bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical characteristics of Pt Schottky contacts on sulfide-treated n-type ZnO
Authors: Kim Sang-Ho , Kim Han-Ki , Seong Tae-Yeon
Published: January 2005

We have investigated the effect of sulfide treatment on the electrical characteristics of Pt contacts on (000-1) n-type ZnO(∼5×1015cm−3) single crystals. The Pt contact on conventionally cleaned ZnO surface shows an ohmic behavior. However, the contact produces a Schottky behavior, when the ZnO surface is etched in a boiling (NH4)2Sx solution. Measurements show that the Schottky barrier height, ideality factor, and leakage current at −5V of the Pt contact on the sulfide-treated ZnO are 0.79eV, 1.51, and 3.75×10−10A, respectively. Auger electron spectroscopy (AES) and x-ray photoelectron spectroscopy (XPS) examinations indicate the formation of ZnS phase at the Pt∕ZnO interface. Based on the capacitance–voltage, AES, and XPS results, a possible mechanism for the formation of good Schottky contacts is given.
Incoherent broad-band cavity-enhanced absorption spectroscopy of liquids
Authors: Fiedler Sven E. , Hese Achim , Ruth Albert A.
Published: January 2005

A new application of incoherent broad-band cavity enhanced absorption spectroscopy (IBBCEAS) to weak transitions in solution through a very straightforward modification of commercially available double-beam UV/VIS absorption spectrometers is reported. The improved sensitivity of the new approach is demonstrated on basis of the weak Franck–Condon inhibited absorption of the fifth C–H stretch overtone in liquid benzene. The theoretical limits of the enhancement of the signal-to-noise ratio of IBBCEAS in comparison with single pass absorption experiments are discussed for a set of given experimental cavity parameters. The optical loss properties of a typical transparent cuvette window in the cavity are also discussed.
External field-frequency lock probe for high resolution solid state NMR
Authors: Paulson Eric K. , Zilm Kurt W.
Published: January 2005

A transmission line lock probe is described for magnetic field stabilization of a high field superconducting magnet with a significant drift rate for high resolution solid state NMR experiments employing a conventional magic angle spinning (MAS) probe. The lock probe connects to the standard spectrometer lock channel and employs a spherical sample bulb containing D2O doped such that the peak is homogeneously broadened despite the sample being displaced from the homogeneous central region of the static magnetic field. Use of a separate lock probe makes it possible to remove the MAS probe for changing samples while maintaining field-frequency lock.
Very high resolution long-baseline water-tube tiltmeter to record small signals from Earth free oscillations up to secular tilts
Authors: d’Oreye Nicolas F. , Zürn Walter
Published: January 2005

A 43m long floatless water-tube tiltmeter has been in operation since 1997 at the Walferdange Underground Laboratory for Geodynamics in the Grand Duchy of Luxembourg. The absence of moving parts makes this instrument particularly simple but does not prevent it from measuring some very small geophysical signals such as the Earth tides with a very favorable signal-to-noise ratio or the successive passages of Love waves circling the globe after major Earthquakes. Its very low noise level and its high resolution up to the long-period seismic band (where for instance the resolution is better than 5×10−12rad) also allows the successful recording of rarely observed grave toroidal and spheroidal free oscillations of the Earth excited by major earthquakes. In the environmental conditions of its installation (in a gypsum mine at 100m depth), the instrument shows a high degree of reliability and a very low drift rate (<0.005microrad∕month). The analytical tilt and horizontal displacement transfer functions computed for this instrument and its sensors can be used to calculate the best geometrical characteristics for the construction of prototypes which should respond to specific requirements for applications in geophysics or geotechnics.
Microwave spectroscopy system for molecules trapped in low temperature condensed media using opto-thermal detection with superconducting thin-film sensor
Authors: Ishiguro Masazumi , Aratono Yasuyuki
Published: January 2005

A simple and widely applicable microwave spectroscopy system for low temperature matrices has been developed. We applied the technique of opto-thermal detection with a superconducting thin-film sensor (STS) for the detection of very weak absorption signals of molecules trapped in quantum solids such as solid para-hydrogen (p-H2). For testing of the system, the microwave transition of an ortho-hydrogen (o-H2) dimer in solid p-H2 was observed. The S∕N ratio of the observed spectrum of the G1 transition at 1.4K was approximately 8. The ultrahigh sensitivity of STS makes it possible not only to obtain sufficient sensitivity but also to make the apparatus very simple especially around the sample cell.
Transition from the constant ion mobility regime to the ion-atom charge-exchange regime for bounded collisional plasmas
Authors: Poggie Jonathan , Sternberg Natalia
Published: January 2005

A numerical and analytical study of a planar, collisional, direct-current, plasma-wall problem is presented. The fluid model for the problem is first validated by comparing numerical solutions with experimental data for low-pressure (∼0.1Pa) electrode sheaths with wall potentials on the order of −100V. For electric potential, ion number density, and ion velocity, good agreement was found between theory and experiment from within the sheath out to the bulk plasma. The frictional drag resulting from ion-neutral collisions is described by a model incorporating both linear and quadratic velocity terms. In order to study the transition from the constant ion mobility regime (linear friction) to the ion-atom charge-exchange collision regime (quadratic friction), the theoretical model was examined numerically for a range of ion temperatures and ion-neutral collision rates. It was found that the solution profiles in the quasineutral plasma depend on the ion temperature. For low ion temperatures they are governed mainly by the ion-atom charge-exchange regime, whereas for high temperatures they are governed by the constant ion mobility regime. Quasineutral plasma models corresponding to these two limiting cases were solved analytically. In particular, an analytical plasma solution is given for the ion-atom charge exchange regime that includes the effects of ion inertia. In contrast to the quasineutral plasma, the sheath is always governed for low to moderate collision rates by the ion-atom charge-exchange regime, independent of the ion temperature. Varying the collision rate, it was shown that when the wall potential is sufficiently high, the sheath cannot be considered collisionless, even if the collision rate is quite small.
Magnetostatic interactions of single-domain nanopillars in quasistatic magnetization states
Authors: Jang Hyuk-Jae , Eames Pete , Dahlberg E. Dan , Farhoud M. , Ross C. A.
Published: January 2005

The magnetostatic interactions and the disorder in an array of cylindrical Ni particles have been quantified. Room-temperature magnetic force microscopy data were used to determine the dipolar energy/particle for first, second, etc., nearest neighbor particles with external magnetic fields applied along the cylinder axes. An Ising-type model, which includes a distribution of anisotropy energies, accurately replicates the experimental dipolar energy/particle data and the observed hysteresis loops. The technique provides a method to quantify the magnetic properties of a magnetic particle system.
Enhancing domain wall motion in magnetic wires by ion irradiation
Authors: Cayssol F. , Menéndez J. L. , Ravelosona D. , Chappert C. , Jamet J.-P. , Ferré J. , Bernas H.
Published: January 2005

The influence of low-energy He ion irradiation on the dynamics of a single Bloch domain wall was studied in magnetic wires based on Pt∕Co∕Pt trilayers exhibiting perpendicular anisotropy. The domain wall velocity is highly enhanced (up to three orders of magnitude) after irradiation at moderate fluence. A study in the thermally activated regime shows that this is consistent with a reduction of the density of pinning centers and of the pinning force. Uniform ion irradiation significantly improves domain wall motion, as required for future magnetic devices.
Difference equation approach to two-thermocouple sensor characterization in constant velocity flow environments
Authors: Hung P. C. , Irwin G. , Kee R. , McLoone S.
Published: January 2005

Thermocouples are one of the most popular devices for temperature measurement due to their robustness, ease of manufacture and installation, and low cost. However, when used in certain harsh environments, for example, in combustion systems and engine exhausts, large wire diameters are required, and consequently the measurement bandwidth is reduced. This article discusses a software compensation technique to address the loss of high frequency fluctuations based on measurements from two thermocouples. In particular, a difference equation (DE) approach is proposed and compared with existing methods both in simulation and on experimental test rig data with constant flow velocity. It is found that the DE algorithm, combined with the use of generalized total least squares for parameter identification, provides better performance in terms of time constant estimation without any a priori assumption on the time constant ratios of the thermocouples.
Array of luminescent Er-doped Si nanodots fabricated by pulsed laser deposition
Authors: Park Seung Min , Bae Chang Hyun , Nam Woosung , Park Sung Chan , Ha Jeong Sook
Published: January 2005

Ordered arrays of Er-doped Si nanodots were fabricated by pulsed laser deposition using an anodic aluminum oxide (AAO) nanopore membrane. Er-doped Si (Si:Er) nanodots with an average diameter of 60–80nm and a periodicity of 100nm were uniformly assembled into hexagonally ordered nanopores of AAO membrane. Photoluminescence (PL) spectra taken from Si:Er nanodots showed an emission peak at 1.54μm, which is due to intra-4f shell transition (I13∕24→I15∕24) of Er3+ ions. Postannealing of nanodot arrays up to 500°C resulted in the enhancement of PL intensities without enlargement or aggregation of the nanodots.
Structure of the carrot defect in 4H-SiC epitaxial layers
Authors: Benamara M. , Zhang X. , Skowronski M. , Ruterana P. , Nouet G. , Sumakeris J. J. , Paisley M. J. , O’Loughlin M. J.
Published: January 2005

Transmission electron microscopy and KOH etching were used to determine the structure of the carrot defect in 4H-SiC epilayers. The defect consists of two intersecting planar faults on prismatic {11¯00} and basal {0001} planes. Both faults are connected by a stair-rod dislocation with Burgers vector 1∕n [101¯0] with n>3 at the crossover. A Frank-partial dislocation with b=1∕12[44¯03] terminates the basal fault.
Nd
:
Ta
2
O
5
rib waveguide lasers
Authors: Unal Bayram , Tai Chao-Yi , Shepherd David P. , Wilkinson James S. , Perney Nicolas M. B. , Netti M. Caterina , Parker Gregory J.
Published: January 2005

Ta 2 O 5 waveguides offer great potential for high-density active photonic crystal circuits and their combination with rare-earth dopants for active devices is of interest for increasing their potential functionality. To this end, neodymium-doped Ta2O5 rib waveguide lasers have been fabricated on an oxidized silicon wafer by rf sputtering and argon ion-beam milling and laser action in this material has been demonstrated. Lasing was observed at wavelenghts between 1060 and 1080 nm and an absorbed pump power threshold of 87 mW was obtained.
Single-crystal field-effect transistors based on copper phthalocyanine
Authors: Zeis R. , Siegrist T. , Kloc Ch.
Published: January 2005

Copper phthalocyanine (Cu–Pc) single crystals were grown by physical vapor transport and field-effect transistors (FETs) on the surface of these crystals were prepared. These FETs function as p-channel accumulation-mode devices. Charge carrier mobilities of up to 1cm2∕Vs combined with a low field-effect threshold were obtained. These remarkable FET characteristics, along with the highly stable chemical nature of Cu–Pc, make it an attractive candidate for device applications.
Enhanced terahertz emission from porous InP (111) membranes
Authors: Reid M. , Cravetchi I. V. , Fedosejevs R. , Tiginyanu I. M. , Sirbu L.
Published: January 2005

Bulk n-InP wafers and porous membrances with (111) crystallographic orientation have been illuminated with 120 fs pulses of 800 nm radiation from a Ti:Sapphire amplified laser system. Terahertz (THz) emission from samples was measured as a function of excitation fluence in the reflection geometry. It was established that the THz emission from both bulk and porous InP (111) saturates at high excitation fluence, emitting comparable levels of far-infrared radiation. Below saturation, however, the emission from the porous InP (111) membrane was found to be approximately an order of magnitude greater in radiated electric field or approximately two orders of magnitude in power relative to the bulk sample. The observed increase in efficiency from the porous, relative to the bulk samples, can be attributed either to the local field enhancement in the porous network for the nonlinear contribution to the radiated THz fields, or to modifications of the transient currents resulting in enhanced THz radiation.
Temperature dependence of a nanomechanical switch
Authors: Badzey Robert L. , Zolfagharkhani Guiti , Gaidarzhy Alexei , Mohanty Pritiraj
Published: January 2005

We present the effect of temperature on the switching characteristics of a bistable nonlinear nanomechanical beam. At megahertz-range frequencies, we find that it is possible to controllably change the state of the system between two stable mechanical states defined by the hysteresis brought on by nonlinear excitation. We find that the introduction of increased temperature results in a loss of switching fidelity, and that temperature acts as an effective source of external noise on the dynamics of the system.
Effects of two-dimensional electron gas on the optical properties of InAs/GaAs quantum dots in modulation-doped heterostructures
Authors: Kim T. W. , Kim J. H. , Lee H. S. , Lee J. Y. , Kim M. D.
Published: January 2005

The Shubnikov–de Haas data showed that the carrier density of two-dimensional electron gas (2DEG) in the GaAs active region containing InAs quantum dot (QD) arrays embedded between modulation-doped Al0.25Ga0.75As/GaAs heterostructures increased with increasing doping concentration in the modulation layer. The transmission electron microscopy images showed that the sizes of the self-assembled InAs vertically stacked QD arrays inserted in the GaAs did not change significantly with increasing carrier density of the 2DEG. The photoluminescence (PL) spectra showed that the peaks corresponding to the interband transitions from the ground electronic subband to the ground heavy-hole subband of the InAs QDs shifted to the higher energy side with increasing density of the 2DEG and that the full width at half maximum of the PL spectrum increased slightly with increasing density of the 2DEG.
Photoemission study of poly(dA)–poly(dT) DNA: Experimental and theoretical approach to the electronic density of states
Authors: Wadati Hiroki , Okazaki Kozo , Niimi Yasuhiro , Fujimori Atsushi , Tabata Hitoshi , Pikus Jared , Lewis James P.
Published: January 2005

We present results of an ultraviolet photoemission spectroscopy study of artificially synthesized poly(dA)–poly(dT) DNA molecules on p-type Si substrates. For comparison, we also present the electronic density of states calculated using an ab initio tight-binding method based on density-functional theory (DFT). Good agreement was obtained between experiment and theory. The spectra of DNA networks on the Si substrate showed that the Fermi level of the substrate is located in the middle of the band gap of DNA. The spectra of thick (∼70nm) DNA films showed a downward shift of ∼2eV compared to the network samples.
Low-force contact heating and softening using micromechanical switches in diffusive-ballistic electron-transport transition
Authors: Jensen Brian D. , Huang Kuangwei , Chow Linda L.-W. , Kurabayashi Katsuo
Published: January 2005

We demonstrate softening of the gold-to-gold contact in surface micromachined microelectromechanical switches under electrostatic force near 30μN, which results from the heating of contact asperities sustaining electron transport. A bias potential that causes the switch contacts to soften is measured for initial contact resistance varying between 0.5 and 300Ω. The asperity sizes in this range are comparable to the electron mean-free path at room temperature. We show that contact spots smaller than the mean-free path require larger bias for softening. Our results can be explained using a model accounting for ballistic electron transport in the contact.
Ultrahigh temperature vibration sensors using aluminum nitride thin films and W∕Ru multilayer electrodes
Authors: Akiyama Morito , Kamohara Toshihiro , Nishikubo Keiko , Ueno Naohiro , Nagai Hideaki , Okutani Takeshi
Published: January 2005

Ultrahigh temperature vibration sensors have been fabricated from highly c-axis-oriented aluminum nitride (AlN) thin films and tungsten/ruthenium (W∕Ru) multilayer bottom electrodes. These films and electrodes were prepared by radio-frequency magnetron sputtering on zirconium oxide (ZrO2) substrates, such as AlN∕W∕Ru∕ZrO2. The vibration sensors resisted the heat treatment of 1450°C for 1h in argon, and after that, peeling and cracks were not observed in the sensor surface. The “tough” behavior of the vibration sensors in the high temperature is probably attributed to the chemical composition change of the W∕Ru multilayer bottom electrodes to Ru60W40 and Ru15W85 solid solutions that prevent chemical reactions and relax thermal stress.
Femtosecond transient fluorescence spectrometer based on parametric amplification
Authors: Fita Piotr , Stepanenko Yuriy , Radzewicz Czeslaw
Published: January 2005

We report an experimental proof-of-principle of a method for recording femtosecond, time-resolved fluorescence spectra in the visible range. The method is based on a noncollinear parametric amplification in a beta barium borate crystal and provides time resolution of the order of 100fs. We demonstrate that with this method, transient fluorescence spectra as wide as 6000cm−1 can be recorded in a single time-delay scan. Fluorescence decay dynamics and transient spectra of Coumarin 6dye dissolved in aniline were measured to test the usefulness of the method.
Dynamic evolution of surface plasmon resonances in metallic nanoslit arrays
Authors: Sun Zhijun , Jung Yun Suk , Kim Hong Koo
Published: January 2005

We have investigated surface plasmon interactions in a metallic nanoslit array structure that shows characteristic transmission spectra with well-defined transmission minima and maxima in the visible-to-infrared range. The time evolution of the surface plasmon resonances occurring in various different regimes of the spectra was analyzed by performing finite-difference time-domain analysis of the plasmon field, energy flow, and polarization charge distributions in the nanoslit array structure. At the transmission dip that corresponds to the surface plasmon resonance at metal/dielectric(substrate) interface, the polarization charges are found to distribute such that they form in-plane standing-wave oscillations along the dielectric side of the metal surface. At the transmission peak, surface plasmon waves oscillate along the periphery of each metal island with a quadrupolar distribution of polarization charges. At the longer wavelength regime, the polarization charges at each island show a dipolar distribution along the array direction. Optical transmission in this regime is found to critically depend on slit width, which affects the near-field coupling between metal islands.
Magnetic field tunable circularly polarized stimulated emission from midinfrared IV-VI vertical emitting lasers
Authors: Fürst J. , Pascher H. , Schwarzl T. , Springholz G. , Böberl M. , Bauer G. , Heiss W.
Published: January 2005

Optically pumped laser emission from a midinfrared PbSe vertically emitting microcavity structure in a magnetic field applied in Faraday geometry is presented. It is shown that the emission line at a wavelength of about 7.9μm splits into two circularly polarized components with opposite helicity. The splitting of the emission line in the magnetic field is caused by different refractive indices of the material inside the microcavity for left- and right-hand circularly polarized light, yielding two resonator modes. Thereby the emission wavelength can be fine tuned by, e.g., 2cm−1 at 30kG. At higher fields the laser emission is 100% circularly polarized. This indicates that lasing in this case originates from completely spin polarized carriers.
Direct observation of interstitial molecular N2 in Si oxynitrides
Authors: Chung Youngsu , Lee Jae Cheol , Shin H. J.
Published: January 2005

High-resolution near edge x-ray absorption spectroscopy and x-ray photoelectron spectroscopy were used to characterize ultrathin plasma-nitrided silicon oxides. The direct observation of interstitial molecular N2 was made by vibrationally resolved N K-edge absorption spectroscopy. The N2 molecules were trapped during the plasma nitridation at the near surface and could be eliminated by annealing via molecular out-diffusion.
Experimental setup for high energy photoemission using synchrotron radiation
Authors: Torelli P. , Sacchi M. , Cautero G. , Cautero M. , Krastanov B. , Lacovig P. , Pittana P. , Sergo R. , Tommasini R. , Fondacaro A. , Offi F. , Paolicelli G. , Stefani G. , Grioni M. , Verbeni R. , Monaco G. , Panaccione G.
Published: January 2005

The instrument VOLPE (volume photoemission from solids) is an experimental setup dedicated to high energy photoemission (PE) experiments. The instrument is equipped with an electrostatic hemispherical spectrometer especially designed to analyze high energy electrons (up to 10 keV) with high resolving power. In order to attain an energy resolution of a few tens of millielectron volts, we designed and constructed a dedicated input lens system, high stability power supplies, and a low dark-count detector and readout electronics. The system has been tested and is now operational on the ID16 beamline at European Synchrotron Radiation Facility, where an optical layout has been developed to perform high energy, high resolution PE experiments. First results show an overall energy resolution (electron + photon) of 71±7meV at 5934 eV. The effective attenuation length of the photoelectrons is estimated to be 5±0.5nm at a kinetic energy of 5 keV.
Local luminescence of ZnO nanowire-covered surface: A cathodoluminescence microscopy study
Authors: Fan H. J. , Scholz R. , Zacharias M. , Gösele U. , Bertram F. , Forster D. , Christen J.
Published: January 2005

Vertically aligned ZnO nanowires were synthesized on sapphire through vapor deposition using Au as a catalyst. In addition to the nanowires, the sample surface contained a thin wetting layer of ZnO clusters. Spatially and spectrally resolved cathodoluminescence (CL) microscopy was applied to correlate the luminescent properties and the sample structure. Local CL spectra and monochromatic images revealed that the nanowires are the major source for a strong and sharp I8 emission line, while two weak emissions at low energies originate exclusively from the wetting layer. Information on stress is also obtained from the relative position of the I8 line.
Electronic insulator-conductor conversion in hydride ion-doped 12CaO∙7Al2O3 by electron-beam irradiation
Authors: Hayashi Katsuro , Toda Yoshitake , Kamiya Toshio , Hirano Masahiro , Yamanaka Minako , Tanaka Isao , Yamamoto Takahisa , Hosono Hideo
Published: January 2005

We report formation of persistent carrier electrons in hydride ion (H−)-incorporated 12CaO∙7Al2O3 (C12A7) by electron-beam irradiation. The electrical conductivity of H−-doped C12A7 single crystals increases with the electron-beam irradiation dose, accompanied with a green coloration attributable to a carrier electron formation. A 25 keV electron beam with a dose of ∼500μCcm−2 fully converts the conductivity in surface layers to the depth of ∼4μm. Carrier electron formation is most likely due to electron-hole pairs generated in the electron excitation volume and subsequent energy transfer to the H− ions. The estimated carrier formation yield per an incident electron is ∼30. These findings may enable a fine patterning of the conductive area without photomasks and photoresists.
Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin
Authors: Polekhina Galina , Giddings Kara Sue , Tweten Rodney K. , Parker Michael W.
Published: January 2005

The cholesterol-dependent cytolysins (CDCs), a superfamily of pore-forming toxins, are characterized by a conserved undecapeptide motif that is believed to be critical for membrane recognition by means of cholesterol. Intermedilysin (ILY), an unusual member of the CDCs, exhibits specificity for human cells and contains nonconservative substitutions in the motif. We show that the cellular specificity of ILY is based on its ability to specifically bind to human cells and does not involve some other feature of the CDC mechanism. Furthermore, cellular recognition by ILY appears to be encoded in domain 4 alone but does not involve the variant undecapeptide of ILY. We show that the undecapeptide is involved in the prepore-to-pore conversion of ILY and so demonstrate a direct connection between the structure of the undecapeptide and the prepore-to-pore transition. We have determined the crystal structure of ILY, which, when compared to the known structure of a prototypical CDC, suggests that the basic aspects of its 3D structure are likely to be conserved in all CDCs.
Distinct roles of insulin and liver X receptor in the induction and cleavage of sterol regulatory elementbinding protein-1c
Authors: Hegarty Bronwyn D. , Bobard Alexandre , Hainault Isabelle , Ferré Pascal , Bossard Pascale , Foufelle Fabienne
Published: January 2005

Sterol regulatory element-binding proteins (SREBPs) are transcription factors central to the regulation of lipid metabolism. The SREBPs are synthesized as precursor proteins that require proteolytic processing to become transcriptionally active. Whereas the regulation of SREBP-1a and -2 cleavage by cellular sterol content is well defined, much less is known about the regulation of SREBP-1c, the predominant SREBP isoform in the liver. Both insulin and liver X receptor α (LXRα) induce SREBP-1c transcription; however, the respective roles of these factors and the mechanism responsible for proteolytic cleavage of this SREBP isoform are not known. In this study, we compare the effects of insulin and LXR agonist TO-901317 on SREBP-1c expression and transcriptional activity in isolated rat hepatocytes. We report that full induction of the mature and transcriptionally active form of SREBP-1c protein requires insulin. Although activation of LXR leads to the induction of
SREBP-1c
gene expression and precursor protein, it has a very poor effect in inducing the mature nuclear form of the transcription factor. This may be due to the induction of
insulin-induced gene-2a
mRNA and protein by LXR activation. The LXR-induced SREBP-1c precursor, however, is rapidly cleaved on acute exposure to insulin via a phosphatidylinositol 3-kinase-dependent mechanism. Finally, we show through experiments in suckling mice that this acute action of insulin to stimulate the proteolytic processing of SREBP-1c is functional
in vivo
.
An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase
Authors: Phan Anh Tuân , Kuryavyi Vitaly , Ma Jin-Biao , Faure Aurélie , Andréola Marie-Line , Patel Dinshaw J.
Published: January 2005

We report on the NMR-based solution structure of the
93del
d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K
+
solution. Within each 16-nt monomer subunit, which contains one A·(G·G·G·G) pentad sandwiched between two G·G·G·G tetrads, all G-stretches are parallel, and all guanines are
anti
with the exception of G1, which is
syn
. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G·G·G·G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A·(G·G·G·G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the
93del
dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.
The genome of the heartwater agent
Ehrlichia ruminantium
contains multiple tandem repeats of actively variable copy number
Authors: Collins Nicola E. , Liebenberg Junita , de Villiers Etienne P. , Brayton Kelly A. , Louw Elmarié , Pretorius Alri , Faber F. Erika , van Heerden Henriette , Josemans Antoinette , van Kleef Mirinda , Steyn Helena C. , van Strijp M. Fransie , Zweygarth Erich , Jongejan Frans , Maillard Jean Charles , Berthier David , Botha Marli , Joubert Fourie , Corton Craig H. , Thomson Nicholas R. , Allsopp Maria T. , Allsopp Basil A.
Published: January 2005

Heartwater, a tick-borne disease of domestic and wild ruminants, is caused by the intracellular rickettsia
Ehrlichia ruminantium
(previously known as
Cowdria ruminantium
). It is a major constraint to livestock production throughout subSaharan Africa, and it threatens to invade the Americas, yet there is no immediate prospect of an effective vaccine. A shotgun genome sequencing project was undertaken in the expectation that access to the complete protein coding repertoire of the organism will facilitate the search for vaccine candidate genes. We report here the complete 1,516,355-bp sequence of the type strain, the stock derived from the South African Welgevonden isolate. Only 62% of the genome is predicted to be coding sequence, encoding 888 proteins and 41 stable RNA species. The most striking feature is the large number of tandemly repeated and duplicated sequences, some of continuously variable copy number, which contributes to the low proportion of coding sequence. These repeats have mediated numerous translocation and inversion events that have resulted in the duplication and truncation of some genes and have also given rise to new genes. There are 32 predicted pseudogenes, most of which are truncated fragments of genes associated with repeats. Rather then being the result of the reductive evolution seen in other intracellular bacteria, these pseudogenes appear to be the product of ongoing sequence duplication events.
Dissecting the molecular control of endothelial NO synthase by caveolin-1 using cell-permeable peptides
Authors: Bernatchez Pascal N. , Bauer Philip M. , Yu Jun , Prendergast Jay S. , He Pingnian , Sessa William C.
Published: January 2005

In endothelia, NO is synthesized by endothelial NO synthase (eNOS), which is negatively regulated by caveolin-1 (Cav-1), the primary coat protein of caveolae. We show that delivery of Cav-1 amino acids 82-101 (Cav) fused to an internalization sequence from Antennapedia (AP) blocks NO release
in vitro
and inflammation and tumor angiogenesis
in vivo
. To characterize the molecular mechanism by which the AP-Cav peptide and Cav-1 mediate eNOS inhibition, we subdivided the Cav portion of AP-Cav into three domains (Cav-A, -B, and -C), synthesized five overlapping peptides (AP-Cav-A, -AB, -B, -BC, and -C), and tested their effects on eNOS-dependent activities. Peptides containing the Cav-B domain (amino acids 89-95) induced time- and dose-dependent inhibition of eNOS-dependent NO release in cultured endothelial cells, NO-dependent inflammation in the ear, and hydraulic conductivity in isolated venules. Alanine scanning of AP-Cav-B revealed that Thr-90 and -91 (T90,91) and Phe-92 (F92) are crucial for AP-Cav-B- and AP-Cav-mediated inhibition of eNOS. Mutation of F92 to A92 in the Cav-1 cDNA caused the loss of eNOS inhibitory activity compared with wild-type Cav-1. These data highlight the importance of amino acids 89-95 and particularly F92 in mediating eNOS inhibition by AP-Cav and Cav-1.
Semiquantitative analysis of intrahepatic CC‐chemokine mRNAs in chronic hepatitis C
Authors: Nischalke Hans Dieter , Nattermann Jacob , Fischer Hans-Peter , Sauerbruch Tilman , Spengler Ulrich , Dumoulin Franz Ludwig
Published: January 2005

BACKGROUND: The mechanisms leading to hepatic injury in chronic hepatitis C virus (HCV) infection are only incompletely understood. Recent data propose a correlation of the intrahepatic expression of the CC chemokine RANTES and the degree of periportal and portal inflammatory liver damage.

Aim: Here, we have studied the intrahepatic mRNA levels of CC chemokines RANTES together with that of other members of this chemokine family (MIP‐1β, MCP‐1, and MCP‐2) in chronic hepatitis C as compared with healthy controls.

Methods: Liver samples from 22 HCV‐infected patients, nine individuals with primary biliary cirrhosis and from 12 normal controls were included into this study. Intrahepatic mRNA levels of CC chemokines RANTES, MIP‐1β, MCP‐1, and MCP‐2 were analyzed by a semi‐quantitative reverse transcription/real‐time polymerase chain reaction assay.

Results: In chronic HCV infection, intrahepatic RANTES mRNA levels were significantly higher than in non‐infected controls (7.2‐fold, p < 0.001) or in the disease control group (2.8‐fold, p < 0.001) and higher levels of RANTES mRNA levels were observed in livers with an advanced stage of liver cell injury (histologic activity index ≥6), although this difference was not statistically significant (p = 0.08). In contrast, mRNA levels of MIP‐1β (p = 0.021) and MCP‐1 (p = 0.021) were significantly lower in HCV liver samples while MCP‐2 expression was similar in all groups analyzed.

Conclusion: The data support the concept of chemokines as mediators of liver cell injury in chronic hepatitis C.
Mast cells are responsible for the lack of anti‐inflammatory effects of morphine in CBA mice
Authors: Stankiewicz Elzbieta , Wypasek Ewa , Plytycz Barbara
Published: January 2005

BACKGROUND and aim: Morphine co‐injection has anti‐inflammatory effects on zymosan‐induced peritonitis in several strains of mice except that of CBA. As peritoneal mast cells (pMCs) are much more numerous in CBA mice than in SWISS mice, the role of pMCs in morphine‐modulated zymosan peritonitis is compared in CBA and SWISS males.

Methods: pMCs were treated in vitro with morphine or C48/80 for comparison of histamine release. In vivo accumulation of leukocytes and histamine in peritoneal exudate were recorded after intraperitoneal injection with morphine, zymosan, or zymosan plus morphine.

Results and conclusion: Morphine induces histamine release by pMCs from CBA mice but not SWISS mice. In vivo morphine‐induced peritonitis is stronger in CBA mice than SWISS mice. Corollary, morphine anti‐inflammatory effects on zymosan peritonitis are reversed in CBA mice by its pro‐inflammatory action through CBA pMCs.
The effects of hemodialysis and peritoneal dialysis on serum homocysteine and C‐reactive protein levels
Authors: Borazan Ali , Aydemir Selim , Sert Mehmet , Yilmaz Ahmet
Published: January 2005

OBJECTIVES: In this study, we aimed to investigate plasma homocysteine (Hcy) and serum C‐reactive protein (CRP) levels in hemodialysis (HD) and continuous ambulatory peritoneal dialysis (CAPD) patients, and the relation among them.

Materials and methods: This study was carried out on 52 HD patients, 26 CAPD patients and a control group of 22 healthy persons. Blood samples were taken from the patients for Hcy and CRP measurements.

Results: Serum CRP level was found to be high in 48.1% of HD patients, 69.2% of CAPD patients and 4.5% of the healthy control group. Plasma Hcy level was found out to be above the normal limits in 73.1% of HD patients, 65.4% of CAPD patients and 9% of the healthy control group. There was a significant positive relation (r = 0.384, p < 0.001) between the levels of plasma Hcy and serum CRP in HD and CAPD patients.

Conclusion: The high levels of Hcy and CRP were found out to be higher in HD and CAPD patients than in the control group. In order to determine the risk rate of Hcy and CRP for coronary artery disease, extensive investigations are required in patients with chronic renal failure that also have coronary artery disease.
Leptin levels in obese women with and without type 2 diabetes mellitus
Authors: Buyukbese Mehmet Akif , Cetinkaya Ali , Kocabas Ramazan , Guven Aytekin , Tarakcioglu Mehmet
Published: January 2005

INTRODUCTION: The role of leptin has been more clear in the endocrinology area after the discovery of its secretion from the adipose tissue. The aim of the study is to investigate the leptin levels in obese women in whom type 2 diabetes mellitus were present or absent.

Materials and methods: Thirty‐five obese women with type 2 diabetes mellitus (group 1) and 34 obese women without type 2 diabetes mellitus (group 2) were enrolled in the study. In both groups the body mass index (BMI), waist circumference, and waist‐to‐hip ratio were measured. Leptin, HbA1c, creatinine and the lipid profile were assessed.

Results: Leptin was found to be statistically significantly lower in group 1 than in group 2 (40.22±17.77 ng/ml versus 50.12±15.51 ng/ml, respectively; p = 0.019). It was well correlated with BMI in group 1 (r = 0.60, p = 0.0001). In group 1 also, correlation of leptin was moderate with creatinine and high‐density lipoprotein‐cholesterol (r = 0.36, p = 0.037 versus r = 0.37, p = 0.027, respectively), whereas triglyceride had a negative correlation (r = ‐0.34, p = 0.046). In group 2, the only significant correlation with leptin was BMI (r = 0.41, p = 0.02). Leptin was also significantly lower in 17 subjects with poorly controlled diabetes mellitus than in 18 well‐controlled diabetics (33.54±15.82 ng/ml versus 44.61±17.54 ng/ml, respectively; p = 0.038).

Conclusion: Since leptin is lower in obese women with diabetes than without diabetes and additionally it is even lower in the poorly controlled diabetes subgroup, we think that further studies are required to make clear the issue for lower leptin levels, whether it is a reason or an outcome.
Expression of nitric oxide synthase and transforming growth factor‐beta in crush‐injured tendon and synovium
Authors: Darmani Homa , Crossan James , Mclellan Sarah D. , Meek Dominic , Curtis Adam
Published: January 2005

THIS study examined the expression of inducible nitric oxide synthase (iNOS) and transforming growth factor‐beta (TGF‐β) in macrophage infiltrates within crush‐injured digital flexor tendon and synovium of control rats and rats treated with N(G)‐nitro‐l‐arginine methyl ester (L‐NAME) (5 mg/kg). Release of TGF‐β from organ cultures of tendon, muscle, and synovium, and the effects of L‐NAME treatment (in vitro and in vivo), on adhesion of peritoneal macrophages to epitenon monolayers were also investigated. The results showed that during normal tendon healing the levels of TGF‐β are high at first and gradually decrease after 3 weeks of injury to slightly above control uninjured levels. However, when L‐NAME was administered at the time of injury, the macrophage infiltrates were expressing high levels of TGF‐β even at 5 weeks after the injury, with no evidence of reduction. In the standard injury, iNOS activity was greatest at the acute phase of the inflammatory response and then gradually returned to normal. Treatment with L‐NAME, however, resulted in inhibition of iNOS activity at 3 days and a reduction in the activity at the later time points examined after injury. We also found greatly increased levels of adhesion of peritoneal macrophages from L‐NAME‐treated rats to epitenon monolayers in vitro, which reflect a chronic imbalance in expression of TGF‐β, which is overexpressed, and nitric oxide, which is underexpressed. The results of the current study show that formation of nitric oxide is an important event in the course of tendon healing since its inhibition results in chronic inflammation and fibrosis due to an imbalance in TGF‐β expression in vivo.
Influence of serotonin on the analgesic effect of granisetron on temporomandibular joint arthritis
Authors: Voog Ülle , Alstergren Per , Leibur Edvitar , Kallikorm Riina , Kopp Sigvard
Published: January 2005

THE influence of circulating serotonin (5‐HT) on the effects of intra‐articular administration of granisetron on temporomandibular joint (TMJ) pain was investigated in 11 patients with chronic polyarthritides. An analgesic effect superior to placebo has been shown previously.

The change in TMJ movement pain intensity was negatively correlated to circulating 5‐HT; that is, the higher the 5‐HT before injection, the greater the reduction of pain intensity. The resting pain intensity reduction was not related to 5‐HT.

In conclusion, this study indicates a stronger short‐term analgesic effect on TMJ movement pain by intra‐articular administration of the 5‐HT3 receptor antagonist granisetron in patients with high levels of circulating 5‐HT.
Peripheral variability and central constancy in mammalian visual system evolution
Authors: Kaskan Peter M. , Franco Edna Cristina S. , Yamada Elizabeth S. , de Lima Silveira Luiz Carlos , Darlington Richard B. , Finlay Barbara L.
Published: January 2005

Neural systems are necessarily the adaptive products of natural selection, but a neural system, dedicated to any particular function in a complex brain, may be composed of components that covary with functionally unrelated systems, owing to constraints beyond immediate functional requirements. Some studies support a modular or mosaic organization of the brain, whereas others emphasize coordination and covariation. To contrast these views, we have analysed the retina, striate cortex (V1) and extrastriate cortex (V2, V3, MT, etc.) in 30 mammals, examining the area of the neocortex and individual neocortical areas and the relative numbers of rods and cones. Controlling for brain size and species relatedness, the sizes of visual cortical areas (striate, extrastriate) within the brains of nocturnal and diurnal mammals are not statistically different from one another. The relative sizes of all cortical areas, visual, somatosensory and auditory, are best predicted by the total size of the neocortex. In the sensory periphery, the retina is clearly specialized for niche. New data on rod and cone numbers in various New World primates confirm that rod and cone complements of the retina vary substantially between nocturnal and diurnal species. Although peripheral specializations or receptor surfaces may be highly susceptible to niche-specific selection pressures, the areal divisions of the cerebral cortex are considerably more conservative.
Coupling between phosphate release and force generation in muscle actomyosin
Authors: Holmes K. C. , Trentham D. R. , Simmons R. , Takagi Y. , Shuman H. , Goldman Y. E.
Published: January 2005

Energetic, kinetic and oxygen exchange experiments in the mid–1980s and early 1990s suggested that phosphate (P
i
) release from actomyosin–adenosine diphosphate P
i
(AM·ADP·P
i
) in muscle fibres is linked to force generation and that P
i
release is reversible. The transition leading to the
force–generating state and subsequent P
i
release were hypothesized to be
separate, but closely linked steps. P
i
shortens single force–generating actomyosin interactions in an isometric optical clamp only if the conditions enable them to last 20–40 ms, enough time for P
i
to dissociate. Until 2003, the
available crystal forms of myosin suggested a rigid coupling between movement of switch II and tilting of the lever arm to generate force, but they did not explain the reciprocal affinity myosin has for actin and nucleotides. Newer crystal forms and other structural
data suggest that closing of the actin–binding cleft opens switch I (presumably decreasing nucleotide affinity). These data are all consistent with the order of events suggested before: myosin·ADP·P
i
binds weakly, then strongly to actin,
generating force. Then P
i
dissociates, possibly further increasing force or sliding.
Smooth muscle myosin: regulation and properties
Authors: Holmes K. C. , Trentham D. R. , Simmons R. , Somlyo Avril V. , Khromov Alexander S. , Webb Martin R. , Ferenczi Michael A. , Trentham David R. , He Zhen-He , Sheng Sitong , Shao Zhifeng , Somlyo Andrew P.
Published: January 2005

The relationship of the biochemical states to the mechanical events in contraction of smooth muscle cross–bridges is reviewed. These studies use direct measurements of the kinetics of Piand ADP release. The rate of release of Pifrom thiophosphorylated cycling cross–bridges held isometric was biphasic with turnovers of 1.8 s–1and 0.3 s–1, reflecting properties and forces directly acting on cross–bridges through mechanisms such as positive strain and inhibition by high–affinity MgADP binding. Fluorescent transients reporting release of an ADP analogue 3'–deac–edaADP were significantly faster in phasic than in tonic smooth muscles. Thiophosphorylation of myosin regulatory light chains (RLCs) increased and positive strain decreased the release rate around twofold. The rates of ADP release from rigor cross–bridges and the steady–state Pirelease from cycling isometric cross–bridges are similar, indicating that the ADP–release step or an isomerization preceding it may limit the ATPase rate. Thus ADP release in phasic and tonic smooth muscles is a regulated step with strain– and dephosphorylation–dependence. High affinity of cross–bridges for ADP and slow ADP release prolong the fraction of the duty cycle occupied by strongly bound AM·ADP state(s) and contribute to the high economy of force that is characteristic of smooth muscle. RLC thiophosphorylation led to structural changes in smooth muscle cross–bridges consistent with our findings that thiophosphorylation and strain modulate product release.
The structure of the rigor complex and its implications for the power stroke
Authors: Holmes K. C. , Trentham D. R. , Simmons R. , Holmes K. C. , Schröder R. R. , Sweeney H. L. , Houdusse Anne
Published: January 2005

Decorated actin provides a model system for studying the strong interaction between actin and myosin. Cryo–energy–filter electron microscopy has recently yielded a 14 Å resolution map of rabbit skeletal actin decorated with chicken skeletal S1. The crystal structure of the cross–bridge from skeletal chicken myosin could not be fitted into the three–dimensional electron microscope map without some deformation. However, a newly published structure of the nucleotide–free myosin V cross–bridge, which is apparently already in the strong binding form, can be fitted into the three–dimensional reconstruction without distortion. This supports the notion that nucleotide–free myosin V is an excellent model for strongly bound myosin and allows us to describe the actin–myosin interface. In myosin V the switch 2 element is closed although the lever arm is down (post–power stroke). Therefore, it appears likely that switch 2 does not open very much during the power stroke. The myosin V structure also differs from the chicken skeletal myosin structure in the nucleotide–binding site and the degree of bending of the backbone ß–sheet. These suggest a mechanism for the control of the power stroke by strong actin binding.