Extending the cereus group genomics to putative food-borne pathogens of different toxicity (open access)

Extending the cereus group genomics to putative food-borne pathogens of different toxicity

The cereus group represents sporulating soil bacteriacontaining pathogenic strains which may cause diarrheic or emetic foodpoisoning outbreaks. Multiple locus sequence typing revealed a presencein natural samples of these bacteria of about thirty clonal complexes.Application of genomic methods to this group was however biased due tothe major interest for representatives closely related to B. anthracis.Albeit the most important food-borne pathogens were not yet defined,existing dataindicate that they are scattered all over the phylogenetictree. The preliminary analysis of the sequences of three genomesdiscussed in this paper narrows down the gaps in our knowledge of thecereus group. The strain NVH391-98 is a rare but particularly severefood-borne pathogen. Sequencing revealed that the strain must be arepresentative of a novel bacterial species, for which the name Bacilluscytotoxis is proposed. This strain has a reduced genome size compared toother cereus group strains. Genome analysis revealed absence of sigma Bfactor and the presence of genes encoding diarrheic Nhe toxin, notdetected earlier. The strain B. cereus F837/76 represents a clonalcomplex close to that of B. anthracis. Including F837/76, three such B.cereus strains had been sequenced. Alignment of genomes suggests that B.anthracis is their common ancestor. Since such strains often emerge fromclinical cases, they merit a special attention. The …
Date: August 24, 2006
Creator: Lapidus, Alla; Goltsman, Eugene; Auger, Sandrine; Galleron, Nathalie; Segurens, Beatrice; Dossat, Carole et al.
Object Type: Article
System: The UNT Digital Library
System-level modeling for geological storage of CO2 (open access)

System-level modeling for geological storage of CO2

One way to reduce the effects of anthropogenic greenhousegases on climate is to inject carbon dioxide (CO2) from industrialsources into deep geological formations such as brine formations ordepleted oil or gas reservoirs. Research has and is being conducted toimprove understanding of factors affecting particular aspects ofgeological CO2 storage, such as performance, capacity, and health, safetyand environmental (HSE) issues, as well as to lower the cost of CO2capture and related processes. However, there has been less emphasis todate on system-level analyses of geological CO2 storage that considergeological, economic, and environmental issues by linking detailedrepresentations of engineering components and associated economic models.The objective of this study is to develop a system-level model forgeological CO2 storage, including CO2 capture and separation,compression, pipeline transportation to the storage site, and CO2injection. Within our system model we are incorporating detailedreservoir simulations of CO2 injection and potential leakage withassociated HSE effects. The platform of the system-level modelingisGoldSim [GoldSim, 2006]. The application of the system model is focusedon evaluating the feasibility of carbon sequestration with enhanced gasrecovery (CSEGR) in the Rio Vista region of California. The reservoirsimulations are performed using a special module of the TOUGH2 simulator,EOS7C, for multicomponent gas mixtures of methane and CO2 or methane andnitrogen. …
Date: April 24, 2006
Creator: Zhang, Yingqi; Oldenburg, Curtis M.; Finsterle, Stefan & Bodvarsson, Gudmundur S.
Object Type: Article
System: The UNT Digital Library
Quantifying the Diffusion of a Fluid through Membranes by RemoteDetection MRI (open access)

Quantifying the Diffusion of a Fluid through Membranes by RemoteDetection MRI

We present a method to measure self-diffusion acrossmembranes without the need for concentration or pressure gradients.Hyperpolarized xenon in combination with remote detection of NMR allowsthe measurement of membrane permeation, even in the gas phase. Theresulting images allow quantification of the amount of fluid diffusedthrough the membrane, and represent an alternative, potentially moreprecise way of measuring a membrane diffusion coefficient. The use ofremote detection of NMR allows for non-invasive signal encoding coupledto sensitive detection, making this approach ideal for the study ofdiffusion in intact devices such as fuel cells or separationsystems.
Date: October 24, 2006
Creator: Telkki, Ville-Veikko; Hilty, Christian; Garcia, Sandra; Harel,Elad & Pines, Alexander
Object Type: Article
System: The UNT Digital Library
Remaining Sites Verification Package for the 100-F-31, 144-F Sanitary Sewer System, Waste Site Reclassification Form 2006-033 (open access)

Remaining Sites Verification Package for the 100-F-31, 144-F Sanitary Sewer System, Waste Site Reclassification Form 2006-033

The 100-F-31 waste site is a former septic system that supported the inhalation laboratories, also referred to as the 144-F Particle Exposure Laboratory (132-F-2 waste site), which housed animals exposed to particulate material. The 100-F-31 waste site has been remediated to achieve the remedial action objectives specified in the Remaining Sites ROD. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.
Date: August 24, 2006
Creator: Dittmer, L. M.
Object Type: Report
System: The UNT Digital Library
Sonoma Persistent Surveillance System (open access)

Sonoma Persistent Surveillance System

Sonoma offers the first cost-effective, broad-area, high-resolution, real-time motion imagery system for surveillance applications. Sonoma is unique in its ability to provide continuous, real-time video imagery of an area the size of a small city with resolutions sufficient to track 8,000 moving objects in the field of view. At higher resolutions and over smaller areas, Sonoma can even track the movement of individual people. The visual impact of the data available from Sonoma is already causing a paradigm shift in the architecture and operation of other surveillance systems. Sonoma is expected to cost just one-tenth the price of comparably sized sensor systems. Cameras mounted on an airborne platform constantly monitor an area, feeding data to the ground for real-time analysis. Sonoma was designed to provide real-time data for actionable intelligence in situations such as monitoring traffic, special events, border security, and harbors. If a Sonoma system had been available in the aftermath of the Katrina and Rita hurricanes, emergency responders would have had real-time information on roads, water levels, and traffic conditions, perhaps saving many lives.
Date: March 24, 2006
Creator: Pennington, D M
Object Type: Report
System: The UNT Digital Library
Observation of amplification of a 1ps pulse by SRS of a 1 ns pulse in a plasma with conditions relevant to pulse compression (open access)

Observation of amplification of a 1ps pulse by SRS of a 1 ns pulse in a plasma with conditions relevant to pulse compression

The compression of a laser pulse by amplification of an ultra short pulse beam Which seeds the stimulated Raman scatter of the first beam has been long been discussed in the context of solid and gas media. We investigate the possibility of using intersecting beams in a plasma to compress nanosecond pulses to picosecond duration by scattering from driven electron waves. Recent theoretical studies have shown the possibility of efficient compression With large amplitude, non-linear Langmuir waves driven either by SRS or non-resonantly. We describe experiments in which a plasma suitable for pulse compression is created , and amplification of an ultra short pulse beam is demonstrated.
Date: May 24, 2006
Creator: Kirkwood, R K; Dewald, E; Wilks, S C; Meezan, N; Niemann, C; Berger, R L et al.
Object Type: Article
System: The UNT Digital Library
Remaining Sites Verification Package for the 141-C Large Animal Barn and Biology Laboratory (Hog Barn), Waste Site Reclassification Form 2006-027 (open access)

Remaining Sites Verification Package for the 141-C Large Animal Barn and Biology Laboratory (Hog Barn), Waste Site Reclassification Form 2006-027

The 141-C waste site is a former large animal barn and biology laboratory within the 100-F Area experimental animal farm. Strontium-90, arsenic, and multiple polycyclic aromatic hydrocarbons were detected within residual demolition debris at concentrations exceeding cleanup criteria. The site has been remediated by removing approximately 900 bank cubic meters of soil and debris within the former building footprint to the Environmental Restoration Disposal Facility. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed that residual contaminant concentrations are protective of groundwater and the Columbia River.
Date: May 24, 2006
Creator: Carlson, R. A.
Object Type: Report
System: The UNT Digital Library
Incompressible Navier-Stokes with particles algorithm designdocument (open access)

Incompressible Navier-Stokes with particles algorithm designdocument

None
Date: July 24, 2006
Creator: Martin, Daniel & Colella, Phillip
Object Type: Report
System: The UNT Digital Library
Phase Transitions Involving Dissociated States of Water at the Electrochemical Ni(111)/H2O Interface (open access)

Phase Transitions Involving Dissociated States of Water at the Electrochemical Ni(111)/H2O Interface

None
Date: April 24, 2006
Creator: Taylor, C; Kelly, R & Neurock, M
Object Type: Report
System: The UNT Digital Library
Elliptically Polarized Modes in RF Cavities (open access)

Elliptically Polarized Modes in RF Cavities

None
Date: May 24, 2006
Creator: Stupakov, G. & Bane, K.
Object Type: Report
System: The UNT Digital Library
Orientation relationship, plasticity, twin relationship, and interfacial structure of the ???' isothermal martensitic transformation in Pu-Ga alloys (open access)

Orientation relationship, plasticity, twin relationship, and interfacial structure of the ???' isothermal martensitic transformation in Pu-Ga alloys

The orientation relationship, habit plane, parent-product interface at the atomic level, twin relationship, and plastic deformation resulting from the {delta} {yields} {alpha}{prime} isothermal martensitic transformation in Pu-Ga alloys are examined using optical microscopy, transmission electron microscopy, and finite element calculations. The {delta} {yields} {alpha}{prime} transformation exhibits a {approx}20% volume collapse when the face-centered cubic {delta} phase transforms to the monoclinic {alpha}{prime} phase, which results in unique and intriguing crystallography and morphology. Here, we show that the orientation relationship is very close to that previously reported by Zocco et al. (1990), but has small rotational misalignments between the two phases both parallel and perpendicular to the [110]{sub {delta}} {parallel}[100]{sub {alpha}{prime}} direction. The amount of plastic deformation is exceedingly large due to the {approx}20% volume collapse and transmission electron microscopy is used to quantify the difference in dislocation density between untransformed {delta}-matrix and regions of {delta} adjacent to the transformed {alpha}{prime}. The twins contained in {alpha}{prime} plates are shown to have a (205){sub {alpha}} orientation as the lattice invariant deformation and are found to be composed of two alternating variants that share a common <020>{sub {alpha}{prime}} direction, but differ by a 60 degree rotation about <020>{sub {alpha}{prime}}. A combination of electron diffraction …
Date: January 24, 2006
Creator: Moore, K; Krenn, C; Wall, M & Schwartz, A
Object Type: Article
System: The UNT Digital Library
Search for B+ ->phi pi+ and B0->phi pi0 Decays (open access)

Search for B+ ->phi pi+ and B0->phi pi0 Decays

A search has been made for the decays B{sup +} {yields} {psi}{pi}{sup +} and B{sup 0} in a data sample of approximately 232 x 10{sup 6} B{bar B} pairs recorded at the {Upsilon}(4S) resonance with the BABAR detector at the PEP-II B-meson Factory at SLAC. No significant signals have been observed, and therefore upper limits have been set on the branching fractions: {Beta}(B{sup +} {yields} {psi}{pi}{sup +}) < 2.4 x 10{sup -7} and {Beta}(B{sup 0} {yields} {psi}{pi}{sup 0}) < 2.8 x 10{sup -7} at 90% probability.
Date: May 24, 2006
Creator: Aubert, B.; Barate, R.; Bona, M.; Boutigny, D.; Couderc, F.; Karyotakis, Y. et al.
Object Type: Report
System: The UNT Digital Library
Elevated Uptake of Th and U by Netted Chain Fern (Woodwardia areloata) (open access)

Elevated Uptake of Th and U by Netted Chain Fern (Woodwardia areloata)

None
Date: March 24, 2006
Creator: KNOX, ANNA
Object Type: Article
System: The UNT Digital Library
Search for the Decay of Neutral B Mesons to a Neutral K Star Meson and a Neutral K Meson Using the BaBar Detector (open access)

Search for the Decay of Neutral B Mesons to a Neutral K Star Meson and a Neutral K Meson Using the BaBar Detector

None
Date: May 24, 2006
Creator: Foulkes, Stephen David & /SLAC /UC, Riverside
Object Type: Report
System: The UNT Digital Library
High-Throughput Plasmid cDNA Library Screening (open access)

High-Throughput Plasmid cDNA Library Screening

Libraries of cDNA clones are valuable resources foranalysing the expression, structure, and regulation of genes, as well asfor studying protein functions and interactions. Full-length cDNA clonesprovide information about intron and exon structures, splice junctionsand 5'- and 3'-untranslated regions (UTRs). Open reading frames (ORFs)derived from cDNA clones can be used to generate constructs allowingexpression of native proteins and N- or C-terminally tagged proteins.Thus, obtaining full-length cDNA clones and sequences for most or allgenes in an organism is critical for understanding genome functions.Expressed sequence tag (EST) sequencing samples cDNA libraries at random,which is most useful at the beginning of large-scale screening projects.However, as projects progress towards completion, the probability ofidentifying unique cDNAs via EST sequencing diminishes, resulting in poorrecovery of rare transcripts. We describe an adapted, high-throughputprotocol intended for recovery of specific, full-length clones fromplasmid cDNA libraries in five days.
Date: May 24, 2006
Creator: Wan, Kenneth H.; Yu, Charles; George, Reed A.; Carlson, JosephW.; Hoskins, Roger A.; Svirskas, Robert et al.
Object Type: Article
System: The UNT Digital Library
Remaining Sites Verification Package for the 118-C-3:3, 105-C French Drains, Waste Site Reclassification Form 2006-016 (open access)

Remaining Sites Verification Package for the 118-C-3:3, 105-C French Drains, Waste Site Reclassification Form 2006-016

The 118-C-3:3 french drains received condensate from the steam heating system in the 105-C Reactor Building. The 118-C-3:3 french drain meets the remedial action objectives specified in the Remaining Sites ROD. The results demonstrate that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.
Date: April 24, 2006
Creator: Carlson, R. A.
Object Type: Report
System: The UNT Digital Library
Remaining Sites Verification Package for the 100-B-1 Surface Chemical and Solid Waste Dumping Area, Waste Site Reclassification Form 2006-003 (open access)

Remaining Sites Verification Package for the 100-B-1 Surface Chemical and Solid Waste Dumping Area, Waste Site Reclassification Form 2006-003

The 100-B-1 waste site was a dumping site that was divided into two areas. One area was used as a laydown area for construction materials, and the other area was used as a chemical dumping area. The 100-B-1 Surface Chemical and Solid Waste Dumping Area site meets the remedial action objectives specified in the Remaining Sites ROD. The results demonstrate that residual contaminant concentrations support future unrestricted land uses that can be represented by a rural-residential scenario. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.
Date: April 24, 2006
Creator: Carlson, R. A.
Object Type: Report
System: The UNT Digital Library
Dsdp5 User Guide - Software for Semidefinite Programming. (open access)

Dsdp5 User Guide - Software for Semidefinite Programming.

DSDP implements the dual-scaling algorithm for semidefinite programming. The source code of this interior-point solver, written entirely in ANSI C, is freely available. The solver can be used as a subroutine library, as a function within the Matlab environment, or as an executable that reads and writes to files. Initiated in 1997, DSDP has developed into an efficient and robust general-purpose solver for semidefinite programming. Although the solver is written with semidefinite programming in mind, it can also be used for linear programming and other constraint cones. The features of DSDP include the following: a robust algorithm with a convergence proof and polynomially bounded complexity under mild assumptions on the data, primal and dual solutions, feasible solutions when they exist or approximate certificates of infeasibility, initial points that can be feasible or infeasible, relatively low memory requirements for an interior-point method, sparse and low-rank data structures, extensibility that allows applications to customize the solver and improve its performance, a subroutine library that enables it to be linked to larger applications, scalable performance for large problems on parallel architectures, and a well-documented interface and examples of its use. The package has been used in many applications and tested for efficiency, robustness, …
Date: January 24, 2006
Creator: Benson, S. J.; Ye, Y. & Science, Mathematics and Computer
Object Type: Report
System: The UNT Digital Library
Conceptual Design of an Antiproton Generation and Storage Facility (open access)

Conceptual Design of an Antiproton Generation and Storage Facility

The Antiproton Generation and Storage Facility (AGSF) creates copious quantities of antiprotons, for bottling and transportation to remote cancer therapy centers. The #12;first step in the generation and storage process is to accelerate an intense proton beam down the Main Linac for injection into the Main Ring, which is a Rapid Cycling Synchrotron that accelerates the protons to high energy. The beam is then extracted from the ring into a transfer line and into a Proton Target. Immediately downstream of the target is an Antiproton Collector that captures some of the antiprotons and focuses them into a beam that is transported sequentially into two antiproton rings. The Precooler ring rapidly manipulates antiproton bunches from short and broad (in momentum) to long and thin. It then performs some preliminary beam cooling, in the fraction of a second before the next proton bunch is extracted from the Main Ring. Pre-cooled antiprotons are passed on to the Accumulator ring before the next antiprotons arrive from the target. The Accumulator ring cools the antiprotons, compressing them into a dense state that is convenient for mass storage over many hours. Occasionally the Accumulator ring decelerates a large number of antiprotons, injecting them into a Deceleration …
Date: October 24, 2006
Creator: Peggs, Stephen
Object Type: Report
System: The UNT Digital Library
Study of Charm Baryons with the BaBar Experiment (open access)

Study of Charm Baryons with the BaBar Experiment

The authors report on several studies of charm baryon production and decays by the BABAR collaboration. They confirm previous observations of the {Xi}'{sub c}{sup 0/+}, {Xi}{sub c}(2980){sup +} and {Xi}{sub c}(3077){sup +} baryons, measure branching ratios for Cabibbo-suppressed {Lambda}{sub c}{sup +} decays and use baryon decays to study the properties of the light-quark baryons, {Omega}{sup -} and {Xi}(1690){sup 0}.
Date: October 24, 2006
Creator: Petersen, Brian Aa.
Object Type: Article
System: The UNT Digital Library
Basic Research Needs for Solid-State Lighting. Report of the Basic Energy Sciences Workshop on Solid-State Lighting, May 22-24, 2006 (open access)

Basic Research Needs for Solid-State Lighting. Report of the Basic Energy Sciences Workshop on Solid-State Lighting, May 22-24, 2006

The workshop participants enthusiastically concluded that the time is ripe for new fundamental science to beget a revolution in lighting technology. SSL sources based on organic and inorganic materials have reached a level of efficiency where it is possible to envision their use for general illumination. The research areas articulated in this report are targeted to enable disruptive advances in SSL performance and realization of this dream. Broad penetration of SSL technology into the mass lighting market, accompanied by vast savings in energy usage, requires nothing less. These new ?good ideas? will be represented not by light bulbs, but by an entirely new lighting technology for the 21st century and a bright, energy-efficient future indeed.
Date: May 24, 2006
Creator: Phillips, J. M.; Burrows, P. E.; Davis, R. F.; Simmons, J. A.; Malliaras, G. G.; So, F. et al.
Object Type: Report
System: The UNT Digital Library
Stringy Instantons and Quiver Gauge Theories (open access)

Stringy Instantons and Quiver Gauge Theories

We explore contributions to the 4D effective superpotential which arise from Euclidean D3 branes (''instantons'') that intersect space-filling D-branes. These effects can perturb the effective field theory on the space-filling branes by nontrivial operators composed of charged matter fields, changing the vacuum structure in a qualitative way in some examples. Our considerations are exemplified throughout by a careful study of a fractional brane configuration on a del Pezzo surface.
Date: October 24, 2006
Creator: Florea, Bogdan; Kachru, Shamit; McGreevy, John & Saulina, Natalia
Object Type: Article
System: The UNT Digital Library
Study of Collective Beam Instabilities using a Correleation-moment Analysis (open access)

Study of Collective Beam Instabilities using a Correleation-moment Analysis

A general formalism for treating simultaneously the transverse coupled bunch and transverse coupled mode instabilities is presented. In this approach, the equations of motion of a coupled multi-bunch beam are expanded to yield a system of equations involving correlation-moments of the transverse and longitudinal motions. After a proper truncation, the system of equations is closed and can be solved. This approach allows us to formulate within one framework several known instability mechanisms including the single bunch mode coupling instability, the coupled bunch instability, the mode coupling instability, and the coupled mode coupled bunch instability as particular cases.
Date: October 24, 2006
Creator: Heifets, S. A. & Chao, A. W.
Object Type: Article
System: The UNT Digital Library
Highly Selective H2 Separation Zeolite Membranes for Coal Gasification Membrane Reactor Applications (open access)

Highly Selective H2 Separation Zeolite Membranes for Coal Gasification Membrane Reactor Applications

Zeolite membranes are thermally, chemically, and mechanically stable. They also have tunable molecular sieving and catalytic ability. These unique properties make zeolite membrane an excellent candidate for use in catalytic membrane reactor applications related to coal conversion and gasification, which need high temperature and high pressure range separation in chemically challenging environment where existing technologies are inefficient or unable to operate. Small pore, good quality, and thin zeolite membranes are needed for highly selective H{sub 2} separation from other light gases (CO{sub 2}, CH{sub 4}, CO). However, zeolite membranes have not been successful for H{sub 2} separation from light gases because the zeolite pores are either too big or the membranes have a large number of defects. The objective of this study is to develop zeolite membranes that are more suitable for H{sub 2} separation. In an effort to tune the size of zeolite pores and/or to decrease the number of defects, medium-pore zeolite B-ZSM-5 (MFI) membranes were synthesized and silylated. Silylation on B-ZSM-5 crystals reduced MFI-zeolite pore volume, but had little effect on CO{sub 2} and CH{sub 4} adsorption. Silylation on B-ZSM-5 membranes increased H{sub 2} selectivity both in single component and in mixtures with CO{sub 2}CO{sub 2}, CH{sub …
Date: September 24, 2006
Creator: Hong, Mei; Noble, Richard D. & Falconer, John L.
Object Type: Report
System: The UNT Digital Library