bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights
Authors: Merabet Assia , Houlleberghs Hellen , Maclagan Kate , Akanho Ester , Bui Tam T. T. , Pagano Bruno , Drake Alex F. , Fraternali Franca , Nikolova Penka V.
Published: February 2010

To assess the potential of mutations from the L1 loop of the tumour suppressor p53 as second-site suppressors, the effect of H115N and S116M on the p53 ‘hot spot’ mutations has been investigated using the double-mutant approach. The effects of these two mutants on the p53 hot spots in terms of thermal stability and DNA binding were evaluated. The results show that: (i) the p53 mutants H115N and S116M are thermally more stable than wild-type p53; (ii) H115N but not S116M is capable of rescuing the DNA binding of one of the most frequent p53 mutants in cancer, R248Q, as shown by binding of R248Q/H115N to gadd45 (the promoter of a gene involved in cell-cycle arrest); (iii) the double mutant R248Q/H115N is more stable than wild-type p53; (iv) the effect of H115N as a second-site suppressor to restore DNA-binding activity is specific to R248Q, but not to R248W; (v) molecular-dynamics simulations indicate that R248Q/H115N has a conformation similar to wild-type p53, which is distinct from that of R248Q. These findings could be exploited in designing strategies for cancer therapy to identify molecules that could mimic the effect of H115N in restoring function to oncogenic p53 mutants.
Anisotropy of tensile stresses and cracking in nonbasal plane AlxGa1−xN/GaN heterostructures
Authors: Young Erin C. , Romanov Alexey E. , Gallinat Chad S. , Hirai Asako , Beltz Glenn E. , Speck James S.
Published: February 2010

Al x Ga 1 − x N films grown on nonpolar m {11¯00} and {112¯2} semipolar orientations of freestanding GaN substrates were investigated over a range of stress states (x≤0.17). Cracking on the (0001) plane was observed beyond a critical thickness in the {11¯00} oriented films, while no cracking was observed for {112¯2} films. Theoretical analysis of tensile stresses in AlxGa1−xN for the relevant planes revealed that anisotropy of in-plane biaxial stress for the nonpolar {11¯00} planes results in the highest normal stresses on the c-planes, consistent with experimental observations. Shear stresses are significant in the semipolar case, suggesting that misfit dislocation formation provides an alternative mechanism for stress relief.
Fast shuttling of ions in a scalable Penning trap array
Authors: Crick D. R. , Donnellan S. , Ananthamurthy S. , Thompson R. C. , Segal D. M.
Published: February 2010

We report on the design and testing of an array of Penning ion traps made from printed circuit board. The system enables fast shuttling of ions from one trapping zone to another, which could be of use in quantum information processing. We describe simulations carried out to determine the optimal potentials to be applied to the trap electrodes for enabling this movement. The results of a preliminary experiment with a cloud of laser cooled calcium ions demonstrate a round-trip shuttling efficiency of up to 75%.
Time asymptotics and entanglement generation of Clifford quantum cellular automata
Authors: Gütschow Johannes , Uphoff Sonja , Werner Reinhard F. , Zimborás Zoltán
Published: February 2010

We consider Clifford quantum cellular automata (CQCAs) and their time-evolution. CQCAs are an especially simple type of quantum cellular automata, yet they show complex asymptotics and can even be a basic ingredient for universal quantum computation. In this work we study the time evolution of different classes of CQCAs. We distinguish between periodic CQCAs, fractal CQCAs, and CQCAs with gliders. We then identify invariant states and study convergence properties of classes of states, such as quasifree and stabilizer states. Finally, we consider the generation of entanglement analytically and numerically for stabilizer and quasifree states.
Submolecular-scale Investigations on metal-phthalocyanine monolayers by frequency modulation atomic force microscopy
Authors: Ichii Takashi , Fukuma Takeshi , Yoda Tadashi , Kobayashi Kei , Matsushige Kazumi , Yamada Hirofumi
Published: February 2010

Copper-phthalocyanine (CuPc) monolayers and cobalt-phthalocyanine monolayers deposited on Au(111) surfaces were investigated by frequency modulation atomic force microscopy (FM-AFM). Submolecular-resolution topographic images were successfully obtained for both samples. Despite the similar molecular geometry of the two molecules, they showed clearly different contrasts in the topographic images. The origin of the contrast is discussed in terms of the relationship of the molecular orbitals and the chemical interaction between the tip and the molecules. In addition, a molecular-resolution surface potential (SP) image was obtained on CuPc monolayers using Kelvin probe force microscopy (KFM) utilizing FM-AFM. The molecular-scale SP contrast was explained by the electric dipole moment at the organic/metal interface. This result suggested the possibility of the detection of the single molecular dipole moment by KFM.
Spectral gap, and split property in quantum spin chains
Authors: Matsui Taku
Published: February 2010

In this article, we consider a class of ground states with spectral gap for quantum spin chains on an integer lattice and we prove that the factorization lemma of Hastings [“Topology and phases in fermionic systems,” J. Stat. Mech.: Theory Exp. 2008, L01001] implies split property (weak statistical independence) of left and right semi-infinite subsystems.
A matching problem revisited for stability analysis of resistive wall modes in flowing plasmas
Authors: Shiraishi J. , Tokuda S. , Aiba N.
Published: February 2010

The classical matching problem for magnetohydrodynamic stability analysis is revisited to study effects of the plasma flow on the resistive wall modes (RWMs). The Newcomb equation, which describes the marginal states and governs the regions except for the resonant surface, is generalized to analyze the stability of flowing plasmas. When there exists no flow, the singular point of the Newcomb equation and the resonant surface degenerate into the rational surface. The location of the rational surface is prescribed by the equilibrium, hence the inner layer, which must contain the resonant surface, can be set a priori. When the flow exists, the singular point of the Newcomb equation splits in two due to the Doppler shift. Additionally, the resonant surface deviates from the singular points and the rational surface if the resonant eigenmode has a real frequency. Since the location of the resonant surface depends on the unknown real frequency, it can be determined only a posteriori. Hence the classical asymptotic matching method cannot be applied. This paper shows that a new matching method that generalizes the asymptotic one to use the inner layer with finite width works well for the stability analysis of flowing plasmas. If the real frequency is limited in a certain range such as the RWM case, the resonance occurs somewhere in the finite region around the singular points, hence the inner layer with finite width can capture the resonant surface.
High energy electron fluxes in dc-augmented capacitively coupled plasmas. II. Effects on twisting in high aspect ratio etching of dielectrics
Authors: Wang Mingmei , Kushner Mark J.
Published: February 2010

In high aspect ratio (HAR) plasma etching of holes and trenches in dielectrics, sporadic twisting is often observed. Twisting is the randomly occurring divergence of a hole or trench from the vertical. Many causes have been proposed for twisting, one of which is stochastic charging. As feature sizes shrink, the fluxes of plasma particles, and ions in particular, into the feature become statistical. Randomly deposited charge by ions on the inside of a feature may be sufficient to produce lateral electric fields which divert incoming ions and initiate nonvertical etching or twisting. This is particularly problematic when etching with fluorocarbon gas mixtures where deposition of polymer in the feature may trap charge. dc-augmented capacitively coupled plasmas (dc-CCPs) have been investigated as a remedy for twisting. In these devices, high energy electron (HEE) beams having narrow angular spreads can be generated. HEEs incident onto the wafer which penetrate into HAR features can neutralize the positive charge and so reduce the incidence of twisting. In this paper, we report on results from a computational investigation of plasma etching of SiO2 in a dc-CCP using Ar/C4F8/O2 gas mixtures. We found that HEE beams incident onto the wafer are capable of penetrating into features and partially neutralizing positive charge buildup due to sporadic ion charging, thereby reducing the incidence of twisting. Increasing the rf bias power increases the HEE beam energy and flux with some indication of improvement of twisting, but there are also changes in the ion energy and fluxes, so this is not an unambiguous improvement. Increasing the dc bias voltage while keeping the rf bias voltage constant increases the maximum energy of the HEE and its flux while the ion characteristics remain nearly constant. For these conditions, the occurrence of twisting decreases with increasing HEE energy and flux.
A Monte Carlo algorithm for computing spin echo small angle neutron scattering correlation functions in real space: Hard sphere liquids
Authors: Shew Chwen-Yang , Chen Wei-Ren
Published: February 2010

A Monte Carlo algorithm is developed to compute the autocorrelation function of liquids and the corresponding spatial correlation function from spin echo small angle neutron scattering (SESANS) spectra. The accuracy of the simulation algorithm is tested with isolated hard spheres and single dumbbells consisting of two hard spheres separated by a given distance. The simulation results accurately reproduce the exact expressions of these two models. To further test the algorithm for many-body systems, two liquid models are considered including hard sphere fluids and hard spheres with an attractive tail. The many-particle Monte Carlo simulation is carried out to obtain the ensemble average of these correlation functions. Meanwhile, the Percus–Yevic (PY) integral equation theory is resorted to compute the autocorrelation function and SESANS spatial correlation function for a density that the PY theory is reasonably applicable. The agreement between simulation and theory indicates that the algorithm is quite robust and can be extended to more complex fluids in the future. Furthermore, we find that the SESANS spatial correlation function is highly sensitive to the interaction potential between particles, which may serve as a useful tool to explore particle interactions in a liquid.
Resistivity dominated by surface scattering in sub-50 nm Cu wires
Authors: Graham R. L. , Alers G. B. , Mountsier T. , Shamma N. , Dhuey S. , Cabrini S. , Geiss R. H. , Read D. T. , Peddeti S.
Published: February 2010

Electron scattering mechanisms in copper lines were investigated to understand the extendibility of copper interconnects when linewidth or thickness is less than the mean free path. Electron-beam lithography and a dual hard mask were used to produce interconnects with linewidths between 25 and 45 nm. Electron backscatter diffraction characterized grain structure. Temperature dependence of the line resistance determined resistivity, which was consistent with existing models for completely diffused surface scattering and line-edge roughness, with little contribution from grain boundary scattering. A simple analytical model was developed that describes resistivity from diffuse surface scattering and line-edge roughness.
Longitudinal and transverse magnetization components in thin films: A resonant magnetic reflectivity investigation using circularly polarized soft x-rays
Authors: Lee J.-S. , Vescovo E. , Arena D. A. , Kao C.-C. , Beaujour J.-M. , Kent A. D. , Jang H. , Park J.-H. , Kim J.-Y.
Published: February 2010

An in-plane vectorial analysis of the magnetization of thin magnetic films is presented. Longitudinal soft x-ray resonant magnetic reflectivity curves display characteristic nodes where the longitudinal scattering component is suppressed by x-ray interference. The transverse magnetic component can be effectively retrieved at these nodal points, despite the use of circular polarization and longitudinal scattering geometry. Using a single geometric configuration, transverse and longitudinal magnetic hysteresis loops can be clearly separated. Calculations based on a Stoner–Wohlfarth model satisfactorily describe both loops. Therefore, this method presents a viable alternative to standard vectorial analysis techniques, with the additional benefit of element specificity.
The trianvil test apparatus: Measurement of shear strength under pressure
Authors: Escobedo J. P. , Field D. P. , LeBlanc M. M. , Florando J. N. , Lassila D. H.
Published: February 2010

An experimental apparatus has been developed for performing shear tests on specimens held under moderately high hydrostatic pressures (up to the order of 10 GPa). This testing procedure experimentally determines the pressure dependent shear strength of thin foil specimens. This information is necessary for models of materials subjected to extreme pressures and can assist in model validation for models such as discrete dislocation dynamics simulations, among others. This paper reports the development of the experimental procedures and the results of initial experiments on thin foils of polycrystalline Ta performed under hydrostatic pressures ranging from 2 to 4 GPa. Subsequent characterization of the samples held under pressure established that the procedure described herein represents a reliable method to impose nearly uniform hydrostatic pressure on thin foil specimens. Both yielding and hardening behavior of Ta are observed to be sensitive to the imposed pressure.
Comparison of electrical, optical, structural, and interface properties of IZO-Ag-IZO and IZO-Au-IZO multilayer electrodes for organic photovoltaics
Authors: Jeong Jin-A , Park Yong-Seok , Kim Han-Ki
Published: February 2010

We compared the electrical, optical, structural, and interface properties of indium zinc oxide (IZO)-Ag-IZO and IZO-Au-IZO multilayer electrodes, as well as the dependence of their electrical and optical properties on the thicknesses of the Ag and Au layers when used for organic solar cells (OSCs). Even though all deposition processes were carried out at room temperature, the IZO-Ag (14 nm)-IZO and IZO-Au (12 nm)-IZO multilayer electrodes exhibited extremely low sheet resistances of 4.15 and 5.49 Ω/sq, and resistivities of 3.9×10−5 and 5.5×10−5 Ω cm, respectively. In spite of its similar electrical properties, the optical transmittance of the IZO-Ag-IZO electrode is much higher than that of the IZO-Au-IZO electrode, due to the more effective antireflection effect of Ag than Au in the visible region. In addition, synchrotron x-ray scattering and scanning electron microscopy examinations showed that the structure and morphology of the Ag and Au layers critically depend on their thicknesses. Moreover, the bulk heterojunction OSC fabricated on the IZO-Ag (14 nm)-IZO multilayer electrode exhibited a higher power conversion efficiency than that fabricated on the IZO-Au-IZO layer, due to its higher transmittance in the 300–600 nm wavelength region corresponding to the absorption wavelength region of the organic active layer.
Charge ordering in PrCuMn6O12 and its behavior under pressure
Authors: Zhang W. , Yao L. D. , Yang L. X. , Liu Z. X. , Jin C. Q. , Yu R. C.
Published: February 2010

Polycrystalline PrCuMn6O12 sample has been successfully synthesized. It has been characterized by x-ray diffraction (XRD), magnetic and magnetotransport measurements at ambient pressure, and transport property measurements under pressures. From the refinements of XRD data, a cubic phase and a trigonal phase with charge ordering state were identified at higher and lower temperatures, respectively. The temperature dependence of the resistance indicates that the phase transition is a first-order transition. Both effective paramagnetic moments of the trigonal and cubic phases can be explained by orbital moment freezing theory. The transport property of the trigonal phase has been fitted with Mott’s law for variable range hopping. Though the magnetoresistance value is not large, the pressure-induced resistance value change of PrCuMn6O12 is positive and achieves 264.8%. The cubic phase is suppressed under pressure and transformed to the trigonal phase at 15 kbar, indicating favor of the charge ordering state under pressure.
Mechanics analysis and atomistic simulations of nanobridge tests
Authors: Chan Wing Kin , Zhang Tong-Yi
Published: February 2010

The present work carries out mechanics analysis and atomistic simulations of nanobridge tests under large deformation. The nanobridge test is a three-point bending test on a nanowire sample with two clamped ends. The bending behavior of a tested nanowire under large deformation is mechanically analyzed, by treating a nanowire as a composite of a three-dimensional core, two-dimensional surfaces, and one-dimensional edges, and approximated by two loading steps corresponding to pure bending and tension, respectively. The two step loadings can be easily implemented in atomistic simulations and yield the strain energy of the tested nanowire in a closed form so that the analysis of simulation results becomes straightforward. Atomistic simulations of nanobridge tests on Si and SiC nanowires were conducted to demonstrate the developed approach. The surface stiffness and edge stiffness determined from the simulations of nanobridge tests are consistent with those determined from the tensile-compressive and pure bending simulations, thereby indicating that the surface stiffness and edge stiffness are material properties, independent of the loading condition, although the size-dependent Young’s modulus is more significant in the nanobridge test than that in the tensile-compressive test.
Phonon sidebands of photoluminescence in single wall carbon nanotubes
Authors: Yu Guili , Liang Qifeng , Jia Yonglei , Dong Jinming
Published: February 2010

The multiphonon-assisted photoluminescence (PL) of the single wall carbon nanotubes (SWNTs) have been studied by solving the Schrödinger equation, showing a set of phonon sidebands, both the Stokes and anti-Stokes lines, which are induced by the longitudinal optical phonon and radial breathing mode phonon. All the calculated results are in a good agreement with the recent experimental PL spectra of the SWNTs [F. Plentz, H. B. Ribeiro, A. Jorio, M. S. Strano, and M. A. Pimenta, Phys. Rev. Lett. 95, 247401 (2005)] and J. Lefebvre and P. Finnie, Phys. Rev. Lett. 98, 167406 (2007)]. In addition, it is very interesting to find in the calculated PL several additional phonon sidebands with rather weak intensities, which are caused by the exciton’s coupling with two kinds of phonons, and expected to be observed in future experiments.
Bulk waves excited by a laser line pulse in a two-layered cylinder
Authors: Pan Y. , Chigarev N. , Audoin B.
Published: February 2010

The acoustic displacements excited by a laser line source under either the ablation or thermoelastic regime are calculated for a two-layered cylinder made of homogeneous and isotropic materials. Two samples made by welding tin in two different copper tubes are considered. Experimental displacements are observed by the laser ultrasonic technique, and corresponding theoretical waveforms are calculated. Good agreement is found in the arrival time, shape, and relative amplitude of various longitudinal and shear bulk waves propagating in the two-layered cylinders, and the waves reflected by the interface are further identified by the ray trajectory analysis. The longitudinal wave reflected at the interface may be used for the nondestructive evaluation of the interface quality.
Luminescence properties of the solvothermally synthesized blue light emitting Mn doped Cu2O nanoparticles
Authors: Das Kajari , Sharma Shailesh N. , Kumar Mahesh , De S. K.
Published: February 2010

The Cu2O nanoparticles having average crystallite diameters ∼8–16 nm were synthesized by a simple solvothermal method. The Mn was doped in the Cu2O sample of crystallite size ∼8 nm. The effects of the size and doping concentration on the crystal structures of the nanoparticles were investigated. The x-ray photoelectron spectroscopy studies clearly showed that the Mn was incorporated into the Cu2O lattice as Mn2+ due to the substitution of the Cu+ ions by Mn2+ ions. The quantum confinement effects were observed in the nanoparticles. The multiple emissions from the Cu2O were quenched in the Mn doped nanoparticles and only blue light emitting Cu2O nanoparticles were obtained due to the transition T42→A61 of Mn. The effects of the doping concentration and the particle size on the relaxations dynamics of the Cu2O nanoparticles were mainly investigated using photoluminescence decay.
Quantum effect on modulational instability of laser radiation in a semiconductor plasma
Authors: Amin M. R.
Published: February 2010

Modulational instability of a high power laser radiation in a homogeneous unmagnetized piezoelectric semiconductor plasma has been investigated analytically. The fluid equations of quantum hydrodynamics coupled with the Maxwell’s equations have been employed to find the nonlinear response of electrons in the piezoelectric semiconductor. The analysis is carried out through the derivation of the nonlinear dispersion relation for the four-wave modulational instability. An expression for the growth rate of the instability including the quantum effect due to Bohm potential has been obtained from the nonlinear dispersion relation. The quantum effect is observed to play a vital role in the four-wave scattering process. For a particular set of parameters, the quantum effect enhances the growth rate of the modulational instability by 37% compared to the growth rate predicted by the classical theory.
In-plane phonon transport in thin films
Authors: Turney J. E. , McGaughey A. J. H. , Amon C. H.
Published: February 2010

The in-plane phonon thermal conductivities of argon and silicon thin films are predicted from the Boltzmann transport equation under the relaxation time approximation. We model the thin films using bulk phonon properties obtained from harmonic and anharmonic lattice dynamics calculations. The input required for the lattice dynamics calculations is obtained from interatomic potentials: Lennard-Jones for argon and Stillinger–Weber for silicon. The effect of the boundaries is included by considering only phonons with wavelengths that fit within the film and adjusting the relaxation times to account for mode-dependent, diffuse boundary scattering. Our model does not rely on the isotropic approximation or any fitting parameters. For argon films thicker than 4.3 nm and silicon films thicker than 17.4 nm, the use of bulk phonon properties is found to be appropriate and the predicted reduction in the in-plane thermal conductivity is in good agreement with results obtained from molecular dynamics simulation and experiment. We include the effects of boundary scattering without employing the Matthiessen rule. We find that the Matthiessen rule yields thermal conductivity predictions that are at most 12% lower than our more accurate results. Our results show that the average of the bulk phonon mean free path is an inadequate metric to use when modeling the thermal conductivity reduction in thin films.
Spin-transfer switching in an epitaxial spin-valve nanopillar with a full-Heusler Co2FeAl0.5Si0.5 alloy
Authors: Sukegawa Hiroaki , Kasai Shinya , Furubayashi Takao , Mitani Seiji , Inomata Koichiro
Published: February 2010

We report magnetization switching by spin-transfer torque in an epitaxial spin-valve nanopillar made with a half-metallic full-Heusler Co2FeAl0.5Si0.5 (CFAS) alloy. The CFAS/Ag/CFAS spin valves showed a magnetoresistance ratio of 7%–9%, and spin-transfer switching was clearly observed in the nanopillar by applying a relatively small dc current (∼106 A/cm2 in current density). Statistical analysis based on a thermal activation model revealed an averaged critical current density (Jc0) of 9.3×106 A/cm2 with a thermal stability factor (KV/kBT) of ∼40.
Annealing effects of in-depth profile and band discontinuity in TiN/LaO/HfSiO/SiO2/Si gate stack structure studied by angle-resolved photoemission spectroscopy from backside
Authors: Toyoda S. , Kamada H. , Tanimura T. , Kumigashira H. , Oshima M. , Ohtsuka T. , Hata Y. , Niwa M.
Published: February 2010

We have investigated annealing effects on in-depth profile and band discontinuity for a metal gate/high-k gate stack structure on a Si substrate using backside angle-resolved photoemission spectroscopy with synchrotron radiation. In-depth profiles analyzed from angle-resolved photoemission spectroscopy show that La atoms diffuse through the HfSiO layer and reach interfacial SiO2 layers by rapid thermal annealing. Chemical shift of Si 2p core-level spectra suggests that there are changes in the band discontinuity at the high-k/SiO2 interface, which is well related to the Vth shift based on the interface dipole model.
Parasitic capacitance effect on programming performance of phase change random access memory devices
Authors: Yeo E. G. , Shi L. P. , Zhao R. , Lim K. G. , Chong T. C. , Adesida I.
Published: February 2010

Parasitic capacitance has increasing implications on the programming performance of phase change random access memory (PCRAM) devices due to increased scaling and high frequency operation. PCRAM devices with larger parasitic capacitance were found to require higher applied voltage to amorphize due to a larger leakage current. The quenching time is also increased due to a longer voltage fall time during amorphization, resulting in a partially crystallized amorphous state. This partial amorphous state requires a lower applied voltage for crystallization, which means improved crystallization performance at the expense of amorphization. Multilevel devices could be implemented by varying the parasitic capacitance to achieve different amorphous resistance.
Left-handed transmission in a simple cut-wire pair structure
Authors: Tung Nguyen Thanh , Thuy Vu Tran Thanh , Park Jin Woo , Rhee Joo Yull , Lee YoungPak
Published: February 2010

It is well known that, together with the plasma behavior of continuous wires, the use of cut-wire pair as a metamagnetic component is to drive the negative permeability in the left-handed combined structure. In this study, we have investigated a strange left-handed transmission in a metamaterial consisting of only conventional cut-wire pair structure without additional adjustment. It is shown that the observed left-handed behavior, which occurs at a frequency three times higher than that for the combined structure, originates from the fundamental negative permittivity provided by the symmetric resonant mode and a negative permeability by the third-order asymmetric resonance. Our results would simplify extremely the fabricating procedure, especially, for terahertz regime as well as reveal many possibilities to design optical devices based on the electromagnetic responses of cut-wire structure.
Effect of leaning angle of gecko-inspired slanted polymer nanohairs on dry adhesion
Authors: Jeong Hoon Eui , Lee Jin-Kwan , Kwak Moon Kyu , Moon Sang Heup , Suh Kahp Yang
Published: February 2010

We present analysis of adhesion properties of angled polymer nanohairs with a wide range of leaning angles from 0° to 45° and ultraviolet (UV)-curable polyurethane acrylate (PUA) materials of two different elastic moduli (19.8 and 320 MPa). It is demonstrated that shear adhesion and adhesion hysteresis can be greatly enhanced by increasing the leaning angle of nanohairs both for soft and hard materials due to increased contact area and reduced structural stiffness.
Investigation of Jahn–Teller splitting with O 1s x-ray absorption spectroscopy in strained Nd1−xCaxMnO3 thin films
Authors: Hsu Daniel , Chen Y. S. , Song M. Y. , Chuang C. H. , Lin Minn-Tsong , Wu W. F. , Lin J. G.
Published: February 2010

Electronic structures of strained Nd1−xCaxMnO3 (NCMO) thin films with x=0 to 0.8 are investigated via x-ray absorption spectroscopy (XAS). The obtained O 1s spectra within the photon energy 529–535 eV can be decomposed into eg↑1, eg↑2, t2g↓, and eg↓ bands. Based on the assigned energy levels of these band states, the energies of magnetic exchange, crystal field and Jahn–Teller (JT) splitting are determined. Particularly, the JT splitting is around 0.8 eV, which is observed with O 1s XAS for the first time in NCMO thin films.
Influence of random roughness on cantilever curvature sensitivity
Authors: Ergincan O. , Palasantzas G. , Kooi B. J.
Published: February 2010

In this work we explore the influence of random surface roughness on the cantilever sensitivity to respond to curvature changes induced by changes in surface stress. The roughness is characterized by the out-of-plane roughness amplitude w, the lateral correlation length ξ, and the roughness or Hurst exponent H(0<H<1). The cantilever sensitivity is found to decrease with increasing roughness (decreasing H and/or increasing ratio w/ξ) or equivalently increasing local surface slope. Finally, analytic expressions of the cantilever sensitivity as a function of the parameters w, ξ, and H are derived in order to allow direct implementation in sensing systems.
The influence of notches on domain dynamics in ferroelectric nanowires
Authors: McMillen M. , McQuaid R. G. P. , Haire S. C. , McLaughlin C. D. , Chang L. W. , Schilling A. , Gregg J. M.
Published: February 2010

The extent to which notches inhibit axial switching of polarization in ferroelectric nanowires was investigated by monitoring the switching behavior of single crystal BaTiO3 wires before and after patterning triangular notches along their lengths. Static zero-field domain patterns suggested a strong domain-notch interaction, implying that notches should act as pinning sites for domain wall propagation. Surprisingly though, notches appeared to assist, rather than inhibit, polar switching. The origin of this effect was rationalized using finite element modeling of the electric field distribution along the notched wire; it was found that the air gap associated with the notch acted to enhance the local field, both in the air, and in the adjacent region of the ferroelectric. It seems that this local field enhancement outweighs any pinning interactions.
A route to improved extraction efficiency of light-emitting diodes
Authors: Zhu H. , Shan C. X. , Wang L. K. , Yang Y. , Zhang J. Y. , Yao B. , Shen D. Z. , Fan X. W.
Published: February 2010

The electroluminescence from an n-MgZnO/i-ZnO/MgO/p-GaN asymmetric double heterojunction has been demonstrated. With the injection of electrons from n-MgZnO and holes from p-GaN, an intense ultraviolet emission coming from the ZnO active layer was observed. It is revealed that the emission intensity of the diode recorded from the MgZnO side is significantly larger than that from the MgO side because of the asymmetric waveguide structure formed by the lower refractive index of MgO than that of MgZnO. The asymmetric waveguide structure reported in this letter may promise a simple and effective route to light-emitting diodes with improved light-extraction efficiency.
Visualizing dynamic interaction between calmodulin and calmodulin-related kinases via a monitoring method in live mammalian cells
Authors: Lee Kyoung Hu , Lee Sangkyu , Lee Woo Yong , Yang Hee Won , Heo Won Do
Published: February 2010

A new visualizing method was developed for monitoring protein-protein (P-P) interactions in live mammalian cells. P-P interactions are visualized by directing localization of a bait protein to endosomes. This method is sufficiently robust to analyze signal-dependent P-P interactions such as calcium-dependent protein interactions. We visualized interactions between activated calmodulin and calmodulin-binding proteins, and observed oscillatory interactions via time-lapse imaging. In addition, this new method can simultaneously monitor multiple P-P interactions in a single live cell, which allows comparison of interactions between several prey proteins and a single bait protein. We observed that CaMKK1 and CaMKIIα bind calmodulin with distinct binding affinities in live cell, which indicates that calcium signaling is fine-tuned by distinct activation patterns of CaM kinases. This method will enable investigation of cellular processes based on dynamic P-P interactions.
The Diagnosis of Viral Respiratory Disease in Older Adults
Authors: Talbot H. Keipp , Falsey Ann R.
Published: February 2010

Viral respiratory disease in older adults has been increasingly recognized as a significant cause of hospitalizations and death. Unfortunately, the recognition and diagnosis of infection due to many viral respiratory pathogens in older adults can be elusive because of atypical clinical presentations and the insensitivity of current laboratory diagnostic tests in this population. For influenza diagnosis, rapid antigen tests followed by viral culture (if antigen test results are negative), can be useful in older adults as long as clinicians are mindful of test limitations. Although specific, rapid antigen tests are insensitive in this population. Erroneous negative results may lead to delays in timely administration of antiviral treatment and institution of appropriate isolation precautions. The increasing availability of new, rapid, and sensitive molecular diagnostics, such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future.
Manganese-induced Trafficking and Turnover of thecis-Golgi Glycoprotein GPP130
Authors: Mukhopadhyay Somshuvra , Bachert Collin , Smith Donald R. , Linstedt Adam D.
Published: February 2010

Manganese is an essential element that is also neurotoxic at elevated exposure. However, mechanisms regulating Mn homeostasis in mammalian cells are largely unknown. Because increases in cytosolic Mn induce rapid changes in the localization of proteins involved in regulating intracellular Mn concentrations in yeast, we were intrigued to discover that low concentrations of extracellular Mn induced rapid redistribution of the mammalian cis-Golgi glycoprotein Golgi phosphoprotein of 130 kDa (GPP130) to multivesicular bodies. GPP130 was subsequently degraded in lysosomes. The Mn-induced trafficking of GPP130 occurred from the Golgi via a Rab-7–dependent pathway and did not require its transit through the plasma membrane or early endosomes. Although the cytoplasmic domain of GPP130 was dispensable for its ability to respond to Mn, its lumenal stem domain was required and it had to be targeted to the cis-Golgi for the Mn response to occur. Remarkably, the stem domain was sufficient to confer Mn sensitivity to another cis-Golgi protein. Our results identify the stem domain of GPP130 as a novel Mn sensor in the Golgi lumen of mammalian cells.
A Fungal Parasite Regulates a Putative Female-Suppressor Gene Homologous to Maize Tasselseed2 and Causes Induced Hermaphroditism in Male Buffalograss
Authors: Chandra Ambika , Huff David R.
Published: February 2010

Parasitically induced hermaphroditism is a fascinating illustration of floral sex organ modification; however, knowledge of how parasites induce hermaphroditism in plants is limited. Here, we show the fungal parasite pistil smut induces development of female sex organs (pistils) in flowers of male buffalograss, potentially by downregulating a putative female-suppressor gene, BdTs2, homologous to maize Tasselseed2 (ZmTs2). Full-length BdTs2, isolated using rapid amplification of cDNA ends, exhibits 89% nucleotide sequence similarity with ZmTs2 and 85% amino acid sequence homology with ZmTs2 protein. Scanning electron micrographs demonstrate that unisexual buffalograss flowers develop through a process of selective abortion of opposite sex organs within hermaphroditic floral primordia. Quantitative real-time polymerase chain reaction showed that high expression levels of BdTs2 within male inflorescences correlate with the selective abortion of gynoecium, leading to the development of unisexual male flowers. RNA in situ hybridization confirmed the expression of BdTs2 precisely within vestigial gynoeciums of male flowers and not in other floral organs of the inflorescence. Furthermore, we show that BdTs2 expression is downregulated by pistil smut infection, which corresponds to the presence of pistils in flowers otherwise destined to become unisexual male. This study provides a potential molecular basis for pistil smut–induced hermaphroditism in male buffalograss.
pH Regulation of Ammonia Secretion by Colletotrichum gloeosporioides and Its Effect on Appressorium Formation and Pathogenicity
Authors: Miyara Itay , Shafran Hadas , Davidzon Maayan , Sherman Amir , Prusky Dov
Published: February 2010

Host-tissue alkalinization via ammonia accumulation is key to Colletotrichum spp. colonization. Using macroarrays carrying C. gloeosporioides cDNAs, we monitored gene expression during the alkalinization process. A set of genes involved in synthesis and catabolism of ammonia accumulation were identified. Expression of NAD+-specific glutamate dehydrogenase (GDH2, encoding ammonia synthesis) and the ammonia exporter AMET were induced at pH 4.0 to 4.5. Conversely, ammonia uptake and transcript activation of the ammonia and glutamate importers (MEP and GLT, respectively) and glutamine synthase (GS1) were higher at pH 6.0 to 7.0. Accumulated ammonia in the wild-type mycelium decreased during ambient alkalinization, concurrent with increased GS1 expression. Δpac1 mutants of C. gloeosporioides, which are sensitive to alkaline pH changes, showed upregulation of the acid-expressed GDH2 and downregulation of the alkaline-expressed GS1, resulting in 60% higher ammonia accumulation inside the mycelium. Δgdh2 strains of C. gloeosporioides, impaired in ammonia production, showed 85% inhibition in appressorium formation followed by reduced colonization on avocado fruit (Persea americana cv. Fuerte) pericarp, while exogenic ammonia addition restored appressoria formation. Thus the modulation of genes involved in ammonia metabolism and catabolism by C. gloeosporioides is ambient pH–dependent. Aside from its contribution to necrotrophic stages, ammonia accumulation by germinating spores regulates appressorium formation and determines the initiation of biotrophic stages of avocado-fruit colonization by Colletotrichum spp.
A Progeny Virus from a Cucumovirus Pseudorecombinant Evolved to Gain the Ability to Accumulate Its RNA-Silencing Suppressor Leading to Systemic Infection in Tobacco
Authors: Asaoka Ryota , Shimura Hanako , Arai Makoto , Masuta Chikara
Published: February 2010

Two isolates of Tomato aspermy virus (TAV), V-TAV and C-TAV, can systemically infect Nicotiana benthamiana but only C-TAV can move systemically in N. tabacum. Any pseudorecombinants between the two strains could not move systemically in tobacco as efficiently as C-TAV. However, a pseudorecombinant consisting of RNAs 1 and 3 of V-TAV and RNA 2 of C-TAV (V1C2V3), which cannot infect tobacco systemically, generated progeny with a mutation in V1 and a recombination in C2 (V1mC2rV3), enabling the virus to move systemically. To avoid further mutation and recombination in the virus, we used Cucumber mosaic virus RNA3 (Y3) for subsequent experiments. Northern blot analyses showed that RNA4A, which encodes the 2b protein (2b), and RNA5 abundantly accumulated in V1mC2rY3-infected tobacco. V1mC2rY3 actually caused higher accumulation of 2b than did V1C2Y3 in Western blots, and overexpression of 2b by the PVX vector enabled V1C2Y3 to move systemically in tobacco, suggesting that 2b accumulation promotes viral systemic movement. Because RNA-silencing suppressor (RSS) activity of 2b was thought to be involved in systemic movement, we compared the RSS activity of 2b for the two TAV isolates; C-TAV 2b had stronger activity than did V-TAV 2b in tobacco in a transient protoplast assay. Our data also demonstrated that 2b and RNA5 play an important role in the evolution of members of genus Cucumovirus by generating mutant/recombinant viruses and viral systemic movement over RNA silencing.
Ascorbic Acid Deficiency in Arabidopsis Induces Constitutive Priming That is Dependent on Hydrogen Peroxide, Salicylic Acid, and the NPR1 Gene
Authors: Mukherjee Madhumati , Larrimore Katherine E. , Ahmed Naushin J. , Bedick Tyler S. , Barghouthi Nadia T. , Traw M. Brian , Barth Carina
Published: February 2010

The ascorbic acid (AA)-deficient Arabidopsis thaliana vtc1-1 mutant exhibits increased resistance to the virulent bacterial pathogen Pseudomonas syringae. This response correlates with heightened levels of salicylic acid (SA), which induces antimicrobial pathogenesis-related (PR) proteins. To determine if SA-mediated, enhanced disease resistance is a general phenomenon of AA deficiency, to elucidate the signal that stimulates SA synthesis, and to identify the biosynthetic pathway through which SA accumulates, we studied the four AA-deficient vtc1-1, vtc2-1, vtc3-1, and vtc4-1 mutants. We also studied double mutants defective in the AA-biosynthetic gene VTC1 and the SA signaling pathway genes PAD4, EDS5, and NPR1, respectively. All vtc mutants were more resistant to P. syringae than the wild type. With the exception of vtc4-1, this correlated with constitutively upregulated H2O2, SA, and messenger RNA levels of PR genes. Double mutants exhibited decreased SA levels and enhanced susceptibility to P. syringae compared with the wild type, suggesting that vtc1-1 requires functional PAD4, EDS5, and NPR1 for SA biosynthesis and pathogen resistance. We suggest that AA deficiency causes constitutive priming through a buildup of H2O2 that stimulates SA accumulation, conferring enhanced disease resistance in vtc1-1, vtc2-1, and vtc3-1, whereas vtc4-1 might be sensitized to H2O2 and SA production after infection.
Conformist learning in nine-spined sticklebacks' foraging decisions
Authors: Pike Thomas W. , Laland Kevin N.
Published: February 2010

Theoretical analyses have reported that in most circumstances where natural selection favours reliance on social learning, conformity (positive frequency-dependent social learning) is also favoured. These findings suggest that much animal social learning should involve a copy-the-majority strategy, yet there is currently surprisingly little evidence for conformist learning among animals. Here, we investigate this possibility in the nine-spined stickleback (
Pungitius pungitius
) by manipulating the number of demonstrator fish at two feeders, one rich and one poor, during a demonstration phase and evaluating how this affects the likelihood that the focal fish copy the demonstrators' apparent choices. As predicted, we observed a significantly increased level of copying with increasing numbers of demonstrators at the richer of the two feeders, with copying increasing disproportionately, rather than linearly, with the proportion of demonstrators at the rich foraging patch. Control conditions with non-feeding demonstrators showed that this was not simply the result of a preference for shoaling with larger groups, implying that nine-spined sticklebacks copy in a conformist manner.
Photoreceptor-based magnetoreception: optimal design of receptor molecules, cells, and neuronal processing
Authors: Ritz Thorsten , Ahmad Margaret , Mouritsen Henrik , Wiltschko Roswitha , Wiltschko Wolfgang
Published: February 2010

The sensory basis of magnetoreception in animals still remains a mystery. One hypothesis of magnetoreception is that photochemical radical pair reactions can transduce magnetic information in specialized photoreceptor cells, possibly involving the photoreceptor molecule cryptochrome. This hypothesis triggered a considerable amount of research in the past decade. Here, we present an updated picture of the radical-pair photoreceptor hypothesis. In our review, we will focus on insights that can assist biologists in their search for the elusive magnetoreceptors.
Gravitational lensing: a unique probe of dark matter and dark energy
Authors: Ellis Richard S.
Published: February 2010

I review the development of gravitational lensing as a powerful tool of the observational cosmologist. After the historic eclipse expedition organized by Arthur Eddington and Frank Dyson, the subject lay observationally dormant for 60 years. However, subsequent progress has been astonishingly rapid, especially in the past decade, so that gravitational lensing now holds the key to unravelling the two most profound mysteries of our Universe—the nature and distribution of dark matter, and the origin of the puzzling cosmic acceleration first identified in the late 1990s. In this non-specialist review, I focus on the unusual history and achievements of gravitational lensing and its future observational prospects.
Interaction of theory and experiment: examples from single molecule studies of nanoparticles
Authors: Marcus Rudolph A.
Published: February 2010

This article is in part the author's perspective on the revolution that has occurred in theoretical chemistry during the past half-century. In this period much of theoretical chemistry has moved from its initial emphasis on analytic treatments, resulting in equations for physical chemical and chemical phenomena, to the detailed computation of many different systems and processes. In the best sense the old and the new are complementary and their coexistence can benefit both. Experiment too has seen major developments. One of the newer types of experiment is that of single molecule studies. They range from those on small inorganic and organic nanoparticles to large biological species. We illustrate some of the issues that arise, using the topic of ‘quantum dots’ (QDs), and choosing a particular inorganic nanoparticle, CdSe, the most studied of these systems. Its study reflects the problems that arise in experiment and in theories in this field. The complementary nature of the conventional ensemble experiments and the new single molecule experiments is described and is illustrated by trajectories for the two types of experiments. The research in the QD field is both experimentally and theoretically a currently ongoing process, for which the answers are not fully known in spite of the large body of research. The detailed role of surface states is part of the problem. The field continues to yield new and unexpected results. In a sense this part of the article is an interim report that illustrates one analytic approach to the topic and where computer calculations and simulations can be expected to provide added insight.
Structural insights into the YAP and TEAD complex
Authors: Li Ze , Zhao Bin , Wang Ping , Chen Fei , Dong Zhenghong , Yang Huirong , Guan Kun-Liang , Xu Yanhui
Published: February 2010

The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50–171)–TEAD1 (residues 194–411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86–100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP–TEAD interaction, and provides a basis for pharmacological intervention of YAP–TEAD hyperactivation in human diseases.