bluuebunny/crossref_metadata_2025 huggingface dataset:
The Perceptual Nature of the Cross-Modal Priming Effect
Authors: Vallet Guillaume , Brunel Lionel , Versace Rémy
Published: November 2009

The aim of this study was to demonstrate that the cross-modal priming effect is perceptual and therefore consistent with the idea that knowledge is modality dependent. We used a two-way cross-modal priming paradigm in two experiments. These experiments were constructed on the basis of a two-phase priming paradigm. In the study phase of Experiment 1, participants had to categorize auditory primes as “animal” or “artifact”. In the test phase, they had to perform the same categorization task with visual targets which corresponded either to the auditory primes presented in the study phase (old items) or to new stimuli (new items). To demonstrate the perceptual nature of the cross-modal priming effect, half of the auditory primes were presented with a visual mask (old-masked items). In the second experiment, the visual stimuli were used as primes and the auditory stimuli as targets, and half of the visual primes were presented with an auditory mask (a white noise). We hypothesized that if the cross-modal priming effect results from an activation of modality-specific representations, then the mask should interfere with the priming effect. In both experiments, the results corroborated our predictions. In addition, we observed a cross-modal priming effect from pictures to sounds in a long-term paradigm for the first time.
On the oxidation ability of the NASA Mars‐1 soil simulant during the thermal volatilization step: Implications for the search of organics on Mars
Authors: Iñiguez Enrique , Navarro‐González Rafael , de la Rosa José , Ureña‐Núñez Fernando , Coll Patrice , Raulin François , McKay Christopher P.
Published: November 2009

The search for organic molecules on Mars has been a major goal in planetary science. Viking performed the first analyses of the Martian soil in 1976, but was unable to detect organics at the ppb level using the thermal volatilization (TV) method. Three decades later, the Phoenix lander conducted analyses of Martian soil samples by TV, and found the release of CO2 from 400 to 680°C that was attributed to Mg or Fe carbonate, adsorbed CO2, or organic molecules. We have previously reported that high levels of iron species present in the soil efficiently oxidize the organics to CO and CO2 by TV. Here we explore in detail the oxidation ability of the organic‐free NASA Mars‐1 soil simulant during TV in molecular hydrogen or in the presence of stearic and mellitic acids. Our results imply that there are two sources of strong oxidizers in palagonite soils: (1) hydroxyl radicals originating from the dehydroxylation of the silica layer matrix at 320°C to 600°C and (2) oxygen atoms released by the reduction of iron(III) to iron(II) species at 320°C to 600°C and of iron(II) to metallic iron at 850–1150°C. These strong oxidizers completely decompose stearic or mellitic acids to carbon dioxide when they are present at low levels (<0.05% wt) in the NASA Mars‐1 soil simulant. Since organics are expected to be present at very low levels on Mars, future space missions utilizing TV will face the challenge of determining if any CO2 released is of inorganic or organic origin.
Ion heating in high‐speed flow channel within the duskside cell of the polar cap ion convection under large IMF‐By condition
Authors: Maeda Sawako , Ogawa Yasunobu , Hosokawa Keisuke , Nozawa Satonori , Oyama Shin‐ichiro , Tsuda Takuo , Brekke Asgeir
Published: November 2009

F region strong sunward ion flow embedded in the duskside cell of expanding polar cap ion convection and coincidental increase in the ion temperature were observed from about 73° to 69° in geomagnetic latitude between 16:00 and 16:48 MLT on 19 August, 2006 from an experiment using the European Incoherent Scatter (EISCAT) radars at Tromsø, Sodankylä and Longyearbyen together with the CUTLASS HF radars. The spatiotemporal structure of the convection map obtained by the SuperDARN HF radars showed that the high‐speed flow channel elongated in 14–17 MLT was moving equatorward. The flow channel appeared during an interval of negative interplanetary magnetic field Bz associated with large positive By. In order to evaluate ion frictional heating and resultant ion temperature increase quantitatively, the experiment was conducted to estimate the ion velocity vector and the ion temperature at the common scattering volume of the EISCAT radars. While the flow channel moved equatorward, the ion temperature increase became less evident at higher part of latitudes within the flow channel, which means that ion frictional heating was depressed where the neutral gases had already responded to the high‐speed ions. The increase in the ion temperature at particular geomagnetic latitude continued for about 20 min, and then ceased while the ion velocity was still enhanced. Ion frictional heating lasted until the neutral wind was accelerated to the equivalent level of the surrounded ion flow.
Self-sustained etch masking: A general concept to initiate the formation of nanopatterns during ion erosion
Authors: Le Roy S. , Barthel E. , Brun N. , Lelarge A. , Søndergård E.
Published: November 2009

A material allowing for rapid and reliable formation of nanopatterned surfaces is an important issue in many areas of science today. Self-organized pattern formation induced by ion erosion is a promising bottom-up approach. In the case of the III-V semiconductors, this method can lead to several remarkable structure types even if the formation mechanism has yet to be found. Through high resolution chemical scanning, transmission electron imaging, and x-ray photo emission, we show through an investigation of GaSb that the capacity of III-V semiconductors to pattern under ion erosion is linked to the phase diagram of these materials. We suggest an original scenario to explain the specific behavior of III-V semiconductors, where one species segregates and acts as a continuously resupplied etching shield. This concept is at variance with the standard Bradley–Harper model and opens interesting perspectives for bottom-up patterning of compound materials.
Low energy photoelectron diffraction analysis at high angular resolution of Cu and Mn/Cu surfaces
Authors: Cousland G. P. , Smith A. E. , Riley J. D. , Stampfl A. P. J.
Published: November 2009

X-ray photoelectron diffraction simulations using a real-space approach are shown to accurately produce the extraordinarily detailed photoelectron diffraction pattern from Cu{111} at an electron kinetic energy of 523.5 eV. These same simulations show that most sensitivity is obtained when using low energy electrons at high angular resolution. Structural differences are observed to be greatest around a kinetic energy of ∼100 eV and many of the features observed in the photoelectron diffraction patterns may be directly related to phenomena observed in low energy electron diffraction patterns from the same surface. For Cu{100}, simulations of buckled surfaces with a Mn overlayer predict that low energy photoelectron diffraction can easily discriminate chemical and structural differences. Even the effects of the relaxed surface of Cu{100} is indeed observable along azimuthal scans around a kinetic energy of 100 eV. Our results show that low energy photoelectron diffraction is extremely sensitive to changes in surface structure if high resolution patterns are acquired.
Investigation of doped calcium aluminosilicate glass: A coupling between thermal-expansion and thermal-diffusion models for assessment of nonradiative relaxation time and characteristic diffusion time
Authors: Souza Filho N. E. , Nogueira A. C. , Rohling J. H. , Baesso M. L. , Medina A. N. , Siqueira A. P. L. , Sampaio J. A. , Vargas H. , Bento A. C.
Published: November 2009

This paper discusses the use of photoacoustic models to obtain the nonradiative relaxation time (τ) and characteristic diffusion time (τβ) for a sample showing visible absorption bands from fluorescent ion-doped low-silica calcium aluminosilicate glass. Two models allowing phase shift analyses, the thermal-expansion and thermal-diffusion models, are briefly reviewed. These models have limitations when the photoacoustic signal depends on both factors, in a coupling mechanism. An alternative model is proposed to take both thermal expansion and thermal diffusion into account with a single temperature solution for the heat-coupled differential equation. This model is simulated for absorbing samples near the thermally thick region. The model is applied to Eu–V codoped glass showing intermediate signal dependence from ω−1.0 to ω−3/2. The nonradiative time and characteristic diffusion time are derived with 33<τ(ms)<39, and τβ(ms)∼70 ms for the Eu-ion and 340<τβ(ms)<710 for the V-ion. Four absorption bands were analyzed (280, 350, 420, and 600 nm), which showed a signal dependence from ω−1.1 to ω−1.52. Absorption coefficients were derived from τβ in the range of 15<β(cm−1)<51, which agreed fairly well with spectrophotometer data for the same ions.
Reactive Ni/Ti nanolaminates
Authors: Adams D. P. , Rodriguez M. A. , McDonald J. P. , Bai M. M. , Jones E. , Brewer L. , Moore J. J.
Published: November 2009

Nickel/titanium nanolaminates fabricated by sputter deposition exhibited rapid, high-temperature synthesis. When heated locally, self-sustained reactions were produced in freestanding Ni/Ti multilayer foils characterized by average propagation speeds between ∼0.1 and 1.4 m/s. The speed of a propagating reaction front was affected by total foil thickness and bilayer thickness (layer periodicity). In contrast to previous work with compacted Ni–Ti powders, no preheating of Ni/Ti foils was required to maintain self-propagating reactions. High-temperature synthesis was also stimulated by rapid global heating demonstrating low ignition temperatures (Tig)∼300–400 °C for nanolaminates. Ignition temperature was influenced by bilayer thickness with more coarse laminate designs exhibiting increased Tig. Foils reacted in a vacuum apparatus developed either as single-phase B2 cubic NiTi (austenite) or as a mixed-phase structure that was composed of monoclinic B19′ NiTi (martensite), hexagonal NiTi2, and B2 NiTi. Single-phase, cubic B2 NiTi generally formed when the initial bilayer thickness was made small.
Optimization of photonics for corrugated thin-film solar cells
Authors: Deparis Olivier , Vigneron Jean Pol , Agustsson Otto , Decroupet Daniel
Published: November 2009

The amount of solar energy reaching the active (photovoltaic) layer in a thin-film solar cell can be increased by reducing the Fresnel reflection losses at the interfaces. By using corrugated interfaces (at the wavelength scale), adiabatic propagation of the electromagnetic radiation is achieved over a broad wavelength range throughout the structure, which leads to an increase in the light that is absorbed in the active layer and, ultimately, to the improvement of the photovoltaic conversion efficiency. In this article, we have considered the case of corrugated thin-film solar cell structures and we have studied theoretically the optimization of such structures from the point of view of photonics. The focus was put on periodic pyramidal interface corrugations because they were similar to those existing at the surface of corrugated transparent electrodes on which active layers can be deposited. Because of their technological importance, we chose to work with fluorine-doped tin oxide as front electrode material and with amorphous silicon as active material. Using an original three dimensional transfer matrix method, we solved the electromagnetic wave propagation problem in the general case of laterally periodic stratified media and we compared this solution with effective medium approximated solution. On the basis of typical pyramid sizes, we demonstrated, through numerical simulations, the optimization of the global light energy intake by means of corrugations of increasing complexity. The best structures were found to be based on pyramid arrays having subwavelength periods and aspect ratio values close to one. Typically, a pyramidal structure with base and height both equal to 300 nm led to a global energy intake equal to I=0.98 (integrated over the spectral range 400–710 nm), which represented a 24% improvement in comparison with the global energy intake of a planar structure (I=0.79).
Reaction pathway analysis for dislocation nucleation from a Ni surface step
Authors: Hara Shotaro , Izumi Satoshi , Sakai Shinsuke
Published: November 2009

Threshold strain required for a thermally activated dislocation nucleation from a Ni surface step has been measured using an atomistic-based reaction pathway analysis. We show that the saddle-point configuration and the stress-dependent activation energy are strongly influenced by the presence of a surface step. Our results provide insight into the previous experimental findings concerning the mechanism on a coherency loss at the Ni∕Cu(001) interface. We conclude that the coherency strain caused by a lattice mismatch between Ni and Cu does not yield a sufficient driving force for the dislocation nucleation.
Electron transport properties of antimony doped SnO2 single crystalline thin films grown by plasma-assisted molecular beam epitaxy
Authors: White M. E. , Bierwagen O. , Tsai M. Y. , Speck J. S.
Published: November 2009

By antimony doping tin oxide, SnO2:Sb (ATO), below 1.0% Sb concentration, controllable n-type doping was realized. Plasma-assisted molecular beam epitaxy has been used to grow high quality single crystalline epitaxial thin films of unintentionally doped (UID) and Sb-doped SnO2 on r-plane sapphire substrates. A UID thickness series showed an electron concentration of 7.9×1018cm−3 for a 26nm film, which decreased to 2.7×1017cm−3 for a 1570nm film, whereas the mobility increased from 15to103cm2∕Vs, respectively. This series illustrated the importance of a buffer layer to separate unintentional heterointerface effects from the effect of low Sb doping. Unambiguous bulk electron doping was established by keeping the Sb concentration constant but changing the Sb-doped layer thickness. A separate doping series correlated Sb concentration and bulk electron doping. Films containing between 9.8×1017 and 2.8×1020 Sb atoms/cm3 generated an electron concentration of 1.1×1018–2.6×1020cm−3. As the atomic Sb concentration increased, the mobility and resistivity decreased from 110to36cm2∕Vs and 5.1×10−2to6.7×10−4Ωcm, respectively. The Sb concentration was determined by secondary ion mass spectrometry. X-ray diffraction and atomic force microscopy measurements showed no detrimental effects arising from the highest levels of Sb incorporation. Temperature dependent Hall measurements established a lower limit for the Sb electron activation energy of 13.2meV and found that films with greater than 4.9×1019electrons∕cm3 were degenerately doped. Within experimental uncertainties, 100% donor efficiency was determined for Sb-doped SnO2 in the range studied.
General decay rate estimate for a viscoelastic equation with weakly nonlinear time-dependent dissipation and source terms
Authors: Liu Wenjun
Published: November 2009

A viscoelastic wave equation in canonical form with weakly nonlinear time-dependent dissipation and source terms is investigated in this paper. For a wider class of relaxation functions and without imposing any restrictive growth assumption on the damping term at the origin, we establish an explicit and general energy decay rate result.
Accelerated interface defect removal in amorphous/crystalline silicon heterostructures using pulsed annealing and microwave heating
Authors: Schulze T. F. , Beushausen H. N. , Hansmann T. , Korte L. , Rech B.
Published: November 2009

We present postdeposition annealing experiments on undoped amorphous-/n-type crystalline silicon [(i)a-Si:H/(n)c-Si/(i)a-Si:H] heterostructures used as precursors for a-Si:H/c-Si high-efficiency solar cells. Comparing conventional hotplate-heating with pulsed microwave-heating we obtain excellent interface passivation and demonstrate that microwave annealing proceeds significantly faster. The effect is ascribed to the details of microwave absorption, which selectively affects Si–H bonds and thus facilitates hydrogen bond reconfiguration needed for interface passivation. Infrared absorption spectroscopy shows that the main contribution to passivation is not stemming from bulk hydrogen reconfiguration. This suggests a hydrogen-rich interface layer, whose occurrence depends on a-Si:H deposition conditions, to be responsible for the fast annealing.
Nanoindentation-induced phase transformation in relaxed and unrelaxed ion-implanted amorphous germanium
Authors: Oliver D. J. , Bradby J. E. , Ruffell S. , Williams J. S. , Munroe P.
Published: November 2009

We have investigated nanoindentation-induced plastic deformation in amorphous germanium (a-Ge) prepared by high-energy self-ion implantation. Using cross-sectional transmission electron microscopy, micro-Raman spectroscopy, and force-displacement curve analysis, we find strong evidence for a pressure-induced metallic phase transformation during indentation. Crystalline diamond-cubic Ge-I is observed in residual indents. Relaxed and unrelaxed structural states of a-Ge exhibit similar behavior on loading, but transform at different pressures on unloading. Both forms are markedly softer mechanically than crystalline Ge. These results assist in furthering the understanding of the intriguing phenomenon known as “explosive crystallization.”
Relaxation of Voronoi shells in hydrated molecular ionic liquids
Authors: Neumayr G. , Schröder C. , Steinhauser O.
Published: November 2009

The relaxation of solvation shells is studied following a twofold strategy based on a direct analysis of simulated data as well as on a solution of a Markovian master equation. In both cases solvation shells are constructed by Voronoi decomposition or equivalent Delaunay tessellation. The theoretical framework is applied to two types of hydrated molecular ionic liquids, 1-butyl-3-methyl-imidazolium tetrafluoroborate and 1-ethyl-3-methyl-imidazolium trifluoromethylsulfonate, both mixed with water. Molecular dynamics simulations of both systems were performed at various mole fractions of water. A linear relationship between the mean residence time and the system’s viscosity is found from the direct analysis independent of the system’s type. The complex time behavior of shell relaxation can be modeled by a Kohlrausch–Williams–Watts function with an almost universal stretching parameter of 1/2 indicative of a square root time law. The probabilistic model enables an intuitive interpretation of essential motional parameters otherwise not accessible by direct analysis. Even more, incorporating the square root time law into the probabilistic model enables a quantitative prediction of shell relaxation from very short simulation studies. In particular, the viscosity of the respective systems can be predicted.
Influence of molecular weight on the solar cell performance of double-crystalline donor-acceptor block copolymers
Authors: Sommer Michael , Hüttner Sven , Steiner Ullrich , Thelakkat Mukundan
Published: November 2009

We investigate the influence of the molecular weight of double-crystalline donor-acceptor block copolymers comprised of poly(3-hexylthiophene) as donor and poly(perylene bisimide acrylate) as acceptor segments on the device performance of polymer solar cells. Two block copolymers 1 and 2 exhibiting different molecular weights but the same composition are compared. Block copolymer 2 with the higher molecular weight shows an improvement in the hole carrier mobility μOFET of more than two orders of magnitude, and an improvement in the external quantum efficiency of one order of magnitude reaching 31%, which is the highest reported value for a block copolymer system.
Electronic states of CuPc chains on the Au(110) surface
Authors: Evangelista F. , Ruocco A. , Gotter R. , Cossaro A. , Floreano L. , Morgante A. , Crispoldi F. , Betti M. G. , Mariani C.
Published: November 2009

The electronic properties of Cu-phthalocyanine (CuPc) molecules flat lying along the channels of the Au(110) reconstructed surface have been investigated by means of ultraviolet and x-ray photoelectron spectroscopy. The ordered chains give rise to a highly ordered single-layer structure with a (5×3) symmetry. Although from the core-level analysis not any significant charge transfer between the molecules and the underlying Au surface is observed, the valence band photoemission data bring to light CuPc-induced features localized at the interface. In particular, energy versus momentum dispersion of an interface state reveals a bandwidth of about 90 meV along the enlarged Au channels, where the CuPc chains are formed, with a defined fivefold symmetry well fitting the CuPc intermolecular distance.
Tribology of the lubricant quantized sliding state
Authors: Castelli Ivano Eligio , Capozza Rosario , Vanossi Andrea , Santoro Giuseppe E. , Manini Nicola , Tosatti Erio
Published: November 2009

In the framework of Langevin dynamics, we demonstrate clear evidence of the peculiar quantized sliding state, previously found in a simple one-dimensional boundary lubricated model [A. Vanossi et al., Phys. Rev. Lett. 97, 056101 (2006)], for a substantially less idealized two-dimensional description of a confined multilayer solid lubricant under shear. This dynamical state, marked by a nontrivial “quantized” ratio of the averaged lubricant center-of-mass velocity to the externally imposed sliding speed, is recovered, and shown to be robust against the effects of thermal fluctuations, quenched disorder in the confining substrates, and over a wide range of loading forces. The lubricant softness, setting the width of the propagating solitonic structures, is found to play a major role in promoting in-registry commensurate regions beneficial to this quantized sliding. By evaluating the force instantaneously exerted on the top plate, we find that this quantized sliding represents a dynamical “pinned” state, characterized by significantly low values of the kinetic friction. While the quantized sliding occurs due to solitons being driven gently, the transition to ordinary unpinned sliding regimes can involve lubricant melting due to large shear-induced Joule heating, for example at large speed.
Effect of pressure on electrospray characteristics
Authors: Marginean Ioan , Page Jason S. , Kelly Ryan T. , Tang Keqi , Smith Richard D.
Published: November 2009

An experimental study of pulsating electrosprays operated at subambient pressure is reported. The pressure domain that affords stable electrospray operation appears to be limited by the vapor pressure of the liquid. The voltage driving the electrospray is shown to have a logarithmic dependence on pressure. The observed scaling amends the relationship currently used to calculate the electric field at the tip of the meniscus of an electrified liquid.
Thermal properties and Brillouin-scattering study of glass, crystal, and “glacial” states in n-butanol
Authors: Hassaine Merzak , Jiménez-Riobóo Rafael J. , Sharapova Irina V. , Korolyuk Oxana A. , Krivchikov Alexander I. , Ramos Miguel A.
Published: November 2009

We investigated through noncommercial calorimetry and elastoacoustic Brillouin experiments the phase diagram of n-butanol and measured the specific heat and the thermal conductivity in a wide low-temperature range for its three different states, namely, glass, crystal, and the so-called “glacial” states. The main aim of the work was to shed light on the controversial issue of these allegedly polyamorphic transitions found in some molecular glass-forming liquids, first reported to occur in triphenyl phosphite and later in n-butanol. Our experimental results show that the obtained glacial state in n-butanol is not a homogenous, amorphous state, but rather a mixture of two different coexisting phases, very likely the (frustrated) crystal phase embedded in a disordered, glassy phase.
Hard repulsive barrier in hot adatom motion during dissociative adsorption of oxygen on Ag(100)
Authors: Hsieh Ming-Feng , Lin Deng-Sung , Gawronski Heiko , Morgenstern Karina
Published: November 2009

Random pairing simulation and low temperature scanning tunneling microscopy (STM) are used to investigate the detailed O2 dissociative adsorption processes at 200 K for various coverages. The distribution of oxygen adatoms shows a strong repulsion between the adsorbates with a radius of ∼0.8 nm. The comparison between STM results and simulation reveals two prominent pairing distances of 2 and 4 nm and their branching ratio is about 2:1. These findings shed new light on the origin of the large intrapair distances found and on the process behind the empirical “eight-site rule.”
Improving replica exchange using driven scaling
Authors: Lee Alexis J. , Rick Steven W.
Published: November 2009

Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can create the need for many replicas for large systems. In this paper, we present a new method in which the potential energy is scaled by a parameter, which has an explicit time dependence. Scaling the potential energy broadens the distribution of energy and reduces the number of replicas necessary to span a given temperature range. We demonstrate that if the system is driven by the time-dependent potential sufficiently slowly, then equilibrium is maintained and energetic and structural properties are identical to those of conventional replica exchange. The method is tested using two systems, the alanine dipeptide and the trpzip2 polypeptide, both in water.
A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis
Authors: Zhang Yu , Yu Hao , Qin Jianhua , Lin Bingcheng
Published: November 2009

Boolean logic performs a logical operation on one or more logic input and produces a single logic output. Here, we describe a microfluidic DNA computing processor performing Boolean logic operations for gene expression analysis and gene drug synthesis. Multiple cancer-related genes were used as input molecules. Their expression levels were identified by interacting with the computing related DNA strands, which were designed according to the sequences of cancer-related genes and the suicide gene. When all the expressions of the cancer-related genes fit in with the diagnostic criteria, positive diagnosis would be confirmed and then a complete suicide gene (gene drug) could be synthesized as an output molecule. Microfluidic chip was employed as an effective platform to realize the computing process by integrating multistep biochemical reactions involving hybridization, displacement, denaturalization, and ligation. By combining the specific design of the computing related molecules and the integrated functions of the microfluidics, the microfluidic DNA computing processor is able to analyze the multiple gene expressions simultaneously and realize the corresponding gene drug synthesis with simplicity and fast speed, which demonstrates the potential of this platform for DNA computing in biomedical applications.
Terahertz vacuum electronic circuits fabricated by UV lithographic molding and deep reactive ion etching
Authors: Shin Young-Min , Barnett Larry R. , Gamzina Diana , Luhmann Neville C. , Field Mark , Borwick Robert
Published: November 2009

The 0.22 THz vacuum electronic circuits fabricated by UV lithography molding and deep reactive ion etching processes are under investigation for submillimeter wave applications. Eigenmode transient simulations show that, accounting for realistic values of our currently achievable fabrication tolerances, the transmission, and dispersion properties of the operation modes of a TE-mode, staggered, double grating circuit are maintained within less than 1 dB and 2% deviation, respectively. Scanning electron microscopy and atomic force microscopy analyses of the fabricated circuit samples demonstrate that both of the microelectromechanical system fabrication approaches produce circuits with ±3–5 μm dimensional tolerance and ∼30 nm surface roughness.
High temperature stable monodisperse superparamagnetic core-shell iron-oxide@SnO2 nanoparticles
Authors: Xu Xiaobin , Ge Mingyuan , Wang Cen , Jiang J. Z.
Published: November 2009

Monodisperse superparamagnetic SnO2-coated iron-oxide nanoparticles (∼16.4 nm) have been synthesized via thermal decomposition. The thickness of SnO2 shells can be controlled from 1–5 nm. As-prepared SnO2-coated iron-oxide nanoparticles with high saturation magnetization (18 A m2/kg), are stable up to 600 °C, which can be formed stable ferrofluid. It was suggested that the SnO2 shell acts as a barrier of preventing the growth of γ-Fe2O3 and consequently, avoiding the γ-Fe2O3-to-α-Fe2O3 phase transition at high temperatures.
Connectivity effects in the segmental self- and cross-reorientation of unentangled polymer melts
Authors: Ottochian A. , Molin D. , Barbieri A. , Leporini D.
Published: November 2009

The segmental (bond) rotational dynamics in a polymer melt of unentangled, linear bead-spring chains is studied by molecular dynamics simulations. To single out the connectivity effects, states with limited deviations from the Gaussian behavior of the linear displacement are considered. Both the self and the cross bond-bond correlations with rank ℓ=1,2 are studied in detail. For ℓ=1 the correlation functions are precisely described by expressions involving the correlation functions of the chain modes. Several approximations concerning both the self- and the cross-correlations with ℓ=1,2 are developed and assessed. It is found that the simplified description of the excluded volume static effects derived elsewhere [D. Molin et al., J. Phys.: Condens. Matter 18, 7543 (2006)] well accounts for the short time cross-correlations. It also allows a proper modification of the Rouse theory which provides quantitative account of the intermediate and the long time decay of the rotational correlations with ℓ=1.
Magnetic and conductive dead layer at the La0.67Ca0.33MnO3–SrTiO3:Nb interface
Authors: Liang S. , Sun J. R. , Wang J. , Shen B. G.
Published: November 2009

Interfacial properties of the La0.67Ca0.33MnO3 films grown on SrTiO3 and SrTiO3:Nb, respectively, have been experimentally studied. An interface layer, ∼13 or ∼4.4 nm for the films on SrTiO3 or SrTiO3:Nb, with degenerated magnetic/conductive properties is found in the film. The most remarkable result is the significantly different layer width on different substrates. The built-in electric field yielded by charge exchange may be responsible for the layer shrinkage in La0.67Ca0.33MnO3/SrTiO3:Nb. A depression of this layer by magnetic field is also observed and ascribed to field-induced enhancement of the double exchange between Mn ions.
Aging of AlGaN quantum well light emitting diode studied by scanning near-field optical spectroscopy
Authors: Pinos A. , Marcinkevičius S. , Yang J. , Bilenko Y. , Shatalov M. , Gaska R. , Shur M. S.
Published: November 2009

Emission from a 285 nm AlGaN quantum well light emitting diode has been studied by scanning near-field optical spectroscopy. The scans revealed micrometer-size domainlike areas emitting with a higher intensity and at a longer wavelength; presumably, because of a lower AlN molar fraction in these regions. Experiments performed on different days have shown that with time, intensity from these spots increases and emission wavelength shifts to the red, indicating a further change in the quantum well alloy composition. This has allowed distinguishing an aging mechanism that involves locally increased current, heating, and atom migration.
Climatic extremes improve predictions of spatial patterns of tree species
Authors: Zimmermann Niklaus E. , Yoccoz Nigel G. , Edwards Thomas C. , Meier Eliane S. , Thuiller Wilfried , Guisan Antoine , Schmatz Dirk R. , Pearman Peter B.
Published: November 2009

Understanding niche evolution, dynamics, and the response of species to climate change requires knowledge of the determinants of the environmental niche and species range limits. Mean values of climatic variables are often used in such analyses. In contrast, the increasing frequency of climate extremes suggests the importance of understanding their additional influence on range limits. Here, we assess how measures representing climate extremes (i.e., interannual variability in climate parameters) explain and predict spatial patterns of 11 tree species in Switzerland. We find clear, although comparably small, improvement (+20% in adjusted D
2
, +8% and +3% in cross-validated True Skill Statistic and area under the receiver operating characteristics curve values) in models that use measures of extremes in addition to means. The primary effect of including information on climate extremes is a correction of local overprediction and underprediction. Our results demonstrate that measures of climate extremes are important for understanding the climatic limits of tree species and assessing species niche characteristics. The inclusion of climate variability likely will improve models of species range limits under future conditions, where changes in mean climate and increased variability are expected.
A histone demethylase is necessary for regeneration in zebrafish
Authors: Stewart Scott , Tsun Zhi-Yang , Belmonte Juan Carlos Izpisua
Published: November 2009

Urodele amphibians and teleost fish regenerate amputated body parts via a process called epimorphic regeneration. A hallmark of this phenomenon is the reactivation of silenced developmental regulatory genes that previously functioned during embryonic patterning. We demonstrate that histone modifications silence promoters of numerous genes involved in zebrafish caudal fin regeneration. Silenced developmental regulatory genes contain bivalent me
3
K4/me
3
K27 H3 histone modifications created by the concerted action of Polycomb (PcG) and Trithorax histone methyltransferases. During regeneration, this silent, bivalent chromatin is converted to an active state by loss of repressive me
3
K27 H3 modifications, occurring at numerous genes that appear to function during regeneration. Loss-of-function studies demonstrate a requirement for a me
3
K27 H3 demethylase during fin regeneration. These results indicate that histone modifications at discreet genomic positions may serve as a crucial regulatory event in the initiation of fin regeneration.
Reovirus nonstructural protein σ1s is required for establishment of viremia and systemic dissemination
Authors: Boehme Karl W. , Guglielmi Kristen M. , Dermody Terence S.
Published: November 2009

Serotype-specific patterns of reovirus disease in the CNS of newborn mice segregate with the viral S1 gene segment, which encodes attachment protein σ1 and nonstructural protein σ1s. The importance of receptor recognition in target cell selection by reovirus implicates the σ1 protein as the primary effector of disease outcome. However, the contribution of σ1s to reovirus disease is unknown. To define the function of σ1s in reovirus pathogenesis, we generated a σ1s-deficient virus by altering a single nucleotide to disrupt the σ1s translational start site. Viruses were recovered that contain nine gene segments from strain type 3 Dearing and either the wild-type or σ1s-null S1 gene segment from strain type 1 Lang. Following peroral inoculation of newborn mice, both viruses replicated in the intestine, although the wild-type virus achieved higher yields than the σ1s-null virus. However, unlike the wild-type virus, the σ1s-deficient virus failed to disseminate to sites of secondary viral replication, including the brain, heart, and liver. Within the small intestine, both viruses were detected in Peyer's patches, but only the wild-type virus reached the mesenteric lymph node. Concordantly, wild-type virus, but not σ1s-deficient virus, was detected in the blood of infected animals. Wild-type and σ1s-null viruses produced equivalent titers following intracranial inoculation, indicating that σ1s is dispensable for viral growth in the murine CNS. These results suggest a key role for σ1s in virus spread from intestinal lymphatics to the bloodstream, thereby allowing the establishment of viremia and dissemination to sites of secondary replication within the infected host.
Identification of microRNA activity by Targets' Reverse EXpression
Authors: Volinia Stefano , Visone Rosa , Galasso Marco , Rossi Elda , Croce Carlo M.
Published: November 2009

Motivation: Non-coding microRNAs (miRNAs) act as regulators of global protein output. While their major effect is on protein levels of target genes, it has been proven that they also specifically impact on the messenger RNA level of targets. Prominent interest in miRNAs strongly motivates the need for increasing the options available to detect their cellular activity.

Results: We used the effect of miRNAs over their targets for the detection of miRNA activity using mRNAs expression profiles. Here we describe the method, called T-REX (from Targets' Reverse EXpression), compare it to other similar applications, show its effectiveness and apply it to build activity maps. We used six different target predictions from each of four algorithms: TargetScan, PicTar, DIANA-microT and DIANA Union. First, we proved the sensitivity and specificity of our technique in miRNA over-expression and knock-out animal models. Then, we used whole transcriptome data from acute myeloid leukemia to show that we could identify critical miRNAs in a real life, complex, clinically relevant dataset. Finally, we studied 66 different cellular conditions to confirm and extend the current knowledge on the role of miRNAs in cellular physiology and in cancer.

Availability: Software is available at http://aqua.unife.it and is free for all users with no login requirement.

Contact:  s.volinia@unife.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Potential Antioxidant Activity of γ‐Oryzanol in Rice Bran as Determined Using an In Vitro Mouse Lymph Axillary Endothelial Cell Model
Authors: Huang Chih‐chun Jean , Xu Zhimin , Godber J. Samuel
Published: November 2009

A mouse lymphatic endothelial cell (SVEC4‐10) in vitro model was developed and found to be effective in the study of antioxidant activity of γ‐oryzanol in rice bran. The critical and vital parameters in developing these cell models included the emulsion preparation of hydrophobic compounds, the consistent management of cell culture, and the selection of cell viability detection methods compatible with the cell lines and the test substances. The SVEC4‐10 cell line had a fast metabolism and consequently could be used to determine antioxidant activity of a test substance in a relatively rapid manner. Results showed that γ‐oryzanol, ferulic acid, and α‐tocopherol could interact with cells such that oxidative damage induced by tert‐butyl hydroperoxide on cellular mitochondrial activity lessened, and in some situations, γ‐oryzanol was a more effective antioxidant than α‐tocopherol. The results also suggested different antioxidant mechanisms among γ‐oryzanol, ferulic acid, and α‐tocopherol. The three major components of γ‐oryzanol generally had higher antioxidant activity than γ‐oryzanol, with 24‐methylene cycloartanyl ferulate relatively more effective. Synergistic antioxidant activity among γ‐oryzanol, ferulic acid, and α‐tocopherol was also found.
Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea
Authors: Xu Mingshuang , Xin Yuhua , Yu Yong , Zhang Jianli , Zhou Yuguang , Liu Hongcan , Tian Jiesheng , Li Ying
Published: November 2009

A novel Gram-negative, orange-pigmented, slightly halophilic, rod-shaped bacterium, strain T30T, was isolated from sediment from the South China Sea. Phylogenetic analysis showed that strain T30Twas a member of the genusErythrobacter, sharing highest 16S rRNA gene sequence similarities withErythrobacteraquimarisJCM 12189T(99.5 %) andErythrobactervulgarisDSM 17792T(99.0 %). Levels of DNA–DNA relatedness between strain T30Tand closely related strains ofErythrobacterspecies ranged from 14.5 to 56.9 %.The isolate lacked bacteriochlorophyllaand contained ubiquinone-10 as the predominant respiratory lipoquinone. The major fatty acids of this strain were C18 : 1ω7c(38.2 %) and C16 : 1ω7c/C16 : 1ω6c(17.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. The DNA G+C content of strain T30Twas 59.5 mol%. On the basis of phenotypic and phylogenetic data, a novel species,Erythrobacter nanhaisediminissp. nov., is proposed; the type strain is T30T(=CGMCC 1.7715T=JCM 16125T).
Weissella beninensis sp. nov., a motile lactic acid bacterium from submerged cassava fermentations, and emended description of the genus Weissella
Authors: Padonou Sègla Wilfrid , Schillinger Ulrich , Nielsen Dennis S. , Franz Charles M. A. P. , Hansen Michael , Hounhouigan Joseph D. , Nago Mathurin C. , Jakobsen Mogens
Published: November 2009

Four Gram-positive, catalase-negative, short rod-shaped or coccoid, heterofermentative lactic acid bacterial strains (2L24P13T, 1L48P15, 1L24P31 and 1L24P34) with unusual phenotypic and genotypic properties were isolated from submerged fermenting cassava on MRS agar. All strains were motile, grew at 15 °C, produceddl-lactic acid from glucose with gas formation and produced ammonia from arginine. Acid was produced fromd-fructose,d-galactose,d-glucose, lactose, maltose,d-mannose, melibiose,d-raffinose, sucrose,N-acetylglucosamine andd-mannitol, but not fromd-arabinose or xylose. 16S rRNA gene sequence analysis revealed that the strains belonged to the genusWeissellaand were most closely related toWeissella ghanensisLMG 24286T.Low DNA−DNA reassociation values were obtained between the isolates andW. ghanensisDSM 19935T. Based on the genetic and phenotypic results, the strains are considered to represent a novel species, for which the nameWeissella beninensissp. nov. is proposed. The type strain is 2L24P13T(=DSM 22752T=LMG 25373T).
Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary
Authors: Xu Xue-Wei , Wu Yue-Hong , Wang Chun-Sheng , Gao Xiao-Hui , Wang Xiao-Gu , Wu Min
Published: November 2009

A strictly aerobic, Gram-negative, non-pigmented bacterial strain, designated LMEB 39T, was isolated from a seawater sample collected from the Yangtze River estuary near the East China Sea and was examined physiologically, chemotaxonomically and phylogenetically. The novel isolate was motile by a single polar flagellum and positive for nitrate reduction and decomposition of casein, gelatin, Tween 20 and Tween 80, but negative for indole production. Chemotaxonomic analysis revealed ubiquinone-8 as the predominant respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. The major fatty acids were C16 : 1ω7c/iso-C15 : 02-OH, C16 : 0, C18 : 1ω7c, C12 : 03-OH, C17 : 1ω8cand C17 : 0. The genomic DNA G+C content was 42.3 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genusPseudoalteromonas. Strain LMEB 39Texhibited the closest phylogenetic affinity toPseudoalteromonas byunsanensisJCM 12483T(97.4 % sequence similarity). The DNA–DNA reassociation values between strain LMEB 39TandP. byunsanensisJCM 12483TandPseudoalteromonas undinaDSM 6065T(97.2 % sequence similarity) were 31.7 and 30.3 %, respectively. On the basis of phenotypic and genotypic data, strain LMEB 39Trepresents a novel species of the genusPseudoalteromonas, for which the namePseudoalteromonas lipolyticasp. nov. is proposed; the type strain is LMEB 39T(=CGMCC 1.8499T=JCM 15903T).
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis
Authors: Stambuk Boris U. , Dunn Barbara , Alves Sergio L. , Duval Eduarda H. , Sherlock Gavin
Published: November 2009

Fuel ethanol is now a global energy commodity that is competitive with gasoline. Using microarray-based comparative genome hybridization (aCGH), we have determined gene copy number variations (CNVs) common to five industrially important fuel ethanol Saccharomyces cerevisiae strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. These strains have significant amplifications of the telomeric SNO and SNZ genes, which are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that increased copy number of these genes confers the ability to grow more efficiently under the repressing effects of thiamin, especially in medium lacking pyridoxine and with high sugar concentrations. These genetic changes have likely been adaptive and selected for in the industrial environment, and may be required for the efficient utilization of biomass-derived sugars from other renewable feedstocks.
Photosynthetic Redox Imbalance Governs Leaf Sectoring in theArabidopsis thalianaVariegation Mutantsimmutans,spotty,var1, andvar2
Authors: Rosso Dominic , Bode Rainer , Li Wenze , Krol Marianna , Saccon Diego , Wang Shelly , Schillaci Lori A. , Rodermel Steven R. , Maxwell Denis P. , Hüner Norman P.A.
Published: November 2009

We hypothesized that chloroplast energy imbalance sensed through alterations in the redox state of the photosynthetic electron transport chain, measured as excitation pressure, governs the extent of variegation in the immutans mutant of Arabidopsis thaliana. To test this hypothesis, we developed a nondestructive imaging technique and used it to quantify the extent of variegation in vivo as a function of growth temperature and irradiance. The extent of variegation was positively correlated (R  2 = 0.750) with an increase in excitation pressure irrespective of whether high light, low temperature, or continuous illumination was used to induce increased excitation pressure. Similar trends were observed with the variegated mutants spotty, var1, and var2. Measurements of greening of etiolated wild-type and immutans cotyledons indicated that the absence of IMMUTANS increased excitation pressure twofold during the first 6 to 12 h of greening, which led to impaired biogenesis of thylakoid membranes. In contrast with IMMUTANS, the expression of its mitochondrial analog, AOX1a, was transiently upregulated in the wild type but permanently upregulated in immutans, indicating that the effects of excitation pressure during greening were also detectable in mitochondria. We conclude that mutations involving components of the photosynthetic electron transport chain, such as those present in immutans, spotty, var1, and var2, predispose Arabidopsis chloroplasts to photooxidation under high excitation pressure, resulting in the variegated phenotype.
ArabidopsisWUSCHEL Is a Bifunctional Transcription Factor That Acts as a Repressor in Stem Cell Regulation and as an Activator in Floral Patterning
Authors: Ikeda Miho , Mitsuda Nobutaka , Ohme-Takagi Masaru
Published: November 2009

Most transcription factors act either as activators or repressors, and no such factors with dual function have been unequivocally identified and characterized in plants. We demonstrate here that the Arabidopsis thaliana protein WUSCHEL (WUS), which regulates the maintenance of stem cell populations in shoot meristems, is a bifunctional transcription factor that acts mainly as a repressor but becomes an activator when involved in the regulation of the AGAMOUS (AG) gene. We show that the WUS box, which is conserved among WOX genes, is the domain that is essential for all the activities of WUS, namely, for regulation of stem cell identity and size of floral meristem. All the known activities of WUS were eliminated by mutation of the WUS box, including the ability of WUS to induce the expression of AG. The mutation of the WUS box was complemented by fusion of an exogenous repression domain, with resultant induction of somatic embryogenesis in roots and expansion of floral meristems as observed upon ectopic expression of WUS. By contrast, fusion of an exogenous activation domain did not result in expanded floral meristems but induced flowers similar to those induced by the ectopic expression of AG. Our results demonstrate that WUS acts mainly as a repressor and that its function changes from that of a repressor to that of an activator in the case of regulation of the expression of AG.