bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of shear-induced and extensional-induced associating polymer assemblies: Brownian dynamics simulation
Authors: Yeom Min Sun , Lee Jysoo
Published: October 2005

In order to examine the difference between shear-induced and extensional-induced associating polymer assemblies at the molecular level, Brownian dynamics simulations with the bead-spring model were carried out for model DNA molecules with sticky spots. The radial distribution of molecules overestimates from that in the absence of flow and increases with increasing Weissenberg number in extensional flow, but slightly underestimates without regard to shear rate in shear flow. The fractional extension progresses more rapidly in extensional flow than in shear flow and the distribution of fractional extension at the formation time has a relatively sharper peak and narrower spectrum in extensional flow than in shear flow. In shear flow, the inducement of the assembly mainly results from the progress of the probability distribution of fractional extension. However, in extensional flow, the assembly is induced by both the progress of the probability distribution and increasing the values of the radial distribution.
Correlation energy functionals dependent on an effective number of electrons: Charged species and equilibrium geometries
Authors: Pérez-Jiménez Ángel J. , Pastor-Abia Luis , Pérez-Jordá José M.
Published: October 2005

Recently proposed spin-dependent and spin-independent correlation energy functionals [Pérez-Jiménez et al., J. Chem. Phys. 116, 10571 (2002)] based on an effective number of electrons Ñ are extended to deal with charged systems. By introducing the concept of an effective atomic number Z̃ analogous to Ñ, the spin-dependent functional in combination with Becke’s exchange [Becke, Phys. Rev. A 38, 3098 (1988)] yields a mean absolute error (MAE) of 5.4kcal∕mol for the 88 ionization potentials and 58 electron affinities included in the extended G2 set, and a MAE of 4.1kcal∕mol for the 312 data comprising the above plus the 148 enthalpies of formation of the extended G2 set and the 18 total energies of the neutral atoms H through Ar. Geometry optimizations performed on the 53 molecules of the G2-1 test set with the above combination of exchange and correlation functionals yield MAEs of 0.017 Å and 1.5° for the 68 bond lengths and 29 angles analyzed as compared with the experimental estimates.
Magnetorelaxometry of magnetic nanoparticles in magnetically unshielded environment utilizing a differential fluxgate arrangement
Authors: Ludwig F. , Mäuselein S. , Heim E. , Schilling M.
Published: October 2005

A magnetorelaxometry system based on a differential fluxgate arrangement is presented. Compared to the single fluxgate setup, the use of two fluxgate magnetometers increases the relaxation signal from the sample by a factor of 2, the signal-to-noise ratio by a factor 2, and allows one to perform magnetorelaxation measurements without any magnetic shielding. For a sample with superparamagnetic Fe3O4 nanoparticles and a volume of 150μl, 100 nmol Fe could be detected, limited by the intrinsic noise of the fluxgate sensors.
Influence of rhodamine 6G doping on the optical properties of TiO2 sol-gel films
Authors: Tomás S. A. , Stolik S. , Palomino R. , Lozada R. , Persson C. , Pepe I. , da Silva A. Ferreira
Published: October 2005

Amorphous titanium dioxide (TiO2) thin films doped with rhodamine 6G (R6G) were deposited on glass substrates by the sol-gel process. The optical properties of the films were characterized by photoacoustic, excitation, and fluorescence spectroscopies. The absorption spectra of the R6G-doped TiO2 films exhibited two well-defined absorption regions: an absorption band over 2.0 eV attributed to rhodamine 6G and a band above 3.0 eV corresponding to TiO2 absorption. While the onset of the R6G absorption band was shifted by 0.06 eV towards lower energies as the R6G doping concentration increased within the interval of 0.01–0.10 mol %, the onset to high absorption (TiO2 band) for the doped films decreased only by 0.01 eV within the same interval. In addition, the optical absorption of undoped rutile-phase bulk TiO2 was calculated and compared to the experimental results. The estimated theoretical value of rutile TiO2 sample was 3.0 eV. This theoretical result shows good agreement when compared with the experimental data of undoped TiO2 sol-gel films, as well as the undoped TiO2 film prepared by sputtering.
Strain-dielectric response of dielectrics as foundation for electrostriction stresses
Authors: Lee Ho Young , Peng Yiyan , Shkel Yuri M.
Published: October 2005

The apparent deformation due to an electric field does not rigorously describe the electrostriction phenomenon. This is in part due to uncertainties in the mechanical constraints at the specimen boundaries. Such constraints are very critical in thin films. Determining the electric-field-induced stress seems to be a more adequate approach to electrostriction. General thermodynamic considerations identify the electrostriction stress through strain derivatives of the dielectric displacement. Consequently, the derivatives of the dielectric coefficients are termed the electrostriction parameters. The strain-dielectric response of a material, which is called dielectrostriction, provides an avenue to study electrostriction. However, controlling the mechanical boundary conditions of a thin-film specimen can be challenging. This problem can be overcome by using a proposed planar capacitor sensor which does not require any mechanical contact with the specimen. The theoretical background and experimental results for the dielectrostriction study of a uniaxially loaded specimen are presented and discussed.
Incorporation of nonadiabatic transition into wave-packet dynamics
Authors: Mil’nikov Gennady V. , Zou Shiyang , Nakamura Hiroki
Published: October 2005

Nonadiabatic wave-packet dynamics is factorized into purely adiabatic propagation and instantaneous localized nonadiabatic transition. A general formula is derived for the quantum-mechanical local nonadiabatic operator which is implemented within the framework of the R-matrix method. The operator can be used for incorporating the nonadiabatic transition in semiclassical wave-packet dynamics.
A radiophotoluminescent glass plate system for medium-sized field dosimetry
Authors: Nakagawa Keiichi , Koyanagi Hiroki , Shiraki Takashi , Saegusa Shigeki , Sasaki Katsutake , Oritate Takashi , Mima Kazuo , Miyazawa Masanori , Ishidoya Tatsuyo , Ohtomo Kuni , Yoda Kiyoshi
Published: October 2005

A two-dimensional radiophotoluminescent system for medium-sized field dosimetry has been developed using a silver-activated phosphate glass plate with a dimension of 120mm×120mm×1mm and a readout unit comprising a UV excitation lamp and a CCD imager. A dose ranging from 0 to 400 cGy, provided by a 6 MV x-ray beam, was delivered to the glass plate oriented perpendicularly to the beam and positioned in a water phantom at a depth of 10 cm, where the center of the glass plate coincided with the linac isocenter. After the dose delivery, the glass plate was placed in the readout system. The CCD output intensity increased linearly with the applied dose. The angular dependence of response on the direction of radiation incidence was measured by rotating the glass plate in the water phantom, indicating that the output remained constant up to 75° from perpendicular incident direction, followed by a steep reduction down to 85% at an angle of 90°. A lateral dose distribution resulting from a 60mm×60mm irradiation was compared between the glass plate and an x-ray film having had the same exposure, showing that the glass plate and the x-ray film led to identical dose distributions. The dose reproducibility for a glass plate and the sensitivity variation among different glass plates were also evaluated.
Validity of the Taylor hypothesis in a random spatially smooth flow
Authors: Burghelea T. , Segre E. , Steinberg V.
Published: October 2005

The validity of the Taylor frozen flow hypothesis in a chaotic flow of a dilute polymer solution in a regime of elastic turbulence is investigated experimentally. By accurate time-dependent measurements of the flow field we study the velocity coherence between pairs of points displaced both in time and space and quantify the degree of applicability of the Taylor hypothesis. Alternatively, the frozen flow assumption is assessed by comparison of the measured velocity structure functions with the ones derived by a frozen flow assumption. The breakdown of the Taylor hypothesis is further discussed in both the context of strong velocity fluctuations and long-range spatial correlations, which are the result of the flow smoothness and lack of scale separation. Different choices of the advection velocity are tested and discussed.
New particle accelerations by magnetized plasma shock waves
Authors: Takeuchi Satoshi
Published: October 2005

Three mechanisms concerning particle accelerations are proposed to account for the high energy of cosmic rays. A model of magnetized plasma clouds is used to simulate a shock-type wave. The attainable energies of test particles colliding with the moving magnetic clouds are investigated by analytical and numerical methods for the three mechanisms. The magnetic trapping acceleration is a new type of particle trapping and acceleration in which, in principle, the test particle is accelerated indefinitely; hence, this mechanism surpasses the Fermi-type acceleration. In the single-step acceleration, the test particle obtains a significant energy gain even though it only experiences a single collision. Lastly, there is the bouncing acceleration by which the test particle is substantially accelerated due to repeated collisions.
Nitrogen incorporation in carbon nitride films produced by direct and dual ion-beam sputtering
Authors: Abrasonis G. , Gago R. , Jimenez I. , Kreissig U. , Kolitsch A. , Möller W.
Published: October 2005

Carbon (C) and carbon nitride (CNx) films were grown on Si(100) substrates by direct ion-beam sputtering (IBS) of a carbon target at different substrate temperatures (room temperature-450 °C) and Ar∕N2 sputtering gas mixtures. Additionally, the effect of concurrent nitrogen-ion assistance during the growth of CNx films by IBS was also investigated. The samples were analyzed by elastic recoil detection analysis (ERDA) and x-ray absorption near-edge spectroscopy (XANES). The ERDA results showed that significant nitrogen amount (up to 20 at. %) was incorporated in the films, without any other nitrogen source but the N2-containing sputtering gas. The nitrogen concentration is proportional to the N2 content in the sputtering beam and no saturation limit is reached under the present working conditions. The film areal density derived from ERDA revealed a decrease in the amount of deposited material at increasing growth temperature, with a correlation between the C and N losses. The XANES results indicate that N atoms are efficiently incorporated into the carbon network and can be found in different bonding environments, such as pyridinelike, nitrilelike, graphitelike, and embedded N2 molecules. The contribution of molecular and pyridinelike nitrogen decreases when the temperature increases while the contribution of the nitrilelike nitrogen increases. The concurrent nitrogen ion assistance resulted in the significant increase of the nitrogen content in the film but it induced a further reduction of the deposited material. Additionally, the assisting ions inhibited the formation of the nitrilelike configurations while promoting nitrogen environments in graphitelike positions. The nitrogen incorporation and release mechanisms are discussed in terms of film growth precursors, ion bombardment effects, and chemical sputtering.
Enhancement of the thermoelectric figure of merit in M∕T∕M (M=Cu or Ni and T=Bi0.88Sb0.12) composite materials
Authors: Yamashita Osamu , Satou Kouji , Odahara Hirotaka , Tomiyoshi Shoichi
Published: October 2005

The resultant thermoelectric figure of merit ZT of M∕T∕M (M=Cu or Ni and T=Bi0.88Sb0.12) composite materials welded with Bi–Sb alloy was measured at 298K as a function of relative thickness of Bi–Sb alloy and compared with ZT values calculated by treating it as an electrical and thermal circuit. It was first clarified experimentally that the observed ZT values of composite materials have a local maximum at an optimum volume fraction (corresponding to the thickness) of Bi–Sb alloy in spite of macroscopic composite materials, owing to a significant enhancement in the Seebeck coefficient. It is sure that the enhancement in α is caused by the boundary Seebeck coefficient generated at the interface between Bi–Sb alloy and a metal. It was thus clarified that the interface effect appears clearly in macroscopic systems. The observed maximum ZT values at 298K reached a surprisingly great value of 0.44 at a relative thickness of approximately 0.7, which corresponds to approximately 1.7 times as large as 0.26 of Bi0.88Sb0.12 alloy and to about half of 0.8–0.9 of commercially utilized bismuth telluride compounds. So enhanced ZT may not be utilizable for a Peltier module, but is available for generators.
Generation of programmable near-Fourier-transform-limited pulses of narrow-band laser radiation from the near infrared to the vacuum ultraviolet
Authors: Seiler R. , Paul Th. , Andrist M. , Merkt F.
Published: October 2005

Fourier-transform-limited pulses of programmable length and shape have been generated in the range λ=720–825nm from the continuous-wave output of a Ti3+-doped sapphire (Ti:Sa) ring laser using a pulsed acousto-optic modulator (AOM). The minimal rise time of the pulses amounts to 10ns and is limited by the size of the cw laser beam in the active medium of the AOM. Amplification of the radiation pulses in Nd:YAG-pumped Ti:Sa crystals into intense pulses of near-infrared (NIR) radiation with pulse energies of up to 15mJ was demonstrated at a repetition rate of 25Hz. Frequency upconversion into the ultraviolet (UV) by frequency doubling (νUV=2νNIR) or by mixing the fundamental NIR radiation with the doubled radiation (νUV=3νNIR) in nonlinear crystals was achieved under conditions where the pulse shapes could be preserved. The pulse energies amounted to up to 1mJ for the doubled radiation and 100μJ for the tripled radiation for NIR pulses of 30ns duration. Vacuum ultraviolet (VUV) radiation pulses of 108–109photons∕pulse at 120000cm−1 were generated by two-photon resonance-enhanced third-harmonic generation in a pulsed gas beam of xenon. The VUV pulse length could be adjusted between 10 and 20ns, and double pulses of VUV radiation separated by a variable delay of up to 100ns could be generated. Frequency chirps arising in the AOM and the pulsed amplification were found to be negligible, but a frequency shift of −5MHz was determined. The bandwidth of the generated radiation was estimated to be 35MHz in the UV at a wave number of ≈40000cm−1 and 55MHz in the VUV at a wave number of ≈120000cm−1 in a Doppler-free measurement of the (5p)6S01→(5p)56p[1∕2](J=0) two-photon resonance of xenon. The absolute accuracy of the wave-number calibration is limited by uncertainties in the positions of NIR lines of I2 taken as reference standard.
Analysis of the dynamics of a mechanical Q-switched CO2 laser: Six-temperature model
Authors: Wang Tie-Jun , Gao Jin-Yue , He Qiong-Yi , Ma Tao , Jiang Yun , Kang Zhi-Hui
Published: October 2005

A six-temperature kinetic model for a CO2-N2-He system is used to describe the dynamic processes of a mechanical Q-switched CO2 laser that is set up using a fast chopper. We put special emphasis on the effect of dynamical parameters on the laser intensity. It takes into account the effects of electrical excitation, energy transfer processes, thermal energy transport, as well as the dissociation of CO2 molecules and rotational relaxation of rotational levels. The results calculated are in satisfactory agreement with experimental data.
Temperature effect on field emission properties and microstructures of polymer-based carbon films
Authors: Guo P. S. , Sun Z. , Huang S. M. , Sun Y.
Published: October 2005

We investigated the field emission properties and resistivity of polymer-based carbon films prepared from poly ethyl-co-phenyl carbyne polymer precursors after treatment at different temperatures. As the heat-treatment temperature increased from 40to1200°C, the emission threshold field decreased from 12.4to2.1V∕μm, the emission current density increased from 0.1to6.1mA∕cm2, and the film resistivity decreased from 108to102Ωcm. The structural changes of the polymer films during the heat-treatment process were analyzed by Raman spectroscopy and atomic force microscopy. Raman analysis of these polymer-based carbon films suggests that the hydrogen content decreased while the sp2 carbon phase increased as the heat-treatment temperature increased. The dependence of the field emission properties of the polymer-based carbon films on the film structures (such as sp3, sp2 phases), film surface morphology and film resistivity is discussed. The enhancement of field emission from polymer-based carbon films was related to the increase of sp2∕sp3 ratio, film conductivity, and surface roughness with the heat-treatment temperature.
Fluorine-enhanced boron diffusion in germanium-preamorphized silicon
Authors: Jacques J. M. , Jones K. S. , Robertson L. S. , Li-Fatou A. , Hazelton C. M. , Napolitani E. , Rubin L. M.
Published: October 2005

Silicon wafers were preamorphized with 60 keV Ge+ or 70 keV Si+ at a dose of 1×1015 atoms∕cm2. F+ was then implanted into some samples at 6 keV at doses ranging from 1×1014 to 5×1015 atoms∕cm2, followed by B+11 implants at 500 eV, 1×1015atoms∕cm2. Secondary-ion-mass spectrometry confirmed that fluorine enhances boron motion in germanium-preamorphized materials in the absence of annealing. The magnitude of boron diffusion scales with increasing fluorine dose. Boron motion in as-implanted samples occurs when fluorine is concentrated above 1×1020atoms∕cm3. Boron atoms are mobile in as-implanted, amorphous material at concentrations up to 1×1019atoms∕cm3. Fluorine directly influences boron motion only prior to activation annealing. During the solid-phase epitaxial regrowth process, fluorine does not directly influence boron motion, it simply alters the recrystallization rate of the silicon substrate. Boron atoms can diffuse in germanium-amorphized silicon during recrystallization at elevated temperatures without the assistance of additional dopants. Mobile boron concentrations up to 1×1020atoms∕cm3 are observed during annealing of germanium-preamorphized wafers.
Granular slumping on a horizontal surface
Authors: Lajeunesse E. , Monnier J. B. , Homsy G. M.
Published: October 2005

We report the results of an experimental investigation of the flow induced by the collapse of a column of granular material (glass beads of diameter d) over a horizontal surface. Two different setups are used, namely, a rectangular channel and a semicircular tube, allowing us to compare two-dimensional and axisymmetric flows, with particular focus on the internal flow structure. In both geometries the flow dynamics and the deposit morphologies are observed to depend primarily on the initial aspect ratio of the granular column a=Hi∕Li, where Hi is the height of the initial granular column and Li its length along the flow direction. Two distinct regimes are observed depending on a: an avalanche of the column flanks producing truncated deposits for small a and a column free fall leading to conical deposits for large a. In both geometries the characteristic time scale is the free fall of the granular column τc=Hi∕g. The flow initiated by Coulomb-like failure never involves the whole granular heap but remains localized in a surface layer whose size and shape depend on a and vary in both space and time. Except in the vicinity of the pile foot where the flow is pluglike, velocity profiles measured at the side wall are identical to those commonly observed in steady granular surface flows: the velocity varies linearly with depth in the flowing layer and decreases exponentially with depth in the static layer. Moreover, the shear rate is constant, γ̇=0.3g∕d, independent of the initial aspect ratio, the flow geometry, position along the heap, or time. Despite the rather complex flow dynamics, the scaled deposit height Hf∕Li and runout distance ΔL∕Li both exhibit simple power laws whose exponents depend on a and on the flow geometry. We show that the physical origin of these power laws can be understood on the basis of a dynamic balance between acceleration, pressure gradient, and friction forces at the foot of the granular pile. Two asymptotic behaviors can be distinguished: the flow is dominated by friction forces at small a and by pressure forces at large a. The effect of the flow geometry is determined primarily by mass conservation and becomes important only for large a.
Gated x-ray intensifier for large format simultaneous imaging
Authors: McCarville T. , Fulkerson S. , Booth R. , Emig J. , Young B. , Anderson S. , Heeter B.
Published: October 2005

Some applications of gated x-ray imagers, pulsed x-ray spectroscopy, for example, benefit if image capture is simultaneous and gain is uniform over the frame. Simultaneity and uniformity are both improved when the voltage gate pulse propagation distance is as short as practical across the micro-channel-plate. This article describes a micro-channel-plate intensifier that captures a 40×100mm2 image in <300ps. A simple transmission line loss model is proposed to explain voltage loss across the micro-channel-plate. The voltage loss exponent was measured to be 0.05∕cm±20%, and used to predict spatial and temporal gain dependence. The spatial and temporal gain profile was measured in detail by capturing images of ∼1ps x-ray bursts created with a short pulse laser. The measured profile is consistent with that predicted using the loss model.
Displacement measurements with resolution in the 15 pm range
Authors: Puppin Ezio
Published: October 2005

An approach to the measurement of mechanical displacements in the picometer range is proposed. The basic idea is to intercept a focused laser beam with a blade whose displacements induce a variation in the intensity of the transmitted light. The smallest detectable displacement depends on the beam diameter and on the resolution of the electronic chain. In our preliminary experiment the beam has been focused with a microscope objective down to a size of 3μm. Two different methods have been used for reducing noise in the electronic chain. In one case the output signal has been normalized to the laser intensity. In the other case the blade position has been modulated at low frequency. In both cases the smallest detectable displacement is in the order of 15 pm.
Influence of top electrode on the current-induced magnetic switching in magnetic nanopillars
Authors: Yang T. , Hamrle J. , Kimura T. , Otani Y.
Published: October 2005

Magnetic nanopillars with variable top electrodes were fabricated to clarify the roles of the spin current and the spin accumulation in the current-induced magnetic switching. The critical switching current is significantly increased when the size of the top electrode is comparable to that of the nanopillar. This result implies that the dominant contribution in the current-induced magnetic switching is not the spin accumulation, but the spin current.
Nanostructured stars of ZnO microcrystals with intense stimulated emission
Authors: Lv Yuzhen , Li Chunping , Guo Lin , Wang Qingxiao , Wang Rongming , Xu Huibin , Yang Shihe , AI Xicheng , Zhang Jianping
Published: October 2005

We demonstrate the synthesis of single-crystalline star-shaped ZnO microcrystals with six arms by a simple solution method. Microscopic and diffraction data reveal that the as-grown products have a wurtzite structure. Each arm of the ZnO microstars has a sharp tip of several nanometers. Under moderate optical excitation, stimulated emission was observed at 388.4nm with a full width at half-maximum (FWHM) of less than 3nm and a threshold of 318kW∕cm2.
Nanoscale recording transducer for perpendicular magnetic recording
Authors: Chomko R. , Litvinov D. , Khizroev Sakhrat
Published: October 2005

A study of a perpendicular magnetic recording transducer with the potential to be utilized at areal densities above 1Tbit∕in.2 is presented. Focused ion beam etching is used to fabricate the transducer via trimming of a regular nanoslider ring head from an air bearing surface. The transducer is compared with a regular ring-type head. With spinstand experiments, it is demonstrated that the overlapping width determines the effective trackwidth in the case of the transducer. With other conditions equal, the transducer indicates substantially higher efficiency. The saturation current values for the transducer and the ring head are measured to be above 350 and 800mAturn, respectively. The performance of the transducer is tested with two types of perpendicular recording media, with and without a soft underlayer, respectively. The experiments indicate that, contrary to the common belief, the medium without a soft underlayer demonstrates the potential for achieving substantially higher areal densities.
Field emission of individual carbon nanotube with in situ tip image and real work function
Authors: Xu Zhi , Bai X. D. , Wang E. G. , Wang Zhong L.
Published: October 2005

The field emission properties of individual multiwalled carbon nanotubes have been measured simultaneously in correlation to the emitter images and their real work functions at tips by the in situ transmission electron microscopy method. The field emission of a single nanotube still follows the Fowler-Nordheim law. The field enhancement factor has been determined by the real work function rather than a given constant. In situ imaging and measurement show that the work function at the nanotube tip depends strongly on its structure and surface condition. This study provides an approach of direct linking field emission with the in situ emitter structure and the real work function at the emitter tip.
Proximity-induced activation of human Cdc34 through heterologous dimerization
Authors: Gazdoiu Stefan , Yamoah Kosj , Wu Kenneth , Escalante Carlos R. , Tappin Inger , Bermudez Vladimir , Aggarwal Aneel K. , Hurwitz Jerard , Pan Zhen-Qiang
Published: October 2005

Cdc34 is an E2-conjugating enzyme required for catalyzing the polyubiquitination reaction mediated by the Skp1·CUL1·F-box (SCF) protein E3 ubiquitin (Ub) ligase. Here, we show that the activity of human Cdc34 in the Ub–Ub ligation reaction was enhanced dramatically by SCF's core Ub ligase module, composed of a heterodimeric complex formed by the ROC1 RING finger protein and the CUL1 C terminus that contains a Nedd8 moiety covalently conjugated at K720. Unexpectedly, we found that N-terminal fusion of a GST moiety to human Cdc34 generated dimeric GST-Cdc34 that was constitutively active in supporting the assembly of K48-linked polyUb chains independently of SCF. Furthermore, fusion of a FK506-binding protein (FKBP) to the N terminus of human Cdc34 yielded FKBP-Cdc34 that was induced to form a dimer upon treatment with the chemical inducer AP20187. The AP20187-induced dimeric form of FKBP-Cdc34 was substantially more active than the monomer in catalyzing Ub–Ub ligation. Thus, juxtaposition of human Cdc34 activates its catalytic capability, suggesting that the SCF-mediated polyubiquitination reaction may require the conversion of Cdc34 from an inactive monomer to a highly active dimeric form.
Functional food science and defence against reactive oxidative species
Authors: Diplock A. T. , Charuleux J.-L. , Crozier-Willi G. , Kok F. J. , Rice-Evans C. , Roberfroid M. , Stahl W. , Viña-Ribes J.
Published: October 2005

This paper assesses critically the science base that underpins the argument that oxidative damage is a significant causative factor in the development of human diseases and that antioxidants are capable of preventing or ameliorating these disease processes. The assessment has been carried out under a number of headings, and some recommendations for future research are made based on the present day knowledge base.
GARSA: genomic analysis resources for sequence annotation
Authors: Dávila Alberto M. R. , Lorenzini Daniel M. , Mendes Pablo N. , Satake Thiago S. , Sousa Gabriel R. , Campos Linair M. , Mazzoni Camila J. , Wagner Glauber , Pires Paulo F. , Grisard Edmundo C. , Cavalcanti Maria C. R. , Campos Maria Luiza M.
Published: October 2005

Summary: Growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools and genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analyzed using the system since it accepts (1) chromatograms, (2) download of sequences from GenBank, (3) Fasta files stored locally or (4) a combination of all three. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), Trypanosoma rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST).

Availability: The GARSA system is freely available under GPL license (). For download requests visit or contact Dr Alberto Dávila.

Contact:  davila@fiocruz.br
Discovering hidden viral piracy
Authors: Kim Eddo , Kliger Yossef
Published: October 2005

Motivation: Viruses and developers of anti-inflammatory therapies share a common interest in proteins that manipulate the immune response. Large double-stranded DNA viruses acquire host proteins to evade host defense mechanisms. Hence, viral pirated proteins may have a therapeutic potential. Although dozens of viral piracy events have already been identified, we hypothesized that sequence divergence impedes the discovery of many others.

Results: We developed a method to assess the number of viral/human homologs and discovered that at least 917 highly diverged homologs are hidden in low-similarity alignment hits that are usually ignored. However, these low-similarity homologs are masked by many false alignment hits. We therefore applied a filtering method to increase the proportion of viral/human homologous proteins. The homologous proteins we found may facilitate functional annotation of viral and human proteins. Furthermore, some of these proteins play a key role in immune modulation and are therefore therapeutic protein candidates.

Contact:  kliger@compugen.co.il
A critical review of interfaces with the peripheral nervous system for the control of neuroprostheses and hybrid bionic systems
Authors: Navarro Xavier , Krueger Thilo B. , Lago Natalia , Micera Silvestro , Stieglitz Thomas , Dario Paolo
Published: October 2005

Abstract  Considerable scientific and technological efforts have been devoted to develop neuroprostheses and hybrid bionic systems that link the human nervous system with electronic or robotic prostheses, with the main aim of restoring motor and sensory functions in disabled patients. A number of neuroprostheses use interfaces with peripheral nerves or muscles for neuromuscular stimulation and signal recording. Herein, we provide a critical overview of the peripheral interfaces available and trace their use from research to clinical application in controlling artificial and robotic prostheses. The first section reviews the different types of non‐invasive and invasive electrodes, which include surface and muscular electrodes that can record EMG signals from and stimulate the underlying or implanted muscles. Extraneural electrodes, such as cuff and epineurial electrodes, provide simultaneous interface with many axons in the nerve, whereas intrafascicular, penetrating, and regenerative electrodes may contact small groups of axons within a nerve fascicle. Biological, technological, and material science issues are also reviewed relative to the problems of electrode design and tissue injury. The last section reviews different strategies for the use of information recorded from peripheral interfaces and the current state of control neuroprostheses and hybrid bionic systems.
Tumor necrosis factor‐α‐converting enzyme is expressed in the inflamed peripheral nervous system
Authors: Kurz Martin , Pischel Heidrun , Hartung Hans‐Peter , Kieseier Bernd C.
Published: October 2005

Abstract  Tumor necrosis factor‐α (TNF‐α) is considered to play a critical role in the pathogenesis of immune‐mediated inflammatory demyelinating disorders of the peripheral nervous system (PNS). Processing of membrane‐bound inactive pro‐TNF‐α into the active soluble cytokine is mediated by a sheddase, the so‐called TNF‐α‐converting enzyme (TACE), a member of the A Disintegrin and Metalloproteinase (ADAM) family. We explored the expression of TACE (ADAM‐17) in sciatic nerves from Lewis rats with experimental autoimmune neuritis (EAN), an animal model of the Guillain‐Barré syndrome (GBS), an immune‐mediated polyradiculoneuropathy. To extend our study to human disease, sural nerve biopsies from GBS patients were investigated by immunohistochemistry. In EAN, T lymphocytes could be defined as the cellular source of ADAM‐17 with peak expression levels at maximum clinical disease severity. Similarly, in human sural nerves, ADAM‐17‐expressing T cells could be localized primarily within the epi‐ and perineurium, whereas in control sections from patients with non‐inflammatory neuropathies, no expression could be depicted. Our findings indicate that ADAM‐17 is upregulated during EAN and expressed in nerves of GBS patients and thus may contribute to the pathogenesis of inflammatory demyelination of the PNS.
Fatigue as the main presenting symptom of chronic inflammatory demyelinating polyradiculoneuropathy: a study of 11 cases
Authors: Boukhris Sami , Magy Laurent , Gallouedec Gaël , Khalil Mohamed , Couratier Philippe , Gil Juan , Vallat Jean‐Michel
Published: October 2005

Abstract  Fatigue has been shown to be more frequent than previously thought in immune‐mediated polyneuropathies. However, fatigue has not been reported as the main cause of referral in chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) patients. Between January 2001 and December 2003, we investigated 11 patients referred for fatigue, for which we established a final diagnosis of CIDP. All patients had at least two clinical examinations including assessment of the fatigue severity scale (FSS) and one electrophysiological and laboratory work up. Additionally, 10 of the 11 patients had a nerve biopsy. There were 11 male patients. Mean age at onset was 53 ± 11 years. Main cause of referral was fatigue in all patients. Additional symptoms included cramps (one case), distal paresthesias (six cases), limb pain (seven cases) and vasomotor disturbances (one case). Cerebrospinal fluid (CSF) analysis displayed a moderate increase in protein content in four patients. Electrophysiological analysis showed abnormalities in all patients. Among 11 patients, one fulfilled the American Academy of Neurology electrodiagnostic criteria for CIDP and three fulfilled the inflammatory neuropathy cause and treatment group or the Nicolas et al. criteria. In the eight remaining patients, a nerve biopsy confirmed the diagnosis of CIDP. Ten patients were treated, among which seven showed a significant improvement based on the FSS scale. This study shows that fatigue is a possible cause of referral for patients with CIDP and, like previous reports, emphasizes the lack of sensitivity of widely accepted electrophysiological criteria of CIDP. Long‐term follow up of these patients is warranted to determine the prognosis of these minimal forms of CIDP and establish the best therapeutic strategy in such cases.
The gene expression signature of relapse in paediatric acute lymphoblastic leukaemia: implications for mechanisms of therapy failure
Authors: Beesley Alex H. , Cummings Aaron J. , Freitas Joseph R. , Hoffmann Katrin , Firth Martin J. , Ford Jette , de Klerk Nicolas H. , Kees Ursula R.
Published: October 2005

Despite significant improvements in the treatment of childhood acute lymphoblastic leukaemia (ALL), the prognosis for relapsing patients remains poor. The aim of this study was to generate a transcriptional profile of relapsed ALL to increase our understanding of the mechanisms involved in therapy failure. RNA was extracted from 11 pairs of cryopreserved pre‐B ALL bone marrow specimens taken from the same patients at diagnosis and relapse, and analysed using HG‐U133A microarrays. Relapse specimens overexpressed genes that are involved with cell growth and proliferation, in keeping with their aggressive phenotype. When tested in 72 independent specimens of pre‐B ALL and T‐ALL, the identified genes could successfully differentiate between diagnosis and relapse in either lineage, indicating the existence of relapse mechanisms common to both. These genes have functions relevant for oncogenesis, drug resistance and metastasis, but are not related to classical multidrug‐resistance pathways. Increased expression of the top‐ranked gene (BSG) at diagnosis was significantly associated with adverse outcome. Several chromosomal loci, including 19p13, were identified as potential hotspots for aberrant gene expression in relapsed ALL. Our results provide evidence for a link between drug resistance and the microenvironment that has previously only been considered in the context of solid tumour biology.
Infections with human herpesvirus 6 variant B delay platelet engraftment after allogeneic haematopoietic stem cell transplantation
Authors: Radonić Aleksandar , Oswald Olivia , Thulke Stefanie , Brockhaus Nina , Nitsche Andreas , Siegert Wolfgang , Schetelig Johannes
Published: October 2005

The clinical significance of human herpesvirus (HHV‐6) infections after allogeneic stem cell transplantation (SCT) remains controversial. We analysed cryoconserved plasma samples from 82 patients after allogeneic SCT by quantitative polymerase chain reaction for HHV‐6 variants A and B. Platelet engraftment was delayed in patients with HHV‐6B infections but not with HHV‐6A infections detected before day +28. In multivariate analysis early HHV‐6B infections and the type of conditioning were associated with platelet engraftment. In conclusion, the two variants of HHV‐6 should be studied separately; early infections with HHV‐6B may contribute to delayed platelet engraftment after allogeneic SCT.
Clone‐specific responses in leaf phenolics of willows exposed to enhanced UVB radiation and drought stress
Authors: Turtola Satu , Rousi Matti , Pusenius Jyrki , Yamaji Keiko , Heiska Susanne , Tirkkonen Veijo , Meier Beat , Julkunen‐Tiitto Riitta
Published: October 2005

The effects of enhanced UVB radiation and drought stress on willow secondary phenolics were studied using the leaves of 8‐week‐old micropropagated plantlets from interspecific hybrids (Salix myrsinites L. ×S. myrsinifolia Salisb.) and pure species (S. myrsinifolia). The plantlets were subjected for 4 weeks to two levels of UVB radiation (ambient, enhanced) and two levels of watering (well‐watered, drought‐stressed) according to a 2 × 2 factorial design. Enhanced UVB radiation increased the total concentration of flavonoids and phenolic acids in all plantlets, while the total concentration of salicylates remained unaffected. Drought stress reduced the total concentration of salicylates and phenolic acids in S. myrsinifolia plantlets, while in hybrids only phenolic acids were affected. The response of phenolic acids to enhanced UVB in drought‐stressed plantlets was different from that in well‐watered ones, indicating that drought stress limited the accumulation of phenolic acids under enhanced UVB radiation. Flavonoids increased in response to enhanced UVB radiation in drought‐stressed plantlets, although drought caused serious physiological stress on growth. There were significant differences between hybrid and S. myrsinifolia plantlets with respect to the composition of phenolics and between families and clones with respect to their concentration. In addition, the response of salicylates, flavonoids and phenolic acids to enhanced UVB and drought stress was clone‐specific, which may indicate that climatic changes will alter the genetic composition of northern forests.
Rehabilitation of patients with haemophilia after orthopaedic surgery: a case study
Authors: STEPHENSEN D.
Published: October 2005

Summary.  Preoperative and postoperative rehabilitation may be useful for improving the recovery of patients undergoing orthopaedic surgery, particularly in those with co‐morbidity or special requirements. This case study, of a patient with haemophilia and inhibitors to factor VIII undergoing total knee replacement, demonstrates the benefits of 6 weeks' preoperative physiotherapy (‘prehabilitation’) combined with 6 weeks' postoperative rehabilitation. The supervised physiotherapy regimen was individually tailored to specifically increase range of motion and muscle strength, enabling rapid mobilization and recovery of function, whilst minimizing the risk of bleeding.
Identifying and managing inhibitor patients requiring orthopaedic surgery – the multidisciplinary team approach
Authors: LUDLAM C.
Published: October 2005

Summary.  Until recently, surgery in haemophilia patients with inhibitors was strongly contraindicated and was therefore often not even contemplated. Inhibitor patients entering the surgical arena face unique challenges; the most frequently encountered problem during surgical intervention is bleeding, and thrombosis is occasionally observed. The activated prothrombin complex concentrate, FEIBATM, and recombinant activated factor VII (rFVIIa) are available as haemostatic cover during surgery. The use of rFVIIa enables inhibitor patients to undergo orthopaedic surgery with an expectation of success, and results are generally good. An organized team approach is critical to this success. However, further information is required to enable different procedures to be optimized in terms of both outcome and safety.
Quality of life before and after surgery: mobility issues, the fear of surgery, inpatient recovery and outpatient rehabilitation
Authors: PEACOCK K.
Published: October 2005

Summary.  A positive life‐changing experience of joint replacement surgery from the point of view of a patient with Factor VII inhibitor.
ESOS: a European study on the orthopaedic status of patients with haemophilia and inhibitors
Authors: DOLAN G.
Published: October 2005

Summary.  Published studies highlight the paucity of data relating to orthopaedic health and quality of life in haemophilia patients with inhibitors. A European Study on the Orthopaedic Status of Patients with Haemophilia and Inhibitors (ESOS) has been set up to address this lack of data. This cross‐sectional retrospective study aims to enrol 400 patients from 50 sites in nine European countries. The primary outcome measure of the study is the burden of orthopaedic complications in patients with severe haemophilia and inhibitors. The data that will be generated should demonstrate the high level of arthropathy in haemophilia patients with inhibitors and show the need to focus on improving orthopaedic health in this rare, but particularly vulnerable, patient population.
Glutamine depletion potentiates leucocyte‐dependent inflammatory events induced by carrageenan or Clostridium difficile toxin A in rats
Authors: Nascimento Silvia B. , Sousa Romualdo B. , Martins Marcos Jullian B. , Souza Gomes Antoniella , Souza Marcellus Henrique L. P. , Guerrant Richard L. , Cunha Fernando Q. , Ribeiro Ronaldo A. , Brito Gerly A. C.
Published: October 2005

This research investigated the effect of glutamine (Gln) depletion on leucocyte‐dependent inflammatory events. Rats were treated intraperitoneally, 16 hr prior to the peak of every parameter evaluated, with either 0·9% NaCl, methionine‐sulphoximine (MSO, an inhibitor of endogenous Gln synthesis, 25 mg/kg) or with MSO + Gln (MSO as above plus Gln 3 g/kg in three doses). MSO‐induced Gln depletion increased paw oedema induced both by carrageenan (Cg) and by Clostridium difficile toxin A (TxA) (66·2% and 45·5%, respectively; P < 0·05). In dextran‐injected animals, oedema and myeloperoxidase (MPO) activity were not modified by Gln depletion. In Cg‐treated paws, Gln depletion increased MPO activity by 44% (P < 0·05), interleukin‐1β (IL‐1β) and tumour necrosis factor‐α (TNF‐α) concentrations by 47% and 52%, respectively (P < 0·05), and immunostaining for TNF‐α in paw tissue. In TxA‐injected paws, Gln depletion increased MPO activity (46%; P < 0·05). Gln depletion increased Cg‐ and TxA‐induced neutrophil migration to subcutaneous air pouches by 56% and 77% (P < 0·05), respectively, but did not affect migration induced by N‐formyl‐methionyl‐leucyl‐phenylalanine (fMLP). Gln infusions reversed all the effects of MSO. Leucocyte counts did not differ between groups. Gln depletion potentiates acute inflammation, possibly by increasing neutrophil migration through resident cell activation and production of IL‐1β and TNF‐α. Gln supplementation reverses these effects and may be useful during inflammatory catabolic stress.
Cbl‐b differentially regulates activation‐induced apoptosis in T helper 1 and T helper 2 cells
Authors: Hanlon Allison , Jang Sihyug , Salgame Padmini
Published: October 2005

We previously reported that ligation of CD3 induces antiapoptotic signals in T helper 2 (Th2) cells, and in contrast causes Th1 cells to undergo apoptosis. Here we show that Cbl‐b is accountable for the unequal response, revealing a previously unknown cell‐specific regulatory function for the molecule. Absence of Cbl‐b resulted in resistance to activation‐induced apoptosis in murine Th1 cells following CD3 ligation, akin to what is observed in Th2 cells containing Cbl‐b. Concurrent with the apoptosis profile, CD3 ligation in the absence of Cbl‐b induced raft mobilization and cytoskeletal rearrangement in Th1 cells. Despite their ability to signal from CD3, Th2 cells did not aggregate their rafts, providing an explanation for cell‐specific activity of Cbl‐b.
MAdCAM‐1 is needed for diabetes development mediated by the T cell clone, BDC‐2·5
Authors: Phillips Jenny M. , Haskins Kathryn , Cooke Anne
Published: October 2005

The NOD‐derived islet‐reactive CD4+ T cell clone, BDC‐2·5, is able to transfer diabetes to neonatal non‐obese diabetic (NOD) mice but is unable to transfer disease to either adult NOD or NOD scid recipients. Transfer of diabetes to adult recipients by BDC‐2·5 is only accomplished by cotransfer of CD8+ T cells from a diabetic donor. To understand why this CD4+ T cell clone is able to mediate diabetes in neonatal but not the adult recipients we examined the ability of the clone to traffic in the different recipients. Our studies showed that MAdCAM‐1 has a very different expression pattern in the neonatal and adult pancreas. Blockade of this addressin prevents the clone from transferring diabetes to neonatal mice, suggesting that the differential pancreatic expression of MAdCAM‐1 in neonatal and adult pancreas provides an explanation of the differences in diabetes development.