bluuebunny/crossref_metadata_2025 huggingface dataset:
Current collection by a cylindrical probe in a partly ionized, collisional plasma
Authors: Pletnev V. , Laframboise J. G.
Published: July 2006

A numerical calculation of ion and electron current collection by a cylindrical Langmuir probe in a partly ionized plasma has been done. The effect of electron and ion collisions with neutrals on the current collected by the probe has been investigated. The validity of the collisionless theory of Laframboise [J. G. Laframboise, University of Toronto, Institute for Aerospace Studies, UTIAS Report No. 100 (1966)] has been studied. The iterative scheme of Laframboise has been combined with Monte Carlo solution of the Boltzmann equation to provide self-consistent steady-state electron and ion density and electric potential distributions as functions of radius. Our model includes elastic ion-neutral and electron-neutral collisions, ionization of neutrals by electron impact, energy loss of electrons due to excitation and ionization of neutrals, and charge-exchange collisions. Our model has been demonstrated by calculating the current collection by a probe in a nitrogen plasma, but it can be applied in other cases because we avoided adjustable parameters. Our results confirm published experimental data which indicate that Laframboise’s theory can be applied when the attracted particles are electrons and ionization processes do not play an important part. When the attracted particles are ions, it is found that charge-exchange collisions in the sheath produce by far the largest contribution to the increase in their collection current. For this situation, collisionless theory can be applied only when the mean distance traveled by ions inside the sheath is much less than the mean free path. The condition that the sheath size is much smaller than the mean free path does not guarantee a collisionless sheath near a cylindrical probe. This condition is in good agreement with experimental results in the literature.
Underlying memory-dominant nature of hysteresis in piezoelectric materials
Authors: Bashash Saeid , Jalili Nader
Published: July 2006

Although the existence of nonlocal memories in hysteresis behavior of piezoelectric materials has been demonstrated, their detailed and thorough properties have yet to be revealed. Along this line, we disclose and demonstrate the underlying memory-dominant nature of hysteresis, and characterize its important properties that must be considered for the accurate prediction of hysteresis trajectory in piezoelectric materials. More specifically, the concept of recording the turning points, targeting the previously recorded turning points, curve alignment, and wiping-out effects at these points are introduced as the basic intellectual properties of hysteresis nonlinearity. A constitutive memory-based mathematical modeling framework is then developed and trained for the precise prediction of a hysteresis path for arbitrarily assigned input profiles. Utilizing a piezoelectric-driven actuator, it is experimentally demonstrated that if the number of memory units is sufficiently selected, model response in the prediction of a hysteresis track is significantly improved.
Effect of substrate roughness on photoluminescence spectra of silicon nanocrystals grown by off axis pulsed laser deposition
Authors: Rani J. R. , Mahadevan Pillai V. P. , Ajimsha R. S. , Jayaraj M. K. , Jayasree R. S.
Published: July 2006

Silicon nanoparticles were prepared by off axis pulsed laser deposition (PLD) technique. The optical properties of Si nanoparticles grown on quartz substrate have been characterized by optical absorption, photoluminescence, Raman, and transmission electron microscopy. TEM has demonstrated that the radius of nanocrystals decreases from 4to0.8nm as the off axis target to substrate distance increases. A blueshift up to 4.2eV is observed in the optical absorption spectra of the Si quantum dots. The slope of log(hν) vs log(α) graph shows that the optical transitions in Si quantum dots are allowed direct, allowed indirect, and direct forbidden transitions which depend on the nature of the substrate used for the growth of silicon. Relaxation of k selection rule is observed in these samples. Photoluminescence (PL) emission consists of an intense broad emission extending over visible to ultraviolet region. The photoluminescence peak energy and intensity are found to be sensitive to the nature of substrate. Possible mechanism of optical absorption and PL origin are discussed in terms of quantum confinement luminescent center model.
Structure and composition dependence of oxygen K edge in CaAl2O4
Authors: Jiang Nan
Published: July 2006

Experimental electron energy-loss spectroscopy of OK edge in CaAl2O4 has been studied in this work. The near edge fine structure of the OK edge has been interpreted with the aid of theoretical calculations in the ground-state approximation. It reveals that the features near the threshold are associated with the coordination of Ca polyhedra. Time-resolved electron energy-loss spectroscopy of OK edge further confirms that the selective elimination of high-order coordinated Ca by electron irradiation results in a threshold shift of the OK edge.
Phase-contrast x-ray imaging for nondestructive evaluation of materials
Authors: Zoofan B. , Kim J.-Y. , Rokhlin S. I. , Frankel G. S.
Published: July 2006

Phase-contrast x-ray imaging has been studied intensively in the past, mainly with applications to low density biological materials. In this work experimental and theoretical aspects of phase-contrast microfocus x-ray imaging of structural materials (metals and polymers) are considered. The diffraction field in an object from a point x-ray source is simulated and the effects of geometrical and material parameters on the x-ray phase-contrast image are obtained. It is shown that higher-order terms should be retained in the asymptotic expansion of the Green function in the image plane to accurately image discontinuities in structural materials. Experimental phase-contrast images of small defects are obtained with a 5μm microfocal x-ray source and compared with those from computer simulation as a function of geometrical magnification and photon energy. The phase-contrast x-ray imaging provides enhanced image contrast and improved edge definition and is important for further development of nondestructive evaluation of structural materials.
Thickness dependence of microstructures in La0.8Ca0.2MnO3 thin films
Authors: Zhang H. D. , Li M. , An Y. K. , Mai Z. H. , Gao J. , Hu F. X. , Wang Y. , Jia C. J.
Published: July 2006

The thickness dependence of microstructures of La0.8Ca0.2MnO3 (LCMO)∕SrTiO3 (STO) thin films was investigated by high-resolution x-ray diffraction, small angle x-ray reflection, grazing incidence x-ray diffraction, scanning electron microscopy, and atomic force microscopy. The results show that all the LCMO films are well oriented in (00l) direction perpendicular to the substrate surface. Self-organized crystalline grains with a tetragonal shape are uniformly distributed on the film surface, indicating the deposition condition being of benefit to the formation of the crystalline grains. With increasing the film thickness, the crystalline quality of the LCMO film is improved, while the surface becomes rougher. There exists a nondesigned cap layer on the upper surface of the LCMO layer for all the samples. The mechanism is discussed briefly.
Crystal structure and ferroelectric properties of rare-earth substituted BiFeO3 thin films
Authors: Uchida Hiroshi , Ueno Risako , Funakubo Hiroshi , Koda Seiichiro
Published: July 2006

The influence of ion modification using rare-earth cations on crystal structures, along with the insulating and ferroelectric properties of BiFeO3 (BFO) thin films was investigated. Rare-earth-substituted BFO films with chemical compositions of (Bi1.00−xREx)Fe1.00O3 (x=0–0.15, RE=La and Nd) were fabricated on (111)Pt∕TiO2∕SiO2∕(100)Si substrates using a chemical solution deposition technique. A crystalline phase of rhombohedral BFO was obtained by heat treatment in a N2 atmosphere at 500°C for 5min. The crystal anisotropy and the Curie temperature of BFO were degraded continuously with increasing contents of La3+ or Nd3+ cations. Ion modification using La3+ and Nd3+ cations up to x=0.05 lowered the leakage current density of the BFO film at room temperature from approximately 10−3 down to 10−6A∕cm2. A polarization (P)-electrical field (E) hysteresis loop measured at 10K revealed that the intrinsic remanent polarization of La3+- and Nd3+-substituted BFO films with x=0.05 (44 and 51μC∕cm2, respectively) was smaller than that of a nonsubstituted BFO film (79μC∕cm2), which is ascribed to the degradation of crystal anisotropy and the Curie temperature of the BFO crystal.
X-ray reflectivity and photoelectron spectroscopy study of interdiffusion at the Si∕Fe interface
Authors: Naik S. R. , Rai S. , Lodha G. S. , Brajpuriya R.
Published: July 2006

We have investigated the nature of silicon on iron interface in electron beam deposited Fe∕Si bilayers, with various iron and silicon thicknesses. The Fe and Si layer thicknesses are varied from 30to330Å and 20to86Å, respectively. Grazing incidence x-ray reflectivity and photoelectron spectroscopy measurements were carried out on these samples to determine interface characteristics. Si on Fe (Si̱Fe) interlayer thickness, roughness, and composition do not depend on the thickness of Fe and Si. The thickness of the interlayer is around 13Å. A systematic variation in silicide concentration across this interface is observed by x-ray photoelectron spectroscopy measurement. Change in the density of states in valence band across this interface is also observed by ultraviolet photoelectron measurement.
Microwave characterization of submicrometer-sized nickel hollow sphere composites
Authors: Deng Yida , Zhao Ling , Shen Bin , Liu Lei , Hu Wenbin
Published: July 2006

In this work, we report on the microwave properties of the nickel hollow spheres (NHSs) synthesized by a facile autocatalytic reduction method. The resonance characterization of the NHS-polyvinyl butyral composite, due to the skin effect, is observed in the microwave frequency. It is shown that the resonant and the matching frequencies of the composite largely depend on the particle size of the spheres.
Large second order optical nonlinearity in thermally poled amorphous niobium borophosphate films
Authors: Dussauze Marc , Malakho Artem , Fargin Evelyne , Manaud Jean Pierre , Rodriguez Vincent , Adamietz Frederic , Lazoryak Bogdan
Published: July 2006

Thin films of sodium niobium borophosphate glass were deposited on silicon wafer and borosilicate glass substrates by radio frequency sputtering. Thermal poling of the films was performed under various voltage conditions. The chemical composition of the films after poling was controlled by x-ray energy dispersive spectroscopy and compared to the initial composition. The second harmonic signals generated by thermal poling were analyzed in reflection mode. The recorded complex Maker fringes pattern signals were simulated and fitted using a multilayer model for the estimation of the second harmonic generation nonlinear coefficients χ(2). The results are compared to previously published χ(2) coefficients obtained for bulk oxide glasses (∼3pm∕V, approximately fourfold as strong as the highest value reported in thermally poled fused silica). Resulting from this study thermally poled niobium sodium borophosphate thin films are revealed of real interest as potential electro-optic devices.
Analytical modeling of silicon thermoelectric microcooler
Authors: Wang Peng , Bar-Cohen Avram , Yang Bao , Solbrekken Gary L. , Shakouri Ali
Published: July 2006

Due to its inherently favorable properties, doped single-crystal silicon has potential application as an on-chip thermoelectric microcooler for advanced integrated circuits. In this paper, an analytical thermal model for silicon microcooler, which couples Peltier cooling with heat conduction and heat generation in the silicon substrate, and which includes heat conduction and heat generation in the metal lead, is derived and used to study the thermal characteristics of silicon thermoelectric microcoolers. The analytical modeling results are shown to be in good agreement with the experimental data and the results from electrothermal numerical simulations. The effects of metal lead, electric contact resistance, silicon doping concentrations, and microcooler sizes on the cooling performance are investigated. The cooling potential of such thermoelectric devices, represented by peak cooling and maximum cooling heat flux on the microcooler surface, is addressed.
Polymer brushes in cylindrical pores: Simulation versus scaling theory
Authors: Dimitrov D. I. , Milchev A. , Binder K.
Published: July 2006

The structure of flexible polymers endgrafted in cylindrical pores of diameter D is studied as a function of chain length N and grafting density σ, assuming good solvent conditions. A phenomenological scaling theory, describing the variation of the linear dimensions of the chains with σ, is developed and tested by molecular dynamics simulations of a bead-spring model. Different regimes are identified, depending on the ratio of D to the size of a free polymer N3∕5. For D>N3∕5 a crossover occurs for σ=σ*=N−6∕5 from the “mushroom” behavior (Rgx=Rgy=Rgz=N3∕5) to the behavior of a flat brush (Rgz=σ1∕3N,Rgx=Rgy=σ−1∕12N1∕2), until at σ**=(D∕N)3 a crossover to a compressed state of the brush, [Rgz=D,Rgx=Rgy=(N3D∕4σ)1∕8<D], occurs. Here coordinates are chosen so that the y axis is parallel to the tube axis, and the z direction normal to the wall of the pore at the grafting site. For D<N3∕5, the coil structure in the dilute regime is a cigar of length Rgy=ND−2∕3 along the tube axis. At σ*=(ND1∕3)−1 the structure crosses over to “compressed cigars,” of size Rgy=(σD)−1. While for ultrathin cylinders (D<N1∕4) this regime extends up to the regime where the pore is filled densely (σ=D∕N), for N1∕4<D<N1∕2 a further crossover occurs at σ***=D−9∕7N−3∕7 to a semidilute regime where Rgy=(N3D∕4σ)1∕8 still exceeds D. For moderately wide tubes (N1∕2<D<N3∕5) a further crossover occurs at σ****=N3D−7, where all chain linear dimensions are equal, to the regime of compressed brush. These predictions are compared to the computer simulations. From the latter, extensive results on monomer density and free chain end distributions are also obtained, and a discussion of pertinent theories is given. In particular, it is shown that for large D the brush height is an increasing function of D−1.
Silicon carbide metal-semiconductor field-effect transistor with and without a low-doped buffer: Influence of substrate traps
Authors: Los Andrei V.
Published: July 2006

Experimental dc and small-signal ac drain-source characteristics are compared for power 4H silicon carbide (SiC) metal-semiconductor field-effect transistors (MESFETs) fabricated on vanadium-compensated semi-insulating substrates, with and without a low-doped p-type buffer layer. Device simulation is performed for the same device structures and simulated current distributions are analyzed together with the experimental data. MESFET transient output characteristics are found to be similar and controlled by carrier trapping in the semi-insulating substrate in both types of the devices at large gate voltages. The trapping was correlated with deep vanadium acceptors by gate-source and drain-source admittance spectroscopies, and gate-source deep level transient spectroscopy in the devices without the buffer, however, neither spectroscopic technique revealed any trap signatures in the devices with the buffer. Measurements of device output characteristics at different temperatures allowed confirming indirectly that trapping takes place at the vanadium acceptors in devices with the buffer similarly to devices without the buffer. Simulations confirm that injection of channel current into the substrate takes place in both types of the MESFETs at large gate voltages.
Applications of Raman spectroscopy in copper chemical mechanical planarization: In situ detection of tantalum layer to dielectric layer transition
Authors: Kondoju S. , Juncker C. , Lucas P. , Raghavan S. , Fischer P. , Oehler A. , Moinpour M.
Published: July 2006

In metal chemical mechanical planarization, in situ detection of barrier to dielectric layer transition is typically done using reflectivity measurements. Introduction of carbon containing low-dielectric constant (k) materials, commonly known as carbon doped oxides (CDOs), as dielectric layers has opened up the possibility of using spectroscopic techniques for detecting such transition. The vibrational frequencies of the bonds between C, H, O, and Si in these low-k materials may be readily detected by spectroscopic techniques such as Raman and infrared spectroscopies. In this work, the use of Raman spectroscopy in detecting the transition from Ta layer to a CDO layer has been explored. An abrasion cell integrated with a Raman spectrometer was used to make the measurements. The sensitivity of the Raman technique is compared with that of the conventional reflectivity technique.
On the correlation between the self-organized island pattern and substrate elastic anisotropy
Authors: Pan E. , Zhu R. , Chung P. W.
Published: July 2006

Self-organized quantum dots pattern depends strongly on the elastic strain energy of the substrate. It is well-known experimentally that for the elastic substrate with a high degree of anisotropy, the epitaxially grown island patterns are different for different growth orientations. In this paper, by incorporating the anisotropic strain energy field into a kinetic Monte Carlo algorithm for adatom diffusion, we show that the self-organized island pattern on the surface of an anisotropic substrate is closely correlated to the elastic energy distribution on the surface. The anisotropic substrates studied are GaAs with different growth orientations (001), (111), and (113). An isotropic substrate Iso (001), reduced from GaAs, is also investigated for the purpose of comparison. The island patterns on these substrates with and without elastic strain energy are presented. Besides the effect of substrate anisotropy, different growth parameters, including temperature, coverage, and interruption time, are further investigated to identify the optimal growth values. It is observed that the strain energy field in the substrate is the key factor that controls the island pattern, and that the latter is closely correlated to the substrate orientation (anisotropy). Our simulated patterns are also in qualitative agreement with recent experimental growth results.
Feynman path integral of Riemann type
Authors: Furuya Kiyoko
Published: July 2006

In this paper, we shall define a kind of operator-valued integration and define the Feynman path integrals of Riemann integral type. It seems that it is one of the best possible conditions of the existence of the path integrals of Riemann integral type for the Schrödinger equation with singular potentials. Our class of potentials is wide enough: the real measurable potential U should be continuous except for a closed set of measure zero.
Dimensional reduction of Dirac operator
Authors: Nikolov Petko A. , Ruseva Gergana R.
Published: July 2006

We construct an explicit example of dimensional reduction of the free massless Dirac operator with an internal SU(3) symmetry, defined on a 12-dimensional manifold that is the total space of a principal SU(3)-bundle over a four-dimensional (nonflat) pseudo-Riemannian manifold. Upon dimensional reduction the free 12-dimensional Dirac equation is transformed into a rather nontrivial four-dimensional one: a pair of massive Lorentz spinor SU(3)-octets interacting with an SU(3)-gauge field with a source term depending on the curvature tensor of the gauge field. The SU(3) group is complicated enough to illustrate features of the general case. It should not be confused with the color SU(3) of quantum chromodynamics where the fundamental spinors, the quark fields, are SU(3) triplets rather than octets.
Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems
Authors: MacDowell Luis G. , Shen Vincent K. , Errington Jeffrey R.
Published: July 2006

Computer simulations are employed to obtain subcritical isotherms of small finite sized systems inside the coexistence region. For all temperatures considered, ranging from the triple point up to the critical point, the isotherms gradually developed a sequence of sharp discontinuities as the system size increased from ∼8 to ∼21 molecular diameters. For the smallest system sizes, and more so close to the critical point, the isotherms appeared smooth, resembling the continuous van der Waals loop obtained from extrapolation of an analytic equation of state outside the coexistence region. As the system size was increased, isotherms in the chemical potential-density plane developed first two, then four, and finally six discontinuities. Visual inspection of selected snapshots revealed that the observed discontinuities are related to structural transitions between droplets (on the vapor side) and bubbles (on the liquid side) of spherical, cylindrical, and tetragonal shapes. A capillary drop model was developed to qualitatively rationalize these observations. Analytic results were obtained and found to be in full agreement with the computer simulation results. The analysis shows that the shape of the subcritical isotherms is dictated by a single characteristic volume (or length scale), which depends on the surface tension, compressibility, and coexistence densities. For small reduced system volumes, the model predicts that a homogeneous fluid is stable across the whole coexistence region, thus explaining the continuous van der Waals isotherms observed in the simulations. When the liquid and vapor free energies are described by means of an accurate mean-field equation of state and surface tensions from simulation are employed, the capillary model is found to describe the simulated isotherms accurately, especially for large systems (i.e., larger than about 15 molecular diameters) at low temperature (lower than about 0.85 times the critical temperature). This implies that the Laplace pressure differences can be predicted for drops as small as five molecular diameters, and as few as about 500molecules. The theoretical study also shows that the extrema or apparent spinodal points of the finite size loops are more closely related to (finite system size) bubble and dew points than to classical spinodals. Our results are of relevance to phase transitions in nanopores and show that first order corrections to nucleation energies in finite closed systems are power laws of the inverse volume.
A new method for analyzing line-tied kink modes in cylindrical geometry
Authors: Evstatiev E. G. , Delzanno G. L. , Finn J. M.
Published: July 2006

A new method for studying linear stability of the m=1 (kink) mode in a cylinder with line-tied boundary conditions is presented. The method is applicable to both resistive and ideal MHD. It is based on expansion in one-dimensional eigenfunctions depending on the radius, satisfying boundary conditions on the cylindrical axis and radial wall. The boundary conditions at the end plates are satisfied by a sum of such radial eigenfunctions. The spectrum of possibly complex axial eigenvalues k is studied and is shown to consist of a continuum part and a discrete part in ideal MHD. Only the discrete part is used to give an approximation to the complete two-dimensional eigenfunction. The method is applied to a special equilibrium magnetic field with constant field line pitch. The role of the individual radial eigenfunctions is explained. It is shown that our method reproduces previously found values of the critical pitch (at marginal stability) for a plasma column in vacuum. The method also suggests important differences between ideal and resistive MHD.
Scanning heterodyne Kerr-effect microscope for imaging of magnetic tracks
Authors: Protopopov Vladimir V. , Lee Sukwon , Kwon Youngkun , Cho Sunghoon , Kim Hyuk , Chae Jonggyn
Published: July 2006

Design and performance of a new type of Kerr microscope based on heterodyne cross-polarized technique is presented. Weak depolarization of the probe beam due to longitudinal magneto-optical Kerr effect is detected by means of heterodyne mixing of the two cross-polarized and frequency shifted waves generated by Zeeman-type He–Ne laser. In comparison with the traditional homodyne method the proposed technique has better sensitivity and spatial resolution. Experimental results of imaging service magnetic tracks on real samples of magnetic disks are presented, showing better contrast and spatial resolution with respect to the images obtained from commercial devices available in the market.
Dependence of spin-transfer switching current on free layer thickness in Co–Fe–B∕MgO∕Co–Fe–B magnetic tunnel junctions
Authors: Kubota Hitoshi , Fukushima Akio , Ootani Yuichi , Yuasa Shinji , Ando Koji , Maehara Hiroki , Tsunekawa Koji , Djayaprawira David D. , Watanabe Naoki , Suzuki Yoshishige
Published: July 2006

Magnetoresistance (MR) and spin-transfer switching (STS) properties were investigated in Co–Fe–B∕MgO∕Co–Fe–B magnetic tunnel junctions as a function of free layer thickness (dFree). The MR ratio was about 140% at dFree⩾2nm. It decreased to about 80% at dFree=1.5nm. Both switching currents and thermal stability were roughly proportional to dFree. The averaged intrinsic switching current density (Jc0av) was 1×107–2×107A∕cm2. The thermal stability of parallel magnetization state was greater than that of antiparallel state. The feasibility of the STS write scheme for nonvolatile magnetic random access memory was discussed.
Exchange anisotropy as a probe of antiferromagnetism in expanded face-centered-tetragonal Mn(001) layers
Authors: Kohlhepp J. T. , Wieldraaijer H. , de Jonge W. J. M.
Published: July 2006

Manganese (Mn) grows coherent and with an expanded metastable face-centered-tetragonal (e-fct) structure on ultrathin fct Co(001)∕Cu(001) template layers. From the temperature dependence of the observed unidirectional Mn∕Co interface exchange anisotropy, an antiferromagnetic state with a blocking temperature around 410K is found for a 21 monolayer thick e-fct Mn(001) film. The temperature dependent coercivity enhancement of the Co films, which is induced by the proximity of the antiferromagnetic Mn layer, suggests a Néel temperature above 410K for this Mn phase.
Influence of indium-tin-oxide thin-film quality on reverse leakage current of indium-tin-oxide/n-GaN Schottky contacts
Authors: Wang R. X. , Xu S. J. , Djurišić A. B. , Beling C. D. , Cheung C. K. , Cheung C. H. , Fung S. , Zhao D. G. , Yang H. , Tao X. M.
Published: July 2006

Indium-tin-oxide (ITO)/n-GaN Schottky contacts were prepared by e-beam evaporation at 200°C under various partial pressures of oxygen. X-ray photoemission spectroscopy and positron beam measurements were employed to obtain chemical and structural information of the deposited ITO films. The results indicated that the observed variation in the reverse leakage current of the Schottky contact and the optical transmittance of the ITO films were strongly dependent on the quality of the ITO film. The high concentration of point defects at the ITO-GaN interface is suggested to be responsible for the large observed leakage current of the ITO/n-GaN Schottky contacts.
Ferromagnetism induced by hydrogen in polycrystalline nonmagnetic Zn0.95Co0.05O
Authors: Deka Sasanka , Joy P. A.
Published: July 2006

Polycrystalline Zn0.95Co0.05O is found to be paramagnetic at room temperature and down to 12K. Optical measurements prove the incorporation of Co2+ ions inside the ZnO lattice in the tetrahedral site. When the paramagnetic sample is heated in Ar∕H2 at 1125K for 2h, ferromagnetism with a very high value of magnetization is observed at room temperature. Hydrogen reduction does not affect the substituted Co2+ ions inside the wurtzite crystal lattice as evidenced from optical studies. X-ray diffraction studies show the presence of Co metal after the reduction process which is the origin of room temperature ferromagnetism.
Self Recognition versus Recognition of others by Biological Motion: Viewpoint-Dependent Effects
Authors: Jokisch Daniel , Daum Irene , Troje Nikolaus F
Published: July 2006

We investigated the influence of viewing angle on performance in recognising the identity of one's own person and familiar individuals such as friends or colleagues from walking patterns. Viewpoint-dependent recognition performance was tested in two groups of twelve persons who knew each other very well. Participants' motion data were acquired by recording their walking patterns in three-dimensional space with the use of a motion capture system. Size-normalised point-light displays of biological motion of these walking patterns, including one's own, were presented to the same group members on a computer screen in frontal view, half-profile view, and profile view. Observers were requested to assign the person's name to the individual gait pattern. No feedback was given. Whereas recognition performance of one's own walking patterns was viewpoint independent, recognition rate for other familiar individuals was better for frontal and half-profile view than for profile view. These findings are discussed in the context of the theory of common coding of motor and visual body representations.
Background Stripes Affect Apparent Speed of Rotation
Authors: Anstis Stuart , Ito Hiroyuki , Cavanagh Patrick
Published: July 2006

A gray line that rotated about its own center against a stationary background of vertical stripes appeared to double in perceptual speed as it rotated through the vertical position and thus momentarily aligned with the background. Four factors may contribute to this speed-up: (i) landmarks, in which the tip of the moving vertical line moves horizontally across the maximum number of stationary stripes; (ii) orientation repulsion of the moving line by the vertical stripes, which may distort the line's perceived position and hence its perceived speed; (iii) the orientation of an induced brightness pattern along the line; and (iv) the motion of the induced brightness pattern, which moves physically most rapidly along the line when the line is near vertical. To test these possibilities, an annulus display provided landmarks but no intersections, and this almost abolished the effect. A rotating-slit display provided an oriented, moving pattern that mimicked the induced brightness but had no landmarks, and this increased the effect. We conclude that the motion, but not the orientation, of the intersections [option (iv)] was responsible for the illusion. The fact that this motion along the length of the line affected the perceived speed of the line orthogonal to its own length indicates a failure on the part of the visual system to fully decouple tangential from radial motion.
A polymorphism within a conserved β1-adrenergic receptor motif alters cardiac function and β-blocker response in human heart failure
Authors: Liggett Stephen B. , Mialet-Perez Jeanne , Thaneemit-Chen Surai , Weber Stewart A. , Greene Scott M. , Hodne Danielle , Nelson Bradley , Morrison Jennifer , Domanski Michael J. , Wagoner Lynne E. , Abraham William T. , Anderson Jeffrey L. , Carlquist John F. , Krause-Steinrauf Heidi J. , Lazzeroni Laura C. , Port J. David , Lavori Philip W. , Bristow Michael R.
Published: July 2006

Heterogeneity of heart failure (HF) phenotypes indicates contributions from underlying common polymorphisms. We considered polymorphisms in the β1-adrenergic receptor (β1AR), a β-blocker target, as candidate pharmacogenomic loci. Transfected cells, genotyped human nonfailing and failing ventricles, and a clinical trial were used to ascertain phenotype and mechanism. In nonfailing and failing isolated ventricles, β1-Arg-389 had respective 2.8 ± 0.3- and 4.3 ± 2.1-fold greater agonist-promoted contractility vs. β1-Gly-389, defining enhanced physiologic coupling under relevant conditions of endogenous expression and HF. The β-blocker bucindolol was an inverse agonist in failing Arg, but not Gly, ventricles, without partial agonist activity at either receptor; carvedilol was a genotype-independent neutral antagonist. In transfected cells, bucindolol antagonized agonist-stimulated cAMP, with a greater absolute decrease observed for Arg-389 (435 ± 80 vs. 115 ± 23 fmol per well). Potential pathophysiologic correlates were assessed in a placebo-controlled trial of bucindolol in 1,040 HF patients. No outcome was associated with genotype in the placebo group, indicating little impact on the natural course of HF. However, the Arg-389 homozygotes treated with bucindolol had an age-, sex-, and race-adjusted 38% reduction in mortality (P= 0.03) and 34% reduction in mortality or hospitalization (P= 0.004) vs. placebo. In contrast, Gly-389 carriers had no clinical response to bucindolol compared with placebo. Those with Arg-389 and high baseline norepinephrine levels trended toward improved survival, but no advantage with this allele and exaggerated sympatholysis was identified. We conclude that β1AR-389 variation alters signaling in multiple models and affects the β-blocker therapeutic response in HF and, thus, might be used to individualize treatment of the syndrome.
Factors regulating the abundance and localization of synaptobrevin in the plasma membrane
Authors: Dittman Jeremy S. , Kaplan Joshua M.
Published: July 2006

After synaptic vesicle fusion, vesicle proteins must be segregated from plasma membrane proteins and recycled to maintain a functional vesicle pool. We monitored the distribution of synaptobrevin, a vesicle protein required for exocytosis, in
Caenorhabditis elegans
motor neurons by using a pH-sensitive synaptobrevin GFP fusion protein, synaptopHluorin. We estimated that 30% of synaptobrevin was present in the plasma membrane. By using a panel of endocytosis and exocytosis mutants, we found that the majority of surface synaptobrevin derives from fusion of synaptic vesicles and that, in steady state, synaptobrevin equilibrates throughout the axon. The surface synaptobrevin was enriched near active zones, and its spatial extent was regulated by the clathrin adaptin AP180. These results suggest that there is a plasma membrane reservoir of synaptobrevin that is supplied by the synaptic vesicle cycle and available for retrieval throughout the axon. The size of the reservoir is set by the relative rates of exo- and endocytosis.
Adaptive evolution by mutations in theFLO11gene
Authors: Fidalgo Manuel , Barrales Ramon R. , Ibeas Jose I. , Jimenez Juan
Published: July 2006

In nature,Saccharomycesyeasts manifest a number of adaptive responses to overcome adverse environments such as filamentation, invasive growth, flocculation and adherence to solid surfaces. CertainSaccharomyceswild yeasts, namely “flor yeasts,” have also acquired the ability to form a buoyant biofilm at the broth surface. Here we report that mutations in a single gene, identified asFLO11, separate these “floating” yeasts from their nonfloating relatives. We have determined that the capability to form a self-supporting biofilm at the liquid surface is largely dependent on two changes in theFLO11gene. First, we identified a 111-nt deletion within a repression region of theFLO11promoter that significantly increasesFLO11gene expression. Secondly, we found rearrangements within the central tandem repeat domain of the coding region that yield a more hydrophobic Flo11p variant. Together, these mutations result in dramatic increase in cell surface hydrophobicity, which in turn confers these yeasts the ability to float by surface tension, an adaptive mechanism to gain direct access to oxygen within oxygen-poor liquid environments.
The 2.7-Å crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase
Authors: Tang Yinyan , Kim Chu-Young , Mathews Irimpan I. , Cane David E. , Khosla Chaitan
Published: July 2006

The x-ray crystal structure of a 194-kDa fragment from module 5 of the 6-deoxyerythronolide B synthase has been solved at 2.7 Å resolution. Each subunit of the homodimeric protein contains a full-length ketosynthase (KS) and acyl transferase (AT) domain as well as three flanking “linkers.” The linkers are structurally well defined and contribute extensively to intersubunit or interdomain interactions, frequently by means of multiple highly conserved residues. The crystal structure also reveals that the active site residue Cys-199 of the KS domain is separated from the active site residue Ser-642 of the AT domain by ≈80 Å. This distance is too large to be covered simply by alternative positioning of a statically anchored, fully extended phosphopantetheine arm of the acyl carrier protein domain from module 5. Thus, substantial domain reorganization appears necessary for the acyl carrier protein to interact successively with both the AT and the KS domains of this prototypical polyketide synthase module. The 2.7-Å KS–AT structure is fully consistent with a recently reported lower resolution, 4.5-Å model of fatty acid synthase stucture, and emphasizes the close biochemical and structural similarity between polyketide synthase and fatty acid synthase enzymology.
Regulatory protein that inhibits both synthesis and use of the target protein controls flagellar phase variation in
Salmonella enterica
Authors: Aldridge Phillip D. , Wu Cheng , Gnerer Joshua , Karlinsey Joyce E. , Hughes Kelly T. , Sachs Matthew S.
Published: July 2006

Flagellin is a major surface antigen for many bacterial species. The pathogen
Salmonella enterica
switches between two alternative, antigenic forms of its flagellin filament protein, either type B or C. This switching (flagellar phase variation) is achieved by stochastic inversion of a promoter that produces both type B flagellin (FljB) and an inhibitor (FljA) of type C flagellin formation. When the
fljB-fljA
operon is expressed, only type B flagella are produced; when the operon is not transcribed, the gene for type C flagellin (
fliC
) is released from inhibition and forms type C flagella. Long thought to be a transcription repressor, the FljA inhibitor is shown here to block both translation and use of the FliC protein by binding to an mRNA region upstream from the translation start codon. Bypass mutants resistant to this inhibition alter this mRNA region, and some prevent FljA–RNA binding. Other bypass mutations are duplications within the leader mRNA that make FljA essential for FliC assembly. Certain bypass mutations allow FljA to block FliC-dependent motility without blocking production of the FliC protein,
per se
. Other mutations in the FliC mRNA leader block expression of the unlinked
fljB
gene. Results suggest that mRNAs for types B and C flagellin compete for occupancy of a site that directs the product toward assembly and that FljA influences this competition. This mechanism may serve to prevent assembly of flagella with a mixture of subunit types, especially during periods of switching from one type to the other.
Drusen, choroidal neovascularization, and retinal pigment epithelium dysfunction in SOD1-deficient mice: A model of age-related macular degeneration
Authors: Imamura Yutaka , Noda Setsuko , Hashizume Kouhei , Shinoda Kei , Yamaguchi Mineko , Uchiyama Satoshi , Shimizu Takahiko , Mizushima Yutaka , Shirasawa Takuji , Tsubota Kazuo
Published: July 2006

Oxidative stress has long been linked to the pathogenesis of neurodegenerative diseases; however, whether it is a cause or merely a consequence of the degenerative process is still unknown. We show that mice deficient in Cu, Zn-superoxide dismutase (SOD1) have features typical of age-related macular degeneration in humans. Investigations of senescent
Sod1
−/−
mice of different ages showed that the older animals had drusen, thickened Bruch’s membrane, and choroidal neovascularization. The number of drusen increased with age, and exposure of young
Sod1
−/−
mice to excess light induced drusen. The retinal pigment epithelial cells of
Sod1
−/−
mice showed oxidative damage, and their β-catenin-mediated cellular integrity was disrupted, suggesting that oxidative stress may affect the junctional proteins necessary for the barrier integrity of the retinal pigment epithelium. These observations strongly suggest that oxidative stress may play a causative role in age-related retinal degeneration, and our findings provide evidence for the free radical theory of aging. In addition, these results demonstrate that the
Sod1
−/−
mouse is a valuable animal model to study human age-related macular degeneration.
Dissecting virulence pathways of
Mycobacterium tuberculosis
through protein–protein association
Authors: Singh Amit , Mai Deborah , Kumar Ashwani , Steyn Adrie J. C.
Published: July 2006

The sudden increase in information derived from the completed
Mycobacterium tuberculosis
(
Mtb
) genome sequences has revealed the need for approaches capable of converting raw genome sequence data into functional information. To date, an experimental system for studying protein–protein association in mycobacteria is not available. We have developed a simple system, termed mycobacterial protein fragment complementation (M-PFC), that is based upon the functional reconstitution of two small murine dihydrofolate reductase domains independently fused to two interacting proteins. Using M-PFC, we have successfully demonstrated dimerization of yeast GCN4, interaction between
Mtb
KdpD and KdpE, and association between Esat-6 and Cfp-10. We established the association between the sensor kinase, DevS, and response regulator, DevR, thereby demonstrating the potential of M-PFC to study protein associations in the mycobacterial membrane. To validate our system, we screened an
Mtb
library for proteins that associate with the secreted antigen Cfp-10 and consistently identified Esat-6 in our screens. Additional proteins that specifically associate with Cfp-10 include Rv0686 and Rv2151c (FtsQ), a component and substrate, respectively, of the evolutionary conserved signal recognition pathway; and Rv3596c (ClpC1), an AAA-ATPase chaperone involved in protein translocation and quality control. Our results provide empirical evidence that directly links the
Mtb
specialized secretion pathway with the evolutionary conserved signal recognition and SecA/SecYEG pathways, suggesting they share secretory components. We anticipate that M-PFC will be a major contributor to the systematic assembly of mycobacterial protein interaction maps that will lead to the development of better strategies for the control of tuberculosis.
Mouse genomic representational oligonucleotide microarray analysis: Detection of copy number variations in normal and tumor specimens
Authors: Lakshmi B. , Hall Ira M. , Egan Christopher , Alexander Joan , Leotta Anthony , Healy John , Zender Lars , Spector Mona S. , Xue Wen , Lowe Scott W. , Wigler Michael , Lucito Robert
Published: July 2006

Genomic amplifications and deletions, the consequence of somatic variation, are a hallmark of human cancer. Such variation has also been observed between “normal” individuals, as well as in individuals with congenital disorders. Thus, copy number measurement is likely to be an important tool for the analysis of genetic variation, genetic disease, and cancer. We developed representational oligonucleotide microarray analysis, a high-resolution comparative genomic hybridization methodology, with this aim in mind, and reported its use in the study of humans. Here we report the development of a representational oligonucleotide microarray analysis microarray for the genomic analysis of the mouse, an important model system for many genetic diseases and cancer. This microarray was designed based on the sequence assembly MM3, and contains ≈84,000 probes randomly distributed throughout the mouse genome. We demonstrate the use of this array to identify copy number changes in mouse cancers, as well to determine copy number variation between inbred strains of mice. Because restriction endonuclease digestion of genomic DNA is an integral component of our method, differences due to polymorphisms at the restriction enzyme cleavage sites are also observed between strains, and these can be useful to follow the inheritance of loci between crosses of different strains.
T lineage differentiation from human embryonic stem cells
Authors: Galić Zoran , Kitchen Scott G. , Kacena Amelia , Subramanian Aparna , Burke Bryan , Cortado Ruth , Zack Jerome A.
Published: July 2006

Harnessing the ability of genetically manipulated human embryonic stem cells (hESC) to differentiate into appropriate lineages could revolutionize medical practice. These cells have the theoretical potential to develop into all mature cell types; however, the actual ability to develop into all hematopoietic lineages has not been demonstrated. Using sequential
in vitro
coculture on murine bone marrow stromal cells, and engraftment into human thymic tissues in immunodeficient mice, we demonstrate that hESC can differentiate through the T lymphoid lineage. Stable transgene expression was maintained at high levels throughout differentiation, suggesting that genetically manipulated hESC hold potential to treat several T cell disorders.
Distinguishing features of δ-proteobacterial genomes
Authors: Karlin Samuel , Brocchieri Luciano , Mrázek Jan , Kaiser Dale
Published: July 2006

We analyzed several features of five currently available δ-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The δ genomes are distinguished from other bacteria by several properties: (
i
) The δ genomes contain two “giant” S1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no S1; (
ii
) in most δ-proteobacterial genomes the major ribosomal protein (RP) gene cluster is near the replication terminus whereas most bacterial genomes place the major RP cluster near the origin of replication; (
iii
) the δ genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amido-transferase complex (Gat CAB) genes that modify Asp-tRNA
Asn
into Asn-tRNA
Asn
and Glu-tRNA
Gln
into Gln-tRNA
Gln
; (
iv
) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among δ genomes; (
v
) the anaerobic δ genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (
vi
) σ
54
activators play a more important role in the δ genomes than in other bacteria. δ genomes have a plethora of enhancer binding proteins that respond to environmental and intracellular cues, often as part of two-component systems; (
vii
) δ genomes encode multiple copies of metallo-β-lactamase enzymes; (
viii
) a host of secretion proteins emphasizing SecA, SecB, and SecY may be especially useful in the predatory activities of
Myxococcus xanthus
; (
ix
) δ proteobacteria drive many multiprotein machines in their periplasms and outer membrane, including chaperone-feeding machines, jets for slime secretion, and type IV pili.
Bdellovibrio
replicates in the periplasm of prey cells. The sulfate-reducing δ proteobacteria metabolize hydrogen and generate a proton gradient by electron transport. The predicted highly expressed genes from δ genomes reflect their different ecologies, metabolic strategies, and adaptations.
Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls
Authors: Bauer Stefan , Vasu Prasanna , Persson Staffan , Mort Andrew J. , Somerville Chris R.
Published: July 2006

To facilitate analysis of plant cell wall polysaccharide structure and composition, we cloned 74 genes encoding polysaccharide-degrading enzymes from
Aspergillus nidulans
,
Aspergillus fumigatus
, and
Neurospora crassa
and expressed the genes as secreted proteins with C-terminal Myc and 6× His tags. Most of the recombinant enzymes were active in enzyme assays, and optima for pH and temperature were established. A subset of the enzymes was used to fragment polysaccharides from the
irregular xylem 9
(
irx9
) mutant of
Arabidopsis
. The analysis revealed a decrease in the abundance of xylan in the mutant, indicating that the
IRX9
gene, which encodes a putative family 43 glycosyltransferase, is required for xylan synthesis.