bluuebunny/crossref_metadata_2025 huggingface dataset:
Initiation of a plume‐ridge interaction in the South Pacific recorded by high‐precision Pb isotopes along Hollister Ridge
Authors: Vlastélic Ivan , Dosso Laure
Published: May 2005

The southern Pacific Ocean offers the rare possibility to study a situation where a spreading ridge (the Pacific‐Antarctic Ridge (PAR)) migrates toward a fixed hot spot (the Louisville hot spot) (Small, 1995). Hollister Ridge is a 450 km long linear structure whose position, between the PAR axis and the most recent edifices of the Louisville hot spot trail, led some authors to suggest that the ridge is genetically related to the hot spot (Small, 1995; Wessel and Kroenke, 1997). Mapping and sampling of the ridge in 1996 revealed, however, that the contribution of the Louisville plume material to its mantle source is minor and suggested that it might be the result of intraplate deformation (Géli et al., 1998; Vlastélic et al., 1998). We report new, highly precise Pb isotopic data from Hollister Ridge, which (1) confirm that the maximal contribution of the Louisville plume, in the centrally, volcanic active part of the ridge, probably does not exceed 20% (15 and 35% for lower and upper limits) and (2) reveal through time an increasing plume influence. The initiation of the Louisville plume involvement in the source of Hollister Ridge is estimated to have occurred between 1.04 and 0.77 Myr ago. It thus followed closely the most recent volcanic activity reported along the Louisville trail (1.11 Ma (Koppers et al., 2004)). This suggests that Hollister Ridge has recorded the dispersion of the Louisville plume as the spreading ridge approached the hot spot. Assuming that the Louisville hot spot is located near the youngest seamount dredged along the Louisville seamount chain, Hollister Ridge lies along the shortest path of pressure release connecting the hot spot to the spreading axis. This path involves, first, an abrupt upwelling across the Eltanin fault system and, subsequently, a more progressive migration toward the spreading axis. Because Hollister Ridge is older than 2.5 Ma, the structure might not be the consequence of the plume‐ridge flow. Instead, Hollister Ridge most likely emplaced through a lithospheric crack (Géli et al., 1998), which, subsequently, may have captured the plume‐ridge flow.
Imaging the seismic structure of the crust and upper mantle beneath the Great Plains, Rio Grande Rift, and Colorado Plateau using receiver functions
Authors: Wilson David , Aster Richard , Ni James , Grand Stephen , West Michael , Gao Wei , Baldridge W. Scott , Semken Steve
Published: May 2005

The seismic structure of the crust and upper mantle of the southwestern United States is examined using receiver functions calculated from teleseismic arrivals recorded in the Colorado Plateau–Rio Grande Rift–Great Plains Seismic Transect (LA RISTRA) experiment. We apply receiver function estimation and filtering methods developed by Wilson and Aster (2005) to produce receiver functions with decreased sensitivity to noise and deconvolutional instability. Crustal thickness and Vp/Vs ratios are estimated using both direct and reverberated P‐to‐S receiver function modes. We apply regularized receiver function migration methods to produce a multiple‐suppressed image of the velocity discontinuity structure of the subsurface. Our results show that crustal thickness averages 44.1 ± 2.3 km beneath the Great Plains (GP) and 45.6 ± 1.1 km beneath the Colorado Plateau (CP). Crustal thinning beneath the Rio Grande Rift (RGR) is broadly symmetric about the rift axis, with the thinnest crust (35 km) located directly beneath the rift axis, suggesting a pure shear stretched lithosphere beneath the RGR. We also observe a prominent northwest dipping discontinuity, ranging from 65 to 85 km deep beneath the CP, and possible subcrustal discontinuities beneath the GP. These discontinuities, along with recent xenolith data, are consistent with preserved ancient lithospheric structures such as relict suture zones associated with Proterozoic subduction. We observe an upper mantle discontinuity at 220–300 km depth that may correlate with similar discontinuities observed beneath eastern North America. We also observe relatively flat discontinuities at 410 and 660 km depth, indicating there is not a large‐scale thermal anomaly beneath the RGR at these depths.
Time-resolved photoluminescence and Raman scattering of InAsSb∕InP quantum dots
Authors: Marcinkevičius Saulius , Qiu Yueming , Leon Rosa , Ibáñez Jordi , Cuscó Ramon , Artús Lluís
Published: May 2005

InAsSb quantum dots (QDs) grown by metalorganic vapor phase epitaxy on In0.53Ga0.47As∕InP under different TMSb∕AsH3 flow ratios have been characterized by means of continuous wave and time-resolved photoluminescence (PL) as well as Raman scattering. It was found that the flow ratio has a very strong influence on the QD composition, PL peak energies, and carrier recombination times. While the samples prepared using low TMSb∕AsH3 flow ratios show a bimodal character with both InAs and InAsSb QDs present, in the structures grown at high flow ratios the InAsSb QDs dominate, showing strong photoluminescence intensity, fast carrier capture and slow recombination.
Superconductivity by means of the subquantum medium coherence
Authors: Agop M. , Ioannou P. D. , Nica P.
Published: May 2005

In the hydrodynamic formulation of the scale relativity theory one shows that a stable vortices distribution of bipolaron type induces superconducting pairs by means of the quantum potential. Then, usual mechanisms (as, for example, the exchange interaction used in the bipolaron theory) are reduced to the coherence on the subquantum medium, the superconducting pairs resulting as a one-dimensional projection of a fractal. The temperature dependences of the superconducting parameters (coherence length, critical speed, pair breaking time, carriers concentration, penetration depth, critical field, critical current) and the concordance with the experimental data and other theories are analyzed.
Self-similarly developing, premixed, turbulent flames: A theoretical study
Authors: Lipatnikov A. N. , Chomiak J.
Published: May 2005

The development of a premixed turbulent flame in a statistically stationary and uniform, planar, one-dimensional flow of a homogeneous mixture is theoretically studied in the case of frozen turbulence. A balance equation for the mean combustion progress variable is proposed to generalize a number of currently available models of premixed turbulent combustion. The equation invokes two unspecified scales and three arbitrary functions to model turbulent diffusion, countergradient transport, and the mean rate of product creation, the rate being assumed to depend straightforwardly on the flame development time t. The equation supplemented with the averaged mass balance equation is analyzed by invoking a single assumption of the self-similarity of the mean flame structure. The assumption, well supported by numerous experiments, allows us to split the aforementioned partial differential balance equations into two ordinary differential equations, which separately model spatial variations of the mean combustion progress variable c¯ and time development of flame thickness Δt. The complementary error function profile of c¯, documented in numerous experiments, is predicted. The profile is independent of mixture properties and turbulence characteristics, as indicated by currently available experimental data. Closures of the countergradient transport term and of the mean rate of product creation are obtained. They substantiate the so-called Zimont equation and generalize it. They also imply that gradient diffusion dominates during the initial stage of flame development, followed by the transition to countergradient turbulent scalar flux ρu″c″¯ in a sufficiently developed flame. A criterion of the transition, obtained in the paper, shows that the transition is promoted by the density ratio. An analytical dependence of a fully developed flame thickness Δt,∞=Δt(t→∞) on the scale of countergradient transport and density ratio is found. Analytical expressions for the development of flame thickness are obtained in the simplified case of a time-independent mean rate of product creation.
Coulomb blockade oscillations in ultrathin gate oxide silicon single-electron transistors
Authors: Wan Yue-Min , Huang Kuo-Dong , Hu S. F. , Sung C. L. , Chou Y. C.
Published: May 2005

Ultrathin oxide-gated (thickness ∼6nm) point-contact junctions have been fabricated to explore single-electron charging effects in strongly gate-dot-coupled polycrystallinesilicon transistors. Current–voltage (I–V) measurements show periodic current oscillations near room temperature. Analysis of the energy-level spacing relates the electron charging energy to a quantum dot of size ∼8nm, and also suggests electron tunneling is via the first excited state. These low-power ∼30pW and low-cost devices can be useful for the next generation nanoelectronics.
Role of dissociative recombination in the excitation kinetics of an argon microwave plasma at atmospheric pressure
Authors: Sáinz A. , Margot J. , García M. C. , Calzada M. D.
Published: May 2005

A collisional radiative model was developed in order to investigate the influence of dissociative recombination on the Saha–Boltzmann plasma equilibrium. As the dissociative recombination products are not well known, their relative importance was tested through comparison with the distribution of line intensities obtained in a microwave argon discharge produced at atmospheric pressure by a surface wave. It was found that the main dissociation products are the ground state and the 4s levels, the 5p and upper levels playing a negligible role. Because the higher levels are only weakly affected by dissociative recombination, they remain in partial local thermodynamic equilibrium. Therefore, the excitation temperature determined from these levels adequately describes the electron temperature. The model well reproduces experimental measurements of excitation temperature, rotational temperature, electron density, and absolute populations of the excited levels.
Site-selective x-ray-excited thermoluminescence and fluorescence of ZrO2 from the local structure of the Zr L3 edge
Authors: Lai Lee-Jene , Chu Tieh-Chi , Hsu Ya-Chuan , Chen Yen-Hsien
Published: May 2005

The results presented are an investigation of the local structure of a ZrO2 sample using site-selective x-ray, excited fluorescence, and thermoluminescence methods. The experimental results demonstrate that fluorescence and thermoluminescence yield an x-ray absorption near-edge structure at the Zr L3 edge that depends on the x-ray photon energy associated with the transition from a Zr 2p3∕2 occupied state to a 4d unoccupied state. Although conventional fluorescence measured by x-ray absorption yields the average structure over all Zr, the thermoluminescence yield measured by x-ray absorption provides information on the local structure of Zr only after a long period of phosphorescence. Furthermore, the x-ray absorption of the ZrO2 sample leads to competitive fluorescence and phosphorescence owing to deexcitation of a core hole.
Unsteady fluid flow separation by the method of averaging
Authors: Kilic M. S. , Haller G. , Neishtadt A.
Published: May 2005

We use the method of averaging to improve recent separation criteria for two-dimensional unsteady fluid flows with no-slip boundaries. Our results apply to general compressible flows that admit a well-defined asymptotic average. Such flows include periodic and quasiperiodic flows, as well as aperiodic flows with a mean component. As an example, we predict and verify the unsteady separation location and angle in variants of an oscillating separation bubble model.
Shell and subshell periodic structures of icosahedral nickel nanoclusters
Authors: Zhang Zhi , Hu Wangyu , Xiao Shifang
Published: May 2005

Using the modified analytic embedded atom method and molecular dynamics, the binding energies and their second order finite differences (stability functions) of icosahedral Ni clusters with shell and subshell periodicity are studied in detail via atomic evolution. The results exhibit shell and subshell structures of the clusters with atoms from 147 to 250 000, and the atomic numbers corresponding to shell or subshell structures are in good agreement with the experimental magic numbers obtained in time-of-flight mass spectra of threshold photoionization, and Martin’s theoretical proposition of progressive formation of atomic umbrellas. Clusters with size from 147 to 561 atoms are energetically investigated via one-by-one atomic evolution and their magic numbers are theoretically proved. For medium-size Ni clusters with 561 to 2057 atoms, the prediction of magic numbers with atomic numbers is performed on the basis of umbrellalike subshell growth in near face-edge-vertex order. The similarity of the energy curves makes it possible to extend the prediction to even larger Ni nanoclusters in hierarchical Mackay icosahedral configurations.
Double torsion testing and finite element analysis for determining the electric fracture properties of piezoelectric ceramics
Authors: Shindo Yasuhide , Narita Fumio , Mikami Masaru
Published: May 2005

This paper presents the results of an experimental and numerical investigation in electric fracture behavior of composite [Pb(Zr,Ti)O3] double torsion (DT) specimens. DT tests were conducted on a commercial piezoelectric ceramic bonded between two metals. Fracture loads under different electric fields were obtained from the experiment. Nonlinear three-dimensional finite element analysis was also employed to calculate the energy release rate for DT specimens based on the exact (permeable) and approximate (impermeable) crack models. The effects of applied electric field and domain switching on the energy release rate are discussed, and the model predictions are compared with the results of the experiments.
Magnetostriction and magnetomechanical coupling of grain-aligned Tb0.33Dy0.67Fey /epoxy-filled composites
Authors: Kwon Oh Yeoul , Kim Hee Yeoun , Cha Seung Il , Hong Soon Hyung
Published: May 2005

The magnetostriction and dynamic magnetomechanical coupling properties of the epoxy-filled composites that were manufactured by replacing the eutectic phase with the epoxy were investigated as a function of the bias field and the RFe2 volume fraction. The composites were prepared with RFe2 volume fractions from 0.34 to 0.88 and were compared with as-grown crystals. The filled composites exhibit a greater maximum strain than do as-grown crystals, strongly dependent on the RFe2 volume fraction. Furthermore, the dynamic magnetomechanical coupling coefficient of the filled composite, which was measured by resonance analysis, shows a maximum value of 0.45at47.2kA∕m, the highest known value for [1–3] composite Terfenol-D and strongly dependent on the volume fraction of RFe2.
Single beam determination of porosity and etch rate in situ during etching of porous silicon
Authors: Foss S. E. , Kan P. Y. Y. , Finstad T. G.
Published: May 2005

A laser reflection method has been developed and tested for analyzing the etching of porous silicon (PS) films. It allows in situ measurement and analysis of the time dependency of the etch rate, the thickness, the average porosity, the porosity profile, and the interface roughness. The interaction of an infrared laser beam with a layered system consisting of a PS layer and a substrate during etching results in interferences in the reflected beam which is analyzed by the short-time Fourier transform. This method is used for analysis of samples prepared with etching solutions containing different concentrations of HF and glycerol and at different current densities and temperatures. Variations in the etch rate and porosity during etching are observed, which are important effects to account for when optical elements in PS are made. The method enables feedback control of the etching so that PS films with a well-controlled porosity are obtainable. By using different beam diameters it is possible to probe interface roughness at different length scales. Obtained porosity, thickness, and roughness values are in agreement with values measured with standard methods.
Ensemble Monte Carlo transport simulations for semiconducting carbon nanotubes
Authors: Verma A. , Kauser M. Z. , Ruden P. P.
Published: May 2005

We report on ensemble Monte Carlo transport simulations for semiconducting, single-wall, zigzag carbon nanotubes. The basis for the Monte Carlo simulations is provided by electronic structure calculations within the framework of a simple tight-binding model that takes the effect of the tube curvature on the band structure into account. The principal scattering mechanisms considered are due to the electron–phonon interactions involving longitudinal acoustic and optical phonons. Using ensemble Monte Carlo simulations, the steady-state and transient characteristics are explored. The steady-state velocity saturates due to optical-phonon scattering, and negative differential mobility is obtained for large electric fields. The results also show interesting transient phenomena that are caused by the limited phase space of these dynamically one-dimensional structures.
Large negative magnetoresistance in quaternary Heusler alloy Ni50Mn8Fe17Ga25 melt-spun ribbons
Authors: Liu Z. H. , Liu H. , Zhang X. X. , Zhang X. K. , Xiao John Q. , Zhu Z. Y. , Dai X. F. , Liu G. D. , Chen J. L. , Wu G. H.
Published: May 2005

Quaternary Heusler alloy Ni50Mn8Fe17Ga25 ribbons have been prepared by the melt-spun method. The ribbons exhibit large negative magnetoresistance (MR){=[R(H)−R(0)]∕R(0)} over a wide temperature region, particularly in the region during the martensitic phase transformation. The MR decreases significantly after annealing. The large MR is isotropic and is mainly attributed to the local magnetic disorders, magnetic clusters, and heterogeneity. The maximum MR at martensitic transformation may be due to the redistribution of electrons and the increase of phase boundary scattering. This feature adds a useful functionality to the already interesting Heusler alloys.
Quantum dot lasers based on a stacked and strain-compensated active region grown by metal-organic chemical vapor deposition
Authors: Nuntawong N. , Xin Y. C. , Birudavolu S. , Wong P. S. , Huang S. , Hains C. P. , Huffaker D. L.
Published: May 2005

We demonstrate an InAs∕GaAs quantum dot (QD) laser based on a strain-compensated, three-stack active region. Each layer of the stacked QD active region contains a thin GaP (Δao=−3.8%) tensile layer embedded in a GaAs matrix to partially compensate the compressive strain of the InAs (Δao=7%) QD layer. The optimized GaP thickness is ∼4MLs and results in a 36% reduction of compressive strain in our device structure. Atomic force microscope images, room-temperature photoluminescence, and x-ray diffraction confirm that strain compensation improves both structural and optical device properties. Room-temperature ground state lasing at λ=1.249μm, Jth=550A∕cm2 has been demonstrated.
Purification and crystallization of tungsten wires fabricated by focused-ion-beam-induced deposition
Authors: Prestigiacomo M. , Bedu F. , Jandard F. , Tonneau D. , Dallaporta H. , Roussel L. , Sudraud P.
Published: May 2005

We studied the behavior of tungsten wires, fabricated by focused-ion-beam-induced deposition and subjected to high current density. We present a simple electrical treatment, which allows an improved wire resistivity of more than 80%. We have distinguished two steps in the treatment. When the current density reaches 1.4×107A∕cm2, Ga atoms segregate and form droplets on the wire. As the current density increases, new droplets appear and merge into a single droplet. At 5.8×107A∕cm2, the droplet evaporates, the resistance is lost and the wire crystallizes. The final resistivity is close to 55 μΩ cm. The same treatment applied to as-deposited platinum wires does not lead to the same observations: neither segregation nor crystallization was found.
Formation of a sheared flow Z pinch
Authors: Golingo R. P. , Shumlak U. , Nelson B. A.
Published: May 2005

The ZaP Flow Z-Pinch project is experimentally studying the effect of sheared flows on Z-pinch stability. It has been shown theoretically that when dVz∕dr exceeds 0.1kVA the kink (m=1) mode is stabilized. [U. Shumlak and C. W. Hartman, Phys. Rev. Lett. 75, 3285 (1995).] Z pinches with an embedded axial flow are formed in ZaP with a coaxial accelerator coupled with a 1m assembly region. Long-lived, quiescent Z pinches are generated throughout the first half cycle of the current. During the initial plasma acceleration phase, the axial motion of the current sheet is consistent with snowplow models. Magnetic probes in the assembly region measure the azimuthal modes of the magnetic field. The amplitude of the m=1 mode is proportional to the radial displacement of the Z-pinch plasma current. The magnetic mode levels show a quiescent period which is over 2000 times the growth time of a static Z pinch. The axial velocity is measured along 20 chords through the plasma and deconvolved to provide a radial profile. Using data from multiple pulses, the time evolution of the velocity profile is measured during formation, throughout the quiescent period, and into the transition to instability. The evolution shows that a sheared plasma flow develops as the Z pinch forms. Throughout the quiescent period, the flow shear is greater than the theoretically required threshold for stability. As the flow shear decreases, the magnetic mode fluctuations increase. The coaxial accelerator provides plasma throughout the quiescent period and may explain the evolution of the velocity profile and the sustainment of the flow Z pinch.
Visualization of nonlinear effects in reflecting internal wave beams
Authors: Peacock Thomas , Tabaei Ali
Published: May 2005

Recent theoretical and numerical investigations predict that localized nonlinear effects in the overlapping region of an incoming and reflected internal wave beam can radiate higher-harmonic beams. We present the first set of experimental visualizations, obtained using the digital Schlieren method, that confirm the existence of radiated higher-harmonic beams. For arrangements in which the angle of propagation of the second harmonic exceeds the slope angle, radiated beams are visualized. When the propagation angle of the second harmonic deceeds the slope angle no radiated beams are detected, as the associated density gradient perturbations are too weak for the experimental method. The case of a critical slope is also reported.
Application of near-field scanning microwave microprobe to electrical current density mapping
Authors: Aga Roberto S. , Wang Xiang , Dizon Jonathan , Noffsinger Jesse , Wu Judy Z.
Published: May 2005

A near-field scanning microwave microprobe (NSMM) has been integrated with electrical current-voltage (I–V) characterization for mapping electrical current density (J) in conducting films at room temperature (RT). In this technique, the focused microwave emitted at the tip of the NSMM was used to alter the local resistance of the sample via heating which results in a voltage response ΔV that depends linearly on the local J and the applied microwave power. In addition to the ΔV map generated during the NSMM scan over a sample, a microwave response map can be recorded simultaneously using the NSMM, providing complementary information of sample morphology and surface impedance. On silver microbridges with predefined patterns, a 10-μm spatial resolution has been demonstrated and better resolution may be achieved with further optimization. Hence, this technique provides a simple and nondestructive method for identification of current-limiting defects in conducting films and may be scaled for reel-to-reel quality control of the high-Tc superconductor coated conductors at RT.
Intensity modulation and polarization rotation of visible light by dielectric planar chiral metamaterials
Authors: Zhang W. , Potts A. , Papakostas A. , Bagnall D. M.
Published: May 2005

We have demonstrated how dielectric planar chiral surfaces can both modulate the intensity and change the polarization state of visible light diffracted from patterned surfaces. These effects are shown to be dependent on the sense of chirality of the surface and the input polarization state of the light. Individual diffracted beams can show variations of over 30% in their intensities for different input polarization states while opposite enantiomeric structures can exhibit differences of over 50%. The size of these effects could make these surfaces particularly promising candidates for the development of solid-state polarization-state detectors.
Off-diagonal elastic constant and sp2-bonded graphitic grain boundary in nanocrystalline-diamond thin films
Authors: Ogi Hirotsugu , Nakamura Nobutomo , Tanei Hiroshi , Hirao Masahiko , Ikeda Ryuji , Takemoto Mikio
Published: May 2005

This letter studies the relationship between the off-diagonal elastic constant C12 and bond configuration in nanocrystalline-diamond (NCD) thin films deposited by the nitrogen-doped chemical vapor deposition method. The film thickness was varied between 2.4 and 11.3μm. The elastic constants were measured by resonant-ultrasound spectroscopy coupled with laser-Doppler interferometry. The diagonal elastic constants C11 and C44, and Young’s modulus in NCD films are smaller than those of the bulk polycrystalline diamond and microcrystalline-diamond (MCD) thin films, and they decrease as the film thickness decreases. However, the off-diagonal elastic constant of the NCD films is significantly larger than that of the bulk diamond, while that of the MCD films is smaller. Micromechanics calculations revealed that this exceptional enhancement of C12 occurs when the material includes randomly distributed thin graphitic plates in the isotropic diamond matrix. Thus, this result indicates that the NCD films consist of sp3-bonded diamond grains and sp2-bonded grain boundaries.
The role of soil water repellency in overland flow generation in pine and eucalypt forest stands in coastal Portugal
Authors: Keizer J. J. , Coelho C. O. A. , Shakesby R. A. , Domingues C. S. P. , Malvar M. C. , Perez I. M. B. , Matias M. J. S. , Ferreira A. J. D.
Published: May 2005

Soil water repellency is now known to occur in diverse soils in various parts of the world. One of the possible adverse effects of soil water repellency is that it can reduce infiltration capacity and hence, on sloping terrain, enhance overland flow and soil erosion. The main aim of the present work is to assess the effects of soil water repellency on surface runoff production in the inner coastal dune areas of central Portugal. This was done for a pine and a eucalypt forest stand and, within each stand, for 2 slopes with contrasting aspect and somewhat different slope angles. Overland flow was measured for 4 pairs of unbounded plots of about 5 m2 at fortnightly intervals from February to October 2001. Over the same period, soil water repellency at and immediately below the soil surface was measured next to the plots at monthly intervals. The runoff–repellency relationship was also studied by carrying out rainfall simulation experiments on 0.24-m2 plots and associated repellency measurements.
The effect of soil water repellency was most clearly demonstrated by statistically significant higher runoff coefficients under strong-to-extremely than under none-to-slightly hydrophobic conditions immediately below the soil surface. Such a difference in runoff over the measurement period was, however, restricted to 2 unbounded plots, both of which were located on the eucalypt slope with a southerly aspect and the greater slope angle. At the scale of these plots, the increase in runoff coefficient due to soil water repellency is moderate, when integrated over the entire period of strong–extremely repellent conditions, but can be quite substantial for individual 2-weekly periods. With respect to the observed differences in runoff between plots, be it plots on the same slope or not, it has proved difficult to distinguish the effect of soil water repellency from that of other factors likely to affect overland flow generation.
Effects of clay amendment on adsorption and desorption of copper in water repellent soils
Authors: Xiong X. , Stagnitti F. , Allinson G. , Turoczy N. , Li P. , LeBlanc M. , Cann M. A. , Doerr S. H. , Steenhuis T. S. , Parlange J.-Y. , de Rooij G. , Ritsema C. J. , Dekker L. W.
Published: May 2005

Copper is an important micronutrient and trace amounts are essential for crop growth. However, high concentrations of copper will produce toxic effects. Australia is increasingly developing production of crops in water repellent soils. Clay amendment, a common amelioration techniques used in Australia, has demonstrated agronomic benefits in increased crop or pasture production. The sorption and desorption of copper and the effect of clay treatment on copper behaviour in a water repellent soil collected from an experimental farm in South Australia is studied. We found that the water repellent soils amended with clay have an increased adsorption capacity of copper. Also the clay-amended soils had an increased ratio of specific sorption to total sorption of copper. The implications of this study to the sustainable agro-environmental management of water repellent soils is discussed.
A new modelling approach to simulate preferential flow and transport in water repellent porous media: Parameter sensitivity, and effects on crop growth and solute leaching
Authors: Kramers G. , van Dam J. C. , Ritsema C. J. , Stagnitti F. , Oostindie K. , Dekker L. W.
Published: May 2005

A modified version of the popular agrohydrological model SWAP has been used to evaluate modelling of soil water flow and crop growth at field situations in which water repellency causes preferential flow. The parameter sensitivity in such situations has been studied. Three options to model soil water flow within SWAP are described and compared: uniform flow, the classical mobile-immobile concept, and a recent concept accounting for the dynamics of finger development resulting from unstable infiltration. Data collected from a severely water-repellent affected soil located in Australia were used to compare and evaluate the usefulness of the modelling options for the agricultural management of such soils.
The study shows that an assumption of uniform flow in a water-repellent soil profile leads to an underestimation of groundwater recharge and an overestimation of plant transpiration and crop production. The new concept of modelling taking finger dynamics into account provides greater flexibility and can more accurately model the observed effects of preferential flow compared with the classical mobile–immobile concept. The parameter analysis indicates that the most important factor defining the presence and extremity of preferential flow is the critical soil water content.
Comparison of the modelling results with the Australian field data showed that without the use of a preferential flow module, the effects of the clay amendments to the soil were insufficiently reproduced in the dry matter production results. This means that the physical characteristics of the soil alone are not sufficient to explain the measured increase in production on clay amended soils. However, modelling with the module accounting for finger dynamics indicated that the preferential flow in water repellent soils that had not been treated with clay caused water stress for the crops, which would explain the decrease in production.
A new modelling approach to simulate preferential flow and transport in water repellent porous media: Model structure and validation
Authors: Ritsema Coen J. , van Dam Jos C. , Dekker Louis W. , Oostindie Klaas
Published: May 2005

Water repellent soil and surface layers exhibit a complex flow and transport mechanism. Knowledge of the underlying principles is essential, for instance, to simulate water availability for crops and to estimate leaching potentials of agrichemicals. The present study aims to introduce and apply a new modelling approach to simulate preferential flow and transport in water repellent porous media, and to test the model on basis of an extensive field tracer experiment. The process of preferential flow and transport has been incorporated in the well-known SWAP model and applied to field data of tracer transport through a water repellent sandy soil in the Netherlands. Flow concept and model structure have been outlined, and simulation results presented. Results indicated early arrival times of bromide tracer in the subsoil in the case where preferential flow has been taken into account in the model. Comparison of measured and computed bromide concentration profiles and bromide recovery rates show close resemblances. Several strategies to alleviate soil water repellency and prevent the occurrence of preferential flow and transport processes are highlighted, such as irrigation scheduling, clay additions, and application of surfactants.
Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases
in vitro
and
in vivo
Authors: Suspène Rodolphe , Guétard Denise , Henry Michel , Sommer Peter , Wain-Hobson Simon , Vartanian Jean-Pierre
Published: May 2005

Because the replication of hepatitis B virus (HBV) proceeds via an obligatory reverse transcription step in the viral capsid, cDNA is potentially vulnerable to editing by cytidine deaminases of the APOBEC3 family. To date only two edited HBV genomes, referred to as G → A hypermutants, have been described
in vivo
. Recent work suggested that HBV replication was indeed restricted by APOBEC3G but by a mechanism other than editing. The issue of restriction has been explored by using a sensitive PCR method allowing differential amplification of AT-rich DNA. G → A hypermutated HBV genomes were recovered from transfection experiments involving APOBEC3B, -3C, -3F, and -3G indicating that all four enzymes were able to extensively deaminate cytidine residues in minus-strand DNA. Unexpectedly, three of the four enzymes (APOBEC3B, -3F, and -3G) deaminated HBV plus-strand DNA as well. From the serum of two of four patients with high viremia, G → A hypermutated genomes were recovered at a frequency of ≈10
-4
, indicating that they are, albeit relatively rare, part of the natural cycle of HBV infection. These findings suggest that human APOBEC3 enzymes can impact HBV replication via cytidine deamination.
Development of a transgenic mouse model susceptible to human coronavirus 229E
Authors: Lassnig Caroline , Sanchez Carlos M. , Egerbacher Monika , Walter Ingrid , Majer Susanne , Kolbe Thomas , Pallares Pilar , Enjuanes Luis , Müller Mathias
Published: May 2005

Human coronavirus (HCoV) 229E is a group 1 coronavirus and is specific to humans. So far, no animal model is available to study the pathogenesis of infection by HCoV-229E. We show here that the expression of aminopeptidase N (APN, also termed CD13), the receptor for HCoV-229E, is required but not sufficient to confer susceptibility
in vivo
. HCoV-229E infection was facilitated by crossing APN transgenic mice into signal transducers and activators of transcription (
Stat
)
1
null mice and by adaptation of HCoV-229E to grow in primary APN transgenic,
Stat1
null fibroblasts. Double transgenic mice allow the study of human coronavirus group 1 infections in an animal model, in particular, viral tropism, replication, recombination, and spread in an immunocompromised situation. Furthermore, these mice provide an important tool for the evaluation of biosafety and efficacy of coronavirus-based vectors.
Topological units of environmental signal processing in the transcriptional regulatory network of
Escherichia coli
Authors: Balázsi G. , Barabási A.-L. , Oltvai Z. N.
Published: May 2005

Recent evidence indicates that potential interactions within metabolic, protein–protein interaction, and transcriptional regulatory networks are used differentially according to the environmental conditions in which a cell exists. However, the topological units underlying such differential utilization are not understood. Here we use the transcriptional regulatory network of
Escherichia coli
to identify such units, called origons, representing regulatory subnetworks that originate at a distinct class of sensor transcription factors. Using microarray data, we find that specific environmental signals affect mRNA expression levels significantly only within the origons responsible for their detection and processing. We also show that small regulatory interaction patterns, called subgraphs and motifs, occupy distinct positions in and between origons, offering insights into their dynamical role in information processing. The identified features are likely to represent a general framework for environmental signal processing in prokaryotes.
An alternative strategy for sustainable pest resistance in genetically enhanced crops
Authors: Mehlo Luke , Gahakwa Daphrose , Nghia Pham Trung , Loc Nguyen Thi , Capell Teresa , Gatehouse John A. , Gatehouse Angharad M. R. , Christou Paul
Published: May 2005

Bacillus thuringiensis(Bt) crystal protein genes encode insecticidal δ-endotoxins that are widely used for the development of insect-resistant crops. In this article, we describe an alternative transgenic strategy that has the potential to generate broader and more sustainable levels of resistance against insect pests. Our strategy involves engineering plants with a fusion protein combining the δ-endotoxin Cry1Ac with the galactose-binding domain of the nontoxic ricin B-chain (RB). This fusion, designated BtRB, provides the toxin with additional, binding domains, thus increasing the potential number of interactions at the molecular level in target insects. Transgenic rice and maize plants engineered to express the fusion protein were significantly more toxic in insect bioassays than those containing the Bt gene alone. They were also resistant to a wider range of insects, including important pests that are not normally susceptible to Bt toxins. The potential impact of fusion genes such as BtRB in terms of crop improvement, resistance sustainability, and biosafety is discussed.
Distinct effectors of platelet-derived growth factor receptor-α signaling are required for cell survival during embryogenesis
Authors: Van Stry Melanie , Kazlauskas Andrius , Schreiber Stuart L. , Symes Karen
Published: May 2005

Platelet-derived growth factor receptor (PDGFR) signaling is essential for normal embryonic development in many organisms, including frog, mouse, zebrafish, and sea urchin. The mode of action of PDGFR signaling during early development is poorly understood, however, mostly because inhibition of signaling through either the PDGFRα or PDGFRβ is embryonic lethal. In
Xenopus
embryos, disruption of PDGFRα signaling causes migrating anterior mesoderm cells to lose direction and undergo apoptosis through the mitochondrial pathway. To understand the mechanism of PDGFRα function in this process, we have analyzed all known effector-binding sites
in vivo
. By using a chemical inducer of dimerization to activate chimera PDGFRαs, we have identified a role for phospholipase Cγ (PLCγ) in protecting cells from death. PDGFRα-mediated cell survival requires PLCγ and phosphatidylinositol 3-kinase signaling, and that PDGFRα with binding sites for these two signaling factors is sufficient for this activity. Other effectors of PDGFRα signaling, Shf, SHP-2, and Crk, are not required for this process. Thus, our findings show that PDGFRα signaling through PLCγ and phosphatidylinositol 3-kinase has a protective role in preventing apoptosis in early development. Furthermore, we demonstrate that small molecule inducers of dimerization provide a powerful system to manipulate receptor function in developing embryos.
Splicing potentiation by growth factor signals via estrogen receptor phosphorylation
Authors: Masuhiro Yoshikazu , Mezaki Yoshihiro , Sakari Matomo , Takeyama Ken-ichi , Yoshida Tasuku , Inoue Kunio , Yanagisawa Junn , Hanazawa Shigemasa , O'Malley Bert W. , Kato Shigeaki
Published: May 2005

Mitogen-activated protein kinase-mediated growth factor signals are known to augment the ligand-induced transactivation function of nuclear estrogen receptor α (ERα) through phosphorylation of Ser-118 within the ERα N-terminal transactivation (activation function-1) domain. We identified the spliceosome component splicing factor (SF)3a p120 as a coactivator specific for human ERα (hERα) activation function-1 that physically associated with ERα dependent on the phosphorylation state of Ser-118. SF3a p120 potentiated hERα-mediated RNA splicing, and notably, the potentiation of RNA splicing by SF3a p120 depended on hER Ser-118 phosphorylation. Thus, our findings suggest a mechanism by which growth factor signaling can regulate gene expression through the modulation of RNA splicing efficiency via phosphorylation of sequence-specific activators, after association between such activators and the spliceosome.
SECISDesign: a server to design SECIS-elements within the coding sequence
Authors: Busch Anke , Will Sebastian , Backofen Rolf
Published: May 2005

Summary: SECISDesign is a server for the design of SECIS-elements and arbitrary RNA-elements within the coding sequence of an mRNA. The element has to satisfy both structure and sequence constraints. At the same time, a certain amino acid similarity to the original protein has to be kept. The designed sequence can be used for recombinant expression of selenoproteins in Escherichia coli.

Availability: The server is available at http://www.bio.inf.uni-jena.de/Software/SECISDesign/index.html

Contact:  backofen@inf.uni-jena.de
Functional annotation from predicted protein interaction networks
Authors: McDermott Jason , Bumgarner Roger , Samudrala Ram
Published: May 2005

Motivation: Progress in large-scale experimental determination of protein–protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes.

Results: We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations.

Availability: Functional predictions for over 50 organisms are available at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/

Contact:  admin@bioverse.compbio.washington.edu

Supplementary information: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nannotation_data/supplement.pdf).
A latent variable model for chemogenomic profiling
Authors: Flaherty Patrick , Giaever Guri , Kumm Jochen , Jordan Michael I. , Arkin Adam P.
Published: May 2005

Motivation: In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure.

Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that requires genes to belong to a single cluster. Drugs such as miconazole and fenpropimorph that have different targets but similar off-target genes are clustered more accurately by the model-based framework. We show that this model is useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles.

Availability: Supplementary information and computer code at http://genomics.lbl.gov/llda

Contact:  flaherty@berkeley.edu
BHUx: A Patent Polyherbal Formulation to Prevent Atherosclerosis
Authors: Tripathi Yamini B. , Singh Birendra K. , Pandey Ravi S. , Kumar Mohan
Published: May 2005

Ayurvedic medicine is a time‐tested system of medicine which has been in clinical use for centuries in India. Being a time‐tested system, it has an edge over other existing systems of health management, especially for dealing with chronic disorders such as coronary artery disease, which is of a complex multi‐etiological nature. Recently, we have shown that BHUx, a patented polyherbal formulation consisting of the aqueous fraction of five medicinal plants of the ayurvedic system, has significant anti‐inflammatory properties through inhibition of cyclooxygenase‐2 and lipoxygenase‐15. Here we have investigated its effect on diet‐induced atherosclerosis in albino rabbits. BHUx was given orally for 3 months to rabbits pre‐treated with an atherogenic diet for 3 months. After 6 months, the dorsal aorta was processed for histological studies for calcium and collagen content. The results demonstrated a remarkable reduction in intimal thickening in the treated animals. In addition, there was less calcification at the intima–medial interface and increased intensity of collagen cap on the surface along with an increase in survival, compared with the sham control. We suggest that BHUx is a potent, multi‐factorial formulation against atherosclerosis.
Prevalence of quadruplexes in the human genome
Authors: Huppert Julian L. , Balasubramanian Shankar
Published: May 2005

Guanine-rich DNA sequences of a particular form have the ability to fold into four-stranded structures called G-quadruplexes. In this paper, we present a working rule to predict which primary sequences can form this structure, and describe a search algorithm to identify such sequences in genomic DNA. We count the number of quadruplexes found in the human genome and compare that with the figure predicted by modelling DNA as a Bernoulli stream or as a Markov chain, using windows of various sizes. We demonstrate that the distribution of loop lengths is significantly different from what would be expected in a random case, providing an indication of the number of potentially relevant quadruplex-forming sequences. In particular, we show that there is a significant repression of quadruplexes in the coding strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA.