bluuebunny/crossref_metadata_2025 huggingface dataset:
Saturation of the fan instability: Nonlinear merging of resonances
Authors: Krafft C. , Volokitin A. , Zaslavsky A.
Published: November 2005

A Hamiltonian self-consistent wave-particle model has been built in order to study the nonlinear interaction of a packet of waves with a nonequilibrium electron distribution in a magnetized background plasma. In particular, this model and the corresponding numerical code allow us to study in detail the excitation by the fan instability of lower hybrid waves interacting resonantly with a strongly anisotropic electron velocity distribution. This paper points out the essential role played by the process of “dynamical merging of resonances,” which results from an instability of the trapped particles’ motion, leading, in its explosive stage, to the amplification of the waves’ amplitudes. Moreover the relaxation phase of the fan instability is shown to lead to a universal distribution of the particles’ velocities, which does not depend on the number of waves and on their distribution in the k space.
First-principles study of some factors controlling the rate of ammonia decomposition on Ni and Pd surfaces
Authors: Stolbov Sergey , Rahman Talat S.
Published: November 2005

Using the plane-wave pseudopotential method within the density-functional theory with the generalized gradient approximation for exchange and correlation potential, we have calculated adsorption energies (Ead), diffusion barrier, and the first dissociation barrier (E1) for NH3 on Ni and Pd surfaces. While the top site is found to be preferred for NH3 adsorption on both Ni(111) and Pd(111), its calculated diffusion barrier is substantially higher for Pd(111) than for Ni(111). We also find that during the first dissociation step (NH3⇒NH2+H), NH2 moves from the top site to the nearest hollow site on Ni(111) and Pd(111) and on the stepped surfaces, Ni(211) and Pd(211), it moves from the initial top site at the step edge to the bridge site in the same atomic chain. Meanwhile H is found to occupy the hollow sites on all four surfaces. On Ni(111), E1 is found to be 0.23eV higher than Ead, while at the step of Ni(211), E1 and Ead are almost equal, suggesting that the probability for the molecule to dissociate is much on the step of Ni(211). In the case of Pd(211), however, we find that the dissociation barrier is much higher than Ead. These trends are in qualitative agreement with the experimental finding that ammonia decomposition rate is much lower on Pd than on Ni.
Quantum-chemical study of CHCl3–SO2 association
Authors: Hippler Michael
Published: November 2005

C H Cl 3 – S O 2 association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Møller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH⋯O hydrogen-bonded complex (ΔE0=−8.73kJ∕mol) with a 2.4Å intermolecular H⋯O distance and two very weak van der Waals complexes (ΔE0=−3.78 and −2.94kJ∕mol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency (“blueshift”) of the CH-stretching vibration compared to the CHCl3 monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance.
Mechanisms of heterogeneous crystal growth in atomic systems: Insights from computer simulations
Authors: Gulam Razul M. S. , Hendry J. G. , Kusalik P. G.
Published: November 2005

In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.
On the suppression of hydrogen degradation in PbZr0.4Ti0.6O3 ferroelectric capacitors with PtOx top electrode
Authors: Huang Chun-Kai , Chang Che-Hao , Wu Tai-Bor
Published: November 2005

The effect of oxygen content in the sputtered Pt oxide (PtOx, x=0.4∼1), top electrode on suppressing the hydrogen degradation of ferroelectric capacitors of PbZr0.4Ti0.6O3 (PZT) was studied. It was found that the ferroelectric property becomes significantly degraded along with a positive voltage offset in the polarization-field hysteresis loop after forming gas (N2+H2) annealing at 200°C of the PZT capacitors made with Pt top electrode. The leakage current in the degraded capacitors also greatly increases due to the reduction of Schottky barrier. However, the degradation of electrical property can be suppressed by using PtOx as top electrode, and the ferroelectric characteristics are well retained ever for capacitors with size shrunk down to submicron scale. The secondary-ion-mass spectroscopy and elastic recoil detection analysis reveal that the catalytic reaction of Pt in dissociation of hydrogen molecules from forming gas can be effectively interrupted by increasing the oxygen content in the PtOx electrode, and the property degradation induced from hydrogen segregation at the interface and incorporation with the PZT layer is thus suppressed. In addition to the superior hydrogen blocking capability, which prevents the detrimental effect of hydrogen doping, a high Schottky barrier is also obtained from the high work function of PtOx electrode.
Magnetization dynamics in arrays of strongly interacting magnetic nanocrystals
Authors: Telem-Shafir Tamar , Markovich Gil
Published: November 2005

Arrays of 6.6nm iron oxide nanocrystals coated with fatty acid molecules were produced using the Langmuir-Blodgett technique. The arrays had a varying number of layers stacked together, going from two dimensional to three dimensional and two different in-plane interparticle separations. While temperature-dependent ac susceptibility measurements of the isolated nanocrystals obeyed the Néel-Brown relaxation law, the array relaxation deviated significantly from this simple law. This deviation together with the observed dc field influence on the susceptibility-temperature curves, the large shifts in blocking temperatures and reduction in susceptibility-temperature curve widths on going from isolated particles to the arrays indicated collective magnetization dynamics during magnetization freezing. A scaling law analysis of this freezing dynamics yielded different powers for the two different interparticle separations with no dependence on dimensionality. In spite of the spin-glass-like behavior, it is possible that small, magnetically ordered domains of nanocrystals form at low temperature.
Dynamic of ion density perturbations observed in a microwave-plasma interaction
Authors: Kamal-Al-Hassan Md. , Ito Hiroaki , Yugami Noboru , Nishida Yasushi
Published: November 2005

The dynamical behavior of ion density perturbations propagated at low-frequency wave nature is experimentally observed in microwave-plasma interaction. An unmagnetized, inhomogeneous laboratory plasma irradiated by an obliquely incident microwave with maximum power P=10kW and pulse width approximately ion plasma period (τpi≈2π∕ωpi) is studied. The p-polarized electric-field component of the interacted microwave of frequency ω0 leads to a nonlinear phenomenon driven by the ponderomotive force by the process of resonance absorption at the critical layer where ω0=ωp is satisfied. The nonlinear ion density perturbations are created from the resonant layer and propagated to an underdense plasma as an electrostatic wave nature.
Photoelectron spectroscopy of S1 toluene: II. Intramolecular dynamics of selected vibrational levels in S1 toluene studied by nanosecond and picosecond time-resolved photoelectron spectroscopies
Authors: Whiteside Paul T. , King Adrian K. , Davies Julia A. , Reid Katharine L. , Towrie Michael , Matousek Pavel
Published: November 2005

We present results which suggest that the photophysics of S1 toluene is significantly more complicated than that of the related molecules p-fluorotoluene or p-difluorobenzene. We have measured a range of photoelectron spectra for a number of S1 internal energies, on different time scales and at different temperatures, in an attempt to unravel the competing processes, but the final conclusion remains outstanding.
Molecular theory of irreversibility
Authors: Pérez-Madrid A.
Published: November 2005

A generalization of the Gibbs entropy postulate is proposed based on the Bogolyubov-Born-Green-Kirkwood-Yvon hierarchy of equations as the nonequilibrium entropy for a system of N interacting particles. This entropy satisfies the basic principles of thermodynamics in the sense that it reaches its maximum at equilibrium and is coherent with the second law. By using a generalization of the Liouville equation describing the evolution of the distribution vector, it is demonstrated that the entropy production is a non-negative quantity. Moreover, following the procedure of nonequilibrium thermodynamics a transport matrix is introduced and a microscopic expression for this is derived. This framework allows one to perform the thermodynamic analysis of nonequilibrium steady states with smooth phase-space distribution functions which, as proven here, constitute the states of minimum entropy production when one considers small departures from stationarity.
Manifestation of ferroelectromagnetism in multiferroic BiMnO3
Authors: Chi Z. H. , Xiao C. J. , Feng S. M. , Li F. Y. , Jin C. Q. , Wang X. H. , Chen R. Z. , Li L. T.
Published: November 2005

Multiferroic BiMnO3 with a highly distorted perovskite structure induced by the stereochemically active 6s2 electron lone pairs of Bi3+ was synthesized at a high pressure of 6 GPa. Magnetization, differential scanning calorimetry, dielectric permittivity, and in situ powder x-ray diffraction as a function of temperature were carried out, respectively. In light of comprehensive evaluation, we can conclude that the synthetic BiMnO3 ceramic displays ferromagnetic and ferroelectric orderings simultaneously, i.e., ferroelectromagnetism below its ferromagnetic Curie temperature TM∼100K.
Nonlinear and linearized algorithms for the Young’s modulus extraction of thin films through the capacitance-voltage measurement of microstructures
Authors: Hu Yuh-Chung , Tu Wei-Hsiang
Published: November 2005

Two high-precision algorithms, based on nonlinear and linearized models, for the Young’s modulus extraction of thin films through the wafer-level capacitance-voltage (C-V) measurement of microstructures are developed and compared with each other. Two microcantilever beams made of single crystalline silicon are used to verify the present methodologies since the Young’s modulus of single crystalline silicon has been well defined. The average value of the Young’s modulus in (110) crystalline plane extracted by the present methods is about 170 GPa, and the error is within 2% compared to the well-defined value of 168 GPa. Thus, the accuracy and precision of the present methodology are verified. The results obtained by the nonlinear algorithm seem to be a little better than the ones obtained by the linearized algorithm. However, the linearized algorithm can provide the Young’s modulus as an explicit function of capacitance and voltage and can self-eliminate the capacitance measurement error from the bias-unrelated parasitic capacitances caused by the layout, the probing lines, or the misalignment of upper and bottom electrodes. The present methods could be accomplished using existing semiconductor testing equipments through probing on the bonding pads of devices because the driving and measured signals are both electrical. Since hardware replacement could be avoided, the present methodology shows substantial advantage over other property-extraction methods for large-scale implementation in semiconductor or microelectromechanical system fabrications.
Collisionality dependence of density peaking in quasilinear gyrokinetic calculations
Authors: Angioni C. , Peeters A. G. , Jenko F. , Dannert T.
Published: November 2005

Linear gyrokinetic calculations and a quasilinear model are applied to compute the radial particle fluxes and investigate the properties of the particle transport in a tokamak plasma induced by ion temperature gradient and trapped electron mode instabilities. The paper focuses on the specific problem of the dependence of anomalous pinch and density peaking on collisionality.
Modulational interaction between the short-wavelength lower-hybrid waves and slow, large-scale density fluctuations
Authors: Üçer Defne , Shapiro Vitali D.
Published: November 2005

Conditions are formulated for modulational instability of two modes with disparate time and space scales, and the modulational interaction of fast and short-wavelength lower-hybrid waves with slow, large-scale inertial Alfvén and ion-acoustic waves is analyzed. Instability is driven by Reynolds’ stresses exerted on plasma by the lower-hybrid waves. Reynolds’ stresses lead to the formation of background density modulations in which the lower-hybrid wave can be localized. It is concluded that the lower-hybrid solitary structures observed in the auroral ionosphere can be created by Reynolds’ stresses of the lower-hybrid waves. In many respects, the observed structures exhibit properties of wave localizations that result from modulational instability.
Effect of isotope mass on simulations of the high-mode pedestal and edge localized modes
Authors: Snyder Stacy E. , Kritz Arnold H. , Bateman Glenn , Onjun Thawatchai , Parail Vassili ,   and EFDA JET Contributors
Published: November 2005

Simulations of Joint European Torus (JET) [P. H. Rebut et al., Nucl. Fusion 25, 1011 (1985)] type I high-mode (H-mode) discharges with edge localized modes (ELMs) are used to study the effect of isotope mass on the height of the pedestal and the frequency of ELMs. A dynamic model for the H-mode pedestal and ELM cycles is employed in the JETTO integrated modeling code [M. Erba et al., Plasma Phys. Control. Fusion 39, 261 (1997)]. The stability criteria that are used to trigger ELM crashes in the JETTO simulations are calibrated with the HELENA and MISHKA ideal magnetohydrodynamic (MHD) stability codes [A. B. Mikhailovskii et al., Plasma Phys. Rep. 23, 713 (1997)]. Results obtained using a pedestal model in which the pedestal width increases with isotope mass are compared with those obtained using a fixed, prescribed pedestal width. In JET type I ELMy H-mode discharges, it is found that the height of the pressure pedestal increases and that the frequency of the ELMs decreases as the isotope mass is increased. Both of these experimentally observed trends are obtained simultaneously in the simulations only if the pedestal width increases with isotope mass. The physical processes that play a significant role in these simulations are described.
A new, explicitly collisional contribution to the gyroviscosity and the radial electric field in a collisional tokamak
Authors: Catto P. J. , Simakov A. N.
Published: November 2005

An additional contribution to the ion viscosity for a collisional plasma is evaluated and found to be the same order as other temperature gradient terms in the collisional perpendicular viscosity. The new contribution arises because of an explicitly collisional portion of the ion distribution function. The evaluation of the Pfirsch-Schlüter radial electric field in a collisional tokamak of arbitrary cross section is extended to retain the new contribution. In a spherical tokamak this new contribution must be retained in determining the radial electric field, while in a conventional tokamak it is small by 1∕q2, where q is the safety factor.
Photocatalyst activation in a pulsed low pressure discharge
Authors: Rousseau A. , Guaitella O. , Gatilova L. , Thevenet F. , Guillard C. , Röpcke J. , Stancu G. D.
Published: November 2005

The effect of combining plasma and photocatalyst for Volatile Organic Compounds (VOC) removal was investigated in a pulsed low-pressure dc discharge. The photocatalyst was TiO2 while the VOC was acetylene (1000 ppm) diluted in dry air. The temporal evolution of C2H2 concentration was measured by Tunable Diode Laser Absorption Spectroscopy (TDLAS) in the mid-infrared region during the plasma pulse (one second). The contribution of external ultraviolet radiation and plasma exposure were quantified, both with and without a photocatalyst. The synergetic effect was clearly demonstrated.
Highly efficient Nd3+:LaB3O6 cleavage microchip laser
Authors: Chen Y. J. , Gong X. H. , Lin Y. F. , Luo Z. D. , Tan Q. G. , Huang Y. D.
Published: November 2005

The improvement of the laser performances of an unprocessed 5.6at.% Nd3+:LaB3O6 cleavage microchip has been reported. Pumped by a Ti:sapphire laser at 871nm, quasi-cw output laser power up to 395mW around 1060nm wavelength with slope efficiency near 52% has been obtained in an end-pumped plano-plano resonator. The influence of the ratio between the cavity mode and pump beam area on the laser performances and laser spectra at various output powers has been investigated. The experimental results have shown that the cleavage technique can become a practical and effective method to obtain the microchip laser medium easily and directly.
Shape change of SiGe islands with initial Si capping
Authors: Wu Y. Q. , Li F. H. , Cui J. , Lin J. H. , Wu R. , Qin J. , Zhu C. Y. , Fan Y. L. , Yang X. J. , Jiang Z. M.
Published: November 2005

The morphologies of self-assembled Ge∕Si(001) islands with initial Si capping at a temperature of 640°C are investigated by atomic force microscopy. Before Si capping, the islands show a metastable dome shape with very good size uniformity. This dome shape changes to a pyramid shape with {103} facets at a Si capping thickness of 0.32nm, and then changes to pyramid shapes with {104} and {105} facets at Si capping thicknesses of 0.42 and 0.64nm, respectively. Noteworthy is that islands with one side retained their dome shape while the other three sides that changed to {103} facets are observed at a Si capping thickness of 0.18nm. These observations indicate that island shape change with Si capping is a kinetic rather than thermodynamic process. The atomic processes associated with this island shape change are kinetically limited at a low temperature of 400°C, and no significant change in size and shape of islands is observed when Si capping layers are deposited at this temperature.
Influence of dual-Ru intermediate layers on magnetic properties and recording performance of CoCrPt–SiO2 perpendicular recording media
Authors: Shi J. Z. , Piramanayagam S. N. , Mah C. S. , Zhao H. B. , Zhao J. M. , Kay Y. S. , Pock C. K.
Published: November 2005

Co Cr Pt – Si O 2 perpendicular recording media containing dual-Ru intermediate layers have been studied. The bottom Ru layer deposited under a higher mobility condition, i.e., low Ar gas pressure and bias on substrate, helps to achieve a good crystalline texture, and the top Ru layer under a lower mobility condition, i.e., high Ar gas pressure, promotes the formation of a columnar microstructure. Three kinds of grain boundaries have been observed. The nucleation field and the coercivity as a function of the thickness and dc bias of the bottom Ru layer have been investigated. Medium noise reduction has been observed for dual-Ru intermediate layer media (dual-Ru media) in comparison with that of single intermediate layer media (single-Ru media). This is mainly attributed to the optimization of the physical grain segregation.
Nonvolatile memory using Al2O3 film with an embedded Al-rich layer
Authors: Nakata Shunji , Saito Kunio , Shimada Masaru
Published: November 2005

This letter describes the capacitance-voltage (C-V) characteristics of a new nonvolatile Al2O3 memory with nanoscale thin film deposited by electron-cyclotron-resonance sputtering. Al-rich Al2O3 was fabricated at a reduced oxygen gas flow rate and used as a charge storage layer of the Al2O3 memory, which is located between the tunnel insulator and blocking insulator. C-V characteristics show a large hysteresis window due to the Al-rich structure, but there is no hysteresis window in the case of stoichiometric Al2O3 structure. This memory will stay nonvolatile for several years or more. The number of electrons injected into the insulator in the case of nanoscale memory cell length is discussed. A discussion of the statistical Gaussian distribution indicates that about 50 localization sites are necessary in Al2O3 memory with 10nm cell length for realizing a 1.8V change of the threshold voltage, which corresponds to the control of ten electrons in the insulator. This structure is easily achieved by the proposed Al-rich Al2O3 memory.
Double injection as a technique to study charge carrier transport and recombination in bulk-heterojunction solar cells
Authors: Juška G. , Arlauskas K. , Sliaužys G. , Pivrikas A. , Mozer A. J. , Sariciftci N. S. , Scharber M. , Österbacka R.
Published: November 2005

Ambipolar charge carrier mobility and recombination in bulk-heterojunction solar cells based on the mixture of regioregular poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene (PCBM) has been studied using injection current transients. The experimental results demonstrate double injection with bimolecular recombination limiting the injection current. We found that charge carrier bimolecular recombination is significantly reduced compared to Langevin recombination. We have measured the temperature and electric field dependence of the reduced bimolecular recombination coefficient and the results suggest that the electron and hole pathways are different and the recombination is controlled by the probability of the carriers to meet at the polymer/PCBM interface.
Unexpected polarization behavior at the aperture of hollow-pyramid near-field probes
Authors: Biagioni P. , Polli D. , Labardi M. , Pucci A. , Ruggeri G. , Cerullo G. , Finazzi M. , Duò L.
Published: November 2005

Polarization in the proximity zone beyond the illuminated aperture of a near-field optical microscope is determined by means of a thin dichroic layer of fluorescent molecules used as a near-field polarization analyzer. Near-field probes of the hollow-pyramid type, with a metal coating and about 100 nm apertures, are used. Surprisingly, it is found that the input polarization is always maintained in the near field, independently of the aperture geometry, in spite of the behavior of the transmitted far field, which may result either isotropic or strongly dichroic depending on the ellipticity of the aperture.
High-efficiency polymer electrophosphorescent diodes based on an Ir (III) complex
Authors: Liu Hong-Mei , He Jian , Wang Peng-Fei , Xie Hong-Zhi , Zhang Xiao-Hong , Lee Chun-Sing , Sun Bao-Quan , Xia Ya-Jun
Published: November 2005

Single-layer high-efficiency green electrophosphorescent light-emitting diodes were fabricated by doping an iridium complex bearing pinene group—tris(5-phenyl-10,10-dimethyl-4-aza- tricycloundeca-2,4,6-triene)Iridium(III)—into a blended host of poly(vinylcarbazole) and 2-(4-biphenylyl)-5-(4-tert-butulphenyl)-1,3,4-oxadiazol. The optimized device shows a turn-on voltage below 4 V, and a very high peak luminescent efficiency of 29.0cd∕A. Comparing with the state-of-the-art electrophosphorescent devices, the present device has a much slower decrease of efficiency with increase of current density; a high efficiency of 20.7cd∕A can still be achieved at a high current density of 150mA∕cm2 (brightness=30800cd∕m2).
Enhanced infrared photovoltaic efficiency in PbS nanocrystal/semiconducting polymer composites: 600-fold increase in maximum power output via control of the ligand barrier
Authors: Zhang S. , Cyr P. W. , McDonald S. A. , Konstantatos G. , Sargent E. H.
Published: November 2005

We report a comparison of photoconductive performance of PbS nanocrystal/polymer composite devices containing either oleic acid-capped or octylamine capped nanocrystals (NCs). The octylamine-capped NCs allow over two orders of magnitude more photocurrent under −1V bias; they also show an infrared photovoltaic response, while devices using oleic acid-capped NCs do not. Further improvement in the photovoltaic performance of films made with octylamine-capped NCs occurs upon thermally annealing the composite layer at 220 °C for 1 h. The procedure leads to a 200-fold increase in short circuit current, a 600-fold increase in maximum power output, and an order of magnitude faster response time.
Hf
O
2
high-k dielectrics grown on (100)Ge with ultrathin passivation layers: Structure and interfacial stability
Authors: Seo J. W. , Dieker Ch. , Locquet J.-P. , Mavrou G. , Dimoulas A.
Published: November 2005

We have investigated the growth of HfO2 thin films on (100)Ge by molecular beam epitaxy. By means of transmission electron microscopy, the structural characteristics of the films grown on clean Ge surfaces are compared with those grown on passivation layers of GeOx and GeOxNy. The interface was found to be very flat and thin, with an interfacial layer one or two monolayer thick. However, traces of Ge in the oxide have been detected when deposited on either one of the interfacial layers, which can be explained by the instability of the interfacial layers grown with an atomic oxygen/nitrogen beam, prior to the HfO2 deposition.
High-frequency magnetic microstrip local bandpass filters
Authors: Kuanr Bijoy K. , Marvin D. L. , Christensen T. M. , Camley R. E. , Celinski Z.
Published: November 2005

This paper presents results for a compact, local bandpass filter. We fabricated the filter using two different ferromagnetic materials, Fe and NiFe, in a microstrip geometry. The different values of saturation magnetization of the two ferromagnets give rise to different gyromagnetic resonance frequencies and provide a local bandpass region between them. The results show that the center frequency of the filter can be tuned over a wide range by adjusting the magnitude of the bias magnetic field. The filter’s bandwidth is almost constant (3.5±0.5GHz) over the entire tuning frequency range (6–26GHz). Theoretical calculations are in good agreement with the experimental results.
First-principles calculation of free Si(100) surface impurity enrichment
Authors: Centoni Scott A. , Sadigh Babak , Gilmer George H. , de la Rubia Tomás Díaz , Musgrave Charles B.
Published: November 2005

Low-temperature crystal growth techniques can deposit silicon films with impurity concentration orders of magnitude above their bulk solubility limits. First-principles calculations were performed of the energies (relative to the bulk) of single substitutional carbon, germanium, boron, and arsenic atoms at several positions within a thin (100) slab of silicon reconstructed as c(4×2). The energies of these impurities were found to be at least 0.2eV lower than in the bulk, corresponding to surface enrichments of 1000 or greater at a temperature of 500°C. General trends can be explained using the concepts of hybridization energy and lone pairs. The large surface reconstruction strain gives rise to this complex potential energy surface, and favors long-ranged order among impurities near the surface. As a result, we expect a complex dependence of trapped impurity concentrations on growth rate and temperature, with a high sensitivity to these parameters when the exchange rate of the impurity with neigboring sites is comparable to the monolayer deposition rate.
The Effect of Contrast upon Perceived Speed: A General Phenomenon?
Authors: Blakemore Mark R , Snowden Robert J
Published: November 2005

The perceived speed of a grating pattern has often been reported to slow as the contrast of the pattern is reduced (though there are some contradictory reports). The mechanism of this perceived slowing has not yet been established nor have the conditions under which the effect occurs (or does not occur). We have therefore examined a range of stimuli that differ upon such aspects as one versus two dimensions, periodic versus nonperiodic, and whether the stimuli occur within a static window. We have also examined a range of stimulus speeds, different types of motion, and simultaneous versus successive presentations. We have found evidence for contrast-induced changes in perceived speed in all our stimuli, and thus suggest that none of the stimulus factors listed above is critical in producing the effect. Though the pattern of results is complex and shows substantial intersubject variation, we generally found that slowly moving patterns presented simultaneously produced the greatest decrease in perceived speed with decreasing contrast. On the other hand faster speeds and successive presentation produced more veridical matches or even an increase in perceived speed with decreasing contrast.
Cognitive Dedifferentiation in Eidetics and Synaesthesia: Hunting for the Ghost Once More
Authors: Glicksohn Joseph , Steinbach Iris , Elimalach-Malmilyan Sigal
Published: November 2005

Both synaesthesia and eidetics have a common characteristic of cognitive dedifferentiation. Synaesthesia (eg colour – hearing) entails the dedifferentiation of the sensory modalities, while eidetic imagery entails the dedifferentiation of imagery and perception. One can profitably gain by investigating both within the same study. Moreover, some of the same issues have arisen in these, hitherto, separate research literatures. This behoves a common framework for analysis and investigation. We applied a technique previously used for identifying child eidetikers, for screening the adult population, looking at both phenomena in the same sample. After screening, we selected a total of twenty-nine individuals for controlled testing of both phenomena and their variants (structural eidetic imagery, typographic eidetic imagery, colour – hearing synaesthesia, colour – mood synaesthesia). Our participants also completed a number of questionnaires of relevance (absorption, dissociation, and hallucination). We found that the personality trait of absorption underlies the commonality of experience tapped by both typographic and structural eidetic imagery. Furthermore, the latter phenomena were found to have a common pseudohallucinatory experiential base. For subjects scoring relatively high on the absorption scale, there is a negative correlation between structural eidetic imagery and colour – mood synaesthetic differentiation, replicating to a degree results reported earlier.
The choice of optimal distance measure in genome-wide datasets
Authors: Glazko Galina , Gordon Alexander , Mushegian Arcady
Published: November 2005

Motivation: Many types of genomic data are naturally represented as binary vectors. Numerous tasks in computational biology can be cast as analysis of relationships between these vectors, and the first step is, frequently, to compute their pairwise distance matrix. Many distance measures have been proposed in the literature, but there is no theory justifying the choice of distance measure.

Results: We examine the approaches to measuring distances between binary vectors and study the characteristic properties of various distance measures and their performance in several tasks of genome analysis. Most distance measures between binary vectors turn out to belong to a single parametric family, namely generalized average-based distance with different exponents. We show that descriptive statistics of distance distribution, such as skewness and kurtosis, can guide the appropriate choice of the exponent. On the contrary, the more familiar distance properties, such as metric and additivity, appear to have much less effect on the performance of distances.

Availability: R code GADIST and Supplementary material are available at

Contact:  gvg@stowers-institute.org
Mining sequence annotation databanks for association patterns
Authors: Artamonova Irena I. , Frishman Goar , Gelfand Mikhail S. , Frishman Dmitrij
Published: November 2005

Motivation: Millions of protein sequences currently being deposited to sequence databanks will never be annotated manually. Similarity-based annotation generated by automatic software pipelines unavoidably contains spurious assignments due to the imperfection of bioinformatics methods. Examples of such annotation errors include over- and underpredictions caused by the use of fixed recognition thresholds and incorrect annotations caused by transitivity based information transfer to unrelated proteins or transfer of errors already accumulated in databases. One of the most difficult and timely challenges in bioinformatics is the development of intelligent systems aimed at improving the quality of automatically generated annotation. A possible approach to this problem is to detect anomalies in annotation items based on association rule mining.

Results: We present the first large-scale analysis of association rules derived from two large protein annotation databases—Swiss-Prot and PEDANT—and reveal novel, previously unknown tendencies of rule strength distributions. Most of the rules are either very strong or very weak, with rules in the medium strength range being relatively infrequent. Based on dynamics of error correction in subsequent Swiss-Prot releases and on our own manual analysis we demonstrate that exceptions from strong rules are, indeed, significantly enriched in annotation errors and can be used to automatically flag them. We identify different strength dependencies of rules derived from different fields in Swiss-Prot. A compositional breakdown of association rules generated from PEDANT in terms of their constituent items indicates that most of the errors that can be corrected are related to gene functional roles. Swiss-Prot errors are usually caused by under-annotation owing to its conservative approach, whereas automatically generated PEDANT annotation suffers from over-annotation.

Availability: All data generated in this study are available for download and browsing at .

Contact:  d.frishman@wzw.tum.de

Supplementary information:
Myokymia in Axonal Disorders
Authors: Kelkar Praful , Kimura Jun
Published: November 2005

Myokymic discharges are spontaneous bursts of individual motor units occurring rhythmically or semirhythmically. Myokymia is typically seen in demyelinating disorders. We present 5 patients with myokymia in axonal disorders, including a case of myokymia after Botox injection, which has not been reported previously.
Parotid Gland Injections of Botulinum Toxin A Are Effective in Treating Sialorrhea in Amyotrophic Lateral Sclerosis
Authors: Scott Kevin R , Kothari Milind J , Venkatesh Y Swami , Murphy Tamara , Simmons Zachary
Published: November 2005

Objective:

The objective of this study was to determine the safety and efficacy of botulinum toxin A in ameliorating refractory sialorrhea and improving quality of life in patients with amyotrophic lateral sclerosis.

Materials and Methods:

Six patients with bulbar ALS received bilateral parotid gland injections of botulinum toxin A.

Results:

No adverse effects occurred. Tissue use decreased in 5 of 7 patients at a dose of 10 units and in 3 of 4 patients at a dose of 20 units. Self-reported quality of life did not change in most.

Conclusions:

Parotid gland injections of botulinum toxin appear safe and may be helpful in some patients with ALS for the treatment of sialorrhea.
Subclinical Sensory Involvement in Monomelic Amyotrophy
Authors: Liao Jenny P , Waclawik Andrew J , Lotz Barend P
Published: November 2005

An 18-year-old woman presented with weakness and atrophy in her hand without associated sensory symptoms, preceding events, or structural abnormalities on neuroimaging. No sensory deficits were detected on neurologic examination. Electrophysiological studies showed not only the expected motor findings for monomelic amyotrophy (MA) in the affected limb, but also markedly reduced sensory nerve action potentials when compared with the unaffected side. These findings suggest that subclinical sensory involvement can exist in patients with otherwise classic presentations of MA.
Parsimony overcomes statistical inconsistency with the addition of more data from the same gene
Authors: Pickett Kurt M. , Tolman Greg L. , Wheeler Ward C. , Wenzel John W.
Published: November 2005

Many authors have demonstrated that the parsimony method of phylogenetic analysis can fail to estimate phylogeny accurately under certain conditions when data follow a model that stipulates homogeneity of the evolutionary process. These demonstrations further show that no matter how much data are added, parsimony will forever exhibit this statistical inconsistency if the additional data have the same distributional properties as the original data. This final component—that the additional data must follow the same distribution as the original data—is crucial to the demonstration. Recent simulations show, however, that if data evolve heterogeneously, parsimony can perform consistently. Here we show, using natural data, that parsimony can overcome inconsistency if new data from the same gene are added to an analysis already exhibiting a condition indistinguishable from inconsistency.

© The Willi Hennig Society 2005.
The Pseudomonas syringae phytotoxin coronatine promotes virulence by overcoming salicylic acid‐dependent defences in Arabidopsis thaliana
Authors: BROOKS DAVID M. , BENDER CAROL L. , KUNKEL BARBARA N.
Published: November 2005

Successful pathogen infection likely involves the suppression of general antimicrobial host defences. One Pseudomonas syringae virulence factor proposed to act in this manner is coronatine (COR), a phytotoxin believed to function as an analogue of one or more jasmonates, a family of plant growth regulators. COR biosynthetic (COR−) mutants of P. syringae pv. tomato strain DC3000 exhibit reduced virulence on Arabidopsis thaliana and tomato. In the present study, three genetically and biochemically defined COR− mutants of DC3000 were used to explore potential effects of COR and its precursors, coronafacic acid (CFA) and coronamic acid (CMA), on defence signalling pathways in A. thaliana. Inoculation with wild‐type DC3000 resulted in the accumulation of several jasmonate‐responsive transcripts, whereas infection with a mutant strain that accumulates CFA, which is structurally similar to methyl jasmonate (MeJA), did not. Thus, COR, but not CFA, stimulates jasmonate signalling during P. syringae infection of A. thaliana. The ability of the COR− mutants to grow to high levels in planta was fully restored in A. thaliana lines deficient for salicylic acid (SA) accumulation. Although the COR− mutants grew to high levels in SA‐deficient plants, disease symptoms were reduced in these plants. Collectively, these results indicate that COR is required both for overcoming or suppressing SA‐dependent defences during growth in plant tissue and for normal disease symptom development in A. thaliana.
Review article: the role of antisecretory therapy in the management of non‐variceal upper gastrointestinal bleeding
Authors: TRIADAFILOPOULOS G.
Published: November 2005

Non‐variceal, upper gastrointestinal bleeding accounts for 300,000 hospitalizations annually in the US and the risk of rebleeding and mortality remain high.

The aim of this study was to review the incidence and causes of non‐variceal upper gastrointestinal haemorrhage, criteria for early discharge, risk stratification and intravenous vs. oral proton‐pump inhibitor use. Peptic ulcer disease accounts for 45% of all admissions for upper gastrointestinal bleeding.

Clinical and endoscopic predictors of adverse outcome have been identified. The Rockall scoring system identifies patients who can be considered for early discharge after endoscopy.

Evidence supports the use of intravenous proton‐pump inhibitor therapy for patients with bleeding ulcers associated with high‐risk stigmata. Patients who are clinically stable and in whom upper endoscopy has shown an ulcer with a clean base or a flat pigmented spot have a low risk for rebleeding and may be discharged early on oral proton‐pump inhibitor therapy. Proton‐pump inhibitor treatment reduces ulcer rebleeding but does not affect overall mortality. In the US, most patients with ulcer bleeding have low‐risk stigmata, and thus, can be treated with oral proton‐pump inhibitors and discharged early.
Cancer stem cells in the mammalian central nervous system
Authors: Pilkington G. J.
Published: November 2005

Abstract. Malignant tumours intrinsic to the central nervous system (CNS) are among the most difficult of neoplasms to treat effectively. The major biological features of these tumours that preclude successful therapy include their cellular heterogeneity, which renders them highly resistant to both chemotherapy and radiotherapy, and the propensity of the component tumour cells to invade, diffusely, the contiguous nervous tissues. The tumours are classified according to perceived cell of origin, gliomas being the most common generic group. In the 1970s transplacental administration of the potent neurocarcinogen, N‐ethyl‐N‐nitrosourea (ENU), enabled investigation of the sequential development of brain and spinal neoplasms by electron microscopy and immunohistochemistry. The significance of the primitive cells of the subependymal plate in cellular origin and evolution of a variety of glial tumours was thereby established. Since then, the development of new cell culture methods, including the in vitro growth of neurospheres and multicellular tumour spheroids, and new antigenic markers of stem cells and glial/neuronal cell precursor cells, including nestin, Mushashi‐1 and CD133, have led to a reappraisal of the histological classification and origins of CNS tumours. Moreover, neural stem cells may also provide new vectors in exciting novel therapeutic strategies for these tumours. In addition to the gliomas, stem cells may have been identified in paediatric tumours including cerebellar medulloblastoma, thought to be of external granule cell neuronal derivation. Interestingly, while the stem cell marker CD133 is expressed in these primitive neuroectodermal tumours (PNETs), the chondroitin sulphate proteoglycan neuronal/glial 2 (NG2), which appears to denote increased proliferative, but reduced migratory activity in adult gliomas, is rarely expressed. This is in contrast to the situation in the histologically similar supratentorial PNETs. A possible functional ‘switch’ between proliferation and migration in developing neural tumour cells may exist between NG2 and ganglioside GD3. The divergent pathways of differentiation of CNS tumours and the possibility of stem cell origin, for some, if not all, such neoplasms remain a matter for debate and continued research, but the presence of self‐renewing neural stem cells in the CNS of both children and adults strongly suggests a role for these cells in tumour initiation and resistance to current therapeutic strategies.
Specific leaf area explains differences in leaf traits between congeneric savanna and forest trees
Authors: HOFFMANN W. A. , FRANCO A. C. , MOREIRA M. Z. , HARIDASAN M.
Published: November 2005

Leaf traits are commonly associated with the life history, distribution and resource requirements of a species. To improve our understanding of the ecological and physiological differences between tropical savanna and forest trees, we compared leaf traits of species native to savanna and gallery (riverine) forests in the Cerrado region of central Brazil.

Congeneric species pairs from 14 different taxonomic families were studied, each with a savanna species and a forest species present at the study site. Only individuals growing in savanna conditions under full sun were studied. We measured foliar nutrients, δ13C, δ15N and specific leaf area (SLA: leaf area per unit leaf mass). We used phylogenetically independent contrasts to compare savanna and forest species and to test for correlations among species traits.

Overall, leaves of forest species had 17% higher N concentration, 32% higher P concentration, and 37% higher K concentration, despite growing in similar soils. Concentrations of all three elements were strongly and positively correlated with SLA.

Forest species had 52% greater SLA, on average, than savanna species, which accounts for the higher foliar nutrient concentrations of these species.

Savanna species had higher δ13C values than forest species, indicating higher water‐use efficiency. The SLA was negatively correlated with δ13C, suggesting that SLA may also account for the higher water‐use efficiency of savanna species.

There was no difference in foliar δ15N between savanna and forest species, but foliar δ15N was negatively correlated with soil pH.

These results contribute to recent studies showing that tropical savanna and forest species represent two distinct functional types, with large differences in ecology and physiology, that have important consequences for the dynamics of savanna–forest boundaries.
Can secondary compounds of an invasive plant affect larval amphibians?
Authors: MAERZ J. C. , BROWN C. J. , CHAPIN C. T. , BLOSSEY B.
Published: November 2005

There is significant concern over the impacts of plant invasions on habitat quality for native fauna. Recent research suggests that non‐native Purple Loosestrife (Lythrum salicaria) invasions may negatively affect the performance of larval American Toad tadpoles (Bufo americanus), and that compounds leached from L. salicaria leaves play a direct or indirect role in this effect.

We raised individual B. americanus and Gray Treefrog (Hyla versicolor) tadpoles on high‐quality diets in aqueous extracts of senescent leaves from L. salicaria, native Broad‐Leaf Cattail (Typha latifolia), and control water to determine whether loosestrife extracts directly affect anuran tadpole performance.

Even at high artificial food levels, B. americanus survival was significantly lower in L. salicaria extracts compared with T. latifolia extracts and a water control. Food level strongly affected B. americanus development, but tadpoles raised in L. salicaria extract were less developed compared with conspecifics raised in cattail extract or water. Unlike B. americanus, Hyla performance was not affected by exposure to any plant extract compared with the water control.

Our study implicates secondary plant compounds as a mechanism underlying the impact of an invasive plant on some but not all native fauna. We hypothesize that high tannin concentrations of L. salicaria leaves have the potential to create environments that are directly toxic to B. americanus tadpoles. We hypothesize that obligate gill breathers such as B. americanus tadpoles are highly sensitive to gill damage caused by high concentrations of phenolics. Other anuran species such as H. versicolor that develop well‐functioning lungs early may be less affected by high tannin concentrations.