bluuebunny/crossref_metadata_2025 huggingface dataset:
Defining HRTEM Resolution: Image Resolutions and Microscope Limits
Authors: O'Keefe MA , Allard LF , Blom DA
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
High Resolution Characterization of Bioengineered Tissue using Multiphoton Microscopy
Authors: Zipfel WR , Bowles RD , Bonassar LJ , Williams RM
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Hybrid Architectures of Metal Oxide Nanostructures Grown on Aligned Carbon Nanotubes
Authors: Ok JG , Juggernauth KA , Sun K , McLane AA , Zhang Y , Tawfick SH , Hart AJ
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Application of Zernike Phase-Contrast Electron Microscopy for Vitrified Complex Biological Specimens
Authors: Fukuda Y , Fukazawa Y , Danev R , Shigemoto R , Nagayama K
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
An X-Ray and Cathodoluminescence Study of Cassiterite (SnO2)
Authors: Wight S , Vicenzi E , Meier D , Benkstein K
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
High Content Imaging for Discovery of Botulinum Neurotoxin Antagonists
Authors: Ruthel G , Kota K , Nuss JE , Bavari S
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Investigating Radiation Damage in Ceramics: the Role of In Situ Microscopy
Authors: Smith KL , Lumpkin GR , Whittle KR , Blackford MG , Zaluzec NJ
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
The Earliest History of Life: Solution to Darwin’s Dilemma
Authors: Schopf JW
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Strain Mapping on Semiconductor Device by Dark Field Electron Holography
Authors: Wang YY , Li J , Bruley J , Domenicucci A , Cooper D , Jean-Luc R
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Microstructure Tomography in the Micro, Nano and Atomic scale – Advanced Access to Understand Local Formation as well as Degradation of Materials Microstructure
Authors: Muecklich F , Engstler M
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Analysis of Local Texture across Layers in Electron-Beam Melted (EBM) Ti-6Al- 4V via Electron Backscatter Diffraction (EBSD)
Authors: Saller B , Porter JR , Van Den Vlekkert T , Walck SD
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Analysis of Metal Nanoparticles in Biological Tissues Specimens Using Various Surface Analytical Techniques
Authors: Smentkowski VS , Denault L , Wark D , Scipioni L , Ferranti D
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
In Situ TEM Studies of Microstructure Evolution Under Ion Irradiation for Nuclear Engineering Applications
Authors: Kaoumi D , Motta AT , Kirk M , Faney T , Wirth B , Bentley J
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Special Approaches to Metallography for Zirconium & Other Reactive Metals
Authors: Sparkowich SD
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Etching and High-Resolution Backscatter Electron Imaging for Semi-Automated Segmentation and Stereology of the Gamma Prime Phase in Ni-based Superalloys
Authors: Payton EJ , Phillips PJ , Mills MJ
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Cells and Viruses at Molecular Resolution: From Structure to Mechanism
Authors: Subramaniam S
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Structural and Compositional Transitions at the Atomic Scale Across Interfaces, Faults and Phase Separations in Complex Oxides
Authors: Williams REA , Dixit M , Mishra R , Genc A , Srinivasan R , Viswanathan GB , McComb DW , Ringnalda J , Dwyer C , Windl W , Fraser HL
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
What microscopy can tell us about Alzheimer's and related diseases
Authors: Welland ME
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Revealing the Microstructure of Super Alloys Using Lucas’ Reagent
Authors: Lucas GM
Published: August 2010

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Magnetosheath for almost‐aligned solar wind magnetic field and flow vectors: Wind observations across the dawnside magnetosheath at X = −12 Re
Authors: Farrugia C. J. , Erkaev N. V. , Torbert R. B. , Biernat H. K. , Gratton F. T. , Szabo A. , Kucharek H. , Matsui H. , Lin R. P. , Ogilvie K. W. , Lepping R. P. , Smith C. W.
Published: August 2010

While there are many approximations describing the flow of the solar wind past the magnetosphere in the magnetosheath, the case of perfectly aligned (parallel or anti‐parallel) interplanetary magnetic field (IMF) and solar wind flow vectors can be treated exactly in a magnetohydrodynamic (MHD) approach. In this work we examine a case of nearly‐opposed (to within 15°) interplanetary field and flow vectors, which occurred on October 24–25, 2001 during passage of the last interplanetary coronal mass ejection in an ejecta merger. Interplanetary data are from the ACE spacecraft. Simultaneously Wind was crossing the near‐Earth (X ∼ −13 Re) geomagnetic tail and subsequently made an approximately 5‐hour‐long magnetosheath crossing close to the ecliptic plane (Z = −0.7 Re). Geomagnetic activity was returning steadily to quiet, “ground” conditions. We first compare the predictions of the Spreiter and Rizzi theory with the Wind magnetosheath observations and find fair agreement, in particular as regards the proportionality of the magnetic field strength and the product of the plasma density and bulk speed. We then carry out a small‐perturbation analysis of the Spreiter and Rizzi solution to account for the small IMF components perpendicular to the flow vector. The resulting expression is compared to the time series of the observations and satisfactory agreement is obtained. We also present and discuss observations in the dawnside boundary layer of pulsed, high‐speed (v ∼ 600 km/s) flows exceeding the solar wind flow speeds. We examine various generating mechanisms and suggest that the most likely cause is a wave of frequency 3.2 mHz excited at the inner edge of the boundary layer by the Kelvin‐Helmholtz instability.
Modes and mechanisms of sea surface temperature low‐frequency variations over the coastal China seas
Authors: Zhang Liping , Wu Lixin , Lin Xiaopei , Wu Dexing
Published: August 2010

In this paper, low‐frequency variability of annual‐mean sea surface temperature in the coastal China seas is studied based on ocean and atmosphere reanalysis products. There are two distinct low‐frequency modes: a basin mode and a north‐south dipole mode. The former is characterized by a uniform warming over the entire coastal oceans, while the latter is characterized by a seesaw pattern over the shelf seas and the South China Sea. The basin mode is associated with global warming, but it is primarily attributed to oceanic advection, with surface heat flux playing a damping effect due to intensification of the latent heat loss. The dipole mode varies coherently with the Pacific Decadal Oscillation. In contrast to the basin mode, the dipole mode is broadly associated with the surface heat flux, with oceanic advection acting to damp sea surface temperature (SST) in the shelf seas but sustain SST in the South China Sea. A further analysis indicates that the basin mode and the dipole mode derived from the annual‐mean SST remain robust in winter and summer, despite some differences in the governing processes. It is found that the summer dipole mode is associated with the Atlantic Multidecadal Oscillation. Therefore, SST over the coastal China seas may be used as a potential indictor of these global‐scale climate changes.
Spectroscopic studies of the heterogeneous reaction between O3(g) and halides at the surface of frozen salt solutions
Authors: Wren Sumi N. , Kahan Tara F. , Jumaa Klaudia B. , Donaldson D. J.
Published: August 2010

Springtime ozone depletion events have been linked to elevated levels of bromine in the polar boundary layer. It has also been suggested that iodine may play an important role in boundary layer chemistry. However, the mechanism(s) for initial halogen activation is not well understood. We report results of experiments using glancing‐angle laser‐induced fluorescence (LIF) and glancing‐angle Raman spectroscopy to investigate the heterogeneous reaction of gas‐phase ozone with bromide and iodide ions at the surface of frozen salt solutions. The results suggest that halides that have been excluded to the ice surface during the freezing process react in the dark and under non‐acidified conditions to produce molecular halogen species. At environmentally relevant bromide concentrations, the reaction proceeds ∼60 times more rapidly at ice surfaces than at the surface of aqueous solutions. At an ozone concentration of ∼8 × 1015 molec cm−3, and sea water concentrations of bromide and iodide, we estimate uptake coefficients γ(Br−) = (1.3 ± 0.5) × 10−8 and γ(I−) = (1.6 ± 0.5) × 10−9. We estimate that at atmospheric ozone concentrations, the uptake coefficients will be approximately a factor of ten greater.
In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS
Authors: Jensen Sheila I , Steunou Anne-Soisig , Bhaya Devaki , Kühl Michael , Grossman Arthur R
Published: August 2010

The relative abundance of transcripts encoding proteins involved in inorganic carbon concentrating mechanisms (CCM), detoxification of reactive oxygen species (ROS) and photosynthesis in the thermophilic cyanobacterium Synechococcus OS-B′ was measured in hot spring microbial mats over two diel cycles, and was coupled with in situ determinations of incoming irradiance and microenvironmental dynamics of O2 and pH. Fluctuations in pH and O2 in the mats were largely driven by the diel cycle of solar irradiance, with a pH variation from ∼7.0 to ∼9.5, and O2 levels ranging from anoxia to supersaturation during night and day, respectively. Levels of various transcripts from mat cyanobacteria revealed several patterns that correlated with incident irradiance, O2 and pH within the mat matrix. Transcript abundances for most genes increased during the morning dark–light transition. Some transcripts remained at a near constant level throughout the light period, whereas others showed an additional increase in abundance as the mat underwent transition from low-to-high light (potentially reflecting changes in O2 concentration and pH), followed by either a decreased abundance in the early afternoon, or a gradual decline during the early afternoon and into the evening. One specific transcipt, psbA1, was the lowest during mid-day under high irradiance and increased when the light levels declined. We discuss these complex in situ transcriptional patterns with respect to environmental and endogenous cues that might impact and regulate transcription over the diel cycle.
Transcriptional activation requires protection of the TATA-binding protein Tbp1 by the ubiquitin-specific protease Ubp3
Authors: Chew Boon Shang , Siew Wee Leng , Xiao Benjamin , Lehming Norbert
Published: August 2010

Tbp1, the TATA-binding protein, is essential for transcriptional activation, and Gal4 and Gcn4 are unable to fully activate transcription in a Saccharomyces cerevisiae TBP1E86D mutant strain. In the present study we have shown that the Tbp1E186D mutant protein is proteolytically instable, and we have isolated intragenic and extragenic suppressors of the transcription defects of the TBP1E186D mutant strain. The TBP1R6S mutation stabilizes the Tbp1E186D mutant protein and suppresses the defects of the TBP1E186D mutant strain. Furthermore, we found that the overexpression of the de-ubiquitinating enzyme Ubp3 (ubiquitin-specific protease 3) also stabilizes the Tbp1E186D mutant protein and suppresses of the defects of the TBP1E186D mutant strain. Importantly, the deletion of UBP3 and its cofactor BRE5 lead to increased degradation of wild-type Tbp1 protein and to defects in transcriptional activation by Gal4 and Gcn4. Purified GST (glutathione transferase)–Ubp3 reversed Tbp1 ubiquitination, and the deletion of UBP3 lead to the accumulation of poly-ubiquitinated species of Tbp1 in a proteaseome-deficient genetic background, demonstrating that Ubp3 reverses ubiquitination of Tbp1 in vitro and in vivo. Chromatin immunoprecipitation showed that Ubp3 was recruited to the GAL1 and HIS3 promoters upon the induction of the respective gene, indicating that protection of promoter-bound Tbp1 by Ubp3 is required for transcriptional activation.
Self‐initiated academic expatriates: Inherent demographics and reasons to expatriate
Authors: Selmer Jan , Lauring Jakob
Published: August 2010

Research on expatriate employees has to date focused mainly on organizational expatriates, so‐called because they have been assigned by a parent company to a host country. Relatively little research has been conducted on self‐initiated expatriate (SIE) employees. Hence, not enough is known about this type of expatriate. This paper examines the inherent demographics of SIEs. Data were collected from 428 expatriate academics from 60 countries, employed in 35 universities in five northern European countries. Results provided support for half of the propositions predicting that SIEs' reasons to expatriate differ according to age and gender. Implications of the findings are discussed.
Optimal control of underactuated mechanical systems: A geometric approach
Authors: Colombo Leonardo , Martín De Diego David , Zuccalli Marcela
Published: August 2010

In this paper, we consider a geometric formalism for optimal control of underactuated mechanical systems. Our techniques are an adaptation of the classical Skinner and Rusk approach for the case of Lagrangian dynamics with higher-order constraints. We study a regular case where it is possible to establish a symplectic framework and, as a consequence, to obtain a unique vector field determining the dynamics of the optimal control problem. These developments will allow us to develop a new class of geometric integrators based on discrete variational calculus.
Modeling the effect of native and laser-induced states on the dielectric breakdown of wide band gap optical materials by multiple subpicosecond laser pulses
Authors: Emmert Luke A. , Mero Mark , Rudolph Wolfgang
Published: August 2010

A model for the multiple-pulse laser-induced breakdown behavior of dielectrics is presented. It is based on a critical conduction band (CB) electron density leading to dielectric breakdown. The evolution of the CB electron density during the pulse train is calculated using rate equations involving transitions between band and mid-gap states (native and laser-induced). Using realistic estimations for the trap density and ionization cross-section, the model is able to reproduce the experimentally observed drop in the multiple-pulse damage threshold relative to the single-pulse value, as long as the CB electron density is controlled primarily by avalanche ionization seeded by multiphoton ionization of the traps and the valence band. The model shows that at long pulse duration, the breakdown threshold becomes more sensitive to presence of traps close (within one photon energy) to the CB. The effect of native and laser-induced defects can be distinguished by their saturation behavior. Finally, measurements of the multiple-pulse damage threshold of hafnium oxide films are used to illustrate the application of the model.
Scaling laws for electrical contact resistance with dissimilar materials
Authors: Zhang Peng , Lau Y. Y.
Published: August 2010

This paper attempts to quantify the effects of contaminants on electrical contact resistance. Based on an idealized model, simple and explicit scaling laws for the electrical contact resistance with dissimilar materials are constructed. The model assumes arbitrary resistivity ratios and aspect ratios in the current channels and their contact region, for both Cartesian and cylindrical geometries. The scaling laws have been favorably tested in several limits, and in sample calculations using a numerical simulation code. From the scaling laws and a survey of the huge parameter space, some general conclusions are drawn on the parametric dependence of the contact resistance on the geometry and on the electrical resistivity in different regions.
Vortex shedding in the wake of a step cylinder
Authors: Morton Chris , Yarusevych Serhiy
Published: August 2010

Flow past a circular cylinder with a single stepwise discontinuity in diameter was investigated numerically for the diameter ratio D/d=2 and two Reynolds numbers, ReD=150 and 300. The primary focus was on vortex shedding and vortex interactions occurring in the cylinder wake. In agreement with previous experimental findings, three distinct spanwise vortex cells were identified in the step-cylinder wake: a single vortex shedding cell in the wake of the small cylinder (the S-cell) and two vortex shedding cells in the wake of the large cylinder, one in the region downstream of the step (the N-cell) and the other away from the step (the L-cell). Due to the differences in vortex shedding frequencies, complex vortex connections occurred in two vortex interaction regions located between the adjacent cells. However, distinct differences in vortex splitting and vortex dislocations were identified in the two regions. The region at the boundary between the S-cell and the N-cell was relatively narrow and its spanwise extent did not fluctuate significantly. In this region, vortex dislocations manifested as half-loop connections between two S-cell vortices of opposite sign. In contrast, the region at the boundary between the N-cell and the L-cell exhibited transient behavior, with large scale vortex dislocations causing cyclic variation in the extent of N-cell vortices. Spectral analysis of velocity data showed that the presence of the N-cell was continuous through all simulations. For ReD=300, small scale streamwise vortices forming in the wake of the large cylinder weaken the primary spanwise vortices and vortex connections, complicating vortex dynamics in the step-cylinder wake. However, no significant Reynolds number effect on the average spanwise extent of the vortex cells and the two transition regions between neighboring cells was observed. Finally, formation of N-cell vortices was shown to be linked to downwash fluctuations near the step.
Fluids density functional theory studies of supramolecular polymers at a hard surface
Authors: McGarrity E. S. , Thijssen J. M. , Besseling N. A. M.
Published: August 2010

We have applied a fluids density functional theory based on that of Yu and Wu [J. Chem. Phys. 116, 7094 (2002)] to treat reversible supramolecular polymers near a hard surface. This approach combines a hard-sphere fluids density functional theory with the first-order thermodynamic perturbation theory of Wertheim. The supramolecular polymers are represented in the theory by hard-spheres with two associating sites. We explore the effects of the bonding scheme, monomer concentration, and association energy upon the equilibrium chain sizes and the depletion lengths. This study is performed on simple systems containing two-site monomers and binary mixtures of two-site monomers combined with end stopper monomers which have only a single association site. Our model has correct behavior in the dilute and overlap regimes and the bulk results can be easily connected to simpler random-flight models. We find that there is a nonmonotonic behavior of the depletion length of the polymers as a function of concentration and that this depletion length can be controlled through the concentration of end stoppers. These results are applicable to the study of colloidal dispersions in supramolecular polymer solutions.
A versatile high resolution scanning tunneling potentiometry implementation
Authors: Druga T. , Wenderoth M. , Homoth J. , Schneider M. A. , Ulbrich R. G.
Published: August 2010

We have developed a new scanning tunneling potentiometry technique which can—with only minor changes of the electronic setup—be easily added to any standard scanning tunneling microscope (STM). This extension can be combined with common STM techniques such as constant current imaging or scanning tunneling spectroscopy. It is capable of performing measurements of the electrochemical potential with microvolt resolution. Two examples demonstrate the versatile application. First of all, we have determined local variations of the electrochemical potential due to charge transport of biased samples down to angstrom length scales. Second, with tip and sample at different temperatures we investigated the locally varying thermovoltage occurring at the tunneling junction. Aside from its use in determining the chemical identity of substances at the sample surface our method provides a controlled way to eliminate the influence of laterally varying thermovoltages on low-bias constant current topographies.
Communication: Feshbach resonances in the water molecule revealed by state-selective spectroscopy
Authors: Grechko Maxim , Maksyutenko Pavlo , Rizzo Thomas R. , Boyarkin Oleg V.
Published: August 2010

We employ triple-resonance vibrational overtone excitation to access quasibound states of water from several fully characterized bound states of the molecule. Comparison of the measured dissociation spectra allows a rigorous assignment of rotational quantum numbers J, nuclear spin and parity, and a tentative vibrational characterization of the observed resonances. Their asymmetrical shapes (Fano profiles) reflect interference of dipole moments for transitions to these resonances with that to the dissociative continuum. The assignments and Fano profile parameters of the resonances stand as a benchmark for the extension of accurate quantum-mechanical calculations to activated complexes of water. The narrow widths of some of these resonances indicate that water molecules may survive for as long as up to 60 ps in states above the dissociation threshold. We consider the possible implication of such long-lived states for the kinetics of water dissociation and the OH+H association reaction.
A molecular dynamics study on the transport of a charged biomolecule in a polymeric adsorbent medium and its adsorption onto a charged ligand
Authors: Riccardi E. , Wang J.-C. , Liapis A. I.
Published: August 2010

The transport of a charged adsorbate biomolecule in a porous polymeric adsorbent medium and its adsorption onto the covalently immobilized ligands have been modeled and investigated using molecular dynamics modeling and simulations as the third part of a novel fundamental methodology developed for studying ion-exchange chromatography based bioseparations. To overcome computational challenges, a novel simulation approach is devised where appropriate atomistic and coarse grain models are employed simultaneously and the transport of the adsorbate is characterized through a number of locations representative of the progress of the transport process. The adsorbate biomolecule for the system studied in this work changes shape, orientation, and lateral position in order to proceed toward the site where adsorption occurs and exhibits decreased mass transport coefficients as it approaches closer to the immobilized ligand. Furthermore, because the ligands are surrounded by counterions carrying the same type of charge as the adsorbate biomolecule, it takes the biomolecule repeated attempts to approach toward a ligand in order to displace the counterions in the proximity of the ligand and to finally become adsorbed. The formed adsorbate-ligand complex interacts with the counterions and polymeric molecules and is found to evolve slowly and continuously from one-site (monovalent) interaction to multisite (multivalent) interactions. Such a transition of the nature of adsorption reduces the overall adsorption capacity of the ligands in the adsorbent medium and results in a type of surface exclusion effect. Also, the adsorption of the biomolecule also presents certain volume exclusion effects by not only directly reducing the pore volume and the availability of the ligands in the adjacent regions, but also causing the polymeric molecules to change to more compact structures that could further shield certain ligands from being accessible to subsequent adsorbate molecules. These findings have significant practical implications to the design and construction of polymeric porous adsorbent media for effective bioseparations and to the synthesis and operation of processes employed in the separation of biomolecules. The modeling and analysis methods presented in this work could also be suitable for the study of biocatalysis where an enzyme is immobilized on the surface of the pores of a porous medium.
Communication: Mode-selective vibrational excitation induced by nonequilibrium transport processes in single-molecule junctions
Authors: Härtle Rainer , Volkovich Roie , Thoss Michael , Peskin Uri
Published: August 2010

In a nanoscale molecular junction at finite bias voltage, the intramolecular distribution of vibrational energy can strongly deviate from the thermal equilibrium distribution and specific vibrational modes can be selectively excited in a controllable way, regardless of the corresponding mode frequency. This is demonstrated for generic models of asymmetric molecular junctions with localized electronic states, employing a master equation as well as a nonequilibrium Green’s function approach. It is shown that the applied bias voltage controls the excitation of specific vibrational modes by tuning the efficiency of vibrational cooling processes due to energy exchange with the leads.
A fine-focusing x-ray source using carbon-nanofiber field emitter
Authors: Sugimoto W. , Sugita S. , Sakai Y. , Goto H. , Watanabe Y. , Ohga Y. , Kita S. , Ohara T.
Published: August 2010

A fine-focusing x-ray source has been constructed employing a field electron emitter prepared by growing carbon-nanofibers (CNFs) on a metal tip. The x-ray source is composed of a CNF field electron emitter, an electrostatic lens, two magnetic lenses, and a W-target for generating x-rays by electron impact. The CNFs provided field electrons with a current density of J∼5×109 A/m2, which was evaluated with the aid of Fowler–Nordheim theory. The electron beam extracted from the CNF emitter was accelerated to the energies of E=10–25 keV, and then focused by the lenses. By recording the x-ray images of test charts, the optimum resolution of the x-ray source was estimated to be approximately Dx=0.5 μm.
A convergence study for the Laguerre expansion in the moment equation method for neoclassical transport in general toroidal plasmas
Authors: Nishimura S. , Sugama H. , Maaßberg H. , Beidler C. D. , Murakami S. , Nakamura Y. , Hirooka S.
Published: August 2010

The dependence of neoclassical parallel flow calculations on the maximum order of Laguerre polynomial expansions is investigated in a magnetic configuration of the Large Helical Device [S. Murakami, A. Wakasa, H. Maaßberg, et al., Nucl. Fusion 42, L19 (2002)] using the monoenergetic coefficient database obtained by an international collaboration. On the basis of a previous generalization (the so-called Sugama–Nishimura method [H. Sugama and S. Nishimura, Phys. Plasmas 15, 042502 (2008)]) to an arbitrary order of the expansion, the 13 M, 21 M, and 29 M approximations are compared. In a previous comparison, only the ion distribution function in the banana collisionality regime of single-ion-species plasmas in tokamak configurations was investigated. In this paper, the dependence of the problems including electrons and impurities in the general collisionality regime in an actual nonsymmetric toroidal configuration is reported. In particular, qualities of approximations for the electron distribution function are investigated in detail.
Axisymmetric simulations of libration-driven fluid dynamics in a spherical shell geometry
Authors: Calkins Michael A. , Noir Jérôme , Eldredge Jeff D. , Aurnou Jonathan M.
Published: August 2010

We report on axisymmetric numerical simulations of rapidly rotating spherical shells in which the axial rotation rate of the outer shell is modulated in time. This allows us to model planetary bodies undergoing forced longitudinal libration. In this study we systematically vary the Ekman number, 10−7≤E≲10−4, which characterizes the ratio of viscous to Coriolis forces in the fluid, and the libration amplitude, Δϕ. For libration amplitudes above a certain threshold, Taylor–Görtler vortices form near the outer librating boundary, in agreement with the previous laboratory experiments of Noir et al. [Phys. Earth Planet. Inter. 173, 141 (2009)]. At the lowest Ekman numbers investigated, we find that the instabilities remain spatially localized at onset in the equatorial region. In addition, nonzero time-averaged azimuthal (zonal) velocities are observed for all parameters studied. The zonal flow is characterized by predominantly retrograde flow in the interior, with a stronger prograde jet in the outer equatorial region. The magnitude of the zonal flow scales as the square of the librational forcing, ϵ2, where ϵ=Δϕf and f is the dimensionless libration frequency defined as the ratio between the libration frequency and the mean angular rotation rate. In addition, the zonal flow is primarily independent of the Ekman number, implying that the zonal flow does not depend on the viscosity of the fluid. The simulations show that the zonal flow is driven by nonlinearities in the Ekman boundary layer; it is not driven by Taylor–Görtler vortices or by inertial waves in the fluid interior. Application of our results suggests that many librating bodies in the solar system are above the onset for centrifugal instabilities, with values up to ∼30 times supercritical. However, the spatial localization of the instabilities at onset in our simulations suggests that their effects are limited on the global dynamics of librating bodies. We find that the zonal flows driven by libration in axisymmetric spherical shells are unlikely to produce significant planetary magnetic fields, but will likely generate nonzero mean torques on the bounding surfaces.
Magnetic states of a rf superconducting quantum interference device containing a double-barrier Josephson junction
Authors: De Luca R.
Published: August 2010

The magnetic properties of a rf superconducting quantum interference device containing one overdamped double-barrier junction are studied. The effective nonsinusoidal expression for the current-phase relation with an additional half harmonic term is used for the double-barrier junction. Devices with inhomogeneous double-barrier junctions show a characteristic feature: for fixed and not too high superconducting loop inductance values, transition from irreversible to reversible magnetic behavior can be induced by increasing the difference in the Josephson coupling of the two junctions.
Revealing substructures of H4 and H5 hole traps in p-type InP using Laplace deep-level transient spectroscopy
Authors: Darwich R. , Mani A. A.
Published: August 2010

New substructures of H4 and H5 hole traps have been revealed using Laplace deep-level transient spectroscopy. Our measurements show that the hole traps H4 and H5 can have at least three components for each. Moreover, the activation energies are deduced and the microscopic nature of these substructures is discussed.
DNA-decorated graphene chemical sensors
Authors: Lu Ye , Goldsmith B. R. , Kybert N. J. , Johnson A. T. C.
Published: August 2010

Graphene is a two-dimensional material with exceptional electronic properties and enormous potential for applications. Graphene’s promise as a chemical sensor material has been noted but there has been little work on practical chemical sensing using graphene, and in particular, how chemical functionalization may be used to sensitize graphene to chemical vapors. Here we show one route towards improving the ability of graphene to work as a chemical sensor by using single stranded DNA as a sensitizing agent. The resulting devices show fast response times, complete and rapid recovery to baseline at room temperature, and discrimination between several similar vapor analytes.
Growth and electronic properties of GaN/ZnO solid solution nanowires
Authors: Han Wei-Qiang , Zhang Yan , Nam Chang-Yong , Black C. T. , Mendez E. E.
Published: August 2010

We have grown single-crystal (Ga1−xZnx)(N1−xOx) solid-solution nanowires using nanostructured ZnGa2O4 precursor prepared by a sol-gel method. From electrical transport measurements in individual nanowire field-effect transistors, we have identified the conduction as n-type and obtained a background carrier density (∼1019 cm−3) and an electron mobility (∼1 cm2/V s) that are consistent with chemical disorder and a large number of charge traps, as confirmed by the devices’ photocurrent response. From the dependence of the device photoresponse on incident light wavelength, we have determined the energy band gap of (Ga0.88Zn0.12)(N0.88O0.12) to be as much as ∼0.6 eV lower than that of GaN or ZnO.
Microwave induced zero-conductance state in a Corbino geometry two-dimensional electron gas with capacitive contacts
Authors: Bykov A. A. , Marchishin I. V. , Goran A. V. , Dmitriev D. V.
Published: August 2010

Microwave induced photoconductivity of a two-dimensional electron gas in selectively doped GaAs/AlAs heterostructures has been studied using the Corbino geometry with capacitive contacts at a temperature T=1.6 K and magnetic field B up to 0.5 T. Zero-conductance states have been observed in the samples under study subject to microwave radiation, similarly to the samples with Ohmic contacts. It has been shown that Ohmic contacts do not play a significant role for observation of zero-conductance states induced by microwave radiation.
Effect of oxygen tension and serum during IVM on developmental competence of bovine oocytes
Authors: Pereira Michele M. , Machado Marco A. , Costa Fernanda Q. , Serapiao Raquel V. , Viana Joao H. M. , Camargo Luiz S. A.
Published: August 2010

With an aim to improve the in vitro production of bovine embryos, the present study investigated the effect of serum and oxygen tension during IVM on oocyte developmental competence. Four experimental groups were evaluated: G1, 10% oestrus cow serum (OCS) with 20% O2; G2, 0.1% polyvinyl alcohol (PVA) with 20% O2; G3, 10% OCS with 5% O2; and G4, 0.1% PVA with 5% O2. The proportion of MII oocytes, blastocyst rates and total cell number were not affected (P > 0.05) when the OCS was replaced with PVA under 5% O2, whereas a higher (P < 0.05) blastocyst rate and total cell number were found with OCS compared with PVA under 20% O2. The apoptosis index was lower in blastocysts from oocytes matured with PVA under 5% O2 (G4) compared with other groups (G1, G2 and G3), but no differences (P > 0.05) were found in maturation and blastocyst rates. Significant differences were found in the amount of specific transcripts in oocytes matured under different conditions. In conclusion maturation with PVA and 5% O2 provides an efficient in vitro culture condition for the maturation of bovine oocytes.
Comparison-based and detection-based approaches to transfer research
Authors: Jarvis Scott
Published: August 2010

This paper offers a number of refinements to Jarvis’s (2000) methodological framework for investigating cross-linguistic effects. According to the original framework, there are three potential consequences of cross-linguistic effects, and any compelling argument for or against the presence of such effects must be based on a consideration of all three consequences. These consequences can be thought of as types of evidence, or premises for transfer, and their investigation requires performance comparisons between individuals, groups, and languages. The present paper has two purposes. The first is to characterize the foundations of a classification scheme that highlights the relationships among these three types of evidence and also indicates that there is yet a fourth type of evidence for cross-linguistic effects that has not yet been taken account of within the framework. The second purpose of this paper is to show that these four types of evidence constitute what can be described as a comparison-based argument for transfer, but that there also exist other valid arguments for transfer, such as what I refer to as the detection-based argument. I describe both the comparison- and detection-based arguments and the types of evidence they entail in relation to number of recent investigations into cross-linguistic influence.
Conventions for sign and speech transcription of child bimodal bilingual corpora in ELAN
Authors: Chen Pichler Deborah , Hochgesang Julie A. , Lillo-Martin Diane , Müller de Quadros Ronice
Published: August 2010

This article extends current methodologies for the linguistic analysis of sign language acquisition to cases of bimodal bilingual acquisition. Using ELAN, we are transcribing longitudinal spontaneous production data from hearing children of Deaf parents who are learning either American Sign Language (ASL) and American English (AE), or Brazilian Sign Language (Libras, also referred to as Língua de Sinais Brasileira/LSB in some texts) and Brazilian Portuguese (BP). Our goal is to construct corpora that can be mined for a wide range of investigations on various topics in acquisition. Thus, it is important that we maintain consistency in transcription for both signed and spoken languages. This article documents our transcription conventions, including the principles behind our approach. Using this document, other researchers can chose to follow similar conventions or develop new ones using our suggestions as a starting point.
Assessing lexical production in deaf signing children with the Boston Naming Test
Authors: Tomasuolo Elena , Fellini Laura , Di Renzo Alessio , Volterra Virginia
Published: August 2010

A picture naming task, the Boston Naming Test, originally developed for spoken language, has been adapted to Italian Sign Language in order to assess the vocabulary of Italian deaf signing children. Thirty deaf and thirty hearing children and adolescents (aged 6–14 years) participated in the study. In the deaf signing group, half of the children attended a bilingual school. Results show no significant differences between deaf and hearing participants in the number of correct responses provided, but do show interesting differences in the lexical accuracy observed for individual items and in error types reported for sign and speech. In the deaf group, children attending a bilingual school performed significantly better than those who did not attend a bilingual programme.
Évaluer les compétences linguistiques des enfants en langue des signes française
Authors: Courtin Cyril , Limousin Fanny , Morgenstern Aliyah
Published: August 2010

Devant l’absence de test d’évaluation des aptitudes linguistiques en langue des signes française (LSF) des enfants signeurs et les besoins exprimés par les nombreux professionnels et chercheurs concernés, nous avons tenté d’adapter à la LSF un test déjà validé pour une autre langue des signes. Notre choix s’est porté sur le test de BSL de Herman et al. (1999), car son usage est relativement simple et peut être utilisé tant pour les besoins de la recherche que par les professeurs de/en LSF. Les résultats obtenus auprès de 129 enfants sourds de parents sourds ou entendants, de différents niveaux de LSF, âgés de 3 à 14 ans, montrent cependant que notre adaptation du test anglais n’est pas valide : le test n’évalue pas ce qu’il était censé évaluer. Ce qui, à première vue, semble un échec offre cependant plusieurs enseignements sur une méthodologie et des pistes à explorer pour construire un test cette fois fiable et valide qui permettrait de revenir sur des questions essentielles telles que l’idée d’âge critique pour le développement linguistique ou cognitif.
α-Arrestins Aly1 and Aly2 Regulate Intracellular Trafficking in Response to Nutrient Signaling
Authors: O'Donnell Allyson F. , Apffel Alex , Gardner Richard G. , Cyert Martha S.
Published: August 2010

Extracellular signals regulate trafficking events to reorganize proteins at the plasma membrane (PM); however, few effectors of this regulation have been identified. β-Arrestins relay signaling cues to the trafficking machinery by controlling agonist-stimulated endocytosis of G-protein–coupled receptors. In contrast, we show that yeast α-arrestins, Aly1 and Aly2, control intracellular sorting of Gap1, the general amino acid permease, in response to nutrients. These studies are the first to demonstrate association of α-arrestins with clathrin and clathrin adaptor proteins (AP) and show that Aly1 and Aly2 interact directly with the γ-subunit of AP-1, Apl4. Aly2-dependent trafficking of Gap1 requires AP-1, which mediates endosome-to-Golgi transport, and the nutrient-regulated kinase, Npr1, which phosphorylates Aly2. During nitrogen starvation, Npr1 phosphorylation of Aly2 may stimulate Gap1 incorporation into AP-1/clathrin-coated vesicles to promote Gap1 trafficking from endosomes to the trans-Golgi network. Ultimately, increased Aly1-/Aly2-mediated recycling of Gap1 from endosomes results in higher Gap1 levels within cells and at the PM by diverting Gap away from trafficking pathways that lead to vacuolar degradation. This work defines a new role for arrestins in membrane trafficking and offers insight into how α-arrestins coordinate signaling events with protein trafficking.
2Struc: the secondary structure server
Authors: Klose D. P. , Wallace B. A. , Janes Robert W.
Published: August 2010

Summary: The defined secondary structure of proteins method is often considered the gold standard for assignment of secondary structure from three-dimensional coordinates. However, there are alternative methods. ‘2Struc: The Secondary Structure Server’ has been created as a single point of access for eight different secondary structure assignment methods. It has been designed to enable comparisons between methods for analyzing the secondary structure content for a single protein. It also includes a second functionality, ‘Compare-the-Protein’ to enable comparisons of the secondary structure features from any one method to be made within a collection of nuclear magnetic resonance models, or between the crystal structures of two different proteins.

Availability:  http://2struc.cryst.bbk.ac.uk

Contact:  r.w.janes@qmul.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Structural genomics of histone tail recognition
Authors: Wang Minghua , Mok Man Wai , Harper Hong , Lee Wen Hwa , Min Jinrong , Knapp Stefan , Oppermann Udo , Marsden Brian , Schapira Matthieu
Published: August 2010

Summary: The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of interactive 3D slides that dissect the structural mechanism underlying the recognition of specific sequences and histone marks. A concise text html-linked to interactive graphics guides the reader through the main features of the interaction. This resource can be used to analyze and compare binding modes across multiple histone recognition modules, to evaluate the chemical tractability of binding sites involved in epigenetic signaling and design small molecule inhibitors.

Availability:  http://www.thesgc.org/resources/histone_tails/

Contact:  matthieu.schapira@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
The use of otolith chemistry to determine the juvenile source of spawning cod in Icelandic waters
Authors: Thorisson Konrad , Jónsdóttir Ingibjörg G. , Marteinsdottir Gudrun , Campana Steven E.
Published: August 2010

Thorisson, K., Jónsdóttir, I. G., Marteinsdottir, G., and Campana, S. E. 2011. The use of otolith chemistry to determine the juvenile source of spawning cod in Icelandic waters. – ICES Journal of Marine Science, 68: 98–106. Chemical fingerprinting was used to discriminate spatial groups of juvenile cod (Gadus morhua) and to backtrack spawning cod in Icelandic waters to their area of origin as 0-group juveniles. Juvenile 0-group cod were collected around Iceland in August 1996 and 1997 to establish the spatial distribution of otolith chemistry at the juvenile stage. Spawning cod from the same year classes were sampled in the same areas in April 2002 and April/May 2003. The core, corresponding to the juvenile otolith, was extracted from the adult otolith and its content of Ba, Mn, and Sr compared with the chemistry of whole otoliths of juveniles of the same year class. High Atlantic inflow into the shelf area north of Iceland in 1997 mixed the juveniles from different areas, and the spawners of that year class were not backtraceable to their origin. For the 1996 year class, however, mixed-stock analysis indicated that most of the spawning cod northwest, north, and northeast of Iceland originated from juveniles off the central part of the north coast. Using otolith chemistry to backtrace the origin of spawners appears well suited for areas with limited mixing, but less well suited for areas or years of high current velocity.
TaDAD2, a Negative Regulator of Programmed Cell Death, Is Important for the Interaction Between Wheat and the Stripe Rust Fungus
Authors: Wang Xiaojie , Tang Chunlei , Zhang Hongchang , Xu Jin-Rong , Liu Bo , LV Jie , Han Dejun , Huang Lili , Kang Zhensheng
Published: August 2010

Defender against cell death (DAD) genes are known to function as negative regulators of cell death in animals. In plants, DAD orthologs are conserved but their role in cell death regulation is not well understood. Here, we report the characterization of the TaDAD2 gene in wheat. The predicted amino acid sequence of TaDAD2 contains typical structural features of DAD proteins, including a signal peptide, three transmembrane regions, and a subunit of oligosaccharyltransferase. Transcripts of TaDAD2 were detected in wheat leaves, culms, roots, florets, and spikelets. The expression level of TaDAD2 was reduced in the initial contact with the stripe rust fungus, subsequently induced and peaked at 18 h postinoculation (hpi), gradually reduced at 24 to 48 hpi, and restored to control level at 72 to 120 hpi. In addition, TaDAD2 exhibited positive transcriptional responses to abiotic stresses after the initial reduction at 1 hpi. Overexpression of TaDAD2 in tobacco leaves inhibited cell death. Furthermore, knocking down TaDAD2 expression by virus-induced gene silencing enhanced the susceptibility of wheat cv. Suwon11 to avirulent race CYR23 and reduced necrotic area at the infection sites. These results indicate that TaDAD2 may function as a suppressor of cell death in the early stages of wheat–stripe rust fungus interaction. However, it is dispensable for or plays an opposite role in hypersensitive response or cell death triggered by an avirulent race of stripe rust fungus at late-infection stages.