bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of polarizations of a laser on absorption in a paraboloid of revolution-shaped welding or drilling cavity
Authors: Ho Ching-Yen
Published: November 2004

The effects of polarizations on the apparent absorptivity or integrated energy absorbed by a paraboloid of revolution-shaped cavity subject to a laser beam are systematically and quantitatively investigated. The incident flux is considered to be a TEM00 mode of a Gaussian distribution specified by the wavelength, spot size, and focal location of the laser beam. Using a Monte Carlo method and neglecting the absorption within the plasma in the cavity, the results show that the predicted energy-transfer efficiency versus incident flux and cavity depth agrees well with the experimental data. The apparent absorption of p polarization is found to be always higher than that of s polarization, even though the latter causes higher energy fluxes absorbed than the former near the critical radius. The apparent absorptivity for s polarization as a function of cavity depth can be divided into three parts: an initial decrease, rapid increase, and gradual increase. Interestingly, the polarization of circularly polarized incoming rays is gradually transformed into s polarization in the course of multiple reflections. The apparent absorptivity as a function of polarizations, specular reflectivity, penetration depth, focal location, and absorptive and refractive indices is also presented.
Analysis of the magnetic anisotropy induced by applying a magnetic field during the quenching process in amorphous ribbons
Authors: Tejedor M. , García J. A. , Carrizo J. , Elbaile L. , Santos J. D. , Mira J. , Rivas J.
Published: November 2004

The magnetic anisotropy induced in amorphous magnetic ribbons by applying a magnetic field to the melt during the solidification process is analyzed. Using a model based on the magnetization curve and on the evolution of the uniaxial torque with the applied magnetic field, the volume fractions of the sample affected by the different magnetic anisotropies are obtained for the ribbons of composition Fe80B20 and Co70Mn5Fe1Mo1Si14B9. The results are compared with those obtained in the ribbons of the same composition but with anisotropies induced by the static magnetic annealing. From these results, the different sources of the field-quenching-induced magnetic anisotropy in those amorphous magnetic ribbons are analyzed.
The magnetoresistance of homogeneous and heterogeneous silver-rich silver selenide
Authors: Beck G. , Korte C. , Janek J. , Gruhl F. , Kreutzbruck M.
Published: November 2004

The magnetoresistance (MR) effect of the low-temperature phase of silver selenide (α-Ag2+δSe) is measured as a function of composition. Very small composition variations in the order of Δδ=10−6 are achieved by coulometric titration and can be performed simultaneously during the MR measurement. A homogeneous Ag2+δSe shows an ordinary magnetoresistance (OMR) effect, which can be well described by the two-band model. For silver selenide with a heterogenous silver excess, we found quite a different MR behavior. Up to a minor silver excess of 1×10−4<δ<1×10−2, a saturating negative MR effect, a linear positive MR effect, or a superposition of both can be measured. The microstructure of the silver-rich Ag2+δSe determines its complicated MR behavior. A heterogeneous silver selenide with a larger silver excess (δ>10−2) shows again an OMR effect.
Cyclostationary shot noise in mesoscopic measurements
Authors: Roschier Leif , Heikkilä Tero T. , Hakonen Pertti
Published: November 2004

We discuss theoretically a setup where a time-dependent current consisting of a dc bias and two sinusoidal harmonics is driven through a sample. If the sample exhibits current-dependent shot noise, the down-converted noise power spectrum varies depending on the local-oscillator phase of the mixer. The theory of this phase-dependent noise is applied to discuss the measurement of the radio-frequency single-electron transistor. We also show that this effect can be used to measure the shot noise accurately even in nonlinear high-impedance samples.
Nonuniform radio-frequency plasma potential due to edge asymmetry in large-area radio-frequency reactors
Authors: Howling A. A. , Sansonnens L. , Ballutaud J. , Hollenstein Ch. , Schmitt J. P. M.
Published: November 2004

In small area capacitive reactors, the rf and dc components of the plasma potential can be assumed to be uniform over all the plasma bulk because of the low plasma resistivity. In large area reactors, however, the rf plasma potential can vary over a long range across the reactor due to rf current flow and the nonzero plasma impedance. A perturbation in rf plasma potential, due to electrode edge asymmetry or the boundary of a dielectric substrate, propagates along the resistive plasma between capacitive sheaths. This is analogous to propagation along a lossy conductor in a transmission line and the damping length of the perturbation can be determined by the telegraph equation. Some consequences are the following: (i) The spatial variation in sheath rf amplitudes causes nonuniform rf power dissipation near to the reactor sidewalls. (ii) The surface charge and potential of a dielectric substrate can be negative and not only positive as for a uniform rf plasma potential. The variation of sheath dc potential across a dielectric substrate causes nonuniform ion energy bombardment. (iii) The self-bias voltage depends on the plasma parameters and on the reactor and substrate dimensions—not only on the ratio of electrode areas. (iv) The nonuniform rf plasma potential in presence of the uniform dc plasma potential leads to nonambipolar dc currents circulating along conducting surfaces and returning via the plasma. Electron current peaks can arise locally at the edge of electrodes and dielectric substrates. Perturbations to the plasma potential and currents due to the edge asymmetry of the electrodes are demonstrated by means of an analytical model and numerical simulations.
Boron diffusion in strained Si: A first-principles study
Authors: Lin Li , Kirichenko Taras , Banerjee Sanjay K. , Hwang Gyeong S.
Published: November 2004

We investigate B diffusion in strained Si by using first-principles density functional theory calculations. An enhancement and an anisotropy of B diffusion in biaxial tensile strained Si are found. The diffusion barrier along the strain plane (channel) is decreased while the barrier in the vertical direction (depth) remains unchanged. This anisotropy comes from the orientation dependence of the saddle point in the diffusion pathway. The formation enthalpy of B-I pair also decreases in strained Si. According to our calculations, for strained Si on a Si0.8Ge0.2 buffer layer, which is widely used in strained metal oxide semiconductor field-effect-transistor, an enhancement of B diffusivity along the channel by a factor ∼4 and a factor ∼2 in the vertical direction are expected for typical rapid thermal anneals.
Escape depth of secondary electrons induced by ion irradiation of submicron diamond membranes
Authors: Richter V. , Fizgeer B. , Michaelson Sh. , Hoffman A. , Kalish R.
Published: November 2004

The emission of secondary electrons from any material is governed by electron excitation in the bulk, their transport to the surface, and their escape through the surface into the vacuum. Here, we address the question of the transport of electrons in polycrystalline diamond and amorphous carbon membranes and discuss the factors that limit it. The results of the measurements of the escape depth of the secondary electrons from the membranes of submicron polycrystalline diamond and amorphous carbon films induced by the hydrogen ion impact are reported here. It is found that the escape depth for the secondary electrons emitted from diamond scales with the grain size of the crystallites in the polycrystalline diamond films and it can be very large. In contrast, for the case of the amorphous carbon membranes, we find this depth to be much shorter. The extremely high electron emission yield, which have been measured following the slowing down of the electrons or ions in diamond, can be explained by the fact that secondary electrons can move rather freely in diamond, hence, can reach the surface from large distances inside the diamond sample.
Orientation and electronic properties of pentacene molecules on SiO2 and GeS(0001) studied using x-ray absorption spectroscopy
Authors: Schwieger T. , Liu X. , Olligs D. , Knupfer M. , Schmidt Th.
Published: November 2004

We present an investigation on the morphology of pentacene molecules, a candidate for organic semiconductors in organic electronic devices. In this case the molecules are deposited on the technologically relevant substrate SiO2. In order to observe possible changes in the morphology of a monolayer of pentacene compared to a much thicker pentacene layer, we have performed x-ray absorption experiments on both films. We did not find significant differences in the orientation of the pentacene molecules as a function of film thickness. The same is true for the orientation of pentacene on the model substrate GeS(0001), however, the molecular orientation is opposite to that of pentacene on SiO2. Whereas the pentacene molecules on GeS(0001) lie flat on the substrate surface, on SiO2 they are standing. These results have important consequences for our understanding of the functionality of organic devices based on pentacene.
Study of HfO2 films deposited on strained Si1−xGex layers by atomic layer deposition
Authors: Damlencourt J.-F. , Weber O. , Renault O. , Hartmann J.-M. , Poggi C. , Ducroquet F. , Billon T.
Published: November 2004

This paper focuses on the growth of HfO2 by atomic layer deposition (ALD) at 350°C on pseudomorphic Si1−xGex thin films (x=15% and 25%). Two different Si1−xGex surface preparations (chemical oxidation and HF “last” treatment) have been investigated to obtain the highest HfO2 film quality with the thinnest interfacial layer possible. The initial stages of the ALD growth on these different surfaces (i.e., hafnium adsorption and chlorine contamination) analyzed by total x-ray fluorescence show that HF last treated Si1−xGex surfaces are more convenient than chemically oxidized ones to grow high quality HfO2 layers. This result is confirmed by x-ray photoelectron spectroscopy investigations of the interfacial layer structure as a function of the surface treatment. As-deposited and annealed thin HfO2 layers (2.5, 3.5, 5, and 8nm) grown on HF last treated Si0.75Ge0.25 strained layers were analyzed by mercury probe. An equivalent oxide thickness as low as 0.7nm was obtained for a 2.5nm as-deposited HfO2 film. Mobility results show that a 22% mobility enhancement is obtained in the entire effective field range with HfO2∕SiGe compared to the HfO2∕Si reference.
Inverse determination of porosity from object’s resonances
Authors: Mitri Farid G.
Published: November 2004

An alternative technique combining vibroacoustography and the finite element method for measuring the porosity parameter P and damping of a chalk sphere immersed in water is presented. This technique is based on the detection of the sphere resonance frequencies which will be compared to the finite element calculations. An optimization procedure based on the least squares method is performed in order to evaluate the “effective” Young’s modulus and damping parameters. Hence, porosity can be estimated by an inverse expression from the effective Young’s modulus.
Power and temperature dependence of low frequency noise in AlGaN∕GaN transmission line model structures
Authors: Vitusevich S. A. , Danylyuk S. V. , Klein N. , Petrychuk M. V. , Belyaev A. E.
Published: November 2004

The low-frequency noise in AlGaN∕GaN transmission line model structures has been investigated for a wide range of ambient temperatures and dissipated powers. A deviation of low-frequency noise from a 1∕f dependence has been observed upon increasing the applied voltage. The effect correlates with the nonlinearity of current-voltage characteristics (CVC). The concept of nonequilibrium 1∕f noise has been introduced to explain 1∕f noise enhancement. A qualitative model connecting non-equilibrium noise with nonlinearity of the CVC via a common origin—nonuniform overheating of the structures—has been suggested. Furthermore, deviations of equilibrium noise from the 1∕f law at low temperatures have been observed and studied.
Simulation of correlated diffusion of Si and B in thermally grown SiO2
Authors: Uematsu Masashi , Kageshima Hiroyuki , Takahashi Yasuo , Fukatsu Shigeto , Itoh Kohei M. , Shiraishi Kenji
Published: November 2004

Simultaneous diffusion of Si and B in thermally grown SiO2 is modeled taking into account the effect of SiO molecules generated at the Si∕SiO2 interface and diffusing into SiO2 to enhance both Si and B diffusion. Based on the model, we simulated experimental profiles of coimplanted Si30 and B in SiO228, which showed increasing diffusivities with decreasing distance from the interface. The simulation results show that the SiO diffusion is so slow that the SiO concentration at the near-surface region critically depends on the distance from the interface. In addition, the simulation explains that the diffusivities of both Si and B increase with longer annealing times because more SiO molecules arrive from the interface. Furthermore, we examined the effect of high-concentration B on the diffusivities of Si and B in SiO2, both of which increase with higher B concentration. The experimental results were simulated assuming that the diffusivity of SiO, which enhances the diffusivities of Si and B, increases with higher B concentration. The present results indicate that Si and B diffusion in SiO2 are correlated via SiO molecules; namely, the enhancement of SiO diffusion at high B concentrations also causes enhanced diffusion of both Si and B.
Coercivity map in perpendicular media investigated by using in situ magnetic force microscopy
Authors: Bai J. , Saito H. , Ishio S.
Published: November 2004

The spatial distribution of coercivities in a CoCrPt-SiO2 granular perpendicular magnetic recording medium was measured by using in situ magnetic force microscopy. The coercivity map that shows the spatial distribution of coercivities was obtained at 1kOe intervals in the medium. The “local” coercivities within microscopic areas of less than 100nm square were evaluated with a good reproducibility. Measuring coercivity map will become a technique for investigating the influence of the spatial distribution of coercivities on the medium noise in perpendicular recording.
Linear tearing modes calculation for diverted tokamak configurations
Authors: Atanasiu C. V. , Günter S. , Lackner K. , Moraru A. , Zakharov L. E. , Subbotin A. A.
Published: November 2004

Writing the expression of the potential energy in terms of the perturbation of the flux function, and performing an Euler minimization, one obtains a system of ordinary differential equations in that perturbation. For a diverted configuration, the usual vanishing boundary conditions for the perturbed flux function at the magnetic axis and at infinity can no longer be used. An approach to fix “natural” boundary conditions for the perturbed flux function just at the plasma boundary has been developed; this replaces the vanishing boundary conditions at infinity. To obtain the necessary metric coefficients from an equilibrium solver, a function exhibiting the same singularity at the X point has been introduced, and thus the separatrix contour was described by a reduced number of moments.
Study of the motions contributing to the Reynolds stress in high and low Reynolds number turbulent boundary layers
Authors: Priyadarshana P. J. A. , Klewicki J. C.
Published: November 2004

Physical experiments are used to explore the properties of the motions contributing to the Reynolds stresses in high and low Reynolds number turbulent boundary layers. The low Reynolds number smooth wall measurements (Rθ=1010, Rθ=2870, and Rθ=4850) were acquired in a large-scale low speed wind tunnel, while the high Reynolds number measurements [Rθ∼O(106)] were acquired at the Surface Layer Turbulence and Environmental Science Test site, Dugway, Utah. These high Reynolds number turbulent boundary layer data were acquired over nearly hydraulically smooth and rough walls. At each Reynolds number and surface roughness, data comparisons were made at approximately yp/2 and 2yp, where yp is the peak position of the Reynolds shear stress. Scale separation effects associated with increasing Rθ are analyzed via spectral measurements (u, v, and u-v cospectra), and by segregating the streamwise and wall-normal velocities according to their frequency content using simultaneous high- and low-pass filtering. A primary observation is that the predominant motions underlying the stress undergo a significant shift from large to intermediate scales as Rθ becomes large, irrespective of surface roughness. Quadrant analysis of the filtered signals is employed to clarify the correlated scales involved in the generation of the stress. Overall, it is apparent that the types of motions contributing to Reynolds stress undergo significant variations at comparable wall-normal locations (relative to yp) over the Reynolds number range explored.
Microstructure and crystal defects in epitaxial ZnO film grown on Ga modified (0001) sapphire surface
Authors: Sun H. P. , Pan X. Q. , Du X. L. , Mei Z. X. , Zeng Z. Q. , Xue Q. K.
Published: November 2004

Surface modification of sapphire (0001) by Ga can eliminate multiple rotation domains in ZnO films. The existence of Ga at ZnO∕sapphire interface was confirmed by x-ray energy dispersive spectroscopy in a transmission electron microscope. Atomic detail of mismatch dislocations at interface was imaged by high resolution transmission electron microscopy. Inside the ZnO film, there is a high density of stacking fault. Both pure gliding of ZnO(0001) plane and condensation of vacancies or interstatials are possible mechanisms to generate the stacking fault.
Sign reversal and tunable rectification in a ballistic nanojunction
Authors: Hackens B. , Gence L. , Gustin C. , Wallart X. , Bollaert S. , Cappy A. , Bayot V.
Published: November 2004

Low-temperature measurements show that an asymmetric mesoscopic junction patterned in a two-dimensional electron gas can exhibit tunable rectification, including sign reversal. Strikingly, we observe that the amplitude and sign of the effect are governed by the conductances of the channels and that rectification is reversed without reversing the asymmetry of the device. Based on the temperature dependence of the rectified voltage, we show that the effect is ballistic and exhibits unexpected features with respect to predictions of available models.
Control of the Rayleigh–Taylor instability in a staged Z pinch
Authors: Rahman H. U. , Ney P. , Rostoker N. , Van Drie A. , Wessel F. J.
Published: November 2004

Z-pinch experiments and computer simulations provide evidence for enhanced stability and current transfer in a staged Z pinch, consisting of an annular krypton shell imploding onto a deuterium gas fill. Visible-streak and Schlieren imaging provide evidence for a multilayer implosion where the outer plasma shell is Rayleigh–Taylor unstable and the inner plasma column is stable. Computer simulations indicate that the discharge current diffuses through the unstable, outer Kr shell. As the discharge current layer implodes onto the deuterium, current is transferred and a stable implosion results, producing a deuterium-compression ratio of 200.
Quantum dot emission from site-controlled InGaN∕GaN micropyramid arrays
Authors: Edwards P. R. , Martin R. W. , Watson I. M. , Liu C. , Taylor R. A. , Rice J. H. , Na J. H. , Robinson J. W. , Smith J. D.
Published: November 2004

In x Ga 1 − x N quantum dots have been fabricated by the selective growth of GaN micropyramid arrays topped with InGaN∕GaN quantum wells. The spatially, spectrally, and time-resolved emission properties of these structures were measured using cathodoluminescence hyperspectral imaging and low-temperature microphotoluminescence spectroscopy. The presence of InGaN quantum dots was confirmed directly by the observation of sharp peaks in the emission spectrum at the pyramid apices. These luminescence peaks exhibit decay lifetimes of approximately 0.5ns, with linewidths down to 650μeV (limited by the spectrometer resolution).
Effects of cathode thickness and thermal treatment on the design of balanced blue light-emitting polymer device
Authors: Chin Byung Doo , Duan Lian , Kim Moo-Hyun , Lee Seong Taek , Chung Ho Kyoon
Published: November 2004

The interface between layered conjugated polymer and electrode is a most important factor to improve the performance and lifetime of polymeric light-emitting devices (PLEDs). In this work, a blue PLED with improved stability was achieved by the combination of optimized cathode structure as well as thermal treatment of light-emitting polymer (LEP). Experimental evidence of the initial luminance “settling in” stage was found to be dependent upon the cathode structure, while the long-term slope of luminance as a function of elapsed time is governed by the annealing conditions. Our study revealed the importance of extrinsic design of device for the improvement of PLED stability. Experimental data shows that a blue PLED annealed at 170°C and 6nm LiF at LiF∕Ca∕Al cathode retained the best lifetime, which can be explained by the improved polymer–metal interface and LEP’s charge mobility.
Influence of hole size on the extraordinary transmission through subwavelength hole arrays
Authors: van der Molen K. L. , Segerink F. B. , van Hulst N. F. , Kuipers L.
Published: November 2004

We show that the extraordinary transmission of light through an array of square subwavelength holes is strongly influenced by the size of the holes. For small, square holes (air fraction below 20%), the dependence of the normalized transmission (transmissivity) on hole width greatly exceeds the expectations on the basis of conventional aperture theory. For larger holes, the transmissivity saturates. Moreover, the positions of the transmission maxima shift when the size is varied.
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emission characteristics of Er3+-doped stoichiometric LiNbO3
Authors: Kang Jeongan , Lee Myeongkyu , Lee Sunkyun , Lim Kisoo , Somu Kumaragurubaran , Takekawa Shunji , Kitamura Kenji
Published: November 2004

The 1.5μm emission characteristics of stoichiometric LiNbO3 crystals with different Er3+ doping levels of 0.2, 0.5, 1.0, and 2.0mol% were investigated. All of the emission decays could be fitted by a single exponential curve. The lifetimes of the 1.5μm transition (I13∕24→I15∕24) were measured to be 3.0–3.2ms, which are about 25% longer than those reported for conventional Er-doped congruent LiNbO3. Our analysis showed that the longer lifetime in stoichiometric LiNbO3 is likely to originate from the reduced density of intrinsic defects.
Fabrication and optical properties of polymeric waveguides containing nanocrystalline quantum dots
Authors: Olsson Ylva K. , Chen Gang , Rapaport Ronen , Fuchs Dan T. , Sundar Vikram C. , Steckel Jonathan S. , Bawendi Moungi G. , Aharoni Assaf , Banin Uri
Published: November 2004

We report on the fabrication of polymer waveguides containing infrared-emitting nanocrystal quantum dots. Both PbSe and InAs nanocrystal quantum dots are incorporated into a fluorinated polymer by a surface functionalization method. The optical properties of the nanocrystal quantum dots are shown to be unaffected by the entire fabrication process. This method may provide a versatile platform for integration of nanocrystal quantum dots into planar photonic circuits.
Direct laser writing of electro-optic waveguide in chromophore-doped hybrid sol–gel
Authors: Zhang Hong Xi , Lu Dong , Liu Tao , Mansuripur Masud , Fallahi Mahmoud
Published: November 2004

To overcome the influence of chromophore absorption and degradation in the ultraviolet spectral range for direct photopatterning of electro-optic devices, a blue laser writing technique operating at 405nm has been used to fabricate electro-optic waveguides from side-chain disperse red-1 doped photosensitive hybrid sol–gel films. The waveguide has good optical confinement and shows an electro-optic coefficient of about 9.0±0.4pm∕V and high temporal stability. The results indicate that the hybrid sol–gel a promising matrix for chromophores, and this technique can find applications in direct patterning of electro-optic devices from nonlinear chromophores-doped photosensitive materials including sol–gels and polymers.
An all-optically prepared and controlled nematic liquid crystal light valve
Authors: Yi Y. W. , Furtak T. E.
Published: November 2004

We describe an optically prepared and controlled nematic liquid crystal device, using derivatized methyl red self-assembled monolayers for surface alignment on both of its windows. This material demonstrates both reversible and irreversible photoinduced anisotropy, depending on the availability of oxygen during illumination. One window of the cell was permanently aligned prior to assembly while the other window retained its sensitivity to the orientation of the polarization of a controlling optical beam, leading to either a uniform or twisted state in the nematic cell. The entire management of the cell was thereby achieved without touching the alignment surfaces.
Dynamic stress-induced low-temperature ordering of FePt
Authors: Lai Chih-Huang , Yang Cheng-Han , Chiang C. C. , Balaji T. , Tseng T. K.
Published: November 2004

The ordering temperature of FePt was significantly reduced to 275°C by introducing a Cu underlayer on the HF-cleaned Si(001) substrate. A coercivity Hc as high as 6200Oe can be achieved after postannealing at 275°C, and Hc can be further increased to 7000Oe after 300°C postannealing. During the formation of copper silicide Cu3Si, the expanded volume induces a dynamic in-plane tensile stress on FePt films, which accelerates the formation of the ordered FePt phase at low temperature. Different from the static stress induced by the lattice mismatch between films and underlayers, the dynamic stress is relaxed after the formation of Cu3Si is completed; therefore, the low-temperature ordering of FePt mainly takes place simultaneously with the evolution of dynamic stress during the formation of Cu3Si. The coercivity of FePt depends on the amount of Cu3Si and on the stress developed by Cu3Si.
Charge distribution mapping by low energy electrons
Authors: Dorozhkin P. S. , Dong Z.-C.
Published: November 2004

We demonstrate how low energy electron point source microscope can be used for quantitative mapping of linear charge distribution along one-dimensional wires. Imaging of electrically biased carbon nanotube ropes suspended across two electrodes showed different charge distributions for three different experimental situations: (1) ropes having good ohmic contacts to both electrodes, (2) ropes with one good and one poor ohmic contacts, and (3) ropes with one end contacted and the other end free standing. The technique gives a linear charge density resolution below 0.1e per nanometer with a spatial resolution better than 10nm. The resolution can be further improved by the proper modification of experimental setup.
The 13C, 15N and 34S signatures of a rocky reef planktivorous fish indicate different coastal discharges of sewage
Authors: Gaston Troy F. , Kostoglidis Antionette , Suthers Iain M.
Published: November 2004

We assessed the effects of primary, secondary and tertiary treated sewage on the stable isotope composition of the viscera and muscle of the zooplanktivorous eastern hula fish (Plesiopidae: Trachinops taeniatus). Fish were collected from three regions during three consecutive summer months for 2 years. In comparison to fish from control sites, the muscle δ15N of fish at outfall sites was significantly enriched by secondary and tertiary treated effluent. We estimate that 30–50% of nitrogen in hula fish near outfalls may be sewage-derived. The δ34S content of muscle was similar at all regions and sites (20–21‰), although it was significantly depleted by 1–2‰ at the tertiary treated outfall site. Detection of a comparatively minor volume of effluent (<6 ML day–1) in fish muscle may be due to its slower tissue turnover rate and the continuous discharge of effluent at outfall sites, compared to major yet sporadic rainfall or oceanographic events. The isotopic composition of hula fish from near a large primary treated sewage outfall off the coast of Sydney was not significantly different from one of the control sites, indicating a regional effect of four outfalls discharging >1000 ML day–1. With increasing upgrades to sewage treatment, stable isotopes may become useful tracers of anthropogenic nutrients in an oligotrophic environment.
A malaria membrane skeletal protein is essential for normal morphogenesis, motility, and infectivity of sporozoites
Authors: Khater Emad I. , Sinden Robert E. , Dessens Johannes T.
Published: November 2004

Membrane skeletons are structural elements that provide mechanical support to the plasma membrane and define cell shape. Here, we identify and characterize a putative protein component of the membrane skeleton of the malaria parasite. The protein, named PbIMC1a, is the structural orthologue of the Toxoplasma gondii inner membrane complex protein 1 (TgIMC1), a component of the membrane skeleton in tachyzoites. Using targeted gene disruption in the rodent malaria species Plasmodium berghei, we show that PbIMC1a is involved in sporozoite development, is necessary for providing normal sporozoite cell shape and mechanical stability, and is essential for sporozoite infectivity in insect and vertebrate hosts. Knockout of PbIMC1a protein expression reduces, but does not abolish, sporozoite gliding locomotion. We identify a family of proteins related to PbIMC1a in Plasmodium and other apicomplexan parasites. These results provide new functional insight in the role of membrane skeletons in apicomplexan parasite biology.
Apoptotic pathways are selectively activated by granzyme A and/or granzyme B in CTL-mediated target cell lysis
Authors: Pardo Julián , Bosque Alberto , Brehm Reina , Wallich Reinhard , Naval Javier , Müllbacher Arno , Anel Alberto , Simon Markus M.
Published: November 2004

Purified cytolytic T lymphocyte (CTL) proteases granzyme (gzm)A and gzmB with sublytic dose of perforin (perf) initiate distinct proapoptotic pathways. Their physiological relevance in CTL-mediated target cell apoptosis is elusive. Using ex vivo virus-immune CD8+ T cells from mice deficient in perf, gzmA and/or gzmB, and the Fas-resistant EL4.F15 tumor target cell, we show that (a) CTL from gzmA−/− or gzmB−/− mice similarly induced early proapoptotic features, such as phosphatidyl serine (PS) exposure on plasma membrane, ΔΨm loss, and reactive oxygen radical generation, though with distinct kinetics; (b) CTL from gzmA−/− but not from gzmB−/− mice activate caspase 3 and 9; (c) PS exposure induced by CTL from gzmA−/− or gzmB−/− mice is prevented, respectively, by caspase inhibitors or by reactive oxygen scavengers without interfering with target cell death; and (d) all gzm-induced apoptotic features analyzed depend critically on perf. Thus, perf is the principal regulator in CTL-mediated and gzm-facilitated intracellular processes. The ability of gzmA and gzmB to induce multiple independent cell death pathways may be the hosts response to circumvent evasion strategies of pathogens and tumors.
Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria
Authors: Rodionov Dmitry A. , Gelfand Mikhail S. , Hugouvieux-Cotte-Pattat Nicole
Published: November 2004

In the plant-pathogenic enterobacterium Erwinia chrysanthemi, almost all known genes involved in pectin catabolism are controlled by the transcriptional regulator KdgR. In this study, the comparative genomics approach was used to analyse the KdgR regulon in completely sequenced genomes of eight enterobacteria, including Erw. chrysanthemi, and two Vibrio species. Application of a signal recognition procedure complemented by operon structure and protein sequence analysis allowed identification of new candidate genes of the KdgR regulon. Most of these genes were found to be controlled by the cAMP-receptor protein, a global regulator of catabolic genes. At the next step, regulation of these genes in Erw. chrysanthemi was experimentally verified using in vivo transcriptional fusions and an attempt was made to clarify the functional role of the predicted genes in pectin catabolism. Interestingly, it was found that the KdgR protein, previously known as a repressor, positively regulates expression of two new members of the regulon, phosphoenolpyruvate synthase gene ppsA and an adjacent gene, ydiA, of unknown function. Other predicted regulon members, namely chmX, dhfX, gntB, pykF, spiX, sotA, tpfX, yeeO and yjgK, were found to be subject to classical negative regulation by KdgR. Possible roles of newly identified members of the Erw. chrysanthemi KdgR regulon, chmX, dhfX, gntDBMNAC, spiX, tpfX, ydiA, yeeO, ygjV and yjgK, in pectin catabolism are discussed. Finally, complete reconstruction of the KdgR regulons in various gamma-proteobacteria yielded a metabolic map reflecting a globally conserved pathway for the catabolism of pectin and its derivatives with variability in transport and enzymic capabilities among species. In particular, possible non-orthologous substitutes of isomerase KduI and a new oligogalacturonide transporter in the Vibrio species were detected.
Nitrate reduction and the nitrogen cycle in archaea
Authors: Cabello Purificación , Roldán M. Dolores , Moreno-Vivián Conrado
Published: November 2004

The nitrogen cycle (N-cycle) in the biosphere, mainly driven by prokaryotes, involves different reductive or oxidative reactions used either for assimilatory purposes or in respiratory processes for energy conservation. As the N-cycle has important agricultural and environmental implications, bacterial nitrogen metabolism has become a major research topic in recent years. Archaea are able to perform different reductive pathways of the N-cycle, including both assimilatory processes, such as nitrate assimilation and N2fixation, and dissimilatory reactions, such as nitrate respiration and denitrification. However, nitrogen metabolism is much less known in archaea than in bacteria. The availability of the complete genome sequences of several members of the eury- and crenarchaeota has enabled new approaches to the understanding of archaeal physiology and biochemistry, including metabolic reactions involving nitrogen compounds. Comparative studies reveal that significant differences exist in the structure and regulation of some enzymes involved in nitrogen metabolism in archaea, giving rise to important conclusions and new perspectives regarding the evolution, function and physiological relevance of the different N-cycle processes. This review discusses the advances that have been made in understanding nitrate reduction and other aspects of the inorganic nitrogen metabolism in archaea.
Glucan synthesis in the genus Lactobacillus: isolation and characterization of glucansucrase genes, enzymes and glucan products from six different strains
Authors: Kralj S. , van Geel-Schutten G. H. , Dondorff M. M. G. , Kirsanovs S. , van der Maarel M. J. E. C. , Dijkhuizen L.
Published: November 2004

Members of the genera Streptococcus and Leuconostoc synthesize various α-glucans (dextran, alternan and mutan). In Lactobacillus, until now, the only glucosyltransferase (GTF) enzyme that has been characterized is gtfA of Lactobacillus reuteri 121, the first GTF enzyme synthesizing a glucan (reuteran) that contains mainly α-(1→4) linkages together with α-(1→6) and α-(1→4,6) linkages. Recently, partial sequences of glucansucrase genes were detected in other members of the genus Lactobacillus. This paper reports, for the first time, isolation and characterization of dextransucrase and mutansucrase genes and enzymes from various Lactobacillus species and the characterization of the glucan products synthesized, which mainly have α-(1→6)- and α-(1→3)-glucosidic linkages. The four GTF enzymes characterized from three different Lb. reuteri strains are highly similar at the amino acid level, and consequently their protein structures are very alike. Interestingly, these four Lb. reuteri GTFs have relatively large N-terminal variable regions, containing RDV repeats, and relatively short putative glucan-binding domains with conserved and less-conserved YG-repeating units. The three other GTF enzymes, isolated from Lactobacillus sakei, Lactobacillus fermentum and Lactobacillus parabuchneri, contain smaller variable regions and larger putative glucan-binding domains compared to the Lb. reuteri GTF enzymes.
Identification of Escherichia coli O157 : H7 genes influencing colonization of the bovine gastrointestinal tract using signature-tagged mutagenesis
Authors: Dziva Francis , van Diemen Pauline M. , Stevens Mark P. , Smith Amanda J. , Wallis Timothy S.
Published: November 2004

Enterohaemorrhagic Escherichia coli (EHEC) cause acute gastroenteritis in humans that may be complicated by life-threatening systemic sequelae. The predominant EHEC serotype affecting humans in the UK and North America is O157 : H7 and infections are frequently associated with contact with ruminant faeces. Strategies to reduce the carriage of EHEC in ruminants are expected to lower the incidence of human EHEC infections; however, the molecular mechanisms underlying persistence of EHEC in ruminants are poorly understood. This paper reports the first comprehensive survey for EHEC factors mediating colonization of the bovine intestines by using signature-tagged transposon mutagenesis. Seventy-nine E. coli O157 : H7 mutants impaired in their ability to colonize calves were isolated and 59 different genes required for intestinal colonization were identified by cloning and sequencing of the transposon insertion sites. Thirteen transposon insertions were clustered in the locus of enterocyte effacement (LEE), which encodes a type III protein secretion system required for the formation of attaching and effacing lesions on intestinal epithelia. A putative structural component of the apparatus (EscN) is essential for intestinal colonization; however, the type III secreted effector protein Map plays only a minor role. Other Type III secretion-associated genes were implicated in colonization of calves by E. coli O157 : H7, including z0990 (ecs0850), which encodes the non-LEE-encoded type III secreted effector NleD and the closely related z3023 (ecs2672) and z3026 (ecs2674) genes which encode homologues of Shigella IpaH proteins. We also identified a novel fimbrial locus required for intestinal colonization in calves by E. coli O157 : H7 (z2199-z2206; ecs2114-ecs2107/locus 8) and demonstrated that a mutant harbouring a deletion of the putative major fimbrial subunit gene is rapidly out-competed by the parent strain in co-infection studies. Our data provide valuable new information for the development of intervention strategies.
The changing nature of hours and employment adjustment in US manufacturing
Authors: Glosser Stuart , Golden Lonnie
Published: November 2004

Has the character of adjustment of labor input in the US manufacturing sector been changing over the last few decades? This question is addressed with time‐series estimation using data through 2001. Impulse responses of employment and average weekly hours to a given shock in output demand are generated from multi‐equation vector autoregressions. The results reveal a marked change in the character of labor input adjustment as compared with the two decades prior to 1979, with some heterogeneity among 18 detailed industries. Adjustment of hours has risen somewhat while adjustment of employment has dropped considerably. This intensifying adjustment of hours vis‐à‐vis employment is consistent with hypotheses regarding employers' potential reactions to a skill‐upgrading of jobs under greater market pressures to restrain cost. US manufacturing employers appear to be increasingly adopting strategies of “lean staffing,” while “hoarding” and shedding work hours, in response to cyclical fluctuation in demand. This phenomenon may be a structural change contributing to a recent “jobless recovery” in the US.
Training provision and regulation: an analysis of the temporary help industry
Authors: Muñoz‐Bullón Fernando
Published: November 2004

This paper studies the juridical rationale for mandatory training provision on Temporary Help Agencies as established in the Spanish Temporary Help Agencies Act, 1994 (Law 14/94). No positive relationship is found between the improvement in Temporary Help Agencies' added value levels and their investments in temps' training. In analyzing this specific provision of Spanish Labor Law we adopt a positive focus to explain its impact on the functioning of the temporary help industry. The application of institutional theory leads us to conclude that efficient use of this legal prescription is limited. The issue is relevant to understanding the economic outcomes of regulation from a law and economics perspective.
Phylogenetic nomenclature is compatible with diverse philosophical perspectives
Authors: Pleijel Fredrik , Härlin Mikael
Published: November 2004

Pleijel, F. & Härlin, M. (2004). Phylogenetic nomenclature is compatible with diverse philosophical perspectives. —Zoologica Scripta,33, 587–591.
In vivo selection for Leishmania donovani miniexon genes that increase virulence in Leishmania major†
Authors: Zhang Wen‐Wei , Matlashewski Greg
Published: November 2004

Different species of Leishmania are responsible for the diverse pathologies associated with leishmaniasis including Leishmania donovani which results in fatal visceral infection and Leishmania major which causes non‐fatal cutaneous infection. In an attempt to identify genotypic differences between these related Old World Leishmania species which contribute to their distinct phenotypic characteristics, we have introduced a L. donovani cosmid library into L. major to select for L. donovani sequences which may increase L. major virulence in BALB/c mice. Through this approach, we have identified a region of the L. donovani genome which increased virulence in both visceral and cutaneous sites and was divergent from the corresponding region of the L. major genome. When these L. donovani sequences were reintroduced into L. major, they enhanced the overall virulence of L. major, increasing its ability to survive in both visceral and cutaneous sites. The region responsible for increased infection levels was determined to be the miniexon gene array derived from chromosome 36 of L. donovani. Pulse field electrophoresis revealed that L. donovani contained miniexon gene sequences in several chromosome locations as opposed to L. major which contains miniexon gene sequences only in chromosome 2. Because of the requirement for miniexon‐derived transcripts in maturation of pre‐mRNAs in trypanosomatids, this observation suggests that the increased expression of miniexon genes is associated with increased virulence. As the genome sequence for Leishmania becomes available, the in vivo selection procedure described within will be useful to identify additional species‐specific sequences responsible for different pathogenic phenotypes associated with Leishmania infection.
The target cell plasma membrane is a critical interface for Salmonella cell entry effector–host interplay
Authors: Cain Robert J. , Hayward Richard D. , Koronakis Vassilis
Published: November 2004

Salmonella species trigger host membrane ruffling to force their internalization into non‐phagocytic intestinal epithelial cells. This requires bacterial effector protein delivery into the target cell via a type III secretion system. Six translocated effectors manipulate cellular actin dynamics, but how their direct and indirect activities are spatially and temporally co‐ordinated to promote productive cytoskeletal rearrangements remains essentially unexplored. To gain further insight into this process, we applied mechanical cell fractionation and immunofluorescence microscopy to systematically investigate the subcellular localization of epitope‐tagged effectors in transiently transfected and Salmonella‐infected cultured cells. Although five effectors contain no apparent membrane‐targeting domains, all six localized exclusively in the target cell plasma membrane fraction and correspondingly were visualized at the cell periphery, from where they induced distinct effects on the actin cytoskeleton. Unexpectedly, no translocated effector pool was detectable in the cell cytosol. Using parallel in vitro assays, we demonstrate that the prenylated cellular GTPase Cdc42 is necessary and sufficient for membrane association of the Salmonella GTP exchange factor and GTPase‐activating protein mimics SopE and SptP, which have no intrinsic lipid affinity. The data show that the host plasma membrane is a critical interface for effector–target interaction, and establish versatile systems to further dissect effector interplay.
Involvement of a novel transcriptional activator and small RNA in post‐transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system
Authors: Vanderpool Carin K. , Gottesman Susan
Published: November 2004

RyaA is a small non‐coding RNA in Escherichia coli that was identified by its ability to bind tightly to the RNA chaperone Hfq. This study reports the role of RyaA in mediating the cellular response to glucose‐specific phosphoenolypyruvate phosphotransferase system (PTS)‐dependent phosphosugar stress. Aiba and co‐workers have shown that a block in the metabolism of glucose 6‐phosphate causes transient growth inhibition and post‐transcriptional regulation of ptsG, encoding the glucose‐specific PTS transporter. We found that RyaA synthesis was induced by a non‐metabolizable glucose phosphate analogue and was necessary for relief of the toxicity of glucose phosphate stress. Expression of RyaA was sufficient to cause a rapid loss of ptsG mRNA, probably reflecting degradation of the message mediated by RyaA:ptsG pairing. The ryaA gene was renamed sgrS, for sugar transport‐related sRNA. Expression of sgrS is regulated by a novel transcriptional activator, SgrR (formerly YabN), which has a putative DNA‐binding domain and a solute‐binding domain similar to those found in certain transport proteins. Our results suggest that under conditions of glucose phosphate accumulation, SgrR activates SgrS synthesis, causing degradation of ptsG mRNA. Decreased ptsG mRNA results in decreased production of glucose transport machinery, thus limiting further accumulation of glucose phosphate.
Effects of crop management patterns on coffee rust epidemics
Authors: Avelino J. , Willocquet L. , Savary S.
Published: November 2004

The effects of crop management patterns on coffee rust epidemics, caused by Hemileia vastatrix, are not well documented despite large amounts of data acquired in the field on epidemics, and much modelling work done on this disease. One main reason for this gap between epidemiological knowledge and understanding for management resides in the lack of links between many studies and actual production situations in the field. Coffee rust epidemics are based on a seemingly simple infection cycle, but develop polycyclic epidemics in a season and polyetic epidemics over successive seasons. These higher‐level processes involve a very large number of environmental variables and, as in any system involving a perennial crop, the physiology of the coffee crop and how it affects crop yield. Crop management is therefore expected to have large effects on coffee rust epidemics because of its immediate effect on the infection cycle, but also because of its cumulative effect on ongoing and successive epidemics. Quantitative examples taken from a survey conducted in Honduras illustrate how crop management, different combinations of shade, coffee tree density, fertilization and pruning may strongly influence coffee rust epidemics through effects on microclimate and plant physiology which, in turn, influence the life cycle of the fungus. We suggest there is a need for novel coffee rust management systems which fully integrate crop management patterns in order to manage the disease in a sustainable way.