bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved pyroelectric detectors for single crystal adsorption calorimetry from 100 to 350 K
Authors: Lew Wanda , Lytken Ole , Farmer Jason A. , Crowe Matthew C. , Campbell Charles T.
Published: February 2010

The adsorption of atoms and molecules on single crystal surfaces allows one to produce well-characterized atomic, molecular, or dissociated adsorbates. Microcalorimetric measurement of the resulting adsorption energies, i.e., single crystal adsorption calorimetry, allows determination of the standard enthalpies of formation of these adsorbates. Methods are described for making an improved heat detector for such measurements, which greatly improves the signal-to-noise ratio, particularly at low temperatures (down to 100 K). The heat detector is an adaptation of a previously introduced design, based on a metallized pyroelectric polymer (β-polyvinylidene fluoride), which is pressed against the back of a single crystal during measurement but removed during sample preparation and annealing. The improvement is achieved by selectively etching the metal coating of the polymer, thus reducing the pyro- and piezoelectric noise from all nonessential regions of the polymer. We, furthermore, describe how to achieve a better thermal contact between the sample and the pyroelectric polymer, without increasing the thermal mass of the detector, resulting in significantly improved sensitivities for both 1 and 127 μm thick samples. The result is a detector which, using 1 μm samples, is ∼40 times more sensitive at 100 K than the traditional polymer-based detector, showing a pulse-to-pulse standard deviation in the heat of adsorption of just 1.3 kJ/mol with gas pulses containing only 1.1% of a monolayer onto Pt(111), for which 1 ML (monolayer) is 1.5×1015 species/cm2. For measurements at 300 K, where especially pyroelectric noise is likely of less concern, the new design improves the sensitivity 3.6-fold compared to the traditional detector. These improvements are furthermore used to propose a new detector design that is able to measure heats of adsorption on samples as thick as 127 μm with reasonable sensitivity.
Splitting induced generation of soliton trains in layered waveguides
Authors: Dreiden G. V. , Khusnutdinova K. R. , Samsonov A. M. , Semenova I. V.
Published: February 2010

We report first experimental registration of the splitting induced generation of a soliton train from a single incident strain soliton in two- and three-layered elastic waveguides. The origin is in the nonlinear response of the wave to an abrupt change of physical properties of the waveguide. We show a good agreement between our experimental results and theoretical estimates, based on a weakly nonlinear solution for the doubly dispersive (Boussinesq type) equation with piecewise constant coefficients for the waveguide made of a piecewise isotropic nonlinearly elastic material.
Influence of free-carrier absorption on terahertz generation from ZnTe(110)
Authors: Harrel Shayne M. , Milot Rebecca L. , Schleicher James M. , Schmuttenmaer Charles A.
Published: February 2010

ZnTe(110) is widely used as a source of terahertz radiation generated by optical rectification. However, when ZnTe(110) is excited with 800 nm light, optical rectification is not the only process which can occur. Specifically, second harmonic generation and two-photon absorption are also possibilities. In addition, free carriers generated by two-photon absorption can absorb terahertz radiation, further reducing the efficiency of optical rectification. We have used terahertz emission spectroscopy to study these effects by analyzing the dependence of the terahertz waveform on excitation fluence. At high excitation fluences, the overall efficiency is reduced and the trailing edge of the waveform is attenuated. A simple model reproduces the measured behavior.
Simulation of a prebunched free-electron laser with planar wiggler and ion channel guiding
Authors: Rouhani M. H. , Maraghechi B.
Published: February 2010

A one-dimensional and nonlinear simulation of a free-electron laser with a prebunched electron beam, a planar wiggler, and ion-channel guiding is presented. Using Maxwell’s equations and full Lorentz force equation of motion for the electron beam, a set of coupled nonlinear differential equations is derived in slowly varying amplitude and wave number approximation and is solved numerically. This set of equations describes self-consistently the longitudinal dependence of radiation amplitude, growth rates, space-charge amplitude, and wave numbers together with the evolution of the electron beam. Because of using full Lorentz force equation of motion, it is possible to treat the injection of the beam into the wiggler. The electron beam is assumed cold, propagates with a relativistic velocity, ions are assumed immobile, and slippage is ignored. The effect of prebunched electron beam on saturation is studied. Ion-channel density is varied and the results for groups I and II orbits are compared with the case when the ion channel is absent. It is found that by using an ion channel/a prebunched electron beam growth rate can be increased, saturation length can be decreased, and the saturated amplitude of the radiation can be increased.
Irradiation uniformity and zooming performances for a capsule directly driven by a 32×9 laser beams configuration
Authors: Temporal M. , Canaud B. , Le Garrec B. J.
Published: February 2010

An inertial confinement fusion capsule directly driven by laser beams has been considered. A ray-tracing package is used to evaluate the uniformity of the energy deposition and the absorption efficiency provided by the direct irradiation of the capsule. Two distinct configurations with a single laser beam or a bundle of nine laser beams associated to 32 directions of irradiation are considered. Assuming a beam-to-beam power imbalance of 5% and a super-Gaussian spatial profile of the beams intensity, is found that the configuration using the bundles provides better irradiation uniformity. The laser beams of each bundle have been divided in two groups of four and five beams with associated different focal spots in order to increase the laser-capsule coupling efficiency. A configuration saving 16% of the laser energy and limiting the irradiation nonuniformity to less than 1% has been individuated.
Interface roughness transport in terahertz quantum cascade detectors
Authors: Lhuillier Emmanuel , Ribet-Mohamed Isabelle , Rosencher Emmanuel , Patriarche Gilles , Buffaz Amandine , Berger Vincent , Carras Mathieu
Published: February 2010

Infrared detectors based on a quantum cascade have been proposed to suppress the dark current which is a limiting factor in quantum well infrared photodetectors. Those detectors have been mainly designed for the midinfrared wavelength. Operating in the terahertz range involves a complete change of regime of transport since the photon energy is lower than the optical phonon energy. Thanks to a two dimensional model of transport, we have identified interface roughness as the key interaction in such a structure. Interface parameters, evaluated by scanning transmission electron microscopy, are used to study their influence on the resistance of the device.
A theoretical study on the dynamic process of the lateral photovoltage in perovskite oxide heterostructures
Authors: Liao Leng , Jin Kui-juan , Ge Chen , Hu Chun-lian , Lu Hui-bin , Yang Guo-zhen
Published: February 2010

The lateral photovoltaic process on the La0.9Sr0.1MnO3/SrNb0.01Ti0.99O3 heterostructure is revealed by solving time-dependent drift-diffusion equations in a two dimensional scenario. We find that both the conventional lateral photovoltage (LPV) effect and the Dember effect contribute to the LPV. Under a low irradiation, the conventional LPV process plays a main role in the lateral photovoltaic process. With the laser pulse energy large enough, the Dember process becomes dominant. Due to the competition between Dember and conventional lateral photovoltage, a laterally modulated photovoltage can be obtained theoretically on the n-type side of the heterostructure.
Alcohol solubility in a lipid bilayer: Efficient grand-canonical simulation of an interfacially active molecule
Authors: Rodgers Jocelyn M. , Webb Michael , Smit Berend
Published: February 2010

We derive a new density-biased Monte Carlo technique which preserves detailed balance and improves the convergence of grand-canonical simulations of a species with a strong preference for an interfacial region as compared to the bulk. This density-biasing technique is applied to the solubility of “alcohol” molecules in a mesoscopic model of the lipid bilayer, a system which has anesthetic implications but is poorly understood.
Subterahertz oscillations from triple-barrier resonant tunneling diodes with integrated patch antennas
Authors: Sekiguchi R. , Koyama Y. , Ouchi T.
Published: February 2010

We report on subterahertz oscillations of resonant tunneling diode oscillators with an integrated patch antenna. The device consists of an InGaAs/InAlAs triple-barrier resonant tunneling diode and a patch antenna on an InP substrate. Current-voltage characteristics indicate a peak current density of 280 kA/cm2, with a peak-valley ratio of about 3 at room temperature. An oscillation frequency of 517 GHz was observed at room temperature through Fourier transformed infrared spectroscopy. The results agree with electromagnetic analysis.
Quantum instanton evaluations of surface diffusion, interior migration, and surface-subsurface transport for H/Ni
Authors: Wang Wenji , Zhao Yi
Published: February 2010

The quantum instanton approximation is extended to investigate dynamical processes of hydrogen on surface, from surface to subsurface, and between interior sites in nickel lattice. The path integral Monte Carlo and adaptive umbrella sampling techniques are employed to manipulate the quantum instanton formula. The free energy profiles along reaction paths, temperature dependence of free energies, and rates as well as diffusion coefficients are calculated for each process. The results manifest that the motions of nickel atoms beneath the surface have little effect on the hydrogen diffusion on Ni(111), and the hydrogen at the fcc binding site is much easier to get into bulk nickel than the one at the hcp site. The temperature dependence of free energy profiles also reveals that the hydrogen in the subsurface octahedral vacancy and interior tetrahedral vacancy becomes unstable at low temperatures, which proposes a temperature dependence of reaction mechanism. In addition, the relaxations of the lattices dramatically lower the free energy barriers except for the process of the hydrogen diffusion on Ni(111). The quantum motions of the lattice atoms affect the free energies little at 300 K, but they hinder the rates by 20%–40% compared with the classical motions of lattice atoms.
Width-dependent hole mobility in top-down fabricated Si-core/Ge-shell nanowire metal-oxide-semiconductor-field-effect-transistors
Authors: Hashemi Pouya , Kim Meekyung , Hennessy John , Gomez Leonardo , Antoniadis Dimitri A. , Hoyt Judy L.
Published: February 2010

Si-core/Ge-shell nanowire p-channel metal-oxide-semiconductor-field-effect-transistors with high-permittivity-dielectric/metal-gate have been demonstrated by selective epitaxial growth of Ge thin-films on the Si-nanowires fabricated by a top-down scheme. Cross-sectional transmission-electron-microscopy reveals that the epitaxial Ge shell exhibits hexagonal {111} facets, and that the Ge is defected, particularly near the Si corners. The hole mobility increases by 40% as the Si-core size is decreased from 70 to 20 nm. Finite-element simulations of the stress profile induced in the Ge channel by the gate stack suggest that a transformation in the transverse stress component from compression to tension plays a role in the mobility enhancement.
Hyaluronan: is it a biomarker for adipose development within bovine muscle?
Authors: Allingham P. G. , Greenwood P. L. , Brown T. J. , Harper G. S.
Published: February 2010

Based on an association with extracellular matrix remodelling, mitosis, proliferation and adipogenic differentiation, the glycosaminoglycan hyaluronan (HA) was assessed as a marker for intramuscular fat (IMF) development (marbling) in bovine loin muscle (longissimus dorsi, LD). Loin samples collected from the quartering site of feedlot-finished Wagyu–Angus and Jersey–Limousin steers were assayed for percentage IMF (IMF%) and HA after assignment of AUS-MEAT marbling scores. There was a moderate phenotypic correlation (r2 = 0.69) between IMF% and marbling score but little variance was explained by HA concentration. Breed was not a significant factor in marbling score or IMF% but did influence the HA concentration of the LD, with Wagyu–Angus steers having 2-fold more HA than Jersey–Limousin steers at the same marbling score. The non-linear decline in fat-adjusted HA levels as marbling score increased suggests that HA concentration was associated with lean growth potential of the muscle rather than adipogenesis. Using a different experimental approach, differences in distribution and amount of HA could not be discerned in histological sections of LD from age-matched Wagyu–Hereford heifers allocated to a low (score 1) or medium (score 3) marbling score group. These findings were consistent with the absence of differences between the two groups for other indicators of fatness (IMF% and P8 fat depth), maturity and myofibre characteristics despite an increase in oxidative capacity of the muscle with age. The data support the conclusion that the concentration of HA in the LD alone was not predictive of development of intramuscular fat.
A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of (CO)
3
Fe(
μ
-S

t

Bu)
3
Ni{SC
6
H
3
-2,6-(mesityl)
2
} and reversible CO addition at the Ni site
Authors: Ohki Yasuhiro , Yasumura Kazunari , Ando Masaru , Shimokata Satoko , Tatsumi Kazuyuki
Published: February 2010

A [NiFe] hydrogenase model compound having a distorted trigonal-pyramidal nickel center, (CO)
3
Fe(
μ
-S

t

Bu)
3
Ni(SDmp), 1 (Dmp = C
6
H
3
-2,6-(mesityl)
2
), was synthesized from the reaction of the tetranuclear Fe-Ni-Ni-Fe complex [(CO)
3
Fe(
μ
-S

t

Bu)
3
Ni]
2
(
μ
-Br)
2
, 2 with NaSDmp at -40 °C. The nickel site of complex 1 was found to add CO or CN

t

Bu at -40 °C to give (CO)
3
Fe(S

t

Bu)(
μ
-S

t

Bu)
2
Ni(CO)(SDmp), 3, or (CO)
3
Fe(S

t

Bu)(
μ
-S

t

Bu)
2
Ni(CN

t

Bu)(SDmp), 4, respectively. One of the CO bands of 3, appearing at 2055 cm
-1
in the infrared spectrum, was assigned as the Ni-CO band, and this frequency is comparable to those observed for the CO-inhibited forms of [NiFe] hydrogenase. Like the CO-inhibited forms of [NiFe] hydrogenase, the coordination of CO at the nickel site of 1 is reversible, while the CN

t

Bu adduct 4 is more robust.
Fiber structure and local coordinates for the Teichmüller space of a bordered Riemann surface
Authors: Radnell David , Schippers Eric
Published: February 2010

We show that the infinite-dimensional Teichmüller space of a Riemann surface whose boundary consists of

n
n

closed curves is a holomorphic fiber space over the Teichmüller space of an

n
n

-punctured surface. Each fiber is a complex Banach manifold modeled on a two-dimensional extension of the universal Teichmüller space. The local model of the fiber, together with the coordinates from internal Schiffer variation, provides new holomorphic local coordinates for the infinite-dimensional Teichmüller space.
Growth Factorerv1-like Modulates Drp1 to Preserve Mitochondrial Dynamics and Function in Mouse Embryonic Stem Cells
Authors: Todd Lance R. , Damin Matthew N. , Gomathinayagam Rohini , Horn Sarah R. , Means Anthony R. , Sankar Uma
Published: February 2010

The relationship of mitochondrial dynamics and function to pluripotency are rather poorly understood aspects of stem cell biology. Here we show that growth factor erv1-like (Gfer) is involved in preserving mouse embryonic stem cell (ESC) mitochondrial morphology and function. Knockdown (KD) of Gfer in ESCs leads to decreased pluripotency marker expression, embryoid body (EB) formation, cell survival, and loss of mitochondrial function. Mitochondria in Gfer-KD ESCs undergo excessive fragmentation and mitophagy, whereas those in ESCs overexpressing Gfer appear elongated. Levels of the mitochondrial fission GTPase dynamin-related protein 1 (Drp1) are highly elevated in Gfer-KD ESCs and decreased in Gfer-overexpressing cells. Treatment with a specific inhibitor of Drp1 rescues mitochondrial function and apoptosis, whereas expression of Drp1-dominant negative resulted in the restoration of pluripotency marker expression in Gfer-KD ESCs. Altogether, our data reveal a novel prosurvival role for Gfer in maintaining mitochondrial fission–fusion dynamics in pluripotent ESCs.
A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
Authors: Chen Liang
Published: February 2010

We conducted a reanalysis of genome-wide histone H3 tail methylation data in mammalian pluripotent and differentiated cells. We show that the promoters marked with histone H3 lysine 27 trimethylation (H3K27me3) tend to have more exonic positions in the promoter regions. However, this is not due to any preferential marking on exons over introns by H3K27me3. The relationship is also independent the status of histone H3 lysine 4 trimethylation (H3K4me3) mark, CpG content and the platforms used in the high-throughput profiling of histone modifications. It provides evidence for the link between histone modifications and transcribed exons in promoter regions.

Contact:  liang.chen@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Alcohol and Depression
Authors: Patel Ishani
Published: February 2010

‘Problem drinking’ is a major national concern as it can lead to long-term serious physical and mental health problems. Alcohol can mimic or accentuate many of the symptoms of depression: low mood, low energy, changes in appetite, weight or sleep pattern, poor concentration, feelings of guilt or worthlessness and suicidal ideation. Many people with depression can develop an alcohol problem as they may ‘self-medicate’ to feel more energetic or cheerful. In severe cases, alcohol misuse can lead to impaired judgement and increase the risk of suicide. Patients with severe depression and alcohol dependence coexisting are considered to have a ‘dual diagnosis’ and often require support from mental health specialist services such as community alcohol team in addition to primary care support.
Alcoholic Pancreatitis
Authors: Potter Andrew
Published: February 2010

Alcohol associated inflammation of the pancreas is an important and serious condition with which the GP must be familiar. The range of disease burden, from a potentially fatal attack of acute pancreatitis to the development of chronic pain, maldigestion and diabetes resulting from chronic pancreatitis must be recognized and managed promptly. Patients with alcoholic pancreatitis therefore require a large input of both primary and secondary care, and the GP has a pivotal role in coordinating this. The aim of this article is to familiarize the reader with the spectrum of alcoholic pancreatitis, its presentation and management and provide a framework to approaching the alcoholic patient with signs and symptoms of pancreatitis.
Evolution of virulence when transmission occurs before disease
Authors: Osnas Erik E. , Dobson Andrew P.
Published: February 2010

Most models of virulence evolution assume that transmission and virulence are constant during an infection. In many viral (HIV and influenza), bacterial (TB) and prion (BSE and CWD) systems, disease-induced mortality occurs long after the host becomes infectious. Therefore, we constructed a model with two infected classes that differ in transmission rate and virulence in order to understand how the evolutionarily stable strategy (ESS) depends on the relative difference in transmission and virulence between classes, on the transition rate between classes and on the recovery rate from the second class. We find that ESS virulence decreases when expressed early in the infection or when transmission occurs late in an infection. When virulence occurred relatively equally in each class and there was disease recovery, ESS virulence increased with increased transition rate. In contrast, ESS virulence first increased and then decreased with transition rate when there was little virulence early in the infection and a rapid recovery rate. This model predicts that ESS virulence is highly dependent on the timing of transmission and pathology after infection; thus, pathogen evolution may either increase or decrease virulence after emergence in a new host.
Sperm midpiece length predicts sperm swimming velocity in house mice
Authors: Firman Renée C. , Simmons Leigh W.
Published: February 2010

Evolutionary biologists have argued that there should be a positive relationship between sperm size and sperm velocity, and that these traits influence a male's sperm competitiveness. However, comparative analyses investigating the evolutionary associations between sperm competition risk and sperm morphology have reported inconsistent patterns of association, and
in vitro
sperm competition experiments have further confused the issue; in some species, males with longer sperm achieve more competitive fertilization, while in other species males with shorter sperm have greater sperm competitiveness. Few investigations have attempted to address this problem. Here, we investigated the relationship between sperm morphology and sperm velocity in house mice (
Mus domesticus
). We conducted
in vitro
sperm velocity assays on males from established selection lines, and found that sperm midpiece size was the only phenotypic predictor of sperm swimming velocity.
Transferring vertically aligned carbon nanotubes onto a polymeric substrate using a hot embossing technique for microfluidic applications
Authors: Mathur A. , Roy S. S. , McLaughlin J. A.
Published: February 2010

We explored the hot embossing method for transferring vertically aligned carbon nanotubes (CNTs) into microfluidic channels, fabricated on poly-methyl-methacrylate (PMMA). Patterned and unpatterned CNTs were synthesized by microwave plasma-enhanced chemical vapour deposition on silicon to work as a stamp. For hot embossing, 115°C and 1 kN force for 2 min were found to be the most suitable parameters for the complete transfer of aligned CNTs on the PMMA microchannel. Raman and SEM studies were used to analyse the microstructure of CNTs before and after hot embossing. The PMMA microparticles with dimensions (approx. 10 µm in diameter) similar to red blood cells were successfully filtered using laminar flow through these microfluidic channels. Finally, a microfluidic-based point-of-care device for blood filtration and detection of bio-molecules is drawn schematically.
Green–Naghdi fluid with non-thermal equilibrium effects
Authors: Straughan B.
Published: February 2010

A. E. Green, FRS and P. M. Naghdi developed a new theory of continuum mechanics based on an entropy identity rather than an entropy inequality. In particular, within the framework of this theory, they developed a new set of equations to describe viscous flow. The new theory additionally involves vorticity and spin of vorticity. We here develop the theory of Green and Naghdi to be applicable to thermal convection in a fluid in which is suspended a collection of minute metallic-like particles. Thus, we develop a non-Newtonian theory we believe capable of describing a nanofluid. Numerical results are presented for copper oxide or aluminium oxide particles in water or in ethylene glycol. Such combinations are used in real nanofluid suspensions.
Dispersion of biased swimming micro-organisms in a fluid flowing through a tube
Authors: Bees Martin A. , Croze Ottavio A.
Published: February 2010

Classical Taylor–Aris dispersion theory is extended to describe the transport of suspensions of self-propelled dipolar cells in a tubular flow. General expressions for the mean drift and effective diffusivity are determined exactly in terms of axial moments and compared with an approximationa laTaylor. As in the Taylor–Aris case, the skewness of a finite distribution of biased swimming cells vanishes at long times. The general expressions can be applied to particular models of swimming micro-organisms, and thus be used to predict swimming drift and diffusion in tubular bioreactors, and to elucidate competing unbounded swimming drift and diffusion descriptions. Here, specific examples are presented for gyrotactic swimming algae.
The reproduction number of seasonal influenza epidemics in Brazil, 1996–2006
Authors: Chowell Gerardo , Viboud Cécile , Simonsen Lone , Miller Mark , Alonso Wladimir J.
Published: February 2010

The transmission dynamics of influenza in tropical regions are poorly understood. Here we explore geographical variations in the reproduction number of influenza across equatorial, tropical and subtropical areas of Brazil, based on the analysis of weekly pneumonia and influenza (P&I) mortality time series in 27 states. The reproduction number (R) was low on average in Brazil (mean = 1.03 (95% CI 1.02–1.04), assuming a serial interval of 3 days). Estimates of the reproduction number were slightly lower for Brazil than for the USA or France (difference in meanR= 0.08,p< 0.01) and displayed less between-year variation (p< 0.001). Our findings suggest a weak gradient in the reproduction number with population size, whereRincreases from low population in the North to high population in the South of Brazil. Our low estimates of the reproduction number suggest that influenza population immunity could be high on average in Brazil, potentially resulting in increased viral genetic diversity and rate of emergence of new variants. Additional epidemiological and genetic studies are warranted to further characterize the dynamics of influenza in the tropics and refine our understanding of the global circulation of influenza viruses.
Productivity responses of a widespread marine piscivore,
Gadus morhua
, to oceanic thermal extremes and trends
Authors: Mantzouni Irene , MacKenzie Brian R.
Published: February 2010

Climate change will have major consequences for population dynamics and life histories of marine biota as it progresses in the twenty-first century. These impacts will differ in magnitude and direction for populations within individual marine species whose geographical ranges span large gradients in latitude and temperature. Here we use meta-analytical methods to investigate how recruitment (i.e. the number of new fish produced by spawners in a given year which subsequently grow and survive to become vulnerable to fishing gear) has reacted to temperature fluctuations, and in particular to extremes of temperature, in cod populations throughout the north Atlantic. Temperature has geographically explicit effects on cod recruitment. Impacts differ depending on whether populations are located in the upper (negative effects) or in the lower (positive effects) thermal range. The probabilities of successful year-classes in populations living in warm areas is on average 34 per cent higher in cold compared with warm seasons, whereas opposite patterns exist for populations living in cold areas. These results have implications for cod dynamics, distributions and phenologies under the influence of ocean warming, particularly related to not only changes in the mean temperature, but also its variability (e.g. frequency of exceptionally cold or warm seasons).
Pseudomonas aeruginosa secreted factors impair biofilm development in Candida albicans
Authors: Holcombe Lucy J. , McAlester Gordon , Munro Carol A. , Enjalbert Brice , Brown Alistair J. P. , Gow Neil A. R. , Ding Chen , Butler Geraldine , O'Gara Fergal , Morrissey John P.
Published: February 2010

Signal-mediated interactions between the human opportunistic pathogensPseudomonas aeruginosaandCandida albicansaffect virulence traits in both organisms. Phenotypic studies revealed that bacterial supernatant from fourP. aeruginosastrains strongly reduced the ability ofC. albicansto form biofilms on silicone. This was largely a consequence of inhibition of biofilm maturation, a phenomenon also observed with supernatant prepared from non-clinical bacterial species. The effects of supernatant on biofilm formation were not mediated via interference with the yeast–hyphal morphological switch and occurred regardless of the level of homoserine lactone (HSL) produced, indicating that the effect is HSL-independent. A transcriptome analysis to dissect the effects of theP. aeruginosasupernatants on gene expression in the early stages ofC. albicansbiofilm formation identified 238 genes that exhibited reproducible changes in expression in response to all four supernatants. In particular, there was a strong increase in the expression of genes related to drug or toxin efflux and a decrease in expression of genes associated with adhesion and biofilm formation. Furthermore, expression ofYWP1, which encodes a protein known to inhibit biofilm formation, was significantly increased. Biofilm formation is a key aspect ofC. albicansinfections, therefore the capacity ofP. aeruginosato antagonize this has clear biomedical implications.
Morphological study of Czochralski-grown lanthanide orthovanadate single crystals and implications on the mechanism of bulk spiral formation
Authors: Cong Hengjiang , Zhang Huaijin , Sun Shangqian , Yu Yonggui , Yu Wentao , Yu Haohai , Zhang Jian , Wang Jiyang , Boughton Robert I.
Published: February 2010

Single crystals of monoclinic Nd:LaVO4with dimensions up to Ø28 × 21 mm have been grown from the near-stoichiometric melt by the Czochralski method, making use of various seed orientations that are perpendicular to the (010), (10{\overline 1}), (001) and (00{\overline 1}) crystal planes. A sample was also prepared with the seed orientation in an arbitrary direction relative to the crystal. The anisotropic properties of the crystal are manifested in the growth morphology of the as-grown crystals, where different degrees of bulk spiral growth were observed. It was also found that employing the (001) or (00{\overline 1}) seed faces severely suppressed the bulk spiral growth, and thus high quality and large-scale Nd:LaVO4crystals were obtained. The constituent segregation coefficients and high-temperature stability, including the melting point, were determined and evaluated. Based on the attachment energy model of Hartman–Perdok theory, morphology predictions were made for monoclinic LaVO4and tetragonal YVO4orthovanadate single crystals. Correlating with the as-grown morphology of both crystals developed along different seed orientations, a theoretical explanation is provided for the influences of seed crystals on bulk spiral formation, crystal quality and utilization ratio. It suggests that breaking the axial symmetry of the ideal atomic level interface between crystal and melt plays a crucial triggering role in bulk spiral formation in the Czochralski growth of lanthanide orthovanadate single crystals. Selecting a proper seed orientation that yields such a highly axially symmetric surface structure consisting of a series of large-area facets with similar growth velocities can greatly reduce bulk spiral formation and thus is preferable in the Czochralski growth of large-sized low-symmetry oxide crystals.
Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee–Richards surfaces (PGALRS)
Authors: Bernstein Herbert J. , Craig Paul A.
Published: February 2010

ThePGALRS(pseudo-Gaussian approximation to Lee–Richards surfaces) algorithm is discussed. By modeling electron density with unphysical pseudo-Gaussian atoms, the Lee–Richards surface can be approximated by a contour level of that density in time approximately linear in the number of atoms. Having that contour level, the atoms and residues closest to that surface can be identified in average timeO[n2/3log(n)] using aNearTree-based nearest neighbor search. If a high-quality Lee–Richards surface is required, then, as a final stage, one of the standard Lee–Richards algorithms can be used but considering only the previously identified surface residues; the typical cost is thereby reduced toO[n2/3log(n)], making the overall average time for all the stepsO(n). For very large macromolecules, such a reduction in computational burden may be essential to being able to render a meaningful molecular surface. This approach extends the feasible range of application for existing molecular surface software, such asMSMS, to larger macromolecules, especially to macromolecules with more than 50 000 atoms, and can be used as a starting point for surface-based (as opposed to backbone-based) motif identification,e.g.usingProMol.
CONEX, a program for angular calibration and averaging of two-dimensional powder scattering patterns
Authors: Gommes Cedric J. , Goderis Bart
Published: February 2010

CONEXis a Windows application for converting series of two-dimensional X-ray powder patterns measured on flat two-dimensional detectors into one-dimensional scattering patterns. It is based on the rigorous use of scattering patterns of calibration samples to determine the three-dimensional position of the detector, with respect to the sample and to the beam. This enables correction of the data for geometric distortions, even when the detector is highly tilted and not centred on the beam.
Coiled-coil conformation of a pentamidine–DNA complex
Authors: Moreno Tadeo , Pous Joan , Subirana Juan A. , Campos J. Lourdes
Published: February 2010

The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)2with pentamidine is presented. The duplex was found to have a mixed structure containing Watson–Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A·T base pairs.
Rapid model building of α-helices in electron-density maps
Authors: Terwilliger Thomas C.
Published: February 2010

A method for the identification of α-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where α-helices appear as tubes of density. The positioning and direction of the α-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. An average of 63% of the α-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled α-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 Å.
FUNCTIONAL PROJECTIONS OF PREDICATES: EXPERIMENTAL EVIDENCE FROM COORDINATE STRUCTURE PROCESSING
Authors: Dubinsky Stanley , Egan Marie , Schmauder A. René , Traxler Matthew J.
Published: February 2010

Abstract. This paper reports the results of six experiments involving an online selfpaced reading task that examine the processing of coordinate small clause predicate phrases versus coordinated argument NPs. The results have particular significance for the analysis of small clause complement has an Agr projection associated with it. An adequate explanation of the processing of small claue coordination is shown to motivate a new parsing principle, Coordination Feature‐matching, which accounts for the longer reading times observed for the coordination of predicates in small clause complements.
Expression of NDRG2 in esophageal squamous cell carcinoma
Authors: Shi Hai , Li Nanlin , Li Shujun , Chen Changsheng , Wang Weizhong , Xu Chunsheng , Zhang Jian , Jin Haifeng , Zhang Hongwei , Zhao Huadong , Song Wenjie , Feng Quanxin , Feng Xiangying , Shen Xin , Yao Libo , Zhao Qingchuan
Published: February 2010

N‐Myc downstream‐regulated gene 2 (NDRG2), a new member of the N‐Myc downstream‐regulated gene family, has been found to be a differentially expressed gene involved in a variety of cancers. The present study aimed to investigate the expression of NDRG2 in esophageal squamous cell carcinoma (ESCC). Immunohistochemistry was performed in 154 samples from patients with ESCC to detect the expression level of NDRG2 and C‐MYC. Results indicated that the expression level of NDRG2 in the cancer samples was significantly lower than that in normal tissues; the trend of C‐MYC was the reverse. The Wilcoxon–Mann–Whitney test showed significant difference in the expression of NDRG2 in patients with different T stage, TNM stage, and differentiation degree of cancers (P = 0.036, 0.031, 0.001, respectively). Patients in stages I and II were followed up for 5 consecutive years and Kaplan–Meier survival analysis demonstrated that the survival time of ESCC patients with high expression of NDRG2 was longer than those with low expression during the 5‐year follow‐up period (P = 0.0018). Cox regression analysis indicated that low expression of NDRG2, cancer stage of pT1, and distant organ metastasis (pM1) were the independent poor prognostic factors of ESCC (P = 0.004, 0.019, 0.0013, respectively). Furthermore, up‐regulation of NDRG2 was introduced to ESCC cell lines (EC9706 and EC109) by plasmid transfection. In vivo and in vitro studies indicated that overexpression of NDRG2 markedly reduced proliferation and promoted the apoptosis of EC9706 and EC109 cells. In summary, our results demonstrated that NDRG2 played an important role in the proliferation of ESCC cells and the expression of NDRG2 in ESCC was closely related with the prognosis.

(Cancer Sci 2010; 101: 1292–1299)
Diagnostic performance of computer tomography, magnetic resonance imaging, and positron emission tomography or positron emission tomography/computer tomography for detection of metastatic lymph nodes in patients with cervical cancer: Meta‐analysis
Authors: Choi Hyuck Jae , Ju Woong , Myung Seung Kwon , Kim Yeol
Published: February 2010

We performed a meta‐analysis to compare diagnostic performances of computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET or PET/CT), for detection of metastatic lymph nodes in patients with cervical cancer. We searched MEDLINE (PubMed), EMBASE and the Cochrane Review database in December 2007. All articles were independently reviewed and selected by three evaluators. We estimated a summary receiver operating characteristic (sROC) curve. The area under the curve (AUC), Q*, and pooled weighted estimates of sensitivity and specificity for each modality by patient‐based and region‐ or node‐based data analyses and conducted pair‐wise comparisons between modalities using the two‐sample Z‐test. Forty‐one of 768 initially identified studies were included in the meta‐analysis. In a patient‐based data analysis, PET or PET/CT showed the highest pooled sensitivity (82%) and specificity (95%), while CT showed 50% and 92%; and MRI, 56% and 91%, respectively. The AUC (0.9641) and Q* (0.9106) of PET or PET/CT were significantly higher than those of MRI (AUC = 0.8270; Q* = 0.7599), both P < 0.001. In region‐ or node‐based data analysis, sensitivities of CT (52%) and PET or PET/CT (54%) were higher than that of MRI (38%), P < 0.02 and P < 0.001, respectively, while specificities of MRI (97%) and PET or PET/CT (97%) were higher than that of CT (92%), both P < 0.001. The AUC and Q* showed no significant difference among CT, MRI, and PET or PET/CT. PET or PET/CT had an overall higher diagnostic performance than did CT or MRI in detecting metastatic lymph nodes in patients with cervical cancer. (Cancer Sci 2010)
Response of native ungulates to drought in semi‐arid Kenyan rangeland
Authors: Augustine David J.
Published: February 2010

The distribution and abundance of native ungulates were measured on commercially managed, semi‐arid rangeland in central Kenya over a 3‐year period that encompassed severe drought and above‐average rainfall. Native ungulate biomass density averaged 5282 kg km−2over the study and was dominated by elephant (Loxodonta africana), impala (Aepyceros melampus) and dik‐dik (Madoqua kirkii). Biomass density of domestic cattle (Bos taurus) averaged 2280 kg km−2during the study. Responses of native ungulates to severe drought were variable. Impala densities were similar to or greater than densities for similar habitat in protected areas, and varied from 12 to 16 km−2during and following the drought to 24–29 km−2following above‐average rainfall. Dik‐dik densities were also greater than densities reported for protected areas and were surprisingly stable throughout the study despite the wide annual fluctuations in rainfall. Elephant migrated out of the region during drought but were present at high densities (2.9–5.2 km−2) during wet seasons, consistent with telemetry studies emphasizing the importance ofAcaciabushland habitat on commercial rangelands for the migratory portion of the Laikipia–Samburu elephant population. Results show that substantial densities of native browsing and mixed‐feeding ungulates can occur on rangeland managed for commercial beef production and suggest that the capacity for ungulates to move over large spatial scales (>100 km2) and to shift distributions in response to locally variable thunderstorms may be important for sustaining these populations.
Historical biogeography of the coffee family (Rubiaceae, Gentianales) in Madagascar: case studies from the tribes Knoxieae, Naucleeae, Paederieae and Vanguerieae
Authors: Wikström N. , Avino M. , Razafimandimbison S. G. , Bremer B.
Published: February 2010

Aim  In Madagascar the family Rubiaceae includes an estimated 650 species representing 95 genera. As many as 98% of the species and 30% of the genera are endemic. Several factors make the Rubiaceae a model system for developing an understanding of the origins of the Malagasy flora. Ancestral area distributions are explicitly reconstructed for four tribes (Knoxieae, Naucleeae, Paederieae and Vanguerieae) with the aim of understanding how many times, and from where, these groups have originated in Madagascar.

Location  Indian Ocean Basin, with a focus on Madagascar.

Methods  Bayesian phylogenetic analyses are conducted on the four tribes. The results are used for reconstructing ancestral areas using dispersal–vicariance analyses. Phylogenetic uncertainties in the reconstructions are accounted for by conducting all analyses on the posterior distribution from the analyses.

Results  Altogether, 11 arrivals in Madagascar (one in Paederieae, five in Knoxieae, three in Vanguerieae, and two in Naucleeae) are reconstructed. The most common pattern is a dispersal event (followed by vicariance) from Eastern Tropical Africa. The Naucleeae and Paederieae in Madagascar differ and originate from Asia. Numerous out‐of‐Madagascar dispersals, mainly in the dioecious Vanguerieae, are reconstructed.

Main conclusions  The four tribes arrived several times in Madagascar via dispersal events from Eastern Tropical Africa, Southern Africa and Tropical Asia. The presence of monophyletic groups that include a number of species only found in Madagascar indicates that much endemism in the tribes results from speciation events occurring well after their arrival in Madagascar. Madagascar is the source of origin for almost all Rubiaceae found on the neighbouring islands of the Comoros, Mascarenes and Seychelles.
Dried leaves of Rosmarinus officinalis as a treatment for streptococcosis in tilapia
Authors: Zilberg D , Tal A , Froyman N , Abutbul S , Dudai N , Golan‐Goldhirsh A
Published: February 2010

Dietary application of dried Rosmarinus officinalis (rosemary) leaves as a treatment for streptococcal infection was studied in tilapia, Oreochromis sp. Feeding with dried rosemary leaves significantly reduced mortality following infection with Streptococcus iniae: 44% mortality in the group fed 8% rosemary, similar to oxytetracycline treatment (43% mortality), and significantly lower than the control (65%). Dietary administration of 16% rosemary significantly reduced mortality because of Streptococcus agalactiae infection in 44 g fish (62% and 76% in 16% rosemary and control, respectively), but not in a similar experiment conducted with 5.5 g fish. The antibacterial effect of rosemary on S. iniae was studied. Activity of rosemary cultivar Israel was reduced during the winter, but there was no significant change in cultivars Oranit and Star. Storage of powdered rosemary leaves at 50 °C resulted in fourfold and eightfold higher MIC24 h values after 3 and 4.5 months, respectively. Storage at −20 °C, 4 °C and 25 °C and autoclaving (120 °C) each resulted in a twofold increase in MIC24 h. Repeated exposures of S. iniae to rosemary did not affect minimal inhibitory concentration, suggesting no development of resistance to rosemary.
Salmonid alphavirus (SAV) and pancreas disease (PD) in Atlantic salmon, Salmo salar L., in freshwater and seawater sites in Norway from 2006 to 2008
Authors: Jansen M D , Taksdal T , Wasmuth M A , Gjerset B , Brun E , Olsen A B , Breck O , Sandberg M
Published: February 2010

A cohort study was initiated in the spring of 2006 to investigate epidemiological aspects and pathogenesis of salmonid alphavirus (SAV) subtype 3 infections and pancreas disease (PD). The aims were to assess involvement of the freshwater production phase, the extent and frequency of subclinical infections and to follow PD‐affected populations throughout the entire seawater production cycle, as well as investigate possible risk factors for PD outbreaks. Fish groups from 46 different Atlantic salmon freshwater sites in six counties were sampled once prior to seawater transfer and followed onto their seawater sites. A total of 51 Atlantic salmon seawater sites were included, and fish groups were sampled three times during the seawater production phase. SAV subtype 3 was not identified by real‐time RT‐PCR from samples collected in the freshwater phase, nor were any SAV‐neutralizing antibodies or histopathological changes consistent with PD. In the seawater phase, SAV was detected in samples from 23 of 36 (63.9%) studied sites located within the endemic region. No SAV subtype 3 was detected in samples from seawater sites located outside the endemic region. The cumulative incidence of PD during the production cycle amongst sites with SAV detected was 87% (20 of 23 sites). Average fish weight at time of PD diagnosis ranged from 461 to 5978 g, because of a wide variation in the timing of disease occurrence throughout the production cycle. Mortality levels following a PD diagnosis varied greatly between populations. The mean percentage mortality was 6.9% (±7.06) (range 0.7–26.9), while the mean duration of increased mortality following PD diagnosis was 2.8 months (±1.11) (range 1–6).