bluuebunny/crossref_metadata_2025 huggingface dataset:
Micelle shape transitions in block copolymer/homopolymer blends: Comparison of self-consistent field theory with experiment
Authors: Greenall M. J. , Buzza D. M. A. , McLeish T. C. B.
Published: July 2009

Diblock copolymers blended with homopolymer may self-assemble into spherical, cylindrical, or lamellar aggregates. Transitions between these structures may be driven by varying the homopolymer diblock molecular weight or composition. Using self-consistent field theory (SCFT), we reproduce these effects. Our results are compared to x-ray scattering and transmission electron microscopy measurements by Kinning et al. and good agreement is found, although the tendency to form cylindrical and lamellar structures is sometimes overestimated due to our neglect of edge effects due to the finite size of these aggregates. Our results demonstrate that SCFT can provide detailed information on the self-assembly of isolated block copolymer aggregates.
Dual formulation of the Lie algebra S-expansion procedure
Authors: Izaurieta F. , Perez A. , Rodriguez E. , Salgado P.
Published: July 2009

The expansion of a Lie algebra entails finding a new bigger algebra G through a series of well-defined steps from an original Lie algebra g. One incarnation of the method, the so-called S-expansion, involves the use of a finite Abelian semigroup S to accomplish this task. In this paper we put forward a dual formulation of the S-expansion method, which is based on the dual picture of a Lie algebra given by the Maurer–Cartan forms. The dual version of the method is useful in finding a generalization to the case of a gauge free differential algebra, which, in turn, is relevant for physical applications in, e.g., supergravity. It also sheds new light on the puzzling relation between two Chern–Simons Lagrangians for gravity in 2+1 dimensions, namely, the Einstein–Hilbert Lagrangian and the one for the so-called “exotic gravity.”
A model of electrical conduction across the grain boundaries in polycrystalline-silicon thin film transistors and metal oxide semiconductor field effect transistors
Authors: Sharma Kiran , Joshi D. P.
Published: July 2009

An electrical conduction model of carrier transport across the grain boundaries (GBs) in polycrystalline silicon (PX-Si) films is developed by considering four conduction mechanisms, a Gaussian energy distribution for GB interface states and the GB scattering effects. The model is applicable over a wide range of temperature and grain size. It is found that the GB scattering potential and the GB distribution parameter are function of temperature but are independent of doping density and grain size. The conduction model is able to explain the dependence of transfer and output characteristics of thin film transistors (TFTs) on the temperature and grain size in the strong inversion regime. The variation of effective mobility and drain current for n-channel TFTs and metal oxide semiconductor field effect transistors with gate bias voltage and grain sizes is also studied. A satisfactory agreement is obtained between the theoretical investigations and the available experimental data.
Isotopic tracing study of the growth of silicon carbide nanocrystals at the SiO2/Si interface by CO annealing
Authors: Pongracz A. , Hoshino Y. , D’Angelo M. , Cavellin C. Deville , Ganem J.-J. , Trimaille I. , Battistig G. , Josepovits K. V. , Vickridge I.
Published: July 2009

The epitaxial growth of β-Sic nanocrystals at the SiO162/Si(100) interface under CO annealing has been studied using C13O18 and isotopically sensitive nuclear reaction analysis and secondary ion mass spectrometry analysis. The results show that the amount of SiC increases linearly with the CO pressure and the annealing time. We demonstrate that the CO diffuses as a molecule in the silica and that for each C atom reacting to form SiC, an oxygen atom is incorporated in the vicinity of the interface. The linear and the parabolic rate constants corresponding to an adapted Deal and Grove model are also determined.
Magnetoelectric behavior of sodium doped lanthanum manganites
Authors: Kalyana Lakshmi Y. , Venkataiah G. , Reddy P. Venugopal
Published: July 2009

Nanocrystalline samples of sodium doped manganites with compositional formula La1−xNaxMnO3 (0.025⩽x⩽0.25) were prepared by polyvinyl alcohol assisted precursor method. After characterizing the samples by x-ray diffraction and transmission electron microscopy a systematic investigation of electrical, magnetic, and thermopower properties has been undertaken. The resistivity data were analyzed using effective medium approximation. From the analysis it has been found that the metallic fraction is increasing up to x=0.10 and remains constant with further doping. A close examination of the resistivity data clearly indicates that the sodium doped samples are slowly transformed from colossal magnetoresistance behavior to charge ordering behavior. Thermoelectric power data at low temperatures were analyzed by considering the magnon drag concept, while the high temperature data were explained by small polaron conduction mechanism.
Application of network identification by deconvolution method to the thermal analysis of the pump-probe transient thermoreflectance signal
Authors: Ezzahri Y. , Shakouri A.
Published: July 2009

The paper discusses the possibility to apply network identification by deconvolution (NID) method to the analysis of the thermal transient behavior due to a laser delta pulse excitation in a pump-probe transient thermoreflectance experiment. NID is a method based on linear RC network theory using Fourier’s law of heat conduction. This approach allows the extraction of the thermal time constant spectrum of the sample under study after excitation by either a step or pulse function. Furthermore, using some mathematical transformations, the method allows analyzing the detail of the heat flux path through the sample, starting from the excited top free surface, by introducing two characteristic functions: the cumulative structure function and the differential structure function. We start by a review of the theoretical background of the NID method in the case of a step function excitation and then show how this method can be adjusted to be used in the case of a delta pulse function excitation. We show how the NID method can be extended to analyze the thermal transients of many optical experiments in which the excitation function is a laser pulse. The effect of the semi-infinite substrate as well as extraction of the interface and thin film thermal resistances will be discussed.
A modified Kolsky bar system for testing ultrasoft materials under intermediate strain rates
Authors: Chen R. , Huang S. , Xia K. , Lu F.
Published: July 2009

A 25 mm aluminum Kolsky bar is modified to test ultrasoft materials under intermediate strain rates (10–100 s−1). In this modified system, an ultralong loading pulse (5–50 ms) is generated using an 800 mm steel striker in combination with a pulse shaper made of 2.5 mm thick soft rubber. For such long loading pulses, the traditional data reduction scheme based on strain gauge measurements is not possible. We use a laser gap gauge to measure the deformation of the sample directly and monitor the low amplitude dynamic loading stresses on the sample with a pair of piezoelectric transducers that are embedded in the bars. A commercial foam rubber is tested to demonstrate the feasibility of our modified Kolsky bar system.
Electrical and magnetic properties of Cr3+ substituted nanocrystalline nickel ferrite
Authors: Patange S. M. , Shirsath Sagar E. , Toksha B. G. , Jadhav S. S. , Jadhav K. M.
Published: July 2009

The magnetic and electrical properties of Cr3+ substituted nickel ferrite synthesized by wet chemical route have been studied. Particle size measured from x-ray diffraction and from transmission electron microscopy images confirms the nanosize dimension of prepared particles. Magnetic parameters such as coercivity and saturation magnetization are measured from vibrating sample magnetometer. Magnetization, ac susceptibility, electrical resistivity, and Mössbauer measurements were carried out. Electrical properties such as ac resistivity as a function of frequency and dc resistivity as a function of temperature were studied for various Cr3+ substitutions in nickel ferrite. The dielectric properties such as dielectric constant (ε′) and dielectric loss (ε″) were also studied. The dielectric constant and dielectric loss obtained for the ferrites prepared through wet chemical route posses a value lower than that of the ceramically prepared samples of the same composition. The resistivity obtained is higher than that of ferrite prepared by ceramic method. The dc resistivity increases with Cr3+ content x. The observed variation in resistivity is explained by Verwey hopping mechanism. The activation energy derived form the temperature variation in resistivity was found to increase with increasing concentration of Cr3+ ions.
A self-consistent treatment of electron transfer in the limit of strong friction via the mixed quantum classical Liouville method
Authors: Shi Qiang , Geva Eitan
Published: July 2009

Electron transfer is investigated at the limit of strong friction. The analysis is based on the generic model of a two-state system bilinearly coupled to a harmonic bath. The dynamics is described within the framework of the mixed quantum classical Liouville (MQCL) equation, which is known to be exact for this model. In the case of zero electronic coupling, it is shown that while the dynamics of the electronic populations can be described by a Markovian quantum Smoluchowski equation, that of the electronic coherences are inherently non-Markovian. A non-Markovian modified Zusman equation is derived in the presence of electronic coupling and shown to be self-consistent in cases where the standard Zusman equation is not.
Numerical evaluations on the asymmetric bias dependence of magnetoresistance in double spin filter tunnel junctions
Authors: Miao G. X. , Moodera J. S.
Published: July 2009

In double spin filter tunnel junctions, the spin information is generated and analyzed purely from the spin filtering effect with nonmagnetic electrodes. In this article we numerically evaluate the bias dependence of magnetoresistance in such tunnel junctions (nonmagnetic metal/spin filter/nonmagnetic insulator/spin filter/nonmagnetic metal), particularly in cases when different spin filter materials are utilized. A large magnetoresistance with nonmonotonic and asymmetric bias dependence is expected within the framework of Wentzel–Kramers–Brillouin approximation. We illustrate the systematic influence of tunnel barrier height, tunnel barrier thickness, and exchange energy splitting on magnetoresistance, particularly focusing on the asymmetric behavior of the magnetoresistance bias dependence.
Characteristics of InAs/GaNAs strain-compensated quantum dot solar cell
Authors: Okada Yoshitaka , Oshima Ryuji , Takata Ayami
Published: July 2009

We have fabricated and compared the performance of GaAs-based p-i-n quantum dot solar cells with ten multilayer stacked structures of self-assembled InAs quantum dots embedded with GaNxAs1−x strain-compensating spacer layers. Reducing the thickness of the spacer layer, and hence increasing the nitrogen composition in GaNxAs1−x, from 40 nm (x=0.5%) to 15 nm (x=1.5%) thereby fulfilling the net strain-balanced condition, resulted in a steady increase in the short-circuit density, while a decreasing trend for the open-circuit voltage was observed. The observed results can be interpreted in terms of the difference in the quantum confinement structure.
Significant increase of light emission efficiency by in situ site-selective etching of InGaN quantum wells
Authors: Fang Zhilai
Published: July 2009

An indium post-treatment of the InGaN epilayers was employed for InGaN-to-GaN interface modification. We find that the treatment could lead to selective etching of the InGaN epilayers around threading dislocations (TDs) due to preferential etching of the chemically active step-correlated TDs and formation of indium-rich InGaN nanostructures on the smooth InGaN surface. The intentionally formed V-shaped pits by site-selective etching of the InGaN epilayers resulted in an increased surface potential barrier at the pit sidewalls due to the relatively thin InGaN single quantum well. The increased energy bandgap of the InGaN active layers around the TDs cores caused the lateral carrier confinement away from nonradiative recombination at the defects and thus significantly enhanced the light emission efficiency.
Negative refraction behaviors in two-dimensional elliptical-rod photonic crystals in a centered rectangular lattice
Authors: Ohlinger Kris , Olvera Isai , Lin Yuankun
Published: July 2009

It is shown that negative refractions exist in two-dimensional photonic crystals consisting of centered rectangular lattices of elliptical dielectric rods in air. These lattices can be considered as deviated structures from well-studied, strict hexagonal lattices. There is a tolerance of negative refractions to deviations of structural parameters from the hexagonal lattice, indicating certain flexibilities for fabrication process for these photonic crystals including the hexagonal one.
The influence of surface tension gradients on drop coalescence
Authors: Blanchette François , Messio Laura , Bush John W. M.
Published: July 2009

We present the results of a combined experimental and numerical investigation of the coalescence of a drop with a liquid reservoir of a miscible but distinct fluid. Particular attention is given to elucidating the influence on the coalescence process of a surface tension difference between drop and reservoir. Drops are gently deposited on the surface of the reservoir, and so coalesce with negligible initial vertical velocity. Depending on the drop size and reservoir composition, partial or total coalescence may occur. Three distinct regimes, depending on the reservoir to drop surface tension ratio, Rσ, are identified and delineated through both experiments and numerics. If Rσ<0.42, droplets are ejected from the top of the drop, while satellite droplets are left in its wake. For 0.42≤Rσ<0.93, only total coalescence is observed. When Rσ≥0.93, partial coalescence is increasingly favored as the reservoir’s surface tension increases.
Vertically aligned silicon microwire arrays of various lengths by repeated selective vapor-liquid-solid growth of n-type silicon/n-type silicon
Authors: Ikedo Akihito , Kawashima Takahiro , Kawano Takeshi , Ishida Makoto
Published: July 2009

Repeated vapor-liquid-solid (VLS) growth with Au and PH3–Si2H6 mixture gas as the growth catalyst and silicon source, respectively, was used to construct n-type silicon/n-type silicon wire arrays of various lengths. Silicon wires of various lengths within an array could be grown by employing second growth over the first VLS grown wire. Additionally, the junction at the interface between the first and the second wires were examined. Current-voltage measurements of the wires exhibited linear behavior with a resistance of 850 Ω, confirming nonelectrical barriers at the junction, while bending tests indicated that the mechanical properties of the wire did not change.
Structural motifs of cholesterol nanoparticles
Authors: Cromie S. R. T. , Ballone P.
Published: July 2009

The growth sequence of gas-phase cholesterol clusters (ChN) with up to N=36 molecules has been investigated by atomistic simulation based on an empirical force field model. The results of long annealings from high temperature show that the geometric motifs characterizing the structure of pure cholesterol crystals already appear in nanometric aggregates. In all clusters molecules tend to align along a common direction. For cluster sizes above the smallest ones, dispersion interactions among the hydrocarbon body and tails of cholesterol cooperate with hydrogen bonding to give rise to a bilayer structure. Analysis of snapshots from the annealing shows that the condensation of hydrogen bonds into a connected network of rings and chains is an important step in the self-organization of cholesterol clusters. The effect of solvation on the equilibrium properties of medium-size aggregates is investigated by short molecular dynamics simulations for the N=30 and N=40 clusters in water at near ambient conditions and in supercritical carbon dioxide at T=400 K.
Accelerating simulation of metastable decay
Authors: Kusaka Isamu
Published: July 2009

We present a new adaptation of umbrella sampling technique in studying nucleation, allowing for a large free energy barrier to be overcome within a time scale accessible to simulation. The method requires a set of order parameters that can distinguish a metastable state and a more stable state toward which the system relaxes, but does not demand that the order parameters be adequate for describing the process around the top of the free energy barrier. To illustrate its effectiveness, the method was implemented using Monte Carlo simulation and was applied to study bubble nucleation in single component truncated and shifted Lennard-Jones fluids. Under the conditions studied, the rate of nucleation, measured in Monte Carlo cycle, was enhanced by a factor ranging from 102 to 107. The simulation also yields various thermodynamic and structural information on the system during nucleation.
Ring-chain structural transitions in a ferromagnetic particles system induced by a dc magnetic field
Authors: Morimoto Hisao , Katano Kunio , Maekawa Toru
Published: July 2009

We carry out statistical analysis of cluster structures formed by ferromagnetic particles in a dc magnetic field based on a flexible chain model. In the absence of a magnetic field, ferromagnetic particles tend to form ring structures. When a dc magnetic field is applied, the rings are broken into chains if the intensity of the field is sufficiently high since the dipole moment of each particle is aligned in the field direction. We analyze the conditions under which ring-chain structural transitions occur and clarify the dependence of the probabilities of the creation of ring and chain structures on control parameters such as the strength of the dipole-dipole interactive energy between particles, the intensity of the magnetic field and the cluster size.
Uniaxial strain relaxation in He+ ion implanted (110) oriented SiGe layers
Authors: Minamisawa R. A. , Buca D. , Trinkaus H. , Holländer B. , Mantl S. , Destefanis V. , Hartmann J. M.
Published: July 2009

Uniaxially strained (011)Si is attractive for high performance p-channel metal oxide semiconductor field effect transistor devices due to the predicted high hole mobilities. Here, we demonstrate the realization of purely uniaxially relaxed (011) SiGe virtual substrates by He+ ion implantation and thermal annealing. Perfect uniaxial relaxation is evidenced by precise ion channeling angular yield scan measurements and plan view transmission electron microscopy as predicted theoretically on the basis of the layer symmetry dependent dislocation dynamics. Strikingly, misfit dislocations propagate exclusively along the [01¯1] direction in the (011) oriented crystal and, in contrast to (100)Si, no crosshatch is formed. We describe dislocation formation and propagation inducing strain relaxation of (011)SiGe and enlighten the differences to (100) oriented SiGe on Si.
Magnetically controlled superconducting weak links
Authors: Van de Vondel J. , Silhanek A. V. , Raes B. , Gillijns W. , Kramer R. B. G. , Moshchalkov V. V. , Sautner J. , Metlushko V.
Published: July 2009

We have designed and characterized a magnetic template which can be switched between chains of parallel and antiparallel field distribution by applying an in-plane magnetic field. The parallel field profile creates highly mobile vortex channels in a superconducting film deposited on top, reproducing the behavior of a weak link as evidenced by the presence of Shapiro steps in the current-voltage characteristics under rf excitation. The Josephson coupling can be fully suppressed by changing the field distribution to the antiparallel state. As a result, a reversible ON/OFF switch for magnetically induced weak links has been demonstrated.
Tunable high transition temperature superconducting quantum interference device magnetometer with gate-voltage-controlled bicrystal junctions
Authors: Chen Kuen-Lin , Sou U. C. , Chen J. C. , Yang H. C. , Jeng J. T. , Ko P. C. , Horng H. E. , Wu C. H. , Chen J. H.
Published: July 2009

A gate-voltage-controlled high transition temperature direct current superconducting quantum interference device (high-Tc dc SQUID) magnetometer was fabricated to study how the electric field effect affects the device’s voltage-flux and voltage-current characteristics. The magnetometer consists of a monolithic YBa2Cu3O7−δ superconducting film and bicrystal junctions covered by a polymethylmethacrylate film as the gate insulator. It was found that the magnetic flux modulated voltage swing of the SQUID magnetometer varies by 48% when the gate voltage is changed from −1.9 to 9.5 V. The variation in voltage swing is attributed to the change of effective capacitance in grain-boundary junctions.
High efficiency organic multilayer photodetectors based on singlet exciton fission
Authors: Lee J. , Jadhav P. , Baldo M. A.
Published: July 2009

We employ an exciton fission process that converts one singlet exciton into two triplet excitons to increase the quantum efficiency of an organic multilayer photodetector beyond 100%. The photodetector incorporates ultrathin alternating donor-acceptor layers of pentacene and C60, respectively. By comparing the quantum efficiency after separate pentacene and C60 photoexcitation we find that singlet exciton fission in pentacene enhances the quantum efficiency by (45±7)%. In quantitative agreement with this result, we also observe that the photocurrent generated from pentacene excitons is decreased by (2.7±0.2)% under an applied magnetic field of H=0.4 T, while the C60 photocurrent is relatively unchanged.
Ab initio design of Ca-decorated organic frameworks for high capacity molecular hydrogen storage with enhanced binding
Authors: Sun Y. Y. , Lee Kyuho , Kim Yong-Hyun , Zhang S. B.
Published: July 2009

Ab initio calculations show that Ca can decorate organic linkers of metal-organic framework, MOF-5, with a binding energy of 1.25 eV. The Ca-decorated MOF-5 can store molecular hydrogen (H2) in both high gravimetric (4.6 wt %) and high volumetric (36 g/l) capacities. Even higher capacities (5.7 wt % and 45 g/l) can be obtained in a rationally designed covalent organic framework system, COF-α, with decorated Ca. Both density functional theory and second-order Møller–Plesset perturbation calculations show that the H2 binding in these systems is significantly stronger than the van der Waals interactions, which is required for H2 storage at near ambient conditions.
Laser operation in nondoped thin films made of a small-molecule organic red-emitter
Authors: Rabbani-Haghighi Hadi , Forget Sébastien , Chénais Sébastien , Siove Alain , Castex Marie-Claude , Ishow Elena
Published: July 2009

Stimulated emission in small-molecule organic films at a high dye concentration is generally hindered by fluorescence quenching, especially in the red region of the spectrum. Here we demonstrate the achievement of high net gains (up to 50 cm−1) around 640 nm in thermally evaporated nondoped films of 4-di(4′-tert-butylbiphenyl-4-yl)amino-4′-dicyanovinylbenzene, which makes this material suitable for green-light pumped single mode organic lasers with low threshold and superior stability. Lasing effect is demonstrated in a distributed Bragg resonator configuration, as well as under the form of random lasing at high pump intensities.
Tuneable optical lenses from diamond thin films
Authors: Kriele A. , Williams O. A. , Wolfer M. , Brink D. , Müller-Sebert W. , Nebel C. E.
Published: July 2009

Nanocrystalline diamond (NCD) membranes of 150 nm thickness and diameters in the millimeter range grown by microwave-assisted chemical-vapor deposition were bulged to investigate their mechanical properties and their use as tuneable optical lenses. The NCD films were grown at different CH4/H2 gas mixtures to vary the sp2/sp3 ratio and thereby to tune their mechanical, optical, and surface morphology properties. By applying gas over pressure the membrane forms a lens shaped geometry. From deflection data we calculated Young’s moduli which decrease with increasing CH4/H2 ratio from 1160 GPa at 0.5% to 900 GPa at 7%. Optical lens applications show a variation in the focal point from infinity to 3.5 mm. The data indicate that NCD is a promising material for tuneable optical lenses applications.
Determination of carrier mobility in disordered organics from current-voltage characteristics
Authors: Wu Y. Z. , Zhang C. R. , Zhang D. J.
Published: July 2009

Electrical field dependent charge carrier mobility of organics was determined by introducing a useful function transformed from simple current-voltage characteristics in an electron-only device. The calculated mobility is consistent with the Poole–Frenkel form for the electrical field between 400 and 1100 V1/2 cm−1/2. The electrical field and carrier distributions in the device were also obtained from the newly introduced function to exhibit behaviors of xα and 1/x1−α (α∼0.15–0.25, for current density from 20 to 500 mA cm−2, x>6 nm, is the distance from cathode), respectively.
Improved thermal stability, interface, and electrical properties of HfO2 films prepared by pulsed laser deposition using in situ ionized nitrogen
Authors: Wang Yi , Wang Hao , Zhang Jun , Wang Hanbin , Ye Cong , Jiang Yong , Wang Qing
Published: July 2009

Nitrogen is incorporated into thin HfO2 films by pulsed laser deposition using in situ ionized nitrogen. The improved thermal stability and interfacial microstructure are further confirmed by high-resolution transmission electron microscopy. The composition of the thin film is investigated by x-ray photoelectron spectroscopy and electron energy-loss spectroscopy. Electrical studies show a property permittivity of 27.7 and low leakage current density were achieved by incorporation of a small amount (about 1 at. %) of nitrogen. The dominant conduction mechanisms of the Pt/HfO2/p-Si structure are trap-assisted tunneling and Schottky emission at low electric field for the gate and substrate injection, respectively.
Atomic migration in molten and crystalline Ge2Sb2Te5 under high electric field
Authors: Yang Tae-Youl , Park Il-Mok , Kim Byoung-Joon , Joo Young-Chang
Published: July 2009

Atomic migration under an electric field, electromigration, in molten and crystalline Ge2Sb2Te5 was studied using a pulsed dc stress to an isolated line structure. Under a single pulse (∼10−3 s), Ge2Sb2Te5 was melted by Joule heating, and an electrostatic force-induced drift of Ge and Sb toward the cathode and Te toward the anode was observed. Effective charge numbers were calculated to be 0.28, 0.38, and −0.29 for Ge, Sb, and Te, respectively. Electromigration in the crystalline state was studied by applying a 10 MHz pulsed dc; constituent elements migrated toward the cathode, which suggests a hole wind-force operating in this phase.
Internal fields in solid electrolytes due to interface effects
Authors: Martin Bjoern , Kliem Herbert
Published: July 2009

The space charge distribution and therefore the distribution of the internal potential in ion-conducting polymers can strongly be influenced by electrode effects. Due to image forces the electrodes attract mobile ions to the electrolyte/electrode interface. Simulations performed with a three-dimensional hopping model yield a charge accumulation of mobile ions at the electrodes as well as a depletion zone near this accumulation layer even without external applied field. The resulting potential shows a maximum in the middle of the sample. Measurements of the surface potential performed with a scanning Kelvin probe using polyethylene oxide confirm the model.
Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme
Authors: English Niall J. , Solomentsev Gleb Y. , O’Brien Paul
Published: July 2009

Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of both external static electric and low-frequency microwave (2.45 GHz) fields of varying intensity. Significant nonthermal field effects were noted, such as marked changes in the protein’s secondary structure relative to the zero-field state, depending on the field conditions, mutation, and orientation with respect to the applied field. This occurred primarily as a consequence of alignment of the protein’s total dipole moment with the external field, although the dipolar alignment of water molecules in both the solvation layer and the bulk was also found to be influential. Substantial differences in behavior were found for proteins with and without overall net charges, particularly with respect to translational motion. Localized motion and perturbation of hydrogen bonds were also found to be evident for charged residues.
Infrared spectra and density functional theory calculations of the tantalum and niobium carbonyl dinitrogen complexes
Authors: Lu Zhang-Hui , Jiang Ling , Xu Qiang
Published: July 2009

Laser-ablated tantalum and niobium atoms react with CO and N2 mixtures in excess neon to produce carbonyl metal dinitrogen complexes, NNMCO (M=Ta, Nb), (NN)2TaCO, and NNTa(CO)2, as well as metal carbonyls and dinitrogen complexes. These carbonylmetal dinitrogen complexes are characterized using infrared spectroscopy on the basis of the results of the isotopic substitution and mixed isotopic splitting patterns. Density functional theory calculations have been performed on these novel species. The good agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts supports the identification of these species from the matrix infrared spectra. Natural bond orbital analysis and plausible reaction mechanisms for the formation of the products are discussed.
Australian pirates: systematics and phylogeny of the Australasian pirate spiders (Araneae:Mimetidae), with a description of the Western Australian fauna
Authors: Harms Danilo , Harvey Mark S.
Published: July 2009

Pirate spiders (Mimetidae) are well known for their specialised feeding ecology. They are vagrant araneophagic predators, enter the webs of their prey spiders and exhibit patterns of aggressive mimicry to overcome the web owner. The mimetid fauna of Australia and New Zealand currently consists of 26 species in the following three genera: Australomimetus Heimer, 1986 (18 species), Mimetus Hentz, 1832 (six species), and Ero C.L. Koch, 1836 (two species). The systematic position of the majority of Australasian mimetids was investigated through phylogenetic techniques utilising morphological character systems of 29 exemplar taxa and 87 characters, including the first examination of spinneret structure in species of Australomimetus. The results support an expanded concept for Australomimetus, which, apart from the introduced Ero aphana (Walckenaer, 1802), is found to contain the entire Australian and New Zealand mimetid fauna, also recorded from Asia. The following taxonomic changes are proposed: A. catulli (Heimer, 1989), comb. nov., A. hannemanni (Heimer, 1989), comb. nov., A. japonicus (Uyemura, 1938), comb. nov., A. mendicus (O. P. Cambridge, 1879), comb. nov. and A. sennio (Urquhart, 1891), comb. nov.; Ero luzoniensis Barrion & Litsinger, 1995 is synonymised with Ero aphana, and A. andreae Heimer, 1989 is synonymised with A. daviesianus Heimer, 1986; Mimetus tikaderi Gajbe, 1992 from India is excluded from Mimetidae, and referred to Liocranidae. The Western Australian mimetid fauna is described for the first time and comprises nine species of Australomimetus, including the following five new species: A. diabolicus, sp. nov., A. djuka, sp. nov., A. dunlopi, sp. nov., A. nasoi, sp. nov. and A. stephanieae, sp. nov. Several species-groups of Australomimetus are identified.
Phylogeny accurately predicts behaviour in Indian Ocean Clitaetra spiders (Araneae:Nephilidae)
Authors: Kuntner Matjaž , Agnarsson Ingi
Published: July 2009

Phylogenies are underutilised, powerful predictors of traits in unstudied species. We tested phylogenetic predictions of web-related behaviour in Clitaetra Simon, 1889, an Afro-Indian spider genus of the family Nephilidae. Clitaetra is phylogenetically sister to all other nephilids and thus important for understanding ancestral traits. Behavioural information on Clitaetra has been limited to only C. irenae Kuntner, 2006 from South Africa which constructs ladder webs. A resolved species-level phylogeny unambiguously optimised Clitaetra behavioural biology and predicted web traits in five unstudied species and a uniform intrageneric nephilid web biology. We tested these predictions by studying the ecology and web biology of C. perroti Simon, 1894 on Madagascar and C. episinoides Simon, 1889 on Mayotte. We confirm predicted arboricolous web architecture in these species. The expected ontogenetic allometric transition from orbs in juveniles to elongate ladder webs in adults was statistically significant in C. perroti, whereas marginally not significant in C. episinoides. We demonstrate the persistence of the temporary spiral in finished Clitaetra webs. A morphological and behavioural phylogenetic analysis resulted in unchanged topology and persisting unambiguous behavioural synapomorphies. Our results support the homology of Clitaetra hub reinforcement with the nephilid hub-cup. In Clitaetra, behaviour was highly predictable and remained consistent with new observations. Our results confirm that nephilid web biology is evolutionarily conserved within genera.
Naming species with no morphological indicators: species status of Galeolaria caespitosa (Annelida:Serpulidae) inferred from nuclear and mitochondrial gene sequences and morphology
Authors: Halt Magdalena N. , Kupriyanova Elena K. , Cooper Steven J. B. , Rouse Greg W.
Published: July 2009

Galeolaria caespitosa Lamarck, 1818 is an endemic, gregarious serpulid annelid, ubiquitous along the intertidal zone of southern Australia, occurring from Queensland to Western Australia. We sampled specimens across this range and utilised morphological features and sequences of mitochondrial (cytochrome-b) and nuclear (ITS2) markers to assess the taxonomic status of this morphospecies. No taxonomically significant morphological differences were observed across the range of G. caespitosa. However, the molecular data revealed the existence of the following two well supported clades that were also geographically concordant for the two markers: an eastern clade, consisting of New South Wales and southern Queensland samples, and a south-western group that encompassed samples from the rest of its range. The minimum pairwise distance between members of the two groups was more than 24% for cytochrome-b, with a maximum of 1% within-group variation. In addition, analysis of molecular variation showed a high proportion (97%) of the total variation distributed among the two groups, indicative of long-term isolation of the two clades. These results suggest that G. caespitosa comprises at least two cryptic species. Here, we discuss the merits of naming new Galeolaria species, given there were no consistent morphological differences detectable and the absence of details on the type locality for G. caespitosa. We conclude that a new species of Galeolaria is warranted and describe it here as G. gemineoa.
Comparison of methods to detect rare and cryptic species: a case study using the red fox (Vulpes vulpes)
Authors: Vine S. J. , Crowther M. S. , Lapidge S. J. , Dickman C. R. , Mooney N. , Piggott M. P. , English A. W.
Published: July 2009

Choosing the appropriate method to detect and monitor wildlife species is difficult if the species is rare or cryptic in appearance or behaviour. We evaluated the effectiveness of the following four methods for detecting red foxes (Vulpes vulpes) on the basis of equivalent person hours in a rural landscape in temperate Australia: camera traps, hair traps (using morphology and DNA from hair follicles), scats from bait stations (using DNA derived from the scats) and spotlighting. We also evaluated whether individual foxes could be identified using remote collection of their tissues. Genetic analysis of hair samples was the least efficient method of detection among the methods employed because of the paucity of samples obtained and the lack of follicles on sampled hairs. Scat detection was somewhat more efficient. Scats were deposited at 17% of bait stations and 80% of scats were amplified with a fox-specific marker, although only 31% of confirmed fox scats could be fully genotyped at all six microsatellite loci. Camera trapping and spotlighting were the most efficient methods of detecting fox presence in the landscape. Spotlighting success varied seasonally, with fox detections peaking in autumn (80% of spotlighting transects) and being lowest in winter (29% of transects). Cameras detected foxes at 51% of stations; however, there was limited seasonality in detection, and success rates varied with camera design. Log-linear models confirmed these trends. Our results showed that the appropriate technique for detecting foxes varies depending on the time of the year. It is suggested that wildlife managers should consider both seasonal effects and species biology when attempting to detect rare or elusive species.
Uncovering Creative Destruction brought about by New Firm Formation: A New Method and Data Source
Authors: Derbyshire James , Brown Ross
Published: July 2009

Atherton (2006) has noted that the current policy preoccupation with increasing start-up levels has been justified in terms of the ‘creative destruction’ it is expected to bring about. However, this article shows that the most commonly employed measures of start-up, and the most common dataset on which they are employed, are inadequate for assessing start-up policy justified in these terms. A new dataset and method is introduced that is better able to uncover creative destruction taking place in the business stock.
Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo
Authors: Anderson Daniel J. , Vargas Jesse D. , Hsiao Joshua P. , Hetzer Martin W.
Published: July 2009

Formation of the nuclear envelope (NE) around segregated chromosomes occurs by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled nuclear membrane components during mitosis. In this study, we show that inner nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes into the emerging NE via their capacity to bind chromatin in a collaborative manner. Despite their redundant functions, decreasing the levels of any of these trans-membrane proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the levels of any of them had the opposite effect. Furthermore, acceleration of NE formation interferes with chromosome separation during mitosis, indicating that the time frame over which chromatin becomes membrane enclosed is physiologically relevant and regulated. These data suggest that functionally distinct classes of chromatin-interacting membrane proteins, which are present at nonsaturating levels, collaborate to rapidly reestablish the nuclear compartment at the end of mitosis.
Control of Healthcare-AssociatedStaphylococcus aureusSurvey of Practices in North Carolina Hospitals
Authors: Weber David J. , Hoffmann Karen K. , Rutala William A. , Pyatt Deborah G.
Published: July 2009

Although patients colonized or infected with methicillin-resistantStaphylococcus aureushave been placed on contact isolation for many years, more recent guidelines recommend enhanced control measures, such as routine active surveillance. We report here the results of a survey of 70 hospitals in North Carolina with regard to current management issues surrounding methicillin-resistantS. aureus.
Benchmarking homology detection procedures with low complexity filters
Authors: Forslund Kristoffer , Sonnhammer Erik LL
Published: July 2009

Background: Low-complexity sequence regions present a common problem in finding true homologs to a protein query sequence. Several solutions to this have been suggested, but a detailed comparison between these on challenging data has so far been lacking. A common benchmark for homology detection procedures is to use SCOP/ASTRAL domain sequences belonging to the same or different superfamilies, but these contain almost no low complexity sequences.

Results: We here introduce an alternative benchmarking strategy based around Pfam domains and clans on whole-proteome data sets. This gives a realistic level of low complexity sequences. We used it to evaluate all six built-in BLAST low complexity filter settings as well as a range of settings in the MSPcrunch post-processing filter. The effect on alignment length was also assessed.

Conclusion: Score matrix adjustment methods provide a low false positive rate at a relatively small loss in sensitivity relative to no filtering, across the range of test conditions we apply. MSPcrunch achieved even less loss in sensitivity, but at a higher false positive rate. A drawback of the score matrix adjustment methods is however that the alignments often become truncated.

Availability: Perl scripts for MSPcrunch BLAST filtering and for generating the benchmark dataset are available at http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/benchmark.tar.gz

Contact:  kristoffer.forslund@sbc.su.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
The SNP ratio test: pathway analysis of genome-wide association datasets
Authors: O'Dushlaine Colm , Kenny Elaine , Heron Elizabeth A. , Segurado Ricardo , Gill Michael , Morris Derek W. , Corvin Aiden
Published: July 2009

Summary: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways.

Availability:  https://sourceforge.net/projects/snpratiotest/

Contact:  codushlaine@gmail.com; colm.odushlaine@tcd.ie

Supplementary information:  Supplementary data are available at Bioinformatics online.
Combination of conditionally replicative adenovirus and standard chemotherapies shows synergistic antitumor effect in pancreatic cancer
Authors: Nelson Amy R. , Davydova Julia , Curiel David T. , Yamamoto Masato
Published: July 2009

Due to devastating prognosis, novel therapies are needed for pancreatic cancer. We are in preparation for a human clinical trial of a conditionally replicative adenovirus (CRAd) we developed. While most patients in the target population are receiving either gemcitabine or 5‐fluorouracil chemotherapy, the combination with CRAd has not yet been studied. This study was designed to evaluate combination therapies with CRAd and current standard chemotherapies in pancreatic cancer. When the combination therapy was testedin vitro, gemcitabine pretreatment showed a synergistic effect in two out of four cell lines whereas CRAd followed by gemcitabine exhibited a synergistic effect in one cell line. With 5‐fluorouracil, pretreatment with 5‐fluorouracil produced a synergistic effect in three cell lines whereas post‐treatment was synergistic in only one cell line. These effects were not fully explained by either induction of cyclooxygenase (Cox) 2 activity or adenoviral receptors with chemotherapeutics. Inin vivoanalyses with Hs766T xenograft, 5‐fluorouracil slightly improved the CRAd antitumor effect but it was not significant. Pretreatment with gemcitabine embodied a significant tumor reduction compared with single therapy with gemcitabine. The most significant antitumor effect occurred when tumors were treated with 5/3COX2CRAdF and subsequent gemcitabine (P = 0.001 vs gemcitabine alone,P = 0.012 vs 5/3COX2CRAdF alone) at day 12. In MIA Paca‐2, pretreatments with either 5‐fluorouracil or gemcitabine improved the CRAd therapeutic effect when administered before CRAd injection (P = 0.03 andP = 0.01, respectively). These experiments indicate the possible benefit of combination therapies, and thus it is not necessary to interrupt chemotherapeutics when receiving CRAd therapy. (Cancer Sci2009); 00: 000–000)
Pregnancy outcome, thyroid dysfunction and fetal goitre after in utero exposure to propylthiouracil: a controlled cohort study
Authors: Rosenfeld Hila , Ornoy Asher , Shechtman Svetlana , Diav‐Citrin Orna
Published: July 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Human pregnancy experience with propylthiouracil has not shown an increased risk of major anomalies, but its use in pregnancy has been associated with fetal or neonatal thyroid dysfunction with or without goitre.

• The rate of these complications has not been prospectively evaluated.

WHAT THIS PAPER ADDS

• Based on prospective data from the Israeli Teratology Information Service, propylthiouracil was not associated with an increased teratogenic risk.

• Hypothyroidism was found in 9.5% (56.8% of whom with goitre) of fetuses or neonates, whereas hyperthyroidism was detected in 10.3%.

• In most cases neonatal thyroid functions normalized without treatment.

AIMS

Propylthiouracil (PTU) is presently considered to be the treatment of choice for hyperthyroidism in pregnancy. It is known to cross the human placenta, and therefore may affect the fetus. The major aims of this study were to evaluate the rate of major anomalies and to report the rate of fetal goitre, accompanied by hypothyroidism, in fetuses/ newborns of mothers after in utero exposure to PTU.

METHODS

Prospective observational controlled cohort study of PTU‐exposed pregnancies of women counselled by the Israeli Teratology Information Service between the years 1994 and 2004 compared with women exposed to nonteratogens.

RESULTS

We followed up 115 PTU‐exposed pregnancies and 1141 controls. The rate of major anomalies was comparable between the groups [PTU 1/80 (1.3%), control 34/1066 (3.2%), P= 0.507]. Hypothyroidism was found in 9.5% of fetuses/neonates (56.8% of whom with goitre). Hyperthyroidism, possibly resulting from maternal disease, was found in 10.3%. Goitres prenatally diagnosed by ultrasound were successfully treated in utero by maternal dose adjustment. In most cases neonatal thyroid functions normalized during the first month of life without any treatment. Median neonatal birth weight was lower [PTU 3145 g (2655–3537) vs. control 3300 g (2968–3600), P= 0.018].

CONCLUSIONS

PTU does not seem to be a major human teratogen. However, it could cause fetal/neonatal hypothyroidism with or without goitre. Fetal thyroid size monitoring and neonatal thyroid function tests are important for appropriate prevention and treatment.
Vestigial and scalloped in the ladybird beetle: a conserved function in wing development and a novel function in pupal ecdysis
Authors: Ohde T. , Masumoto M. , Morita‐Miwa M. , Matsuura H. , Yoshioka H. , Yaginuma T. , Niimi T.
Published: July 2009

In Drosophila melanogaster, Vestigial (Vg) and Scalloped (Sd) form a transcription factor complex and play a crucial role in wing development. To extend our knowledge of insect wing formation, we isolated vg and sd homologues from two ladybird beetle species, Henosepilachna vigintioctopunctata and Harmonia axyridis. Although the ladybird beetle vg homologues had only low homology with D. melanogaster vg, ectopic expression of H. vigintioctopunctata vg induced wing‐like tissues in antennae and legs of D. melanogaster. Subsequent larval RNA interference (RNAi) analysis in H. vigintioctopunctata demonstrated conserved functions of vg and sd in wing development, and an unexpected novel function of sd in pupal ecdysis. Furthermore, our results can be applied to the production of a flightless ladybird beetle for biological control purposes using larval RNAi.