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At least 1,225 records · Page 68

Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks

In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r 2 ). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993–1994 and a single case from 2011 as well as links between two isolates from over 30 years ago. The identification of these potential links shows that JSpecies Tetra analysis can be a useful tool in rapidly assessing genetic relatedness of Lm isolates during outbreak investigations and for comparing historical isolates. In conclusion, our analyses led to the identification of a highly related clonal group involved in two separate outbreaks, stone fruit and caramel apple, and suggests the possibility of a new genotype that may be better adapted for certain foods and/or environment.

59 BASIC BIOLOGICAL SCIENCES↗

Gamma-ray spectrometry as a tool for exploring archaeological nuclear facilities: a case study from the Nevada Test Site Nuclear Rocket Development Station

Since its first demonstration in the early 2000s, the exploration of gamma-ray spectrometry (GRS) applications as a geophysical tool in archaeology remains nascent. While intentional neutron activation, which requires a gamma-ray analysis, has seen increasing use as a geoforensics technique in archaeology, little or no research has been published concerning the possibility of GRS as an industrial archaeological tool for use in exploring nuclear sites or facilities where neutron activation and surface contamination may have already occurred. Consequently, the use of GRS as a geophysical tool for the archaeological investigation of abandoned or decommissioned nuclear facilities is proposed, demonstrated, and discussed using a case study from the Nevada Test Site Nuclear Rocket Development Station.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

AmeriFlux FLUXNET-1F US-xTL NEON Toolik (TOOL)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xTL NEON Toolik (TOOL). This is the FLUXNET version of the carbon flux data for the site US-xTL NEON Toolik (TOOL) produced by applying the standard ONEFlux (1F) software. Site Description - The Toolik field site is located in a remote wilderness area at the Toolik Field Station which is on land managed by the Bureau of Land Management. The area is underlain by continuous permafrost, which exerts a major influence on hydrology and the distribution, structure, and function of terrestrial and aquatic ecosystems. Because of its location between the Brooks Range and the coastal plain, the vegetation and soils at TOOL are representative of much of the Alaskan foothills tundra. This terrestrial field site is collocated with NEON’s Toolik Lake aquatic site. The closest city, Fairbanks, Alaska is 400 miles away. The Dalton Highway (also known as the Haul Road or Pipeline Road), which traverses the middle of the state from Fairbanks to Prudhoe Bay, provides access to the area.

Network), NEON (National Ecological Observatory↗

Coal Power Plant Reinvestment Visualization Tool

This tool, available at https://energycommunities.gov/coal-power-plant-reinvestment-visualization-tool/, serves as a public database and map for the purposes of enabling state and local economic development officials, project developers, and power plant owners to identify and pursue opportunities for plant and community reinvestment. The Coal Power Plant Reinvestment Visualization Tool focuses on coal power plants that have been closed or set-to-retire, alongside key infrastructure characteristics that are relevant for potential redevelopment reinvestment opportunities, including the opportunity to query these data based off pre-defined or user-set queries to identify opportunities for coal power facility reinvestment to support solar, wind, manufacturing, and nuclear. These Data for visualization and query include, but are not limited to: • Electric Transmission Lines • EPA Brownfield Sites (assessed with Federal funding) • Petroleum Terminals • Ports • Railroads • Others The tool will be updated periodically to provide relevant information to enable state and local economic development officials, project developers, and power plant owners to identify and pursue opportunities for economic revitalization and community reinvestment. Within this application data are focused on U.S. power plants with coal generation, where at least one on-site generator utilizes or utilized coal as a fuel source, including planned retirements through 2058 (EIA, 2024). Additional information on energy communities and revitalization opportunities can be accessed on the Interagency Working Group on Coal & Power Plant Communities & Economic Revitalization Energy Communities website (https://energycommunities.gov).

Closures↗

Smart CO2 Transport-Route Planning Tool

NETL has developed the Smart CO2 Transport-Route Planning Tool to help inform energy transport planning and development. The stand-alone, open-source tool applies data-driven, geospatial and machine-learning informed logic to identify potential routes or evaluate existing corridors based on current legislation, best construction practices, and more. Underpinning the interactive tool, is NETL’s CO2 Transport Planning Database (https://edx.netl.doe.gov/dataset/ccs-pipeline-route-planning-database-v1). This geospatial resource contains more than 70 gigabytes of data representing more than 60 critical factors for the spatial routing of CO2 transport, including land use requirements, existing infrastructure, high consequence areas, and natural hazards.

Bipartisan Infrastructure Law↗

Summary Report for the SINBAD Search Tool Project

The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.

Cunha Da Silva, Alice↗

Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil Shale/Sands

In our research, we are taking the novel approach of developing and applying high performance computing, computational fluid dynamics (CFD)-based simulation tools to a modified in-situ process for production of oil from oil shale. The simulation tools being developed capture the relevant physical processes and data from a large-scale system. The modified in-situ application is a pilot-scale heat transfer process inside Red Leaf Resources EcoShale capsule. We demonstrate the need to understand fluid flow behavior in the convective channels of the rubblized shale bed as convective heating greatly decreases the time required to heat the oil shale to the production temperature when compared with conductive heating alone. We have developed and implemented a geometry creation strategy for a representative section of the EcoShale capsule, developed a meshing approach to deal with the complicated geometry and produce a well-behaved mesh, analyzed the effects of boundary conditions on the simulation results, and devised a new operator splitting solution algorithm that reduces computational costs by taking advantage of the differing convective and conductive time scales occurring in the simulation. These simulation tools can be applied to a wide range of processes involving convective fluid flow heating in rubblized beds.

04 OIL SHALES AND TAR SANDS↗

Online Analysis of Wind and Solar Part I: Ramping Tool

To facilitate wider penetration of renewable resources without compromising system reliability concerns arising from the lack of predictability of intermittent renewable resources, a tool for use by California Independent System Operator (CAISO) power grid operators was developed by Pacific Northwest National Laboratory (PNNL) in conjunction with CAISO with funding from California Energy Commission. This tool predicts and displays additional capacity and ramping requirements caused by uncertainties in forecasts of loads and renewable generation. The tool is currently operational in the CAISO operations center. This is one of two final reports on the project.

ancillary services↗

Online Analysis of Wind and Solar Part II: Transmission Tool

To facilitate wider penetration of renewable resources without compromising system reliability concerns arising from the lack of predictability of intermittent renewable resources, a tool for use by California Independent System Operator (CAISO) power grid operators was developed by Pacific Northwest National Laboratory (PNNL) in conjunction with CAISO with funding from California Energy Commission. The tool analyzes and displays the impacts of uncertainties in forecasts of loads and renewable generation on: (1) congestion, (2) voltage and transient stability margins, and (3) voltage reductions and reactive power margins. The impacts are analyzed in the base case and under user-specified contingencies. A prototype of the tool has been developed and implemented in software.

probabilistic load and wind forecasts↗

Collaboration Leads to State-of-the-Art Energy Auditing Tool: Project Highlights (Fact Sheet)

This fact sheet describes the tablet-based simuwatt Audit tool, which uses NREL's advanced energy modeling framework and building energy audit processes, collaboration tools, in-app media, and private company concept3D's geometric capture software combined with real-time connections to large sets of standardized data to perform building energy audits faster than traditional methods. By integrating the NREL Building Component Library, utility rates, weather information, and energy conservation measures, the tool provides investment-grade audits that cost 75% less than traditional audits and stores the data in a consistent and reusable format.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High Performance Computing Productivity Study - Evaluation of Parallel Tools Platform (PTP) Eclipse Plug-In

This report is a DARPA funded Work For Others (WFO) evaluation of the Parallel Tools Platform (PTP) version 5.0.3 (Released October 18, 2011). PTP is currently being developed and supported as an open source product managed by Project Lead Greg Watson and team at IBM plus several other contributors. The tool has been in development since 2005 with a goal of providing an infrastructure for the integration of high performance computing tools. Basic functionality such as source code editing, compiling, launching, and debugging, plus more advanced features including performance monitoring and deployment have been bundled into an Eclipse Integrated Development Environment (IDE) plug-in to give parallel application programmers the features and improved productivity gained from using a common, well established development platform. The evaluation encompasses the basic aspects of using PTP, beginning with the installation and configuration of the plug-in, followed by code development and debugging. Each aspect is evaluated based on the expectations of my experience as an Eclipse user and is presented in the following format: • Feature description • User Experience • Evaluation The feature description is based on the provided documentation for PTP and the ‘generic’ expectations of what the feature should provide. The user experience reveals the actual use and exercise of the feature – specifically in the context and perspective of the evaluation platform provided by Lawrence Livermore National Laboratory. The evaluation of each feature includes the overall outcome of the user experience, along with the expectations that were not met, met, or exceeded along with any issues that were encountered.

97 MATHEMATICS AND COMPUTING↗

Field Assessment of Energy Audit Tools for Retrofit Programs

This project focused on the use of home energy ratings as a tool to promote energy retrofits in existing homes. A home energy rating provides a quantitative appraisal of a home's asset performance, usually compared to a benchmark such as the average energy use of similar homes in the same region. Home rating systems can help motivate homeowners in several ways. Ratings can clearly communicate a home's achievable energy efficiency potential, provide a quantitative assessment of energy savings after retrofits are completed, and show homeowners how they rate compared to their neighbors, thus creating an incentive to conform to a social standard. An important consideration is how rating tools for the retrofit market will integrate with existing home energy service programs. For residential programs that target energy savings only, home visits should be focused on key efficiency measures for that home. In order to gain wide adoption, a rating tool must be easily integrated into the field process, demonstrate consistency and reasonable accuracy to earn the trust of home energy technicians, and have a low monetary cost and time hurdle for homeowners. Along with the Home Energy Score, this project also evaluated the energy modeling performance of SIMPLE and REM/Rate.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Recovery Act: Advanced Interaction, Computation, and Visualization Tools for Sustainable Building Design

Current building energy simulation technology requires excessive labor, time and expertise to create building energy models, excessive computational time for accurate simulations and difficulties with the interpretation of the results. These deficiencies can be ameliorated using modern graphical user interfaces and algorithms which take advantage of modern computer architectures and display capabilities. To prove this hypothesis, we developed an experimental test bed for building energy simulation. This novel test bed environment offers an easy-to-use interactive graphical interface, provides access to innovative simulation modules that run at accelerated computational speeds, and presents new graphics visualization methods to interpret simulation results. Our system offers the promise of dramatic ease of use in comparison with currently available building energy simulation tools. Its modular structure makes it suitable for early stage building design, as a research platform for the investigation of new simulation methods, and as a tool for teaching concepts of sustainable design. Improvements in the accuracy and execution speed of many of the simulation modules are based on the modification of advanced computer graphics rendering algorithms. Significant performance improvements are demonstrated in several computationally expensive energy simulation modules. The incorporation of these modern graphical techniques should advance the state of the art in the domain of whole building energy analysis and building performance simulation, particularly at the conceptual design stage when decisions have the greatest impact. More importantly, these better simulation tools will enable the transition from prescriptive to performative energy codes, resulting in better, more efficient designs for our future built environment.

99 GENERAL AND MISCELLANEOUS↗

Assessment of Energy Storage Alternatives in the Puget Sound Energy System Volume 2: Energy Storage Evaluation Tool

This volume presents the battery storage evaluation tool developed at Pacific Northwest National Laboratory (PNNL), which is used to evaluate benefits of battery storage for multiple grid applications, including energy arbitrage, balancing service, capacity value, distribution system equipment deferral, and outage mitigation. This tool is based on the optimal control strategies to capture multiple services from a single energy storage device. In this control strategy, at each hour, a look-ahead optimization is first formulated and solved to determine battery base operating point. The minute by minute simulation is then performed to simulate the actual battery operation. This volume provide background and manual for this evaluation tool.

25 ENERGY STORAGE↗

White Paper on the Use of Team Calendars with the JIRA Issue Tracking System and Confluence Collaboration Tools for the xLPR Project

ORNL was tasked by xLPR project management to propose a team calendar for use within the xLPR consortium. Among various options that were considered, the approach judged by ORNL to best fit the needs of the xLPR project is presented in this document. The Atlassian Team Calendars plug-in used with the Confluence collaboration tool was recommended for several reasons, including the advantage that it provides for a tight integration between Confluence (found at https://xlpr.ornl.gov/wiki ) and xLPR s JIRA issue tracking system (found at https://xlpr.ornl.gov/jira ). This document is divided into two parts. The first part (Sections 1-6) consists of the white paper, which highlights some of the ways that Team Calendars can improve com mun ication between xLPR project managers, group leads, and team members when JIRA is applied for both issue tracking and change-management activities. Specific points emphasized herein are as follows: The Team Calendar application greatly enhances the added value that the JIRA and Confluence tools bring to the xLPR Project. The Team Calendar can improve com mun ication between xLPR project managers, group leads, and team members when JIRA is applied for both issue tracking and change-management activities. The Team Calendar works across different email tools such as Outlook 2011, Outlook 2010, Outlook 2007, Google Calendars and Mac s iCalendar to name a few. xLPR users can now access the wiki Confluence (with embedded Team Calendars) directly from JIRA without having to re-validate their login. The second part consists of an Annex (Section 7), which describes how users can subscribe to Team Calendars from different calendar applications. Specific instructions are given in the Annex that describe how to Import xLPR Team Calendar to Outlook Version Office 2010 Import xLPR Team Calendar to Outlook Version Office 2007 Subscribe to Team Calendar from Google Calendar The reader is directed to Section 4 for instructions on adding events to the Team Calendar or accessing ORNL staff for assistance with such additions. To seek help with your questions and problems regarding the content of this document, please contact Hilda Klasky at klaskyhb@ornl.gov

97 MATHEMATICS AND COMPUTING↗

Foundational Tools for Petascale Computing

The Paradyn project has a history of developing algorithms, techniques, and software that push the cutting edge of tool technology for high-end computing systems. Under this funding, we are working on a three-year agenda to make substantial new advances in support of new and emerging Petascale systems. The overall goal for this work is to address the steady increase in complexity of these petascale systems. Our work covers two key areas: (1) The analysis, instrumentation and control of binary programs. Work in this area falls under the general framework of the Dyninst API tool kits. (2) Infrastructure for building tools and applications at extreme scale. Work in this area falls under the general framework of the MRNet scalability framework. Note that work done under this funding is closely related to work done under a contemporaneous grant, “High-Performance Energy Applications and Systems”, SC0004061/FG02-10ER25972, UW PRJ36WV.

97 MATHEMATICS AND COMPUTING↗

Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT) Final Report

A partnership across government, academic, and private sectors has created a novel system that enables climate researchers to solve current and emerging data analysis and visualization challenges. The Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT) software project utilizes the Python application programming interface (API) combined with C/C++/Fortran implementations for performance-critical software that offers the best compromise between "scalability" and “ease-of-use.” The UV-CDAT system is highly extensible and customizable for high-performance interactive and batch visualization and analysis for climate science and other disciplines of geosciences. For complex, climate data-intensive computing, UV-CDAT’s inclusive framework supports Message Passing Interface (MPI) parallelism as well as taskfarming and other forms of parallelism. More specifically, the UV-CDAT framework supports the execution of Python scripts running in parallel using the MPI executable commands and leverages Department of Energy (DOE)-funded general-purpose, scalable parallel visualization tools such as ParaView and VisIt. This is the first system to be successfully designed in this way and with these features. The climate community leverages these tools and others, in support of a parallel client-server paradigm, allowing extreme-scale, server-side computing for maximum possible speed-up.

54 ENVIRONMENTAL SCIENCES↗

Advanced Epi Tools for Gallium Nitride Light Emitting Diode Devices

Over the course of this program, Applied Materials, Inc., with generous support from the United States Department of Energy, developed a world-class three chamber III-Nitride epi cluster tool for low-cost, high volume GaN growth for the solid state lighting industry. One of the major achievements of the program was to design, build, and demonstrate the world’s largest wafer capacity HVPE chamber suitable for repeatable high volume III-Nitride template and device manufacturing. Applied Materials’ experience in developing deposition chambers for the silicon chip industry over many decades resulted in many orders of magnitude reductions in the price of transistors. That experience and understanding was used in developing this GaN epi deposition tool. The multi-chamber approach, which continues to be unique in the ability of the each chamber to deposit a section of the full device structure, unlike other cluster tools, allows for extreme flexibility in the manufacturing process. This robust architecture is suitable for not just the LED industry, but GaN power devices as well, both horizontal and vertical designs. The new HVPE technology developed allows GaN to be grown at a rate unheard of with MOCVD, up to 20x the typical MOCVD rates of 3{micro}m per hour, with bulk crystal quality better than the highest-quality commercial GaN films grown by MOCVD at a much cheaper overall cost. This is a unique development as the HVPE process has been known for decades, but never successfully commercially developed for high volume manufacturing. This research shows the potential of the first commercial-grade HVPE chamber, an elusive goal for III-V researchers and those wanting to capitalize on the promise of HVPE. Additionally, in the course of this program, Applied Materials built two MOCVD chambers, in addition to the HVPE chamber, and a robot that moves wafers between them. The MOCVD chambers demonstrated industry-leading wavelength yield for GaN based LED wafers and industry-leading uptime enabled in part by a novel in-situ cleaning process developed in this program.

36 MATERIALS SCIENCE↗