bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of opacity models for stellar interior, inertial fusion, and high energy density plasmas
Authors: Bailey J. E. , Rochau G. A. , Mancini R. C. , Iglesias C. A. , MacFarlane J. J. , Golovkin I. E. , Blancard C. , Cosse Ph. , Faussurier G.
Published: March 2009

Theoretical opacities are required for calculating energy transport in plasmas. In particular, understanding stellar interiors, inertial fusion, and Z pinches depends on the opacities of mid-atomic-number elements over a wide range of temperatures. The 150–300 eV temperature range is particularly interesting. The opacity models are complex and experimental validation is crucial. For example, solar models presently disagree with helioseismology and one possible explanation is inadequate theoretical opacities. Testing these opacities requires well-characterized plasmas at temperatures high enough to produce the ion charge states that exist in the sun. Typical opacity experiments heat a sample using x rays and measure the spectrally resolved transmission with a backlight. The difficulty grows as the temperature increases because the heating x-ray source must supply more energy and the backlight must be bright enough to overwhelm the plasma self-emission. These problems can be overcome with the new generation of high energy density (HED) facilities. For example, recent experiments at Sandia’s Z facility [M. K. Matzen , Phys. Plasmas12, 055503 (2005)] measured the transmission of a mixed Mg and Fe plasma heated to 156±6 eV. This capability will also advance opacity science for other HED plasmas. This tutorial reviews experimental methods for testing opacity models, including experiment design, transmission measurement methods, accuracy evaluation, and plasma diagnostics. The solar interior serves as a focal problem and Z facility experiments illustrate the techniques.
Frustrating the lamellar ordering transition of polystyrene-block-polyisoprene with a C60 additive
Authors: Zhao Yue , Hashimoto Takeji , Douglas Jack F.
Published: March 2009

Thermal fluctuations in block copolymer (BCP) materials characteristically drive the ordering phase transition order from second to first order by the well known Brazovskii mechanism and there have been many observations of jumps in x-ray and neutron scattering intensity data at the order-disorder transition (ODT) that signal this phenomenon. However, the existence of quenched disorder can either destroy the ODT or restore the second-order nature of this type of phase transition. The present work considers how the dispersion of C60 (“buckyballs”), which is prone to clustering in polymeric media, into poly(styrene)-block-poly(isoprene) to see how this nanoparticle additive alters the qualitative character of the BCP ordering. Small angle x-ray scattering indicates that a small amount (≈1 mass %) of C60 causes the BCP to remain disordered over a wide temperature range so that a phase transition no longer exists. This phenomenon offers both technological problems and opportunities.
A high pressure cell for simultaneous osmotic pressure and x-ray diffraction measurements
Authors: Gauthé Béatrice L. L. E. , Heron Andrew J. , Seddon John M. , Ces Oscar , Templer Richard H.
Published: March 2009

In this paper, we report on a novel osmotic cell, developed to simultaneously subject a sample to osmotic stress and measure structural changes by small angle x-ray diffraction. The osmotic cell offers many advantages over more conventional methods of osmotically stressing soft materials to measure their structural response. In particular, a full osmotic analysis can be performed with a single small sample (25 μl). This reduces sample handling and the associated systematic errors, as well as enabling tight control and monitoring of the thermodynamic environment during osmosis, thereby increasing measurement precision. The cell design enables control of osmotic pressure to ±0.04 bar over a pressure range of 1–100 bar, and temperature control to ±0.05 °C. Under these conditions, the lattice spacing in lyotropic structures was resolved to better than ±0.005 Å. Using the osmotic cell, we demonstrate good agreement with previous conventional measurements on the energy of dehydrating the fluid lamellar phase of dioleoylphosphatidylcholine in water.
Spectroscopic properties and stability of the SH⋅H2O open shell complex
Authors: Du Shiyu , Francisco Joseph S.
Published: March 2009

High level quantum chemical calculations on the open shell SH⋅H2O complex have been carried out using coupled-cluster theory. Two stable isomers of the complex are found. The equilibrium geometries, binding energies, and spectroscopic properties for both isomers of the SH⋅H2O open shell complex are presented. The bonding feature of the complexes is compared with another important open shell complex OH⋅H2O using the natural bond orbital theory.
Electronic nonadiabatic interactions and ultrafast internal conversion in phenylacetylene radical cation
Authors: Reddy V. Sivaranjana , Mahapatra S.
Published: March 2009

Quantum chemistry and dynamics of the ground X̃ 2B1 and low-lying excited Ã 2A2, B̃ 2B2, and C̃ 2B1 electronic states of phenylacetylene radical cation are examined here in striving to understand its photostability, long-lived excited electronic states, and resolved (<10 meV) vibrational energy level spectrum. The electronic potential energy surfaces and their nonadiabatic coupling are computed ab initio. A model Hamiltonian is constructed in a diabatic electronic basis for the nuclear dynamical simulations from first principles. Analysis of electronic structure data reveals the relevance of 24 vibrational degrees of freedom in the quantum dynamics of the X̃-Ã-B̃-C̃ coupled electronic states of the radical cation. The complex vibrational energy level spectrum of this coupled electronic manifold is calculated and assigned. Theoretical results are in excellent accord with the experimental photoelectron spectroscopy data. The agreements and discrepancies of the theoretical results are also recorded and discussed with the mass-analyzed threshold ionization and photoinduced Rydberg ionization and photodissociation spectroscopy results of the X̃ and C̃ electronic states, respectively. The lifetimes of the excited electronic states of phenylacetylene radical cation are estimated from the decay of electronic population and are discussed in relation to the available experimental data.
Multivariate frequency domain analysis of protein dynamics
Authors: Matsunaga Yasuhiro , Fuchigami Sotaro , Kidera Akinori
Published: March 2009

Multivariate frequency domain analysis (MFDA) is proposed to characterize collective vibrational dynamics of protein obtained by a molecular dynamics (MD) simulation. MFDA performs principal component analysis (PCA) for a bandpass filtered multivariate time series using the multitaper method of spectral estimation. By applying MFDA to MD trajectories of bovine pancreatic trypsin inhibitor, we determined the collective vibrational modes in the frequency domain, which were identified by their vibrational frequencies and eigenvectors. At near zero temperature, the vibrational modes determined by MFDA agreed well with those calculated by normal mode analysis. At 300 K, the vibrational modes exhibited characteristic features that were considerably different from the principal modes of the static distribution given by the standard PCA. The influences of aqueous environments were discussed based on two different sets of vibrational modes, one derived from a MD simulation in water and the other from a simulation in vacuum. Using the varimax rotation, an algorithm of the multivariate statistical analysis, the representative orthogonal set of eigenmodes was determined at each vibrational frequency.
Relaxation of intense inhomogeneous charged beams
Authors: Nunes R. P. , Pakter R. , Rizzato F. B. , Endler A. , Souza E. G.
Published: March 2009

This work analyzes the dynamics of inhomogeneous, magnetically focused high intensity beams of charged particles. Initial inhomogeneities lead to density waves propagating transversely in the beam core, and the presence of transverse waves eventually results in particle scattering. Particle scattering off waves in the beam core ultimately generates a halo of particles with concomitant emittance growth. Emittance growth indicates a beam relaxing to its final stationary state, and the purpose of the present paper is to describe halo and emittance in terms of test particles moving under the action of the inhomogeneous beam. To this end an average Lagrangian approach for the beam is developed. This approach, aided by the use of conserved quantities, produces results in nice agreement with those obtained with full N-particle numerical simulations.
Arm splitting and backfiring of spiral waves in media displaying local mixed-mode oscillations
Authors: Gao Qingyu , Zhang Lu , Wang Qun , Epstein I. R.
Published: March 2009

The behavior of spiral waves is investigated in a model of reaction-diffusion media supporting local mixed-mode oscillations for a range of values of a control parameter. This local behavior is accompanied by the formation of nodes, at which the arms of the simple spiral waves begin to split. With further parameter changes, this nodal structure loses stability, becoming quite irregular, eventually evolving into turbulence, while the local dynamics increases in complexity. The breakup of the spiral waves arises from a backfiring instability of the nodes induced by the arm splitting. This process of spiral breakup in the presence of mixed-mode oscillations represents an alternative to previously described scenarios of instability of line defects and superspirals in media with period-doubling and quasiperiodic oscillations, respectively.
Structure and molecular dynamics of crystalline and liquid anthracene and naphthalene: Possible transient rotator phase of naphthalene
Authors: Bordat Patrice , Brown Ross
Published: March 2009

We examine the structural and dynamical properties of the crystal and liquid states of anthracene and naphthalene, with special attention to melting. This molecular dynamics study is based on an all-atom force field, which we optimized for simulations of solid and liquid anthracene, over wide ranges of temperature and pressure. The force field is shown to be transferable to naphthalene. Local ordering of the simulated liquids is in fair agreement with structures deduced in the literature from X-ray scattering, while providing a much more detailed picture. In analogy with the rich polymorphism of substituted benzene and naphthalene complexes, we find for naphthalene (but not anthracene) a two-step melting process with a transient rotator phase in which rotational jumps precede the onset of full melting with translational diffusion.
Effects of isomer coexistence and solvent-induced core switching in the photodissociation of bare and solvated (CS2)2− anions
Authors: Habteyes Terefe , Velarde Luis , Sanov Andrei
Published: March 2009

The photodissociation of the (CS2)2− dimer anion, known to exist in the form of several electronic and structural isomers, has been investigated at 532, 355, and 266 nm. The observed anionic fragments are CS2− and C2S2− at 532 nm, and C2S2−, CS2−, CS3−, S2−, and S− at 355 and 266 nm. In addition to the photon energy, the fractional yields of the photofragments depend on the ion source conditions and solvation of the dimer anion. Specifically, the (C2S2−+S2−)/CS2− product ratio is significantly higher when (CS2)2− is formed in the presence of water in the precursor gas mixture, even though the parent anion itself does not include H2O. On the other hand, an abrupt decrease in the above product ratio is observed upon the addition of solvent molecules (CS2 or H2O) to the (CS2)2− anion. Since the variation of this product ratio exhibits positive correlation with the relative intensity of the photoelectron band assigned to the C2v (B21) covalent structure of C2S4− by Habteyes et al. [J. Phys. Chem. A 112, 10134 (2008)], this structure is suggested as the primary origin of the C2S2− and S2− photoproducts. The switching of the fragmentation yield from C2S2− and S2− to other products upon solvation is ascribed to the diminished presence of the C2v (B21) dimer-anion structure relative to the CS2− based clusters. This population shift is attributed to the more effective solvation of the latter. The CS2− based clusters are suggested as the origin of the S− photoproduct, while CS3− is formed through the secondary S−+CS2 intracluster association reaction.
Directional bending sensor with temperature insensitivity using a sampled chirped fiber Bragg grating
Authors: Han Young-Geun
Published: March 2009

A simple and practical scheme for a directional bending sensor based on a sampled chirped fiber Bragg grating is proposed. The proposed sensing method has temperature insensitivity. The wavelength spacing in the reflection spectrum of a sampled chirped fiber Bragg grating is changed by bending because of the modification of the chirp ratio. As positive or negative bending is applied to the sampled chirped fiber Bragg grating embedded on a flexible cantilever beam, the wavelength spacing increases or decreases because of the induction of the tension and the compression strain gradient along the fiber grating. However, the wavelength spacing is not changed by the applied temperature. Since the effect of the temperature variation along the grating length remains the same, the chirp ratio is independent of the applied temperature change. Regardless of temperature change, it is therefore possible to measure the direction and the variation of bending.
Nonuniformity for rotated beam illumination in directly driven heavy-ion fusion
Authors: Runge J. , Logan B. G.
Published: March 2009

A key issue in heavy-ion beam inertial confinement fusion is target interaction, especially implosion symmetry. In this paper the two-dimensional beam irradiation nonuniformity on the surface of a spherical target is studied. This is a first step to studies of three-dimensional dynamical effects on target implosion. So far nonrotated beams have been studied. Because normal incidence may increase Rayleigh–Taylor instabilities, it has been suggested to rotate beams (to increase average uniformity) and hit the target tangentially. The level of beam irradiation uniformity, beam spill and normal incidence is calculated in this paper. In MATHEMATICA the rotated beams are modeled as an annular integrated Gaussian beam. To simplify the chamber geometry, the illumination scheme is not a 4π system, but the beams are arranged on few polar rings around the target. The position of the beam spot rings is efficiently optimized using the analytical model. The number of rings and beams, rotation radii and widths are studied to optimize uniformity and spilled intensity. The results demonstrate that for a 60-beam system on four rings peak-to-valley nonuniformities of under 0.5% are possible.
Conditions to cancel the laser polarization dependence of a subwavelength tip
Authors: Houard J. , Vella A. , Vurpillot F. , Deconihout B.
Published: March 2009

Using laser assisted atom probe tomography, we investigate the polarization dependence of the absorption coefficient of a subwavelength Al tip illuminated by an ultrashort laser pulse. In practice, we find an equilibrium condition as a function of the incident wavelength for which the atom evaporation rate becomes independent of the wave polarization. It is experimentally shown that this condition only depends on the ratio between the tip radius and the laser wavelength. Furthermore, our calculations demonstrate that a transverse local plasmon polariton mode can be resonantly excited at the tip apex.
Calculation of long time classical trajectories: Algorithmic treatment and applications for molecular systems
Authors: Schwetlick Hartmut , Zimmer Johannes
Published: March 2009

We study the problem of finding a path that joins a given initial state with a final one, where the evolution is governed by classical (Hamiltonian) dynamics. A new algorithm for the computation of long time transition trajectories connecting two configurations is presented. In particular, a strategy for finding transition paths between two stable basins is established. The starting point is the formulation of the equation of motion of classical mechanics in the framework of Jacobi’s principle; a shortening procedure inspired by Birkhoff’s method is then applied to find geodesic solutions. Numerical examples are given for Müller’s potential and the collinear reaction H2+H→H+H2.
Structural diversity of the soluble trimers of the human amylin(20–29) peptide revealed by molecular dynamics simulations
Authors: Mo Yuxiang , Lu Yan , Wei Guanghong , Derreumaux Philippe
Published: March 2009

The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20–29 of sequence SNNFGAILSS (hIAPP20–29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20–29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20–29 fibril with out-of-register antiparallel β-strands, and two forms of seeded hIAPP20–29 fibril, with in-register antiparallel or in-register parallel β-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20–29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 μs. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20–29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide β-sheets and antiparallel β-strands are more probable than parallel β-strands. One MD-predicted out-of-register antiparallel three-stranded β-sheet matches exactly the FTIR-derived unseeded hIAPP20–29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel β-sheets as reported for seeded hIAPP20–29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.
Amplified spontaneous emission and collisional transfer from the fg+(P3) ion-pair state of I2
Authors: Ridley Trevor , Lawley Kenneth P. , Donovan Robert J.
Published: March 2009

The work presented here extends previous studies of amplified spontaneous emission (ASE) between ion-pair (charge-transfer) states of I2 and shows that ASE can occur between states correlating with different states of the cation, namely, f0g+(P30) and D0u+(P32), despite the smaller transition dipole moment between them. A value of 0.34 e Å is obtained for the transition dipole under experimental conditions where the f0g+(P30)→D0u+(P32) ASE is eliminated. No F0u+(P30)←f0g+(P30) ASE transfer is observed despite the combination of favorable Franck–Condon factors and transition dipoles. The F0u+(P30)←f0g+(P30) transfer is shown to be purely collisional and a propensity for transfers involving the smallest energy mismatch is observed.
On the temperature dependence of the nonexponentiality in glass-forming liquids
Authors: Cangialosi Daniele , Alegría Angel , Colmenero Juan
Published: March 2009

Using a simple mathematical formalism, we show that temperature dependent nonexponential relaxation found in glass-forming liquids and amorphous polymers, often resulting in a decrease in the stretching exponent when decreasing temperature, can be suitably described assuming the combination of an intrinsic stretched response and the existence of temperature independent heterogeneities. The effect of the latter is incorporated by assuming a Gaussian distribution of Vogel temperatures. Comparison with experimental data of a large number of glass formers showed that this approach is able to quasiquantitatively describes the temperature dependence of the stretching exponent using the width of the distribution as the single fitting parameter. According to this approach, the rapidity of the decrease in the stretching exponent with decreasing temperature depends not only on the magnitude of the standard deviation of Vogel temperatures but also on the value of the intrinsic stretching exponent and on the fragility of the glass former. The latter result is able to rationalize, at least partially, the empirical correlation between the fragility and the stretching exponent at Tg.
Scalable implementation of strongly coupled cavity-quantum dot devices
Authors: Dousse A. , Suffczyński J. , Braive R. , Miard A. , Lemaître A. , Sagnes I. , Lanco L. , Bloch J. , Voisin P. , Senellart P.
Published: March 2009

Using low temperature in situ optical lithography, we fabricate pillar microcavities with quality factors around 2×104. Each pillar embeds a spatially and spectrally resonant single InGaAs quantum dot (QD). Light-matter strong coupling regime is reached for 100% of the fabricated pillars for which the resonance can be tuned through temperature. This is a demonstration of scalable and deterministic implementation of strongly coupled cavity-QD devices.
Polarity-dependent photoemission spectra of wurtzite-type zinc oxide
Authors: Ohashi Naoki , Adachi Yutaka , Ohsawa Takeo , Matsumoto Kenji , Sakaguchi Isao , Haneda Hajime , Ueda Shigenori , Yoshikawa Hideki , Kobayashi Keisuke
Published: March 2009

Electronic structures of the polar and nonpolar surfaces of ZnO were investigated by hard x-ray photoelectron spectroscopy (HXPES) using synchrotron radiation. The profile of HXPES spectra in the valence band region varied with the crystalline orientation (polarity) of the surface. This polarity dependence was always found in the HXPES spectra regardless of sample conditions such as surface treatment and doping. The possible origin of the polarity dependence of HXPES spectra is discussed in terms of spontaneous polarization.
An acoustic emission study of the effect of a magnetic field on the martensitic transition in Ni2MnGa
Authors: Ludwig Benno , Strothkaemper Christian , Klemradt Uwe , Moya Xavier , Mañosa Lluís , Vives Eduard , Planes Antoni
Published: March 2009

Acoustic emission measurements during the martensitic transition of a Ni–Mn–Ga magnetic shape-memory alloy reveal the intermittent and jerky character of the transition. The distribution of the amplitude of the acoustic emission events shows power law behavior, which reflects the absence of characteristic scales in the process. In this paper we show that the distribution is affected by an applied magnetic field, which proves that the transition dynamics is strongly influenced by magnetostructural coupling taking place at multiple length scales. The martensitic start temperature and the power law exponent of the amplitude distribution are measured in dependence of the applied field.
Thermoelectric properties of tetrahedrally bonded wide-gap stannite compounds Cu2ZnSn1−xInxSe4
Authors: Shi X. Y. , Huang F. Q. , Liu M. L. , Chen L. D.
Published: March 2009

It is usually accepted that good thermoelectric (TE) materials should be narrow-gap semiconductors. Here we show an example that the tetrahedrally bonded stannite compound Cu2ZnSnSe4 with a band gap of 1.44 eV can also exhibit a high figure of merit at intermediate temperature. The highly distorted structure strives for the relatively low thermal conductivity, and the tunability of the electrical properties were demonstrated through doping. The maximum ZT of Cu2ZnSn0.90In0.10Se4 reaches 0.95 at 850 K. This work may open a way for exploring high-performance TE materials with the family of widely existing tetrahedrally bonded semiconductors.
Solid state nanogaps for differential measurements of molecular properties
Authors: Moody Benjamin , McCarty Gregory S.
Published: March 2009

This paper demonstrates the production and probing of solid state nanogaps. These nanogaps can be inexpensively and controllably produced using a combination of molecular and standard photolithography. These nanogaps are implemented for chemical monitoring by using surface enhanced Raman spectroscopy to collect molecular information at the nanogap and current-voltage traces to probe the charge transport of the nanogap. These data show that the oligonucleotides used as the molecular resist are degraded, that some of the degraded oligonucleotides are removed, and then new oligonucleotides are adsorbed.
Investigation of hepatic fibrosis in rats with x-ray diffraction enhanced imaging
Authors: Li Hui , Zhang Lu , Wang Xueyan , Wang Tailing , Wang Baoen , Zhao Xinyan , Luo Shuqian
Published: March 2009

X-ray diffraction enhanced imaging (DEI) is a phase contrast technique that generates excellent contrast of biological soft tissues compared to conventional absorption radiography. We explore the application of DEI in the diagnosis of hepatic fibrosis. The produced refraction contrast images of fibrous rat liver samples show clearly abnormal liver architectures. Moreover, by comparing to histological pictures, different stages of fibrosis are discriminated, and the corresponding morphological features are analyzed. Besides, quantitative analyses of texture features are presented. The results reported herein show that DEI can be a potential noninvasive technique to diagnose and stage hepatic fibrosis.
Interface resistivity and lifetime of thin film transistors exposed to ambient air
Authors: Petrović Andraž , Bratina Gvido
Published: March 2009

We found that different contributions to the resistivity in pentacene-based organic thin film transistors exhibit different time dependences upon extended exposure to ambient air. Our Kelvin force microscopy data show that contact resistance at the drain/source interface and the resistance of the pentacene channel initially decrease and after approximately 6 h monotonically increase. The contact resistance at the source/pentacene interface, on the other hand, initially decreases and exhibits only minor increase after 6 h. Such behavior is interpreted in terms of competing effect of oxygen and water penetration in the pentacene channel and in the interfacial region.
Electron transport properties of irradiated polyimide thin films in single track regime
Authors: Murugaraj Pandiyan , Mainwaring David , Siegele Rainer
Published: March 2009

We have prepared a suite of polyimide thin films containing spatially separated one-dimensional conductive-nanowires by ion-beam irradiation exhibiting temperature dependent electrical resistance consistent with thermally activated electron hopping with activation energies about 1 eV arising from localized states spatially distributed along the ion tracks. Dielectric measurements showed the formation of high dielectric constant interphase regions surrounding each ion track generated during the irradiation process, responsible for space-charge accumulation which influences electron transport within the ion tracks. This behavior suggests a role for space-charge effects and dielectric properties in this interphase region in the control of electron transport within single track nanowires.
Terahertz pulsed imaging of frozen biological tissues
Authors: Hoshina Hiromichi , Hayashi Aya , Miyoshi Norio , Miyamaru Fumiaki , Otani Chiko
Published: March 2009

Recently, terahertz wave imaging has been shown to have potential in medical and biological applications. However, absorption by liquid water in tissues hinders the measurement of thick samples. In this study, porcine tissue was frozen to temperatures below −33 °C to prevent this absorption. Consequently, the striated muscle and adipose tissue could be clearly distinguished in the terahertz time-domain spectra owing to the difference in absorbance values and refractive indices. We demonstrated two-dimensional map of absorbance and terahertz pulse delay, which clearly shows the spatial distribution of the tissues.
Direct-gap exciton and optical absorption in the Ge/SiGe quantum well system
Authors: Kuo Yu-Hsuan , Li Yin-Shun
Published: March 2009

The ground-level direct-gap excitons and quantum-confined Stark effect (QCSE) electroabsorption in the Ge/SiGe quantum well structures are studied using the tunneling resonance modeling and the variational method. The exciton radius, transition energy, binding energy, and optical oscillator strength are calculated for various quantum well thicknesses (5–35 nm) and vertical electric fields (0–105 V/cm) simultaneously. The relative direct-gap-to-indirect-gap absorption ratios are compared. A quantum well implementation scheme with relatively broad thickness range of ∼5–15 nm can provide moderate excitonic absorption and contrast ratio for long wavelength operation. This investigation will improve the QCSE electroabsorption efficiency in the Ge quantum well system.
Transparent indium gallium zinc oxide transistor based floating gate memory with platinum nanoparticles in the gate dielectric
Authors: Suresh Arun , Novak Steven , Wellenius Patrick , Misra Veena , Muth John F.
Published: March 2009

A transparent memory device has been developed based on an indium gallium zinc oxide thin film transistor by incorporating platinum nanoparticles in the gate dielectric stack as the charge storage medium. The transfer characteristics of the device show a large clockwise hysteresis due to electron trapping and are attributed to the platinum nanoparticles. Effect of the gate bias stress (program voltage) magnitude, duration, and polarity on the memory window characteristics has been studied. Charge retention measurements were carried out and a loss of less than 25% of the trapped elec-trons was observed over 104 s indicating promising application as nonvolatile memory.
Durum wheat (Triticum durum Desf.) in rotation with faba bean (Vicia faba var. minor L.): long-term simulation case study
Authors: Garofalo P. , Di Paolo E. , Rinaldi M.
Published: March 2009

The aim of this work was to apply the CropSyst simulation model to evaluate the effect of faba bean cultivation as a break crop in the continuous durum wheat cropping system in southern Italy. The model was previously calibrated and validated for durum wheat and faba bean on data derived from experiments carried out in southern Italy (for different years and treatments), comparing observed and simulated crop growth, yield, soil water, and nitrogen output variables.
The validation showed good agreement between simulated and observed values for cumulative above-ground biomass, green area index, and soil water content for both crops and grain yield for durum wheat; a negative correlation for grain yield in faba bean was observed due to a reduction in harvest index in the well-watered crop, which the model does not simulate well.
Subsequently, a long-term analysis was carried out to study the effects on durum wheat of introducing a legume crop in rotation with the cereal in 2 and 3-year sequences.
A long-term simulation, based on 53 years of daily measured weather data, showed that faba bean, due to a lower level of transpirated water (on average 247 mm for durum wheat and 197 mm for faba bean), allowed for greater soil water availability at durum wheat sowing for the cereal when in rotation with a legume crop (on average, +84 mm/m for durum wheat following the faba bean), with positive effects for nitrogen uptake, above-ground biomass, and grain yield of wheat. The yield increase of wheat when following a faba bean crop was on average +12%, but this effect was amplified in drier years (up to 135%).
In conclusion, the case study offered the potential to confirm the positive results previously obtained in long/medium-term field experiments on the introduction of faba bean in rotation with durum wheat, as well as reduction in the chemical application of nitrogen.
The resolution and potential value of Australian seasonal rainfall forecasts based on the five phases of the Southern Oscillation Index
Authors: Vizard Andrew L. , Anderson Garry A.
Published: March 2009

We assess the resolution of the Southern Oscillation Index (SOI) seasonal rainfall forecasting system and calculate the loss in potential value of the forecasting system using a cost/loss model. Forecasts of the probability of a ‘dry’ autumn, winter, spring, and summer were obtained for 226 towns across Australia, based on the 5 phases of the SOI. For every town the variance ratio, the observed forecast variance as a proportion of the variance of a perfect forecasting system, was calculated for each season. Value score curves, showing the expected value of the forecasts as a proportion of the expected value of perfect information, were calculated for every town for each season. Maps of variance ratio and maps of mean value scores across Australia were produced by ordinary kriging. In all seasons and regions the SOI forecasting system had a variance ratio of less than 0.20, indicating that resolution and skill were never high. Variance ratios greater than 0.10 only occurred in parts of south-eastern Australia and the Cape York region during spring and in the Townsville region during summer. The variance ratio was less than 0.05 for the majority of Australia during autumn, winter, and summer.
The mean value scores for actions that are only triggered by a large shift in the forecast from climatology were uniformly close to zero in all seasons and regions, indicating that little or no value can be derived in such cases. Actions triggered by a moderate shift of the forecast were also generally associated with low value scores. Mean value scores above 0.20 were limited to actions with a decision threshold close to climatology and only occurred in parts of south-eastern Australia and the Cape York region during spring and in the Townsville region during summer. We conclude that the imperfect resolution of the SOI forecasting system has a substantial effect on potential value. The forecasting system can potentially deliver value to users with actions that are triggered by a small shift in the forecast from climatology, especially in eastern Australia during spring, but not to users with actions that are only triggered by a large shift of the forecasts from climatology.
Publish and Be Damned
Authors: Ozimek John
Published: March 2009

The revolution in technology has turned us all into publishers and has wide-reaching implications for policing obscenity, says John Ozimek
Keeping It Clean
Authors: Finkelstein Seth
Published: March 2009

Obscenity online is posing some of the greatest challenges to free speech advocates and censors. Seth Finkelstein explains why
THE CASE OF AVIAN INFLUENZA IN TURKEY
Authors: Kasapoglu Aytül , Odabas Yonca , Kaya Nilay
Published: March 2009

The primary concern of this paper is to inquire about the associations between socio-demographic and psychological variables related to avian influenza in Turkey. The data were collected from a survey given to a sample of 247 females and 223 males from six regions in Turkey. Statistical analysis revealed that gender, education level, and socio-economic status had significant impacts on knowledge, attitudes, and responsible behavior. Participants who were more aware of the impacts of nature made important suggestions at both the national and international level.
Marko Kaksonen: Tracking the inner secrets of endocytosis
Authors: Sedwick Caitlin
Published: March 2009

Kaksonen is probing the function and regulation of the endocytic machinery in yeast using live-cell microscopy and genetics.
Akt regulates L-type Ca2+ channel activity by modulating Cavα1 protein stability
Authors: Catalucci Daniele , Zhang Deng-Hong , DeSantiago Jaime , Aimond Franck , Barbara Guillaume , Chemin Jean , Bonci Désiré , Picht Eckard , Rusconi Francesca , Dalton Nancy D. , Peterson Kirk L. , Richard Sylvain , Bers Donald M. , Brown Joan Heller , Condorelli Gianluigi
Published: March 2009

The insulin IGF-1–PI3K–Akt signaling pathway has been suggested to improve cardiac inotropism and increase Ca2+ handling through the effects of the protein kinase Akt. However, the underlying molecular mechanisms remain largely unknown. In this study, we provide evidence for an unanticipated regulatory function of Akt controlling L-type Ca2+ channel (LTCC) protein density. The pore-forming channel subunit Cavα1 contains highly conserved PEST sequences (signals for rapid protein degradation), and in-frame deletion of these PEST sequences results in increased Cavα1 protein levels. Our findings show that Akt-dependent phosphorylation of Cavβ2, the LTCC chaperone for Cavα1, antagonizes Cavα1 protein degradation by preventing Cavα1 PEST sequence recognition, leading to increased LTCC density and the consequent modulation of Ca2+ channel function. This novel mechanism by which Akt modulates LTCC stability could profoundly influence cardiac myocyte Ca2+ entry, Ca2+ handling, and contractility.
N-glycans are direct determinants of CFTR folding and stability in secretory and endocytic membrane traffic
Authors: Glozman Rina , Okiyoneda Tsukasa , Mulvihill Cory M. , Rini James M. , Barriere Herve , Lukacs Gergely L.
Published: March 2009

N-glycosylation, a common cotranslational modification, is thought to be critical for plasma membrane expression of glycoproteins by enhancing protein folding, trafficking, and stability through targeting them to the ER folding cycles via lectin-like chaperones. In this study, we show that N-glycans, specifically core glycans, enhance the productive folding and conformational stability of a polytopic membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR), independently of lectin-like chaperones. Defective N-glycosylation reduces cell surface expression by impairing both early secretory and endocytic traffic of CFTR. Conformational destabilization of the glycan-deficient CFTR induces ubiquitination, leading to rapid elimination from the cell surface. Ubiquitinated CFTR is directed to lysosomal degradation instead of endocytic recycling in early endosomes mediated by ubiquitin-binding endosomal sorting complex required for transport (ESCRT) adaptors Hrs (hepatocyte growth factor–regulated tyrosine kinase substrate) and TSG101. These results suggest that cotranslational N-glycosylation can exert a chaperone-independent profolding change in the energetic of CFTR in vivo as well as outline a paradigm for the peripheral trafficking defect of membrane proteins with impaired glycosylation.
Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle
Authors: Zhang Yongjun , Tu Yizeng , Zhao Jianping , Chen Ka , Wu Chuanyue
Published: March 2009

Aberrant Src activation plays prominent roles in cancer progression. However, how Src is activated in cancer cells is largely unknown. Genetic Src-activating mutations are rare and, therefore, are insufficient to account for Src activation commonly found in human cancers. In this study, we show that reversion-induced LIM (RIL), which is frequently lost in colon and other cancers as a result of epigenetic silencing, suppresses Src activation. Mechanistically, RIL suppresses Src activation through interacting with Src and PTPL1, allowing PTPL1-dependent dephosphorylation of Src at the activation loop. Importantly, the binding of RIL to Src is drastically reduced upon Src inactivation. Our results reveal a novel Src inactivation cycle in which RIL preferentially recognizes active Src and facilitates PTPL1-mediated inactivation of Src. Inactivation of Src, in turn, promotes dissociation of RIL from Src, allowing the initiation of a new Src inactivation cycle. Epigenetic silencing of RIL breaks this Src inactivation cycle and thereby contributes to aberrant Src activation in human cancers.
Scab formation and wound healing of plant tissue by soldier aphid
Authors: Kutsukake Mayako , Shibao Harunobu , Uematsu Keigo , Fukatsu Takema
Published: March 2009

In the social aphidNipponaphis monzeni, a unique gall-repairing behaviour has been known: when a hole is made on the gall, many soldier nymphs discharge body fluid on the breach, which promptly solidifies and plugs the hole. Here, we experimentally investigated the subsequent fate of repaired galls and their inhabitants. Irrespective of natural repair by soldier nymphs or artificial repair with adhesive, repaired galls survived significantly better than non-repaired galls. Within a month after repair, the plant tissue around the hole proliferated and sealed up the hole. Many soldier nymphs were localized at the hole area and extermination of inhabiting aphids by insecticides aborted the gall regeneration, indicating that the gall regeneration requires inhabiting aphids, wherein soldier nymphs are likely to play a major role. This study provides an unprecedented case of scab formation and wound healing, which occurs at an animal–plant interface: scab derived from insect body fluid promptly plugs damaged plant tissue and subsequently the insects actively stimulate regeneration of the plant tissue, whereby the compromised plant tissue recovers. We suggest that the novel system may have evolved in the aphid lineage through enhancement and recruitment of the pre-existing capabilities of haemolymph coagulation and gall formation.
Targeting mitotic chromosomes: a conserved mechanism to ensure viral genome persistence
Authors: Feeney Katherine M , Parish Joanna L
Published: March 2009

Viruses that maintain their genomes as extrachromosomal circular DNA molecules and establish infection in actively dividing cells must ensure retention of their genomes within the nuclear envelope in order to prevent genome loss. The loss of nuclear membrane integrity during mitosis dictates that paired host cell chromosomes are captured and organized by the mitotic spindle apparatus before segregation to daughter cells. This prevents inaccurate chromosomal segregation and loss of genetic material. A similar mechanism may also exist for the nuclear retention of extrachromosomal viral genomes or episomes during mitosis, particularly for genomes maintained at a low copy number in latent infections. It has been heavily debated whether such a mechanism exists and to what extent this mechanism is conserved among diverse viruses. Research over the last two decades has provided a wealth of information regarding the mechanisms by which specific tumour viruses evade mitotic and DNA damage checkpoints. Here, we discuss the similarities and differences in how specific viruses tether episomal genomes to host cell chromosomes during mitosis to ensure long-term persistence.
The scleritome ofPaterimitra: an Early Cambrian stem group brachiopod from South Australia
Authors: Skovsted Christian B , Holmer Lars E , Larsson Cecilia M , Högström Anette E.S , Brock Glenn A , Topper Timothy P , Balthasar Uwe , Stolk Sandra Petterson , Paterson John R
Published: March 2009

Early Cambrian tommotiids are problematic fossil metazoans with external organophosphatic sclerites that have been considered to be basal members of the lophophorate stem group. Tommotiids are almost exclusively known from isolated or rarely fused individual sclerites, which made previous reconstructions of the actual organism highly conjectural. However, the recent discovery of the first articulated specimens of the tommotiidEccentrothecarevealed a tubular sclerite arrangement (scleritome) that limited the possible life habit to sessile filter feeding and thus further supported a lophophorate affinity. Here, we report the first articulated specimens of a second tommotiid taxon,Paterimitrafrom the Early Cambrian of the Arrowie Basin, South Australia. Articulated specimens ofPaterimitraare composed of two bilaterally symmetrical sclerite types and an unresolved number of small, asymmetrical and irregular crescent-shaped sclerites that attached to the anterior margin of the symmetrical sclerites. Together, the sclerites form an open cone in which the symmetrical sclerites are joined together and form a small posterior opening near the base of the scleritome, while the irregular crescent-shaped sclerites defined a broad anterior opening. The coniform scleritome ofPaterimitrais interpreted to have attached to hard substrates via a pedicle that emerged through the small posterior opening (sometimes forming a tube) and was probably a sessile filter feeder. The scleritome ofPaterimitracan be derived from the tubular scleritome ofEccentrothecaby modification of basal sclerites and reduction in tube height, and probably represents a more derived member of the brachiopod stem group with the paired symmetrical sclerites possibly homologous to brachiopod valves.
Seasonal host dynamics drive the timing of recurrent epidemics in a wildlife population
Authors: Begon Michael , Telfer Sandra , Smith Matthew J , Burthe Sarah , Paterson Steve , Lambin Xavier
Published: March 2009

The seasonality of recurrent epidemics has been largely neglected, especially where patterns are not driven by forces external to the population. Here, we use data on cowpox virus in field voles to explore the seasonal patterns in wildlife (variable abundance) populations and compare these with patterns previously found in humans. Timing in our system was associated with both the number and the rate of recruitment of susceptible hosts. A plentiful and sustained supply of susceptible hosts throughout the summer gave rise to a steady rise in infected hosts and a late peak. A meagre supply more limited in time was often insufficient to sustain an increase in infected hosts, leading to an early peak followed by a decline. These seasonal patterns differed from those found in humans, but the underlying association found between the timing and the supply of susceptible hosts was similar to that in humans. We also combine our data with a model to explore these differences between humans and wildlife. Model results emphasize the importance of the interplay between seasonal infection and recruitment and suggest that our empirical patterns have a relevance extending beyond our own system.
Allometry of visceral organs in living amniotes and its implications for sauropod dinosaurs
Authors: Franz Ragna , Hummel Jürgen , Kienzle Ellen , Kölle Petra , Gunga Hanns-Christian , Clauss Marcus
Published: March 2009

Allometric equations are often used to extrapolate traits in animals for which only body mass estimates are known, such as dinosaurs. One important decision can be whether these equations should be based on mammal, bird or reptile data. To address whether this choice will have a relevant influence on reconstructions, we compared allometric equations for birds and mammals from the literature to those for reptiles derived from both published and hitherto unpublished data. Organs studied included the heart, kidneys, liver and gut, as well as gut contents. While the available data indicate that gut content mass does not differ between the clades, the organ masses for reptiles are generally lower than those for mammals and birds. In particular, gut tissue mass is significantly lower in reptiles. When applying the results in the reconstruction of a sauropod dinosaur, the estimated volume of the coelomic cavity greatly exceeds the estimated volume of the combined organ masses, irrespective of the allometric equation used. Therefore, substantial deviation of sauropod organ allometry from that of the extant vertebrates can be allowed conceptually. Extrapolations of retention times from estimated gut contents mass and food intake do not suggest digestive constraints on sauropod dinosaur body size.