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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Evaluation of a Machine-Learning Algorithm for Treatment Planning in Prostate Low-Dose-Rate Brachytherapy

Purpose: This work presents the application of a machine learning (ML) algorithm to automatically generate high-quality, prostate low-dose-rate (LDR) brachytherapy treatment plans. The ML algorithm can mimic characteristics of preoperative treatment plans deemed clinically acceptable by brachytherapists. The planning efficiency, dosimetry, and quality (as assessed by experts) of preoperative plans generated with an ML planning approach was retrospectively evaluated in this study. Methods and Materials: Preimplantation and postimplantation treatment plans were extracted from 100 high-quality LDR treatments and stored within a training database. The ML training algorithm matches similar features from a new LDR case to those within the training database to rapidly obtain an initial seed distribution; plans were then further fine-tuned using stochastic optimization. Preimplantation treatment plans generated by the ML algorithm were compared with brachytherapist (BT) treatment plans in terms of planning time (Wilcoxon rank sum, α = 0.05) and dosimetry (1-way analysis of variance, α = 0.05). Qualitative preimplantation plan quality was evaluated by expert LDR radiation oncologists using a Likert scale questionnaire. Results: The average planning time for the ML approach was 0.84 ± 0.57 minutes, compared with 17.88 ± 8.76 minutes for the expert planner (P=.020). Preimplantation plans were dosimetrically equivalent to the BT plans; the average prostate V150% was 4% lower for ML plans (P=.002), although the difference was not clinically significant. Respondents ranked the ML-generated plans as equivalent to expert BT treatment plans in terms of target coverage, normal tissue avoidance, implant confidence, and the need for plan modifications. Respondents had difficulty differentiating between plans generated by a human or those generated by the ML algorithm. Conclusions: Prostate LDR preimplantation treatment plans that have equivalent quality to plans created by brachytherapists can be rapidly generated using ML. The adoption of ML in the brachytherapy workflow is expected to improve LDR treatment plan uniformity while reducing planning time and resources.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRSDate not supplied

Assessing the use of UAS-related terms in ASRS using Seed Topic Modeling

Context: The NASA Aviation Safety Reporting System (ASRS) is a voluntary confidential aviation safety reporting system. The ASRS receives reports from pilots, air traffic controllers, flight attendants and other involved in aviation operations. The reports are de-identified and coded by ASRS expert safety analysts. The de-identified reports are then disseminated to the aviation community in a number of ways including entry into an online database. Augmenting the discovery of topics of user interest in this online database would therefore be beneficial to the community it serves. Aim: We propose and execute an experiment to assess the use of seed term topic modeling using the database narratives to identify UAS reports. The use of seed term topic modeling would enable users to identify groups of related narratives associated to a topic of their interest. Method: We use a newly curated field in ASRS reports which identify UAS from non-UAS reports in combination of different set of UAS related terms to assess if seed topic modeling can be used in ASRS.

LDA↗
DOE OSTI2021

Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2022

The hierarchical organization of autocatalytic reaction networks and its relevance to origin of life

Abiogenesis has long been suspected to require that chemical reaction networks contain multiple autocatalytic cores, but little is known about what features of these networks allow for the gradual accretion of complexity. To identify realistic scenarios for the emergence of life-like properties, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds”. We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

Zhen Peng↗
DOE OSTI2014

A modern Monte Carlo investigation of the TG-43 dosimetry parameters for an {sup 125}I seed already having AAPM consensus data

Purpose: To investigate potential causes for differences in TG-43 brachytherapy dosimetry parameters in the existent literature for the model IAI-125A{sup 125}I seed and to propose new standard dosimetry parameters. Methods: The MCNP5 code was used for Monte Carlo (MC) simulations. Sensitivity of dose distributions, and subsequently TG-43 dosimetry parameters, was explored to reproduce historical methods upon which American Association of Physicists in Medicine (AAPM) consensus data are based. Twelve simulation conditions varying{sup 125}I coating thickness, coating mass density, photon interaction cross-section library, and photon emission spectrum were examined. Results: Varying{sup 125}I coating thickness, coating mass density, photon cross-section library, and photon emission spectrum for the model IAI-125A seed changed the dose-rate constant by up to 0.9%, about 1%, about 3%, and 3%, respectively, in comparison to the proposed standard value of 0.922 cGy h{sup −1} U{sup −1}. The dose-rate constant values by Solberg et al. [“Dosimetric parameters of three new solid core {sup 125}I brachytherapy sources,” J. Appl. Clin. Med. Phys. 3, 119–134 (2002)], Meigooni et al. [“Experimental and theoretical determination of dosimetric characteristics of IsoAid ADVANTAGE™ {sup 125}I brachytherapy source,” Med. Phys. 29, 2152–2158 (2002)], and Taylor and Rogers [“An EGSnrc Monte Carlo-calculated database of TG-43 parameters,” Med. Phys. 35, 4228–4241 (2008)] for the model IAI-125A seed and Kennedy et al. [“Experimental and Monte Carlo determination of the TG-43 dosimetric parameters for the model 9011 THINSeed™ brachytherapy source,” Med. Phys. 37, 1681–1688 (2010)] for the model 6711 seed were +4.3% (0.962 cGy h{sup −1} U{sup −1}), +6.2% (0.98 cGy h{sup −1} U{sup −1}), +0.3% (0.925 cGy h{sup −1} U{sup −1}), and −0.2% (0.921 cGy h{sup −1} U{sup −1}), respectively, in comparison to the proposed standard value. Differences in the radial dose functions between the current study and both Solberg et al. and Meigooni et al. were <10% for r ≤ 5 cm, and increased for r > 5 cm with a maximum difference of 29% at r = 9 cm. In comparison to Taylor and Rogers, these differences were lower (maximum of 2% at r = 9 cm). For the similarly designed model 6711 {sup 125}I seed, differences did not exceed 0.5% for 0.5 ≤ r ≤ 10 cm. Radial dose function values varied by 1% as coating thickness and coating density were changed. Varying the cross-section library and source spectrum altered the radial dose function by 25% and 12%, respectively, but these differences occurred at r = 10 cm where the dose rates were very low. The 2D anisotropy function results were most similar to those of Solberg et al. and most different to those of Meigooni et al. The observed order of simulation condition variables from most to least important for influencing the 2D anisotropy function was spectrum, coating thickness, coating density, and cross-section library. Conclusions: Several MC radiation transport codes are available for calculation of the TG-43 dosimetry parameters for brachytherapy seeds. The physics models in these codes and their related cross-section libraries have been updated and improved since publication of the 2007 AAPM TG-43U1S1 report. Results using modern data indicated statistically significant differences in these dosimetry parameters in comparison to data recommended in the TG-43U1S1 report. Therefore, it seems that professional societies such as the AAPM should consider reevaluating the consensus data for this and others seeds and establishing a process of regular evaluations in which consensus data are based upon methods that remain state-of-the-art.

61 RADIATION PROTECTION AND DOSIMETRY↗
NASA NTRS2019

Space Launch System and Missions to Near Rectilinear Halo Orbits

The first major evolution of NASA’s Space Launch System (SLS) will begin its flights starting in the mid-2020’s. This new configuration, called Block 1B, replaces the Interim Cryogenic Propulsion Stage with a larger Exploration Upper Stage (EUS). The additional capability provided by the new upper stage will allow SLS to send heavier payloads into deep space. One destination of interest to the SLS program is called a Near Rectilinear Halo Orbit (NRHO). This is a type of lunar orbit with multiple advantages for deep space exploration. These benefits include Earth/lunar access, low station-keeping requirements, and high communication potential with Earth. Therefore, it is a leading candidate for the proposed Lunar Orbital Platform-Gateway (LOP-G). This paper will provide a detailed assessment of the SLS Block 1B requirements and capabilities for sending payloads to an NRHO. Analysts at Marshall Space Flight Center are producing a multi-year mission availability scan for the SLS Block 1B configuration to a predefined NRHO orbit. The analysis produces an optimized trajectory for each day of the scan window. A maximized payload and minimized propellant requirement are determined for each day. All maneuvers from launch to the end of the Trans-Lunar-Injection (TLI) are being modeled as finite burns. Injections into an NRHO are being modeled as impulsive maneuvers. The payload element is arbitrary, but includes sufficient mass to represent a large habitat or propulsion module. The resulting parameters of payload capability, delta-v requirements, and launch windows length vary over the course of the scan. Many launch days in the scan are eliminated in post-processing as they violate mission constraints such as payload mass and propellant usage to insert into an NRHO. Based off previous one-year scan results for the SLS Block 1B Design Analysis Cycle 2 (DAC-2), it is expected that there will be one to three days per week where the payload is able to insert into an NRHO within SLS constraints objectives. This scan provides results for longer than one-year, allowing analysts to better understand the launch availability and energy requirements of SLS Block 1B over time. The in-space mission design and scans utilize Copernicus, an n-body trajectory optimization tool originally developed out of the University of Texas at Austin with further development at Johnson Space Center in Houston, TX. To seed the in-space trajectory, Copernicus uses a plugin to call a database of SLS ascent trajectories optimized in the Program to Simulate Optimized Trajectories II (POST2). The ascent trajectories are developed using a framework that parametrizes payload mass and LEO inclination, and targets a 100 nmi (nautical mile) altitude circular parking orbit. Though this analysis is specific to the SLS program, it will provide a summary of mission design benefits and constraints associated with generic NRHO access, and may be applied to other programs or concepts that will utilize this orbit.

Statham, T. L.↗
DOE OSTI2018

Auto-generated materials database of Curie and Néel temperatures via semi-supervised relationship extraction

article presents an auto-generated database of 39,822 records containing chemical compounds and their associated Curie and Néel magnetic phase transition temperatures. The database was produced using natural language processing and semi-supervised quaternary relationship extraction, applied to a corpus of 68,078 chemistry and physics articles. Evaluation of the database shows an estimated overall precision of 73%. Therein, records processed with the text-mining toolkit, ChemDataExtractor, were assisted by a modified Snowball algorithm, whose original binary relationship extraction capabilities were extended to quaternary relationship extraction. Consequently, its machine learning component can now train with ≤500 seeds, rather than the 4,000 originally used. Data processed with the modified Snowball algorithm affords 82% precision. Database records are available in MongoDB, CSV and JSON formats which can easily be read using Python, R, Java and MatLab. As a result, this makes the database easy to query for tackling big-data materials science initiatives and provides a basis for magnetic materials discovery.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Grounding annotations in published literature with an emphasis on the functional roles used in metabolic models

Accurate genome annotations in databases are a critical resource available to the scientific community for analysis and research. Inaccurate and inconsistent annotations exist as a result of errors generated from mass automated annotation, and currently act as a barrier to the application of bioinformatics. The purpose of this effort was to improve the SEED by improving the connection of functional roles to literature references. Direct literature references (DLits), found through searches of PubMed and other online databases such as SwissProt, were attached to protein sequences within the PubSEED to provide literature support for the roughly 2,500 distinct functional roles used to construct metabolic models within the Model SEED. Only DLits in which a researcher asserted the function of a protein were attached to sequences. Starting from a list of 1,072 functional roles that did not previously have DLit support, we were able to connect sequences to literature for 655 functional roles, at least 484 of which were in the original list of unsupported roles. When added to the existing set of sequences having DLits, the resulting set of DLit-sequence pairs (the foundation set) now connects approximately 4,300 DLits to approximately 5,600 distinct protein sequences obtained from approximately 16,000 genes (some of these genes have identical protein sequences). From the foundation set, we construct projection sets such that each set contains one member of the foundation set and projections of its functional role onto similar genes. The projection sets revealed 120 inconsistent annotations within the SEED. Two types of inconsistencies were corrected through manual annotation in the PubSEED: instances in which two identical protein sequences had been annotated with different functions, and instances when projected functions contradicted previous annotations. 26,785 changes to gene function assignment, 219 of which were to previously uncharacterized proteins, resulted in a more consistent and accurate set of input data from which to construct revised metabolic models within the Model SEED.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigation of divertor detachment induced through neon seeding and density ramp on HL-3

A new self-consistent 1D scrape-off layer model has been recently developed in BOUT++ framework, named SD1D, which includes equations for various particle species (e.g. main plasma, neutrals and impurities) and couples open databases like ADAS and AMJUEL. It is able to quickly and effectively simulate divertor detachment experiments. In this work, a typical detachment experiment (shot #6270) on HL-3 with neon seeding is simulated using the SD1D code. It is found that the target electron temperature and the target ion saturation current in the simulations are consistent with experimental results measured by Langmuir probes on the target plate. The variation of D α radiation intensity in the divertor is qualitatively similar to the measured D α signal. Following the experimental validations, different upstream densities are set in the simulations to study the impurity distribution under different plasma density conditions. It is found that increasing upstream density can be helpful for the control of the neon radiation front (closer to the target). In this work we also compare two detachment regimes in simulations. Based on the same initial experimental parameters (shot #6270) on HL-3, a scan of upstream density and a scan of neon seeding rate are carried out respectively. It is found that the role of atomic and molecular processes is different in the two detachment regimes. The current density roll-over is ascribed to a drop in the divertor ion source, and the variation of D α radiation intensity via different excitation channels is associated with the relevant collisional reaction sources.

BOUT++↗
DOE OSTI2019

Constructing a Tandem Mass Spectral Library for Forensic Ricin Identification

Ricin, a protein found in castor seeds, is a lethal toxin that is designated as a category 2 select agent. Because castor seeds are easy to obtain and the toxin can be easily extracted, cases of attempted ricin poisoning are relatively common. A shotgun proteomics method for ricin identification has recently been developed (manuscript in preparation), in which ricin peptides are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by proteomics database search, and peptide-spectrum matches are verified and compared to standard spectra by a human expert. To make this process more reproducible, objective, and high-throughput, we have created a ricin spectral library for peptide identification to supplement the human review step. To construct these spectral libraries, two pure ricin samples (from a proposed standard reference material) and crude castor seed extracts were digested with trypsin and analyzed using a standard shotgun LC-MS/MS protocol. Spectral libraries were created from the filtered search results from four database search tools. The library was then used in a search using SpectraST on samples from castor seeds. Analysis showed that the spectral library search resulted in more peptides identified from crude castor seed samples compared to MS-GF+ and Sequest plus Percolator. These results suggest that computational comparison of putative ricin peptide spectra to library spectra can be an effective method of confirming the presence of ricin, and that spectral library search may be suitable to augment the more manual and subjective aspects of the currently recommended human expert review.

Spectral Library, Ricin, forensic, proteomic↗
DOE OSTI2018

Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome

Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits. Location: Tundra biome. Time period: Data collected between 1964 and 2016. Major taxa studied: 295 tundra vascular plant species. Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post-hoc clustering of species-level traits. Results: Traditional functional groups explained significant differences in trait expression, particularly among traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post-hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression. Main conclusion: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra ecosystem change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insight for ecological prediction and modelling.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Mining the Gravity Mutants of Arabidopsis

Gravity mutants are a valuable resource for understanding gravity perception, signaling, and response in plants. A review of 190 publications resulted in a list of 97 loci with mutations that caused a gravitropic phenotype. While all these mutants show some form of gravity phenotype, several are also generally defective in growth. After removing these nonspecific mutants, 76 loci were deemed to have true gravity mutants. The gene list was then used to create a sortable database containing key factors of gravity signaling as well as data on methodologies and the development of mutant lines. Indexing this database has allowed us to pull out trends that were not visible in individual publications. For example, mutants that are unable to rearrange starch statoliths make up a larger proportion of the described inflorescence stems mutants than any other organ. Comparing these statolith mutants across organs shows that root and inflorescence stems consistently display different phenotypes for the same class of defect. The more severe gravity defects are most commonly described in root tissue while other tissues are more likely to show only a delayed or reduced response to gravity. The experience of members of the GeneLab plant Analytics Working Group (AWG) in data visualization and gene mapping have sparked new ideas for utilizing this database. Knowledge of shared traits, mutant development, and growth can provide a new resource for the production of seed lines specialized for their response to gravity.

gravitropism↗
DOE OSTI2024

The root cause of disruptive NTMs and paths to stable operation in DIII-D ITER baseline scenario plasmas

Analyses of the DIII-D ITER Baseline Scenario database support that the disruptive m,n=2,1 magnetic islands are pressure gradient driven, non-linear instabilities seeded in a sequence of stochastic transient magnetic perturbations, and that the current profile relaxation does not affect the m,n=2,1 island onset rate. At low torque, these Neoclassical Tearing Modes are most commonly seeded by non-linear 3-wave coupling when the differential rotation between the q=1 & q=2 rational surfaces approaches zero. Lack of statistically significant difference between the current profiles of stable and unstable states, as well as lack of correlation between the tearing mode onset rate and the current profile relaxation both reject causality between the current profile evolution and the 2,1 magnetic island onsets in these plasmas. These support that preserving the differential rotation between the q=1 and q=2 rational surfaces is key to long pulse stable operation in the plasma scenario planned for ITER, while optimization of the current profile within the explored parameter space may lead to much weaker improvements than sustaining the differential rotation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Supporting Building Portfolio Investment and Policy Decision Making through an Integrated Building Utility Data Platform

The American Recovery and Reinvestment Act stimulus funding of 2009 for smart grid projects resulted in the tripling of smart meters deployment. In 2012, the Green Button initiative provided utility customers with access to their real-time1 energy usage. The availability of finely granular data provides an enormous potential for energy data analytics and energy benchmarking. The sheer volume of time-series utility data from a large number of buildings also poses challenges in data collection, quality control, and database management for rigorous and meaningful analyses. In this paper, we will describe a building portfolio-level data analytics tool for operational optimization, business investment and policy assessment using 15-minute to monthly intervals utility data. The analytics tool is developed on top of the U.S. Department of Energy’s Standard Energy Efficiency Data (SEED) platform, an open source software application that manages energy performance data of large groups of buildings. To support the significantly large volume of granular interval data, we integrated a parallel time-series database to the existing relational database. The time-series database improves on the current utility data input, focusing on real-time data collection, storage, analytics and data quality control. The fully integrated data platform supports APIs for utility apps development by third party software developers. These apps will provide actionable intelligence for building owners and facilities managers. Unlike a commercial system, this platform is an open source platform funded by the U.S. Government, accessible to the public, researchers and other developers, to support initiatives in reducing building energy consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2018

Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Intraspecific trait variation within natural populations (i.e. intra-population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource-limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. Here, we propose that during invasion, IPTV and its relative change in response to key resource enrichment may increase with the resource deficit of invaded sites, and that this relationship may facilitate plant invasions into resource-limited environments. We analyzed the invasion trend, IPTV and its response to water enrichment, and moisture variability among populations of an annual grass Brachypodium hybridum in California, United States. We incorporated a genotyping-by-sequencing approach, a common garden experiment that had two water level treatments, and public plant and climate databases. Our hypothesis was supported by the observation that for populations that invaded sites with higher spring moisture deficit, both their seed biomass IPTV (for the water-enriched treatment only) and relative change of the IPTV across water treatments were larger when examined in the common garden experiment. A generally north to south spreading direction was found in these B. hybridum populations, towards a drier and warmer climate exhibiting higher moisture deficit for plant growth. Our results suggest a role for interactions between IPTV (rather than trait means) and environmental resource availability in promoting plant invasions, providing new insights into the significance of IPTV in shaping plant geographic distributions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2007

Optical Measurements in a Combustor Using a 9-Point Swirl-Venturi Fuel Injector

This paper highlights the use of two-dimensional data to characterize a multipoint swirl-venturi injector. The injector is based on a NASA-conceived lean direct injection concept. Using a variety of advanced optical diagnostic techniques, we examine the flows resultant from multipoint, lean-direct injectors that have nine injection sites arranged in a 3 x 3 grid. The measurements are made within an optically-accessible, jet-A-fueled, 76-mm by 76-mm flame tube combustor. Combustion species mapping and velocity measurements are obtained using planar laser-induced fluorescence of OH and fuel, planar laser scatter of liquid fuel, chemiluminescence from CH*, NO*, and OH*, and particle image velocimetry of seeded air (non-fueled). These measurements are used to study fuel injection, mixedness, and combustion processes and are part of a database of measurements that will be used for validating computational combustion models.

Hicks, Yolanda R.↗
DOE OSTI2016

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

Background. A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped. Results. Two high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly. Conclusions. The information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electron cyclotron emission detection of neoclassical tearing modes for control for ITER

Successful operation of ITER requires control of magnetic instabilities including neoclassical tearing modes (NTMs) that can degrade confinement and lead to disruption. Low latency detection by electron cyclotron emission (ECE) diagnostics has been demonstrated in a few current experiments. Using a synthetic diagnostic, we demonstrate low latency NTM detection for ITER with plasmas described by ITER IMAS database scenarios and with realistic limitations imposed on the instrumentation by these high temperature scenarios. 2/1 NTMs are detected 430 ms after magnetic island seeding and before island locking. The radiometer configuration was optimized using simulation, and the smallest detectable island size was explored. Island sizes of ∼3 cm are detectable at the 2/1 surface. The simulated signals incorporate recent physics models for island growth and rotation, which show early locking and continued island growth after locking and before disruption. This work determines limits for ITER ECE spatial resolution imposed by relativistic broadening of channels, which informs hardware design. Real-time detection is demonstrated in hardware that is required by ITER, including on an NI PXI-7853R FPGA system. Development of a synthetic diagnostic and details of the hardware will be discussed.

Cyclotron radiation↗