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 …

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. …

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.

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.

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 …

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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.

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}.

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.

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.

The accumulation of mildly deleterious missense mutations inindividual human genomes has been proposed to be a genetic basis forcomplex diseases. The plausibility of this hypothesis depends onquantitative estimates of the prevalence of mildly deleterious de novomutations and polymorphic variants in humans and on the intensity ofselective pressure against them. We combined analysis of mutationscausing human Mendelian diseases, human-chimpanzee divergence andsystematic data on human SNPs and found that about 20 percent of newmissense mutations in humans result in a loss of function, while about 27percent are effectively neutral. Thus, more than half of new missensemutations have mildly deleterious effects. These mutations give rise tomany low frequency deleterious allelic variants in the human populationas evident from a new dataset of 37 genes sequenced in over 1,500individual human chromosomes. Surprisingly, up to 70 percent of lowfrequency missense alleles are mildly deleterious and associated with aheterozygous fitness loss in the range 0.001-0.003. Thus, the low allelefrequency of an amino acid variant can by itself serve as a predictor ofits functional significance. Several recent studies have reported asignificant excess of rare missense variants in disease populationscompared to controls in candidate genes or pathways. These studies wouldbe unlikely to work if most rare variants were neutral …

The Department of Energy (DOE) selected Caustic-Side Solvent Extraction (CSSX) as the preferred technology for the removal of radioactive cesium from High-Level Waste (HLW) at the Savannah River Site (SRS). Before the full-scale Salt Waste Processing Facility (SWPF) becomes operational, a portion of dissolved saltcake waste will be processed through a Modular CSSX Unit (MCU). The MCU employs the CSSX process, a continuous process that uses a novel solvent to extract cesium from waste and concentrate it in dilute nitric acid. Of primary concern is Cs-137 which makes the solution highly radioactive. Since the MCU does not have the capacity to wait for sample results while continuing to operate, the Waste Acceptance Strategy is to perform inline analyses. Gamma-ray monitors are used to: measure the Cs-137 concentration in the decontaminated salt solution (DSS) before entering the DSS Hold Tank; measure the Cs-137 concentration in the strip effluent (SE) before entering the SE Hold Tank; and verify proper operation of the solvent extraction system by verifying material balance within the process. Since this gamma ray monitoring system application is unique, specially designed shielding was developed and software was written and acceptance tested by Savannah River National Laboratory (SRNL) personnel. The software …

We study the transverse-momentum distribution of hadrons produced in semi-inclusive deep-inelastic scattering. We consider cross sections for various combinations of the polarizations of the initial lepton and nucleon or the produced hadron, for which we perform the resummation of large double-logarithmic perturbative corrections arising at small transverse momentum. We present phenomenological results for the process ep {yields} e{pi}X for the typical kinematics in the COMPASS experiment. We discuss the impact of the perturbative resummation and of estimated non-perturbative contributions on the corresponding cross sections and their spin asymmetry.

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

In this paper, we review experiences with programs to support the deployment of photovoltaics (PV) in new, market-rate homes, drawing upon interviews with program managers around the country, project data, and publicly-available documentation on program design, impacts, and experiences. We focus on state clean energy funds, which have been established in 14 U.S. states to build markets for clean energy resources, as well as a select number of other state or local organizations whose activities are particularly noteworthy. We describe the types of programs implemented and their impacts to date, and discuss key issues and lessons learned for initiatives aimed at growing the new home market for PV.

The initial multi-mode interfacial velocity and density perturbations present at the onset of a small Atwood number, incompressible, miscible, Rayleigh-Taylor instability-driven mixing layer have been quantified using a combination of experimental techniques. The streamwise interfacial and spanwise interfacial perturbations were measured using high-resolution thermocouples and planar laser-induced fluorescence (PLIF), respectively. The initial multi-mode streamwise velocity perturbations at the two-fluid density interface were measured using particle-image velocimetry (PIV). It was found that the measured initial conditions describe an initially anisotropic state, in which the perturbations in the streamwise and spanwise directions are independent of one another. The evolution of various fluctuating velocity and density statistics, together with velocity and density variance spectra, were measured using PIV and high-resolution thermocouple data. The evolution of the velocity and density statistics is used to investigate the early-time evolution and the onset of strongly-nonlinear, transitional dynamics within the mixing layer. The early-time evolution of the density and vertical velocity variance spectra indicate that velocity fluctuations are the dominant mechanism driving the instability development. The implications of the present experimental measurements on the initialization of Reynolds-averaged turbulent transport and mixing models and of direct and large-eddy simulations of Rayleigh-Taylor instability-induced turbulence are discussed.

Recently, while performing extensive EUV irradiation endurance testing on Ru-capped multilayer mirrors in the presence of elevated partial pressures of water and hydrocarbons, NIST has observed that the amount of EUV-induced damage actually decreases with increasing levels of water vapor above {approx} 5 x 10{sup -7} Torr. It is thought that the admitted water vapor may interact with otherwise stable, condensed carbonaceous species in an UHV vacuum system to increase the background levels of simple gaseous carbon-containing molecules. Some support for this hypothesis was demonstrated by observing the mitigating effect of very small levels of simple hydrocarbons with the intentional introduction of methyl alcohol in addition to the water vapor. It was found that the damage rate decreased by at least an order of magnitude when the partial pressure of methyl alcohol was just one percent of the water partial pressure. These observations indicate that the hydrocarbon components of the vacuum environment under actual testing conditions must be characterized and controlled to 10{sup -11} Torr or better in order to quantify the damage caused by high levels of water vapor. The possible effects of exposure beam size and out-of-band radiation on mirror lifetime testing will also be discussed.

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A nine-month monitored field study of the performance of automated roller shades and daylighting controls was conducted in a 401 m{sup 2} unoccupied, furnished daylighting mockup. The mockup mimicked the southwest corner of a new 110 km{sub 2} commercial building in New York, New York, where The New York Times will be the major tenant. This paper focuses on evaluating the performance of two daylighting control systems installed in separate areas of an open plan office with 1.2-m high workstation partitions: (1) Area A had 0-10 V dimmable ballasts with an open-loop proportional control system and an automated shade controlled to reduce window glare and increase daylight, and (2) Area B had digital addressable lighting interface (DALI) ballasts with a closed-loop integral reset control system and an automated shade controlled to block direct sun. Daylighting control system performance and lighting energy use were monitored. The daylighting control systems demonstrated very reliable performance after they were commissioned properly. Work plane illuminance levels were maintained above 90% of the maximum fluorescent illuminance level for 99.9{+-}0.5% and 97.9{+-}6.1% of the day on average over the monitored period, respectively, in Areas A and B. Daily lighting energy use savings were significant in both Areas …

From examination of only 4 deg{sup 2} of sky in the NOAO Deep Wide-Field Survey (NDWFS) region, we have identified the first radio-loud quasar at a redshift z > 6. The object, FIRST J1427385+331241, was discovered by matching the FLAMEX IR survey to FIRST survey radio sources with NDWFS counterparts. One candidate z > 6 quasar was found, and spectroscopy with the Keck II telescope confirmed its identification, yielding a redshift z = 6.12. The object is a Broad Absorption Line (BAL) quasar with an optical luminosity of M{sub B} {approx} -26.9 and a radio-to-optical flux ratio {approx} 60. Two Mg II absorptions systems are present at redshifts of z = 2.18 and z = 2.20. We briefly discuss the implications of this discovery for the high-redshift quasar population.

A 3{omega} transmitted beam diagnostic has been commissioned on the Omega Laser at the Laboratory for Laser Energetics, University of Rochester [Soures et.al., Laser Part. Beams 11 (1993)]. Transmitted light from one beam is collected by a large focusing mirror and directed onto a diagnostic platform. The near field of the transmitted light is imaged; the system collects information from twice the original f-cone of the beam. Two gated optical cameras capture the near field image of the transmitted light. Thirteen spatial positions around the measurement region are temporally resolved using fast photodiodes to allow a measure of the beam spray evolution. The Forward stimulated Raman scattering and forward simulated Brillion scattering are spectrally and temporally resolved at 5 independent locations within twice the original f-cone. The total transmitted energy is measured in two spectral bands ({delta}{lambda} < 400 nm and {delta}{lambda} > 400 nm).

This paper presents the history of Professor T. D. Lee's seminal work on the theory of relativistic heavy ion collisions, and the founding and development of the Riken Brookhaven Center. A number of anecdotes are given about Prof. Lee, and his strong positive effect on his colleagues, particularly young physicists.