bluuebunny/crossref_metadata_2025 huggingface dataset:
A local coherent-state approximation to system-bath quantum dynamics
Authors: Martinazzo Rocco , Nest Mathias , Saalfrank Peter , Tantardini Gian Franco
Published: November 2006

A novel quantum method to deal with typical system-bath dynamical problems is introduced. Subsystem discrete variable representation and bath coherent-state sets are used to write down a multiconfigurational expansion of the wave function of the whole system. With the help of the Dirac-Frenkel variational principle, simple equations of motion—a kind of Schrödinger-Langevin equation for the subsystem coupled to (pseudo) classical equations for the bath—are derived. True dissipative dynamics at all times is obtained by coupling the bath to a secondary, classical Ohmic bath, which is modeled by adding a friction coefficient in the derived pseudoclassical bath equations. The resulting equations are then solved for a number of model problems, ranging from tunneling to vibrational relaxation dynamics. Comparison of the results with those of exact, multiconfiguration time-dependent Hartree calculations in systems with up to 80 bath oscillators shows that the proposed method can be very accurate and might be of help in studying realistic problems with very large baths. To this end, its linear scaling behavior with respect to the number of bath degrees of freedom is shown in practice with model calculations using tens of thousands of bath oscillators.
Decay rate of the excited surface electron states on liquid helium
Authors: Monarkha Yu. P. , Sokolov S. S.
Published: November 2006

The low temperature bound of the decay rate of the excited surface electron states on liquid helium is theoretically studied. It is shown that the lifetime and dephasing time of the surface electron states are strongly limited by spontaneous emission of couples of short-wavelength capillary wave quanta (ripplons). These two-ripplon scattering processes are of the second order in the nonlinear interaction Hamiltonian. In contrast to the usual one-ripplon scattering contribution, the decay rate found here cannot be substantially reduced, neither by lowering of the temperature nor by external magnetic field, which is important for a recently discussed implementation of quantum bits in such a system.
Interfacial atomic structures, energetics and band offsets of Ge:ZrO2 interfaces
Authors: Tse Koon-Yiu , Robertson John
Published: November 2006

Future field effect transistors may use germanium as a high mobility channel material instead of silicon, and high dielectric constant (κ) oxides such as ZrO2 and HfO2 instead of SiO2 as the gate dielectric. First principles calculations of the polar (100) and nonpolar (110) Ge:ZrO2 interfaces are presented. A number of interface configurations that satisfy the valence bonding requirements are constructed and their relaxed structures, total energies, interface electronic states, and band offsets are calculated. For the polar (100) interfaces, the results are quite similar to those of (100) Si:ZrO2. There are numerous semiconducting O-terminated interfaces. The most stable O-terminated interface for a 1×1 surface unit cell has three coordinated oxygen sites. The interface with a tenfold coordinated Zr is the most stable metal-terminated interface, but it is metallic which makes this interface not useful for devices. The band offsets of the O-terminated interfaces have a relatively narrow range, whereas the Zr-terminated band offsets exhibit a range of 0.9eV.
Shot noise limited, microwave bandwidth photodetector design
Authors: Milford G. N. , Harb C. C. , Huntington E. H.
Published: November 2006

We present a methodology for designing wideband, shot noise limited photodetectors using commercially available components and microwave engineering techniques. We use this methodology to design and construct a photodetector using wideband microwave amplifiers and a 3.5GHz bandwidth photodiode. Consistent with our analytic models, the photodetector exhibits linear behavior up to a level of 6.5dB clearance between shot noise and dark noise from 2.0to3.5GHz at 10mA of photocurrent, reducing to 3.5dB of clearance at 6.4GHz.
Microfabricated electromagnetic filters for millikelvin experiments
Authors: le Sueur Hélène , Joyez Philippe
Published: November 2006

In this article we report on the design, fabrication, and tests of microfabricated broadband filters suitable for proper electromagnetic thermalization of electrical lines connected to sensitive quantum electronics experiments performed at dilution fridge temperatures. Compared to previous such miniature filters, the new design improves on performance and reliability. These filters can be packed in space-saving cases with either single or multicontact connector. Measured performance in the accessible range compares well to simulations. We use these simulations to discuss the effectiveness of these filters for electromagnetic thermalization at 30mK.
Extended microtunnels in GaN prepared by wet chemical etch
Authors: Huang Hsin-Hsiung , Zeng Hung-Yu , Lee Chi-Ling , Lee Shih-Chang , Lee Wei-I
Published: November 2006

It is demonstrated in GaN that microtunnels extended beyond hundreds of microns can be easily achieved using wet chemical etch. To obtain this result, specially designed structures of GaN layers are first grown on sapphire substrates with metal-organic chemical vapor deposition and subsequently with hydride vapor phase epitaxy techniques. The prepared samples are then chemically etched in molten KOH. With the designed structure of GaN layers, extended microtunnels with triangular cross sections are formed. The crystallographic planes of the triangular bevels belong to the {112¯2} family. The etch rate of the tunnel can be as high as 10μm∕min at proper etching conditions.
CO adsorption on pure and binary-alloy gold clusters: A quantum chemical study
Authors: Joshi Ajay M. , Tucker Mark H. , Delgass W. Nicholas , Thomson Kendall T.
Published: November 2006

We performed density-functional theory analysis of nondissociative CO adsorption on 22 binary Au-alloy (AunMm) clusters: n=0–3, m=0–3, and m+n=2 (dimers) or 3 (trimers), M=Cu∕Ag∕Pd∕Pt. We report basis-set superposition error corrections to adsorption energies and include both internal energy of adsorption (ΔUads) and Gibbs free energy of adsorption (ΔGads) at standard conditions (298.15K and 1atm). We found onefold (atop) CO binding on all the clusters except Pd2 (twofold/bridged), Pt2 (twofold/bridged), and Pd3 (threefold). In agreement with the experimental results, we found that CO adsorption is thermodynamically favorable on pure Au∕Cu clusters but not on pure Ag clusters and also observed the following adsorption affinity trend: Pd>Pt>Au>Cu>Ag. For alloy dimers we found the following patterns: Au2>MAu>M2 (M=Ag∕Cu) and M2>MAu>Au2 (M=Pd∕Pt). Alloying Ag∕Cu dimers with (more reactive) Au enhanced adsorption and the opposite effect was observed for Pd∕Pt dimers. The Ag–Au, Cu–Au, and Pd–Au trimers followed the trends observed on dimers: Au3>MAu2>M2Au>M3 (M=Ag∕Cu) and Pd3>Pd2Au>PdAu2>Au3. Interestingly, Pt–Au trimers reacted differently and alloying with Au systematically increased the adsorption affinity: PtAu2>Pt2Au>Pt3>Au3. A strikingly different behavior of Pt is also manifested by the triplet spin state and onefold (atop) binding in Pt3–CO which is in contradiction with the singlet spin state and threefold binding in Pd3–CO. We found a linear correlation between CO binding energy (BE) and elongation of the CO bond. For Ag–Au and Cu–Au clusters, the increase in CO BE (and elongation of the C–O bond which is probably due to the back donation) is accompanied by the decrease in the cluster-CO distance suggesting that the donation (from 5σ highest occupied molecular orbital in CO to cluster lowest unoccupied molecular orbital) mechanism also contributes to the BE. For Pd–Au clusters, the cluster-CO distance (and CO bond length) increases with increase in the BE, suggesting that the donation mechanism may not be important for those clusters. No clear trend was observed for Pt–Au clusters.
Propagation of Alfvén waves in shear flows: Nature of driven longitudinal velocity and density fluctuations
Authors: Kaghashvili Edisher Kh. , Raeder Joachim , Webb Gary M. , Zank Gary P.
Published: November 2006

The nature of driven longitudinal velocity fluctuations and density fluctuations is studied when there is an Alfvén wave propagating in the medium characterized by an inhomogeneous velocity field. A system of governing equations that describes driven fluctuations is obtained and the properties of this system are analyzed. For some circumstances considering general properties of the Alfvén wave, the system allows us to obtain analytical solutions for driven waves that can be compared with ones obtained by numerical integration of the wave interaction equations. It is shown that for the low β plasma, the analytical solutions are in a good agreement with the numerical ones. The natural frequencies of individual wave components (“uncoupled natural frequencies”) are analyzed and how these frequencies are related to the natural frequencies of the coupled system are shown. In the summary, it is discussed where this process can be important. The possible observations in different areas where its signature can be found are outlined.
Discontinuous molecular dynamics simulation study of polymer collapse
Authors: Opps Sheldon B. , Polson James M. , Risk Nick Abou
Published: November 2006

Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different versions of the model were employed, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter λ determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a λ-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the θ-point values λθ separating the coil from the globule state. For each model we construct coil-globule phase diagrams in terms of λ and the particle density ρ. Additionally, we explore for each model the effects of varying the range of the attractive interactions on the phase boundary separating the coil and globule phases. The results are analyzed in terms of a simple Flory-type theory of the collapse transition.
Diluted magnetic semiconductors with high Curie temperature based on C1b compounds: CoTi1−xFexSb
Authors: Kroth Kristian , Balke Benjamin , Fecher Gerhard H. , Ksenofontov Vadim , Felser Claudia , Lin Hong-Ji
Published: November 2006

Diluted magnetic semiconductors were prepared by substituting titanium in the semiconducting compound CoTiSb with iron. The structural, electronic, and magnetic properties of the pure and doped materials were investigated. It was found that substitution of up to 10% Ti by Fe does not affect the crystalline structure. Self-consistent calculations of the electronic structure predict the material to be a half-metallic ferromagnet. The Curie temperature of the Fe substituted alloy is far above room temperature (>700K), thus making that material a serious candidate for future electronic applications, in particular, for magnetoelectronics and spintronics.
Temperature mapping and thermal lensing in large-mode, high-power laser diodes
Authors: Chan P. K. L. , Pipe K. P. , Plant J. J. , Swint R. B. , Juodawlkis P. W.
Published: November 2006

The authors use high-resolution charge-coupled device based thermoreflectance to derive two dimensional facet temperature maps of a λ=1.55μm InGaAsP∕InP watt-class laser that has a large (>5×5μm2) fundamental optical mode. Recognizing that temperature rise in the laser will lead to refractive index increase, they use the measured temperature profiles as an input to a finite-element mode solver, predicting bias-dependent spatial mode behavior that agrees well with experimental observations. These results demonstrate the general usefulness of high-resolution thermal imaging for studying spatial mode dynamics in photonic devices.
Intermolecular and interlayer interactions in copper phthalocyanine films as measured with microspot photoemission spectroscopy
Authors: Sugiyama Takeharu , Sasaki Toshihide , Kera Satoshi , Ueno Nobuo , Munakata Toshiaki
Published: November 2006

The authors have applied photoemission microspectroscopy to copper phthalocyanine films grown on a graphite surface with a lateral resolution of 0.3μm and an energy resolution of 30meV. The photoemission peak due to the highest occupied molecular orbital was found to be at binding energies of 1.13, 1.23, 1.38, and 1.5eV, depending on film thickness. From the thickness and light-polarization dependence, the peaks were assigned to originate from isolated molecules, the first layer, the second layer, and multilayer, respectively. They demonstrate the capability of photoemission microspectroscopy to resolve electronic states modified by fine differences of molecular environments.
Aromatic Hydrogen Isotope Exchange Reactions Catalyzed by Iridium Complexes in Aqueous Solution
Authors: Lukey CA , Long MA , Garnett JL
Published: November 2006

Sodium hexachloroiridate (III) and sodium hexachloroiridate (IV) have been used as homogeneous catalysts for hydrogen isotope exchange between benzenoid compounds and water. The ideal solvent consisted of 50 mole % acetic acid/water, and the optimum temperature was found to be 160°C. Under these conditions the rate of incorporation of deuterium into benzene was significant (typically 15% D in 6 h), and reduction to iridium metal was minimized. The active catalytic species was identified as a solvated iridium(III) species, which is also postulated to be the active catalyst in solutions containing hexachloroiridate (IV). The kinetics of exchange in benzene catalysed by sodium hexachloroiridate (III) were elucidated, and found to be more complex than for the corresponding sodium tetrachloroplatinate (II) catalysed exchange, in that a two-term rate dependence was found for catalyst concentration and the reaction was inversely dependent on hydrogen ion concentration. The reaction was found to be independent of chloride ion concentration, this confirming that the active catalyst is a solvated species. Isotopic labelling in all compounds was confined to the aromatic ring, and most substituted benzenes exhibited deactivation of the ortho positions, indicating that a dissociative π-complex exchange mechanism was operating. This was confirmed by exchange into naphthalene, where it was found that labelling was predominantly in the β position. Facile exchange into nitrobenzene provided good evidence of homogeneous catalysis, and not catalysis by precipitated metal.
Thermodynamics of Viscous Flow in Ethane-1,2-diol+Water Binary Mixtures
Authors: Corradini F , Marchetti A , Tagliazucchi M , Tassi L , Tosi G
Published: November 2006

Kinematic viscosities (v) of pure ethane-1,2-diol (component 1) and of nine mixtures with water (component 2) were measured at 19 temperatures ranging from -10 to +80°C, and for binary compositions covering the whole miscibility field expressed by the relation 0 ≤ X1 ≤ 1. The property fitted some empirical equations in terms of the dependences v = v(T) and v(X1), where T is the thermodynamic temperature and X1 is the mole fraction of ethane-1,2-diol. Furthermore, the excess function (vE) and the excess Gibbs energy of activation of viscous flow (∆G*E) have been investigated. The trend of vE against binary composition of the mixtures shows negative deviations from ideal behaviour, while the contrary is true for ∆G*E The results indicate specific molecular interactions between the components, and an overview is given on the basis of the molecular dynamics of the pure species.
Copper-Catalyzed Oxidation of Cyanide by Peroxide in Alkaline Aqueous Solution
Authors: Beattie JK , Polyblank GA
Published: November 2006

The oxidation of cyanide by peroxide in alkaline aqueous solution is catalysed by copper complexes. In the presence of excess cyanide, copper(II) is reduced to form the tricyanocuprate (I) complex. The cyanogen oxidation product is hydrolysed with disproportionation to cyanate and cyanide:2CuII+2CN-→ 2CuI+(CN)2(CN)2+2OH- → OCN-+CN-+H2OCuI+3CN- ↔ Cu(CN)32-The stoichiometry and kinetics of the catalysed oxidation have been investigated. Hydrogen peroxide oxidizes coordinated cyanide with a rate that is first order in peroxide and first order in copper but independent of cyanide concentration in the presence of excess cyanide. Cu(CN)32-+H2O2→ Cu(CN)2-+OCN-+H2O Cu(CN)2-+CN-↔ Cu(CN)32- When the excess cyanide is consumed and Cu(CN)2- becomes the dominant species, the reaction becomes more complex and less efficient. Under certain conditions the stoichiometry revealed a peroxide-to-Cu(CN)2- ratio of about 6 : 1, instead of the minimum of 2.5:1 required for the oxidation of the coordinated cyanide to cyanate and the CuI to Cu(OH)2. This suggests that peroxide is consumed by a copper- catalysed disproportionation, in competition with oxidation of the coordinated cyanide. An intermediate yellow complex forms while peroxide is present, before Cu(OH)2 finally precipitates. The consequence of this mechanism is that the most efficient process for the destructive oxidation of cyanide has a high cyanide-to-copper ratio, to minimize the final concentration of Cu(CN)2- which consumes peroxide inefficiently. The rate of the reaction depends on the concentration of copper, however, which must be large enough for a satisfactory turnover.
Reactivity and Ground State Effects of Silicon in Organic Chemistry
Authors: White JM
Published: November 2006

The strong σ donor ability of the C- Si bond manifests itself in many unusual properties of silicon-containing organic compounds. This review discusses the effect that silicon substituents have on the ground-state properties of organic compounds and on their reactivities, from this viewpoint.
Structure-Activity Correlations for Psychotomimetics. III. Tryptamines
Authors: Clare BW
Published: November 2006

Based on electronic properties calculated by the semiempirical PM3 method, a quantitative structure-activity relationship has been derived for a group of psychotomimetic tryptamines. Data analysis by partial least squares reveals two significant components. The major property affecting potency was the difference in energy between the highest occupied and lowest unoccupied molecular orbital. Less significant was the effect of molecular size, shape and polarizability, in particular, the dimension in the direction of the ethylamine side chain, involving the substituents on the amine nitrogen. The results are consistent with earlier studies on phenylalkylamines.
Neutron Powder Diffraction Study of Molybdenum and Tungsten Dioxides
Authors: Bolzan AA , Kennedy BJ , Howard CJ
Published: November 2006

Neutron powder diffraction data for MoO2 [P21/c, a 5.6102(3), b 4.8573(2), c 5.6265(3) Ǻ, β 120.915(2)°] and WO2 [P21/c, a 5.5769(2), b 4.8986(1), c 5.6644(2) Ǻ, β 120.678(1)] have been employed to refine structural parameters by the Rietveld method. The results confirm previous studies but have considerably greater precision.
The Structure Determination of Simonyellin—a New Lichen Naphthopyran
Authors: Elix JA , Elix JA , Feige GB , Feige GB , Lumbsch HT , Lumbsch HT , Mies B , Mies B , Wardlaw JH , Wardlaw JH , Willis AC , Willis AC
Published: November 2006

The structure of simonyellin (5,9-dihydroxy-4-methoxy-7-methyl-1H,6H-naphtho[1,8-cd]pyran-1,6-dione), a naphthopyran from the lichen Simonyella variegata Steiner, has been established by X-ray structure analysis of a corresponding tetraacetate derivative. Crystals of simonyellin tetraacetate are triclinic, Pī, a 10.974(2), b 11.282(3), c 20.634(3)Ǻ, α 92.23(2)°, β 100.03(1)°, γ 117.80(2)°; Z 4. Refinement of 2754 data with I > 3σ(I) gave conventional R factors of 0.043 and 0.034.
3D structure of amyloid protofilaments of β
2
-microglobulin fragment probed by solid-state NMR
Authors: Iwata Kentaro , Fujiwara Toshimichi , Matsuki Yoh , Akutsu Hideo , Takahashi Satoshi , Naiki Hironobu , Goto Yuji
Published: November 2006

Understanding the structure and formation of amyloid fibrils, the filamentous aggregates of proteins and peptides, is crucial in preventing diseases caused by their deposition and, moreover, for obtaining further insight into the mechanism of protein folding and misfolding. We have combined solid-state NMR, x-ray fiber diffraction, and atomic force microscopy to reveal the 3D structure of amyloid protofilament-like fibrils formed by a 22-residue K3 peptide (Ser
20
-Lys
41
) of β
2
-microglobulin, a protein responsible for dialysis-related amyloidosis. Although a uniformly
13
C,
15
N-labeled sample was used for the NMR measurements, we could obtain the 3D structure of the fibrils on the basis of a large number of structural constraints. The conformation of K3 fibrils was found to be a β-strand–loop–β-strand with each K3 molecule stacked in a parallel and staggered manner. It is suggested that the fibrillar conformation is stabilized by intermolecular interactions, rather than by intramolecular hydrophobic packing as seen in globular proteins. Together with thermodynamic studies of the full-length protein, formation of the fibrils is likely to require side chains on the intermolecular surface to pack tightly against those of adjacent monomers. By revealing the structure of β
2
-microglobulin protofilament-like fibrils, this work represents technical progress in analyzing amyloid fibrils in general through solid-state NMR.
Micromanipulation Studies of Chromatin Fibers in Xenopus Egg Extracts Reveal ATP-dependent Chromatin Assembly Dynamics
Authors: Yan Jie , Maresca Thomas J. , Skoko Dunja , Adams Christian D. , Xiao Botao , Christensen Morten O. , Heald Rebecca , Marko John F.
Published: November 2006

We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening–closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy difference between core histone octamers on and off DNA. Addition of ATP led to highly dynamic behavior with time courses exhibiting processive runs of assembly and disassembly not observed in the ATP-depleted case. With ATP present, application of forces of 2 pN led to nearly complete fiber disassembly. Our study suggests that ATP hydrolysis plays a major role in nucleosome rearrangement and removal and that chromatin in vivo may be subject to highly dynamic assembly and disassembly processes that are modulated by DNA tension.
Rapid identification of clinically relevant Nocardia species using real-time PCR with SYBR Green and melting-curve analysis
Authors: Alfaresi Mubarak , Elkosh Abida
Published: November 2006

The objective of this study was to develop and evaluate a rapid new method of identifying clinically relevant Nocardia species. DNA extracted from different Nocardia strains was used in a real-time PCR assay with SYBR Green and melting-curve analysis to identify Nocardia species. Ten control strains and four bacterial strains of closely related genera were employed, and samples from 28 patients were used. All Nocardia strains were identified correctly, and there was no cross-reaction with strains from genera closely related to Nocardia. The sensitivity and specificity of the method were 90 and 100 %, respectively. This method can be used to rapidly detect Nocardia species in culture, without cross-reaction with other closely related genera.
Genetic characterization of multidrug resistance in Shigella spp. from Japan
Authors: Ahmed Ashraf M. , Furuta Kimi , Shimomura Kei , Kasama Yoshio , Shimamoto Tadashi
Published: November 2006

This study characterized the genetic basis of antimicrobial resistance of a number of Shigella spp. isolated from humans from 2000 to 2004 in Hiroshima prefecture, Japan. A total of 26 isolates of Shigella spp. were included in this study. Antimicrobial susceptibility tests revealed high levels of resistance, especially to ampicillin, streptomycin, trimethoprim, tetracycline, nalidixic acid and ciprofloxacin. PCR and DNA sequencing were used for screening and characterization of antibiotic-resistance determinants. PCR sequencing analysis revealed the presence of only one type of class 1 integron in one isolate of Shigella sonnei. This class 1 integron was 1904 bp and contained two gene cassettes: a probable esterase/lipase (estX) and aadA1, which confers resistance to streptomycin and spectinomycin. Two types of class 2 integron were identified in this study. One was the classic type (2158 bp) and carried the three conserved resistance gene cassettes of the class 2 integron, dfrA1, sat1 and aadA1, which confer resistance to trimethoprim, streptothricin and streptomycin/spectinomycin, respectively. This type was detected in both Shigella sonnei (14 isolates) and Shigella flexneri (five isolates). The other type was shorter (1313 bp) and carried only two gene cassettes, dfrA1 and sat1. This integron was detected in a single isolate of Shigella sonnei. PFGE patterns showed limited diversity within clusters of the same species. Furthermore, an extended-spectrum β-lactamase gene, bla
OXA-30, which confers resistance to ampicillin, was characterized in all isolates of Shigella flexneri except the oldest strain, which was isolated in 2000. Southern blot hybridization and conjugation experiments showed that bla
OXA-30 was located in the chromosome.
Comparative analysis of Etest and broth microdilution method (AFST-EUCAST) for trends in antifungal drug susceptibility testing of Brazilian Cryptococcus neoformans isolates
Authors: Dias Amanda L. T. , Matsumoto Flavia E. , Melhem Marcia S. C. , da Silva Eriques G. , Auler Marcos E. , de Siqueira Antonio M. , Paula Claudete R.
Published: November 2006

A prospective study was performed to evaluate the correlation between the proposed standard of the Antifungal Susceptibility Testing Subcommittee of the European Committee on Antibiotic Susceptibility Testing (AFST-EUCAST) (document 7.1) and the commercial system Etest for determining the MICs of flucytosine, amphotericin B, fluconazole, itraconazole and voriconazole for a collection of 100 clinical and environmental isolates of Cryptococcus neoformans. The agreements among Etest MICs within ±2 log2 dilutions of AFST-EUCAST standard MICs were greater for flucytosine, fluconazole and voriconazole (76, 78 and 88 %, respectively) than for amphotericin B (5 %), the lowest agreement, and itraconazole (67 %). Overall, the correlation coefficients were statistically significant (P<0.05), and it is suggested that the Etest and AFST-EUCAST method are reliable alternatives and present good correlation for all drugs evaluated except amphotericin B. However, the observed differences related to MICs for susceptible, susceptible dose dependent and resistant strains between the methods suggest that it will be necessary to carry out further studies, including assessment of interlaboratory agreement and correlation of MICs by different methods with in vivo response.
Reduction and analysis of SANS and USANS data using IGOR Pro
Authors: Kline Steven R.
Published: November 2006

A software package is presented for performing reduction and analysis of small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) data. A graphical interface has been developed to visualize and quickly reduce raw SANS and USANS data into one- or two-dimensional formats for interpretation. The resulting reduced data can then be analyzed using model-independent methods or non-linear fitting to one of a large and growing catalog of included structural models. The different instrumental smearing effects for slit-smeared USANS and pinhole-smeared SANS data are handled automatically during analysis. In addition, any number of SANS and USANS data sets can be analyzed simultaneously. The reduction operations and analysis models are written in a modular format for extensibility, allowing users to contribute code and models for distribution to all users. The software package is based on Igor Pro, providing freely distributable and modifiable code that runs on Macintosh and Windows operating systems.
X-ray diffraction cell for studying solid–gas reactions under gas pressures to 100 bar
Authors: Gray E. MacA. , Cookson D. J. , Blach T. P.
Published: November 2006

A pressure cell designed for high-energy X-ray diffraction in transmission mode is described. The cell is intended for use at temperatures up to 573 K with samples that are large enough to permit the real-time determination of the amount of absorbed gas by measuring the gas pressure. The design is driven by the need to ensure that the sample temperature is constant and uniform, despite the heat flow accompanying the reaction between the gas and the sample. The use of the cell is illustrated by its application to elucidating the hydriding phase transformation in the LaNi5–H2system.
Three-dimensional small-angle neutron scattering of shear-induced phase separation in a dynamically asymmetric polymer mixture
Authors: Koizumi Satoshi , Suzuki Jun-ichi
Published: November 2006

A polymer mixture of polystyrene (PS)/poly(vinyl methyl ether) (PVME) has been investigated by using a three-dimensional small-angle neutron scattering (3D-SANS) method. PS and PVME exhibit a large difference in the glass transition temperatureTg. Therefore, dynamical asymmetry is strongly enhanced in an intermediate temperature region between theTgvalues of neat PS and PVME. In the intermediate temperature region, a shear deformation was imposed on the polymer mixture to enhance the concentration fluctuations,i.e.shear-induced phase separation. By rotating the film specimen, which was rapidly quenched after deformation, 3D-SANS due to shear-induced phase separation was observed successfully. In theqx=qyplane of the sample coordinate system, whereqis a component of scattering vectorq, it was possible to observe SANS of `double-lobe' shape, with the minor axes of the lobes inclined towardsqx=qy, whereqx,qyandqz, denote the shear, velocity gradient and vorticity directions in reciprocal space, respectively. Abnormal `butterfly' scattering was observed in a section cut through the 3D-SANS in theqxqzplane. The 3D-SANS thus obtained is discussed in comparison with a model of dynamical coupling between stress and diffusion.
Hydrophobic `lock and key' recognition of N-4-nitrobenzoylamino acid by strychnine
Authors: Białońska Agata , Ciunik Zbigniew
Published: November 2006

During racemic resolution of N-4-nitrobenzoyl-DL-amino acids (alanine, serine and aspartic acid) by a fractional crystallization of strychninium salts, crystals of both diastereomeric salts were grown, and the crystal structures of strychninium N-4-nitrobenzoyl-L-alaninate methanol disolvate (1a), strychninium N-4-nitrobenzoyl-D-alaninate dihydrate (1b), strychninium N-4-nitrobenzoyl-D-serinate dihydrate (2a), strychninium N-4-nitrobenzoyl-L-serinate methanol solvate hydrate (2b), strychninium hydrogen N-4-nitrobenzoyl-L-aspartate 3.75 hydrate (3a) and strychninium hydrogen N-4-nitrobenzoyl-D-aspartate 2.25 hydrate (3b) were determined. The strychninium cations form corrugated layers, which are separated by hydrogen-bonded anions and solvent molecules. Common features of the corrugated layers are deep hydrophobic grooves at their surfaces, which are occupied by the 4-nitrobenzoyl groups of suitable anions. The hydrophobic `lock and key' recognition of 4-nitrobenzoyl groups of amino acid derivatives in deep grooves of the strychnine self-assembly causes the resulting surface to have more hydrophilic properties, which are more appropriate for interactions in the hydrophilic environments from which strychninium salts were crystallized. In the crystal structure of (2a) and (3a), such hydrophobic `lock and key' recognition is responsible for the lack of N—H+...O− hydrogen bonds that are usually formed between the protonated tertiary amine N atom of the strychninium cation and the deprotonated carboxyl group of the resolved acid. In the crystal structure of (2a) and (3a), the protonated amine N atom is a donor of hydrogen bonds, while the hydroxyl group of the serine derivative and water molecules are their acceptors. In light of the hydrophobic recognition, chiral discrimination depends on the nature of the hydrogen-bond networks, which involve anions, solvent molecules and the protonated amine N atom of strychninium cations.
Competing hydrogen-bonding patterns and phase transitions of 1,2-diaminoethane at varied temperature and pressure
Authors: Budzianowski Armand , Olejniczak Anna , Katrusiak Andrzej
Published: November 2006

1,2-Diaminoethane has been in-situ pressure- and temperature-frozen; apart from two known low-temperature phases, Iα and II, three new phases, Iβ, Iγ and III, have been observed and their structures determined by X-ray diffraction. The measurements at 0.1 MPa were carried out at 274, 243 and 224 K, and 296 K measurements were made at 0.15 GPa (phase Iα), at 0.3 and 1.1 GPa (phase Iβ), at 1.5 GPa (phase Iγ), and at 0.2, 0.3 and 0.5 GPa (phase III). All these phases are monoclinic, space group P21/c, but the unit-cell dimension of phases Iα and III are very different at 296 K: a
Iα = 5.078 (5), b
Iα = 7.204 (8), c
Iα = 5.528 (20) Å, β
Iα = 115.2 (2)° at 0.15 GPa, and a
III = 5.10 (3), b
III = 5.212 (2), c
III = 7.262 (12) Å, β
III = 111.6 (4)° at 0.2 GPa, respectively; in both phases Z = 2. An ambient-pressure low-temperature phase II has been observed below 189 K. Discontinuities in the unit-cell dimensions and in the N...N distance mark the isostructural transition between phases Iα and Iβ at 0.2 GPa, which can be attributed to a damping process of the NH2 group rotations. In phase Iγ the unit-cell parameter a doubles and Z increases to 4. The molecule has inversion symmetry in all the structures determined. 1,2-Diaminoethane can be considered as a simple structural ice analogue, but with NH...N hydrogen bonds and with the H-atom donors (four in one molecule) in excess over H-atom acceptors (two per molecule). Thus, the transformations of 1,2-diaminoethane phases involving the conformational dynamics affect the hydrogen-bonding geometry and molecular association in the crystal. The 1,2-diaminoethane:1,2-dihydroxyethane mixture has been separated by pressure-freezing, and a solid 1,2-diaminoethane crystal in liquid 1,2-dihyroxyethane has been obtained.
Electron-diffraction structure refinement of Ni4Ti3 precipitates in Ni52Ti48
Authors: Tirry Wim , Schryvers Dominique , Jorissen Kevin , Lamoen Dirk
Published: November 2006

The atomic coordinates of the crystal structure of nanoscale Ni4Ti3 precipitates in Ni-rich NiTi is refined by means of a least-squares method based on intensity measures of electron-diffraction patterns. The optimization is performed in combination with density functional theory calculations and has yielded an R\bar 3 symmetry with slightly different atomic positions when compared with the existing structure. The new unit cell offers a better understanding of the lattice deformation from the B2 matrix.
Structural characterization of a new high-pressure phase of GaAsO4
Authors: Santamaría-Pérez David , Haines Julien , Amador Ulises , Morán Emilio , Vegas Angel
Published: November 2006

As in SiO2 which, at high pressures, undergoes the α-quartz → stishovite transition, GaAsO4 transforms into a dirutile structure at 9 GPa and 1173 K. In 2002, a new GaAsO4 polymorph was found by quenching the compound from 6 GPa and 1273 K to ambient conditions. The powder diagram was indexed on the basis of a hexagonal cell (a = 8.2033, c = 4.3941 Å, V = 256.08 Å3), but the structure did not correspond to any known structure of other AXO4 compounds. We report here the ab initio crystal structure determination of this hexagonal polymorph from powder data. The new phase is isostructural to β-MnSb2O6 and it can be described as a lacunary derivative of NiAs with half the octahedral sites being vacant, but it also contains fragments of the rutile-like structure.
Bayesian modelling and ROC analysis to predict placebo responders using clinical score measured in the initial weeks of treatment in depression trials
Authors: Gomeni Roberto , Merlo‐Pich Emilio
Published: November 2006

What is already known about this subject

• In major depressive disorder an appreciable percentage (40%) of patients in antidepressant trials will have a placebo response.

• In these trials, early changes (i.e. within the first 4 weeks) of the clinical score scale (e.g. HAMD‐17) are associated with response at end‐point.

• Unpredictable placebo response is one of the major reasons for clinical trial failure in the evaluation of antidepressant drugs.

What this study adds

• Provides a model to describe the time course of individual and population placebo response.

• Provides a methodology to forecast the individual probability to be placebo responder based on early HAMD‐17 measurements with an assessment of the prognostic power.

• Provides a methodological framework to implement a population enrichment strategy in the design of clinical trials for the assessment of novel antidepressant drugs.

Aims  To develop a probabilistic and longitudinal model describing the time course of Hamilton's Rating Scale for Depression (HAMD‐17) total score in patients with major depressive disorders treated with placebo and to develop predictive models to estimate the response at end‐point given HAMD‐17 measurements at weeks 2 and 4.

Methods  Patients (n = 691) from seven clinical trials were analysed in WinBUGS using a Bayesian approach. The whole dataset was randomly split in a learning (359 patients for model definition) and a test dataset (332 patients for assessment of model predictive performance). The analysis of the learning dataset assumed uninformative priors, whereas the analysis of the test dataset used the posterior parameter estimates of the learning dataset as priors. ROC curve analysis estimated the optimal sensitivity/specificity cut‐off between false‐negative and false‐positive rates and determined the prognostic allocation rule for patients to responder and nonresponder groups.

Results  A Weibull/linear model accurately described the population and individual HAMD‐17 time course. The total area under the ROC curve, ranging from 0.76 (logistic model with data at week 2) to 0.86 (longitudinal model with data at week 4), provided a measure of the prognostic discriminatory power of early HAMD‐17 measures using the two models. The best placebo‐responder classification score (86.32% true and 13.68% false positive) was associated with the longitudinal model with HAMD‐17 measures at week 4.

Conclusion  Results showed the relevance of the Bayesian approach to predict HAMD‐17 score at study end and to classify a patient as a placebo responder given the uncertainty in parameters derived from historical data and early HAMD‐17 measurements.
Different isoforms of the Wilms’ tumour protein WT1 have distinct patterns of distribution and trafficking within the nucleus
Authors: Dutton J. R. , Lahiri D. , Ward A.
Published: November 2006

Abstract.  The Wilms’ tumour suppressor gene WT1 encodes multiple isoforms of a transcription factor essential for correct mammalian urogenital development. Maintenance of the correct isoform ratio is critical. In humans, perturbation of this ratio causes Frasier syndrome, which is characterized by developmental defects of the kidney and urogenital tract. Different WT1 isoforms are thought to regulate transcription and participate in mRNA processing, functions reflected by a complex sub‐nuclear distribution. However, the role of individual WT1 isoforms remains unclear and pathways leading to WT1 sub‐nuclear localization are completely unknown. Here we use cells expressing green fluorescent protein‐tagged WT1 to demonstrate that the two major WT1 isoforms occupy separate and dynamic intranuclear locations in which one isoform, WT1+KTS, preferentially associates with the nucleolus. The alternatively spliced zinc finger region is found to be critical for the initial sub‐nuclear separation of WT1 isoforms, but interactions between different isoforms influence the sub‐nuclear distribution of WT1. We illustrate how disruption of WT1 nuclear distribution might result in disease. This study contributes to the emerging picture of intranuclear protein trafficking.
Role of FGF1, FGF2 and FGF7 in the development of the pancreas from control and streptozotocin‐treated hamsters
Authors: Inchovska M. , Ogneva V. , Martinova Y.
Published: November 2006

Abstract.  Although progress has been made with respect to the growth and transcription factors implicated in pancreatic development, many questions remain unsolved. It has been established that during embryonic life, both endocrine and acinar cells are derived from pancreatic epithelial precursor cells. Growth factors control the proliferation of precursor cells and their ability to differentiate into mature cells, both in pre‐natal and in early post‐natal life. Pancreatic development during the early post‐natal period is an area of great interest for many scientists. In this study we have examined the structure characteristics, functional and proliferative activity of control and diabetic hamster pancreatic ductal, exocrine and β cells, following treatment with FGFs 1, 2 and 7 in vitro. Light and electron microscopic studies indicated active synthetic processes in these cells under the influence of the investigated FGFs. In our experimental model of diabetes, the labelling index of the cells was significantly higher than in corresponding control groups of hamsters. We established that FGF2 at a concentration of 10 ng/l was responsible for the most prominent effect on ductal cells and β cells in the diabetic groups. FGF1 at a concentration of 10 ng/l displayed the highest stimulatory effect on exocrine cells in the diabetic groups at post‐natal day 10. Taken together these data strongly suggest that FGF1 and FGF2 induce proliferation of pancreatic epithelial cells during the early post‐natal period whereas FGF7 is not strictly specific for pancreatic cell proliferation.
Study of selected quality and agronomic characteristics and their interrelationship in Kabuli‐type chickpea genotypes (Cicer arietinum L.)
Authors: Khattak Amal Badshah , Khattak Gul Sanat Shah , Mahmood Zahid , Bibi Nizakat , Ihsanullah Ihsanullah
Published: November 2006

Impact of genotype on quality, agronomic characteristics and their interrelationship in Kabuli‐type chickpea was investigated to provide significant feedback to breeder for selection/evolution of the most suitable varieties. Seven genotypes were studied for seventeen physical, chemical and agronomic characteristics. The effect of Kabuli‐type chickpea genotype on the physicochemical parameters, cooking time and agronomic characteristics were significant. Maximum seed size and volume were recorded for CC98/99 (0.32 g and 0.26 mL seed−1, respectively), density and swelling index for the genotype FLIP97‐179C (having minimum seed size and volume), while the rest of the genotypes were statistically the same. Weight, volume after hydration, hydration capacity and swelling capacity followed the same pattern. Maximum moisture, protein and mineral concentration were noted in CC98/99. Seed protein concentration for the remaining genotypes was statistically non‐significant from one another. Longer period was taken by CM 2000 for flowering and maturity (130 and 181 days, respectively). Minimum time to flowering and maturity was taken by CC98/99. Genotype CC 98/99 outyielded all other genotypes (2107 kg ha−1). Seed size and seed volume were strongly and positively correlated with protein content, weight after hydration, volume after hydration, hydration and swelling capacities (r = 0.83–1.0). Strong correlation was also noted among different agronomic characters.
Time trends in population cholesterol levels 1986–2004: influence of lipid‐lowering drugs, obesity, smoking and educational level. The northern Sweden MONICA study
Authors: ELIASSON M. , JANLERT U. , JANSSON J.‐H. , STEGMAYR B.
Published: November 2006

Objectives.  To explore time trends in population total cholesterol.

Design and setting.  Five population‐based cross‐sectional surveys, 1986–2004 in the northern Sweden MONICA study included 8827 men and women.

Results.  Age‐adjusted cholesterol level declined in men, 25–64 years old, from 6.38 to 5.78 mmol L−1 and in women from 6.32 to 5.51 mmol L−1. Between 1994 and 2004, subjects 65–74 years old were included, and their levels also decreased, in men from 6.35 to 5.76 mmol L−1 and in women from 7.11 to 6.24 mmol L−1. The decrease was continuous over surveys and age groups, except in young and middle‐aged men where no further decline was found after 1999. Cohorts born 1920–1939 showed decreased cholesterol over the period, whilst no change was noted for those born thereafter. In 2004, one‐fourth of men and one‐third of women 25–74 years achieved levels below 5.0 mmol L−1. Subjects with low educational level, body mass index ≥25 or smokers all had higher cholesterol levels which persisted during the 18‐year period. In 2004, the 9% who used lipid‐lowering drugs are estimated to contribute, at most, to 0.13 mmol L−1 lower cholesterol in the population.

Conclusion.  Large decreases in cholesterol levels occurred in the 18‐year period. Less smoking may contribute to, and increasing obesity attenuate, this trend whilst lipid‐lowering drugs have had little effect until recently. Socio‐economic inequalities persist.
Cytomegalovirus infection in renal transplant recipients
Authors: Carstens J. , Andersen H.K. , Spencer E. , Madsen M.
Published: November 2006

Abstract:We have retrospectively analyzed the incidence of cytomegalovirus (CMV) infection in 250 consecutive renal allograft transplants performed in 244 recipients. The mean follow‐up was 35.1±25.4 months. Immunosuppression was cyclosporine‐ or tacrolimus‐based triple therapy. CMV infection prophylaxis with ganciclovir for 3 months post transplant was prescribed in CMV‐seronegative recipients of allografts from seropositive donors (D+R−) and in all recipients treated with OKT3. CMV antigenemia was monitored by the pp65‐antigen assay. Thirteen of 57 D+R− recipients (22.8%) developed CMV antigenemia. One recipient had a breakthrough of CMV antigenemia during ganciclovir prophylaxis; 12 D+R− recipients developed CMV antigenemia 147.5±173.8 days after transplantation. Four of 13 (30.7%) D+R− recipients had asymptomatic CMV infection, 8 (61.6%) had CMV infection with non‐specific symptoms including fever, and 1 (7.7%) developed CMV pneumonia. Six of 13 (46.1%) D+R− patients had been treated with intensified immunosuppressive therapy before CMV infection. In the low‐risk CMV groups (D+R+; D−R+; D−R−), 28 recipients (14.5%) developed CMV antigenemia 42.5±15.2 days post transplantation. Ten of the 28 (35.7%) recipients had asymptomatic CMV infection, 17 (60.7%) developed CMV infection with non‐specific symptoms, and 1 (3.6%) developed CMV pneumonia. Twenty‐one of 28 (75.0%) had intensified immunosuppressive therapy before CMV infection. In conclusion, ganciclovir prophylaxis diminished and delayed the onset of CMV infection but did not totally prevent it from occurring in D+R− renal transplant recipients. Clinicians should be vigilant to the possibility of CMV infection in both seronegative and seropositive recipients, especially after anti‐rejection therapy.