bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometric interpretation of previtrification in hard sphere liquids
Authors: Brito Carolina , Wyart Matthieu
Published: July 2009

We derive a microscopic criterion for the stability of hard sphere configurations and we show empirically that this criterion is marginally satisfied in the glass. This observation supports a geometric interpretation for the initial rapid rise in viscosity with packing fraction or previtrification. It also implies that barely stable soft modes characterize the glass structure, whose spatial extension is estimated. We show that both the short-term dynamics and activation processes occur mostly along those soft modes and we study some implications of these observations. This article synthesizes new and previous results [C. Brito and M. Wyart, Europhys. Lett. 76, 149 (2006); C. Brito and M. Wyart, J. Stat. Mech.: Theory Exp. 2007, L08003] in a unified view.
Self-assembled Mn5Ge3 nanomagnets close to the surface and deep inside a Ge1−xMnx epilayer
Authors: Lechner R. T. , Holý V. , Ahlers S. , Bougeard D. , Stangl J. , Trampert A. , Navarro-Quezada A. , Bauer G.
Published: July 2009

Under defined growth conditions ferromagnetic hexagonal Mn5Ge3 precipitates are formed in cubic Ge1−xMnx epilayers. To study the topotaxial relationship of these nanomagnets we perform x-ray diffraction experiments in coplanar as well as in grazing incidence geometries at synchrotron sources. Additionally, to the well defined topotaxial relation derived for buried nanomagnets deep within the Ge layer, we found an additional class of Mn5Ge3 precipitates very close to the surface, with larger inclusion diameter and several different crystallographic orientations with respect to the buried ones.
Iteration stability for simple Newtonian stellar systems
Authors: Price Richard H. , Markakis Charalampos , Friedman John L.
Published: July 2009

For an equation of state in which pressure is a function only of density, the analysis of Newtonian stellar structure is simple in principle if the system is axisymmetric or consists of a corotating binary. It is then required only to solve two equations: one stating that the “injection energy,” κ, a potential, is constant throughout the stellar fluid, and the other being the integral over the stellar fluid to give the gravitational potential. An iterative solution of these equations generally diverges if κ is held fixed, but converges with other choices. To understand the mathematical reasons for this, we start the iteration from an approximation that is perturbatively different from the actual solution and, for the current study, confine ourselves to spherical symmetry. A cycle of iteration is treated as a linear “updating” operator, and the properties of the linear operator, especially its spectrum, determine the convergence properties. We analyze updating operators both in the finite dimensional space corresponding to a finite difference representation of the problem and in the continuum, and we find that the fixed-κ operator is self-adjoint and generally has an eigenvalue greater than unity; in the particularly important case of a polytropic equation of state with index greater than unity, we prove that there must be such an eigenvalue. For fixed central density, on the other hand, we find that the updating operator has only a single eigenvector with zero eigenvalue and is nilpotent in finite dimension, thereby giving a convergent solution.
Asymptotic flatness at spatial infinity in higher dimensions
Authors: Tanabe Kentaro , Tanahashi Norihiro , Shiromizu Tetsuya
Published: July 2009

A definition of asymptotic flatness at spatial infinity in d dimensions (d≥4) is given using the conformal completion approach. Then we discuss asymptotic symmetry and conserved quantities. As in four dimensions, in d dimensions we should impose a condition at spatial infinity that the “magnetic” part of the d-dimensional Weyl tensor vanishes at a faster rate than the “electric” part does in order to realize the Poincare symmetry as asymptotic symmetry and construct the conserved angular momentum. However, we found that an additional condition should be imposed in d>4 dimensions.
Viscoelastic properties of crystals
Authors: Williams Stephen R. , Evans Denis J.
Published: July 2009

We examine the question of whether fluids and crystals are differentiated on the basis of their zero frequency shear moduli or their limiting zero frequency shear viscosity. We show that while fluids, in contrast with crystals, do have a zero value for their shear modulus, in contradiction to a widespread presumption, a crystal does not have an infinite or exceedingly large value for its limiting zero frequency shear viscosity. In fact, while the limiting shear viscosity of a crystal is much larger than that of the liquid from which it is formed, its viscosity is much less than that of the corresponding glass that may form assuming the liquid is a good enough glass former.
Random matrices with external source and KP τ functions
Authors: Wang Dong
Published: July 2009

In this paper we prove that the partition function in the random matrix model with external source is a KP τ function.
Diffusion in a nonequilibrium binary mixture of hard spheres swelling at different rates
Authors: Popov Alexander V. , Hernandez Rigoberto
Published: July 2009

The nonequilibrium dynamics of a probe in a driven binary mixture of effective hard-sphere particles has been measured computationally in molecular dynamics simulations so as to obtain a better understanding of the energy and spatial correlations that persist through the coupling between the binary components. The driving of the particles is manifested through a change of the effective volume (or equivalently, diameter of the hard spheres) and each component is assumed to have a different time-dependent profile. Such a driving is possible in a suspension of one-component colloidal mesogens, for example, in which the particle volume has been seen to change with pH or temperature changes in the solution. It can also be realized by growing nanoparticles during a nucleation process. The full particle dynamics has been projected onto Langevin-type models of the probe motion by representing the environment using two different reservoirs and distinct bath-probe coupling coefficients with different nonstationary properties. The bath particles corresponding to each reservoir swell with time at various rates, nonsynchronously changing their volume fractions. Under the assumption of a weak bath-bath interactions, the coupling coefficients between the probe and two baths are expressed via those in the case of a simple—consisting of one bath—environment. The general form of the resulting irreversible Langevin equation is in agreement with the MD simulations of a hard sphere probe particle diffusing in the nonstationary binary mixture.
Oscillating current observed in field emission from a single zinc oxide nanostructure and the physical mechanism
Authors: Xiao Z. M. , She J. C. , Li Z. B. , Yang Y. H. , Yang G. W. , Deng S. Z. , Chen Jun , Xu N. S.
Published: July 2009

A phenomenon of field emission instability is reported. Field emission current oscillation was observed when a single zinc oxide (ZnO) one dimensional nanostructure operated at high current density. As a result, the radius curvature of the nanoemitter apex was sharpened to less than 15 nm. This indicates the oscillation was associated with melting of the emitter material. We found that the oscillation may be ascribed to (i) the behavior of charging and (ii) the shape changing of a metallic liquid ball that exists at the tip apex under high electric field. The net force of electric force and surface tension modifies the radius of the apex periodically, which results in the oscillation of field emission current. This finding may enhance the understanding of the physical process of field emission from ZnO nanostructures.
Grazing incidence small angle x-ray scattering study of the structure of nanoporous ultralow-k dielectrics prepared by plasma enhanced chemical vapor deposition
Authors: Jousseaume V. , Gourhant O. , Zenasni A. , Maret M. , Simon J.-P.
Published: July 2009

This paper focuses on the structure of nanoporous SiOCH thin films deposited using a porogen approach by plasma enhanced chemical vapor deposition (PECVD). The grazing incidence small angle x-ray scattering signal demonstrates the existence of a biphase pattern in hybrid films, deposited by PECVD. After porogen removal, there are few differences between pore pattern of optimized ultraviolet (UV) illuminated and thermally treated samples: anisotropy of the pore pattern is observed in both samples, probably due to the porogen degradation. Finally, a kinetic study of porogen degradation by UV shows that the porous structure develops in only a few minutes.
Particle clusters settling under gravity in a viscous fluid
Authors: Alabrudziński Sławomir , Ekiel-Jeżewska Maria L. , Chehata-Gómez Daniel , Kowalewski Tomasz A.
Published: July 2009

Clusters made of a small number of close solid spherical particles at a random configuration, sedimenting through a viscous fluid at small Reynolds number, were experimentally investigated at a short-time scale. The cluster settling velocities were measured and shown to be well approximated by the ensemble-averaged formula derived earlier for the uniform distribution of the point particles inside a spherical volume. It was emphasized that the “effective radius” of this volume in general should be smaller than the actual radius of a cluster made of the spheres, and the relation between both radii was determined. The formula was also shown to account well for the gravitational settling of rigid conglomerates, measured and computed elsewhere.
High-repetition-rate optical delay line using a micromirror array and galvanometer mirror for a terahertz system
Authors: Kitahara Hideaki , Tani Masahiko , Hangyo Masanori
Published: July 2009

We developed a high-repetition-rate optical delay line based on a micromirror array and galvanometer mirror for terahertz time-domain spectroscopy. The micromirror array is fabricated by using the x-ray lithographic technology. The measurement of terahertz time-domain waveforms with the new optical delay line is demonstrated successfully up to 25 Hz.
Development of a simultaneous dual-ablation apparatus and preparation of compositionally gradient (Sr1−xEux)Al2O4 thin films
Authors: Kusaka Yu , Suzuki Tsuneo , Kato Ariyuki , Yunogami Takashi , Nakayama Tadachika , Suematsu Hisayuki , Niihara Koichi
Published: July 2009

A simultaneous dual-ablation apparatus using a pulsed laser was developed for preparation of compositionally gradient thin films to explore novel compounds. Unlike other compositionally gradient thin film preparation apparatus, two targets rotated by motors were installed in and two beams splitted from a single laser were introduced to a vacuum chamber. With this apparatus, a (Sr1−xEux)Al2O4 compositionally gradient thin film was prepared. The phase and the photoluminescence properties were investigated. The Eu optimal composition for the emission intensity in the (Sr1−xEux)Al2O4 system was found to be x=0.06.
The role of threading dislocations and unintentionally incorporated impurities on the bulk electron conductivity of In-face InN
Authors: Gallinat Chad S. , Koblmüller Gregor , Speck James S.
Published: July 2009

The origin of bulk electrons in In-face InN has been studied by considering the effects of both unintentionally incorporated impurities and threading dislocation densities on electron transport properties. The concentration of unintentionally incorporated oxygen and hydrogen scaled with the bulk electron concentration while threading dislocations had no discernable effect on the electron concentration. We conclude that unintentional impurities were the significant source of electrons and threading dislocations acted only as scattering centers limiting the electron mobility in as-grown InN films. Further, we present In-face InN growth techniques controlling the incorporation of oxygen and hydrogen and reducing threading dislocation densities.
Magnetized microplasmas generated in a narrow quartz tube
Authors: Yoshiki Hiroyuki
Published: July 2009

Magnetized He and Ar microplasmas in a narrow quartz tube having an inner diameter of 1 mm (referred to as magnetized capillary microplasmas) are reported. A capillary microplasma can be magnetized by the occurrence of a radio frequency (rf) oscillating E×B drift motion along the tube axis, provided that the external magnetic field is perpendicular to both the rf electric field and the tube axis and that the Larmor radius of an electron is sufficiently smaller than both the electron mean free path and the tube radius. When a magnetic flux density of 0.4 T was applied, a magnetized capillary microplasma could be generated at gas pressures lower than 1.5 kPa because the electron cyclotron frequency exceeds the electron-neutral collision frequency. However, plasma ignition at low gas pressure below 4 kPa was hardly taken place without a strong magnetic field. The Ar atomic excitation temperature was estimated by optical emission spectroscopy and found to increase dramatically from 5000 to 15 000 K when the gas pressure was reduced from 4 to 0.2 kPa. This implies an increase in the electron temperature. Furthermore, Ar ionic emission (Ar II) lines were clearly observed under the magnetized plasma conditions.
Dynamics of chemically powered nanodimer motors subject to an external force
Authors: Tao Yu-Guo , Kapral Raymond
Published: July 2009

The chemically powered self-propelled directed motions of nanodimer motors confined in a rectangular channel and subject to an applied external conservative force are investigated using hybrid molecular dynamics/multiparticle collision dynamics. The influence of factors, such as dimer sizes, chemical reaction type, and the nature of the interaction potentials between dimer monomers and solvent molecules, on the propulsion force and friction constant are examined. The stall force, for which the nanodimer has zero net velocity, and the thermodynamic efficiency of the motor are calculated. Both irreversible and reversible chemical reactions are considered. The simulation results are compared to theoretical predictions which are able to capture the major features of the self-propelled motion.
A Car–Parrinello and path integral molecular dynamics study of the intramolecular lithium bond in the lithium 2-pyridyl-N-oxide acetate
Authors: Durlak Piotr , Latajka Zdzisław , Berski Sławomir
Published: July 2009

Lithium bonding in lithium 2-pyridyl-N-oxide acetate has been investigated using classic Car–Parrinello molecular dynamics (CPMD) and the path integral approach [path integrals molecular dynamics (PIMD)]. The simulations have been performed in 300 K. Structures, energies, and lithium trajectories have been determined. The CPMD results show that the lithium atom is generally equidistant between heavy atoms in the (O⋯Li⋯O) bridge. Applying quantum effects through the PIMD leads to similar conclusion. The theoretical lithium 2-pyridyl-N-oxide acetate infrared spectrum has also been determined using the CPMD calculations. This shows very good agreement with available experimental results and reproduces well the broad low-frequency band observed experimentally. In order to gain deeper understanding of the nature of the lithium bonding topological analysis of the electron localization function has been applied.
On the complex behavior of strain relaxation in (In,Ga)As/GaAs(001) quantum dot molecules
Authors: Hanke M. , Dubslaff M. , Schmidbauer M. , Wang Zh. M. , Mazur Yu. I. , Lytvyn P. M. , Lee J. H. , Salamo G. J.
Published: July 2009

A detailed growth scenario of surface quantum dot molecules (QDM) in the system (In,Ga)As/GaAs(001) has been investigated in terms of shape and elastic strain evolution. QDMs are grown by a combined approach using droplet epitaxy for initial homoepitaxial GaAs mounds, which subsequently serve as nucleation spots for surrounding (In,Ga)As surface quantum dots. Atomic force micrographs trace a detailed pathway toward the final QDM containing up to six quantum dots with perfect inherent symmetry. Synchrotron-based grazing incidence diffraction together with grazing incidence small angle x-ray scattering reveal a relaxation behavior, which for all growth stages comprises a strained lattice along [1¯10] and partial elastic relaxation along [110]. Numerical finite element calculations on the three-dimensional strain profile support the experimental findings.
Opening the light extraction cone of high index substrates with plasmonic gratings: Light emitting diode applications
Authors: Drezet A. , Przybilla F. , Laux E. , Mahboub O. , Genet C. , Ebbesen T. W. , Bouillard J. S. , Zayats A. , Spevak I. S. , Zayats A. V. , Nikitin A. Yu , Martín-Moreno L.
Published: July 2009

The opening of the light extraction cone of a high index substrate (GaP) is demonstrated using plasmonic gratings. We show that the excitation of surface plasmons on the metal grating leads to the extraction of light otherwise undergoing total internal reflection in the substrate with high efficiency. This effect has an immediate application in the context of light emitting diodes, where resonant metal gratings are promising for the design of dual purpose electric contact/extraction structures.
Micromagnet-superconducting hybrid structures with directional current flow dependence for persistent current switching
Authors: Ozmetin Ali Esad , Yapici Murat Kaya , Zou Jun , Lyuksyutov Igor F. , Naugle Donald G.
Published: July 2009

This letter reports on a microfabricated magnet-superconducting hybrid structure (Co–SiO2–Pb82Bi18) showing the dependence of the critical current (Ic) on the current flow direction. With external magnetic field, intermittent superconducting and normally conducting regions are formed on the Pb82Bi18 film due to field localization created by the Co stripes, which is verified by scanning Hall probe microscopy measurements. Superconducting and normal conduction paths are created parallel and perpendicular to the Co stripes, providing directional dependency on the current flow. By changing the orientation of the ferromagnetic stripes with respect to the superconducting film, the hybrid structure could be adapted to realize a low-power persistent current switch.
Converse magnetoelectric effect in ferromagnetic shape memory alloy/piezoelectric laminate
Authors: Chen S. Y. , Wang D. H. , Han Z. D. , Zhang C. L. , Du Y. W. , Huang Z. G.
Published: July 2009

In laminates, the converse magnetoelectric (CME) effect is often achieved by an elastic coupling between magnetostrictive and piezoelectric layers. Here the authors report on an alternative mechanism for obtaining CME. In a transition-metals-based ferromagnetic shape memory alloy/piezoelectric ceramic laminated composite, the stress-induced martensitic transformation is utilized to gain the magnetic changes, which gives rise to a giant CME effect consequently. The strong CME is observed at room temperature over a broad bandwidth, under weak magnetic bias and electric field.
A model of the exchange bias setting process in magnetic read sensors
Authors: Barker J. , Craig B. , Lamberton R. , Johnston A. , Chantrell R. W. , Heinonen O.
Published: July 2009

A model of the acquisition of exchange bias during the high temperature annealing process used to set the bias direction in the antiferromagnet is described. The model is applied to the investigation of the process of setting the bias direction in the antiferromagnetic layer, which comprises a high-temperature anneal in a field sufficiently large to saturate the ferromagnetic layers. It is shown that there is an optimal setting temperature depending on the material parameters. The temperature dependence of the antiferromagnetic anisotropy is shown to be an important factor in achieving maximum exchange bias.
Tunneling magnetoresistance sensors for high resolutive particle detection
Authors: Albon C. , Weddemann A. , Auge A. , Rott K. , Hütten A.
Published: July 2009

Arrays of tunnel magnetoresistance sensors based on MgO as insulating layer are employed to detect magnetic microbeads. For single bead detection, elliptically shaped sensors of axis lengths of 400 and 100 nm are used. Due to high shape anisotropy a linear response of the sensor signal in a magnetic field range between −500 and 500 Oe can be reported. By performing static detection measurements of magnetic microbeads, a distinct signal shape correlated with the position of beads in respect to the sensor can be observed. The experimental data are compared to micromagnetic simulations carried out on a trilayer model.
Frustration driven stripe domain formation in Co/Pt multilayer films
Authors: Davies J. E. , Hellwig O. , Fullerton E. E. , Winklhofer M. , Shull R. D. , Liu Kai
Published: July 2009

We report microscopic mechanisms for an unusual magnetization reversal behavior in Co/Pt multilayers where some of the first-order reversal curves protrude outside of the major loop. Transmission x-ray microscopy reveals a fragmented stripe domain topography when the magnetic field is reversed prior to saturation, in contrast to an interconnected pattern when reversing from a saturated state. The different domain nucleation and propagation behaviors are due to unannihilated domains from the prior field sweep. These residual domains contribute to random dipole fields that impede the subsequent domain growth and prevent domains from growing as closely together as for the interconnected pattern.
Perception of Illuminant Colour Changes across Real Scenes
Authors: de Almeida Vasco M N , Nascimento Sérgio M C
Published: July 2009

In a complex natural scene the colour and intensity of the illumination may vary considerably across the scene. Changes in intensity can easily be detected but the same does not seem to be true of colour changes. We investigated the extent to which chromatic changes of the illuminant are detected and the relation of detection performance with colour constancy and scene interpretation. The stimuli were complex real 3-D scenes rendered with spatial colour gradients of which the extremes had correlated colour temperatures within the range 25 000 K–3300 K. Observers' sensitivity to these spatial changes of the illuminant was found to be low and critically dependent on scene composition. Also, even in extreme conditions where colour constancy is known to fail, changes in the color of the illuminant across the scenes could not be perceived. These results suggest that insensitivity to spatial changes of the colour of the illuminant is a strong phenomenon and that it holds regardless of colour constancy.
Synthesis of Epoxides Catalyzed by a Halide-Free Reaction-Controlled Phase-Transfer Catalytic System: [(CH3(CH2)17)2N(CH3)2]3[PW4O32]/H2O2/Dioxan/Olefin
Authors: Ding Yong , Ma Baochun , Tong Dejie , Hua Hui , Zhao Wei
Published: July 2009

The epoxidation of alkenes was successfully catalyzed by a recyclable catalytic system: [(CH3(CH2)17)2N(CH3)2]3[PW4O32]/H2O2/dioxan/olefin. This new catalytic system is not only capable of catalyzing homogeneous epoxidation of alkenes with a unique reaction-controlled phase-transfer character, but also avoids the use of chlorinated solvents. The reactions were conducted in a biphasic mixture of aqueous H2O2/dioxan, and many kinds of alkenes could be efficiently converted to the corresponding epoxides in high yields. Both new and used [(CH3(CH2)17)2N(CH3)2]3[PW4O32] catalyst was characterized by 31P magic angle spin NMR, and IR.
Recent Advances in the Total Synthesis of Polyketide Natural Products as Promising Anticancer Agents
Authors: Paterson Ian , Findlay Alison D.
Published: July 2009

A growing number of complex polyketides, isolated from a variety of marine and terrestrial sources, present novel scaffolds for the development of cancer therapeutic agents. However, the low natural abundance of such lead compounds often precludes full biological evaluation, which demands the development of efficient synthetic routes to afford a sustainable supply. In this account, we provide an overview of the total synthesis of several representative anticancer polyketides – dolastatin 19, spirangien A, reidispongiolide A, and spongistatin 1/altohyrtin A – based on versatile aldol methodology developed in our group.
Synthesis and Photophysical Properties of a Conformationally Flexible Mixed Porphyrin Star-Pentamer
Authors: Bell Toby D. M. , Bhosale Sheshanath V. , Ghiggino Kenneth P. , Langford Steven J. , Woodward Clint P.
Published: July 2009

The synthesis of a porphyrin star-pentamer bearing a free-base porphyrin core and four zinc(ii) metalloporphyrins, which are tethered by a conformationally flexible linker about the central porphyrin’s antipody, is described. The synthetic strategy is highlighted by the use of olefin cross metathesis to link the five chromophores together in a directed fashion in high yield. Photoexcitation into the Soret absorption band of the zinc porphyrin chromophores at 425 nm leads to a substantial enhancement of central free-base porphyrin fluorescence, indicating energy transfer from the photoexcited zinc porphyrin (outer periphery) to central free-base porphyrin. Time-resolved fluorescence decay profiles required three exponential decay components for satisfactory fitting. These are attributed to emission from the central free-base porphyrin and to two different rates of energy transfer from the zinc porphyrins to the free-base porphyrin. The faster of these decay components equates to an energy-transfer rate constant of 3.7 × 109 s–1 and an efficiency of 83%, whereas the other is essentially unquenched with respect to reported values for zinc porphyrin fluorescence decay times. The relative contribution of these two components to the initial fluorescence decay is ~3:2, similar to the 5:4 ratio of cis and trans geometric isomers present in the pentamer.
Organoiodine-Catalyzed Oxidative Spirocyclization of Phenols using Peracetic Acid as a Green and Economic Terminal Oxidant
Authors: Minamitsuji Yutaka , Kato Daishi , Fujioka Hiromichi , Dohi Toshifumi , Kita Yasuyuki
Published: July 2009

The use of peracetic acid as a green and economical terminal oxidant in fluoroalcohol solvents could provide a practical iodoarene-catalyzed oxidation of phenols to give spirodienones. Acetic acid and water were the only co-products and waste, and thus this catalytic approach utilizing fluoroalcohol media could simplify the reaction workup procedure for product isolation.
The culture of rent, factionalism, and corruption: a political economy of rent in the Arab World
Authors: Hafez Ziad
Published: July 2009

This paper is an attempt at showing the relationship between a rent-based economy, factionalism and corruption. The premise is that without an understanding of the culture of rent, factionalism and corruption, attempts at political and economic reform will not succeed.
Marian Walhout: Transcriptional mapmaker
Authors: Short Ben
Published: July 2009

Walhout uses the genome as a base camp for exploring transcriptional regulation.
Differentiation of Eleven Fusarium spp. Isolated from Sugar Beet, Using Restriction Fragment Analysis of a Polymerase Chain Reaction–Amplified Translation Elongation Factor 1α Gene Fragment
Authors: Nitschke Elke , Nihlgard Maria , Varrelmann Mark
Published: July 2009

Sugar beet in Europe is commonly grown in wheat and maize crop rotations and subsequently pile-stored for several weeks. Beet is threatened by the colonization of saprophytic as well as pathogenic Fusarium spp. A tool for reliable identification based on sequence information of the translation elongation factor 1α (TEF-1α) gene was developed for the numerous Fusarium spp. being isolated from sugar beets. In all, 65 isolates from different species (Fusarium avenaceum, F. cerealis, F. culmorum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. redolens, F. solani, F. tricinctum, and F. venenatum) were obtained from sugar beet at different developmental stages from locations worldwide. Database sequences for additional species (F. sporotrichioides, F. poae, F. torulosum, F. hostae, F. sambucinum, F. subglutinans, and F. verticillioides), isolated from sugar beets in previous studies, were included in the analysis. Molecular sequence analysis of the partial TEF-1α gene fragment revealed sufficient variability to differentiate between the Fusarium spp., resulting in species-dependent separation of the isolates analyzed. This interspecific divergence could be translated into a polymerase chain reaction restriction fragment length polymorphism assay using only two subsequent restriction digests for the differentiation of 17 of 18 species.
Triticum mosaic virus: A Distinct Member of the Family Potyviridae with an Unusually Long Leader Sequence
Authors: Tatineni Satyanarayana , Ziems Amy D. , Wegulo Stephen N. , French Roy
Published: July 2009

The complete genome sequence of Triticum mosaic virus (TriMV), a member in the family Potyviridae, has been determined to be 10,266 nucleotides (nt) excluding the 3′ polyadenylated tail. The genome encodes a large polyprotein of 3,112 amino acids with the “hall-mark proteins” of potyviruses, including a small overlapping gene, PIPO, in the P3 cistron. The genome of TriMV has an unusually long 5′ nontranslated region of 739 nt with 12 translation initiation codons and three small open reading frames, which resemble those of the internal ribosome entry site containing 5′ leader sequences of the members of Picornaviridae. Pairwise comparison of 10 putative mature proteins of TriMV with those of representative members of genera in the family Potyviridae revealed 33 to 44% amino acid identity within the highly conserved NIb protein sequence and 15 to 29% amino acid identity within the least conserved P1 protein, suggesting that TriMV is a distinct member in the family Potyviridae. In contrast, TriMV displayed 47 to 65% amino acid sequence identity with available sequences of mature proteins of Sugarcane streak mosaic virus (SCSMV), an unassigned member of the Potyviridae. Phylogenetic analyses of the complete polyprotein, NIa-Pro, NIb, and coat protein sequences of representative species of six genera and unassigned members of the family Potyviridae suggested that TriMV and SCSMV are sister taxa and share a most recent common ancestor with tritimoviruses or ipomoviruses. These results suggest that TriMV and SCSMV should be classified in a new genus, and we propose the genus Poacevirus in the family Potyviridae, with TriMV as the type member.
Association of Soil Chemical and Physical Properties with Pythium Species Diversity, Community Composition, and Disease Incidence
Authors: Broders K. D. , Wallhead M. W. , Austin G. D. , Lipps P. E. , Paul P. A. , Mullen R. W. , Dorrance A. E.
Published: July 2009

A high-throughput baiting and identification process identified more than 7,000 isolates of Pythium from 88 locations in Ohio. Isolates were identified using direct-colony polymerase chain reaction followed by single-strand conformational polymorphism, and communities were assembled using the Jaccard similarity coefficient and cluster analysis. Both univariate and multivariate statistics were used to evaluate differences in soil properties between communities, and canonical discriminant analysis (CDA) was used to assess the strength of the association of soil variables within communities from 83 of the locations. In all, 21 species of Pythium were identified but only 6 were recovered from >40% of the locations. Five communities were formed using the cluster analysis, and significant differences were observed in disease incidence, as well as soil pH, calcium, magnesium, and cation exchange capacity between communities. Stepwise multiple discriminant analysis and CDA identified pH, calcium, magnesium, and field capacity as contributing the most to the separation of the five Pythium communities. There was a strong association between abiotic soil components and the structure of Pythium communities, as well as diversity of Pythium spp. collected from agronomic production fields in Ohio.
Characterization of Genetic Components Involved in Durable Resistance to Stripe Rust in the Bread Wheat ‘Renan’
Authors: Dedryver F. , Paillard S. , Mallard S. , Robert O. , Trottet M. , Nègre S. , Verplancke G. , Jahier J.
Published: July 2009

Stripe rust, caused by Puccinia striiformis f. tritici, is one of the most widespread and destructive wheat diseases in areas where cool temperatures prevail. The wheat cv. Renan, carrying the specific gene Yr17, has shown effective resistance for a long time, even though some pathotypes overcame the Yr17 gene. The objectives of this study were to locate and map genetic loci associated with adult-plant resistance (APR) to stripe rust in a recombinant inbred line population derived from a cross between Renan (resistant) and Récital (susceptible). Field assays were performed for 4 years (1995, 1996, 2005, and 2006) to score disease-progress data and identify APR quantitative trait loci (QTLs). Three QTLs, QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B, with resistance alleles derived from Renan were detected in 1995 to 1996 with the 237E141 pathotype, which is avirulent against genotypes carrying Yr17. These QTLs were stable and explained a major part of the phenotypic variation seen in 2005 to 2006, when the 237E141 V17 pathotype was used. Each of these QTLs contributed ≈4 to 15% of the phenotypic variance and was effective at different adult plant stages. Interactions were observed between some markers of the Yr17 gene and three Renan QTLs: QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B. Resistance based on the combination of different APR types should provide durable resistance to P. striiformis.
Xanthomonas axonopodis pv. glycines Soybean Cultivar Virulence Specificity Is Determined by avrBs3 Homolog avrXg1
Authors: Athinuwat Dusit , Prathuangwong Sutruedee , Cursino Luciana , Burr Thomas
Published: July 2009

Three races of Xanthomonas axonopodis pv. glycines were identified on pustule disease resistant and susceptible soybean cultivars based on virulence phenotype. For race 3, an avrBs3 homolog, avrXg1 was identified that conferred resistance expressed as a hypersensitive response on resistant cultivar Williams 82. Mutations in two predicted functional domains of avrXg1 resulted in gained virulence on Williams 82 and an increase in bacterial population number on susceptible cultivars. Expression of avrXg1 in race 1, that is predicted to confer a nonspecific HR, led to virulence on susceptible cultivars Spencer and PI 520733. Expression of avrXg1 in race 2, that is predicted of carrying avrBs3-like genes, resulted in gained virulence and fitness of pathogen on both resistant and susceptible cultivars. The results demonstrate multifunctions for avrXg1 dependent on pathogen and plant genetic backgrounds.
Empirical Evidence for Various Evolutionary Hypotheses on Species Demonstrating Increasing Mortality with Increasing Chronological Age in the Wild
Authors: Libertini Giacinto
Published: July 2009

Many species show a significant increase in mortality with increasing chronological age in the wild. For this phenomenon, three possible general hypotheses are proposed, namely that: (1) it has no adaptive meaning; (2) it has an adaptive meaning; (3) the ancestry is the pivotal determinant. These hypotheses are evaluated according to their consistency with the empirical evidence. In particular, (1) the existence of many species with a constant, or almost constant, mortality rate, especially the so-called “animals with negligible senescence”; (2) the inverse correlation, observed in mammals and birds in the wild, between extrinsic mortality and the proportion of deaths due to intrinsic mortality; (3) the existence of highly sophisticated, genetically determined, and regulated mechanisms that limit and modulate cell duplication capacities and overall cell functionality. On the whole, the hypothesis of an adaptive meaning appears to be consistent with the empirical evidence, while the other two hypotheses hardly appear compatible.
Reactivity to alcohol assessment measures: an experimental test
Authors: Walters Scott T. , Vader Amanda M. , Harris T. Robert , Jouriles Ernest N.
Published: July 2009

Aims  Previous research has suggested that alcohol screening and assessment may affect drinking.

Design  This study was a randomized test of reactivity to alcohol assessment questionnaires among a group of heavy drinking college students.

Setting and participants  A total of 147 university students completed a screening questionnaire and were randomized to either immediate assessment or delayed assessment. The immediate assessment group completed a set of drinking questionnaires at baseline, 3, 6 and 12 months, while the delayed assessment group completed questionnaires only at 12 months.

Measurements  Primary outcomes included overall volume of drinking, risky drinking and use of risk reduction behaviors.

Findings  We found a significant effect of assessment on measures of risky drinking and risk reduction behaviors, but not on overall volume of drinking. Specifically, at 12 months, participants who had previously completed drinking assessments had a lower peak blood alcohol concentration (BAC) (d = −0.373), were more likely to report a low score on the Alcohol Use Disorders Identification Test (AUDIT; odds ratio = 2.55) and tended to use more strategies to moderate their alcohol consumption (d = 0.352). Risk reduction behaviors that were affected tended to be those that limited alcohol consumption, rather than those that minimized consequences.

Conclusions  These results may have implications for the development of brief interventions.
The impact of changing nicotine replacement therapy licensing laws in the United Kingdom: findings from the International Tobacco Control Four Country Survey
Authors: Shahab Lion , Cummings K. Michael , Hammond David , Borland Ron , West Robert , McNeill Ann
Published: July 2009

Aim  To evaluate the impact of a new licence for some nicotine replacement therapy products (NRT) for cutting down to stop (CDTS) on changes in the pattern of NRT use.

Design  Quasi‐experimental design comparing changes in NRT use across two waves of a population‐based, replenished‐panel, telephone survey conducted before and after the introduction of new licensing laws in the United Kingdom with changes in NRT use in three comparison countries (Australia, Canada and United States) without a licensing change.

Participants  A total of 7386 and 7013 smokers and recent ex‐smokers participating in the 2004 and/or 2006/7 survey.

Measurements  Data were collected on demographic and smoking characteristics as well as NRT use and access. In order to account for interdependence resulting from some participants being present in both waves, generalized estimation equations with an exchangeable correlation matrix were used to assess within‐country changes and linear and logistic regressions to assess between‐country differences in adjusted analyses.

Findings  NRT use was more prevalent in the United Kingdom and increased across waves in all countries but no wave × country interaction was observed. There was no evidence that the licensing change increased the prevalence of CDTS or the use of NRT (irrespective of how it was accessed) for CDTS in the United Kingdom relative to comparison countries. There was also no evidence for a change in concurrent smoking and NRT use among smokers not attempting to stop in the United Kingdom relative to comparison countries.

Conclusion  The addition of the CDTS licence for some NRT products in the United Kingdom appears to have had very limited, if any, impact on NRT use in the first year after the licence change.
Early weaning and alcohol disorders in offspring: biological effect, mediating factors or residual confounding?
Authors: Alati Rosa , Van Dooren Kate , Najman Jake M. , Williams Gail M. , Clavarino Alexandra
Published: July 2009

Aims This study explores associations between early weaning and alcohol use disorders in youth and mechanisms by which these associations may operate. Design We used data from the Mater University Study of Pregnancy and its outcomes, an Australian birth cohort study based in Brisbane. Setting and participants: This study is based on a subsample of 2370 participants for whom complete data were available at age 21 years. Length and method of breastfeeding were assessed at 6 months. Measurements Alcohol use disorders were assessed at age 21 using the life‐time version of the Composite International Diagnostic Interview—computerized version (CIDI‐Auto). We adjusted for maternal age, marital status, education, alcohol, tobacco use, anxiety, depression and maternal attitudes towards the baby. Attention Deficit and Hyperactivity Disorders (ADHD) and Intellect Quotient (IQ) were measured with the Child Behaviour Checklist (5 years) and the Ravens SM (14 years), respectively. Findings Those who had been weaned within 2 weeks of being born and breastfed at regular intervals were at increased risk of meeting criteria for alcohol use disorders at age 21 [odds ratio (OR) 1.71, 95% confidence interval (CI):1.07, 2.72]. Conclusion This study confirms a small but robust association between early weaning and increased risk of alcohol use disorders.
Ascites improves upon plus serum sodium model for end‐stage liver disease (MELD) for predicting mortality in patients with advanced liver disease
Authors: SOMSOUK M. , GUY J. , BIGGINS S. W. , VITTINGHOFF E. , KOHN M. A. , INADOMI J. M.
Published: July 2009

Background  The clinical impact of ascites has historically been well recognized; however, its value is unclear in the context of current prognostic models.

Aim  To determine whether ascites can improve risk discrimination beyond model for end‐stage liver disease (MELD) and serum sodium (MELDNa).

Methods  Consecutive cirrhotic patients were evaluated for ascites on the basis of an outpatient CT along with concurrent MELD and Na values. Cox models were used to determine the added value of ascites for predicting 1‐year mortality. Increases in the C‐index, integrated discrimination improvement (IDI) and the net reclassification index (NRI) were used to assess improvements in discrimination after the addition of ascites.

Results  A total of 1003 patients had Na and MELD scores available within 30 days of the CT scan. A total of 60 deaths occurred within 1 year, with mortality higher in patients with ascites (21.4% vs. 4.0%, HR 6.08, 95% CI 3.62–10.19, P < 0.0005). In the presence of ascites, the MELD and MELDNa scores underestimated mortality risk when the scores were less than 21. The addition of ascites to the MELDNa model substantially improved discrimination by the C‐index (0.804 vs. 0.770, increase of 3.4%, 95% CI 0.2–9.9%), IDI (1.8%, P = 0.016) and NRI (15.8%, P = 0.0006).

Conclusion  The incorporation of radiographic ascites significantly improves upon MELDNa for predicting 1‐year mortality. The presence of ascites may help identify patients at increased risk for mortality, not otherwise captured by either MELD or MELDNa.
3D seismic imaging of a Tertiary Dyke Swarm in the Southern North Sea, UK
Authors: Wall Mostyn , Cartwright Joe , Davies Richard , McGrandle Andrew
Published: July 2009

We use three‐dimensional (3D) seismic reflection and magnetic data to interpret and describe the 3D geometry of igneous dykes in the southern North Sea. The dykes were emplaced into Paleozoic and Mesozoic sediments and have a common upper termination in Early Tertiary sediments. We interpret the dykes to be part of the British Tertiary volcanic province and estimate the age of the dykes to be 58 Ma. The dykes are characterized by a narrow 0.5–2 km wide vertical disturbance of seismic reflections that have linear plan view geometry. Negative magnetic anomalies directly align with the vertical seismic disturbance zones and indicate the presence of igneous material. Linear coalesced collapse craters are found above the dykes. The collapse craters have been defined and visualized in 3D. Collapse craters have formed above the dyke due to the release of volatiles at the dyke tip and resulting volume loss. Larger craters have potentially formed due to explosive phreatomagmatic interaction between magma and pore water. The collapse craters are a new Earth analogue to Martian pit chain craters.
Wind velocity perturbation of soil respiration measurements using closed dynamic chambers
Authors: Suleau M. , Debacq A. , Dehaes V. , Aubinet M.
Published: July 2009

Soil respiration measurements performed with closed dynamic chambers are very sensitive to pressure differences inside and outside the chamber: differences as small as 1 Pa can induce errors that are of the same magnitude as the flux itself. The problem is usually solved by adding a vent to the experimental set‐up. However, although this may give acceptable results in most cases, it is not effective at sites that are very exposed to wind. At the CarboEurope–IP agricultural site of Lonzée (Belgium), on bare soil, we used a vent composed of a vertical tube whose upper end was placed between two horizontal plates. Whilst this system worked properly in low‐wind conditions, it led to a significant flux over‐estimation (up to 300%) under strong wind conditions. We analysed the causes of this error and attributed it to a dynamic pressure effect at the vent, leading to air aspiration from within the chamber. We suggest that this is because the wind at the vent level was not the same as that experienced in the chamber, because of the large vertical wind speed gradient close to the soil. Another vent geometry was then proposed that positioned the vent at the chamber level. This new design was tested on both manual and automatically operated chambers. It was found to be efficient in windy conditions as most of the artificial correlation between soil respiration measurements and wind speed had disappeared.
Conserved aromatic and basic amino acid residues in the pore region of Caenorhabditis elegans spastin play critical roles in microtubule severing
Authors: Matsushita‐Ishiodori Yuka , Yamanaka Kunitoshi , Hashimoto Hiroshi , Esaki Masatoshi , Ogura Teru
Published: July 2009

Mutations of human spastin, an AAA (ATPases associated with diverse cellular activity) family protein, cause an autosomal dominant form of hereditary spastic paraplegia, which is characterized by weakness, spasticity and loss of the vibratory sense in the lower limbs. Recently, it has been reported that spastin displays microtubule‐severing activity. We also previously reported that Caenorhabditis elegans spastin homologue SPAS‐1 displays microtubule severing. However, the detailed molecular mechanism of microtubule severing remains unknown. Here, we describe that SPAS‐1 forms a stable hexamer in a concentration‐dependent manner and that ATPase activity of SPAS‐1 is greatly stimulated by microtubules. Furthermore, MTBD (microtubule‐binding domain) of SPAS‐1 is essential for binding to microtubules. Taken these results together, we propose that MTBD of SPAS‐1 plays a critical role in enrichment of SPAS‐1 to microtubules, where SPAS‐1 is concentrated and able to form a stable hexamer, subsequently its ATPase activity is stimulated. On the other hand, our mutational analyses revealed that the conserved aromatic and basic amino acid residues in the pore region are important for microtubule severing. We also detected the direct interaction of the extremely acidic C‐terminal polypeptide of tubulin with SPAS‐1. Consequently, we propose that the central pore residues are important for the recognition of substrates.