bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic field structure evolution in rotating magnetic field plasmas
Authors: Petrov Yuri , Yang Xiaokang , Huang Tian-Sen
Published: July 2008

A study of magnetic field structure evolution during 40-ms plasma discharge has been performed in a new device with 80cmlong/40cm diameter cylindrical chamber, in which a plasma current Ip≈2kA was driven and sustained by a rotating magnetic field. The main focus of the experiments is on how the changes in externally applied magnetic field affect the current profile and magnetic field in plasma. During plasma discharge, a pulse current was briefly fed to a magnetic coil located at the midplane (middle coil). The magnetic field in cross section of plasma was scanned with pickup probes. Two regimes were studied: without and with an external toroidal field (TF) produced by axial Iz current. With a relatively small current (Im⩽600A) in the middle coil, the plasma current is boosted up to 5kA. The magnetic flux surfaces become extended along the axial Z direction, sometimes with the formation of doublet shape plasma. The regime without TF appears to be less stable, presumably due to the reversal of plasma current in central area of plasma column.
Structural characterization of sputtered hydrogenated amorphous carbon films by solid state nuclear magnetic resonance
Authors: Cho Gyunggoo , Yen Bing K. , Klug Christopher A.
Published: July 2008

Solid state nuclear magnetic resonance (NMR) methods have been used to investigate the effect of H content on the structure of sputtered hydrogenated amorphous carbon a-C:H films. Carbon-13 NMR spectra of a-C:H consist of two broad peaks at 135 and 40 ppm, which correspond to the sp2 and sp3 carbons, respectively. Surprisingly, the sp2/sp3 carbon ratio (2.0±0.3) is relatively independent of the H content in the range of 13%–35%. Hence, all a-C:H films contain approximately 66% graphitelike sp2 carbon. Cross polarization and spectral editing experiments reveal that the nonprotonated (quaternary) sp3 carbon fraction reaches as high as 30% at low H concentrations of 13%–23%. As the H content exceeds 23%, however, quaternary carbon bonds are terminated by H atoms to form protonated sp3 carbons, such as methylene (CH2) and methine (CH). Our results show that the hardness of a-C:H correlates with the quaternary carbon fraction rather than the sp2/sp3 ratio, as commonly believed. We also report the first extensive studies of both H1 and C13 spin-lattice relaxation for sputtered a-C:H. Relaxation data for hydrogen and carbon indicate that the unpaired electrons are probably equally distributed among sp2 and sp3 carbons. Moreover, the number of unpaired electrons in the a-C:H samples is relatively independent of H content, as revealed by spin counting experiments. C13 and H1 magnetization recovery curves for samples with H content up to 28% can be fitted with a single exponential, which is in contrast to the biexponential behavior reported for plasma-enhanced chemical vapor deposition (PECVD) a-C:H films. Hence, our results for sputtered a-C:H films do not support the model of proton-rich and proton-deficient regions proposed for PECVD carbon.
Shear-induced effects in hyperbranched-linear polyelectrolyte complexes
Authors: Dalakoglou G. K. , Karatasos K. , Lyulin S. V. , Lyulin A. V.
Published: July 2008

Static and dynamic properties of complexes formed by hyperbranched polymers with linear polyelectrolytes are studied under the influence of steady shear flow by means of Brownian dynamics simulations. Models of peripherally charged hyperbranched molecules bearing two extreme topological structures and different molecular weights complexed with linear neutralizing chains are subjected to a range of shear rates starting from a low-shear regime toward the complex-breaking point. Examination of the stability limit, shape and mass distribution parameters, and dynamics in different lengths and timescales is performed as a function of the applied shear. The results described illustrate features of the generic behavior that should be expected from such systems under conditions of steady shear flow.
Model dielectric functions for AlxGa1−xAs alloys of arbitrary compositions
Authors: Jung Y. W. , Kim T. J. , Yoon J. J. , Kim Y. D. , Aspnes D. E.
Published: July 2008

Many optical models have been used to construct analytic composition-dependent dielectric functions of AlxGa1−xAs alloys. However, these models incorporate various unphysical assumptions to improve their fits to data. Here, we provide the parameters needed to calculate dielectric functions of AlxGa1−xAs for 1.5≤E≤6.0 eV and 0≤x≤1 by means of the parametric model of Johs et al. [Thin Solid Films 313–314, 137 (1998)], which eliminates these problems. A representative example concerning interface analysis is discussed, where it is necessary to construct a dielectric function of an alloy of essentially arbitrary composition.
Coercivity generation of surface Nd2Fe14B grains and mechanism of fcc-phase formation at the Nd/Nd2Fe14B interface in Nd-sputtered Nd–Fe–B sintered magnets
Authors: Fukagawa Tomoki , Hirosawa Satoshi
Published: July 2008

The coercivity of surface grains of a Nd–Fe–B sintered magnet can be measured unequivocally if the magnet is a thin slab with the orientation of its c-axis parallel to the largest surface. Due to the loss of part of the neodymium-rich grain boundary phase, the surface Nd2Fe14B grains have low coercivity after machining. When a Nd layer is sputter deposited on the surface and annealed in the temperature range from 500 to 675 °C, the surface coercivity recovers to its full value, which is identical to the coercivity of the bulk magnet from which the slab was cut. Transmission electron microscopy has indicated the formation of a fcc interfacial phase having a lattice constant a=0.548 nm between the surface grains and the Nd layer in the specimen whose surface coercivity was recovered. In addition to a double hexagonal closed packed phase (metallic Nd), A-type Nd2O3 has been observed in the inner region of the Nd film away from the interface. A-type Nd2O3 having a hexagonal structure with a=0.382 nm and c=0.598 nm is the most stable phase of the neodymium oxides with 2:3 stoichiometry. Since the fcc phase is derived from metastable C-type Nd2O3 having a cubic structure with a=1.108 nm, the fcc phase is also a metastable phase. Therefore it is considered that the formation of the fcc phase results from the interfacial energy with the Nd2Fe14B grains.
Synthesis and magnetic properties of self-assembled FeRh nanoparticles
Authors: Jia Z. , Harrell J. W. , Misra R. D. K.
Published: July 2008

We report here the synthesis and magnetization behavior of tunable FeRh magnetic nanoparticles with both controllable composition and size. FexRh1−x (x=0.35,0.44,0.51) nanoparticles of 4–20nm size range were fabricated using a polyol coreduction process. The stoichiometry of FexRh1−x nanoparticles was altered by tuning the molar ratio of rhodium acetylacetonate and iron acetylacetonate. The particle size was tunable via control of surfactant concentration. Magnetic measurements were made for films of the particles cast onto silicon wafers. The coercivity of Fe51Rh49 nanoparticles was ∼250Oe at room temperature after annealing at 700°C for 2h, indicating CsCl-type phase transition. The temperature dependent magnetization measurement of annealed Fe51Rh49 confirmed the antiferromagnetic-ferromagnetic transition and was supported by x-ray diffraction measurements.
Electrical investigation of V-defects in GaN using Kelvin probe and conductive atomic force microscopy
Authors: Lochthofen A. , Mertin W. , Bacher G. , Hoeppel L. , Bader S. , Off J. , Hahn B.
Published: July 2008

We report on the electrical characterization of V-defects in GaN-based heterostructures via Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy (C-AFM). The KPFM measurements show for n- and p-doped GaN top layers an increase in the work function within the V-defects. Surprisingly, an increase in the current flow within the V-defects is found by C-AFM in case of the n-doped structure, while current flow into the V-defect is suppressed for the p-doped structure. For a consistent explanation of these results we suggest a model, which is based on an increase in the electron affinity of the {10−11}-surfaces within the V-defects as compared to the planar (0001)-surface.
An integrable coupled hybrid lattice and its exact solutions
Authors: Jia M. , Liu P. , Lou S. Y.
Published: July 2008

A coupled hybrid lattice system is proposed. The model can be considered as one of the discrete forms of the coupled integrable Korteweg–de Vries system which is a special case of some physically significant models. The Lax integrability of the coupled hybrid lattice system is proved. By using a simple function expansion approach, various novel types of exact solutions such as the kink-soliton lattice, the bell-staggered soliton lattice, the kink-kink breather lattice, and the soliton-soliton breather lattice, are found.
Riemannian geometry of noncommutative surfaces
Authors: Chaichian M. , Tureanu A. , Zhang R. B. , Zhang Xiao
Published: July 2008

A Riemannian geometry of noncommutative n-dimensional surfaces is developed as a first step toward the construction of a consistent noncommutative gravitational theory. Historically, as well, Riemannian geometry was recognized to be the underlying structure of Einstein’s theory of general relativity and led to further developments of the latter. The notions of metric and connections on such noncommutative surfaces are introduced, and it is shown that the connections are metric compatible, giving rise to the corresponding Riemann curvature. The latter also satisfies the noncommutative analog of the first and second Bianchi identities. As examples, noncommutative analogs of the sphere, torus, and hyperboloid are studied in detail. The problem of covariance under appropriately defined general coordinate transformations is also discussed and commented on as compared to other treatments.
Organometallic vapor phase epitaxial growth of GaN on ZrN∕AlN∕Si substrates
Authors: Oliver Mark H. , Schroeder Jeremy L. , Ewoldt David A. , Wildeson Isaac H. , Rawat Vijay , Colby Robert , Cantwell Patrick R. , Stach Eric A. , Sands Timothy D.
Published: July 2008

An intermediate ZrN∕AlN layer stack that enables the epitaxial growth of GaN on (111) silicon substrates using conventional organometallic vapor phase epitaxy at substrate temperatures of ∼1000°C is reported. The epitaxial (111) ZrN layer provides an integral back reflector and Ohmic contact to n-type GaN, whereas the (0001) AlN layer serves as a reaction barrier, as a thermally conductive interface layer, and as an electrical isolation layer. Smooth (0001) GaN films less than 1μm thick grown on ZrN∕AlN∕Si yield 0002 x-ray rocking curve full width at half maximum values as low as 1230arcsec.
X-pinch x-ray sources driven by a 1μs capacitor discharge
Authors: Appartaim R. K. , Maakuu B. T.
Published: July 2008

X pinches formed from tungsten, molybdenum, titanium, aluminum, and alloys, such as constantan and nichrome with diameters of 13–25μm, have been imploded with a 300kA, 1μs quarter-period capacitor discharge and observed with an array of diagnostics including time-integrated optical photography, x-ray pinhole cameras, x-ray Si photodiodes, a flat crystal spectrograph, and a Nd:YAG laser interferometry/schlieren system. The results of these comprehensive observations are presented. When a single, central hot spot is formed with the right choice of wire and x-ray filter, it is observed to be highly localized, very bright and small enough that point projection radiography can be routinely demonstrated for a simple biological specimen. For an aluminum X pinch, spectroscopic measurements indicate that the hot spots have a plasma density and electron temperature consistent with ∼1020cm−3 and ∼320–350eV, respectively.
Two-photon transitions in hydrogen atoms embedded in weakly coupled plasmas
Authors: Paul S. , Ho Y. K.
Published: July 2008

The pseudostate method has been applied to calculate energy eigenvalues and corresponding eigenfunctions of the hydrogen atom in Debye plasma environments. Resonant two-photon transition rates from the ground state of atomic hydrogen to 2s and 3s excited states have been computed as a function of photon frequency in the length and velocity gauges for different Debye lengths. A two-photon transparency is found in correspondence to each resonance for 1s–3s. The transparency frequency and resonance enhancement frequency vary significantly with the Debye length.
Influence of film thickness on the crystallization of Ni-doped amorphous silicon samples
Authors: Ferri F. A. , Zanatta A. R.
Published: July 2008

This work reports on the crystallization of amorphous silicon (a-Si) films doped with 1 at. % of nickel. The films, with thicknesses ranging from 10 to 3000 nm, were deposited using the cosputtering method onto crystalline quartz substrates. In order to investigate the crystallization mechanism in detail, a series of undoped a-Si films prepared under the same deposition conditions were also studied. After deposition, all a-Si films were submitted to isochronal thermal annealing treatments up to 1000 °C and analyzed by Raman scattering spectroscopy. Based on the present experimental results, it is possible to state that (a) when compared to the undoped a-Si films, those containing 1 at. % of Ni crystallize at temperatures ∼100 °C lower, and that (b) the film thickness influences the temperature of crystallization that, in principle, tends to be lower in films thinner than 1000 nm. The possible reasons associated to these experimental observations are presented and discussed in view of some experimental and thermodynamic aspects involved in the formation of ordered Si–Si bonds and in the development of Ni-silicide phases.
Role of C in the formation and kinetics of nanovoids induced by He+ implantation in Si
Authors: D’Angelo D. , Mirabella S. , Bruno E. , Pulvirenti G. , Terrasi A. , Bisognin G. , Berti M. , Bongiorno C. , Raineri V.
Published: July 2008

The formation and growth of nanovoids in a C-doped Si layer after He+ implantation and thermal annealing are reported. A structure consisting of 240 nm of Si, 20 nm of Si doped with C at 0.8 at. %, and 240 nm of Si cap was realized by molecular beam epitaxy onto a (100) Si Czochralsky substrate. Three sets of samples were implanted with He+ at 30 keV and different doses of 8×1015, 3×1016, and 5×1016 cm−2 and subsequently annealed at 800 °C in N2 atmosphere. Cross-section transmission electron microscopy was used to determine the void size and location. The tensile strain of the C-doped layer was measured by high-resolution x-ray diffraction. Our studies report the double role of C in the formation and evolution of nanovoids. After the low dose implantation, the C-doped layer still shows tensile strain due to substitutional C, and voids are localized only within this layer. At higher implantation doses, all the C atoms have been displaced from substitutional sites. No more strain is present in the C-doped layer and the presence of large cavities in its neighborhood is strongly inhibited. This work shows how localized strain in epitaxial films can be effectively used to drive nanovoid formation and evolution.
Exact solutions for nonlinear propagation of slow ion acoustic monotonic double layers and a solitary hole in a semirelativistic plasma
Authors: El-Kalaawy O. H. , Ibrahim R. S.
Published: July 2008

A small-amplitude slow ion acoustic monotonic double layer in an unmagnetized plasma consisting of relativistic drifting cold electrons and nonrelativistic drifting thermal ions is investigated. By using the reductive perturbation method, Schamel–Korteweg–de Vries (SKdV) and Schamel equations are derived. We used the linearization transformation to obtained the solutions of the SKdV and Schamel equations. The method is based upon a linearization principle that can be applied on nonlinearities which have a polynomial form. We illustrate the potential of the method by finding solutions of the SKdV and Schamel equations. Furthermore, we show that the monotonic double-layer solution is a nonlinear extension of the slow ion acoustic solitary hole having a negative trapping parameter in a semi relativistic plasma.
Numerical and experimental study of the fluid dynamics of a flapping wing with low order flexibility
Authors: Toomey Jonathan , Eldredge Jeff D.
Published: July 2008

A simple canonical problem for understanding the role of flexibility in flapping wing flight is investigated numerically and experimentally. The problem consists of a two-dimensional two-component wing structure connected by a single hinge with a damped torsion spring. One component of the wing is driven with hovering flapping wing kinematics, while the other component responds passively to the fluid dynamic and inertial/elastic forces. Numerical simulations are carried out with the viscous vortex particle method with strongly coupled body dynamics. The experiments are conducted in a water tank with suspended particles for flow visualization. The system is analyzed in several different kinematic test cases that are designed to span a broad parametric range of flapping. Hinge deflection is used as the primary metric for comparison; the agreement between computation and experiment is very good in all cases. The trajectories of shed vortices are also compared, again with favorable agreement. Fluid forces and moments are computed in the numerical simulation at two different Reynolds numbers. It is found that the rate and timing of wing rotation primarily controls the generation of lift; in contrast, the translational acceleration has little effect. Likewise, kinematics with rotation transition well separated from translation transition are captured utilizing rotation-only kinematics. Reynolds number has little effect on the wing deflection but does influence the mean lift generated by the wing.
Study of phase transition in (Pb,Ba)TiO3 thin films
Authors: Pontes F. M. , Santos L. S. , Pontes D. S. L. , Longo E. , Neto S. Claro , Leite E. R. , Chiquito A. J. , Pizani P. S.
Published: July 2008

Dielectric and Raman scattering experiments were performed on polycrystalline Pb1−xBaxTiO3 thin films (x=0.40 and 0.60) as a function of temperature. The dielectric study on single phase compositions revealed that a diffuse-type phase transition occurred upon transformation of the cubic paraelectric to the tetragonal ferroelectric phase in all thin films, which showed a broadening of the dielectric peak. Diffusivity was found to increase with increasing barium contents in the composition range under study. In addition, the temperature dependence of Raman scattering spectra was investigated through the ferroelectric phase transition. The temperature dependence of the phonon frequencies was used to characterize the phase transitions. Raman modes persisted above the tetragonal to cubic phase transition temperature, although all optical modes should be Raman inactive. The origin of these modes was interpreted as a breakdown of the local cubic symmetry by chemical disorder. The lack of a well-defined transition temperature and the presence of broadbands in some temperature intervals above the paraferroelectric phase transition temperature suggest a diffuse-type phase transition.
Spin transfer induced coherent microwave emission with large power from nanoscale MgO tunnel junctions
Authors: Houssameddine D. , Florez S. H. , Katine J. A. , Michel J.-P. , Ebels U. , Mauri D. , Ozatay O. , Delaet B. , Viala B. , Folks L. , Terris B. D. , Cyrille M.-C.
Published: July 2008

In low resistance-area product MgO magnetic tunnel junction nanopillars, we observe high integrated power (up to 43nW), narrow linewidth (down to 10MHz), spin transfer induced microwave emission at frequencies up to 14GHz due to precession of the free layer magnetization at room temperature. Although all devices were fabricated on the same wafer, they present bimodal transport and precessional characteristics. The devices in which the narrowest linewidths were observed exhibited low resistance and tunneling magnetoresistance (30%), while maintaining large integrated power.
Pseudomorphic SiGe∕Si(001) layers synthesized by gas immersion laser doping
Authors: Fossard Frédéric , Boulmer Jacques , Débarre Dominique , Perrossier Jean-Luc , Bachelet Cyril , Fortuna Franck , Mathet Véronique , Bouchier Daniel
Published: July 2008

We report on the synthesis of SiGe layers on silicon by gas immersion laser doping. GeCl4 molecules are adsorbed on the surface and further incorporated into the Si top layer by a pulsed laser induced melt/regrowth process. Structural and chemical characterizations of the SiGe layers have been performed by using complementarily Rutherford backscattering spectrometry and x-ray Diffraction which indicate that Ge incorporation in the Si matrix results in a fully strained SiGe layer with gradual Ge concentrations reaching up to 18.5% near the surface.
Digital smoothing of the Langmuir probe I-V characteristic
Authors: Magnus F. , Gudmundsson J. T.
Published: July 2008

Electrostatic probes or Langmuir probes are the most common diagnostic tools in plasma discharges. The second derivative of the Langmuir probe I-V characteristic is proportional to the electron energy distribution function. Determining the second derivative accurately requires some method of noise suppression. We compare the Savitzky–Golay filter, the Gaussian filter, and polynomial fitting to the Blackman filter for digitally smoothing simulated and measured I-V characteristics. We find that the Blackman filter achieves the most smoothing with minimal distortion for noisy data.
Multichannel digital phase sensitive detection using a field programmable gate array development platform
Authors: Lascos Steven J. , Cassidy Daniel T.
Published: July 2008

This paper describes the development and performance of digital phase sensitive detectors (PSDs) based on a field programmable gate array (FPGA) logic device. A FPGA development system combined with a custom analog data acquisition board provides a powerful platform for the development of digital signal processing systems. Conventional performance metrics for digital PSDs are determined by the analog front-end devices and do not represent improvements to the PSD itself. FPGAs offer a scalable platform on which digital PSDs can be implemented with enhanced capabilities including simultaneous demodulation of multiple independent analog signals at multiple frequencies with arbitrary demodulation functions. Circuits for providing dynamic frequency tracking and ultrafine (<0.001°) phase resolution are presented.
Tip-enhanced near-field Raman spectroscopy with a scanning tunneling microscope and side-illumination optics
Authors: Yi K. J. , He X. N. , Zhou Y. S. , Xiong W. , Lu Y. F.
Published: July 2008

Conventional Raman spectroscopy (RS) suffers from low spatial resolution and low detection sensitivity due to the optical diffraction limit and small interaction cross sections. It has been reported that a highly localized and significantly enhanced electromagnetic field could be generated in the proximity of a metallic tip illuminated by a laser beam. In this study, a tip-enhanced RS system was developed to both improve the resolution and enhance the detection sensitivity using the tip-enhanced near-field effects. This instrument, by combining RS with a scanning tunneling microscope and side-illumination optics, demonstrated significant enhancement on both optical sensitivity and spatial resolution using either silver (Ag)-coated tungsten (W) tips or gold (Au) tips. The sensitivity improvement was verified by observing the enhancement effects on silicon (Si) substrates. Lateral resolution was verified to be below 100 nm by mapping Ag nanostructures. By deploying the depolarization technique, an apparent enhancement of 175% on Si substrates was achieved. Furthermore, the developed instrument features fast and reliable optical alignment, versatile sample adaptability, and effective suppression of far-field signals.
An integrated approach to piezoactuator positioning in high-speed atomic force microscope imaging
Authors: Yan Yan , Wu Ying , Zou Qingze , Su Chanmin
Published: July 2008

In this paper, an integrated approach to achieve high-speed atomic force microscope (AFM) imaging of large-size samples is proposed, which combines the enhanced inversion-based iterative control technique to drive the piezotube actuator control for lateral x-y axis positioning with the use of a dual-stage piezoactuator for vertical z-axis positioning. High-speed, large-size AFM imaging is challenging because in high-speed lateral scanning of the AFM imaging at large size, large positioning error of the AFM probe relative to the sample can be generated due to the adverse effects—the nonlinear hysteresis and the vibrational dynamics of the piezotube actuator. In addition, vertical precision positioning of the AFM probe is even more challenging (than the lateral scanning) because the desired trajectory (i.e., the sample topography profile) is unknown in general, and the probe positioning is also effected by and sensitive to the probe-sample interaction. The main contribution of this article is the development of an integrated approach that combines advanced control algorithm with an advanced hardware platform. The proposed approach is demonstrated in experiments by imaging a large-size (50μm) calibration sample at high-speed (50Hz scan rate).
Breaking single-walled carbon nanotube bundles by Joule heating
Authors: Wei Yang , Liu Peng , Jiang Kaili , Liu Liang , Fan Shoushan
Published: July 2008

Electrical breakdown induced by Joule heating was employed to make a well-aligned surface structure from single-walled carbon nanotube (SWCNT) bundles. The surfaces at the breaking ends are tip abundant and composed of SWCNTs of high quality. In addition, the radial breathing mode frequencies of the CNT tips have a downshift than the as-grown SWCNTs, due to the higher thermal stability of wider SWCNTs and the strong intertube interactions. The ends can provide emission currents of about 100μA, and a pixel based on these potential electron emitters was developed for lateral field emission displays.
Evaporation-induced assembly of biomimetic polypeptides
Authors: Keyes Joseph , Junkin Michael , Cappello Joseph , Wu Xiaoyi , Wong Pak Kin
Published: July 2008

We report an evaporation assisted plasma lithography (EAPL) process for guided self-assembly of a biomimetic silk-elastinlike protein (SELP). We demonstrate the formation of SELP structures from millimeter to submicrometer range on plasma-treatment surface templates during an evaporation-induced self-assembly process. The self-assembly processes at different humidities and droplet volumes were investigated. The process occurs efficiently in a window of optimized operating conditions found to be at 70% relative humidity and 8μl volume of SELP solution. The EAPL approach provides a useful technique for the realization of functional devices and systems using these biomimetic materials.
Cubic zirconia as a dynamic compression window
Authors: Dolan D. H. , Ao T.
Published: July 2008

Symmetric impact experiments were used to characterize the elastic response of ⟨100⟩ cubic zirconia crystals under shock wave compression. Elastic response was determined from the apparent velocity structure upon free surface release and the preservation of light passing through the compressed sample. The Hugoniot and window correction were determined below 9GPa, and the estimated elastic limit was found to be near 10GPa. These results indicate that cubic zirconia may serve as a useful alternate to sapphire in dynamic compression experiments.
Orientation of H platelets under local stress in Si
Authors: Reboh S. , Beaufort M. F. , Barbot J. F. , Grilhé J. , Fichtner P. F. P.
Published: July 2008

Hydrogen is implanted into (001) silicon under the strain field of previously formed overpressurized helium plates. Upon thermal annealing, the hydrogen atoms precipitate into platelet structures oriented within specific {111} or {001} variant determined through the local symmetry of the strain. The behavior is understood in terms of elastic interactions and is described via energy minimization calculations, predicting the formation and distribution of each platelet orientation variant. Our results demonstrate the concept that sublocal organized arrangements of precipitates can be obtained within nanosize domains using local strain fields.
Probing quantum confinement of single-walled carbon nanotubes by resonant soft-x-ray emission spectroscopy
Authors: Zhong Jun , Chiou Jauwern , Dong Chungli , Song Li , Liu Chang , Xie Sishen , Cheng Huiming , Pong Way-Faung , Chang Chinglin , Chen Yangyuan , Wu Ziyu , Guo Jinghua
Published: July 2008

We report the band-structure changes near Fermi level for single-walled carbon nanotubes (SWNTs) with diameters down to 1nm from the study of soft-x-ray absorption and resonant emission spectroscopy. The observed quantum confinement of SWNTs affects both π and σ bands and bandgap through the rehybridization of π and σ orbitals. The significant changes of electronic structure are proved to be a measure for the mean diameter of the macroscopic amounts of SWNTs.
Carbon nanotube formation by laser direct writing
Authors: Wu Yu-Tsung , Su Huan-Chieh , Tsai Chung-Min , Liu Kuo-Liang , Chen Guo-Dung , Huang Ren-Hong , Yew Tri-Rung
Published: July 2008

This letter presents carbon nanotube (CNT) formation by laser direct writing using 248nm KrF excimer pulsed laser in air at room temperature, which was applied to irradiate amorphous carbon (a-C) assisted by Ni catalysts underneath for the transformation of carbon species into CNTs. The CNTs were synthesized under appropriate combination of laser energy density and a-C thickness. The growth mechanism and key parameters to determine the success of CNT formation were also discussed. The demonstration of the CNT growth by laser direct writing in air at room temperature opens an opportunity of in-position CNT formation at low temperatures.
Modulated precursor flow epitaxial growth of AlN layers on native AlN substrates by metal-organic chemical vapor deposition
Authors: Kim Hee Jin , Choi Suk , Yoo Dongwon , Ryou Jae-Hyun , Dupuis Russell D. , Dalmau R. F. , Lu P. , Sitar Z.
Published: July 2008

We have investigated the growth of AlN layers on bulk AlN substrates by modulated precursor flow epitaxial growth using metal-organic and hydride precursors as well as by conventional metal-organic chemical vapor deposition growth. A nanopit-containing morphology was observed for an AlN layer grown by conventional growth, while atomically smooth and pit-free surface was achieved for an AlN layer created by modulated precursor flow epitaxial growth. For similar growth set-point temperatures, nanopit-free surfaces were observed for AlN layers created by conventional growth on sapphire substrates. This is believed to be due to the difference in the temperature of the growing surface, as evidenced by finite element method thermal profiling and the morphology change of the AlN layer with decreasing temperature observed for growth of AlN on sapphire substrates. The AlN layers grown by modulated precursor flow epitaxial growth on the AlN bulk substrates also have excellent crystalline qualities with narrow x-ray rocking curve peak linewidths of 36 and 61arcsec for the (002) and (102) diffraction conditions, respectively.
(Zr,Hf)Co(Sb,Sn) half-Heusler phases as high-temperature (>700°C) p-type thermoelectric materials
Authors: Culp Slade R. , Simonson J. W. , Poon S. Joseph , Ponnambalam V. , Edwards J. , Tritt Terry M.
Published: July 2008

By substituting Sn for Sb, the potential of stable (Zr,Hf)Co(Sb,Sn) half-Heusler phases, as p-type thermoelectric materials, for high-temperature power generation has been examined. Sn concentration as much as ∼20%–30% is required to realize high power factor values. Substitution of heavier Hf, which reduces the thermal conductivity (κ) via mass fluctuation scattering, nonetheless maintains high mobility. As a result, the thermoelectric figure of merit ZT, for these not-yet-optimized materials, which we found to be ZT=0.5 at 1000K (measured) and ZT=0.6 at 1100K (extrapolated), surpasses the industry benchmark for a p-type material set by SiGe alloys.
Soluble receptor-mediated selective inhibition of VEGFR and PDGFRβ signaling during physiologic and tumor angiogenesis
Authors: Kuhnert Frank , Tam Betty Y. Y. , Sennino Barbara , Gray John T. , Yuan Jenny , Jocson Angeline , Nayak Nihar R. , Mulligan Richard C. , McDonald Donald M. , Kuo Calvin J.
Published: July 2008

The simultaneous targeting of both endothelial cells and pericytes via inhibition of VEGF receptor (VEGFR) and PDGFβ receptor (PDGFRβ) signaling, respectively, has been proposed to enhance the efficacy of antiangiogenic tumor therapy. Clinical and preclinical modeling of combined VEGFR and PDGFRβ signaling inhibition, however, has used small molecule kinase inhibitors with inherently broad substrate specificities, precluding detailed examination of this hypothesis. Here, adenoviral expression of a soluble VEGFR2/Flk1 ectodomain (Ad Flk1-Fc) in combination with a soluble ectodomain of PDGFRβ (Ad sPDGFRβ) allowed highly selective inhibition of these pathways. The activity of Ad sPDGFRβ was validated
in vitro
against PDGF-BB and
in vivo
with near-complete blockade of pericyte recruitment in the angiogenic corpus luteum, resulting in prominent hemorrhage, thus demonstrating an essential function for PDGF signaling during ovarian angiogenesis. Combination therapy with Ad PDGFRβ and submaximal doses of Ad Flk1-Fc produced modest additive antitumor effects; however, no additivity was observed with maximal VEGF inhibition in numerous s.c. models. Notably, VEGF inhibition via Ad Flk1-Fc was sufficient to strongly suppress tumor endothelial and pericyte content as well as intratumoral PDGF-B mRNA, obscuring additive Ad sPDGFRβ effects on pericytes or tumor volume. These studies using highly specific soluble receptors suggest that additivity between VEGFR and PDGFRβ inhibition depends on the strength of VEGF blockade and appears minimal under conditions of maximal VEGF antagonism.
Listeria monocytogenes
multidrug resistance transporters activate a cytosolic surveillance pathway of innate immunity
Authors: Crimmins Gregory T. , Herskovits Anat A. , Rehder Kai , Sivick Kelsey E. , Lauer Peter , Dubensky Thomas W. , Portnoy Daniel A.
Published: July 2008

To gain insight into the interaction of intracellular pathogens with host innate immune pathways, we performed an unbiased genetic screen of
Listeria monocytogenes
mutants that induced an enhanced or diminished host innate immune response. Here, we show that the major facilitator superfamily of bacterial multidrug resistance transporters (MDRs) controlled the magnitude of a host cytosolic surveillance pathway, leading to the production of several cytokines, including type I IFN. Mutations mapping to repressors of MDRs resulted in ectopic expression of their cognate transporters, leading to host responses that were increased up to 20-fold over wild-type bacteria, and a 20-fold decrease in bacterial growth
in vivo
. Mutation of one of the MDRs, MdrM, led to a 3-fold reduction in the IFN-β response to
L. monocytogenes
infection, indicating a pivotal role for MdrM in activation of the host cytosolic surveillance system. Bacterial MDRs had previously been associated with resistance to antibiotics and other toxic compounds. This report links bacterial MDRs and host immunity. Understanding the mechanisms through which live pathogens activate innate immune signaling pathways should lead to the discovery of adjuvants, vaccines, and perhaps new classes of therapeutics. Indeed, we show that the mutants identified in this screen induced vastly altered type I IFN response
in vivo
as well.
Interaction of nitric oxide with a functional model of cytochrome
c
oxidase
Authors: Collman James P. , Dey Abhishek , Decreau Richard A. , Yang Ying , Hosseini Ali , Solomon Edward I. , Eberspacher Todd A.
Published: July 2008

Cytochrome
c
oxidase (CcO) is a multimetallic enzyme that carries out the reduction of O
2
to H
2
O and is essential to respiration, providing the energy that powers all aerobic organisms by generating heat and forming ATP. The oxygen-binding heme a
3
should be subject to fatal inhibition by chemicals that could compete with O
2
binding. Near the CcO active site is another enzyme, NO synthase, which produces the gaseous hormone NO. NO can strongly bind to heme a
3
, thus inhibiting respiration. However, this disaster does not occur. Using functional models for the CcO active site, we show how NO inhibition is avoided; in fact, it is found that NO can protect the respiratory enzyme from other inhibitors such as cyanide, a classic poison.
Impact of Hydrogen Peroxide Vapor Room Decontamination onClostridium difficileEnvironmental Contamination and Transmission in a Healthcare Setting
Authors: Boyce John M. , Havill Nancy L. , Otter Jonathan A. , McDonald L. Clifford , Adams Nicholas M. T. , Cooper Timothea , Thompson Angela , Wiggs Lois , Killgore George , Tauman Allison , Noble-Wang Judith
Published: July 2008

Objective.

To determine whether hydrogen peroxide vapor (HPV) decontamination can reduce environmental contamination with and nosocomial transmission ofClostridium difficile.

Design.

A prospective before-after intervention study.

Setting.

A hospital affected by an epidemic strain ofC. difficile.

Intervention.

Intensive HPV decontamination of 5 high-incidence wards followed by hospital-wide decontamination of rooms vacated by patients withC. difficile-associated disease (CDAD). The preintervention period was June 2004 through March 2005, and the intervention period was June 2005 through March 2006.

Results.

Eleven (25.6%) of 43 cultures of samples collected by sponge from surfaces before HPV decontamination yieldedC. difficile,compared with 0 of 37 cultures of samples obtained after HPV decontamination (P< .001). On 5 high-incidence wards, the incidence of nosocomial CDAD was significantly lower during the intervention period than during the preintervention period (1.28 vs 2.28 cases per 1,000 patient-days;P= .047). The hospital-wide CDAD incidence was lower during the intervention period than during the preintervention period (0.84 vs 1.36 cases per 1,000 patient-days;P= .26). In an analysis limited to months in which the epidemic strain was present during both the preintervention and the intervention periods, CDAD incidence was significandy lower during the intervention period than during the preintervention period (0.88 vs 1.89 cases per 1,000 patient-days;P= .047).

Conclusions.

HPV decontamination was efficacious in eradicating C.difficilefrom contaminated surfaces. Further studies of the impact of HPV decontamination on nosocomial transmission ofC. difficileare warranted.
Caenorhabditis elegansTeneurin,ten-1, Is Required for Gonadal and Pharyngeal Basement Membrane Integrity and Acts Redundantly with Integrinina-1and Dystroglycandgn-1
Authors: Trzebiatowska Agnieszka , Topf Ulrike , Sauder Ursula , Drabikowski Krzysztof , Chiquet-Ehrismann Ruth
Published: July 2008

The Caenorhabditis elegans teneurin ortholog, ten-1, plays an important role in gonad and pharynx development. We found that lack of TEN-1 does not affect germline proliferation but leads to local basement membrane deficiency and early gonad disruption. Teneurin is expressed in the somatic precursor cells of the gonad that appear to be crucial for gonad epithelialization and basement membrane integrity. Ten-1 null mutants also arrest as L1 larvae with malformed pharynges and disorganized pharyngeal basement membranes. The pleiotropic phenotype of ten-1 mutant worms is similar to defects found in basement membrane receptor mutants ina-1 and dgn-1 as well as in the mutants of the extracellular matrix component laminin, epi-1. We show that the ten-1 mutation is synthetic lethal with mutations of genes encoding basement membrane components and receptors due to pharyngeal or hypodermal defects. This indicates that TEN-1 could act redundantly with integrin INA-1, dystroglycan DGN-1, and laminin EPI-1 in C. elegans development. Moreover, ten-1 deletion sensitizes worms to loss of nidogen nid-1 causing a pharynx unattached phenotype in ten-1;nid-1 double mutants. We conclude that TEN-1 is important for basement membrane maintenance and/or adhesion in particular organs and affects the function of somatic gonad precursor cells.
Consequences of Individual N-glycan Deletions and of Proteasomal Inhibition on Secretion of Active BACE
Authors: Vanoni Omar , Paganetti Paolo , Molinari Maurizio
Published: July 2008

BACE is an aspartic protease involved in the production of a toxic peptide accumulating in the brain of Alzheimer's disease patients. After attainment of the native structure in the endoplasmic reticulum (ER), BACE is released into the secretory pathway. To better understand the mechanisms regulating protein biogenesis in the mammalian ER, we determined the fate of five variants of soluble BACE with 4, 3, 2, 1, or 0 N-linked glycans. The number of N-glycans displayed on BACE correlated directly with folding and secretion rates and with the yield of active BACE harvested from the cell culture media. Addition of a single N-glycan was sufficient to recruit the calnexin chaperone system and/or for oligosaccharide de-glucosylation by the ER-resident α-glucosidase II. Addition of 1–4 N-glycans progressively enhanced the dissociation rate from BiP and reduced the propensity of newly synthesized BACE to enter aberrant soluble and insoluble aggregates. Finally, inhibition of the proteasome increased the yield of active BACE. This shows that active protein normally targeted for destruction can be diverted for secretion, as if for BACE the quality control system would be acting too stringently in the ER lumen, thus causing loss of functional polypeptides.
Translationally Repressed mRNA Transiently Cycles through Stress Granules during Stress
Authors: Mollet Stephanie , Cougot Nicolas , Wilczynska Ania , Dautry François , Kress Michel , Bertrand Edouard , Weil Dominique
Published: July 2008

In mammals, repression of translation during stress is associated with the assembly of stress granules in the cytoplasm, which contain a fraction of arrested mRNA and have been proposed to play a role in their storage. Because physical contacts are seen with GW bodies, which contain the mRNA degradation machinery, stress granules could also target arrested mRNA to degradation. Here we show that contacts between stress granules and GW bodies appear during stress-granule assembly and not after a movement of the two preassembled structures. Despite this close proximity, the GW body proteins, which in some conditions relocalize in stress granules, come from cytosol rather than from adjacent GW bodies. It was previously reported that several proteins actively traffic in and out of stress granules. Here we investigated the behavior of mRNAs. Their residence time in stress granules is brief, on the order of a minute, although stress granules persist over a few hours after stress relief. This short transit reflects rapid return to cytosol, rather than transfer to GW bodies for degradation. Accordingly, most arrested mRNAs are located outside stress granules. Overall, these kinetic data do not support a direct role of stress granules neither as storage site nor as intermediate location before degradation.
BioBayes: A software package for Bayesian inference in systems biology
Authors: Vyshemirsky Vladislav , Girolami Mark
Published: July 2008

Motivation: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values of kinetic parameters, about the general structure of the model and about the behaviour of biochemical species which cannot be observed directly. The methods of Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions. We present a software package for applying the Bayesian inferential methodology to problems in systems biology.

Results: Described herein is a software package, BioBayes, which provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package is extensible allowing additional modules to be included by developers. There are no other such packages available which provide this functionality.

Availability:  http://www.dcs.gla.ac.uk/BioBayes/

Contact:  vvv@dcs.gla.ac.uk
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
Authors: Ji Shuiwang , Sun Liang , Jin Rong , Kumar Sudhir , Ye Jieping
Published: July 2008

Motivation: Regulation of gene expression in space and time directs its localization to a specific subset of cells during development. Systematic determination of the spatiotemporal dynamics of gene expression plays an important role in understanding the regulatory networks driving development. An atlas for the gene expression patterns of fruit fly Drosophila melanogaster has been created by whole-mount in situ hybridization, and it documents the dynamic changes of gene expression pattern during Drosophila embryogenesis. The spatial and temporal patterns of gene expression are integrated by anatomical terms from a controlled vocabulary linking together intermediate tissues developed from one another. Currently, the terms are assigned to patterns manually. However, the number of patterns generated by high-throughput in situ hybridization is rapidly increasing. It is, therefore, tempting to approach this problem by employing computational methods.

Results: In this article, we present a novel computational framework for annotating gene expression patterns using a controlled vocabulary. In the currently available high-throughput data, annotation terms are assigned to groups of patterns rather than to individual images. We propose to extract invariant features from images, and construct pyramid match kernels to measure the similarity between sets of patterns. To exploit the complementary information conveyed by different features and incorporate the correlation among patterns sharing common structures, we propose efficient convex formulations to integrate the kernels derived from various features. The proposed framework is evaluated by comparing its annotation with that of human curators, and promising performance in terms of F1 score has been reported.

Contact: jieping.ye@asu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.