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At least 1,009 records · Page 56

A Survey of Open Source Software Repositories in the U.S. Department of Energy’s National Laboratories

There are 17 national laboratory systems in the United States operating under the auspices of the U.S. Department of Energy (DOE). These government labs employ tens of thousands of people engaging in research software engineering activities across a variety of missions. To support this work, many open source projects are maintained. Further, many of these projects have broad utility to the computing community at large and domain scientists in a variety of fields. However, the complexity and decentralized nature of the laboratory system has resulted in a situation where no one entity even knows about all the open source software projects in this ecosystem, let alone crude metrics of their health. In this article, we do the first external inventory of open source software repositories with a nexus to DOE labs. We posit that a project’s need for sustainability support can be determined by comparing measures of active use to measures of active maintenance.

97 MATHEMATICS AND COMPUTING↗

Local order, disorder, and everything in between: using 91 Zr solid-state NMR spectroscopy to probe zirconium-based metal–organic frameworks

Characterization of metal centers in metal–organic frameworks (MOFs) is critical for rational design and further understanding of structure–property relationships. The short-range structure about Zr atoms is challenging to properly elucidate in many Zr MOFs, particularly when local disorder is present. Static 91 Zr solid-state NMR spectra of the seven zirconium MOFs UiO-66, UiO-66-NH 2 , UiO-67, MOF-801, MOF-808, DUT-68 and DUT-69 have been acquired at high magnetic fields of 35.2 T and 19.6 T, yielding valuable information on the local structure, site symmetry and order about Zr. 91 Zr NMR is very sensitive to differences in MOF short-range structure caused by guest molecules, linker substitution and post-synthetic treatment. Complementary density functional theory (DFT) calculations assist in the interpretation and assignment of 91 Zr solid-state NMR spectra, lend insight into structural origins of 91 Zr NMR parameters and enable determination of local Zr coordination environments. This approach can be extended to many other materials containing zirconium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GMLC Technical Assistance to States

This presentation provides an overview of the U.S. Department of Energy's Grid Modernization Laboratory Consortium (GMLC) efforts to provide customized technical support specific to state public utility commissions (PUCs), specifically on the integration of distributed energy resources (DERs). The goals are to increase awareness of existing materials and support to help state PUCs move forward on DER interconnection activities, to help participants make connections to colleagues with similar challenges (and solutions), and to help the GMLC/National Renewable Energy Laboratory project team understand context and implementation challenges.

DER↗

Apple Bitter Rot: Biology, Ecology, Omics, Virulence Factors, and Management of Causal Colletotrichum Species

ABSTRACT Apple bitter rot is caused by various Colletotrichum spp. that threaten apple production globally resulting in millions of dollars in damage annually. The fungus causes a decline in fruit quality and yield, eventually rotting the fruit and rendering it inedible. The pathogen is difficult to keep out of orchards because of its broad host range and transmissibility by rain splash and insects. Once the disease manifests, pathogen identification is difficult due to evolving taxonomy and similar morphology between species. Current management strategies are threatened by an increase in fungicide resistance and regulations on many multisite fungicides, leading to a pressing need for new management options for control. This review aims to summarise the most current knowledge regarding the biology, virulence factors, ecology, omics and emerging management strategies for Colletotrichum species that cause apple bitter rot. Taxonomy Colletotrichum species—Domain Eukaryota, Kingdom Fungi, Phylum Ascomycota, Class Sordariomycetes, Order Glomerellales, Family Glomerellaceae, Genus Colletotrichum . Biology Hemibiotrophic pathogen with a wide host range that establishes a biotrophic interaction where it penetrates host plants using appressoria followed by a switch to necrotrophy causing rot symptoms. Toxins Cercosporin, colletotrichins, colletotric acid, ferricrocin. Host Range The host range varies by species but largely occurs on dicotyledonous plants and is less prevalent on monocots as well as gymnosperms, ferns, mosses and animals (e.g., insects). Disease Symptoms Symptoms often manifest as flat to sunken necrotic areas on fruit. Lesions on leaves and fruit can have concentric rings with abundant pathogen sporulation. Disease Control Colletotrichum spp. are primarily managed by single‐site quinone outside inhibitor (Qol), methyl benzimidazole carbamate (MBC), demethylation inhibitor (DMI) fungicides, and multisite dithiocarbamate and phthalimide fungicides. Susceptibility may vary with species, strain specificity, or geographic region. Other management options include clean stock production, cultural practices, resistance breeding, and biological control through the introduction of protective or competing microorganisms.

Boeckman, Nathanial J. [Plant Pathology Laboratory↗

Hyperspectral leaf reflectance of grasses varies with evolutionary lineage more than with site

Abstract To predict ecological responses at broad environmental scales, grass species are commonly grouped into two broad functional types based on photosynthetic pathway. However, closely related species may have distinctive anatomical and physiological attributes that influence ecological responses, beyond those related to photosynthetic pathway alone. Hyperspectral leaf reflectance can provide an integrated measure of covarying leaf traits that may result from phylogenetic trait conservatism and/or environmental conditions. Understanding whether spectra‐trait relationships are lineage specific or reflect environmental variation across sites is necessary for using hyperspectral reflectance to predict plant responses to environmental changes across spatial scales. We measured hyperspectral leaf reflectance (400–2400 nm) and 12 structural, biochemical, and physiological leaf traits from five grass‐dominated sites spanning the Great Plains of North America. We assessed if variation in leaf reflectance spectra among grass species is explained more by evolutionary lineage (as captured by tribes or subfamilies), photosynthetic pathway (C 3 or C 4 ), or site differences. We then determined whether leaf spectra can be used to predict leaf traits within and across lineages. Our results using redundancy analysis ordination (RDA) show that grass tribe identity explained more variation in leaf spectra (adjusted R 2 = 0.12) than photosynthetic pathway, which explained little variation in leaf spectra (adjusted R 2 = 0.00). Furthermore, leaf reflectance from the same tribe across multiple sites was more similar than leaf reflectance from the same site across tribes (adjusted R 2 = 0.12 and 0.08, respectively). Across all sites and species, trait predictions based on spectra ranged considerably in predictive accuracies ( R 2 = 0.65 to <0.01), but R 2 was >0.80 for certain lineages and sites. The relationship between Vc max , a measure of photosynthetic capacity, and spectra was particularly promising. Chloridoideae, a lineage more common at drier sites, appears to have distinct spectra‐trait relationships compared with other lineages. Overall, our results show that evolutionary relatedness explains more variation in grass leaf spectra than photosynthetic pathway or site, but consideration of lineage‐ and site‐specific trait relationships is needed to interpret spectral variation across large environmental gradients.

Pau, Stephanie [Department of Geography University↗

Data for: Miscanthus × giganteus changes soil structure and increases maximum water holding capacity

The data provided include results from a comparative study evaluating the impact of Miscanthus × giganteus (miscanthus) versus maize on soil structural properties and maximum water holding capacity (MWHC) across two Iowa sites. The dataset includes MWHC values determined using the Funnel Filter Paper Drainage (FFPD) method, as well as additional measurements of MWHC following structural disruption of the soil to isolate the effect of aggregation. It also contains three-dimensional micro-computed tomography (microCT) data used to quantify total porosity and pore size distribution (PSD) of soil aggregates at a 5 µm resolution. All data are provided as raw replicate-level measurements, organized by site, crop, and depth, along with processed summary files in table form in CSV (.csv) format to support reproducibility and downstream analysis.

Misanthus x giganteus↗

Guidance on EPAct section 707 Emergency Repair and Restoration Vehicle Exclusions: EPAct State and Alternative Fuel Provider Fleet Program Guidance Document

Section 707 of the Energy Policy Act of 2005 (EPAct 2005) amended section 301(9)(E) of EPAct 1992 by adding to the list of vehicles excluded from the definition of "fleet" a new subcategory of emergency motor vehicles, i.e., "vehicles directly used in the emergency repair of transmission lines and in the restoration of electricity service following power outages, as determined by the Secretary." Like other excluded vehicles, these light-duty vehicles (LDVs) do not count (1) when determining whether a fleet is covered under the U.S. Department of Energy's (DOE) State and Alternative Fuel Provider Fleet Program (Program), and (2) for fleets that are covered under the Program, when calculating annual alternative fuel vehicle (AFV)-acquisition requirements. If AFV models of excluded vehicles are acquired, however, a fleet may count them toward their acquisition requirement by including them in the calculation of the number of AFVs acquired. Exclusion Process.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

Epidemiology, Clinical Features, and Outcomes of Coccidioidomycosis, Utah, 2006–2015

On the basis of a 1957 geographic Coccidioides seropositivity survey, 3 counties in southwestern Utah, USA, were considered coccidioidomycosis-endemic, but there has been a paucity of information on the disease burden in Utah since. We report findings from a recent clinical and epidemiologic study of coccidioidomycosis in Utah. To describe clinical characteristics, we identified all coccidioidomycosis cases in an integrated health system in the state during 2006–2015. For epidemiologic analysis, we used cases reported to the Utah Department of Health during 2009–2015. Mean state incidence was 1.83 cases/100,000 population/year. Washington County, in southwestern Utah, had the highest incidence, 17.2 cases/100,000 population/year. In a generalized linear model with time as a fixed effect, mean annual temperature, population, and new construction were associated with regional variations in incidence. Using these variables in a spatiotemporal model, we estimated the adjusted regional variation by county to predict areas where Coccidioides infections might increase.

60 APPLIED LIFE SCIENCES↗

Predictive models of the genetic bases underlying budding yeast fitness in multiple environments

Abstract The ability of organisms to adapt and survive depends on the effects of genes and the environment on fitness. However, the multigenic nature of fitness and genotype-by-environment interactions hinder our understanding of the genetic basis of fitness. Here, we established fitness prediction models for 35 environments using machine learning and existing fitness data and different genetic variant types for a Saccharomyces cerevisiae population. Models revealed that the predictive ability of genetic variants varied across environments, with copy number variants explaining the majority of fitness variation in most cases. Model interpretation showed that different variant types identified distinct gene sets associated with predictive variants. These gene sets were significantly enriched in experimentally validated genes affecting fitness in only a subset of environments, indicating that many genes influencing fitness remain unexplored. Notably, non-experimentally validated genes were more important than validated ones for fitness predictions. Gene contributions to predictions were both isolate- and environment-dependent, pointing to gene-by-gene and gene-by-environment interactions. Furthermore, models uncovered experimentally validated and novel candidate genetic interactions for a well-characterized stress, the fungicide benomyl. These findings highlight the feasibility of identifying the genetic basis of fitness by using different genetic variant types and offer novel targets for future functional analysis.

DNA copy number variations↗

Real-space simulations of the hyperbolic plasmon polaritons in 1T′ tungsten ditelluride

Recent discoveries of hyperbolic surface plasmon polaritons (SPPs) in 1T′ WTe 2 have garnered significant attention in 2D materials and nanophotonics. In this study, we employ finite-element simulations to investigate the real-space characteristics of hyperbolic SPPs in thin WTe 2 flakes. Our results show that the SPPs exhibit a pronounced sensitivity to excitation energy and sample thickness. By analyzing the plasmonic field patterns, we extract key plasmonic parameters including plasmon wavelengths, hyperbolic angles, and plasmonic figures of merit. In addition, we examine SPP modes in stacked WTe 2 flakes with varying twist angles, demonstrating that the plasmonic field patterns can be effectively tuned by adjusting the twist angle. Notably, as the twist angle increases, the SPPs undergo a topological transition from open hyperbolic modes to closed elliptic modes. This twist-engineering capability offers promising potential for the development of tunable plasmonic devices based on WTe 2 .

2D materials↗