bluuebunny/crossref_metadata_2025 huggingface dataset:
Near band-edge luminescence and evidence of the weakening of the N-conduction-band coupling for partially relaxed and high nitrogen composition GaAs1−xNx epilayers
Authors: Coaquira J. A. H. , Pinault M.-A. , Litvinchuk A. P. , Bhusal L. , Freundlich Alex
Published: October 2007

Photoluminescence and absorption spectroscopy experiments are implemented on as-grown and thermally annealed GaAs1−xNx epilayers grown on GaAs(001) having a nitrogen content in the range of 0.4%–7.1%. At low temperature, photoluminescence spectra exhibit two sets of features: (i) a relatively broad peak at low energy in the vicinity of the band gap predicted by the band anticrossing model (BAC) and (ii) sharp excitonic features at higher energy (over 100meV above the band gap for x>4%). An enhancement of the photoluminescence response of excitonic emissions and a notable intensity reduction of the deeper luminescence were systematically observed for samples subjected to high-temperature postgrowth annealing treatments. For pseudomorphically strained low nitrogen-containing epilayers (x<2%), and by taking into account the strain magnitude and the average substitutional nitrogen concentration (as extracted from x-ray analysis), excitonic energies and corresponding band gaps (as determined by absorption spectroscopy) are well described within the framework of the BAC model. The extracted binding energies of split heavy- and light-hole excitons are found to be consistent with the expected increase of electron effective masses. For thick partially relaxed epilayers (1%<x<2%) and relaxed epilayers with high nitrogen content (x>4%), the fundamental band gap of GaAsN is found at significantly higher energies than those predicted by the BAC model using the commonly accepted nitrogen coupling parameter CNM=2.7eV. To account, within the BAC framework, for the apparent deceleration in the band-gap reduction rate requires the use of a smaller coupling constant (CNM=2.0eV), which suggests a weakening of the strength of the interaction between the localized nitrogen state and the conduction band of the host matrix. This observation seems to be associated with the increasing population of N-related defects.
Atomic and molecular emissions of the laser-induced plasma during zinc and zinc oxide target ablation
Authors: Acquaviva S. , D’Anna E. , De Giorgi M. L.
Published: October 2007

Optical emission spectroscopic investigations of the plasma produced during KrF excimer laser ablation of Zn and ZnO targets, in vacuum and in oxygen gas environment, are presented. The plume luminescence is mainly due to Zn excited atoms and ions, but the contribution of atomic and molecular oxygen, as well as of particulates, cannot be neglected. In particular, we detect emissions in the spectral regions around 380 and 530 nm, corresponding to the UV and green photo-luminescence bands of the zinc oxide. Moreover, we study the temporal evolution of atomic and ionic ejected species by space- and time-resolved spectroscopy and analyze the results by means of empirical models, in order to infer information about plasma dynamics.
A comparison of zinc oxide thin-film transistors on silicon oxide and silicon nitride gate dielectrics
Authors: Carcia P. F. , McLean R. S. , Reilly M. H. , Crawford M. K , Blanchard E. N. , Kattamis A. Z. , Wagner S.
Published: October 2007

We compared the properties of ZnO thin-film transistors in the inverted coplanar geometry on thermally grown silicon oxide gate dielectric to devices on silicon nitride, grown by plasma-enhanced chemical vapor deposition at 150 °C or magnetron sputtering at room temperature. The ZnO semiconductor was sputtered without substrate heating at oxygen partial pressures in the range of 10−5−10−4 Torr. At the lowest oxygen partial pressure, transistor characteristics were similar for all dielectrics. The field-effect mobility approached ∼5 cm2/V s and devices generally operated in depletion mode. With increasing oxygen partial pressure, the mobility decreased by 1000× on SiO2, whereas the decrease on silicon nitride was considerably smaller. On SiO2 the threshold voltage was >30 V but <5 V on silicon nitride. Devices on SiO2 operated in enhancement mode, whereas they operated in depletion mode on PECVD silicon nitride. Photoluminescence of ZnO revealed that deep-level emission depended on the specific dielectric on which ZnO was grown. Green emission for ZnO on chemically vapor-deposited silicon nitride was consistent with the presence of oxygen vacancies in ZnO. Yellow emission for ZnO on silicon oxide was associated with electron acceptor defects, such as oxygen adsorbed in grain boundaries or interstitially in ZnO. We concluded that differences in transistor properties were attributable to modification of ZnO defect chemistry, mediated by growth on a specific dielectric.
Nucleation and growth of Ti2AlN thin films deposited by reactive magnetron sputtering onto MgO(111)
Authors: Beckers M. , Schell N. , Martins R. M. S. , Mücklich A. , Möller W. , Hultman L.
Published: October 2007

The nucleation and growth of Ti2AlN thin films on MgO(111) substrates during dual direct current reactive magnetron cosputtering from Ti and Al targets in an Ar∕N2 atmosphere at a substrate temperature of 690 °C have been investigated. Time and thickness dependent in situ specular x-ray reflectivity and x-ray diffraction in combination with cross-sectional transmission electron microscopy and Rutherford backscattering spectroscopy reveal the formation of competing phases for slight N superstoichiometry with respect to Ti2AlN. The stoichiometry deviations initiate the layer-by-layer growth of a ∼380 Å thick epitaxial N-substoichiometric cubic (Ti1−xAlx)Ny layer. N-vacancy driven diffusion of Ti and Al leads to decomposition of this metastable solid solution into nanosized cubic TiNy′ and AlNy″ domains as well as to a solid-state reaction with the MgO(111) by formation of a Mg2(Al:Ti)O4 spinel, reducing the transformed (Ti1−xAlx)Ny layer thickness down to ∼60 Å. Local AlNy″ domains serve as templates for Ti2AlN nucleation at higher thicknesses. At the same time TiNy′ and AlNy″ serve as a sink for excess gas phase N during the subsequent polycrystalline Ti2AlN growth with random (Ti1−xAlx)Ny renucleation as a tissue phase along Ti2AlN grain boundaries. The individual Ti2AlN grains with vertical sizes up to the total thickness retain local epitaxy to the substrate, with basal planes nonparallel to the substrate interface. Concurrently the (Ti1−xAlx)Ny layer is further reduced by inward Ti2AlN grain growth along the basal planes.
Effect of film viscoelasticity on the finite deformation of a spherical bubble
Authors: Haimin Wang , Jianmin Ma , Wen Zhang
Published: October 2007

According to the strain energy density function for finite deformation of viscoelastic material, the relaxation function of the Maxwell mode, and the deformation gradient tensor of the bubble, a stress equation for finite deformation of a protein bubble is derived. By using the above stress equation and the dynamics equation of the bubble, an equation describing the relation between the relative deformation rate of the inner radius and time is developed for finite deformation. Based on this equation and the nonlinear properties of finite deformation, the effect of the pressure difference, the thickness and viscosity of the film, the initial size of the bubble, and the initial gas pressure in the bubble on the radial deformation of the protein bubble are analyzed by numerical simulation. The results show that during the contraction of the bubble, an oscillation with degressive amplitude is associated. The variation tendencies of vibration frequency and amplitude and the balance size of the bubble are closely related to the applied load, the viscoelasticity of the film, and the initial bubble size. Increasing the thickness and viscosity of protein film or decreasing the initial bubble size can counteract the vibration of the bubble wall and thus, can enhance the load-bearing capacity of the protein bubble.
Single crystalline BaTiO3 thin films synthesized using ion implantation induced layer transfer
Authors: Park Young-Bae , Diest Kenneth , Atwater Harry A.
Published: October 2007

Layer transfer of BaTiO3 thin films onto silicon-based substrates has been investigated. Hydrogen and helium ions were co-implanted to facilitate ion-implantation-induced layer transfer of films from BaTiO3 single crystals. From thermodynamic equilibrium calculations, we suggest that the dominant species during cavity nucleation and growth are H2, H+, H2O, Ba2+ and Ba–OH, and that the addition of hydrogen to the Ba–Ti–O system can effectively suppress volatile oxide formation during layer transfer and subsequent annealing. After ion implantation, BaTiO3 layers contain microstructural defects and hydrogen precipitates in the lattice, but after layer transfer, the single crystal is found to be stoichiometric. Using direct wafer bonding and layer splitting, single crystal BaTiO3 thin films were transferred onto amorphous Si3N4 and Pt substrates. Micro-Raman spectroscopy indicated that the density of defects generated by ion implantation in BaTiO3 can be significantly reduced during post-transfer annealing, returning the transferred layer to its single crystal state. Characterization using piezoresponse force microscopy shows that the layer transferred thin films are ferroelectric, with domain structures and piezoresponse characteristics similar to that of bulk crystals.
Optical characterization of urethane/urea elastomers undoped and doped with magnetic nanoparticles subjected to a uniaxial strain
Authors: Sena C. , Godinho M. H. , Neto A. M. Figueiredo
Published: October 2007

We report on the optical characterization of urethane/urea elastomers (PU/PBDO), based on polypropylene oxide and polybutadiene diol, pure and doped with ferrofluid. The ratios in wt % of PU and PBDO investigated are 40/60, 50/50, 60/40, and 80/20. The incorporation of nanoparticles in the elastomeric matrices strongly depends upon the ratio of PU/PBDO, which corresponds to different degrees of cross linking. The nanoparticles were also found to act as impurities in the elastomeric matrix by reducing the initial induced anisotropy promoted by film casting and preparation. Optical experiments show that the strain-induced optical birefringence is linear with the stress in both pure and doped elastomers.
GaN quantum dot superlattices grown by molecular beam epitaxy at high temperature
Authors: Xu Tao , Zhou Lin , Wang Yiyi , Özcan Ahmet S. , Ludwig K. F. , Smith David J. , Moustakas T. D.
Published: October 2007

In this paper, we report the growth of GaN quantum dot superlattices (QDSLs) with AlN barriers on (0001) sapphire substrates by molecular beam epitaxy at relatively high temperature (770°C) using the modified Stranski-Krastanov growth mode. Observations with atomic force microscopy show that the height distribution of the dots depends strongly on the number of GaN monolayers (MLs) grown on the AlN barriers. Specifically, the height distribution consists of two Gaussian distributions (bimodal) for coverages of 3 or 4 ML, and becomes a single Gaussian distribution for 5 and 6 ML of coverage. Furthermore, the density of quantum dots increases with the degree of coverage and saturates at 2×1011dots∕cm2. An increase in the number of stacks in the superlattice structure with 4 ML coverage also leads to a more pronounced bimodal height distribution. Electron microscopy observations indicate that the GaN QDs are truncated pyramids faceted along the {11¯03} planes and suggest that larger dots are associated with threading dislocations which presumably provide low-energy nucleation sites. Transmission electron microscopy studies also indicate that most of the larger dots are nucleated next to edge-type dislocations, while most of the smaller dots are located in dislocation-free regions. These GaN QDSLs were also studied by grazing-incidence small angle x-ray scattering and grazing-incidence x-ray diffraction methods. The average lateral deviation and the vertical correlation length between QD positions for two successive layers were determined to be 1.4nm and 190nm, respectively. A GaN QD growth model is proposed to explain the phenomenon.
Er
3
+
diffusion in congruent LiNbO3 crystal in Li-enriched atmosphere
Authors: Zhang De-Long , Jia Qi-Shen , Hua Ping-Rang , Pei-Zhang  , Zhang Wen-Jun , Yang Qing-Zhong , Liu Hong-Li , Cui Yu-Ming , Pun E. Y. B.
Published: October 2007

The thermal diffusion of Er3+ into X- and Z-cut congruent LiNbO3 crystal in Li-enriched atmosphere [i.e., vapor transport equilibration (VTE)], created by Li3NbO4–LiNbO3 two-phase powder at the temperature around 1130°C, was attempted. Single-crystal x-ray diffraction, micro-Raman, photoluminescence spectroscopy, and secondary ion mass spectrometry (SIMS) were used to study the crystalline phase with respect to Er3+ ion and the Er3+ diffusivity. The results show that the thickness of the Er film coated should not be thicker than 10nm for an X-cut plate and 15nm for a Z-cut plate. In this case, the diffusion is complete if the duration is long enough (>150h) and the Er3+ ions in the diffused layer still retain the LiNbO3 phase. On the other hand, if the initial thickness of the Er metal film is thicker than 10nm for the X-cut plate and 15nm for the Z-cut plate, the diffusion will be incomplete no matter how long the duration is. This is because the residual Er3+ ions form irremovable ErNbO4 grains on the surface of the crystal. SIMS analysis on an X-cut VTE (1130°C∕192h) and a Z-cut VTE (1129°C∕158h) crystal coated, respectively, with 10 and 15nm thick Er film reveals that the Er diffusion shows obvious anisotropy with the mean diffusion coefficients of 0.0155 and 0.0957μm2∕h, respectively. The surface concentrations are 1.5×1020 and 1.0×1020at.∕cm3, respectively. The diffused Er3+ ions follow the stretched-exponential decay profile with a stretching factor of 1.85 and 3.5, respectively. The Li∕Nb ratio in the Er-diffused layer is similar to 99.4% for the X-cut sample coated with 10nm thick Er film and 99.3% for the Z-cut crystal coated with 15nm thick Er film. The rms roughness of the diffused surface is better than 6 and 4nm for the X-cut and Z-cut samples, respectively.
Liouvillian perturbations of black holes
Authors: Couch W. E. , Holder C. L.
Published: October 2007

We apply the well-known Kovacic algorithm to find closed form, i.e., Liouvillian solutions, to the differential equations governing perturbations of black holes. Our analysis includes the full gravitational perturbations of Schwarzschild and Kerr, the full gravitational and electromagnetic perturbations of Reissner-Nordstrom, and specialized perturbations of the Kerr-Newman geometry. We also include the extreme geometries. We find all frequencies ω, in terms of black hole parameters and an integer n, which allow Liouvillian perturbations. We display many classes of black hole parameter values and their corresponding Liouvillian perturbations, including new closed-form perturbations of Kerr and Reissner-Nordstrom. We also prove that the only type 1 Liouvillian perturbations of Schwarzschild are the known algebraically special ones and that type 2 Liouvillian solutions do not exist for extreme geometries. In cases where we do not prove the existence or nonexistence of Liouvillian perturbations we obtain sequences of Diophantine equations on which decidability rests.
Optimization of cone target geometry for fast ignition
Authors: Nakamura Tatsufumi , Sakagami Hitoshi , Johzaki Tomoyuki , Nagatomo Hideo , Mima Kunioki , Koga James
Published: October 2007

Electron energy characteristics generated by the irradiation of ultraintense laser pulses onto solid targets are controlled by using cone targets. Two parameters characterizing the laser-cone interaction are introduced, which are cone angle and the ratio of the laser spot size to the cone tip size. By changing these parameters, the energy absorption rate, laser irradiance at the cone tip, and electron acceleration at the cone tip and side wall are controlled. The optimum cone targets for fast ignition are 30° cone angle with double-cone geometry, and a tip size comparable to the core size, with the irradiation of a laser pulse with a spot size of about four times the cone tip size. Cone targets have the possibility to enhance the maximum energy of laser-accelerated protons by using a smaller angle cone depending on the laser f-number.
A new high performance battery-operated electrometer
Authors: He Meilu , Marzocca Pier , Dhaniyala Suresh
Published: October 2007

Design and analysis of a new low-noise, fast-response, high-sensitivity, compact electrometer are described. This electrometer are battery operated and capable of measuring currents down to the femtoampere level. The portable, high performance nature of the electrometer renders it applicable for deployment in compact instruments for applications such as aerosol particle counters. A parametric experimental study is conducted to determine the role of different components on the performance of the electrometer. Under an ideal configuration, the electrometer has a step-up response time of ∼3s. Experiments with the electrometer used for particle counting measurements suggest that the new electrometer has high accuracy and sensitivity in comparison to the Keithley 6514 electrometer. The response of the electrometer used in particle counting studies is consistent with that of an optical single particle counter used in comparison experiments. A damping component introduced to reduce possible spike currents in the electrometer is also seen to reduce noise and almost have no effect on response time. The electrometer response characteristics are presented in detail.
Analysis of photomixer receivers for continuous-wave terahertz radiation
Authors: Gregory I. S. , Evans M. J. , Page H. , Malik S. , Farrer I. , Beere H. E.
Published: October 2007

We examine the electrical properties of photomixer receivers for the homodyne detection of continuous-wave terahertz radiation and analyze the coupling between the incoming terahertz field and the current flowing in the receiver circuit for two designs of photomixer. Significantly, we find that the optimum geometry for a photomixer receiver is very different to the optimized emitter designs despite the optical symmetry between the generation and detection processes.
Design and characterization of a temporal analysis of products reactor
Authors: Leppelt R. , Hansgen D. , Widmann D. , Häring T. , Bräth G. , Behm R. J.
Published: October 2007

We describe an improved temporal analysis of products (TAP) reactor design whose main new features in comparison to the recent TAP-2 design of Gleaves et al. [Appl. Catal. A 160, 55 (1997)] are the use of a turbomolecular pump, piezoelectrically driven pulse valves, and a newly designed, differentially pumped gate valve. The gate valve allows fast and simple changes between high pressure operation, in which in situ catalyst treatment can be performed, and the analytic mode with a direct line-of-sight connection to the analysis chamber and the mass spectrometer. The heating system and pulse valves are located outside the vacuum chamber, resulting in a system that is easy to operate and modify. The high stability and reproducibility of the pulse intensity allows for direct, quantitative evaluation of single-pulse and multipulse experiments. The performance of the system is demonstrated using the CO oxidation over a Au∕TiO2 catalyst as test reaction.
Infrared spectra of the OCS trimer
Authors: Afshari Mahin , Dehghani M. , Abusara Z. , Moazzen-Ahmadi N. , McKellar A. R. W.
Published: October 2007

Infrared spectra of the barrel-shaped trimer (OCS)3, previously known from its microwave spectrum, are reported for the first time. The observations are carried out in a supersonic slit-jet expansion of a He+OCS gas mixture which is probed with a tunable diode laser. Three rotationally resolved bands associated with the ν1 fundamental vibration of OCS (2062.20cm−1) are observed, at about 2047, 2053, and 2077cm−1. Small perturbations are noted in the 2077cm−1 band and may also be present in the 2053cm−1 band, which is weak and hence more difficult to analyze precisely. Employing a variety of evidence, we suggest a plausible assignment for the nature of the OCS vibrations in each of the three bands.
The measure of a measurement
Authors: Jorgensen Palle E. T.
Published: October 2007

We identify a fractal scale s in a family of Borel probability measures μ on the unit interval which arises independently in quantum information theory and in wavelet analysis. The scales s we find satisfy s∊R+ and s≠1, some s<1 and some s>1. We identify these scales s by considering the asymptotic properties of u(J)∕∣J∣s where J are dyadic subintervals, and ∣J∣→0.
Comparative study of atmospheric pressure low and radio frequency microjet plasmas produced in a single electrode configuration
Authors: Kim Dan Bee , Rhee J. K. , Gweon B. , Moon S. Y. , Choe W.
Published: October 2007

Microsize jet-type plasmas were generated in a single pin electrode structure source for two separate input frequencies of 50kHz and 13.56MHz in the ambient air. The copper pin electrode radius was 360μm, and it was placed in a Pyrex tube with a radius of 3mm for helium gas supply. Due to the input frequency difference, the generated plasmas showed distinct discharge characteristics for their plasma physical appearances, electrical properties, gas temperatures, and optical properties. Strengths and weaknesses of both plasmas were discussed for further applications.
Determination of InN–GaN heterostructure band offsets from internal photoemission measurements
Authors: Mahmood Zahid Hasan , Shah A. P. , Kadir Abdul , Gokhale M. R. , Ghosh Sandip , Bhattacharya Arnab , Arora B. M.
Published: October 2007

Band discontinuities at the InN–GaN heterointerface are experimentally determined from internal photoemission spectroscopy measurements on n+ InN on GaN epilayers. The photocurrent shows two threshold energies, one at 1.624eV and the other at 2.527eV. From these, we obtain the band offsets ΔEv=0.85eV and ΔEc=1.82eV.
Data acquisition system for an advanced x-ray imaging crystal spectrometer using a segmented position-sensitive detector
Authors: Nam U. W. , Lee S. G. , Bak J. G. , Moon M. K. , Cheon J. K. , Lee C. H.
Published: October 2007

A versatile time-to-digital converter based data acquisition system for a segmented position-sensitive detector has been developed. This data acquisition system was successfully demonstrated to a two-segment position-sensitive detector. The data acquisition system will be developed further to support multisegmented position-sensitive detector to improve the photon count rate capability of the advanced x-ray imaging crystal spectrometer system.
Bistability and nonlinear gain in 1.55μm vertical cavity semiconductor optical amplifiers: Theory and experiments
Authors: Hurtado Antonio , Henning Ian D. , Adams Michael J.
Published: October 2007

We report experimental measurements of power and wavelength optical bistability and nonlinear gain in two 1.55μm vertical-cavity semiconductor optical amplifiers operated in reflection. Anticlockwise and clockwise nonlinear switching and bistability, both with high on-off contrast ratio up to 3.5:1, have been observed in the optical power and wavelength domains. Theoretical modeling gives excellent agreement with the experimental measurements.
Femtosecond laser-written quasi-phase-matched waveguides in lithium niobate
Authors: Thomas Jens , Heinrich Matthias , Burghoff Jonas , Nolte Stefan , Ancona Antonio , Tünnermann Andreas
Published: October 2007

We report on thermally stable optical waveguides written in periodically poled lithium niobate with a femtosecond laser using a two line approach. Both fundamental and second harmonic light at 1064 and 532nm are guided with low damping losses. In a 10-mm-long sample a conversion efficiency of 58% was achieved.
Nanolasers to enable data storage beyond 10Tbit∕in.2
Authors: Ikkawi Rabee , Amos Nissim , Krichevsky Alexander , Chomko Roman , Litvinov Dmitri , Khizroev Sakhrat
Published: October 2007

A focused ion beam (FIB) fabricated nanolaser is demonstrated to be able to focus light with power of over 250nW into a 30nm spot. To fabricate a nanolaser, a 100nm thick aluminum film was deposited on the emitting edge of a diode laser. FIB was used to etch various apertures into the film. The power was measured by a scanning near-field optical microscope in the near-field regime with a 10nm separation between the probe and the air bearing surface of the nanolaser. Out of four different shapes under study, “C”-shape aperture was found to have the highest throughput.
Fibroblast growth factor receptor 2 regulates proliferation and Sertoli differentiation during male sex determination
Authors: Kim Yuna , Bingham Nathan , Sekido Ryohei , Parker Keith L. , Lovell-Badge Robin , Capel Blanche
Published: October 2007

Targeted mutagenesis ofFgf9in mice causes male-to-female sex reversal. Among the four FGF receptors, FGFR2 showed two highly specific patterns based on antibody staining, suggesting that it might be the receptor-mediating FGF9 signaling in the gonad. FGFR2 was detected at the plasma membrane in proliferating coelomic epithelial cells and in the nucleus in Sertoli progenitor cells. This expression pattern suggested thatFgfr2might play more than one role in testis development. To test the hypothesis thatFgfr2is required for male sex determination, we crossed mice carrying a floxed allele ofFgfr2with two differentCrelines to induce a temporal or cell-specific deletion of this receptor. Results show that deletion ofFgfr2in embryonic gonads phenocopies deletion ofFgf9and leads to male-to-female sex reversal. Using these twoCrelines, we provide the first genetic evidence thatFgfr2plays distinct roles in proliferation and Sertoli cell differentiation during testis development.
Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote,
Dictyostelium discoideum
, with a role in cytokinesis
Authors: Zhang Haiyu , Gómez-Garcı́a Marı́a R. , Shi Xiaobing , Rao Narayana N. , Kornberg Arthur
Published: October 2007

Polyphosphate kinase 1 (PPK1), the principal enzyme responsible for reversible synthesis of polyphosphate (poly P) from the terminal phosphate of ATP, is highly conserved in bacteria and archaea.
Dictyostelium discoideum
, a social slime mold, is one of a few eukaryotes known to possess a PPK1 homolog (DdPPK1). Compared with PPK1 of
Escherichia coli
, DdPPK1 contains the conserved residues for ATP binding and autophosphorylation, but has an N-terminal extension of 370 aa, lacking homology with any known protein. Polyphosphate or ATP promote oligomerization of the enzyme
in vitro
. The DdPPK1 products are heterogeneous in chain length and shorter than those of
E. coli
. The unique DdPPK1 N-terminal domain was shown to be necessary for its enzymatic activity, cellular localization, and physiological functions. Mutants of DdPPK1, as previously reported, are defective in development, sporulation, and predation, and as shown here, in late stages of cytokinesis and cell division.
Cloning and characterization of the biosynthetic gene cluster for kutznerides
Authors: Fujimori Danica Galonić , Hrvatin Siniša , Neumann Christopher S. , Strieker Matthias , Marahiel Mohamed A. , Walsh Christopher T.
Published: October 2007

Kutznerides, actinomycete-derived cyclic depsipetides, consist of six nonproteinogenic residues, including a highly oxygenated tricyclic hexahydropyrroloindole, a chlorinated piperazic acid, 2-(1-methylcyclopropyl)-glycine, a β-branched-hydroxy acid, and 3-hydroxy glutamic acid, for which biosynthetic logic has not been elucidated. Herein we describe the biosynthetic gene cluster for the kutzneride family, identified by degenerate primer PCR for halogenating enzymes postulated to be involved in biosyntheses of these unusual monomers. The 56-kb gene cluster encodes a series of six nonribosomal peptide synthetase (NRPS) modules distributed over three proteins and a variety of tailoring enzymes, including both mononuclear nonheme iron and two flavin-dependent halogenases, and an array of oxygen transfer catalysts. The sequence and organization of NRPS genes support incorporation of the unusual monomer units into the densely functionalized scaffold of kutznerides. Our work provides insight into the formation of this intriguing class of compounds and provides a foundation for elucidating the timing and mechanisms of their biosynthesis.
Transactivation of Vascular Endothelial Growth Factor Receptor-2 by Interleukin-8 (IL-8/CXCL8) Is Required for IL-8/CXCL8-induced Endothelial Permeability
Authors: Petreaca Melissa L. , Yao Min , Liu Yan , DeFea Kathryn , Martins-Green Manuela
Published: October 2007

Interleukin-8 (IL-8/CXCL8) is a chemokine that increases endothelial permeability during early stages of angiogenesis. However, the mechanisms involved in IL-8/CXCL8-induced permeability are poorly understood. Here, we show that permeability induced by this chemokine requires the activation of vascular endothelial growth factor receptor-2 (VEGFR2/fetal liver kinase 1/KDR). IL-8/CXCL8 stimulates VEGFR2 phosphorylation in a VEGF-independent manner, suggesting VEGFR2 transactivation. We investigated the possible contribution of physical interactions between VEGFR2 and the IL-8/CXCL8 receptors leading to VEGFR2 transactivation. Both IL-8 receptors interact with VEGFR2 after IL-8/CXCL8 treatment, and the time course of complex formation is comparable with that of VEGFR2 phosphorylation. Src kinases are involved upstream of receptor complex formation and VEGFR2 transactivation during IL-8/CXCL8-induced permeability. An inhibitor of Src kinases blocked IL-8/CXCL8-induced VEGFR2 phosphorylation, receptor complex formation, and endothelial permeability. Furthermore, inhibition of the VEGFR abolishes RhoA activation by IL-8/CXCL8, and gap formation, suggesting a mechanism whereby VEGFR2 transactivation mediates IL-8/CXCL8-induced permeability. This study points to VEGFR2 transactivation as an important signaling pathway used by chemokines such as IL-8/CXCL8, and it may lead to the development of new therapies that can be used in conditions involving increases in endothelial permeability or angiogenesis, particularly in pathological situations associated with both IL-8/CXCL8 and VEGF.
Acclimation ofSaccharomyces cerevisiaeto Low Temperature: A Chemostat-based Transcriptome Analysis
Authors: Tai Siew Leng , Daran-Lapujade Pascale , Walsh Michael C. , Pronk Jack T. , Daran Jean-Marc
Published: October 2007

Effects of suboptimal temperatures on transcriptional regulation in yeast have been extensively studied in batch cultures. To eliminate indirect effects of specific growth rates that are inherent to batch-cultivation studies, genome-wide transcriptional responses to low temperatures were analyzed in steady-state chemostats, grown at a fixed specific growth rate (0.03 h−1). Although in vivo metabolic fluxes were essentially the same in cultures grown at 12 and at 30°C, concentrations of the growth-limiting nutrients (glucose or ammonia) were higher at 12°C. This difference was reflected by transcript levels of genes that encode transporters for the growth-limiting nutrients. Several transcriptional responses to low temperature occurred under both nutrient-limitation regimes. Increased transcription of ribosome-biogenesis genes emphasized the importance of adapting protein-synthesis capacity to low temperature. In contrast to observations in cold-shock and batch-culture studies, transcript levels of environmental stress response genes were reduced at 12°C. Transcription of trehalose-biosynthesis genes and intracellular trehalose levels indicated that, in contrast to its role in cold-shock adaptation, trehalose is not involved in steady-state low-temperature adaptation. Comparison of the chemostat-based transcriptome data with literature data revealed large differences between transcriptional reprogramming during long-term low-temperature acclimation and the transcriptional responses to a rapid transition to low temperature.
Epidermal Growth Factor Increases the Interaction between Nucleolin and Heterogeneous Nuclear Ribonucleoprotein K/Poly(C) Binding Protein 1 Complex to Regulate the Gastrin mRNA Turnover
Authors: Lee Pin-Tse , Liao Pao-Chi , Chang Wen-Chang , Tseng Joseph T.
Published: October 2007

Gastrin, a gastrointestinal hormone responsible for gastric acid secretion, has been confirmed as a growth factor for gastrointestinal tract malignancies. High expression of gastrin mRNA was observed in pancreatic and colorectal cancer; however, the mechanism is unclear. Epidermal growth factor (EGF) was found to increase gastrin mRNA stability, indicating mRNA turnover regulation mechanism is involved in the control of gastrin mRNA expression. Using biotin-labeled RNA probe pull-down assay combined with mass spectrometry analysis, we identified the heterogeneous nuclear ribonucleoprotein K (hnRNP K) and poly(C) binding protein 1 (PCBP1) bound with the C-rich region in gastrin mRNA 3′ untranslated region. Nucleolin bound with the AGCCCU motif and interacted with hnRNP K were also demonstrated. Under EGF treatment, we observed the amount of nucleolin interacting with hnRNP K and gastrin mRNA increased. Using small interfering RNA technology to define their functional roles, we found hnRNP K, PCBP1, and nucleolin were all responsible for stabilizing gastrin mRNA. Moreover, nucleolin plays a crucial role in mediating the increased gastrin mRNA stability induced by EGF signaling. Besides, we also observed hnRNP K/PCBP1 complex bound with the C-rich region in the gastrin mRNA increased nucleolin binding with gastrin mRNA. Finally, a novel binding model was proposed.
CellLine, a stochastic cell lineage simulator
Authors: Ribeiro Andre S. , Charlebois Daniel A. , Lloyd-Price Jason
Published: October 2007

Summary: We present CellLine, a simulator of the dynamics of gene regulatory networks (GRN) in the cells of a lineage. From user-defined reactions and initial substance quantities, it generates cell lineages, i.e. genealogic pedigrees of cells related through mitotic division. Each cell's dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time delayed reactions.

The cells of the lineage can be individually subject to ‘perturbations’, such as gene deletion, duplication and mutation. External interventions, such as adding or removing a substance at a given moment, can be specified. Cell differentiation lineages, where differentiation is stochastically driven or externally induced, can be modeled as well. Finally, CellLine can generate and simulate the dynamics of multiple copies of any given cell of the lineage.

As examples of CellLine use, we simulate the following systems: cell lineages containing a model of the P53-Mdm2 feedback loop, a differentiation lineage where each cell contains a 4 gene repressilator (a bistable circuit), a model of the differentiation of the cells of the retinal mosaic required for color vision in Drosophila melanogaster, where the differentiation pathway depends on one substance's concentration that is controlled by a stochastic process, and a 9 gene GRN to illustrate the advantage of using CellLine rather than simulating multiple independent cells, in cases where the cells of the lineage are dynamically correlated.

Availability: The CellLine program, instructions and examples are available at http://www.cs.tut.fi/~sanchesr/CellLine/CellLine.html

Contact:  andre.sanchesribeiro@tut.fi
First Report of Pierce's Disease in New Mexico
Authors: Randall Jennifer J. , Radionenko Maxim , French Jason M. , Goldberg Natalie P. , Hanson Stephen F.
Published: October 2007

In the fall of 2006, Vitis vinifera Chardonnay grapevines from two vineyards in southern New Mexico exhibited leaf scorch and dieback symptoms consistent with Pierce's disease. ELISA, PCR, and culturing assays all detected the presence of Xylella fastidiosa, the causal agent of Pierce's disease, in symptomatic tissue from both vineyards confirming Pierce's disease in New Mexico. Phylogenetic analysis indicates that isolates from New Mexico grapes are closely related to a X. fastidiosa isolate recently found in the landscape plant Chitalpa tashkentensis in New Mexico.

Accepted for publication 20 April 2007. Published 2 October 2007.
The Expansion of AFTA: Widening and Deepening?
Authors: Menon Jayant
Published: October 2007

Regional trading arrangements (RTAs) have recently tended to both widen and deepen. This paper examines the impact of widening and assesses progress with deepening in the ASEAN Free Trade Area (AFTA). Widening of AFTA has seen its membership grow from six to nine countries (and perhaps ten in 1998). Widening has increased AFTA's diversity, with the emergence of a two‐tier structure of developed and under‐developed segments. An AFTA‐Plus program is designed to deepen regional integration. Apart from harmonising customs procedures and tariff nomenclature, and fast‐tracking a common customs valuation method, progress has been limited.
The effect of environmental salinity on the proteome of the sea bass (Dicentrarchus labrax L.)
Authors: Ky C. L. , De Lorgeril J. , Hirtz C. , Sommerer N. , Rossignol M. , Bonhomme F.
Published: October 2007

The European sea bass, Dicentrarchus labrax L., tolerates a range of salinities from freshwater to hyper‐saline. To study differences in protein expression, fish were reared in both freshwater and seawater. After 3‐month acclimation, gill and intestine epithelia were collected and the soluble protein extracted. In all, 362 spots were differentially expressed in the gills and intestines of fishes reared in seawater compared to those from freshwater. Fifty differential protein spots were excised from a colloidal Coomassie‐stained gel. Nine separate protein spots were identified unambiguously by mass spectrometry and database searching. Among the six proteins over‐expressed in gill cells in seawater, five were cytoskeleton proteins and one was the aromatase cytochrome P450. In gill cells under freshwater conditions, the two over‐expressed proteins identified were the prolactin receptor and the major histocompatibility complex class II β‐antigen. In intestinal cells under freshwater conditions, the Iroquois homeobox protein Ziro5 was upregulated over ninefold. The expression of these proteins, their possible direct or indirect roles in the adaptation of D. labrax to salinity, and their correspondences with a previous study are discussed.
Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar × Meishan F2 family using a high‐density gene map
Authors: Čepica S. , Bartenschlager H. , Geldermann H.
Published: October 2007

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low‐density linkage maps in a wild boar × Meishan F2 family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F‐ratio values for all QTL. Maxima of F‐ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.
Assessment of soy aeroallergen levels in different work environments
Authors: Gómez‐Ollés S. , Cruz M. J. , Bogdanovic J. , Wouters I. M. , Doekes G. , Sander I. , Morell F. , Rodrigo M. J.
Published: October 2007

Background
Airborne soybean hull proteins are known causes of asthma epidemics around harbours and soy processing plants. Soy flour dust proteins may cause occupational allergy in food and feed industries.

Objective
To compare enzyme immunoassays (EIAs) for soy hull and soy flour aeroallergens, exposure assessment in various work environments.

Methods
Airborne dust samples (n=324) from soy unloading and/or processing plants, the animal feed industry and pig stables were analysed by two soy flour assays: one assay for measuring complete soy hull proteins and two assays for measuring the purified low‐molecular‐weight (LMW) soy hull allergens.

Results
Immunoblotting confirmed strong differences between antibody specificities and soy preparations. The results of the two soy flour assays and the assay for measuring complete soy hull proteins were highly correlated (r>0.85). The two LMW soy hull assays also showed a strong mutual correlation (r=0.91), but much less correlation with assays for measuring soy flour and complete soy hull. The levels of LMW soy hull proteins were the highest at sites of soybean unloading or processing, while soy flour levels were particularly high in the soy and animal feed industry.

Conclusions
The optimal EIA procedure for soy aeroallergen exposure assessment depends on the type of work environment and the local soy dust composition. Thus, the type of work environment should always be taken into account in future soy allergy studies in order to prevent a possible underestimation of the workers' actual risk of developing soy allergy.
Risk factors for asthma at 3.5 and 7 years of age
Authors: Mitchell E. A. , Robinson E. , Black P. N. , Becroft D. M. O. , Clark P. M. , Pryor J. E. , Thompson J. M. D. , Waldie K. E. , Wild C. J.
Published: October 2007

BackgroundIt has been suggested that factors in early life including exposure to allergens and microbes may influence the development of asthma.

ObjectiveTo identify risk factors for asthma in early childhood.

MethodsEight‐hundred and seventy‐one children of European mothers were enrolled at birth, of whom 385 (44.2%) were born small for gestational age (SGA) and 486 were appropriate for gestational age (AGA). Data were collected at birth, 12 months, 3.5 years of age (y) and 7 y. The outcome of interest (current wheeze) was defined as a positive response to the question: ‘Has your child had wheezing or whistling in the chest in the last 12 months?’

ResultsParticipation rate was 85.4% at 1 y, 63.1% at 3.5 y and 68.0% at 7 y. The prevalence of asthma was 23.8% at 3.5 y and 18.1% at 7 y. Antibiotic use in the first year of life and day care in the first year of life were associated with increased risk of wheeze at 7 y [odds ratio (OR)=4.3 95% confidence interval (CI) (1.8–10.1) and OR=2.8 95% CI (1.2–6.5), respectively], but not at 3.5 y. Exposure to dogs was a risk factor for asthma at both ages [OR=2.1 95% CI (1.1–3.8)] as was sleeping on a used cot mattress in the first year of life [OR=1.8 95% CI (1.0–3.2)].

ConclusionsThere was a significant association between antibiotic use and day care in the first year of life and wheezing at 7 y but not at 3.5 y. This strengthens the argument that these factors increase the risk of asthma. We have also made the novel observation that sleeping on a used mattress in the first year of life is a risk factor for wheezing at 3.5 and 7 y.

Capsule summaryThis prospective study of 871 children made the novel observation that sleeping on a used mattress in the first year of life was a risk factor for wheezing at 3.5 and 7 y.
Rainfall impact effects on ageing casts of a tropical anecic earthworm
Authors: Mariani L. , Jiménez J. J. , Torres E. A. , Amézquita E. , Decaëns T.
Published: October 2007

We investigated the erodibility of surface casts produced by an anecic earthworm of the Colombian savannahs by means of indoor rain simulations. The kinetic energy applied to samples, 21.62 J minute−1 m−2, was estimated to be equivalent to 41% of the energy of the more intense period of a local storm. The erodibility of casts was assessed at different stages of their ageing along with the effects of repeated wetting‐drying cycles. Bare soil cores and soil cores of the same size with a cast on their surface (soil + cast) were used as controls. Saturated hydraulic conductivity (HC) was measured to test whether casts enhance soil water permeability. Fresh, almost liquid, individual casts were completely dispersed by a 2‐hour rainfall simulation at a dispersion rate of 0.9 ± 0.5% of sample minute−1. After 5 hours drying at 32°C and 79% relative humidity, casts were as moist as fresh casts (non‐significant Mann–Whitney U‐test) but had a solid appearance and were no longer dispersed by raindrop impact. Under simulated rainfall, dry casts were very slowly fragmented into large aggregates (> 5 mm). The HC of casts was increased by repeated cycles of wetting and drying but unaffected by length of air‐drying and natural ageing, and averaged 7 (3, n = 6), 20 (3, n = 7) and 32 (1, n = 45) cm hour−1 for bare soil, soil + cast and all casts, respectively (standard error, sample size). Except for bare soil, these values were greater than the greatest rainfall intensities recorded locally. The consequences for soil erosion, nutrient losses and water infiltration are discussed.
Emission of herbivore‐induced volatile terpenoids from two hybrid aspen (Populus tremula×tremuloides) clones under ambient and elevated ozone concentrations in the field
Authors: BLANDE JAMES D. , TIIVA PÄIVI , OKSANEN ELINA , HOLOPAINEN JARMO K.
Published: October 2007

Tropospheric ozone levels are continuously rising due to human activities in the 21st century. Although the phytotoxic impact of ozone on plants has been well documented, the effect of ozone on plant emissions has received little attention. We have conducted a field‐based investigation utilizing two clones of hybrid aspen (Populus tremula L. ×P. tremuloides Michx.) in a free‐air ozone concentration enrichment (FACE) facility. The effects of chronic exposure to moderately increased concentrations of ozone on insect‐induced terpene emissions by these trees were investigated. We used two herbivore species, Phyllobius piri, and Epirrita autumnata, both of which can reach outbreak levels on deciduous trees in Northern Europe. Our results indicated only very small changes in emissions due to increased ozone levels, but showed induction of some terpenes, particularly the monoterpene trans‐β‐ocimene and the homoterpene (E)‐4,8‐dimethyl‐1,3,7‐nonatriene, in response to insect feeding. Here, we consider the positive aspects of conducting this type of study in the field and consider the possible influences of other field‐based environmental factors.