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At least 1,639 records · Page 91

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↗

Observations of gamma-ray emission in solar flares

Solar flare associated gamma ray observations are reviewed. Data cover He-3, line emission, and absolute intensity associated with gamma ray production. Results are given in graphs and tables.

Forrest, D. J.↗

Time-varying oscillations in the solar soft X-ray flux as observed from Skylab

Observations obtained by the Skylab/Apollo telescope S-056 X-ray experiment were used to study the time-varying oscillations in the solar soft X-ray flux during a flare. The observations consisted of count rates measured every 2.5 s by sealed, gas-filled counters operating over the 2.5-7.25-A and 6.1-20.0-A wavelength ranges. The power spectra for two other intervals were computed to determine whether the observed oscillations were flare-associated or instrumental in origin. The data indicate that the oscillations in the flare-associated X-ray flux are caused by waves which are generated during the flare and which periodically increase the electron density. No oscillations were observed during quiet periods.

Teuber, D. L.↗

New interpretations of shock-associated noise with and without screech

Anomalous trends in present convergent nozzle (Mach 1) shock associated noise analyses and predictions, with particular emphasis on the roles of screech and jet temperature, are discussed. Experimentally measured values of shock associated noise are used to reassess data trends, including both frequency and sound pressure level. The data used includes model-scale nozzles, varying in nominal diameter from 5 cm to 13 cm, and full scale engine nozzles up to 48 cm. All data were obtained at static conditions. From this reassessment of the measured data, new empirical methods for the prediction of shock associated noise are developed. Separate procedures are presented for screech free and screech contaminated shock associated noise. In the present approach, shock associated noise spectra are developed from considerations that include the peak sound pressure level and its frequency, the low frequency sound pressure level slope, and the high frequency sound pressure level slope or roll-off; the latter is shown to vary with directivity angle.

Vonglahn, U.↗

Detection and mapping of volcanic rock assemblages and associated hydrothermal alteration with Thermal Infrared Multiband Scanner (TIMS) data Comstock Lode Mining District, Virginia City, Nevada

Thermal Infrared Multispectral Scanner (TIMS) data were acquired over the Virginia City area on September 12, 1984. The data were acquired at approximately 1130 hours local time (1723 IRIG). The TIMS data were analyzed using both photointerpretation and digital processing techniques. Karhuen-Loeve transformations were utilized to display variations in radiant spectral emittance. The TIMS image data were compared with color infrared metric camera photography, LANDSAT Thematic Mapper (TM) data, and key areas were photographed in the field.

Taranik, James V.↗

Propagation of solar flare-associated interplanetary shock waves in the heliospheric meridional plane

An analysis is conducted for 149 flare-associated shock wave events based on interplanetary scintillation observational data. All of the flare-associated shock waves tend to propagate toward the low latitude region near the solar equator for flares that are located in both the solar Northern and Southern Hemispheres. Also, the fastest propagation directions tend toward the heliospheric current sheet near 1 AU. This tendency is caused by the dynamic action of near-sun magnetic forces on the ejected coronal plasma that traverses the helmet-like magnetic topologies near the sun outward to the classical topology that is essentially parallel to the heliospheric current sheet.

Wei, Fengsi↗

ArcGIS Digitization of Apollo Surface Traverses

The Apollo surface activities were documented in extraordinary detail, with every action performed by the astronauts while on the surface recorded either in photo, audio, film, or by written testimony [1]. The samples and in situ measurements the astronauts collected while on the lunar surface have shaped our understanding of the geologic history of the Moon, and the earliest history and evolution of the inner Solar System. As part of an ongoing LASERfunded effort, we are digitizing and georeferencing data from astronaut traverses and spatially associating them to available, co-registered remote sensing data. Here we introduce the products produced so far for Apollo 15, 16, and 17 missions.

Petro, N. E.↗

Satellite Data Reveals a Recent Increase in Shifting Cultivation and Associated Carbon Emissions in Laos

Although shifting cultivation is the major land use type in Laos, the spatial-temporal patterns and the associated carbon emissions of shifting cultivation in Laos are largely unknown. This study provides a nationwide analysis of the spatial-temporal patterns of shifting cultivation and estimations of the associated carbon emissions in Laos over the last three decades. This study found that shifting cultivation has been expanding and intensifying in Laos, especially in the last five years. The newly cultivated land from 2016-2020 accounted for 4.5% (±1.2%) of the total land area of Laos. Furthermore, the length of fallow periods has been continuously declining, indicating that shifting cultivation is becoming increasingly intensive. Combining biomass derived from GEDI (Global Ecosystem Dynamics Investigation) and shifting cultivation maps and area estimates, we found that the net carbon emissions from shifting cultivation declined in 2001-2015 but increased in 2016-2020. The largest carbon source is conversion from intact forests to shifting cultivation, which contributed to 89% of the total emissions from 2001 to 2020. In addition, there were increased emissions from intensified use of fallow land. This research provides useful information for policymakers in Laos to understand the changes in shifting cultivation and improve land use management. This study not only supports REDD+ (Reducing Emissions from Deforestation and forest Degradation) reporting for Laos but also provides a methodology for tracking carbon emissions and removals of shifting cultivation.

Shifting cultivation↗

SNF Data Visualization on the Centralized Used Fuel Resource for Information Exchange (CURIE) Website

To better inform stakeholders regarding the nature of spent nuclear fuel (SNF) at utility sites, an online data visualization system has been created for the U.S. Department of Energy's Office of Nuclear Energy (DOENE). The data visualization system is part of the Centralized Used Fuel Resource for Information Exchange (CURIE) website, hosted by the Oak Ridge National Laboratory (ORNL) for DOE-NE. The visualization employs a database that is part of an analysis tool known as the Used Nuclear Fuel Storage, Transportation and Disposal Analysis Resource and Data System (UNF-ST[and]DARDS). Because many of the previous document management and sharing tools related to SNF have been terminated (or are inaccessible), a new tool, the CURIE, was developed for DOE-NE and launched on March 1, 2013 at http://curie.ornl.gov. In addition to supporting DOE SNF programs, CURIE is a national resource that is accessible to industry, vendor, federal, and laboratory partners, as well as other stakeholders. CURIE's architecture was initially based on previous work that supported DOE's Bioenergy Technologies Office on the Bioenergy Knowledge Discovery Framework (KDF). The site uses an open-source search engine, Apache Solr, which provides intuitive search results based on a faceted search method similar to that used by Amazon.com{sup R}. This algorithm helps to ensure that finding documents and data is straightforward. SNF data visualization capability was added to the CURIE website which provides a capability to post and access documents and data related to the management of SNF. CURIE currently maintains over 4,100 documents and the Siting Experience Database (SED), which was developed in response to a near-term recommendation by the Blue Ribbon Commission on America's Nuclear Future (BRC). The SED is a database of the experience that has been gained and relevant documentation that has been produced in efforts to site nuclear waste facilities, both in the US and abroad. Most of these documents are publicly accessible. In addition, CURIE maintains a current calendar of related events, an SNF image gallery, featured documents, and external links to related databases and websites. CURIE also maintains private groups (or communities) to facilitate collaborative development through sharing and editing documents that are not publicly available. There are more than 250 registered users in 23 different communities within CURIE.ORNL has also been developing UNF-ST[and]DARDS to provide a controlled source of technical data for various waste management system analysis/evaluation tools, access to key technical data, and analysis capabilities for characterizing the SNF inventory. UNF-ST[and]DARDS also provides enhanced capabilities to assess safety, risk, and uncertainty throughout the integrated waste management system. This paper describes the UNF-ST[and]DARDS data available for visualization and the associated visualization techniques used by CURIE to display this data.

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Tissue decomposition from dual energy CT data for MC based dose calculation in particle therapy

Purpose: The authors describe a novel method of predicting mass density and elemental mass fractions of tissues from dual energy CT (DECT) data for Monte Carlo (MC) based dose planning. Methods: The relative electron density ϱ{sub e} and effective atomic number Z{sub eff} are calculated for 71 tabulated tissue compositions. For MC simulations, the mass density is derived via one linear fit in the ϱ{sub e} that covers the entire range of tissue compositions (except lung tissue). Elemental mass fractions are predicted from the ϱ{sub e} and the Z{sub eff} in combination. Since particle therapy dose planning and verification is especially sensitive to accurate material assignment, differences to the ground truth are further analyzed for mass density, I-value predictions, and stopping power ratios (SPR) for ions. Dose studies with monoenergetic proton and carbon ions in 12 tissues which showed the largest differences of single energy CT (SECT) to DECT are presented with respect to range uncertainties. The standard approach (SECT) and the new DECT approach are compared to reference Bragg peak positions. Results: Mean deviations to ground truth in mass density predictions could be reduced for soft tissue from (0.5±0.6)% (SECT) to (0.2±0.2)% with the DECT method. Maximum SPR deviations could be reduced significantly for soft tissue from 3.1% (SECT) to 0.7% (DECT) and for bone tissue from 0.8% to 0.1%. MeanI-value deviations could be reduced for soft tissue from (1.1±1.4%, SECT) to (0.4±0.3%) with the presented method. Predictions of elemental composition were improved for every element. Mean and maximum deviations from ground truth of all elemental mass fractions could be reduced by at least a half with DECT compared to SECT (except soft tissue hydrogen and nitrogen where the reduction was slightly smaller). The carbon and oxygen mass fraction predictions profit especially from the DECT information. Dose studies showed that most of the 12 selected tissues would profit significantly (up to 2.2%) from DECT material decomposition with no noise present. The ϱ{sub e} associated with an absolute noise of ±0.01 and Z{sub eff} associated with an absolute noise of ±0.2 resulted in ±10% standard variation in the carbon and oxygen mass fraction prediction. Conclusions: Accurate stopping power prediction is mainly determined by the correct mass density prediction. Theoretical improvements in range predictions with DECT data in the order of 0.1%–2.1% were observed. Further work is needed to quantify the potential improvements from DECT compared to SECT in measured image data associated with artifacts and noise.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Calcium and Bone Homeostasis During 4-6 Months Space Flight

Bone and calcium homeostasis are altered by weightlessness. We previously reported calcium studies on three subjects from the first joint US/Russian mission to Mir. We report here data on an additional three male subjects, whose stays on Mir were 4 (n= 1) and 6 (n=2) mos. Data were collected before, during, and after the missions. Inflight studies were conducted at 2-3 mos. Endocrine and biochemical indices were measured, along with 3-wk calcium tracer studies. Percent differences are reported compared to preflight. Ionized calcium was unchanged (2.8 +/-2.1 %) during flight. Calcium absorption was variable inflight, but was decreased after landing. Vitamin D stores were decreased 35 +/-24% inflight, similar to previous reports. Serum PTH was decreased 59 +/-9% during flight (greater than we previously reported), while 1,25(OH)(sub 2)-Vitamin D was decreased in 2 of 3 subjects. Markers of bone resorption (e.g., crosslinks) were increased in all subjects. Bone-specific alkaline phosphatase was decreased (n=1) or unchanged (n=2), while osteocalcin was decreased 34 +/-23%. Previously presented data showed that inflight bone loss is associated with increased resorption and unchanged/decreased formation. The data reported here support these earlier findings. These studies will help to extend our understanding of space flight-induced bone loss, and of bone loss associated with diseases such as osteoporosis or paralysis.

Smith, Scott M.↗

Design of satellite flexibility experiments

A preliminary study has been completed to begin development of a flight experiment to measure spacecraft control/flexible structure interaction. The work reported consists of two phases: identification of appropriate structural parameters which can be associated with flexibility phenomena, and suggestions for the development of an experiment for a satellite configuration typical of near-future vehicles which are sensitive to such effects. Recommendations are made with respect to the type of data to be collected and instrumentation associated with these data. The approach consists of developing the equations of motion for a vehicle possessing a flexible solar array, then linearizing about some nominal motion of the craft. A set of solutions are assumed for array deflection using a continuous normal mode method and important parameters are exposed. Inflight and ground based measurements are distinguished. Interrelationships between these parameters, measurement techniques, and input requirements are discussed which assure minimization of special vehicle maneuvers and optimization of data to be obtained during the normal flight sequence.

Kaplan, M. H.↗

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced Computational Framework for Environmental Management ZEM, Version 1.x

Typically environmental management problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly integration into a series of models with different complexity for various types of model analyses where the data are applied as soft and hard model constraints. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions). To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian- Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org). The ZEM framework is open-source and can be applied to any environmental management site. The framework will be open-source and released under GPL V3 license.

Vesselinov, VelimirV.↗

ZEM: Integrated Framework for Real-Time Data and Model Analyses for Robust Environmental Management Decision Making - 16438

Typically environmental management (EM) problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly analysis, assimilation and integration into a series of models with different complexity for various types of model-based analyses. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions). To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian-Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is predominantly coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org) and incorporates the MADS computational tools (Model Analysis and Decision Support; http://mads.lanl.gov). We demonstrate the application of ZEM for data and model analyses at the LANL Chromium site. The ZEM framework will be released as open-source code and can be applied to any environmental management site. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗