bluuebunny/crossref_metadata_2025 huggingface dataset:
Tests of relative earthquake location techniques using synthetic data
Authors: Lin Guoqing , Shearer Peter
Published: April 2005

We compare three relative earthquake location techniques using tests on synthetic data that simulate many of the statistical properties of real travel time data. The methods are (1) the hypocentroidal decomposition method of Jordan and Sverdrup (1981), (2) the source‐specific station term method (SSST) of Richards‐Dinger and Shearer (2000), and (3) the modified double‐difference method (DD) of Waldhauser and Ellsworth (2000). We generate a set of synthetic earthquakes, stations, and arrival time picks in half‐space velocity models. We simulate the effect of travel time variations caused by random picking errors, station terms, and general three‐dimensional velocity structure. We implement the algorithms with a common linearized approach and solve the systems using a conjugate gradient method. We constrain the mean location shift to be zero for the hypocentroidal decomposition and double‐difference locations. For a single compact cluster of events, these three methods yield very similar improvements in relative location accuracy. For distributed seismicity, the DD and SSST algorithms both provide improved relative locations of comparable accuracy. We also present a new location technique, termed the shrinking box SSST method, which provides some improvement in absolute location accuracy compared to the SSST method. In our implementation of these algorithms, the SSST method runs significantly faster than the DD method.
Implications of climate change for freshwater inflows to the Arctic Ocean
Authors: Arnell Nigel W.
Published: April 2005

Observational evidence suggests that river inflows to the Arctic Ocean have increased over the last 30 years. Continued increases have the potential to alter the freshwater balance in the Arctic and North Atlantic Oceans and hence the thermohaline circulation. Simulations with a macroscale hydrological model and climate change scenarios derived from six climate models and two emissions scenarios suggest increases of up to 31% in river inflows to the Arctic by the 2080s under high emissions and up to 24% under lower emissions, although there are large differences between climate models. Uncertainty analysis suggests low sensitivity to model form and parameterization but higher sensitivity to the input data used to drive the model. The addition of up to 0.048 sverdrup (Sv, 106 m3 s−1) is a large proportion of the 0.06–0.15 Sv of additional freshwater that may trigger thermohaline collapse. Changes in the spatial distribution of inflows to the Arctic Ocean may influence circulation patterns within the ocean.
The yeast cyclin-dependent kinase inhibitor Sic1 and mammalian p27Kip1 are functional homologues with a structurally conserved inhibitory domain
Authors: BARBERIS Matteo , DE GIOIA Luca , RUZZENE Maria , SARNO Stefania , COCCETTI Paola , FANTUCCI Piercarlo , VANONI Marco , ALBERGHINA Lilia
Published: April 2005

In Saccharomyces cerevisiae, Sic1, an inhibitor of Cdk (cyclin-dependent kinase), blocks the activity of S-Cdk1 (Cdk1/Clb5,6) kinase that is required for DNA replication. Deletion of Sic1 causes premature DNA replication from fewer origins, extension of the S phase and inefficient separation of sister chromatids during anaphase. Despite the well-documented relevance of Sic1 inhibition of S-Cdk1 for cell cycle control and genome instability, the molecular mechanism by which Sic1 inhibits S-Cdk1 activity remains obscure. In this paper, we show that Sic1 is functionally and structurally related to the mammalian Cki (Cdk inhibitor) p27Kip1 of the Kip/Cip family. A molecular model of the inhibitory domain of Sic1 bound to the Cdk2–cyclin A complex suggested that the yeast inhibitor might productively interface with the mammalian Cdk2–cyclin A complex. Consistent with this, Sic1 is able to bind to, and strongly inhibit the kinase activity of, the Cdk2–cyclin A complex. In addition, comparison of the different inhibitory patterns obtained using histone H1 or GST (glutathione S-transferase)–pRb (retinoblastoma protein) fusion protein as substrate (the latter of which recognizes both the docking site and the catalytic site of Cdk2–cyclin A) offers interesting suggestions for the inhibitory mechanism of Sic1. Finally, overexpression of the KIP1 gene in vivo in Saccharomyces cerevisiae, like overexpression of the related SIC1 gene, rescues the cell cycle-related phenotype of a sic1Δ strain. Taken together, these findings strongly indicate that budding yeast Sic1 and mammalian p27Kip1 are functional homologues with a structurally conserved inhibitory domain.
Characteristics of glutamine metabolism in human precision-cut kidney slices: a 13C-NMR study
Authors: VITTORELLI Anne , GAUTHIER Catherine , MICHOUDET Christian , MARTIN Guy , BAVEREL Gabriel
Published: April 2005

The metabolism of glutamine, a physiological substrate of the human kidney, plays a major role in systemic acid–base homoeostasis. Not only because of the limited availability of human renal tissue but also in part due to the lack of adequate cellular models, the mechanisms regulating the renal metabolism of this amino acid in humans have been poorly characterized. Therefore given the renewed interest in their use, human precision-cut renal cortical slices were incubated in Krebs–Henseleit medium (118 mM NaCl, 4.7 mM KCl, 1.18 mM KH2PO4, 1.18 mM MgSO4·7H2O, 24.9 mM NaHCO3 and 2.5 mM CaCl2·2H2O) with 2 mM unlabelled or 13C-labelled glutamine residues. After incubation, substrate utilization and product formation were measured by enzymatic and NMR spectroscopic methods. Glutamate accumulation tended to plateau but glutamine removal and ammonia, alanine and lactate production as well as flux through GLDH (glutamate dehydrogenase) increased to various extents with time for up to 4 h of incubation indicating the metabolic viability of the slices. Valproate, a stimulator of renal glutamine metabolism, markedly and in a dose-dependent fashion increased ammonia production. With [3-13C]glutamine as a substrate, and in the absence and presence of valproate, [13C]glutamate, [13C]alanine and [13C]lactate accounted for 81 and 96%, 34 and 63%, 30 and 46% of the glutamate, alanine and lactate accumulations measured enzymatically respectively. The slices also metabolized glutamine and retained their reactivity to valproate during incubations lasting for up to 48 h. These results demonstrate that, although endogenous metabolism substantially operates in the presence of glutamine, human precision-cut renal cortical slices are metabolically viable and strongly respond to the ammoniagenic effect of valproate. Thus, this experimental model is suitable for metabolic and pharmaco-toxicological studies.
Nitric oxide consumption through lipid peroxidation in brain cell suspensions and homogenates
Authors: KEYNES Robert G. , GRIFFITHS Charmaine H. , HALL Catherine , GARTHWAITE John
Published: April 2005

Mechanisms which inactivate NO (nitric oxide) are probably important in governing the physiological and pathological effects of this ubiquitous signalling molecule. Cells isolated from the cerebellum, a brain region rich in the NO signalling pathway, consume NO avidly. This property was preserved in brain homogenates and required both particulate and supernatant fractions. A purified fraction of the particulate component was rich in phospholipids, and NO consumption was inhibited by procedures that inhibited lipid peroxidation, namely a transition metal chelator, the vitamin E analogue Trolox and ascorbate oxidase. The requirement for the supernatant was accounted for by its content of ascorbate which catalyses metal-dependent lipid peroxidation. The NO-degrading activity of the homogenate was mimicked by a representative mixture of brain lipids together with ascorbate and, under these conditions, the lipids underwent peroxidation. In a suspension of cerebellar cells, there was a continuous low level of lipid peroxidation, and consumption of NO by the cells was decreased by approx. 50% by lipid-peroxidation inhibitors. Lipid peroxidation was also abolished when NO was supplied at a continuously low rate (∼100 nM/min), which explains why NO consumption by this process is saturable. Part of the activity remaining after the inhibition of lipid peroxidation was accounted for by contaminating red blood cells, but there was also another component whose activity was greatly enhanced when the cells were maintained under air-equilibrated conditions. A similar NO-consuming process was present in cerebellar glial cells grown in tissue culture but not in blood platelets or leucocytes, suggesting a specialized mechanism.
Bulgecin A: a novel inhibitor of binuclear metallo-β-lactamases
Authors: SIMM Alan M. , LOVERIDGE E. Joel , CROSBY John , AVISON Matthew B. , WALSH Timothy R. , BENNETT Peter M.
Published: April 2005

Bulgecin A, a sulphonated N-acetyl-D-glucosamine unit linked to a 4-hydroxy-5-hydroxymethylproline ring by a β-glycosidic linkage, is a novel type of inhibitor for binuclear metallo-β-lactamases. Using steady-state kinetic analysis with nitrocefin as the β-lactam substrate, bulgecin A competitively inhibited the metallo-β-lactamase BceII from Bacillus cereus in its two-zinc form, but failed to inhibit when the enzyme was in the single-zinc form. The competitive inhibition was restored by restoring the second zinc ion. The single-zinc metallo-β-lactamase from Aeromonas veronii bv. sobria, ImiS, was not inhibited by bulgecin A. The tetrameric L1 metallo-β-lactamase from Stenotrophomonas maltophilia was subject to partial non-competitive inhibition, which is consistent with a kinetic model in which the enzyme bound to inhibitor retains catalytic activity. Docking experiments support the conclusion that bulgecin A co-ordinates to the zinc II site in metallo-β-lactamases via the terminal sulphonate group on the sugar moiety.
Mode of action of xylogalacturonan hydrolase towards xylogalacturonan and xylogalacturonan oligosaccharides
Authors: ZANDLEVEN Joris , BELDMAN Gerrit , BOSVELD Margaret , BENEN Jaques , VORAGEN Alphons
Published: April 2005

XGH (xylogalacturonan hydrolase; GH 28) is an enzyme that is capable of degrading XGA (xylogalacturonan), which is a polymer of α-D-galacturonic acid, highly substituted with β-D-xylose. XGA is present in cell walls of various plants and exudates, such as gum tragacanth. XGA oligosaccharides were derived from an XGH digestion of gum tragacanth, then fractionated, and analysed for their sugar composition and structure by matrix-assisted laser-desorption ionization–time-of-flight MS and nanospray MS. Several oligosaccharides from XGA were identified with different galacturonic acid/xylose ratios including five oligosaccharide isomers. Although XGH can act as an endo-enzyme, product-progression profiling showed that the disaccharide GalAXyl was predominantly produced from XGA by XGH, which indicated also an exolytic action. The latter was further supported by degradation studies of purified oligosaccharide GalA4Xyl3. It was shown that XGH acted from the non-reducing end towards the reducing end of this oligosaccharide, and showed the processive character of XGH. The results from this study further show that although XGH prefers to act between two xylosidated GalA units, it tolerates unsubstituted GalA units in its −1 and +1 subsites.
Role of compartmentalized redox-active iron in hydrogen peroxide-induced DNA damage and apoptosis
Authors: TENOPOULOU Margarita , DOULIAS Paschalis-Thomas , BARBOUTI Alexandra , BRUNK Ulf , GALARIS Dimitrios
Published: April 2005

Jurkat cells in culture were exposed to oxidative stress in the form of continuously generated hydrogen peroxide, obtained by the addition of glucose oxidase to the medium. This treatment induced a rapid, dose-dependent increase in the ICIP (intracellular calcein-chelatable iron pool). Early destabilization of lysosomal membranes and subsequent nuclear DNA strand breaks were also observed, as evaluated by the Acridine Orange relocation test and the comet assay respectively. Somewhat later, these effects were followed by a lowered mitochondrial membrane potential, with release of cytochrome c and apoptosis-inducing factor. These events were all prevented if cells were pretreated with the potent iron chelator DFO (desferrioxamine) for a period of time (2–3 h) long enough to allow the drug to reach the lysosomal compartment following fluid-phase endocytosis. The hydrophilic calcein, a cleavage product of calcein acetoxymethyl ester following the action of cytosolic esterases, obviously does not penetrate intact lysosomal membranes, thus explaining why ICIP increased dramatically following lysosomal rupture. The rapid decrease in ICIP after addition of DFO to the medium suggests draining of cytosolic iron to the medium, rather than penetration of DFO through the plasma membrane. Most importantly, these observations directly connect oxidative stress and resultant DNA damage with lysosomal rupture and the release of redox-active iron into the cytosol and, apparently, the nucleus.
Ixolaris: a Factor Xa heparin-binding exosite inhibitor
Authors: MONTEIRO Robson Q. , REZAIE Alireza R. , RIBEIRO José M. C. , FRANCISCHETTI Ivo M. B.
Published: April 2005

Ixolaris is a two-Kunitz TFPI (tissue factor pathway inhibitor) from the tick salivary gland. In contrast with human TFPI, Ixolaris binds tightly to the zymogen FX (Factor X) and to dansyl-Glu-Gly-Arg-chloromethyl ketone-treated FXa (DEGR-FXa; active-site-blocked FXa), indicating that exosites are involved in the FX(a)–Ixolaris interaction. Here we provide evidence that Ixolaris binds specifically to the FXa HBE (heparin-binding exosite), since (i) it markedly decreases the inhibition of FXa by the antithrombin–heparin but not the antithrombin–pentasaccharide complex, (ii) it impairs FXa binding to Sepharose-immobilized heparin, and (iii) it allosterically modulates the catalytic activity of FXa for small chromogenic substrates (S-2765). By using a series of recombinant FXa mutants in which the HBE is mutated, we have identified the importance of amino acids involved in the enzyme–inhibitor interaction as being in the following order: Arg-93≫Arg-165≥Lys-169>Lys-236>Lys-96>Arg-240>Arg-125. Ixolaris at appropriate concentrations also inhibits thrombin formation in vitro by the assembled prothrombinase complex, a process that is critically dependent on the FXa HBE. Ixolaris is the first inhibitor characterized to date that binds specifically to the FXa HBE.
Bifunctional promoter of type IV collagen COL4A5 and COL4A6 genes regulates the expression of α5 and α6 chains in a distinct cell-specific fashion
Authors: SUND Malin , MAESHIMA Yohei , KALLURI Raghu
Published: April 2005

Type IV collagen is present ubiquitously in basement membranes. A bifunctional promoter regulates the expression of the α1/α2 genes, and the α3/α4 and the α5/α6 genes are also considered to be regulated by putative bifunctional promoters. Unlike the other type IV collagen chains, the α5(IV) and α6(IV) chains do not always co-localize and are present in distinct basement membranes. To address such dichotomy in the α5(IV) and α6(IV) gene regulation, we cloned a mouse genomic DNA fragment containing the promoter region between the two transcription start sites of these genes and we then placed this putative promoter sequence between the chloramphenicol acetyltransferase and Luciferase reporter genes, so that these genes would be transcribed in opposite directions in this unique construct. Glomerular endothelial cells and mesangial cells generate the kidney glomerular basement membrane, which always contains the α5(IV) chain but not the α6(IV) chain. In contrast, the basement membranes of Bowman's capsule and distal tubuli (produced by the tubular epithelial cells) contain the α6(IV) chain. We demonstrate that, in response to TGF-β (transforming growth factor β), epidermal growth factor, vascular endothelial growth factor and platelet-derived growth factor, expression from the α5(IV) gene is significantly enhanced in the glomerular endothelial cells and mesangial cells, but not expression from the α6(IV) gene. In contrast, the expression from the α6(IV) gene, and not that from the α5(IV) gene, was significantly enhanced in response to growth factors in the tubular epithelial cells. Our results demonstrate that the proximal bifunctional promoter regulates the expression of the α5(IV) and α6(IV) genes in a cell-specific manner and offers the first demonstration of the promoter plasticity in growth factor regulation of type IV collagen genes in different tissues of the body.
Sensitivity of plant mitochondrial terminal oxidases to the lipid peroxidation product 4-hydroxy-2-nonenal (HNE)
Authors: WINGER Alison M. , MILLAR A. Harvey , DAY David A.
Published: April 2005

We have investigated the effect of the lipid peroxidation product, HNE (4-hydroxy-2-nonenal), on plant mitochondrial electron transport. In mitochondria isolated from Arabidopsis thaliana cell cultures, HNE inhibited succinate-dependent oxygen consumption via the Aox (alternative oxidase), but had minimal effect on respiration via Cox (cytochrome c oxidase). Maximal Cox activity, measured with reduced cytochrome c as substrate, was only slightly inhibited by high concentrations of HNE, at which Aox was completely inhibited. Incubation with HNE prevented dimerization of the Aox protein, suggesting that one site of modification was the conserved cysteine residue involved in dimerization and activation of this enzyme (CysI). However, a naturally occurring isoform of Aox lacking CysI and unable to be dimerized, LeAox1b from tomato (Lycopersicon esculentum), was equally sensitive to HNE inhibition, showing that other amino acid residues in Aox also interact with HNE. The presence of HNE in vivo in Arabidopsis cell cultures was also investigated. Induction of oxidative stress in the cell cultures by the addition of hydrogen peroxide, antimycin A or menadione, caused a significant increase in hydroxyalkenals (of which HNE is the most prominent). Western blotting of mitochondrial proteins with antibodies against HNE adducts, demonstrated significant modification of proteins during these treatments. The implications of these results for the response of plants to reactive oxygen species are discussed.
Dispersion of the Raman depolarization ratio of HDO in water and heavy water from 295to368K, and from concentrated NaClO4∕D2O∕H2O
Authors: Walrafen George E.
Published: April 2005

The dispersion of the Raman depolarization ratio ρL was measured for HDO in H2O and in D2O. ρL for the decoupled OD stretch displays a maximum at 2575±15cm−1 at 296K and a minimum at 2675±15cm−1, in agreement with the isosbestic point 2570±10cm−1, and the enthalpy dispersion maximum, 2650–2675cm−1, respectively. However, three extrema were uncovered in ρL for the OH stretch of HDO in D2O, and their positions agree with the frequencies of a minimum and a maximum in the enthalpy dispersion and with the isosbestic frequency. The frequency of the ρL maximum (OH stretch) lies just above the frequency corresponding to the joint angle-frequency probability maximum. [Lawrence and Skinner, J. Chem. Phys. 118, 264 (2003)]. The low- and high-frequency minima in ρL (OH stretch), correspond, respectively, to very strong H-bonds, and extremely weak, long, bent H bonds. The frequencies of the maxima and minima in ρL for the decoupled OH and OD stretches are independent of temperature within experimental error between 295 and 368K. ρL was also measured for the OD stretch from saturated NaClO4 in D2O∕H2O; it displays a maximum at 2560±20cm−1 and a sharp minimum at 2650±5cm−1. The shape of the dispersion of (β∕α)2≈ρL for HDO in D2O was calculated with the aid of the molecular dynamics results of Lawrence and Skinner. β2 is the anisotropic polarizability and α is the isotropic polarizability. A maximum resulted in the calculated dispersion at 3400±10cm−1, in excellent agreement with the measured maximum of 3395±15cm−1. The H-bond angles decrease far below 180° as the OH-stretching frequency increases to 3700cm−1 and above. Such small H-bond angles, and very large O–O distances, are tantamount to broken H-bonds and are thought to produce the minimum in ρL near 2650cm−1.
The elastic constants and related properties of β-HMX determined by Brillouin scattering
Authors: Stevens Lewis L. , Eckhardt Craig J.
Published: April 2005

By scattering from a variety of acoustic phonons, a complete stiffness tensor has been determined for crystalline β-HMX. The results are compared with recent experimental and theoretical determinations of the elastic constants and bulk modulus. Reasons for disagreement are discussed in terms of experimental limitations and anharmonic effects. The observed ordering of stiffness constants, C11 (18.4 GPa), C22 (14.4 GPa), and C33 (12.4 GPa), is qualitatively associated with physical phenomena including cleavage planes, patterns in crystal growth, and molecular packing. This interpretation is further corroborated by the linear compressibilities plotted in three crystallographic planes. The Voigt–Reuss–Hill bulk and shear moduli were found to be 9.9 and 3.7 GPa, respectively. The elasticity of β-HMX is also discussed in relation to proposed mechanisms for the initiation of detonation.
Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules
Authors: Praprotnik Matej , Janežič Dušanka
Published: April 2005

A series of molecular dynamics (MD) simulations of nonlinear molecules has been performed to test the efficiency of newly introduced semianalytical second-order symplectic time-reversible MD integrators that combine MD and the standard theory of molecular vibrations. The simulation results indicate that for the same level of accuracy, the new algorithms allow significantly longer integration time steps than the standard second-order symplectic leap-frog Verlet method. Since the computation cost per integration step using new MD integrators with longer time steps is approximately the same as for the standard method, a significant speed-up in MD simulation is achieved.
Quantum and transport mobilities in an AlGaAs∕GaAs parabolic quantum-well structure
Authors: Yu G. , Studenikin S. A. , SpringThorpe A. J. , Aers G. C. , Austing D. G.
Published: April 2005

We study quantum and transport mobilities in a parabolic quantum-well structure when one or more subbands are occupied. We developed an original analytical method to extract the quantum mobility from the multiple occupied subband transport characteristics at low temperature. We tune the carrier density and hence the subband structure of the parabolic quantum well over a wide range by illumination with a red light-emitting diode. In order to obtain the quantum mobilities, Fourier transforms of the first differential of the experimental magnetoresistance traces (ρxx versus magnetic field) are taken and fitted by a conductivity tensor model in the same magnetic field range. We find that both the quantum and transport mobilities increase nonlinearly with increasing carrier density for both the first and second subbands and conclude that the intersubband scattering is predominantly large angle.
Density dependence of trace tritium transport in H-mode Joint European Torus plasma
Authors: Voitsekhovitch I. , Garbet X. , McDonald D. C. , Zastrow K.-D. , Adams M. , Baranov Yu. , Belo P. , Bertalot L. , Budny R. , Conroy S. , Cordey J. G. , Garzotti L. , Mantica P. , McCune D. , Ongena J. , Parail V. , Popovichev S. , Stork D. , Whiteford A. D. ,   JET EFDA contributors
Published: April 2005

Tritium transport in edge localized mode (ELM) high confinement (H-mode) plasmas is analyzed here as a function of density for discharges from the recent trace tritium experimental campaign performed on Joint European Torus. In this campaign small amounts of tritium have been puffed or injected (with neutral beam injectors) into deuterium plasmas [K.-D. Zastrow, J. M. Adams, Yu. Baranov et al., Plasma Phys. Controlled Fusion 46, B255 (2004)]. Information about the tritium has been obtained from the evolution of the profiles of neutron emission simulated via the TRANSP [R. J. Goldston, D. C. McCune, H. H. Towner, S. L. Davis, R. J. Hawryluk, and G. L. Schmidt, J. Comput. Phys. 43, 61 (1981)] and SANCO (L. Lauro-Taroni, B. Alper, R. Giannella, K. Lawson, F. Marcus, M. Mattioli, P. Smeulders, and M. Von Hellermann, Proceedings of the 21st European Conference on Controlled Fusion and Plasma Physics, Montpelier, France, 1994) codes. A strong inverse correlation of tritium transport with plasma density is found in this analysis. The low tritium transport at high density is close to neoclassical values while the transport becomes strongly anomalous in low density plasmas. The thermal transport does not exhibit such a strong density dependence, leading to a varying ratio of thermal to tritium transport in these discharges. An interpretation of the density effects on the trace tritium transport, partially based on the test particle simulations in plasmas with stochastic magnetic field, is proposed. A simple model for the tritium diffusion coefficient and convective velocity, which includes the modification of the neoclassical particle diffusion in presence of electromagnetic turbulence [A. I. Smolyakov and P. N. Yushmanov, Nucl. Fusion 35, 383 (1993)] completed with an empirical density dependence, is developed. This model has positive β dependence in agreement with the results of the similarity experiments performed for trace tritium transport.
Structure formation by modulational interactions between lower-hybrid and dispersive Alfvén waves
Authors: Hall J. O. , Shukla P. K. , Eliasson B.
Published: April 2005

The nonlinear interaction between finite amplitude lower-hybrid (LH) and dispersive Alfvén (DA) waves is considered. For this purpose, a set of equations is derived, which governs the three-dimensional dynamics of nonlinearly coupled LH and DA waves propagating obliquely to an external magnetic field. The interaction between the two wave modes is mediated by the Reynolds stress of the LH waves and the density perturbation associated with the DA wave. Additional terms due to self-interaction nonlinearity of the DA wave are included in order to describe large-amplitude DA waves. Three-wave decay and modulational interactions of the system are analyzed by means of a newly derived nonlinear dispersion relation, which predicts the instability of a finite-amplitude LH pump wave. The fully nonlinear dynamics and the LH wave collapse are studied by solving the governing equations numerically.
Optical and microstructural studies of InGaN∕GaN single-quantum-well structures
Authors: Graham D. M. , Soltani-Vala A. , Dawson P. , Godfrey M. J. , Smeeton T. M. , Barnard J. S. , Kappers M. J. , Humphreys C. J. , Thrush E. J.
Published: April 2005

We have studied the low-temperature (T=6K) optical properties of a series of InGaN∕GaN single-quantum-well structures with varying indium fractions. With increasing indium fraction the peak emission moves to lower energy and the strength of the exciton–longitudinal-optical (LO)-phonon coupling increases. The Huang–Rhys factor extracted from the Fabry–Pérot interference-free photoluminescence spectra has been compared with the results of a model calculation, yielding a value of approximately 2nm for the in-plane localization length scale of carriers. We have found reasonable agreement between this length scale and the in-plane extent of well-width fluctuations observed in scanning transmission electron microscopy high-angle annular dark-field images. High-resolution transmission electron microscopy images taken with a short exposure time and a low electron flux have not revealed any evidence of gross indium fluctuations within our InGaN quantum wells. These images could not, however, rule out the possible existence of small-scale indium fluctuations, of the order of a few at. %.
Characteristics of confinement and stability in large helical device edge plasmas
Authors: Komori A. , Sakakibara S. , Morisaki T. , Watanabe K. Y. , Narushima Y. , Toi K. , Ohdachi S. , Masuzaki S. , Kobayashi M. , Shoji M. , Ohyabu N. , Ida K. , Tanaka K. , Kawahata K. , Narihara K. , Morita S. , Peterson B. J. , Sakamoto R. , Yamada H. , Ikeda K. , Kaneko O. , Kobayashi M. , Kubo S. , Miyazawa J. , Nagaoka K. , Nakanishi H. , Ohkubo K. , Oka Y. , Osakabe M. , Shimozuma T. , Takeiri Y. , Tsumori K. , Yamada I. , Yoshimura Y. , Yoshinuma M. , Motojima O. ,   LHD Experimental Group
Published: April 2005

Recent progress in the heating capability in the large helical device [O. Motojima et al., Phys. Plasmas 6, 1843 (1999)] has allowed the highest average β value (4.1%) obtained in the helical devices, and enables exploration of magnetohydrodynamics (MHD) stability in this β region. MHD activities in the periphery are found to become stable spontaneously from the inner region to the outer region when the averaged β value exceeds a threshold, and then a flattening of the electron temperature profile is observed around the resonant surface. Such a flattening can be formed externally by producing an m∕n=1∕1 magnetic island, and the complete stabilization of the m∕n=1∕1 mode is demonstrated by the moderate island width. In addition, attempts to control peripheral plasmas are also performed by using a limiter and a local island divertor utilizing the m∕n=1∕1 island, to improve plasma confinement and, especially, to stabilize pressure-driven modes in the present study. The stabilization of peripheral MHD modes is obtained with both approaches, and this indicates that these are available to the production of higher-β plasmas without edge MHD activities.
Variance reduction for Monte Carlo solutions of the Boltzmann equation
Authors: Baker Lowell L. , Hadjiconstantinou Nicolas G.
Published: April 2005

We show that by considering only the deviation from equilibrium, significant computational savings can be obtained in Monte Carlo evaluations of the Boltzmann collision integral for flow problems in the small Mach number (Ma) limit. The benefits of this variance reduction approach include a significantly reduced statistical uncertainty when the deviation from equilibrium is small, and a flow-velocity signal-to-noise ratio that remains approximately constant with Ma in the Ma⪡1 limit. This results in stochastic Boltzmann solution methods whose computational cost for a given signal-to-noise ratio is essentially independent of Ma for Ma⪡1; our numerical implementation demonstrates this for Mach numbers as low as 10−5. These features are in sharp contrast to current particle-based simulation techniques in which statistical sampling leads to computational cost that is proportional to Ma−2, making calculations at small Ma very expensive.
Experimental investigation of self-induced thermocapillary convection for an evaporating meniscus in capillary tubes using micro–particle image velocimetry
Authors: Buffone C. , Sefiane K. , Christy J. R. E.
Published: April 2005

The present paper reports an experimental investigation of the self-induced liquid convection for an evaporating meniscus in small capillary tubes. The strong evaporative cooling at the triple contact line leads to a variation in temperature along the liquid–vapor interface, which generates a gradient of surface tension that in turn drives the observed convection. Ethanol and methanol in three tube sizes (600, 900, and 1630 μm) were investigated in this study. The flow pattern in the liquid phase has been characterized using a micro–particle image velocimetry (PIV) technique with a vector spatial resolution of 640 nm. Thermocapillary Marangoni convection is observed in horizontal diametrical sections of the horizontally oriented capillary tubes as two contrarotating vortices of similar strength, whereas in vertical diametrical sections a single clockwise vortex is mostly present. This distortion of the flow pattern could be attributed to gravity. The distortion and loss of symmetry in the vertical section is found to exhibit an oscillatory behavior. The convection (represented by the vorticity) is found to be stronger for more volatile liquids and smaller tube sizes. The vorticity normalized with the convective time scale is found to be higher for the less volatile liquid and to increase with the tube radius. Therefore, a further correction of the normalized vorticity using a dimensionless liquid saturated vapor pressure leads to a parameter that is found independent of the tube size and the liquid properties, suggesting that the phenomena described here are universal and dictated by the local conditions near the triple line.
Circumferential-mode, quasi-ring-type, magnetoelectric laminate composite—a highly sensitive electric current and∕or vortex magnetic field sensor
Authors: Dong Shuxiang , Bai John G. , Zhai Junyi , Li Jie-Fang , Lu G.-Q. , Viehland D. , Zhang Shujun , Shrout T. R.
Published: April 2005

A quasi-ring-type magnetoelectric (ME) laminate composite consisting of a circumferentially poled piezoelectric Pb(Zn1∕3Nb2∕3O)3-4.5at.%PbTiO3single-crystal ring and two circumferentially magnetized magnetostrictive TERFENOL-D rings was fabricated and found to have a giant ME voltage coefficient of 2.2V∕Oe, or equivalently a ME field coefficient of 5.5V∕cmOe, over the frequency range of 0.5<f<105Hz. This circumferential-mode quasiring ME laminate can detect ac currents (noncontact) as small as 10−7A, and∕or a vortex magnetic field as small as 6×10−12Tesla. In addition, we demonstrated current sensing capability of the quasiring laminate in a power electronics module.
Epitaxial condition and polarity in GaN grown on a HfN-buffered Si(111) wafer
Authors: Xu X. , Armitage R. , Shinkai Satoko , Sasaki Katsutaka , Kisielowski C. , Weber E. R.
Published: April 2005

Single-crystal GaN thin films have been deposited epitaxially on a HfN-buffered Si(111) substrates by molecular-beam epitaxy. The microstructural and compositional characteristics of the films were studied in detail by transmission electron microscopy (TEMs). Cross-sectional TEM investigations have revealed the crystallographic orientation relationship in different GaN∕HfN∕Si layers. GaN film polarity is studied by conventional TEM and convergent beam electron diffraction simulations, and the results show that the GaN film has a Ga polarity with relatively high density of inversion domains. Based on our observations, growth mechanisms related to the structural properties are discussed.
Electroluminescence in polymer-fullerene photovoltaic cells
Authors: Kim Heejoo , Kim Jin Young , Park Sung Heum , Lee Kwanghee , Jin Youngeup , Kim Jinwoo , Suh Hongsuk
Published: April 2005

We report electroluminescence (EL) in photovoltaic (PV) cells based on semiconducting polymer-fullerene composites. By applying a forward bias to the PV cells, the devices exhibited a clear EL action with a peak around 1.5 eV. We ascribe this peak to an “electric field-assisted exciplex” formed between the electrons in the fullerenes and the holes in the polymers, thereby resulting in radiative recombination in the composites. This finding is totally unexpected because of a strong photoluminescence quenching in the same materials. Since the same devices also showed typical photovoltaic effects under illumination, our results demonstrate a dual functionality in one device; polymer photovoltaic cells and polymer light-emitting diodes.
Toward the formation of three-dimensional nanostructures by electrochemical etching of silicon
Authors: Kleimann P. , Badel X. , Linnros J.
Published: April 2005

We report a simple technique to form various kinds of three-dimensional structures in silicon. The process flow is only composed of two steps: lithography and electrochemical etching (“LEE”). The LEE process is an easy and low-cost solution for the fabrication of high-aspect-ratio structures such as walls, tubes, and pillars. Here we demonstrate the possibility to apply the LEE process on the submicrometer scale, indicating that it is a promising tool for silicon nanomachining.
Low symmetry phase in (001) BiFeO3 epitaxial constrained thin films
Authors: Xu Guangyong , Hiraka H. , Shirane G. , Li Jiefang , Wang Junling , Viehland D.
Published: April 2005

The lattice of (001)-oriented BiFeO3 epitaxial thin film has been identified by synchrotron x-ray diffraction. By choosing proper scattering zones containing the fixed (001) reflection, we have shown that low-symmetry phases similar to a MA phase exist in the thin film at room temperature. These results demonstrate a change in phase stability from rhombohedral in bulk single crystals, to a modified monoclinic structure in epitaxial thin films.
Structure change of pyrochlore Sm2Ti2O7 at high pressures
Authors: Zhang F. X. , Manoun B. , Saxena S. K. , Zha C. S.
Published: April 2005

Structural evolution of pyrochlore titanate Sm2Ti2O7 at high pressures was investigated by in situ Raman and x-ray diffraction methods. An intermediate phase was found at high pressures. The structure is a distorted pyrochlore, where anions are disordered after 40GPa while the cations are still somewhat ordered up to 51GPa. When the pyrochlore structure is severely distorted by external pressure, it transforms completely to an amorphous phase quenchable to room conditions.
Ascochyta blight of chickpea (Cicer arietinum L.): a review of biology, pathogenicity, and disease management
Authors: Pande S. , Siddique K. H. M. , Kishore G. K. , Bayaa B. , Gaur P. M. , Gowda C. L. L. , Bretag T. W. , Crouch J. H.
Published: April 2005

Ascochyta blight (AB), caused by Ascochyta rabiei is a major disease of chickpea (Cicer arietinum L.), especially in areas where cool, cloudy, and humid weather persists during the crop season. Several epidemics of AB causing complete yield loss have been reported. The fungus mainly survives between seasons through infected seed and in infected crop debris. Despite extensive pathological and molecular studies, the nature and extent of pathogenic variability in A. rabiei have not been clearly established. Accumulation of phenols, phytoalexins (medicarpin and maackiain), and hydrolytic enzymes has been associated with host-plant resistance (HPR). Seed treatment and foliar application of fungicides are commonly recommended for AB management, but further information on biology and survival of A. rabiei is needed to devise more effective management strategies. Recent studies on inheritance of AB resistance indicate that several quantitative trait loci (QTLs) control resistance. In this paper we review the biology of A. rabiei, HPR, and management options, with an emphasis on future research priorities.
Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat
Authors: Zwart R. S. , Thompson J. P. , Godwin I. D.
Published: April 2005

Pratylenchus thornei and P. neglectus are two species of root-lesion nematode that cause substantial yield losses in wheat. No commercially available wheat variety has resistance to both species. A doubled-haploid population developed from a cross between the synthetic hexaploid wheat line CPI133872 and the bread wheat Janz was used to locate and tag quantitative trait loci (QTLs) associated with resistance to both P. thornei and P. neglectus. Wheat plants were inoculated with both species of nematode in independent replicated glasshouse trials repeated over 2 years. Known locations of wheat microsatellite markers were used to construct a framework map. After an initial single-marker analysis to detect marker-trait linkages, chromosome regions associated with putative QTLs were targetted with microsatellite markers to increase map density in the chromosome regions of interest. In total, 148 wheat microsatellite markers and 21 amplified fragment length polymorphism markers were mapped. The codominant microsatellite marker Xbarc183 on the distal end of chromosome 6DS was allelic for resistance to both P. thornei and P. neglectus. The QTL were designated QRlnt.lrc-6D.1 and QRlnn.lrc-6D.1, for the 2 traits, respectively. The allele inherited from CPI133872 explained 22.0–24.2% of the phenotypic variation for P. thornei resistance, and the allele inherited from Janz accounted for 11.3–14.0% of the phenotypic variation for P. neglectus resistance. Composite interval mapping identified markers that flank a second major QTL on chromosome 6DL (QRlnt.lrc-6D.2) that explained 8.3–13.4% of the phenotypic variation for P. thornei resistance. An additional major QTL associated with P. neglectus resistance was detected on chromosome 4DS (QRlnn.lrc-4D.1) and explained a further 10.3–15.4% of the phenotypic variation. The identification and tagging of nematode resistance genes with molecular markers will allow appropriate allele combinations to be selected, which will aid the successful breeding of wheat with dual nematode resistance.
Assessment of internal quality attributes of mandarin fruit. 1. NIR calibration model development
Authors: Guthrie J. A. , Walsh K. B. , Reid D. J. , Liebenberg C. J.
Published: April 2005

The utility of near infrared spectroscopy as a non-invasive technique for the assessment of internal eating quality parameters of mandarin fruit (Citrus reticulata cv. Imperial) was assessed. The calibration procedure for the attributes of TSS (total soluble solids) and DM (dry matter) was optimised with respect to a reference sampling technique, scan averaging, spectral window, data pre-treatment (in terms of derivative treatment and scatter correction routine) and regression procedure. The recommended procedure involved sampling of an equatorial position on the fruit with 1 scan per spectrum, and modified partial least squares model development on a 720–950-nm window, pre-treated as first derivative absorbance data (gap size of 4 data points) with standard normal variance and detrend scatter correction. Calibration model performance for the attributes of TSS and DM content was encouraging (typical Rc2 of >0.75 and 0.90, respectively; typical root mean squared standard error of calibration of <0.4 and 0.6%, respectively), whereas that for juiciness and total acidity was unacceptable. The robustness of the TSS and DM calibrations across new populations of fruit is documented in a companion study.
A genetic linkage map in autotetraploid lucerne adapted to northern Australia, and use of the map to identify DNA markers linked to resistance to Phytophthora medicaginis
Authors: Musial J. M. , Aitken K. S. , Mackie J. M. , Irwin J. A. G.
Published: April 2005

Phytophthora root rot, caused by Phytophthora medicaginis, is a major limitation to lucerne (Medicago sativa L.) production in Australia and North America. Quantitative trait loci (QTLs) involved in resistance to P. medicaginis were identified in a lucerne backcross population of 120 individuals. A genetic linkage map was constructed for tetraploid lucerne using 50 RAPD (randomly amplified polymorphic DNA), 104 AFLP (amplified fragment length polymorphism) markers, and one SSR (simple sequence repeat or microsatellite) marker, which originated from the resistant parent (W116); 13 markers remain unlinked. The linkage map contains 18 linkage groups covering 2136.5 cM, with an average distance of 15.0 cM between markers. Four of the linkage groups contained only either 2 or 3 markers. Using duplex markers and repulsion phase linkages the map condensed to 7 homology groups and 2 unassigned linkage groups. Three regions located on linkage groups 2, 14, and 18, were identified as associated with root reaction and the QTLs explained 6–15% of the phenotypic variation. The research also indicates that different resistance QTLs are involved in conferring resistance in different organs. Two QTLs were identified as associated with disease resistance expressed after inoculation of detached leaves. The marker, W11-2 on group 18, identified as associated with root reaction, contributed 7% of the phenotypic variation in leaf response in our population. This marker appears to be linked to a QTL encoding a resistance factor contributing to both root and leaf reaction. One other QTL, not identified as associated with root reaction, was positioned on group 1 and contributed to 6% of the variation. This genetic linkage map provides an entry point for future molecular-based improvement of lucerne in Australia, and markers linked to the QTLs we have reported should be useful for marker-assisted selection for partial resistance to P. medicaginis in lucerne.
Pulling Out Threads from the Cosmic Tapestry: Defining Filaments of Galaxies
Authors: Pimbblet Kevin A.
Published: April 2005

Filaments of galaxies are the dominant feature of modern large-scale redshift surveys. They can account for up to perhaps half of the baryonic mass budget of the Universe and their distribution and abundance can help constrain cosmological models. However, there remains no single, definitive way in which to detect, describe, and define what filaments are and their extent. This work examines a number of physically motivated, as well as statistical, methods that can be used to define filaments and examines their relative merits.
Mud bath dermatitis due to cinnamon oil
Authors: García‐Abujeta José Luis , De Larramendi Carlos Hernando , Berna José Pomares , Palomino Elena Muñoz
Published: April 2005

A case of long‐lasting, extensive eczematous and bullous dermatitis affecting exposed areas (arms and legs), beginning within 24 hr after having a mud bath with cinnamon essential oil in a spa, in a 74‐year‐old woman, is reported. Patch tests with the GEIDC standard battery and the dental battery (including clove essence and eugenol), cinnamon essence and its components were carried out 5 years later. Fragrance mix, cinnamon essence, eugenol, cinnamic alcohol and cinnamic aldehyde yielded a positive result. To our knowledge, this is the first case of cinnamon dermatitis after a mud bath.
Impact of introducing guidelines on anticoagulant reversal
Authors: Salamat A. , Seaton J. , Watson H. G.
Published: April 2005

summary. The production of clinical guidelines has become an accepted and lauded part of modern medicine. It is also widely perceived that these guidelines provide some sort of panacea for the problems that medicine faces. Our experience suggests otherwise. Triggered by on going anecdotal evidence of poor practice, we reviewed the effect on practice of a recently introduced local guideline on the management of major bleeding in patients on warfarin. Comparing 34 patients treated before and 48 patients after the introduction of the guideline, we found no significant improvement in prothrombin complex concentrate dosing or administration of vitamin K. The only improvement witnessed was in early assessment of the effect of the intervention on coagulation which improved from 10 to 35% of cases. Of major concern, in 10% of cases, there was no documentation to confirm or refute that prothrombin complex concentrate (PCC), which had been issued, had actually been administered to the patient.

The production and widespread dissemination of this local guideline did not achieve significant improvement in clinical practice. Possible reasons for failure to adhere to the guideline are discussed.
Frequency distribution of human platelet antigens in the Indian population
Authors: Kulkarni B. , Mohanty D. , Ghosh K.
Published: April 2005

summary.  This study was undertaken with an aim of establishing the frequency distribution of various human platelet antigens (HPA) in Indian populations by means of DNA‐based technology. A total of 1164 people belonging to various population groups were studied for the frequency distribution of HPA. DNA extraction was performed from peripheral venous blood samples. Polymerase chain reaction allele‐specific amplification technique was used for HPA genotyping. The HPA bands were visualized by using ethidium bromide‐stained agarose gel, after electrophoresis. The homozygosity of the HPA‐1b/1b genotype was found to be significantly higher (P < 0·05) in the Parsi population group and Vatalia Prajapati population group, compared to Maharashtrians. Frequency distribution of HPA‐1b in our populations was found to be slightly lower than that reported in some western populations. This study has established a DNA technique to diagnose cases of NAITP definitively and to treat these cases during the neonatal period, and also gives the frequency distribution of HPA in some of the Indian population.