bluuebunny/crossref_metadata_2025 huggingface dataset:
Helium induced nanoscopic morphology on tungsten under fusion relevant plasma conditions
Authors: Baldwin M.J. , Doerner R.P.
Published: January 2008

Polished W discs exposed to pure He plasma in the PISCES-B linear-divertor-plasma simulator at 1120 and 1320 K are found to develop deeply nanostructured surface layers consisting of a conglomerate of amorphous ‘nanorods’. The growth of the thickness of the nanostructured layer is explored for exposure times spanning 300–(2.2 × 104) s in He plasmas of density n
e ∼ 4 × 1018 m−3 and temperature T
e ∼ 6–8 eV where the average He-ion surface-impact energy is ∼60 eV, below the threshold for physical sputtering. A nanostructured layer in excess of 5 µm thick is observed for the longest exposure time explored. The kinetics of the layer growth are found to follow Fick's law, characterized by an effective diffusive mechanism with coefficients of diffusion: D
1120 K = 6.6 ± 0.4 × 10−12 cm2 s−1 and D
1320 K = 2.0± 0.5 × 10−11 cm2 s−1. The diffusion of He atoms in W is considered too rapid to explain the observed growth of surface modification and points to the interplay of other mechanisms, such as the availability of thermal vacancies and/or the slower diffusion of He through the forming nanostructured layer.
Sawtooth stability in neutral beam heated plasmas in TEXTOR
Authors: Chapman I.T. , Pinches S.D. , Koslowski H.R. , Liang Y. , Krämer-Flecken A. , de Bock M.
Published: January 2008

The experimental sawtooth behaviour in neutral beam injection (NBI) heated plasmas in TEXTOR is described. It is found that the sawtooth period is minimized with a low NBI power oriented in the same direction as the plasma current. As the beam power is increased in the opposite direction to the plasma current, the sawtooth period increases to a maximum before it begins to shorten once more. Results from both magnetohydrodynamic stability modelling including toroidal flows and modelling of the kinetic effects of the fast ions resulting from NBI heating are also presented. This model combining the gyroscopic and kinetic effects upon the stability of then= 1 internal kink mode—thought to be associated with sawtooth oscillations—qualitatively recovers the sawtooth behaviour exhibited in the experiment. It is proposed that the sawtooth period is minimized in the co-NBI direction at the point at which the stabilization of the kink mode due to rotation is weakest. This occurs when the plasma rotation induced by the NBI balances the intrinsic rotation of the plasma. The sawtooth behaviour in the counter-NBI regime is attributed to a subtle balance of the competing stabilization from the toroidal rotation and destabilization from the presence of energetic ions.
Preparation and Characterization of Si3N4-TiN Nanocomposite viain situCo-deposition in Liquid Ammonia
Authors: Yang Mei , Lu Ming-li , Zhu Hong-min
Published: January 2008

A new method of TiN/Si3N4 nanocomposite synthesis was described and tested. TiCl4 and SiCl4 used as the starting materials and sodium as the reduction agent were conducted in liquid ammonia respectively. TiCl4 and SiCl4 were reduced simultaneously and titanium nitride/silicon nitride nanocomposite powders were obtained by in situ co-deposition at temperatures around 45C. X-ray diffraction patterns indicate that the product was amorphous and the by-product was sodium chloride. The product powders were heated up to 1600C and crystallization to TiN and -Si3N4 happened. Due to presence of TiN, the crystallization of silicon nitride in the mixture was later than that of pure silicon nitride. Transmission electron microscopy images show the average size of powders range from 10 nm to 40 nm and scanning electron microscopy images conformed that Ti and Si elements were dispersed uniformly. A green bulk nitride composite containing 20%TiN with the mean grain size of 100300 nm and fracture toughness of 10.11.1 m1/2MPa, was obtained by spark plasma sintering at 15001600C. The effect of TiN additive on microstructure and mechanical properties of composite bulk was discussed.
Preparation of High-Orderly TiO2 Nanotubes in Organic Solution and Characterization of C-doped TiO2
Authors: Fan Xiao-yan , Zhang Yun-huai , Xiao Peng , Hu Fu , Zhang Huai
Published: January 2008

High-orderly TiO2 nanotube arrays were fabricated by anodic oxidation of pure titanium substrate in organic electrolyte containing fluoride. Different morphological nanotubes of titania were obtained through controlling the different anodization voltages and durations. The length of the longest nanotubes was approximately 60 m and the length-to-width aspect ratio was about 600. The nanotube layers were then annealed at different temperatures (450, 550, and 650C) in air for 2 h. The samples were characterized by scanning electron microscopy, X-ray diffraction (XRD), energy dispersive X-Ray (EDS) and UV-Vis spectrometer. The XRD results demonstrated that the as-anodized samples were amorphous and the structure changed to antanse and rutile when the samples were annealed at higher temperature. The EDS microanalysis indicated the presence of carbon in the TiO2 nanotubes. The result of degradation of methylene blue showed clearly that the photocatalytic activity of C-doped TiO2 nanotubes increased by 10%.
Surface Modification of Vapor-grown Carbon Nanofibers in Radio Frequency Plasma
Authors: Liu Hong-yan , Yang Yong-zhen , Ji Wei-yun , Liu Xu-guang , Xu Bing-she
Published: January 2008

Vapor-grown carbon nanofibers (VGCNFs) were treated in radio frequency (RF) plasma to activate their surface and thus to improve the compatibility with the matrix in polymer composites. The surface of VGCNFs was modified in atmospheres containing different ratios of O2 and Ar. Fourier transform infrared spectroscopy and thermogravimetric measurement shows that when the O2 content in mixture gases was 5%, C-O and O-H functional groups were produced abundantly in the surface of the VGCNFs. When O2 content increased to 8%, most of the surface of carbon fibers was severely oxidized, resulting in defects in structures of the inner layers of VGCNFs.
Preparation and Optical Properties of CdTe/CdOnH2O Core/shell Nano-composites in Aqueous Solution
Authors: Zhang Xiao , Zhou Xing-ping , Ni Si-yu , Dai Guo-liang , Wang Yin-sheng
Published: January 2008

The deposition of CdOnH2O on CdTe nanoparticles was studied in an aqueous phase. The CdTe nanocrystals (NCs) were prepared in aqueous solution through the reaction between Cd2+ and NaHTe in the presence of thioglycolic acid as a stabilizer. The molar ratio of the Cd2+ to Te2- in the precursory solution played an important role in the photoluminescence of the ultimate CdTe NCs. The strongest photoluminescence was obtained under 4.0 of [Cd2+]/[Te2-] at pH~8.2. With the optimum dosage of Cd(II) hydrous oxide deposited on the CdTe NCs, the photoluminescence was enhanced greatly. The photoluminescence of these nanocomposites was kept constant in the pH range of 8.010.0, but dramatically decreased with an obvious blue-shifted peak while the pH was below 8.0. In addition, the photochemical oxidation of CdTe NCs with cadmium hydrous oxide deposition was markedly inhibited.
Preparation and Performances of RuO2/TiO2 Films Photocatalyst Supported on Float Pearls
Authors: Yao Bing-hua , Wang Li-ming , Wang Cheng , Wang Yi-xun , Zhao Gao-yang
Published: January 2008

RuO2/TiO2 films were deposited on float pearls (FP) by the sol-gel-dipping method. The substrates were coated with RuO2/TiO2 precursor sol, air-dried at 120C and further heated at 500C to obtain the coupled photocatalyst of RuO2/TiO2 films supported on FP (RuO2/TiO2/FP). The structure of coupled photocatalyst was characterized by SEM, XRD, and FT-IR technique, respectively. The results showed TiO2 has anatase structure and doped RuO2 was highly dispersed on the surface of TiO2 particles as amorphous. The average thickness of RuO2/TiO2 films (3 layers) on FP was determined to be about 1 m. This study was carried out under the following conditions: volume 60 mL, initial concentration of beta-cypermethrin (BEC) 45 mg/L, pH 6.5, amount of RuO2/TiO2/PF 5 g/L, air flow rate 200 mL/min, reaction time 60 min. The degradation rates of BEC are 88.1% (125 W Hg lamp), 82.8% (8 W UV lamp), and 75.1% (8 W solar lamp), respectively. The photocatalytic degradation of BEC was experimentally demonstrated to follow the Langmuir-Hinshelwood kinetic model, and the reaction rate constant (17.5 mg/(L min)) and the adsorption constant (3.486 L/g) were determined, respectively. It was also found that the RuO2/TiO2/FP photocatalyst has significantly the visible light photoactivity for degradation of BEC.
A Comparison of Chinese and American Indian (Chumash) Medicine
Authors: Adams James D. , Garcia Cecilia , Lien Eric J.
Published: January 2008

Chinese and Chumash traditional medical approaches are similar in terms of disease causation, use of acupuncture or healing touch, plants, spiritual and philosophical approaches. This article provides a brief comparison and discussion of Chinese and Chumash traditional medical practices. A table of 66 plants is presented along with Chinese and Chumash uses of each plant. These uses are compared and contrasted.
Enhancement of jellyfish (Aurelia aurita) populations by extensive aquaculture rafts in a coastal lagoon in Taiwan
Authors: Lo Wen-Tseng , Purcell Jennifer E. , Hung Jia-Jang , Su Huei-Meei , Hsu Pei-Kai
Published: January 2008

Lo, W-T., Purcell, J. E., Hung, J-J., Su, H-M., and Hsu, P-K. 2008. Enhancement of jellyfish (Aurelia aurita) populations by extensive aquaculture rafts in a coastal lagoon in Taiwan. – ICES Journal of Marine Science, 65: 453–461. Blooms of the moon jellyfish, Aurelia aurita, often occur in coastal waters that are heavily affected by human construction, such as harbours. Tapong Bay is a hypertrophic lagoon in southwestern Taiwan that was studied between August 1999 and September 2004. The removal of extensive oyster-culture rafts in June 2002 provided a “natural” experiment to examine the effects of aquaculture on processes and communities in the lagoon. The removal caused many changes in the ecosystem, including increases in flushing, light penetration, dissolved oxygen, salinity, chlorophyll a, primary production, and zooplankton, but decreases in nutrients, periphyton, and dramatically reduced populations of bivalves, zooplanktivorous fish, and jellyfish (A. aurita). We conclude that environmental and trophic conditions were favourable for jellyfish throughout the study period. Therefore, we believe that aquaculture rafts enhanced jellyfish populations by three probable mechanisms: the rafts provided substrate and shading for the larval settlement and polyp colony formation, and the rafts restricted water exchange in the lagoon. Aquaculture is increasing rapidly in Asia, and the problems associated with jellyfish may also increase.
Pedigree-free animal models: the relatedness matrix reloaded
Authors: Frentiu Francesca D , Clegg Sonya M , Chittock John , Burke Terry , Blows Mark W , Owens Ian P.F
Published: January 2008

Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance–covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland's pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rankRmatrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of theRmatrix in order to maximize the signal to noise ratio. Using reduced-rankRmatrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.
Wild pedigrees: the way forward
Authors: Pemberton J.M
Published: January 2008

Metrics derived from pedigrees are key to investigating several major issues in evolutionary biology, including the quantitative genetic architecture of traits, inbreeding depression, and the evolution of cooperation and inbreeding avoidance. There is merit in studying these issues in natural populations experiencing spatially and temporally variable environmental conditions, since these analyses may yield different results from laboratory studies and allow us to understand population responses to rapid environmental change. Partial pedigrees are now available for several natural populations which are the subject of long-term individual-based studies, and analyses using these pedigrees are leading to important insights. Accurate pedigree construction supported by molecular genetic data is now feasible across a wide range of taxa, and even where only imprecise pedigrees are available it is possible to estimate the consequences of imprecision for the questions of interest. In outbred diploid populations, the pedigree approach is superior to analyses based on marker-based pairwise estimators of coancestry.
Introduction. Evolutionary dynamics of wild populations: the use of long-term pedigree data
Authors: Kruuk L.E.B , Hill W.G
Published: January 2008

Studies of populations in the wild can provide unique insights into the forces driving evolutionary dynamics. This themed issue of
Proc. R. Soc. B
focuses on new developments in long-term analyses of animal populations where pedigree information has been collected. These address fundamental questions in evolutionary biology concerning the genetic basis of phenotypic diversity, patterns of natural and sexual selection, the occurrence of inbreeding and inbreeding depression, and speciation. Contributions include the analysis of evolutionary responses to climate change, exploration of the genetic basis of senescence, the exploitation of advances in molecular genetic technology, and reviews of developments in quantitative genetic methodology. We discuss here common themes, specific problems and pointers for future research.
Quality scores and SNP detection in sequencing-by-synthesis systems
Authors: Brockman William , Alvarez Pablo , Young Sarah , Garber Manuel , Giannoukos Georgia , Lee William L. , Russ Carsten , Lander Eric S. , Nusbaum Chad , Jaffe David B.
Published: January 2008

Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We describe general methods for improved quality scores and accurate automated polymorphism detection, and apply them to data from the Roche (454) Genome Sequencer 20. We assess our methods using known-truth data sets, which is critical to the validity of the assessments. We developed informative, base-by-base error predictors for this sequencer and used a variant of the phred binning algorithm to combine them into a single empirically derived quality score. These quality scores are more useful than those produced by the system software: They both better predict actual error rates and identify many more high-quality bases. We developed a SNP detection method, with variants for low coverage, high coverage, and PCR amplicon applications, and evaluated it on known-truth data sets. We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data.
Delaunay ends of constant mean curvature surfaces
Authors: Kilian M. , Rossman W. , Schmitt N.
Published: January 2008

The generalized Weierstrass representation is used to analyze the asymptotic behavior of a constant mean curvature surface that arises locally from an ordinary differential equation (ODE) with a regular singularity. We prove that a holomorphic perturbation of an ODE that represents a Delaunay surface generates a constant mean curvature surface which has a properly immersed end that is asymptotically Delaunay. Furthermore, that end is embedded if the Delaunay surface is unduloidal.
Quantum cohomology of the Grassmannian and alternate Thom–Sebastiani
Authors: Kim Bumsig , Sabbah Claude
Published: January 2008

We introduce the notion of an alternate product of Frobenius manifolds and we give, after Ciocan-Fontanine et al., an interpretation of the Frobenius manifold structure canonically attached to the quantum cohomology of G(r,n+1) in terms of alternate products. We also investigate the relationship with the alternate Thom–Sebastiani product of Laurent polynomials.
Three-Dimensional Modeling and Geometrical Influence on the Hydraulic Performance of a Control Valve
Authors: Palau-Salvador Guillermo , González-Altozano Pablo , Arviza-Valverde Jaime
Published: January 2008

The ability to understand and manage the performance of hydraulic control valves is important in many automatic and manual industrial processes. The use of computational fluid dynamics (CFD) aids in the design of such valves by inexpensively providing insight into flow patterns, potential noise sources, and cavitation. Applications of CFD to study the performance of complex three-dimensional (3D) valves, such as poppet, spool, and butterfly valves, are becoming more common. Still, validation and accuracy remain an issue. The Reynolds-averaged Navier–Stokes equations were solved numerically using the commercial CFD package FLUENT V6.2 to assess the effect of geometry on the performance of a 3D control valve. The influence of the turbulence model and of a cavitation model was also investigated. Comparisons were made to experimental data when available. The 3D model of the valve was constructed by decomposing the valve into several subdomains. Agreement between the numerical predictions and measurements of flow pressure was less than 6% for all cases studied. Passive flow control, designed to minimize vortical structures at the piston exit and reduce potential cavitation, noise, and vibrations, was achieved by geometric smoothing. In addition, these changes helped to increase Cv and reduce the area affected by cavitation as it is related to the jet shape originated at the valve throat. The importance of accounting for full 3D geometry effects in modeling and optimizing control valve performance was demonstrated via CFD. This is particularly important in the vicinity of the piston. It is worth noting that the original geometry resulted in a lower Cv with higher velocity magnitude within the valve, whereas after smoothing Cv increased and served to delay cavitation inception.
Analysis of Coherent Structures in the Far-Field Region of an Axisymmetric Free Jet Identified Using Particle Image Velocimetry and Proper Orthogonal Decomposition
Authors: Shinneeb A.-M. , Balachandar R. , Bugg J. D.
Published: January 2008

This paper investigates an isothermal free water jet discharging horizontally from a circular nozzle (9mm) into a stationary body of water. The jet exit velocity was 2.5m∕s and the exit Reynolds number was 22,500. The large-scale structures in the far field were investigated by performing a proper orthogonal decomposition (POD) analysis of the velocity field obtained using a particle image velocimetry system. The number of modes used for the POD reconstruction of the velocity fields was selected to recover 40% of the turbulent kinetic energy. A vortex identification algorithm was then employed to quantify the size, circulation, and direction of rotation of the exposed vortices. A statistical analysis of the distribution of number, size, and strength of the identified vortices was carried out to explore the characteristics of the coherent structures. The results clearly reveal that a substantial number of vortical structures of both rotational directions exist in the far-field region of the jet. The number of vortices decreases in the axial direction, while their size increases. The mean circulation magnitude is preserved in the axial direction. The results also indicate that the circulation magnitude is directly proportional to the square of the vortex radius and the constant of proportionality is a function of the axial location.
A Grid-Free Lagrangian Approach of Vortex Method and Particle
Trajectory Tracking Method Applied to Internal Fluid-Solid Two-Phase
Flows
Authors: Iso Yoshiyuki , Kamemoto Kyoji
Published: January 2008

We have developed a numerical simulation scheme combining a vortex method and a particle trajectory tracking method, which is applicable to internal unsteady two-phase flows. It is a completely grid-free Lagrangian–Lagrangian simulation, which is able to simulate the primary effect of vortical flow on the unsteady particle motion and dispersion. It can handle unsteady high Reynolds number flows. So far, no one has applied this kind of method internal multiphase flows, though many industrial multiphase flows are internal. In this study, internal liquid-solid two-phase flows in a vertical channel and a mixing tee have been calculated by the new method, in which use of the vortex introduction model enables the simulation of the dynamic behavior of separation or reattachment. In the mixing tee, solid particle phenomena such as depositions or particle-wall collisions have been simulated and measured. Numerical results based on simple two-dimensional flow and one-way model show good agreement with the experimental data. The results show that turbulent vortices dominate particle motion. It has been shown that the present method can be useful in the design of industrial multiphase flows with particle mixing, dispersion, deposition, and particle-wall collision because it is possible to simulate the effect of turbulent vortices on the particle motion.
Discrete Particle Study of Turbulence Coupling in a Confined Jet Gas-Liquid Separator
Authors: Strasser Wayne
Published: January 2008

A 3D computational fluid dynamics investigation of particle-induced flow effects and liquid entrainment from an industrial-scale separator has been carried out using the Eulerian–Lagrangian two-way coupled multiphase approach. A differential Reynolds stress model was used to predict the gas phase turbulence field. The dispersed (liquid) phase was present at an intermediate mass loading (0.25) but low volume fraction (0.05). A discrete random walk method was used to track the paths of the liquid droplet releases. It was found that gas phase deformation and turbulence fields were significantly impacted by the presence of the liquid phase; these effects have been parametrically quantified. Substantial enhancement of both the turbulence and the anisotropy of the continuous phase by the liquid phase was demonstrated. It was also found that a large number (⩾1000) of independent liquid droplet release events were needed to make conclusions about liquid entrainment. Known plant run conditions and entrainment rates validated the numerical method.
Analysis of Turbulent Mixing Jets in a Large Scale Tank
Authors: Lee Si Y. , Dimenna Richard A. , Leishear Robert A. , Stefanko David B.
Published: January 2008

Flow evolution models were developed to evaluate the performance of the new advanced design mixer pump for sludge mixing and removal operations with high-velocity liquid jets in one of the large-scale Savannah River Site waste tanks, Tank 18. This paper describes the computational model, the flow measurements used to provide validation data in the region far from the jet nozzle, and the extension of the computational results to real tank conditions through the use of existing sludge suspension data. A computational fluid dynamics approach was used to simulate the sludge removal operations. The models employed a three-dimensional representation of the tank with a two-equation turbulence model. Both the computational approach and the models were validated with onsite test data reported here and literature data. The model was then extended to actual conditions in Tank 18 through a velocity criterion to predict the ability of the new pump design to suspend settled sludge. A qualitative comparison with sludge removal operations in Tank 18 showed a reasonably good comparison with final results subject to significant uncertainties in actual sludge properties.
Transgenic Inhibition of Synaptic Transmission Reveals Role of CA3 Output in Hippocampal Learning
Authors: Nakashiba Toshiaki , Young Jennie Z. , McHugh Thomas J. , Buhl Derek L. , Tonegawa Susumu
Published: January 2008

The hippocampus is an area of the brain involved in learning and memory. It contains parallel excitatory pathways referred to as the trisynaptic pathway (which carries information as follows: entorhinal cortex → dentate gyrus → CA3 → CA1 → entorhinal cortex) and the monosynaptic pathway (entorhinal cortex → CA1 → entorhinal cortex). We developed a generally applicable tetanus toxin–based method for transgenic mice that permits inducible and reversible inhibition of synaptic transmission and applied it to the trisynaptic pathway while preserving transmission in the monosynaptic pathway. We found that synaptic output from CA3 in the trisynaptic pathway is dispensable and the short monosynaptic pathway is sufficient for incremental spatial learning. In contrast, the full trisynaptic pathway containing CA3 is required for rapid one-trial contextual learning, for pattern completion–based memory recall, and for spatial tuning of CA1 cells.
NMR Imaging of Catalytic Hydrogenation in Microreactors with the Use of para-Hydrogen
Authors: Bouchard Louis-S. , Burt Scott R. , Anwar M. Sabieh , Kovtunov Kirill V. , Koptyug Igor V. , Pines Alexander
Published: January 2008

Catalysis is vital to industrial chemistry, and the optimization of catalytic reactors attracts considerable resources. It has proven challenging to correlate the active regions in heterogeneous catalyst beds with morphology and to monitor multistep reactions within the bed. We demonstrate techniques, using magnetic resonance imaging and para-hydrogen (
p
-H
2
) polarization, that allow direct visualization of gas-phase flow and the density of active catalyst in a packed-bed microreactor, as well as control over the dynamics of the polarized state in space and time to facilitate the study of subsequent reactions. These procedures are suitable for characterizing reactors and reactions in microfluidic devices where low sensitivity of conventional magnetic resonance would otherwise be the limiting factor.
Aspergillus
Section
Fumigati
: Antifungal Susceptibility Patterns and Sequence-Based Identification
Authors: Alcazar-Fuoli Laura , Mellado Emilia , Alastruey-Izquierdo Ana , Cuenca-Estrella Manuel , Rodriguez-Tudela Juan L.
Published: January 2008

This study analyzed 28
Aspergillus
strains belonging to the section
Fumigati
that were isolated from clinical samples in Spain. All isolates sporulated slowly and were unable to grow at 48°C. Phylogenetic analysis based on sequencing of partial sequences of the β-tubulin and rodlet A genes was used to classify the 28 strains into six different clades (
Neosartorya hiratsukae
,
Neosartorya pseudofischeri
,
Aspergillus viridinutans
,
Aspergillus lentulus
,
Aspergillus fumigatiaffinis
, and
Aspergillus fumisynnematus
). Antifungal susceptibility testing showed heterogeneous patterns and grouped the strains together by species. Most
A. lentulus
and
A. fumigatiaffinis
isolates showed high MICs of amphotericin B (geometric mean [GM] MICs, ≥4.5 μg/ml), itraconazole (GM MICs, ≥6 μg/ml), voriconazole (GM MICs, ≥3 μg/ml), and ravuconazole (GM MICs, ≥3 μg/ml);
N pseudofischeri
and
A. viridinutans
showed high MICs of itraconazole (GM MICs, ≥8 μg/ml), voriconazole (GM MICs, ≥3.33 μg/ml), and ravuconazole (GM MICs, ≥2 μg/ml); and
N. hiratsukae
and
A. fumisynnematus
were susceptible to all the antifungals tested. In conclusion, a number of different species whose morphological features resemble those of
Aspergillus fumigatus
could succeed in producing invasive infections in the susceptible host. In addition, some of them showed high MICs for most of the antifungals available for the treatment of patients infected with these organisms. The epidemiology and clinical relevance of these species should therefore be addressed.
Convergent In Vivo and In Vitro Selection of Ceftazidime Resistance Mutations at Position 167 of CTX-M-3 β-Lactamase in Hypermutable
Escherichia coli
Strains
Authors: Stepanova Marina N. , Pimkin Maxim , Nikulin Anatoly A. , Kozyreva Varvara K. , Agapova Elena D. , Edelstein Mikhail V.
Published: January 2008

We report on a novel CTX-M extended-spectrum β-lactamase (ESBL), designated CTX-M-42, with enhanced activity toward ceftazidime. CTX-M-42 was identified in a hypermutable
Escherichia coli
nosocomial isolate (isolate Irk2320) and is a Pro167Thr amino acid substitution variant of CTX-M-3. By molecular typing of ESBL-producing
E. coli
strains previously isolated in the same hospital ward, we were able to identify a putative progenitor (strain Irk1224) of Irk2320, which had a mutator phenotype and harbored the CTX-M-3 β-lactamase. To reproduce the natural evolution of CTX-M-3, we selected for ceftazidime resistance mutations in
bla
CTX-M-3
gene in vitro both in clinical isolate Irk1224 and in laboratory-derived hypermutable (
mutD5
) strain GM2995. These experiments yielded CTX-M-3
Pro167Ser
and CTX-M-3
Asn136Lys
mutants which conferred higher levels of resistance to ceftazidime than to cefotaxime. CTX-M-3
Asn136Lys
had a level of low activity toward ampicillin, which may explain its absence from clinical isolates. We conclude that the selection of CTX-M-42 could have occurred in vivo following treatment with ceftazidime and was likely facilitated by the hypermutable background.
Characterization of a Novel Human Immunodeficiency Virus Type 1 Protease Inhibitor, A-790742
Authors: Dekhtyar Tatyana , Ng Teresa I. , Lu Liangjun , Masse Sherie , DeGoey David A. , Flosi William J. , Grampovnik David J. , Klein Larry L. , Kempf Dale J. , Molla Akhteruzzaman
Published: January 2008

A-790742 is a potent human immunodeficiency virus type 1 (HIV-1) protease inhibitor, with 50% effective concentrations ranging from 2 to 7 nM against wild-type HIV-1. The activity of this compound is lowered by approximately sevenfold in the presence of 50% human serum. A-790742 maintained potent antiviral activity against lopinavir-resistant variants generated in vitro as well as against a panel of molecular clones containing proteases derived from HIV-1 patient isolates with multiple protease mutations. During in vitro selection, A-790742 selected two primary mutations (V82L and I84V) along with L23I, L33F, K45I, A71V/A, and V77I in the pNL4-3 background and two other mutations (A71V and V82G) accompanied by M46I and L63P in the HIV-1 RF background. HIV-1 pNL4-3 clones with a single V82L or I84V mutation were phenotypically resistant to A-790742 and ritonavir. Taking these results together, A-790742 displays a favorable anti-HIV-1 profile against both the wild type and a large number of mutants resistant to other protease inhibitors. The selection of the uncommon V82L and V82G mutations in protease by A-790742 suggests the potential for an advantageous resistance profile with this protease inhibitor.
Spontaneous Deletion of the Methicillin Resistance Determinant,
mecA
, Partially Compensates for the Fitness Cost Associated with High-Level Vancomycin Resistance in
Staphylococcus aureus
Authors: Noto Michael J. , Fox Paige M. , Archer Gordon L.
Published: January 2008

Treatment of infections caused by
Staphylococcus aureus
is often confounded by the bacterium's ability to develop resistance to chemotherapeutic agents. Methicillin-resistant
S. aureus
(MRSA) arises through the acquisition of staphylococcal chromosomal cassette
mec
(SCC
mec
), a genomic island containing the methicillin resistance determinant,
mecA
. In contrast, resistance to vancomycin can result from exposure to the drug, a mechanism that is not dependent upon a gene acquisition event. Here we describe three MRSA strains that became resistant to vancomycin during passage in the presence of increasing concentrations of the drug. In each case two derivative strains were isolated, one that had lost
mecA
and one that retained
mecA
during passage. Strain 5836VR lost
mecA
by the site-specific chromosomal excision of SCC
mec
, while the other two strains (strains 3130VR and VP32) deleted portions of their SCC
mec
elements in a manner that appeared to involve IS
431
. Conversion to vancomycin resistance caused a decrease in the growth rate that was partially compensated for by the deletion of
mecA
. In mixed-culture competition experiments, vancomycin-resistant strains that lacked
mecA
readily outcompeted their
mecA
-containing counterparts, suggesting that the loss of
mecA
during conversion to vancomycin resistance was advantageous to the organism.
Inhibition of Human Immunodeficiency Virus Type 1 Replication in Human Cells by Debio-025, a Novel Cyclophilin Binding Agent
Authors: Ptak Roger G. , Gallay Philippe A. , Jochmans Dirk , Halestrap Andrew P. , Ruegg Urs T. , Pallansch Luke A. , Bobardt Michael D. , de Béthune Marie-Pierre , Neyts Johan , De Clercq Erik , Dumont Jean-Maurice , Scalfaro Pietro , Besseghir Kamel , Wenger Roland M. , Rosenwirth Brigitte
Published: January 2008

Debio-025 is a synthetic cyclosporine with no immunosuppressive capacity but a high inhibitory potency against cyclophilin A (CypA)-associatedcis-transprolyl isomerase (PPIase) activity. A lack of immunosuppressive effects compared to that of cyclosporine was demonstrated both in vitro and in vivo. For three cyclosporines, the inhibitory potential against PPIase activity was quantitatively correlated with that against human immunodeficiency virus type 1 (HIV-1) replication. Debio-025 selectively inhibited the replication of HIV-1 in a CD4+cell line and in peripheral blood mononuclear cells: potent activity was demonstrated against clinical isolates of various HIV-1 subtypes, including isolates with multidrug resistance to reverse transcriptase and protease inhibitors. Simian immunodeficiency virus and HIV-2 strains were generally resistant to inhibition by Debio-025; however, some notable exceptions of sensitive HIV-2 clinical isolates were detected. In two-drug combination studies, additive inhibitory effects were found between Debio-025 and 19 clinically used drugs of different classes. Clinical HIV-1 isolates that are naturally resistant to Debio-025 and that do not depend on CypA for infection were identified. Comparison of the amino acid sequences of the CypA binding domain of the capsid (CA) protein from Debio-025-sensitive and -resistant HIV-1 isolates indicated that resistance was mostly associated with an H87Q/P exchange. Mechanistically, cyclosporines competitively inhibit the binding of CypA to the HIV-1 CA protein, which is an essential interaction required for early steps in HIV-1 replication. By real-time PCR we demonstrated that early reverse transcription is reduced in the presence of Debio-025 and that late reverse transcription is almost completely blocked. Thus, Debio-025 seems to interfere with the function of CypA during the progression/completion of HIV-1 reverse transcription.
Outer Membrane Protein DsrA Is the Major Fibronectin-Binding Determinant of
Haemophilus ducreyi
Authors: Leduc Isabelle , White C. Dinitra , Nepluev Igor , Throm Robert E. , Spinola Stanley M. , Elkins Christopher
Published: January 2008

The ability to bind extracellular matrix proteins is a critical virulence determinant for skin pathogens.
Haemophilus ducreyi
, the etiological agent of the genital ulcer disease chancroid, binds extracellular matrix components, including fibronectin (FN). We investigated
H. ducreyi
FN binding and report several important findings about this interaction. First, FN binding by
H. ducreyi
was greatly increased in bacteria grown on heme and almost completely inhibited by hemoglobin. Second, wild-type strain 35000HP bound significantly more FN than did a
dsrA
mutant in two different FN binding assays. Third, the expression of
dsrA
in the
dsrA
mutant restored FN binding and conferred the ability to bind FN to a non-FN-binding
Haemophilus influenzae
strain. Fourth, an anti-DsrA monoclonal antibody partially blocked FN binding by
H. ducreyi
. The hemoglobin receptor, the collagen-binding protein, the
H. ducreyi
lectin, the fine-tangle pili, and the outer membrane protein OmpA2 were not involved in
H. ducreyi
FN binding, since single mutants bound FN as well as the parent strain did. However, the major outer membrane protein may have a minor role in FN binding by
H. ducreyi
, since a double
dsrA momp
mutant bound less FN than did the single
dsrA
mutant. Finally, despite major sequence differences, DsrA proteins from both class I and class II
H. ducreyi
strains mediated FN and vitronectin binding. We concluded that DsrA is the major factor involved in FN binding by both classes of
H. ducreyi
strains.
Regulatory Roles of CD1d-Restricted NKT Cells in the Induction of Toxic Shock-Like Syndrome in an Animal Model of Fatal Ehrlichiosis
Authors: Stevenson H. L. , Crossley E. C. , Thirumalapura N. , Walker D. H. , Ismail N.
Published: January 2008

CD1d-restricted NKT cells are key players in host defense against various microbial infections. Using a murine model of fatal ehrlichiosis, we investigated the role of CD1d-restricted NKT cells in induction of toxic shock-like syndrome caused by gram-negative, lipopolysaccharide-lacking, monocytotropicEhrlichia. Our previous studies showed that intraperitoneal infection of wild-type (WT) mice with virulentEhrlichia(Ixodes ovatus Ehrlichia[IOE]) results in CD8+T-cell-mediated fatal toxic shock-like syndrome marked by apoptosis of CD4+T cells, a weak CD4+Th1 response, overproduction of tumor necrosis factor alpha and interleukin-10, and severe liver injury. Although CD1d−/−mice succumbed to high-dose IOE infection similar to WT mice, they did not develop signs of toxic shock, as shown by elevated bacterial burdens, low serum levels of tumor necrosis factor, normal serum levels of liver enzymes, and the presence of few apoptotic hepatic cells. An absence of NKT cells restored the percentages and absolute numbers of CD4+and CD8+T cells and CD11b+cells in the spleen compared to WT mice and was also associated with decreased expression of Fas on splenic CD4+lymphocytes and granzyme B in hepatic CD8+lymphocytes. Furthermore, our data show that NKT cells promote apoptosis of macrophages and up-regulation of the costimulatory molecule CD40 on antigen-presenting cells, including dendritic cells, B cells, and macrophages, which may contribute to the induction of pathogenic T-cell responses. In conclusion, our data suggest that NKT cells mediateEhrlichia-induced T-cell-mediated toxic shock-like syndrome, most likely via cognate and noncognate interactions with antigen-presenting cells.
Fibronectin Binding and Proteolytic Degradation byLeishmaniaand Effects on Macrophage Activation
Authors: Kulkarni Manjusha M. , Jones Eric A. , McMaster W. Robert , McGwire Bradford S.
Published: January 2008

Infection by vector-borne protozoa of the genusLeishmaniaoccurs by the deposition of parasites within the skin of the mammalian host, where they eventually bind to and are phagocytized by Mφs. Our previous work supported the idea that parasites can interact with extracellular matrix and basement membrane proteins, such as fibronectin (FN), within the skin, leading to enhanced invasion. In this report, we extend these findings and show that both promastigotes and amastigotes ofLeishmaniaspecies can bind directly to soluble FN and laminin (LM) and that promastigotes express a distinct surface protein of ∼60 kDa that binds both FN and LM. Promastigotes of multipleLeishmaniaspecies can rapidly degrade FN by using surface-localized and secreted metalloprotease (leishmanolysin). FN degradation at the surfaces of amastigotes is leishmanolysin dependent, whereas both secreted leishmanolysin and cysteine protease B contribute to extracellular FN degradation.Leishmania-degraded FN decreased the production of reactive oxygen intermediates by parasite-infected macrophages and affected the accumulation of intracellular parasites. These findings show that both parasite stages ofLeishmaniaspecies bind to and proteolytically degrade FN at the parasite surface and distantly through secreted proteases and that degraded forms of FN can influence the activation state of parasite-infected macrophages.
Attenuated Endocytosis and Toxicity of a Mutant Cholera Toxin with Decreased Ability To Cluster Ganglioside GM
1
Molecules
Authors: Wolf Anne A. , Jobling Michael G. , Saslowsky David E. , Kern Eli , Drake Kimberly R. , Kenworthy Anne K. , Holmes Randall K. , Lencer Wayne I.
Published: January 2008

Cholera toxin (CT) moves from the plasma membrane (PM) of host cells to the endoplasmic reticulum (ER) by binding to the lipid raft ganglioside GM
1
. The homopentomeric B-subunit of the toxin can bind up to five GM
1
molecules at once. Here, we examined the role of polyvalent binding of GM
1
in CT action by producing chimeric CTs that had B-subunits with only one or two normal binding pockets for GM
1
. The chimeric toxins had attenuated affinity for binding to host cell PM, as expected. Nevertheless, like wild-type (wt) CT, the CT chimeras induced toxicity, fractionated with detergent-resistant membranes extracted from toxin-treated cells, displayed restricted diffusion in the plane of the PM in intact cells, and remained bound to GM
1
when they were immunoprecipitated. Thus, binding normally to two or perhaps only one GM
1
molecule is sufficient for association with lipid rafts in the PM and toxin action. The chimeric toxins, however, were much less potent than wt toxin, and they entered the cell by endocytosis more slowly, suggesting that clustering of GM
1
molecules by the B-subunit enhances the efficiency of toxin uptake and perhaps also trafficking to the ER.
Further Characterization of
Vibrio vulnificus
Rugose Variants and Identification of a Capsular and Rugose Exopolysaccharide Gene Cluster
Authors: Grau Brenda L. , Henk Margaret C. , Garrison Katherine L. , Olivier Brett J. , Schulz Randall M. , O'Reilly Kathy L. , Pettis Gregg S.
Published: January 2008

Capsular polysaccharide (CPS) is a major virulence factor in
Vibrio vulnificus
, and encapsulated strains have an opaque, smooth (OpS) colony morphology, while nonencapsulated strains have a translucent, smooth (TrS) colony morphology. Previously, we showed that OpS and TrS parental strains can yield a third colony type, rugose (R), and that the resulting strains, with the OpR and TrR phenotypes, respectively, form copious biofilms. Here we show that while OpR and TrR strains both produce three-dimensional biofilm structures that are indicative of rugose extracellular polysaccharide (rEPS) production, OpR strains also retain expression of CPS and are virulent in an iron-supplemented mouse model, while TrR strains lack CPS and are avirulent. Chlorine resistance assays further distinguished OpR and TrR isolates as exposure to 3 μg/ml NaOCl eradicated both OpS and OpR strains, while both TrS and TrR strains survived, but at rates which were significantly different from one another. Taken together, these results further emphasize the importance of CPS for virulence of
V. vulnificus
and establish a correlation between CPS expression and chlorine sensitivity in this organism. Using reverse transcriptase PCR, we also identified a nine-gene cluster associated with both CPS and rEPS expression in
V. vulnificus
, designated the
wcr
(
c
apsular and
r
ugose polysaccharide) locus, with expression occurring primarily in R variants. The latter results set the stage for characterization of functional determinants which individually or collectively contribute to expression of multiple EPS forms in this pathogen.
In Vitro Analysis of Tobramycin-Treated
Pseudomonas aeruginosa
Biofilms on Cystic Fibrosis-Derived Airway Epithelial Cells
Authors: Anderson Gregory G. , Moreau-Marquis Sophie , Stanton Bruce A. , O'Toole George A.
Published: January 2008

P. aeruginosa
forms biofilms in the lungs of individuals with cystic fibrosis (CF); however, there have been no effective model systems for studying biofilm formation in the CF lung. We have developed a tissue culture system for growth of
P. aeruginosa
biofilms on CF-derived human airway cells that promotes the formation of highly antibiotic-resistant microcolonies, which produce an extracellular polysaccharide matrix and require the known abiotic biofilm formation genes
flgK
and
pilB
. Treatment of
P. aeruginosa
biofilms with tobramycin reduced the virulence of the biofilms both by reducing bacterial numbers and by altering virulence gene expression. We performed microarray analysis of these biofilms on epithelial cells after treatment with tobramycin, and we compared these results with gene expression of (i) tobramycin-treated planktonic
P. aeruginosa
and (ii) tobramycin-treated
P. aeruginosa
biofilms on an abiotic surface. Despite the conservation in functions required to form a biofilm, our results show that the responses to tobramycin treatment of biofilms grown on biotic versus abiotic surfaces are different, as exemplified by downregulation of genes involved in
Pseudomonas
quinolone signal biosynthesis specifically in epithelial cell-grown biofilms versus plastic-grown biofilms. We also identified the gene PA0913, which is upregulated by tobramycin specifically in biofilms grown on CF airway cells and codes for a probable magnesium transporter, MgtE. Mutation of the PA0913 gene increased the bacterial virulence of biofilms on the epithelial cells, consistent with a role for the gene in the suppression of bacterial virulence. Taken together, our data show that analysis of biofilms on airway cells provides new insights into the interaction of these microbial communities with the host.