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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Genomic and phenotypic characterization of multidrug-resistant Salmonella enterica serovar Reading isolates involved in a turkey-associated foodborne outbreak

Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella -associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading ( S . Reading) linked to 358 human infections in 42 US states and Canada. Since S . Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S . Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S . Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S . Reading human isolates. Of the 41 S . Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S . Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S . Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

Analysis of generic scramjet external nozzle flowfields employing simulant gases

Experimental and computational results are presented for a generic scramjet nozzle/afterbody model. Mixtures of argon and Freon were employed as simulant scramjet exhaust gases because they correctly model the inviscid simulation parameters of actual scramjet combustion products, allowing test and analysis at significantly reduced temperatures. Air was also employed as an exhaust gas to provide experimental and computational comparisons with simulant gas effects. Several computational aerodynamic analysis codes, employing different levels of theoretical modeling, were applied to compute solutions about the scramjet geometry. The solutions are compared with measured surface static and flowfield pitot pressure data taken in a Mach 6 freestream.

Tatum, Kenneth E.↗
NASA NTRS1993

COSMIC monthly progress report

Activities of the Computer Software Management and Information Center (COSMIC) are summarized for the month of August, 1993. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are discussed. Ten articles were prepared for publication in the NASA Tech Brief Journal. These articles (included in this report) describe the following software items: (1) MOM3D - A Method of Moments Code for Electromagnetic Scattering (UNIX Version); (2) EM-Animate - Computer Program for Displaying and Animating the Steady-State Time-Harmonic Electromagnetic Near Field and Surface-Current Solutions; (3) MOM3D - A Method of Moments Code for Electromagnetic Scattering (IBM PC Version); (4) M414 - MIL-STD-414 Variable Sampling Procedures Computer Program; (5) MEDOF - Minimum Euclidean Distance Optimal Filter; (6) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (Macintosh Version); (7) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (IBM PC Version); (8) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (UNIX Version); (9) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (DEC VAX VMS Version); and (10) TFSSRA - Thick Frequency Selective Surface with Rectangular Apertures. Activities in the areas of marketing, customer service, benefits identification, maintenance and support, and dissemination are also described along with a budget summary.

Source record↗
NASA NTRS2003

MOD06 Optical and Microphysical Retrievals

Major efforts over the past six months included: (1) submission of MOD06 Optical and Microphysical Retrieval recompetition proposal, (2) delivery of a MODIS Atmosphere Level-3 update, (3) delivery of the MODIS Atmosphere s new combined Level-2 product, (4) development of an above-cloud precipitable water research algorithm and a multi-layer cloud detection algorithm, (5) continued development of a Fortran 90 version of the retrieval code for use with MAS as well as operational MODIS processing, (6) preliminary analysis of CRYSTAL-FACE field experiment in July 2002, (7) continued analysis of data obtained during the SAFARI 2000 dry season campaign in southern Africa, and the Arctic FIRE-ACE experiment.

King, Michael D.↗
NASA NTRS2003

VLSI design of turbo decoder for integrated communication system on a chip applications

A high-throughput low-power turbo decoder core has been developed for integrated communication system applications such as satellite communications, wireless LAN, digital TV, cable modem, Digital Video Broadcast (DVB), and xDSL systems. The turbo decoder is based on convolutional constituent codes, which outperform all other Forward Error Correction techniques. This turbo decoder core is parameterizable and can be modified easily to fit any size for advanced communication system-on-chip products. The turbo decoder core provides Forward Error Correction of up to 15 Mbits/sec on a 0.13-micron CMOS FPGA prototyping chip at a power of 0.1 watts.

turbo decoder↗
NASA NTRS2009

Wind-US User's Guide, Version 2.0

Wind-US is a computational platform which may be used to numerically solve various sets of equations governing physical phenomena. Currently, the code supports the solution of the Euler and Navier-Stokes equations of fluid mechanics, along with supporting equation sets governing turbulent and chemically reacting flows. Wind-US is a product of the NPARC Alliance, a partnership between the NASA Glenn Research Center (GRC) and the Arnold Engineering Development Center (AEDC) dedicated to the establishment of a national, applications-oriented flow simulation capability. The Boeing Company has also been closely associated with the Alliance since its inception, and represents the interests of the NPARC User's Association. The "Wind-US User's Guide" describes the operation and use of Wind-US, including: a basic tutorial; the physical and numerical models that are used; the boundary conditions; monitoring convergence; the files that are read and/or written; parallel execution; and a complete list of input keywords and test options.

Towne, Charles E.↗
NASA NTRS2012

Low-Cost Telemetry System for Small/Micro Satellites

A Software Defined Radio (SDR) concept uses a minimum amount of analog/radio frequency components to up/downconvert the RF signal to/from a digital format. Once in the digital domain, all other processing (filtering, modulation, demodulation, etc.) is done in software. The project will leverage existing designs and enhance capabilities in the commercial sector to provide a path to a radiation-hardened SDR transponder. The SDR transponder would incorporate baseline technologies dealing with improved Forward Error Correcting (FEC) codes to be deployed to all Near Earth Network (NEN) ground stations. By incorporating this FEC, at least a tenfold increase in data throughput can be achieved. A family of transponder products can be implemented using common platform architecture, allowing new products to be more quickly introduced into the market. Software can be reused across products, reducing software/hardware costs dramatically. New features and capabilities, such as encoding and decoding algorithms, filters, and bit synchronizers, can be added to the existing infrastructure without requiring major new capital expenditures, allowing implementation of advanced features in the communication systems. As new telecommunication technologies emerge, incorporating them into the SDR fabric will be easily accomplished with little or no requirements for new hardware. There are no preferred flight platforms for the SDR technology, so it can be used on any type of orbital or sub-orbital platform, all within a fully radiation hardened design.

Sims, William↗
NASA NTRS2016

Wind-US Users Guide Version 4.0

Wind-US is a computational platform which may be used to numerically solve various sets of equations governing physical phenomena. Currently, the code supports the solution of the Euler and Navier-Stokes equations of fluid mechanics, along with supporting equation sets governing turbulent and chemically reacting flows. Wind-US is a product of the NPARC Alliance, a partnership between the NASA Glenn Research Center (GRC) and the Arnold Engineering Development Complex (AEDC) dedicated to the establishment of a national, applications-oriented flow simulation capability. The Boeing Company has also been closely associated with the Alliance since its inception, and represents the interests of the NPARC User's Association. The "Wind-US User's Guide" describes the operation and use of Wind-US, including: a basic tutorial; the physical and numerical models that are used; the boundary conditions; monitoring convergence; the files that are read and/or written; parallel execution; and a complete list of input keywords and test options. For current information about Wind-US and the NPARC Alliance, please see the Wind-US home page at http://www.grc.nasa.gov/WWW/winddocs/ and the NPARC Alliance home page at http://www.grc.nasa.gov/WWW/wind/.

fluid dynamics↗
NASA NTRS2010

Kepler Mission's Focal Plane Characterization Models Implementation

The Kepler Mission photometer is an unusually complex array of CCDs. A large number of time-varying instrumental and systemic effects must be modeled and removed from the Kepler pixel data to produce light curves of sufficiently high quality for the mission to be successful in its planet-finding objective. After the launch of the spacecraft, many of these effects are difficult to remeasure frequently, and various interpolations over a small number of sample measurements must be used to determine the correct value of a given effect at different points in time. A library of software modules, called Focal Plane Characterization (FC) Models, is the element of the Kepler Science Data Pipeline (hereafter "pipeline") that handles this. FC, or products generated by FC, are used by nearly every element of the SOC processing chain. FC includes Java components: database persistence classes, operations classes, model classes, and data importers; and MATLAB code: model classes, interpolation methods, and wrapper functions. These classes, their interactions, and the database tables they represent, are discussed. This paper describes how these data and the FC software work together to provide the pipeline with the correct values to remove non-photometric effects caused by the photometer and its electronics from the Kepler light curves. The interpolation mathematics is reviewed, as well as the special case of the sky-to-pixel,pixel-to-sky coordinate transformation code, which incorporates a compound model that is unique in the SOC software.

mission↗
DOE OSTI2025

Practical Implementation of GPU-based Computing at the Grid Edge for Resilience Scenarios

This paper presents a practical implementation of GPU-accelerated computing at the grid edge to enhance power system resilience through next-generation smart meters. Advanced Metering Infrastructure (AMI) systems rely predominantly on centralized processing architectures, which limit real-time response capabilities during grid disturbances. This work proposes the integration of GPU-enabled computational platforms directly within smart meter to enable local execution support for power system analytics, fault detection algorithms, and optimization routines. The proposed framework uses the Julia programming language to leverage highperformance parallel computing capabilities while maintaining code portability and development efficiency. We use two experimental scenarios to benchmark the computational feasibility of this approach: sparse linear system solutions representative of power flow analyses, and multi-stage production cost simulations incorporating unit commitment and economic dispatch operations. Results demonstrate that computationally intensive power system algorithms, such as those supporting resilience scenario calculations, can be effectively executed at the distribution edge using commercially available embedded GPU hardware. Keywords—GPU acceleration, edge computing, smart meters, grid resilience, AMI, resilience.

De Souza, Reubun [School of Electrical Engineering↗
DOE OSTI2024

Building Science Advisor (BSA): A Tool to Assist in the Design and Education of Durable Envelopes

The moisture durability of a building envelope component can be difficult to predict. It depends on the materials used, the location in the assembly, the macro- and microclimate of the building, the air tightness of the interior environment and construction quality. Modern building codes require more insulation and tighter construction but provide little guidance about how to ensure these energy-efficient assemblies are designed and built to retain moisture durability. Furthermore, as new products are introduced to the market, builders are increasingly uncertain about the long-term durability of their building envelope designs. As building envelopes get tighter and better insulated, moisture management is key to a durable and high-performing wall assembly.

Desjarlais, Andre↗
DOE OSTI2023

Advanced Fuel Cycle Cost Basis Report: Supporting Documents 2 Production Based Costing

The purpose of this section is to outline a method of cost analysis whereby a significantly better representation of “should achieve” costs may be attained for NOAK systems. Based on economists’ notions of producer theory, and grounded in the cost analysts’ and project managers’ tool called the Work Breakdown Structure (WBS), this section describes best practices in cost estimation. It then illustrates how the Code of Accounts (COA) structure, developed by the Economic Modeling Working Group (EMWG) of the Generation IV International Forum in “Cost Estimating Guidelines for Generation IV Nuclear Energy Systems [EMWG 2007] (hereafter “Gen IV Guidelines Document”), can be used to differentiate “should achieve” versus “did experience” costs.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

3-D Geologic Controls of Hydrothermal Fluid Flow at Brady Geothermal Field, Nevada using PCA

In many hydrothermal systems, fracture permeability along faults provides pathways for groundwater to transport heat from depth. Faulting generates a range of deformation styles that cross-cut heterogeneous geology, resulting in complex patterns of permeability, porosity, and hydraulic conductivity. Vertical connectivity (a through going network of permeable areas that allows advection of heat from depth to the shallow subsurface) is rare and is confined to relatively small volumes that have highly variable spatial distribution. This local compartmentalization of connectivity represents a significant challenge to understanding hydrothermal circulation and for exploring, developing, and managing hydrothermal resources. Here, we present an evaluation of the geologic characteristics that control this compartmentalization in hydrothermal systems through 3-D analysis of the Brady geothermal field in western Nevada. A published 3-D geologic map of the Brady area is used as a basis to develop structural and geological variables that are hypothesized to control or effect permeability or connectivity. The 3-D distribution of these variables is compared to the distribution of productive and non-productive fluid flow intervals along production wells and non-productive wells via principal component analysis (PCA). This comparison elucidates which geologic and structural variables are most closely associated with productive fluid flow intervals. Results indicate that production intervals at Brady are located: (1) within or near to known and stress-loaded macro-scale faults, and (2) in areas of high fault and fracture density. This submission includes the published journal article detailing this work, the published 3-D geologic map of the Brady Geothermal Area used as a basis to develop structural and geological variables that are hypothesized to control or effect permeability or connectivity, 3-D well data, along which geologic data were sampled for PCA analyses, and associated metadata file. This work was done using existing R programs.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems

Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O -phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O -phosphoserine (Sep) onto tRNA Cys . Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNA Cys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m 1 G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O -phosphoseryl-tRNA Sec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cross sections and calculated yields of some radionuclides of yttrium, strontium and rubidium formed in proton-induced reactions on enriched strontium-86: possibility of production of 85g Sr, 83 Rb and 82m Rb in no-carrier-added form

Here, cross sections of the 86 Sr(p,3n) 84m Y, 86 Sr(p,αn) 82m Rb, and 86 Sr(p,x) 85g Sr reactions were measured from their respective thresholds up to 16.2 MeV and from 23.0 to 44.1 MeV at FZJ, and from 14.3 to 24.5 MeV at LBNL, using 96.4% enriched 86 SrCO 3 as target material. Thin targets prepared by sedimentation were irradiated with protons in a stacked-form, and the induced radioactivity was measured by high-resolution γ-ray spectrometry. Nuclear model calculations based on the code TALYS reproduced our experimental cross section data well. From the excitation functions, the integral yields of the above three radionuclides were calculated. The yield of 85g Sr via the natSr(n,γ) process was also measured using the TRIGA Mark-II reactor at AERE, Savar. A comparison of the reactor and cyclotron production of carrier-added 85g Sr is given. The production possibilities of the three investigated radionuclides in no-carrier-added forms at a 30 MeV cyclotron via new routes are discussed.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Investigation of Frozen Chemistry for Molten Salt Reactors (MSRs)

Understanding accident progression and the potential/conditions for fission product release from fuel is necessary to evaluate safety for any nuclear reactor system. Molten Salt Reactors (MSRs) under development need such analysis to support safety evaluations. Fission product chemistry specific to MSR concepts is a critical area that introduces distinct considerations relative to the current state-of-knowledge in reactor safety, primarily developed for water-moderated nuclear reactor systems. In Light Water Reactor (LWR) systems, it is necessary to capture the chemical interaction of fission products with the reactor evironment, containment and confinement systems. The overall effects at this point are relatively well understood for the purposes of performing safety evaluations. A key insight from LWR studies is that fission product chemical behavior can be reasonably captured by modeling approaches where the chemistry is "frozen". These modeling approaches assume that radionuclide reaction and speciation can be represented by chemical classes, each with characteristic transport behavior that is invariant under a broad range of thermochemical conditions. However, radionuclides can exhibit a range of behavior in the liquid salt-melt phase of the coolant used in MSRs. Radionuclides, salt, and the metal containment surfaces (i.e. pipes) can co-exist in dynamic equilibrium that could evolve with small system mass changes. A detailed investigation to the degree the equilibrium state can dynamically evolve with changes in the conditions of the molten salt mixture has not been previously conducted. It is currently not well understood where frozen chemistry assumptions are valid. Expanding the state-of-knowledge in this regard is relevant to better assessing the range of chemical effects that should be incorporated as part of MSR safety assessments. This investigation used the Oak Ridge Isotope GENeration (ORIGEN) module of the Standardized Computer-Analysis for Licensing Evaluation (SCALE) code to generate simulated radionuclide inventories for the MSR Experiment (MSRE) and then modeled reactor chemical speciation using the Molten Salt Thermodynamic Database – Thermochemical (MSTDB-TC) coupled with Thermochimica. The effect of composition variation during decay of fission product inventory in a molten salt over a period of 500 days prolonged post- at multiple temperatures was studied. Mass fractions for fluorine and berilium were varied in order to probe the effects of free fluorine control. Finally, speciation of fluoride reactors were showed by comparing MSRE readionuclide inventories with a FLiBe based molten salt breeder reactor (MSBR). The results showed that fission product mass change has little effect on phase mass changes and vapor pressures for fluoride species, but differ with varying carrier and fuel salt compositions. However, iodine species were found to have a vapor pressure not only dependent on temperature, but also the free fluorine potential, releasing iodine when the free fluorine potential is equal to the iodine inventory. This observation, however, arose under free fluorine potentials that are very unlikely to be realized in typical molten salt mixtures. Despite this observation, temperature was found to be the dominant parameter that drove phase change and fission product species vapor pressure. The results indicate that the current frozen chemistry approach is adequate for MSR analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Numerical evaluation of AGR-2 fission product release

The AGR-2 experiment produced normal operation and accident condition fuel performance data for tri-structural isotropic (TRISO) particles with UCO and UO 2 kernels. Data for compacts with no failed particles and for compacts with one or more failed particles are available. To model the fission product diffusion and release from these compacts, it is important to consider the computational mesh as well as the heat conduction and mass diffusion properties of the materials in a TRISO particle. Code and solution verification studies with the Bison fuel performance code were performed to show that the code is computing correct solutions. Bison comparisons to post-irradiation examination data and PARFUME predictions were made for several sets of compacts. Furthermore, these comparisons considered silver, cesium, strontium, and krypton with and without failed particles. Bison predictions closely match those of PARFUME, while both codes generally overpredict post-irradiation examination data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

An MLIR-based Compiler Flow for System-Level Design and Hardware Acceleration

The generation of custom hardware accelerators for applications implemented within high-level productive programming frameworks requires considerable manual effort. To automate this process, we introduce \sodaopt, a compiler tool that extends the MLIR infrastructure. \sodaopt automatically searches, outlines, tiles, and pre-optimizes relevant code regions to generate high-quality accelerators through high-level synthesis. \sodaopt can support any high-level programming framework and domain-specific language that interface with the MLIR infrastructure. By leveraging MLIR, \sodaopt solves compiler optimization problems with specialized abstractions. Backend synthesis tools connect to \sodaopt through progressive intermediate representation lowerings. \sodaopt interfaces to a design space exploration engine to identify the combination of compiler optimization passes and options that provides high-performance generated designs for different backends and targets. We demonstrate the practical applicability of the compilation flow by exploring the automatic generation of accelerators for deep neural networks operators outlined at arbitrary granularity and by combining outlining with tiling on large convolution layers. Experimental results with kernels from the PolyBench benchmark show that \sodaopt high-level optimizations improve execution delays of synthesized accelerators up to 60x. We also show that for the selected kernels, our solution outperforms the current of state-of-the art in more than 70% of the benchmarks and provides better average speedup in 55% of them.

Bohm Agostini, Nicolas↗