the economic solar energy challenge identified by the NAE in their Grand Challenges of the 21st Century. In this project, we conducted a directed series of experiments to determine morphology-property correlations in bulk heterojunction films by careful control of the OPV structure and morphology. Unlike most research undertaken in the PV arena, this is mostly a fundamental study that does not set out to evaluate new materials or produce devices, but rather we wish to understand from first principles how the molecular structure of polymer-fullerene mixtures determined using neutron scattering (small angle neutron scattering and neutron reflection) affects device characteristics and consequently performance. While this seems a very obvious question to ask, this critical understanding is far from being realized despite the wealth of studies into OPV’s and is severely limiting organic PV devices from achieving their theoretical potential. Despite the fundamental nature of proposed work, it is essential to remain technologically relevant and therefore to ensure we address these issues we have developed relationships on the fundamental nature of structure-processing-property paradigm as applied to future need for large area, flexible OPV devices. Nanoscale heterojunction systems consisting of fullerenes dispersed in conjugated polymers are promising materials candidates for achieving high performance organic photovoltaic (OPV) devices. In order to understand the phase behavior in these devices, neutron reflection is used to determine the behavior of model conjugated polymer-fullerene mixtures. Neutron reflection is particularly useful for these types of thin film studies since the fullerene generally have a high scattering contrast with respect to most polymers. We are studying model bulk heterojunction (BHJ) films based on mixtures of poly(3-hexyl thiophene)s (P3HT), a widely used photoconductive polymer, and different fullerenes (C60, PCBM and bis-PCBM). The characterization technique of neutron reflectivity measurements have been used to determine film morphology in a direction normal to the film surfaces. The novelty of the approach over previous studies is that the BHJ layer is sandwiched between a PEDOT/PSS and Al layers in real device configuration. Using this model system, the effect of typical thermal annealing processes on the film development as a function of the polythiophene-fullerene mixtures is measured.

14 SOLAR ENERGY↗
DOE OSTI2015

Distinguishing Pu Metal from Pu Oxide and Determining α-ratio using Fast Neutron Counting

We describe a new method for determining the ratio of the rate of (α, n) source neutrons to the rate of spontaneous fission neutrons, the so called α-ratio. This method is made possible by fast neutron counting with liquid scintillator detectors, which can determine the shape of the fast neutron spectrum. The method utilizes the spectral difference between fission spectrum neutrons from Pu metal and the spectrum of (α, n) neutrons from PuO 2 . Our method is a generalization of the Cifarelli-Hage method for determining k eff for fissile assemblies, and also simultaneously determines k eff along with the α-ratio.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2017

Novel Methods to Determine Feeder Locational PV Hosting Capacity and PV Impact Signatures

Often PV hosting capacity analysis is performed for a limited number of distribution feeders. For medium - voltage distribution feeders, previous results generally analyze less than 20 feeders, and then the results are extrapolated out to similar types of feeders. Previous hosting capacity research has often focused on determining a single value for the hosting capacity for the entire feeder, whereas this research expands previous hosting capacity work to investigate all the regions of the feeder that may allow many different hosting capacity values wit h an idea called locational hosting capacity (LHC)to determine the largest PV size that can be interconnected at different locations (buses) on the study feeders. This report discusses novel methods for analyzing PV interconnections with advanced simulati on methods. The focus is feeder and location - specific impacts of PV that determine the locational PV hosting capacity. Feeder PV impact signature are used to more precisely determine the local maximum hosting capacity of individual areas of the feeder. T he feeder signature provides improved interconnection screening with certain zones that show the risk of impact to the distribution feeder from PV interconnections.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2019

Determining Cs-137 Background Body Burdens for Wild Pigs at Savannah River Site

In Gaines and Novak, an effective method for determining the background 137 Cs body burden for the white-tailed deer population on the SRS was developed, using data collected during public hunts combined with gamma overflight data to determine the areas contaminated by site activities. However, a background 137 Cs body burden for the wild pigs present on the SRS has not been developed to date. In this work, we applied the Gaines and Novak methods to determine the 137 Cs background concentration in wild pigs. The determination of a site-specific home range for wild pigs on SRS with establishing background hunt compartments for calculating the background body burdens of 137 Cs resulted in an upper bound concentration in wild pigs on SRS of 1.97 pCi/g. This value bounds 95% of the possible 137 Cs contamination value for wild pigs from the background compartments with 95% confidence. Therefore, it is recommended that 1.97 pCi/g be used in the SRS Hunter Dose Tracking System as the background 137 Cs concentration for wild pigs on SRS. This concentration should be decay corrected from the year 2014. It is also recommended that this assessment of background concentrations in SRS wild pigs (and whitetailed deer) be performed at least every five years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Determination of Stress-Free Lattice Spacing (D₀) for Residual Stress Relaxation Measurement in Ni-based Superalloys by Neutron Diffraction

The residual stress and its relaxation in critical engineering components are key to structural materials reliability. The determination of residual stress in bulk engineering structures like Ni-based superalloys can be conducted by measuring the lattice strain with penetrating neutron diffraction. The state-of-the-art engineering diffraction beamline VULCAN at the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS) provides the critical capability to evaluate the residual strain/stress relaxation in engineering component thanks to the high flux and event data features. By the means of residual stress/strain calculation, it is critical to accurately determine the stress-free lattice spacing d₀, which can be altered by the change of chemistry, unrelieved stress, and measurement scheme. Here we reported d₀ determination for determining residual stress relaxation and distribution in Alloy 718 superalloys after different quenching treatments. Selection of locations for d₀ measurement was discussed by considering the neutron path, attenuation and sample alignment. A dynamic d₀ that resulted from atom diffusion and chemistry change was estimated as function of time for the in-situ relaxation characterization. It demonstrated how the dynamic d₀ values may influence on the strain calculation in different thermally treated samples. The results highlight the importance of dynamic d₀ for in-situ relaxation involving chemical changes and provide guidance to the dynamic d₀ measurement and simulation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Determination of particle-dependent light response for defining detector response functions

This study comprehensively characterizes two scintillation detectors, an organic deuterated liquid and a stilbene crystal, concerning their response to charged particles such as electrons, protons, alphas, and carbon nuclei. The Birks function was used to determine the detectors’ response to charged particles, enabling the determination of particle-dependent light responses. The particle-dependent light characterization was used to determine detector response functions (DRF) using Geant in combination with Gamma Detector Response and Analysis Software (GADRAS). These DRFs enhance GADRAS by enabling full spectral analysis functionality for previously underrepresented detector materials. Additionally, neutron-specific DRFs are determined for neutron energy spectrum unfolding applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Determination of Leaf Water Content by Visible and Near-Infrared Spectrometry and Multivariate Calibration in Miscanthus

Leaf water content is one of the most common physiological parameters limiting efficiency of photosynthesis and biomass productivity in plants including Miscanthus. Therefore, it is of great significance to determine or predict the water content quickly and non-destructively. In this study, we explored the relationship between leaf water content and diffuse reflectance spectra in Miscanthus . Three multivariate calibrations including partial least squares (PLS), least squares support vector machine regression (LSSVR), and radial basis function (RBF) neural network (NN) were developed for the models of leaf water content determination. The non-linear models including RBF_LSSVR and RBF_NN showed higher accuracy than the PLS and Lin_LSSVR models. Moreover, 75 sensitive wavelengths were identified to be closely associated with the leaf water content in Miscanthus . The RBF_LSSVR and RBF_NN models for predicting leaf water content, based on 75 characteristic wavelengths, obtained the high determination coefficients of 0.9838 and 0.9899, respectively. The results indicated the non-linear models were more accurate than the linear models using both wavelength intervals. These results demonstrated that visible and near-infrared (VIS/NIR) spectroscopy combined with RBF_LSSVR or RBF_NN is a useful, non-destructive tool for determinations of the leaf water content in Miscanthus , and thus very helpful for development of drought-resistant varieties in Miscanthus .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

General-Purpose Bayesian Tensor Learning With Automatic Rank Determination and Uncertainty Quantification

A major challenge in many machine learning tasks is that the model expressive power depends on model size. Low-rank tensor methods are an efficient tool for handling the curse of dimensionality in many large-scale machine learning models. The major challenges in training a tensor learning model include how to process the high-volume data, how to determine the tensor rank automatically, and how to estimate the uncertainty of the results. While existing tensor learning focuses on a specific task, this paper proposes a generic Bayesian framework that can be employed to solve a broad class of tensor learning problems such as tensor completion, tensor regression, and tensorized neural networks. We develop a low-rank tensor prior for automatic rank determination in nonlinear problems. Our method is implemented with both stochastic gradient Hamiltonian Monte Carlo (SGHMC) and Stein Variational Gradient Descent (SVGD). We compare the automatic rank determination and uncertainty quantification of these two solvers. We demonstrate that our proposed method can determine the tensor rank automatically and can quantify the uncertainty of the obtained results. We validate our framework on tensor completion tasks and tensorized neural network training tasks.

Bayesian inference↗
DOE OSTI2020

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

59 BASIC BIOLOGICAL SCIENCES↗