bluuebunny/crossref_metadata_2025 huggingface dataset:
Luminophore application method of anodized aluminum pressure sensitive paint as a fast responding global pressure sensor
Authors: Sakaue Hirotaka
Published: July 2005

Luminophore application studies of dipping deposition method on anodized aluminum pressure sensitive paint (AA-PSP) are presented. Studies include the solvent dependency on the application, and the steady-state and unsteady-state characterizations, such as the luminescent signal level, pressure sensitivity, and response time. Solvents were varied by their polarity index. It is found that the solvent in the dipping deposition greatly influences the luminophore application onto anodized aluminum, the luminescent signal level, and the pressure sensitivity. The maximum signal level is obtained from acetone as a solvent. However, dichloromethane gives the highest at low pressure region below 5kPa. The maximum pressure sensitivity of 0.62 is obtained from dichloromethane as a solvent. Solvent in the dipping deposition affects the response time. However, its effect is within the 10% of thickness uncertainty of AA-PSP. At 10μm thickness of AA-PSP, its response time is characterized as 35μs at 90% pressure rise to a step change of pressure.
Design of a simple low cost tethersonde data acquisition system for meteorological measurements
Authors: John Thomas , Garg S. C. , Maini H. K. , Chaunal D. S. , Yadav V. S.
Published: July 2005

A tethersonde instrument for vertical sounding in the lowest height region of the atmosphere designed using commercially available solid state sensors is presented. This instrumentation which was developed for high-resolution measurements of the vertical profiles of atmospheric temperature, humidity, and pressure to study the evolution of radiation fog in winter over Delhi, measures the pressure (800–1100milli-bar), temperature (0–35°C), and relative humidity (0–100% RH) and includes an eight-channel 12bit data acquisition unit and a low-power digital, FM telemetry system operating at 173MHz and uses a PC printer port connection for real-time data logging and operates from a single 9V supply. It is capable of providing data to high resolutions of better than 0.01°C for temperature, 0.07mb for pressure, 0.1% for the relative humidity, and the system has a response time of ∼50s. The sonde can accommodate up to six different sensors according to sounding requirements. The data are serially streamed into the PC and the identification of data from the different sensors is accomplished by using a sync word which is included as a part of the data stream. The sonde has been flown quite successfully a number of times and the flights made thus far have shown excellent performance. The design implementation facilitates easy recalibrations of the individual sensors and their replacement upon failure.
Microscopic four-point atomic force microscope probe technique for local electrical conductivity measurement
Authors: Ju Yang , Ju Bing-Feng , Saka Masumi
Published: July 2005

A micro-four-point probe technique for local electrical conductivity measurement is presented. An atomic force microscope (AFM) probe was fabricated into four parallel electrodes isolated from each other. Electrodes separated by a distance as small as 1.0μm were used to perform the current and electrical potential measurements. This technique is a combination of the principles of the four-point probe method and standard AFM. The equipment is capable of simultaneously measuring both surface topography and local electrical conductivity. Experiments show the microprobe to be mechanically flexible and robust. The repeatable conductivity measurement on the submicron surface of thin aluminum and indium tin oxide films demonstrates the capability of the equipment and its possible extension to characterize microdevices and samples.
Low temperature fluorescence thermometer application of long afterglow phosphorescent SrAl12O19:Eu2+,Dy3+ crystals
Authors: Katsumata T. , Kohno Y. , Kubo H. , Komuro S. , Morikawa T.
Published: July 2005

Photoluminescence from long afterglow phosphorescent SrAl12O19:Eu2+,Dy3+ phosphor crystals have been studied for a fluorescence thermometer at a temperature lower than 200K. Broadband emissions peaking at λ=404 and 519nm are observed from the crystals at room temperature. The λ=519nm emission is strongly coupled with hole traps generated by the auxiliary activator, which dominates long afterglow phosphorescence from the crystals. The lifetime of the λ=519nm emission was, therefore, much longer than that at λ=404nm. The intensity of the λ=404nm emission decreases with decreasing temperature and it also decreases with increasing in the intensity of λ=371nm emissions due to P7∕26-S7∕28 transition. The intensity of λ=371nm emissions is found to be extremely sensitive to the temperature below 200K. The peak intensity ratio between λ=371nm emissions and the λ=404nm emission is effective for the highly sensitive measurement of a temperature lower than 200K.
Fast high-voltage amplifiers for driving electro-optic modulators
Authors: Müller Holger
Published: July 2005

We describe five high-voltage (60 to 550 V peak to peak), high-speed (1–300 ns risetime; 1.3–300 MHz bandwidth) linear amplifiers for driving capacitive or resistive loads such as electro-optic modulators. The amplifiers use bipolar transistors in various topologies. Two used electron tubes to overcome the speed limitations of high-voltage semiconductors. All amplifiers have been built. Measured performance data is given for each.
Hybrid Monte Carlo implementation of the Fourier path integral algorithm
Authors: Chakravarty Charusita
Published: July 2005

This paper formulates a hybrid Monte Carlo implementation of the Fourier path integral (FPI-HMC) approach with partial averaging. Such a hybrid Monte Carlo approach allows one to generate collective moves through configuration space using molecular dynamics while retaining the computational advantages associated with the Fourier path integral Monte Carlo method. In comparison with the earlier Metropolis Monte Carlo implementations of the FPI algorithm, the present HMC method is shown to be significantly more efficient for quantum Lennard-Jones solids and suggests that such algorithms may prove useful for efficient simulations of a range of atomic and molecular systems.
Acoustic excitation of stationary streamwise structures in a separation region on a straight wing
Authors: Brylyakov A. P. , Zanin B. Yu. , Kovrizhina V. N. , Zharkova G. M.
Published: July 2005

An effect of sound on the flow with a transitional separation bubble on a wing model at low subsonic freestream velocity was experimentally investigated. Using hot-wire measurements and liquid-crystal visualization, stationary streamwise structures were found to appear in the reattachment region. Quantitative characteristics of the disturbances upcoming during the breakdown to turbulence were measured.
Theoretical investigation upon Kármán constant and relevance to drag reduction
Authors: Yoshizawa Akira , Matsuo Yuichi , Abe Hiroyuki
Published: July 2005

The Kármán constant in the logarithmic-velocity profile is investigated in a theoretical manner. In the layer of nearly constant shear stress abbreviated as the constant-stress layer, a shifted logarithmic-velocity profile occurs, which is reduced to the usual profile with the aid of the concept of effective Kármán coefficient. The coefficient is linked to the thickness of the viscosity-dominated layer and depends on location and Reynolds number. At a fixed Reynolds number, the coefficient tends to a constant value at the outer edge of the constant-stress layer, whose infinite-Reynolds-number limit corresponds to the Kármán constant. In the present framework, thickening of the buffer layer leads to the decrease in the coefficient or the increase in the volume flow. This finding is discussed in light of the relationship of the buffer-layer thickening with the drag reduction by polymer additives.
Energy distributions of gallium nanoclusters
Authors: Poland Douglas
Published: July 2005

Starting with the heat-capacity data of Breaux et al., [J. Am. Chem. Soc. 126, 8629 (2004)] we use the maximum-entropy method to calculate energy distribution functions for gallium-ion nanoclusters over a wide temperature range (100–1050 K). Specifically, we calculate energy distributions for clusters containing n=39 and n=45 gallium atoms. For the case of n=39 clusters the energy distribution gets systematically broader as a function of temperature with no indication of any marked structural change in the cluster. On the other hand, the energy distribution for the n=45 cluster first gets broader as a function of temperature but then gets narrower again as the temperature is further increased, indicating that there is some kind of structural transition taking place in this cluster species.
A rotatable flat coil for static solid-state nuclear magnetic resonance spectroscopy
Authors: Rainey Jan K. , DeVries Jeffrey S. , Sykes Brian D.
Published: July 2005

A holder allowing rotation of a flat coil relative to the static magnetic field (B0) of a nuclear magnetic resonance (NMR) spectrometer over the range of orientations from parallel to perpendicular has been built and incorporated into a two-channel wide line static solid-state NMR probe. Radiofrequency induction by the coil is perpendicular to B0 for all rotational angles. Such a coil holder provides ready access to an additional directional variable for experiments exploiting sample orientation such as those using planar-supported oriented phospholipid bilayers. Rotation of the flat coil is demonstrated using P31 NMR of oriented phospholipid and peptide bilayers sandwiched between pairs of mica substrates.
Small amplitude oscillations of a thin beam immersed in a viscous fluid near a solid surface
Authors: Green Christopher P. , Sader John E.
Published: July 2005

The hydrodynamic loading on a solid body moving in a viscous fluid can be strongly affected by its proximity to a surface. In this article, we calculate the hydrodynamic load on an infinitely long rigid beam of zero thickness that is undergoing small amplitude oscillations. The presence of a solid surface an arbitrary distance from the beam is rigorously accounted for using a boundary integral formulation.
Interface magnetization profiling by x-ray magnetometry of marker impurities on Fe∕GaAs(001)-(4×6)
Authors: Giovanelli L. , Panaccione G. , Rossi G. , Fabrizioli M. , Tian C. S. , Gastelois P. L. , Fujii J. , Back C. H.
Published: July 2005

We use Co atoms dispersed in a ferromagnetic Fe film as a magnetic marker material to probe the magnetic properties of the Fe film grown epitaxially on GaAs(001)-(4×6). X-ray magnetic circular dichroism on CoL2,3 edges has been used to perform, in a Mössbauer-like experiment, a layer-dependent analysis. We find an enhancement of the Co orbital magnetic moment near the interface with the GaAs substrate, as well as a decrease of the spin magnetic moment when approaching the interface and at the surface of the Fe film.
Linear instability analysis of an electrified coaxial jet
Authors: Li Fang , Yin Xie-Yuan , Yin Xie-Zhen
Published: July 2005

A temporal linear instability analysis of an electrified coaxial jet inside a coaxial electrode is carried out in this paper. The analytic dispersion equation is derived. The characteristic of the temporal instability is investigated and effects of the parameters, including the dimensionless electrostatic force, the dimensionless velocity difference, the density ratio, the inner and the outer diameter ratios, and the Weber numbers, are discussed systematically. The axisymmetric and the helical modes are both considered. Two independent unstable modes, mode 1 and mode 2, are identified. Among all the parameters the dimensionless electrostatic force has remarkable influence on mode 1. It can change mode 1 from the Rayleigh regime to the wind induced regime, and to the atomization regime by increasing the electric-field intensity. Nevertheless, the dimensionless electrostatic force has no apparent effect on mode 2. The behaviors of mode 2 resemble those of a coaxial jet not having electric field. The surface tensions on the inner and the outer interfaces induce instability of the inner and the outer interfaces in the region of long wavelength and suppress the growth rate in the region of short wavelength.
200 mm wafer-scale substrate transfer of 0.13μmCu∕low-k (Black Diamond™) dual-damascene interconnection to glass substrates
Authors: Teh W. H. , Kumar R. , Kwong D. L.
Published: July 2005

We report a low-temperature (350 °C) pulsed-voltage anodic bonding followed by grind/etch-back method for 200 mm wafer-scale substrate transfer of 0.13μmCu∕low-k (Black Diamond™) dual-damascene interconnection to glass substrates. Standard back-end-of-line (BEOL) 3kÅSiN∕3kÅ undoped Si glass passivating films were used as buffer layers between donor wafer and glass wafer to facilitate the bonding. We demonstrate removal of the silicon bulk layer to leave behind a transparent (∼1.25μm thick) 0.13μm BEOL circuit on a 1-mm-thick glass wafer. The quality of the mechanical and electrical integrity of the deep submicron BEOL circuit is confirmed by focused ion beam-scanning electron microscopy microscopy and I-V characterization on via chain test structures. This technique has potential applications for bioelectronics and optoelectronics integration schemes.
Low-field magnetodielectric effect in terbium iron garnets
Authors: Hur N. , Park S. , Guha S. , Borissov A. , Kiryukhin V. , Cheong S.-W.
Published: July 2005

Materials exhibiting low-field magnetoelectric and magnetodielectric (MD) effects are necessary for utilization of these effects in multifunctional devices. Since large magnetic fields (H) or electric fields (E) are required to produce any significant effect in existing single-phase magnetoelectrics, recent efforts have been largely devoted to the investigation of laminates or thin film composites made of piezoelectric and magnetostrictive materials. In this work, we report large MD effect Δε∕ε∼3% at remarkably low fields (H<2kOe) in a single-phase material, terbium iron garnet. Our results suggest a route towards future applications of the MD effect in advanced devices.
Quantifying the effect of metal-rich precipitates on minority carrier diffusion length in multicrystalline silicon using synchrotron-based spectrally resolved x-ray beam-induced current
Authors: Buonassisi T. , Istratov A. A. , Pickett M. D. , Marcus M. A. , Hahn G. , Riepe S. , Isenberg J. , Warta W. , Willeke G. , Ciszek T. F. , Weber E. R.
Published: July 2005

Synchrotron-based, spectrally resolved x-ray beam-induced current (SR-XBIC) is introduced as a technique to locally measure the minority carrier diffusion length in semiconductor devices. Equivalence with well-established diffusion length measurement techniques is demonstrated. The strength of SR-XBIC is that it can be combined in situ with other synchrotron-based analytical techniques, such as x-ray fluorescence microscopy (μ-XRF) and x-ray absorption microspectroscopy (μ-XAS), yielding information about the distribution, elemental composition, chemical nature, and effect on minority carrier diffusion length of individual transition metal species in multicrystalline silicon. SR-XBIC, μ-XRF, and μ-XAS measurements were performed on intentionally contaminated multicrystalline silicon, revealing a strong correlation between local concentrations of copper and nickel silicide precipitates and a decrease of minority carrier diffusion length. In addition, the reduction of minority carrier diffusion length due to submicron-sized Cu3Si and NiSi2 precipitates could be decoupled from the influence of homogeneously distributed nanoprecipitates and point defects.
Frequency-dependent optical constants and conductivities of hydrogen-functionalized single-walled carbon nanotubes
Authors: Kang Chul , Maeng In Hee , Oh Seung Jae , Son Joo-Hiuk , Jeon Tae-In , An Kay Hyeok , Lim Seong Chu , Lee Young Hee
Published: July 2005

The frequency-dependent optical constants and electrical conductivities of hydrogen-functionalized single-walled carbon nanotubes (SWNTs) have been measured from the 0.2 to 1.5 THz region using a terahertz time domain spectroscopy. The indices of refraction and electrical conductivities of the sample after hydrogen functionalization were smaller than those of the sample before hydrogen functionalization. The experimental results were fitted using the Maxwell–Garnett model, and a reduction of plasma frequency was observed. This can be attributed to the fact that the hydrogen functionalization has reduced the number of free carriers with the bonding change from sp2 to sp3.
Raman studies of Ge-promoted stress modulation in 3C–SiC grown on Si(111)
Authors: Zgheib Ch. , McNeil L. E. , Kazan M. , Masri P. , Morales F. M. , Ambacher O. , Pezoldt J.
Published: July 2005

We present a study of the stress state in cubic silicon carbide (3C–SiC) thin films (120 and 300 nm) grown by solid-source molecular-beam epitaxy (SSMBE) on Si(111) substrates modified by the deposition of germanium prior to the carbonization of Si. μ-Raman measurements were used to determine the residual stress existing in the 3C–SiC layers. The stress is found to decrease linearly with increasing Ge quantity but with different strength depending on the 3C–SiC thickness deposited after the introduction of Ge. Based on secondary ions mass spectroscopy (SIMS) and transmission electron microscopy (TEM) analyses it is suggested that the Ge introduced prior to the carbonization step remains in the near-interface region and reduces the Si outdiffusion, which further reduces the stress state of the 3C–SiC layers.
Ballistic bit addressing in a magnetic memory cell array
Authors: Schumacher H. W.
Published: July 2005

A ringing free bit addressing scheme for magnetic memories like magnetic random access memory (MRAM) is proposed. As in standard MRAM addressing schemes the switching of a selected cell is obtained by the combination of two half-select field pulses. Numerical solutions of a single spin model of an MRAM cell show that the pulse parameters can be chosen such that the application of the half select pulse induces a full precessional turn of the magnetization (no switch) whereas the superposition of two half select pulses induces a half precessional turn (switch). With well adapted pulse parameters both full-select and half-select switching occurs on ballistic trajectories characterized by the absence of ringing after magnetic pulse decay. Such ballistic bit addressing allows ultrahigh MRAM clock rates.
Very wide bandwidth hot electron bolometer heterodyne detectors based on single-walled carbon nanotubes
Authors: Yngvesson K. S.
Published: July 2005

A hot electron bolometer heterodyne detector is proposed that has the potential for achieving intermediate frequency bandwidths of several hundred GHz. The concept relies on experimentally measured ballistic∕quasiballistic transport properties of single-wall carbon nanotubes and the measured temperature dependence of the resistance of such tubes. Receiver noise temperatures of a few thousand Kelvin, and local oscillator powers of 1μW or less are estimated.
Light-induced resonant transmittance through a gold film
Authors: Smolyaninov Igor I. , Hung Yu-Ju , Davis Christopher C.
Published: July 2005

We report the experimental observation of photoinduced resonant transmission of light through a gold film deposited on a chalcogenide glass surface. This effect is caused by the formation of a photoinduced diffraction grating in the chalcogenide glass near the gold film surface by an optical pump beam. The transmittance of a probe beam is resonantly enhanced due to grating-induced coupling to surface electromagnetic excitations on the gold film surface. This observation demonstrates the feasibility of all-optical signal processing using the extraordinary light transmission of thin metal films.
Low-frequency noise and tunneling magnetoresistance in Fe(110)∕MgO(111)∕Fe(110) epitaxial magnetic tunnel junctions
Authors: Guerrero R. , Aliev F. G. , Villar R. , Hauch J. , Fraune M. , Güntherodt G. , Rott K. , Brückl H. , Reiss G.
Published: July 2005

We report on tunneling magnetoresistance (TMR), current–voltage (I–V) characteristics and low-frequency noise in epitaxially grown Fe(110)∕MgO(111)∕Fe(110) magnetic tunnel junctions (MTJs) with dimensions from 2×2 to 20×20μm2. The evaluated MgO energy barrier (0.50±0.08eV), the barrier width (13.1±0.5Å) as well as the resistance times area product (7±1MΩμm2) show relatively small variation, confirming a high quality epitaxy and uniformity of all MTJs studied. The noise power, though exhibiting large variation, was observed to be roughly anticorrelated with the TMR. Surprisingly, for the largest junctions we observed a strong enhancement of the normalized low-frequency noise in the antiparallel magnetic configuration. This behavior could be related to an interplay between the magnetic state and the local barrier defects structure of the epitaxial MTJs.
Extraction of a nearly monoenergetic ion beam using a pulsed plasma
Authors: Xu Lin , Economou Demetre J. , Donnelly Vincent M. , Ruchhoeft Paul
Published: July 2005

A nearly monoenergetic ion beam was extracted from a capacitively coupled pulsed Ar plasma. The electron temperature decayed rapidly in the afterglow, resulting in uniform plasma potential, and minimal energy spread for ions extracted in the afterglow. Ion energy was controlled by a dc bias on a ring electrode surrounding the plasma. Langmuir probe measurements indicated that this bias simply raised the plasma potential without heating the electrons in the afterglow. A rejection grid downstream of the plasma allowed ions to pass only during a selected time window in the afterglow. The energy spread was 3.4 eV full width at half maximum for a peak ion beam energy of 102.0 eV. This energy spread is about an order of magnitude narrower than the beam extracted from the continuous plasma.
Asymmetric quantum-confined Stark effects of hierarchical self-assembly of GaAs∕AlxGa1−xAs quantum dots
Authors: Li Shu-Shen , Xia Jian-Bai
Published: July 2005

Quantum-confined Stark effects in GaAs∕AlxGa1−xAs self-assembled quantum dots are investigated theoretically in the framework of effective-mass envelope function theory. The electron and hole energy levels and optical transition energies are calculated in the presence of an electric field in different directions. In our calculation, the effect of finite offset, valence-band mixing, the effects due to the different effective masses of electrons and holes in different regions, and the real quantum dot structures are all taken into account. The results show that the electron and hole energy levels and the optical transition energies can cause blueshifts when the electric field is applied along the opposite to the growth direction. Our calculated results are useful for the application of hierarchical self-assembly of GaAs∕AlxGa1−xAs quantum dots to photoelectric devices.
Buckling properties of carbon nanotube bundles
Authors: Liew K. M. , Wong C. H. , Tan M. J.
Published: July 2005

In the study described herein, we observed the buckling behavior of carbon nanotube (CNT) bundles under axial compression using molecular dynamics (MD) simulations. We found that the critical buckling loads of CNT bundles are much higher than that of an individual single-walled carbon nanotube (SWCNT). The addition of SWCNTs into a CNT bundle results in as much as a fivefold increase in its buckling load. The long-range van der Waals interactions also improve the overall rigidity of the CNT bundles. The larger the CNT bundle, the greater the significance of the van der Waals interactions. We also found that the buckling load of a CNT bundle is directly proportional to that of a SWCNT.
Cross-sectional Raman spectra of InN epifilms
Authors: Chen J. W. , Chen Y. F. , Lu H. , Schaff W. J.
Published: July 2005

Cross-sectional Raman spectroscopy was performed on InN epifilms. We found direct evidence for the existence of residual strain along the growth direction of the InN films. This result is very useful for the understanding of the depth dependence of the physical properties. We also found that cross-sectional Raman spectroscopy can be used to study certain vibration modes that are normally not observable in the normal surface Raman configuration.
Aluminum gallium nitride ultraviolet photodiodes with buried p-layer structure
Authors: Sheu J. K. , Lee M. L. , Lai W. C.
Published: July 2005

An Al0.21Ga0.79N∕GaNp-i-n photodiode was designed with a heavily doped buried p+-GaN layer associating an n++-In0.3Ga0.7N layer to form a p+∕n++ tunneling junction under the Al0.21Ga0.79p-i-n heterostructure. In contrast to conventional AlGaN-based p-i-n photodiodes, the inverted devices can have a low-resistivity n-type AlGaN top contact layer with a typical zero-bias peak responsivity of 0.1A∕W at 315 nm corresponding to a quantum efficiency of around 39%. The zero-bias rejection ratio was about four orders of magnitude over the ultraviolet and visible regions of the spectrum. The typical dark current of the inverted devices was below 30 pA at a reverse bias of below 1.5 V. The leakage current at a 10 V reverse bias was as high as 5 nA caused by the presence of cracks in the Al0.21Ga0.79 layers.
Many-body optical gain and intraband relaxation time of wurtzite InGaN∕GaN quantum-well lasers and comparison with experiment
Authors: Park Seoung-Hwan , Ahn Doyeol , Park E. H. , Yoo T. K. , Lee Yong-Tak
Published: July 2005

The optical gain and the intraband relaxation time of wurtzite InGaN∕GaN QW lasers are investigated theoretically considering the non-Markovian gain model with many-body effects. Gain spectra are compared with those obtained from the experiment. The calculated intraband relaxation time is about 24fs at the subband edge and gradually increases with the energy. The intraband relaxation time is shown to be nearly independent of the sheet carrier density in an investigated range. The calculated gain spectra is in good agreement with the experiment. The intraband relaxation time τin obtained from fitting with experiment is 25fs. This value agrees well with the calculated value (∼24fs) at the subband edge, for which most of optical transitions occur.
Multiple implantations into Si: Influence of the implantation sequence on ion range profiles
Authors: Posselt M. , Mäder M. , Lebedev A. , Grötzschel R.
Published: July 2005

In successive implantations of p- and∕or n-dopants, the implantation sequence may affect the ion range distributions. This is demonstrated for two consecutive implantations into the [001] channel direction: (i) 35keV B followed by 50keV As and (ii) 50keV As followed by 35keV B. The defects formed in the first implantation cause enhanced dechanneling of the subsequently implanted ions and, therefore, influence the shape of the range distributions in the second implantation step. The experimental range profiles can be reproduced very well by atomistic computer simulations that take into account damage accumulation or dynamic annealing during a single implantation step as well as the influence of the defects formed by the preceding implantation steps.
Reversible surface functionalization of carbon nanotubes for fabrication of field-effect transistors
Authors: Zhang Zhi-Bin , Cardenas Juan , Campbell Eleanor E. B. , Zhang Shi-Li
Published: July 2005

Evidence of the adsorption of sodium dodecyl sulfate (SDS) residuals on single-walled carbon nanotubes (SWNTs) is shown using x-ray photoelectron spectroscopy. The adsorption of SDS on semiconducting SWNTs (s-SWNTs) is believed to result in deposition and alignment of s-SWNTs between predefined electrode pairs using ac dielectrophoresis. However, the presence of SDS on SWNTs degrades electrical properties of the fabricated devices. Attempts at surface cleaning, aimed at removal of the SDS residuals and formation of an improved contact between the SWNTs and the metal, are described.
Chemical states and electronic structure of a HfO2∕Ge(001) interface
Authors: Seo Kang-Ill , McIntyre Paul C. , Sun Shiyu , Lee Dong-Ick , Pianetta Piero , Saraswat Krishna C.
Published: July 2005

We report the chemical bonding structure and valence band alignment at the HfO2∕Ge(001) interface by systematically probing various core level spectra as well as valence band spectra using soft x rays at the Stanford Synchrotron Radiation Laboratory. We investigated the chemical bonding changes as a function of depth through the dielectric stack by taking a series of synchrotron photoemission spectra as we etched through the HfO2 film using a dilute hydrogen fluoride solution. We found that a very nonstoichiometric GeOx layer exists at the HfO2∕Ge interface. The valence band spectra near the Fermi level in each different film structure were carefully analyzed, and as a result, the valence band offset between Ge and GeOx was determined to be ΔEv (Ge–GeOx)=2.2±0.15eV, and that between Ge and HfO2, ΔEv (Ge–HfO2)=2.7±0.15eV.
Junctional adhesion molecule-A-deficient polymorphonuclear cells show reduced diapedesis in peritonitis and heart ischemia-reperfusion injury
Authors: Corada Monica , Chimenti Stefano , Cera Maria Rosaria , Vinci Maria , Salio Monica , Fiordaliso Fabio , De Angelis Noeleen , Villa Antonello , Bossi Mario , Staszewsky Lidia I. , Vecchi Annunciata , Parazzoli Dario , Motoike Toshiyuki , Latini Roberto , Dejana Elisabetta
Published: July 2005

Junctional Adhesion Molecule-A (JAM-A) is a transmembrane adhesive protein expressed at endothelial junctions and in leukocytes. Here we report that JAM-A is required for the correct infiltration of polymorphonuclear leukocytes (PMN) into an inflamed peritoneum or in the heart upon ischemia-reperfusion injury. The defect was not observed in mice with an endothelium-restricted deficiency of the protein but was still detectable in mice transplanted with bone marrow fromJAM-A-/-donors. Microscopic examination of mesenteric and heart microvasculature ofJAM-A-/-mice showed high numbers of PMN adherent on the endothelium or entrapped between endothelial cells and the basement membrane.In vitro, in the absence ofJAM-A, PMN adhered more efficiently to endothelial cells and basement membrane proteins, and their polarized movement was strongly reduced. This paper describes a nonredundant role of JAM-A in controlling PMN diapedesis through the vessel wall.
A tool for filtering information in complex systems
Authors: Tumminello M. , Aste T. , Di Matteo T. , Mantegna R. N.
Published: July 2005

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties.
Gene targeting of VEGF-A in thymus epithelium disrupts thymus blood vessel architecture
Authors: Müller Susanna M. , Terszowski Grzegorz , Blum Carmen , Haller Corinne , Anquez Viviane , Kuschert Stephen , Carmeliet Peter , Augustin Hellmut G. , Rodewald Hans-Reimer
Published: July 2005

The thymus harbors an organ-typical dense network of branching and anastomosing blood vessels. To address the molecular basis for morphogenesis of this thymus-specific vascular pattern, we have inactivated a key vascular growth factor, VEGF-A, in thymus epithelial cells (TECs). Both
Vegf-A
alleles were deleted in TECs by a complementation strategy termed nude mouse [mutated in the transcription factor
Foxn1
(forkhead box N1)] blastocyst complementation. Injection of
Foxn1
+/+
ES cells into

Foxn1
nu/nu

blastocysts reconstituted a functional thymus. By dissecting thymus stromal cell subsets, we have defined, in addition to medullary TECs (mTECs) and cortical TECs (cTECs), another prominent stromal cell subset designated cortical mesenchymal cells (cMes). In chimeric thymi, mTECs and cTECs but not cMes were exclusively ES cell-derived. According to this distinct origin, the
Vegf-A
gene was deleted in mTECs and cTECs, whereas cMes still expressed
Vegf-A
. This genetic mosaic was associated with hypovascularization and disruption of the organ-typical network of vascular arcades. Thus, vascular growth factor production by TECs is required for normal thymus vascular architecture. These experiments provide insights into
Foxn1
-dependent and
Foxn1
-independent stromal cell development and demonstrate the value of this chimeric approach to analyzing gene function in thymus epithelium.
Two-dimensional atomic crystals
Authors: Novoselov K. S. , Jiang D. , Schedin F. , Booth T. J. , Khotkevich V. V. , Morozov S. V. , Geim A. K.
Published: July 2005

We report free-standing atomic crystals that are strictly 2D and can be viewed as individual atomic planes pulled out of bulk crystals or as unrolled single-wall nanotubes. By using micromechanical cleavage, we have prepared and studied a variety of 2D crystals including single layers of boron nitride, graphite, several dichalcogenides, and complex oxides. These atomically thin sheets (essentially gigantic 2D molecules unprotected from the immediate environment) are stable under ambient conditions, exhibit high crystal quality, and are continuous on a macroscopic scale.
The TatA component of the twin-arginine protein transport system forms channel complexes of variable diameter
Authors: Gohlke Ulrich , Pullan Lee , McDevitt Christopher A. , Porcelli Ida , de Leeuw Erik , Palmer Tracy , Saibil Helen R. , Berks Ben C.
Published: July 2005

The Tat system mediates Sec-independent transport of folded precursor proteins across the bacterial plasma membrane or the chloroplast thylakoid membrane. Tat transport involves distinct high-molecular-weight TatA and TatBC complexes. Here we report the 3D architecture of the TatA complex from
Escherichia coli
obtained by single-particle electron microscopy and random conical tilt reconstruction. TatA forms ring-shaped structures of variable diameter in which the internal channels are large enough to accommodate known Tat substrate proteins. This morphology strongly supports the proposal that TatA forms the protein-conducting channel of the Tat system. One end of the channel is closed by a lid that might gate access to the channel. On the basis of previous protease accessibility measurements, the lid is likely to be located at the cytoplasmic side of the membrane. The observed variation in TatA diameter suggests a model for Tat transport in which the number of TatA protomers changes to match the size of the channel to the size of the substrate being transported. Such dynamic close packing would provide a mechanism to maintain the membrane permeability barrier during transport.
NMR data collection and analysis protocol for high-throughput protein structure determination
Authors: Liu Gaohua , Shen Yang , Atreya Hanudatta S. , Parish David , Shao Ying , Sukumaran Dinesh K. , Xiao Rong , Yee Adelinda , Lemak Alexander , Bhattacharya Aneerban , Acton Thomas A. , Arrowsmith Cheryl H. , Montelione Gaetano T. , Szyperski Thomas
Published: July 2005

A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that allows one to capitalize on high spectrometer sensitivity: a set of five G-matrix Fourier transform NMR experiments for resonance assignment based on highly resolved 4D and 5D spectral information is acquired in conjunction with a single simultaneous 3D15N,13Caliphatic,13Caromatic-resolved [1H,1H]-NOESY spectrum providing1H-1H upper distance limit constraints. The protocol was integrated with methodology for semiautomated data analysis and used to solve eight NMR protein structures of the Northeast Structural Genomics Consortium pipeline. The molecular masses of the hypothetical target proteins ranged from 9 to 20 kDa with an average of ≈14 kDa. Between 1 and 9 days of instrument time were invested per structure, which is less than ≈10–25% of the measurement time routinely required to date with conventional approaches. The protocol presented here effectively removes data collection as a bottleneck for high-throughput solution structure determination of proteins up to at least ≈20 kDa, while concurrently providing spectra that are highly amenable to fast and robust analysis.
Avicinylation (thioesterification): A protein modification that can regulate the response to oxidative and nitrosative stress
Authors: Haridas Valsala , Kim Sung-Oog , Nishimura Goshi , Hausladen Alfred , Stamler Jonathan S. , Gutterman Jordan U.
Published: July 2005

Avicins are a recently discovered family of plant-derived terpenoid molecules that possess proapoptotic, antiinflammatory, and cytoprotective properties in mammalian cells. Previous work demonstrating that avicins can exert their effects by suppressing or activating the redox-sensitive transcription factors NF-κB and nuclear factor-erythroid 2 p45-related factor (Nrf2), respectively, has raised the idea that they may react with critical cysteine residues. To understand the molecular mechanism through which avicins regulate protein function, we examined their effects on the paradigmatic redox-responsive transcriptional activator, OxyR of
Escherichia coli
, which protects bacterial cells against oxidative and nitrosative stresses.
In vitro
transcription assays demonstrated that avicins activate OxyR and its target genes
katG
and
oxyS
in a DTT-reversible manner. In addition,
katG
-dependent hydroperoxidase I activity was enhanced in avicin-treated bacteria. Mass spectrometric analysis of activated OxyR revealed thioesterification of the critical regulatory cysteine, Cys-199, to an avicin fragment comprising the outer monoterpene side chain. Our results indicate that avicinylation can induce adaptive responses that protect cells against oxidative or nitrosative stress. More generally, transesterification may represent a previously undescribed thiol-directed posttranslational modification, which extends the code for redox regulation of protein function.
Ku86 preserves chromatin integrity in cells adapted to high NaCl
Authors: Dmitrieva Natalia I. , Celeste Arkady , Nussenzweig André , Burg Maurice B.
Published: July 2005

Cells adapted to high NaCl have many DNA breaks both in cell culture and in the renal inner medullain vivo; yet they survive, function, and even proliferate. Here, we show that Ku86 is important for maintaining chromosomal integrity despite the continued presence of DNA breaks. The Ku heterodimer is part of DNA-dependent PK (DNA-PK), a complex that contributes by nonhomologous end joining to repair of double-strand breaks. We demonstrate that cells deficient in Ku86, but not cells deficient in DNA-PKcs (the catalytic subunit of DNA-PK), are hypersensitive to high NaCl as manifested by profound inhibition of proliferation, aberrant mitosis, and increased chromosomal fragmentation. Lower eukaryotes, including the soil nematodeCaenorhabditis elegans, lack a DNA-PKcs homologue but are able to adapt to high NaCl. We show that cells ofC. elegansadapted to high NaCl have many DNA breaks, similar to the mammalian cells adapted to high NaCl. Ku86 mutantC. elegansas well asC. elegansfed with cku86 dsRNA also display hypersensitivity to high NaCl, characterized by a reduced number of progeny and prolonged generation time in high NaCl. We propose that Ku86 ameliorates the effects of high NaCl-induced DNA breaks in adapted cells by supporting alignment of the broken ends of the DNA and thus maintaining integrity of the fragmented chromatin.
Activation of β-catenin by carcinogenic
Helicobacter pylori
Authors: Franco Aime T. , Israel Dawn A. , Washington Mary K. , Krishna Uma , Fox James G. , Rogers Arlin B. , Neish Andrew S. , Collier-Hyams Lauren , Perez-Perez Guillermo I. , Hatakeyama Masanori , Whitehead Robert , Gaus Kristin , O'Brien Daniel P. , Romero-Gallo Judith , Peek Richard M.
Published: July 2005

Persistent gastritis induced by
Helicobacter pylori
is the strongest known risk factor for adenocarcinoma of the distal stomach, yet only a fraction of colonized persons ever develop gastric cancer. The
H. pylori
cytotoxin-associated gene (
cag
) pathogenicity island encodes a type IV secretion system that delivers the bacterial effector CagA into host cells after bacterial attachment, and
cag
+
strains augment gastric cancer risk. A host effector that is aberrantly activated in gastric cancer precursor lesions is β-catenin, and activation of β-catenin leads to targeted transcriptional up-regulation of genes implicated in carcinogenesis. We report that
in vivo
adaptation endowed an
H. pylori
strain with the ability to rapidly and reproducibly induce gastric dysplasia and adenocarcinoma in a rodent model of gastritis. Compared with its parental noncarcinogenic isolate, the oncogenic
H. pylori
strain selectively activates β-catenin in model gastric epithelia, which is dependent on translocation of CagA into host epithelial cells. β-Catenin nuclear accumulation is increased in gastric epithelium harvested from gerbils infected with the
H. pylori
carcinogenic strain as well as from persons carrying
cag
+
vs.
cag
-
strains or uninfected persons. These results indicate that
H. pylori
-induced dysregulation of β-catenin-dependent pathways may explain in part the augmentation in the risk of gastric cancer conferred by this pathogen.
Histology and affinity of the earliest armoured vertebrate
Authors: Sansom Ivan J , Donoghue Philip C.J , Albanesi Guillermo
Published: July 2005

Arandaspids are the earliest skeletonizing vertebrates known from articulated remains. Despite a wealth of data, their affinity remains questionable because they exhibit a random mixture of primitive and derived characteristics. We constrain the affinity of arandaspids by providing the first detailed characterization of their dermoskeleton which is revealed to be three-layered, composed of a basal laminated, cancellous middle and tubercular superficial layers. All three layers are composed of acellular bone but the superficial layer also includes dentine and enameloid, comprising the tubercles. As such, the composition of the arandaspid dermoskeleton is common to heterostracans and astraspids, supporting existing hypotheses of early vertebrate phylogeny. This emphasizes the peculiarity of existing interpretations of aranadaspid anatomy and there is need for a complete reappraisal of the existing anatomical data.
Climate change causing phase transitions of walleye pollock (Theragra chalcogramma) recruitment dynamics
Authors: Ciannelli Lorenzo , Bailey Kevin M , Chan Kung-Sik , Belgrano Andrea , Stenseth Nils Chr
Published: July 2005

In 1976 the North Pacific climate shifted, resulting in an average increase of the water temperature. In the Gulf of Alaska the climate shift was followed (i.e. early 1980s) by a gradual but dramatic increase in the abundance of groundfish species that typically prey on pre-recruitment stages of walleye pollock. In the present study we used a previously parameterized model to investigate the effect of these climate and biological changes on the recruitment dynamics of walleye pollock in the Gulf of Alaska. Simulations covered the 1970–2000 time frame and emphasized the medium-to-long temporal scale (i.e. about 5–10 years) of environmental variability. Results showed that during periods characterized by high sea surface temperature and high predation on juvenile pollock stages, recruitment variability and magnitude were below average, and recruitment control was delayed to stages older than the 0-group. Opposite dynamics (i.e. high abundance and variability, and early recruitment control) occurred during periods characterized by low temperature and predation. These results are in general agreement with empirical observations, and allowed us to formulate causal explanations for their occurrence. We interpreted the delay of recruitment control and the reduction of variability as an effect of increased constraint on the abundance of post age-0 stages, in turn imposed by high density dependence and predation mortality. On the other hand, low density-dependence and predation favoured post age-0 survival, and allowed for an unconstrained link between larval and recruitment abundance. Our findings demonstrate that the dominant mechanisms of pollock survival change over contrasting climate regimes. Such changes may in turn cause a phase transition of recruitment dynamics with profound implications for the management of the entire stock.
Spiders that decorate their webs at higher frequency intercept more prey and grow faster
Authors: Li Daiqin
Published: July 2005

Many orb-weaving spiders decorate their webs with extra, bright white, ultraviolet light reflecting silk. Previous studies suggest that these decorations increase a spider's foraging efficiency by improving web attractiveness, which is known as the prey-attraction hypothesis. One assumption of this hypothesis is that individuals which decorate their webs at a higher frequency are expected to have a higher growth rate. Using a decoration-building orb-weaving spider,
Argiope versicolor
, I show a strong positive relationship between the growth rate in terms of weight gain and the frequency of decoration-building, as well as the rate of insect interception. This is the first study to reveal a fitness consequence of decorating behaviour in spiders.
Do femaleDrosophila melanogasteradaptively bias offspring sex ratios in relation to the age of their mate?
Authors: Long Tristan A.F , Pischedda Alison
Published: July 2005

Modification of offspring sex ratios in response to parental quality is predicted when the long-term fitness returns of sons and daughters differ. One factor that may influence a mother's sex allocation decision is the quality (or attractiveness) of her mate. We investigated whether the sex ratios of offspring produced by femaleDrosophila melanogasterare biased with respect to the age of the males to which they are mated, and whether there is an adaptive basis for this phenomenon. We found that females mated to old males (13 d post-eclosion) initially produced a greater proportion of daughters than did females mated to young males (1 d post-eclosion). This pattern does not appear to be due to a systematic difference in the numbers or mortality of the X- and Y-bearing sperm originating from old and young fathers, as the overall sex ratios of all offspring produced from a single copulation did not differ between broods fathered by the two types of males. The sons of older males fared worse in competitive mating assays than did the sons of younger males, while daughters of old and young males were of comparable fitness. These results suggest that there is an adaptive basis for the observed sex ratio modification.