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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses

Pneumonic tularemia is a highly debilitating and potentially fatal disease caused by inhalation of Francisella tularensis. Most of our current understanding of its pathogenesis is based on the highly virulent F. tularensis subsp. tularensis strain SCHU S4. However, multiple sources of SCHU S4 have been maintained and propagated independently over the years, potentially generating genetic variants with altered virulence. In this study, the virulence of four SCHU S4 stocks (NR-10492, NR-28534, NR-643 from BEI Resources and FTS-635 from Battelle Memorial Institute) along with another virulent subsp. tularensis strain, MA00-2987, were assessed in parallel. In the Fischer 344 rat model of pneumonic tularemia, NR-643 and FTS-635 were found to be highly attenuated compared to NR-10492, NR-28534, and MA00-2987. In the NZW rabbit model of pneumonic tularemia, NR-643 caused morbidity but not mortality even at a dose equivalent to 500x the LD 50 for NR-10492. Genetic analyses revealed that NR-10492 and NR-28534 were identical to each other, and nearly identical to the reference SCHU S4 sequence. NR-643 and FTS-635 were identical to each other but were found to have nine regions of difference in the genomic sequence when compared to the published reference SCHU S4 sequence. Given the genetic differences and decreased virulence, NR-643/FTS-635 should be clearly designated as a separate SCHU S4 substrain and no longer utilized in efficacy studies to evaluate potential vaccines and therapeutics against tularemia. View Full-Text

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum , Clostridium sporogenes , and Clostridium argentinense

At least 40 toxin subtypes of botulinum neurotoxins (BoNTs), a heterogenous group of bacterial proteins, are produced by seven different clostridial species. A key factor that drives the diversity of neurotoxigenic clostridia is the association of bont gene clusters with various genomic locations including plasmids, phages and the chromosome. Analysis of Clostridium sporogenes BoNT/B1 strain CDC 1632, C. argentinense BoNT/G strain CDC 2741, and Clostridium parabotulinum BoNT/B1 strain DFPST0006 genomes revealed bont gene clusters within plasmid-like sequences within the chromosome or nested in large contigs, with no evidence of extrachromosomal elements. A nucleotide sequence (255,474 bp) identified in CDC 1632 shared 99.5% identity (88% coverage) with bont/B1-containing plasmid pNPD7 of C. sporogenes CDC 67071; CDC 2741 contig AYSO01000020 (1.1 MB) contained a ~140 kb region which shared 99.99% identity (100% coverage) with plasmid pRSJ17_1 of C. argentinense BoNT/G strain 89G; and DFPST0006 contig JACBDK0100002 (573 kb) contained a region that shared 100% identity (99%) coverage with the bont/B1-containing plasmid pCLD of C. parabotulinum Okra. This is the first report of full-length plasmid DNA-carrying complete neurotoxin gene clusters integrated in three distinct neurotoxigenic species: C. parabotulinum, C. sporogenes and C. argentinense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Description of Pegethrix niliensis sp. nov., a Novel Cyanobacterium from the Nile River Basin, Egypt: A Polyphasic Analysis and Comparative Study of Related Genera in the Oculatellales Order

In this paper, we examine the filamentous cyanobacterial strain NILCB16 and describe it as a new species within the genus Pegethrix. The original population was sampled from a mat growing in an irrigation canal in the Nile River, Egypt. Initially classified under Plectonema or Planktolyngbya, the strain is a potential producer of the toxins microcystin and β-N-Methylamino-L-Alanine (BMAA). Additionally, we reviewed the taxonomic relationships between the Oculatellales genera. To describe the new species, we conducted a polyphasic study, encompassing 16S rRNA gene phylogenetic analyses performed using both Maximum Likelihood and Bayesian methods, sequence identity (p-distance) analysis, 16S-23S ITS secondary structures, and morphological and habitat comparisons. The phylogenetic analysis revealed that strain NILCB16 clustered within the Pegethrix clade with strong phylogenetic support, but in a distinct position from other species in the genus. The strain shared a maximum 16S rRNA gene identity of 97.3% with P. qiandaoensis and 96.1% with the type species, P. bostrychoides. Morphologically, NILCB16 can be differentiated from other species in the genus by its lack of false branching. Our phylogenetic analyses also show that Pegethrix, Cartusia, Elainella, and Maricoleus are clustered with strong phylogenetic support. They exhibit high 16S rRNA gene identity and are morphologically indistinguishable, suggesting they could potentially be merged into a single genus in the future.

Hentschke, Guilherme Scotta (ORCID:000000034396024↗
DOE OSTI2023

Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150–200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Pitting Propagation Behavior on Low Alloy AISI 4130 (UNS G41300) Steel Exposed to Various Alkali and Alkaline Earth Metal Chlorides

Pit propagation studies were conducted to elucidate whether alkali and alkali earth metal cations such as Na+ and Rb+ present in the form of metal chloride salts such as RbCl affect pitting behavior in distinctly different manner than NaCl. Pit propagation studies were conducted on a low alloy steel using one-dimensional (1-D) pit method over pit depths from 300-1000 µm. LSV and EIS of planar electrodes of 4130 in a range of Cl- solutions were conducted and revealed no detected differences in impedance, open circuit, corrosion potential (Ecorr), passive current density (ipass), and pitting potential (Epit) as a function of salt type. In the case of one-dimensional pits during fast downward scan rates, the saturation potential (Esat) varied as a function of cation identity when pit depths were shallow. Mass transported limited current density also differed with cations in shallow pits when various alkali metal and alkaline metal cations were present. The limiting current density was increased for RbCl relative to NaCl The pit surface potential (Esurf) of activated pit surfaces reached Ecorr prior to establishing a condition where the pit electrolyte surface concentration (Csurf) was less than the critical concentration for active acidified pitting (i.e. Csurf<Ccrit) in this marginally passivating steel. For various Esurf and pit current density (ipit) combinations at constant Csurf where Ccrit< Csurf < Csat, E-log(i) plots were constructed using the method of Tianshu to create IR ohmic voltage corrected Tafel plots for various fixed pit solution concentrations. Under these conditions, the influence of cation identity on charge transfer controlled kinetics indicated slight differences in Tafel behavior where RbCl was slightly more aggressive than NaCl for low alloy steel oxidation. Differences in metal cation identity exert no effect on passive or breakdown on planar electrodes and only effect pit propagation stage in shallow pits.

Demarest, Chalres↗
DOE OSTI2023

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bounds on spectral gaps of Hyperbolic spin surfaces

We describe a method for constraining Laplacian and Dirac spectra of two dimensional compact orientable hyperbolic spin manifolds and orbifolds. The key ingredient is an infinite family of identities satisfied by the spectra. These spectral identities follow from the consistency between 1) the spectral decomposition of functions on the spin bundle into irreducible representations of SL(2,R) and 2) associativity of pointwise multiplication of functions. Applying semidefinite programming methods to our identities produces rigorous upper bounds on the Laplacian spectral gap as well as on the Dirac spectral gap conditioned on the former. In several examples, our bounds are nearly sharp; a numerical algorithm based on the Selberg trace formula shows that the [0;3,3,5] orbifold, a particular surface with signature [1;3], and the Bolza surface nearly saturate the bounds at genus 0, 1 and 2 respectively. Under additional assumptions on the number of harmonic spinors carried by the spin-surface, we obtain more restrictive bounds on the Laplacian spectral gap. In particular, these bounds apply to hyperelliptic surfaces. We also determine the set of Laplacian spectral gaps attained by all compact orientable two-dimensional hyperbolic spin orbifolds. We show that this set is upper bounded by 12.13798; this bound is nearly saturated by the [0;3,3,5] orbifold, whose first non-zero Laplacian eigenvalue is λ^(0)_1 ≈ 12.13623.

Spectral theory↗
DOE OSTI2024

Factorized visual representations in the primate visual system and deep neural networks

Object classification has been proposed as a principal objective of the primate ventral visual stream and has been used as an optimization target for deep neural network models (DNNs) of the visual system. However, visual brain areas represent many different types of information, and optimizing for classification of object identity alone does not constrain how other information may be encoded in visual representations. Information about different scene parameters may be discarded altogether (‘invariance’), represented in non-interfering subspaces of population activity (‘factorization’) or encoded in an entangled fashion. In this work, we provide evidence that factorization is a normative principle of biological visual representations. In the monkey ventral visual hierarchy, we found that factorization of object pose and background information from object identity increased in higher-level regions and strongly contributed to improving object identity decoding performance. We then conducted a large-scale analysis of factorization of individual scene parameters – lighting, background, camera viewpoint, and object pose – in a diverse library of DNN models of the visual system. Models which best matched neural, fMRI, and behavioral data from both monkeys and humans across 12 datasets tended to be those which factorized scene parameters most strongly. Notably, invariance to these parameters was not as consistently associated with matches to neural and behavioral data, suggesting that maintaining non-class information in factorized activity subspaces is often preferred to dropping it altogether. Thus, we propose that factorization of visual scene information is a widely used strategy in brains and DNN models thereof.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Control system estimation and design for aerospace vehicles with time delay

The problems of estimation and control of discrete, linear, time-varying systems are considered. Previous solutions to these problems involved either approximate techniques, open-loop control solutions, or results which required excessive computation. The estimation problem is solved by two different methods, both of which yield the identical algorithm for determining the optimal filter. The partitioned results achieve a substantial reduction in computation time and storage requirements over the expanded solution, however. The results reduce to the Kalman filter when no delays are present in the system. The control problem is also solved by two different methods, both of which yield identical algorithms for determining the optimal control gains. The stochastic control is shown to be identical to the deterministic control, thus extending the separation principle to time delay systems. The results obtained reduce to the familiar optimal control solution when no time delays are present in the system.

Allgaier, G. R.↗
NASA NTRS1972

Electromagnetic inverse scattering

A three-dimensional electromagnetic inverse scattering identity, based on the physical optics approximation, is developed for the monostatic scattered far field cross section of perfect conductors. Uniqueness of this inverse identity is proven. This identity requires complete scattering information for all frequencies and aspect angles. A nonsingular integral equation is developed for the arbitrary case of incomplete frequence and/or aspect angle scattering information. A general closed-form solution to this integral equation is developed, which yields the shape of the scatterer from such incomplete information. A specific practical radar solution is presented. The resolution of this solution is developed, yielding short-pulse target resolution radar system parameter equations. The special cases of two- and one-dimensional inverse scattering and the special case of a priori knowledge of scatterer symmetry are treated in some detail. The merits of this solution over the conventional radar imaging technique are discussed.

Bojarski, N. N.↗
NASA NTRS1978

Petrographic and petrological studies of lunar rocks

Clasts, rind glass, matrix glass, and matrix minerals from five Apollo 15 glass-coated breccias (15255, 15286, 15465, 15466, and 15505) were studied optically and with the SEM/microprobe. Rind glass compositions differ from sample to sample, but are identical, or nearly so, to the local soil, suggesting their origin by fusion of that soil. Most breccia samples contain green or colorless glass spheres identical to the Apollo 15 green glasses. These glasses, along with other glass shards and fragments, indicate a large soil component is present in the breccias. Clast populations include basalts and gabbros containing phases highly enriched in iron, indicative of extreme differentiation or fractional crystallization. Impact melts, anorthosites, and minor amounts of ANT suite material are also present among the clasts. Tektite glasses, impact melts, and breccias from the Zhamanshin structure, USSR, were also studied. Basic tektite glasses were found to be identical in composition to impact melts from the structure, but no satisfactory parent material has been identified in the limited suite of samples available.

Winzer, S. R.↗
NASA NTRS1989

Wiring Viterbi decoders (splitting deBruijn graphs)

A new Viterbi decoder, capable of decoding convolutional codes with constraint lengths up to 15, is under development for the Deep Space Network (DSN). A key feature of this decoder is a two-level partitioning of the Viterbi state diagram into identical subgraphs. The larger subgraphs correspond to circuit boards, while the smaller subgraphs correspond to Very Large Scale Integration (VLSI) chips. The full decoder is built from identical boards, which in turn are built from identical chips. The resulting system is modular and hierarchical. The decoder is easy to implement, test, and repair because it uses a single VLSI chip design and a single board design. The partitioning is completely general in the sense that an appropriate number of boards or chips may be wired together to implement a Viterbi decoder of any size greater than or equal to the size of the module.

Collins, O.↗
NASA NTRS1991

Error associated with a reduced order linear model of a spur gear pair

The paper proposes a reduced-order analytical model of a spur gear pair which consists of two identical spur gears, two identical flexible shafts, and four identical rolling element bearings of a given radial stiffness. The error associated with the undamped eigensolution is estimated by a comparison with a benchmark finite element model.

Kahraman, A.↗
NASA NTRS1954

Heat transfer, diffusion, and evaporation

Although it has long been known that the differential equations of the heat-transfer and diffusion processes are identical, application to technical problems has only recently been made. In 1916 it was shown that the speed of oxidation of the carbon in iron ore depends upon the speed with which the oxygen of the combustion air diffuses through the core of gas surrounding the carbon surface. The identity previously referred to was then used to calculate the amount of oxygen diffusing to the carbon surface on the basis of the heat transfer between the gas stream and the carbon surface. Then in 1921, H. Thoma reversed that procedure; he used diffusion experiments to determine heat-transfer coefficients. Recently Lohrisch has extended this work by experiment. A technically very important application of the identity of heat transfer and diffusion is that of the cooling tower, since in this case both processes occur simultaneously.

GASES - DIFFUSION↗
NASA NTRS1993

Tension fracture of laminates for transport fuselage. Part 2: Large notches

Tests were conducted on over 200 center-crack specimens to evaluate: (a) the tension-fracture performance of candidate materials and laminates for commercial fuselage applications; and (b) the accuracy of several failure criteria in predicting response. Crack lengths of up to 12 inches were considered. Other variables included fiber/matrix combination, layup, lamination manufacturing process, and intraply hybridization. Laminates fabricated using the automated tow-placement process provided significantly higher tension-fracture strengths than nominally identical tape laminates. This confirmed earlier findings for other layups, and possibly relates to a reduced stress concentration resulting from a larger scale of repeatable material inhomogeneity in the tow-placed laminates. Changes in material and layup result in a trade-off between small-notch and large-notch strengths. Toughened resins and 0 deg-dominate layups result in higher small-notch strengths but lower large-notch strengths than brittle resins, 90 deg and 45 deg dominated layups, and intraply S2-glass hybrid material forms. Test results indicate that strength-prediction methods that allow for a reduced order singularity of the crack-tip stress field are more successful at predicting failure over a range of notch sizes than those relying on the classical square-root singularity. The order of singularity required to accurately predict large-notch strength from small-notch data was affected by both material and layup. Measured crack-tip strain distributions were generally higher than those predicted using classical methods. Traditional methods of correcting for finite specimen width were found to be lacking, confirming earlier findings with other specimen geometries. Fracture tests of two stiffened panels, identical except for differing materials, with severed central stiffeners resulted in nearly identical damage progression and failure sequences. Strain-softening laws implemented within finite element models appear attractive to account for load redistribution in configured structure due to damage-induced crack tip softening

Walker, Tom H.↗
NASA NTRS1994

Development and initial test of the University of Wisconsin global isentropic-sigma model

The description of a global version of the University of Wisconsin (UW) hybrid isentropic-sigma (theta-sigma) model and the results from an initial numerical weather prediction experiment are presented in this paper. The main objectives of this initial test are to (1) discuss theta-sigma model development and computer requirements, (2) demonstrate the ability of the UW theta-sigma model for global numerical weather prediction using realistic orography and parameterized physical processes, and (3) compare the transport of an inert trace constituent against a nominally 'identical' sigma coordinate model. Initial and verifying data for the 5-day simulations presented in this work were supplied by the Goddard Earth Observing System (GEOS-1) data assimilation system. The time period studied is 1-6 February 1985. This validation experiment demonstrates that the global UW theta-sigma model produces a realistic 5-day simulation of the mass and momentum distributions when compared to both the identical sigma model and GEOS-1 verification. Root-mean-square errors demonstrate that the theta-sigma model is slightly more accurate than the nominally identical sigma model with respect to standard synoptic variables. Of particular importance, the UW theta-sigma model displays a distinct advantage over the conventional sigma model with respect to the prognostic simulation of inert trace constituent transport in amplifying baroclinic waves of the extratropics. This is especially true in the upper troposphere and stratosphere where the spatial integrity and conservation of an inert trace constituent is severely compromised in the sigma model compared to the theta-sigma model.

Zapotocny, Tom H.↗
NASA NTRS1996

Temperature measurement involving nanostructured thermal barrier coating using a multiwavelength pyrometer

It has been reported that erroneous results were obtained when a conventional pyrometer was used to measure the surface temperature of turbine engine components. Temperatures discrepancies were observed in components which were identical, except that one had its measured surface covered by a nanostructured thermal barrier coating (TBC) whereas the other component's surface was not so coated. These components were placed in an identical environment, receiving identical heat fluxes. A pyrometer measured the TBC covered surface hundreds degrees lower. These coatings were about 25 (mu)m thick, consisting of hundreds of layers of finer structures. The TBC's had very low thermal conductivity, heat flux calculations indicated that the temperatures of the coated surface should exhibit much higher temperature than the uncoated surface. Because these coatings were transparent to radiation from the visible to the infrared region, the temperatures measured by the pyrometer should be the temperature of the covered surface. Turbo components' performance and service life depend critically on the temperatures that it would experience; it is therefore important to know accurately and confidently the real surface temperature. Out of these concerns, an investigation into the measurement of nanostructured material surface temperature was carried out.

Ng, Daniel↗
NASA NTRS1996

Effective Numerical Methods for Solving Elliptical Problems in Strengthened Sobolev Spaces

Fourth-order elliptic boundary value problems in the plane can be reduced to operator equations in Hilbert spaces G that are certain subspaces of the Sobolev space W(sub 2)(exp 2)(Omega) is identical with G(sup (2)). Appearance of asymptotically optimal algorithms for Stokes type problems made it natural to focus on an approach that considers rot w is identical with (D(sub 2)w - D(sub 1)w) is identical with vector of u as a new unknown vector-function, which automatically satisfies the condition div vector of u = 0. In this work, we show that this approach can also be developed for an important class of problems from the theory of plates and shells with stiffeners. The main mathematical problem was to show that the well-known inf-sup condition (normal solvability of the divergence operator) holds for special Hilbert spaces. This result is also essential for certain hydrodynamics problems.

D'yakonov, Eugene G.↗