bluuebunny/crossref_metadata_2025 huggingface dataset:
Time-dependent density functional theory with the generalized restricted-unrestricted approach
Authors: Oprea Corneliu I. , Telyatnyk Lyudmyla , Rinkevicius Zilvinas , Vahtras Olav , Ågren Hans
Published: May 2006

This work presents the derivation, implementation, and first applications of the generalized restricted-unrestricted method based on the density functional Kohn-Sham formalism. By using a spin-restricted Kohn-Sham representation for the reference state the well-known spin contamination problem is avoided, while the unrestricted representation of the perturbation response retains a proper description of spin polarization. The formulation is a generalization of our previous implementation of the restricted-unrestricted method [Z. Rinkevicius et al., J. Chem. Phys. 121, 7614 (2004)], as it accounts for the full unrestricted response instead of describing the spin polarization in terms of triplet operators only. The purpose of this paper is to investigate the role of the generalization employed and demonstrate its numerical performance. For this purpose we focus on isotropic hyperfine coupling constants of a set of organic radicals and transition metal compounds. For both classes of molecules we observe that the effect of neglecting singlet excitation operators in the response part of restricted-unrestricted formalism changes the calculated hyperfine coupling parameters by a few MHz. The obtained results confirm the validity of the approximation used in the simplified restricted-unrestricted approach, i.e. spin polarization can, in most cases, be adequately described by an account of only triplet operators in the response term.
Semidirect sums of Lie algebras and discrete integrable couplings
Authors: Ma Wen-Xiu , Xu Xi-Xiang , Zhang Yufeng
Published: May 2006

A relation between semidirect sums of Lie algebras and integrable couplings of lattice equations is established, and a practicable way to construct integrable couplings is further proposed. An application of the resulting general theory to the generalized Toda spectral problem yields two classes of integrable couplings for the generalized Toda hierarchy of lattice equations. The construction of integrable couplings using semidirect sums of Lie algebras provides a good source of information on complete classification of integrable lattice equations.
Effects of hot electrons on the stability of a dipolar plasma
Authors: Krasheninnikova Natalia S. , Catto Peter J.
Published: May 2006

The effects of a hot species on plasma stability in a dipole magnetic field is investigated by considering the interchange stability of a plasma of fluid background electrons and ions with a small fraction of hot kinetic electrons. The species diamagnetic drift and magnetic drift frequencies are assumed to be of the same order, and the wave frequency is assumed to be much larger than the background, but much less than the hot drift frequencies. An arbitrary total pressure dispersion relation is derived and analyzed to obtain the general requirements for stability in dipolar geometry. As an application of the theory, a special separable form of a point dipole equilibrium is considered. This analysis shows that a weak drift resonance with the slowly moving hot electrons modifies the simple magnetohydrodynamic interchange stability condition. Destabilization by this weak drift resonance can be avoided by carefully controlling the hot electron density and temperature profiles. A strong hot electron destabilization due to magnetic drift reversal is found not to occur in point dipole geometry. The results can be applied to dipole experiments employing electron cyclotron heating.
Effect of long-range elastic interactions on the toroidal moment of polarization in a ferroelectric nanoparticle
Authors: Wang Jie , Zhang Tong-Yi
Published: May 2006

The effect of long-range (LR) elastic interactions on the toroidal moment of polarization in a two-dimensional ferroelectric particle is investigated using a phase field model. The phase field simulations exhibit vortex patterns with purely toroidal moments of polarization and negligible macroscopic polarization when the spontaneous strains are low and the simulated ferroelectric size is small. However, a monodomain structure with a zero toroidal moment of polarization is formed when the spontaneous strains are high in small simulated ferroelectrics, indicating that, because of the LR elastic interactions, high values of spontaneous strains hinder the formation of polarization vortices in ferroelectric particles.
Generation of filamentary structures by beam-plasma interaction
Authors: Wang X. Y. , Lin Y.
Published: May 2006

The previous simulations by Wang and Lin [Phys. Plasmas. 10, 3528, (2003)] showed that filaments, frequently observed in space plasmas, can form via the interaction between an ion beam and a background plasma. In this study, the physical mechanism for the generation of the filaments is investigated by a two-dimensional hybrid simulation, in which a field-aligned ion beam with relative beam density nb=0.1 and beam velocity Vb=10VA is initiated in a uniform plasma. Right-hand nonresonant ion beam modes, consistent with the linear theory, are found to be dominant in the linear stage of the beam-plasma interaction. In the later nonlinear stage, the nonresonant modes decay and the resonant modes grow through a nonlinear wave coupling. The interaction among the resonant modes leads to the formation of filamentary structures, which are the field-aligned structures (k⊥B) of magnetic field B, density, and temperature in the final stage. The filaments are nonlinearly generated in a prey-predator fashion by the parallel and oblique resonant ion beam modes, which meanwhile evolve into two types of shear Alfvén modes, with one mainly propagating along the background field B0 and the other obliquely propagating. The filamentary structures are found to be phase standing in the plasma frame, but their amplitude oscillates with time. In the dominant filament mode, fluctuations in the background ion density, background ion temperature, and beam density are in phase with the fluctuations in B, whereas the significantly enhanced beam temperature is antiphase with B. It is found that the filaments are produced by the interaction of at least two ion beam modes with comparable amplitudes, not by only one single mode, thus their generation mechanism is different from other mechanisms such as the stimulated excitation by the decay of an Alfvén wave.
Properties of the acoustic mode in partially ionized and dusty plasmas
Authors: Vranjes J. , Poedts S.
Published: May 2006

The properties of current-driven ion-acoustic (IA) and dust-acoustic (DA) modes in partially ionized plasmas are investigated. The current is oriented along the magnetic field lines and the mode is assumed to propagate at an angle with respect to the current. For highly collisional light plasma components, the fluid equations in the parallel direction are used. In the case of unmagnetized heavy species, which provide the mode inertia (ions for the IA mode and grains for the DA mode), the oblique perturbations will have an acoustic nature. For an arbitrary collision frequency of heavy species with neutrals, a kinetic description is used for the heavy species. For the DA mode, the dispersion equation is solved first in the limits of an electron-depleted plasma, showing that the mode has a minimum instability threshold at a large angle of propagation. This feature is primarily due to the collisions. For higher values of the charge on the grains, this minimum vanishes but the threshold becomes considerably lower. The full dispersion equation, with electrons having a current with an opposite sign compared to ions, is solved numerically yielding both a lower frequency and a smaller increment. A similar angle-dependent threshold and increment are found for the IA mode as well.
Relativistic electron beam acceleration by Compton scattering of extraordinary waves
Authors: Sugaya R.
Published: May 2006

Relativistic transport equations, which demonstrate that relativistic and nonrelativistic particle acceleration along and across a magnetic field and the generation of an electric field transverse to the magnetic field, are induced by nonlinear wave-particle scattering (nonlinear Landau and cyclotron damping) of almost perpendicularly propagating electromagnetic waves in a relativistic magnetized plasma were derived from the relativistic Vlasov-Maxwell equations. The relativistic transport equations show that electromagnetic waves can accelerate particles in the k″ direction (k″=k−k′). Simultaneously, an intense cross-field electric field, E0=B0×vd∕c, is generated via the dynamo effect owing to perpendicular particle drift to satisfy the generalized Ohm’s law, which means that this cross-field particle drift is identical to the E×B drift. On the basis of these equations, acceleration and heating of a relativistic electron beam due to nonlinear wave-particle scattering of electromagnetic waves in a magnetized plasma were investigated theoretically and numerically. Two electromagnetic waves interact nonlinearly with the relativistic electron beam, satisfying the resonance condition of ωk−ωk′−(k⊥−k⊥′)vd−(k∥−k∥′)vb≃mωce, where vb and vd are the parallel and perpendicular velocities of the relativistic electron beam, respectively, and ωce is the relativistic electron cyclotron frequency. The relativistic transport equations using the relativistic drifted Maxwellian momentum distribution function of the relativistic electron beam were derived and analyzed. It was verified numerically that extraordinary waves can accelerate the highly relativistic electron beam efficiently with βmec2≲1GeV, where β=(1−vb2∕c2)−1∕2.
Transient behavior at the nanoscale
Authors: Ma Yuefei , Seminario Jorge M.
Published: May 2006

Transient and steady state responses of a system to an input are well-known features of materials and systems in science and engineering. These responses depend on the intrinsic parameters of the system and on the nature of the input. We find that a system comprised of nanosized features no longer shows the typical stationary characteristics as their microscopic or solid-state counterparts. Interestingly, because of the chemistry of the nanostructure, thermal motion of the atoms, and external fields, the nanosized system shows extended electrical transient behavior, compatible with highly nonlinear features such a negative differential resistance and hysteresis.
NMR high-resolution magic angle spinning rotor design for quantification of metabolic concentrations
Authors: Holly R. , Damyanovich A. , Peemoeller H.
Published: May 2006

A new high-resolution magic angle spinning nuclear magnetic resonance technique is presented to obtain absolute metabolite concentrations of solutions. The magnetic resonance spectrum of the sample under investigation and an internal reference are acquired simultaneously, ensuring both spectra are obtained under the same experimental conditions. The robustness of the technique is demonstrated using a solution of creatine, and it is shown that the technique can obtain solution concentrations to within 7% or better.
Characterization of Si p-i-n diode for scanning transmission ion microanalysis of biological samples
Authors: Devès G. , Matsuyama S. , Barbotteau Y. , Ishii K. , Ortega R.
Published: May 2006

The performance of a silicon p-i-n diode (Hamamatsu S1223-01) for the detection of charged particles was investigated and compared with the response of a standard passivated implanted planar silicon (PIPS) detector. The photodiode was characterized by ion beam induced charge collection with a micrometer spatial resolution using proton and alpha particle beams in the 1–3MeV energy range. Results indicate that homogeneity, energy resolution, and reproducibility of detection of charged particles enable the use of the low cost silicon p-i-n device as a replacement of conventional PIPS detector during scanning transmission ion microanalysis experiments. The Si p-i-n diode detection setup was successfully applied to scanning transmission ion microscopy determination of subcellular compartments on human cancer cultured cells.
Photoluminescence from GaN nanopowder: The size effect associated with the surface-to-volume ratio
Authors: Kudrawiec R. , Nyk M. , Syperek M. , Podhorodecki A. , Misiewicz J. , Strek W.
Published: May 2006

Nanosized GaN powder with the average grain size changing from ∼10to∼30nm has been obtained by combustion method with some modifications and its optical properties have been investigated by photoluminescence (PL). The GaN band-gap-related PL band at ∼3.4eV and surface-related PL bands centered at ∼2.0 and ∼2.8eV have been observed for this powder. The relative intensities between observed PL bands change in favor of the surface-related PL band with the decrease of the grain size. This phenomenon has been attributed to the change in the surface-to-volume ratio.
Synthesis of wurtzite ZnSe nanorings by thermal evaporation
Authors: Leung Y. P. , Choy Wallace C. H. , Markov I. , Pang G. K. H. , Ong H. C. , Yuk T. I.
Published: May 2006

In this study, free standing crystalline ZnSe nanorings and nanowires have been fabricated on Au coated Si substrates by simple thermal evaporation of ZnSe powders. Ring- or wirelike morphology can be achieved in a controllable manner by using different reactor pressures during growth, while all the other conditions remain the same. Our results show that the ZnSe nanorings are wurtzite phase instead of the zinc-blende phase, observed in typical one-dimensional ZnSe nanostructures. The growth mechanism of the nanorings has been discussed, and the cathodoluminescence of the nanorings has been described.
Observation of minority-carrier traps in InGaN∕GaN multiple-quantum-well light-emitting diodes during deep-level transient spectroscopy measurements
Authors: Kim Jae Wook , Song G. Hugh , Lee Jhang W.
Published: May 2006

An unusual appearance of a peak in the deep-level transient spectroscopy (DLTS) data for minority-carrier traps from an InGaN∕GaN multiple-quantum-well (MQW) light-emitting diode, under a bias condition provided by a square pulse of varying height superimposed over the reverse-bias voltage, is newly observed and analyzed. The peak is attributed to hole traps, having the estimated activation energy of 0.7eV, in the last one (toward the p side) among the GaN barrier layers in the MQW structure. We have found that the ΔC∕Cr-versus temperature pattern from the DLTS measurement agrees well with the pattern predicted from the model of hole traps, i.e., the minority-carrier traps, in the MQW barrier layer, whose occupation probability is governed by the local hole quasi-Fermi level.
Direct-band-gap Ga(NAsP)-material system pseudomorphically grown on GaP substrate
Authors: Kunert B. , Volz K. , Koch J. , Stolz W.
Published: May 2006

Compressively strained Ga(NAsP) multi-quantum-well heterostructures with As concentration above 85% have been grown pseudomorphically on GaP substrates by metal organic vapor phase epitaxy. Detailed structural analysis applying high-resolution x-ray diffraction proves the high crystalline perfection of the samples. Optical spectroscopy appyling photoluminescence and excitation spectroscopy verify the direct-band-gap characteristic of this novel material system. The comparison of the experimental data with elemental calculations via the band anticrossing model demonstrates that the formation of direct band structure can be understood by the strong bowing of the band gap energy typical for diluted III-V nitrides.
Comparison of interfacial and electrical characteristics of HfO2 and HfAlO high-k dielectrics on compressively strained Si1−xGex
Authors: Curreem K. K. S. , Lee P. F. , Wong K. S. , Dai J. Y. , Zhou M. J. , Wang J. , Li Quan
Published: May 2006

Interfacial reactions and electrical properties of HfO2 and HfAlO high-k gate dielectric films on strained Si1−xGex (x=17%) fabricated by pulsed-laser deposition were investigated. The dielectric films were characterized by x-ray photoelectron spectroscopy, transmission electron microscopy, and electrical measurements. We found that alloying of HfO2 with alumina can reduce the GeOx formation at the interfacial layer and thus reduce the Ge diffusion during the film post-thermal annealing process. Such suppression effect significantly improved the electrical properties of the dielectric films.
Structural Characterization of Some Complexes of Group 13 Metal(III) Nitrates with N,N′-Bidentate Bases
Authors: Junk Peter C. , Skelton Brian W. , White Allan H.
Published: May 2006

The structural characterization of several novel complexes of gallium(iii) and indium(iii) nitrates, crystallized with 2,2′-bipyridyl (bpy) and 1,10-phenanthroline (phen) from nitromethane solution, is presented. The adduct In(NO3)3:bpy (1:2) is of the form [(ONO2)(O2NO)2In(bpy)2], rather than [(ONO2)3ML2] as found for the larger M = Ln (rare earth), Bi, despite similar 2-symmetry. Several hydroxo-bridged dimers, [L2M(OH)2ML2](NO3)4(·S) are also presented, the cations all of the same isomeric form. [(ONO2)(bpy)In(OH)2In(bpy)(O2NO)], interestingly, displays two different forms within the one crystal, by virtue of different dispositions of the coordinated nitrate. The structures of related cis-[(phen)2GaBr2]Br(·S) and [(en)2In(OH)2In(en)2](NO3)4 (en = H2N(CH2)2NH2) are also described, the latter isomorphous with its cobalt(iii) counterpart.
Structure of the Molecular Receptor 1,4,7,10-Tetrakis[(S)-2-hydroxy-2-phenylethyl]-1,4,7,10-tetraazacyclododecane: A Combined X-Ray Crystallographic and Theoretical Study Producing an Assessment of the Crystal Packing Energy
Authors: Smith Christopher B. , Buntine Mark A. , Lincoln Stephen F. , Taylor Max R. , Wainwright Kevin P.
Published: May 2006

X-Ray crystallography demonstrates that the guest molecule binding cavity within the molecular receptor ligand 1,4,7,10-tetrakis[(S)-2-hydroxy-2-phenylethyl]-1,4,7,10-tetraazacyclododecane, (S)-thpec12, is a poorly defined conical region stabilized by three O–H···O hydrogen bonds and a single O–H···N hydrogen bond. Two similar, but crystallographically independent, molecules exist within the unit cell. Ab initio calculations, using Gaussian 03 (LanL2DZ basis set at the Hartree–Fock level of theory), predict that these have steric energies of 97.73 and 97.06 kJ mol−1, respectively, above that of the minimum energy (gas phase) conformer of the same hydrogen-bonding configuration, which is believed to be the structure of global minimum energy. The mean of these energies (97.4 kJ mol−1) represents a best estimate of the crystal packing energy for (S)-thpec12, some of which is seen to be expended in rotating the phenyl rings away from the positions favoured in the gas phase. The ability of the CdII complex of (S)-thpec12 to act as a molecular receptor for aromatic anions is demonstrated by the isolation of two inclusion compounds in which p-nitrophenolate and anthraquinone-2-sulfonate are retained.
Chiral Heterocyclic Ligands. XIII. Synthesis and X-Ray Crystal Structure of a Chiral, Unidirectional, Silver Coordination Polymer
Authors: Fitchett Christopher M. , Steel Peter J.
Published: May 2006

The chiral bridging ligand 2 is shown to react with silver nitrate to produce a new type of chiral coordination polymer with a unidirectional ladder-like structure.
A New Way To Detect Noncovalently Bonded Complexes of Biomolecules from Liquid Micro-Droplets by Laser Mass Spectrometry
Authors: Morgner Nina , Barth Hans-Dieter , Brutschy Bernhard
Published: May 2006

A new version of laser mass-spectrometry is presented, which allows the quantitative analysis of specific biocomplexes in native solution. On-demand micro droplets, injected into vacuum, are irradiated by mid IR-laser pulses. Above a certain intensity threshold they explode due to the transmitted energy, setting free a fraction of the charged biomolecules which are then mass-analyzed. Amounts of analyte in the attomolar range may be detected with the ion intensity being linear over a wide range of molarity. Evidence is given that this method is soft, tolerant against various buffers, reflects properties of the liquid phase, and suitable for studying noncovalently bonded specific complexes. This is highlighted by results from antibiotics specifically binding into the minor groove of duplex DNA.
An Interpenetrating Coordination Polymer Containing Weak Hydrogen Bonds and Argentophilic Interactions
Authors: Duriska Martin B. , Batten Stuart R. , Price David J.
Published: May 2006

The structure of the coordination polymer [Ni(en)2][Ag(CN)2]2[Ag2(CN)2] (1; en = ethylenediamine) contains 2D (6,3) sheets in which trans-Ni(en)2{Ag(CN)2}2 moieties bridge between zigzag Ag(CN) chains. The sheets are puckered, and show 3-fold 2D → 2D parallel interpenetration. The structure also contains weak N–H···π(CN) and argentophilic Ag···Ag interactions between the 2D sheets.
Photoswitchable Sensitization of Porphyrin Excited States
Authors: Straight Stephen D. , Terazono Yuichi , Kodis Gerdenis , Moore Thomas A. , Moore Ana L. , Gust Devens
Published: May 2006

Light-driven molecular switches consisting of a porphyrin covalently linked to a fulgimide photochrome antenna have been prepared. Light absorbed by the cyclic form of the fulgimide is transferred to the porphyrin with ≥ 95% efficiency, generating the porphyrin first excited singlet state. Irradiation with visible light photoisomerizes the fulgimide to the open form, which does not absorb above 450 nm, and antenna function is abolished. UV irradiation converts the fulgimide back into the cyclic form, re-establishing efficient energy transfer. Photoisomerization of the fulgimide thus controls generation of the porphyrin excited state, which may then be used to carry out a variety of useful photochemical processes.
Photoinduced Electron Transfer Processes in Rotaxanes Containing [60]Fullerene and Ferrocene: Effect of Axle Charge on Light-Induced Molecular Motion
Authors: Sandanayaka Atula S. D. , Sasabe Hisahiro , Araki Yasuyuki , Kihara Nobuhiro , Furusho Yoshio , Takata Toshikazu , Ito Osamu
Published: May 2006

Two rotaxanes containing [60]fullerene (C60) as pendants on a crown-ether necklace, to which ferrocene (Fc) as axle stoppers were added, have been synthesized. One rotaxane has an ammonium cation in the centre of the axle (C60;Fc)Rot+ and the other has a neutral axle (C60;Fc)Rot. Optimized structures, calculated using a molecular orbital method, suggest that in the ground states (C60;Fc)Rot+ has a shorter distance between C60 and Fc than that of (C60;Fc)Rot. In both rotaxanes, efficient intra-rotaxane photoinduced electron-transfer processes have been observed by the selective excitation of C60 which acts as a photosensitized electron acceptor. The rates and efficiencies of the charge-separation and charge-recombination processes were evaluated by time-resolved fluorescence and transient absorption measurements with changing solvent polarity. From the different kinetic parameters between (C60;Fc)Rot+ and (C60;Fc)Rot, the light-induced molecular motions of these rotaxanes in the excited states and charge-separated states were separately revealed.
Synthesis and Evaluation of a Molecularly Imprinted Polymer Selective to 2,4,6-Trichloroanisole
Authors: Schwarz Lachlan , Bowyer Michael C. , Holdsworth Clovia I. , McCluskey Adam
Published: May 2006

In the wine industry 2,4,6-trichloroanisole (TCA) has been identified as the primary contaminant responsible for ‘cork taint’. A molecularly imprinted polymer (MIP) selective for TCA was prepared in three porogens (hexane, acetonitrile, and dichloromethane) of varying polarities using non-covalent molecular imprinting techniques. Target rebinding to the MIP was found to be most effective in its porogenic solvent and highest in dichloromethane (imprinting factor = 3.65). Competitive binding assays performed against a range of close structural analogues demonstrated a preference for the target molecule.
Rotational Energy Distributions of Benzene Liberated from Aqueous Liquid Microjets: A Comparison between Evaporation and Infrared Desorption
Authors: Maselli Olivia J. , Gascooke Jason R. , Kobelt Sarah L. , Metha Gregory F. , Buntine Mark A.
Published: May 2006

We have measured the rotational energy distribution of benzene molecules both evaporated and desorbed by an IR laser from a liquid microjet. Analysis of the 601 vibronic band of benzene has shown that the benzene molecules evaporating from the liquid microjet surface have a rotational temperature of 157 ± 7 K. In contrast, the rotational temperature of benzene molecules desorbed from the liquid microjet by a 1.9 μm laser pulse is 82 ± 5 K. However, in both cases careful inspection of the spectral profiles shows that the experimental rotational distributions are non-Boltzmann, displaying an underpopulation of high rotational states and a relative overpopulation of the low rotational states. The non-equilibrium evaporation and desorption spectral profiles are consistent with a model that involves transfer of internal energy into translation upon liberation from the condensed phase.
Coordination Networks with Carborane Anions: Ag(I) and Nitrogen Bridging Ligands
Authors: Cunha-Silva Luís , Ahmad Ruksanna , Hardie Michaele J.
Published: May 2006

New crystalline coordination networks based on Ag(i) and N-bridging ligands — pyrazine (pyz), 4,4′-bipyridine (bpy), and 2,3-bis-(2-pyridyl)pyrazine (bppz) — incorporating carborane monoanions (CB11H12)− or [Co(C2B9H11)2]− were isolated and characterized using single crystal X-ray diffraction, microanalysis, and infrared spectroscopy. All the complexes with the bpy and bppz ligands reveal 1D coordination infinite chains involving the Ag(i) and the ligands, and layered extended structures with rows of carborane anions between the layers of chains. Interestingly, two polymorphs of the complex [Ag(bpy)(CH3CN)][Co(C2B9H11)2] were observed. The complex [Ag(pyz)(CH3CN)2][Co(C2B9H11)2] shows a 1D coordination polymer, while the pyz complex with the smaller carborane anion {[Ag(pyz)](CB11H12)} exhibits a 3D coordination network structure with four Ag···H−B interactions between the silver centre and carborane anions.
A Planar Silver(I) Complex with a 'Simple' 2,2?-Bipyridine Ligand
Authors: Constable Edwin C. , Housecroft Catherine E. , Kariuki Benson M. , Smith Christopher B.
Published: May 2006

The phenol-functionalized 2,2′-bipyridine ligand 1 forms a silver(i) complex containing [Ag(1)2]+ cations that are best described as having a planar coordination environment.
Integration of EXAFS, Spectroscopic, and DFT Techniques for Elucidation of the Structure of Reactive Diiron Compounds
Authors: Bondin Mark I. , Borg Stacey J. , Cheah Mun Hon , Foran Garry , Best Stephen P.
Published: May 2006

Strategies for modelling the EXAFS of a range of compounds with structural features common to the diiron subsite of the [FeFe] hydrogenase H-centre are compared, and this has allowed identification of highly constrained models that still permit expression of the main structural characteristics of the compounds. Despite giving self-consistent values of the iron–scatterer distances, the EXAFS analysis fails to give unambiguous identification of the stereochemistry and composition of the compounds, and this necessitates the integration of results obtained using other spectroscopic and computational approaches. The combination of infrared spectroscopy, EXAFS, and ab initio DFT calculations are shown to provide a particularly potent approach for the study of metal carbonyl compounds of this class. In this case the EXAFS-derived iron–scatterer distances provide the basis of the starting point for DFT geometry optimization calculations, and the final distances together with the calculated infrared spectrum provides a means of validating the computed geometry. The approach is applied both to compounds of known structure and to the examination of the unstable products of chemical or electrochemical reduction.
Avidin–Biotin Assembling of Horseradish Peroxidase Multi-Monomolecular Layers on Electrodes
Authors: Limoges Benoît , Savéant Jean-Michel , Yazidi Dounia
Published: May 2006

The strong avidin–biotin affinity is used to stack up successive monomolecular layers of horseradish peroxidase on carbon electrodes. After a biotinylated immunoglobulin is adsorbed on the electrode surface, alternate deposition of neutravidin and biotinylated HRP allows the assemblage of up to 16 successive active HRP layers. The film build-up is followed by cyclic voltammetry using an osmium complex as soluble mediator and H2O2 as substrate. The variation of the resulting catalytic responses with H2O2 concentration exhibit characteristics qualitatively consistent with the catalysis-inhibition reaction scheme previously established for monomolecular layers. In most cases the catalytic activity increases steadily with the number of monomolecular layers, leading to a significant increase of the analytical sensitivity of the derivatized electrode.
Kinetic Model for the Degradation of MTBE by Fenton's Oxidation
Authors: Al Ananzeh Nada , Bergendahl John A. , Thompson Robert W.
Published: May 2006

Environmental Context.Since the early 1990s, methyl tert-butyl ether (MTBE), a possible human carcinogen, has been used as a gasoline oxygenate at concentrations of up to 15% by volume; however, a fraction of the MTBE produced has inevitably been released to the environment. And, spills at gasoline service stations have resulted in local groundwater contamination levels of MTBE over 100 mg L−1, because of its very high water solubility. Advanced oxidation is a common technique for mineralizing organic contaminants, but the reaction chemistry needs to be better understood to facilitate design of remediation systems.
Abstract.A kinetic model for the degradation of methyl tert-butyl ether (MTBE) in batch reactors with Fenton’s oxidation (Fe2+/ H2O2) in aqueous solutions was developed. This kinetic model consists of equations accounting for (1) hydrogen peroxide chemistry in aqueous solution, (2) iron speciation, and (3) MTBE oxidation. The mechanisms of MTBE degradation, and the resultant pathways for the formation and degradation of the byproducts, were proposed on the basis of previous studies. A set of stiff nonlinear ordinary differential equations that describe the rate of formation of each species in this batch system was solved using Matlab (R13) software. The kinetic model was validated with published experimental data. The degradation of MTBE by Fenton’s oxidation is predicted well by the model, as are the formation and degradation of byproducts, especially methyl acetate (MA) and tert-butyl alcohol (TBA). Finally, a sensitivity analysis based on calculating the sum of the squares of the residuals (SSR) after making a perturbation of one rate constant at a time was applied to discern the effect of each reaction on MTBE disappearance.
Prediction of Zinc and Cadmium Phytoavailability Within a Contaminated Agricultural Site using DGT
Authors: Cornu Jean-Yves , Denaix Laurence
Published: May 2006

Environmental Context.In some agricultural areas, soils are contaminated by trace elements. This contamination of cultivated soils may constitute a serious problem for human health through the accumulation of metals in the edible parts of crops. In order to assess the risk for human health associated with metal contamination of soil, we need to develop simple tools like Diffusive Gradients in Thin Films (DGT) for predicting crop metal accumulation. The present study focuses on an agricultural site contaminated with fallout from industrial dust and reveals that DGT could be a predictive tool of zinc accumulation in lettuce.
Abstract.Risk assessment of metal contamination in cultivated soils needs to address metal phytoavailability. The technique of diffusive gradients in thin films (DGT) has been shown to be a promising tool to assess metal phytoavailability in a wide range of soils. The present study has examined the ability of the DGT method to predict metal phytoavailability within a contaminated agricultural site. Lettuce (Lactuva sativa cv Appia) was grown in nine metal-contaminated soils differing mainly by their pH. Metal concentrations (Zn, Cd) in plant shoots were compared with total soil metal concentrations and free ion metal concentrations in soil pore waters, and effective concentrations, CE, measured by DGT. Plant Zn concentrations were highly related to CE, suggesting DGT can be a sensitive tool able to assess Zn phytoavailability within mildly contaminated agricultural soils. Plant Cd concentrations were less closely related to CE, signifying that processes other than Cd re-supply from the solid phase may occur during soil–plant transfer of Cd.
Tidal stirring and mixing on the Australian North West Shelf
Authors: Katsumata K.
Published: May 2006

Strong tides on the Australian North West Shelf lead to vigorous vertical stirring and mixing. This activity near the shelf break is directly quantified with a numerical model. The model has a spatial and temporal resolution of about 800 m and 13 s respectively. The model result shows internal tides steepening as they shoal onto the slope, which is near critical for the semidiurnal tide. The main energy balance of the internal tides is between incoming internal tidal energy flux and the dissipation. The vertical and horizontal distribution of the heat flux carried by the internal tides is complex and difficult to parameterise. When area-averaged in the model region (38 km by 36 km), the vertical heat flux is in the order of –10−5 deg m s−1 (positive upward). This translates to a vertical diffusivity of 10−4 to 10−2 m2 s−1, which is an order of magnitude larger than the subgrid vertical diffusion. Both the warming and cooling rates caused by the convergence and divergence of the heat flux are in the order of 10−6 deg s−1. The neap-spring modulation of the semidiurnal tide did not significantly modify these estimates. These values can explain the vertical heat exchange inferred from large-scale analysis of the heat budget on the Shelf.
Dynamics of the Ningaloo Current off Point Cloates, Western Australia
Authors: Woo Mun , Pattiaratchi Charitha , Schroeder William
Published: May 2006

The Ningaloo Current (NC) is a wind-driven, northward-flowing current present during the summer months along the continental shelf between the latitudes of 22° and 24°S off the coastline of Western Australia. The southward flowing Leeuwin Current is located further offshore and flows along the continental shelf break and slope, transporting warm, relatively fresh, tropical water poleward. A recurrent feature, frequently observed in satellite images (both thermal and ocean colour), is an anti-clockwise circulation located offshore Point Cloates. Here, the seaward extension of the coastal promontory blocks off the broad, gradual southern shelf, leaving only a narrow, extremely steep shelf to the north. The reduction in the cross-sectional area, from the coast to the 50 m contour, between southward and northward of the promontory is ~80%. Here, a numerical model study is undertaken to simulate processes leading to the development of the recirculation feature offshore Point Cloates. The numerical model output reproduced the recirculation feature and indicated that a combination of southerly winds, and coastal and bottom topography, off Point Cloates is responsible for the recirculation. The results also demonstrated that stronger southerly winds generated a higher volume transport in the NC and that the recirculation feature was dependent on the wind speed, with stronger winds decreasing the relative strength of the recirculation.
Corroborating the ages of walleye pollock (Theragra chalcogramma)
Authors: Kimura Daniel K. , Kastelle Craig R. , Goetz Betty J. , Gburski Christopher M. , Buslov Alexander V.
Published: May 2006

Fish ageing researchers have long recognised the importance of validating age-reading methodologies. The strongest age validations require the acquisition of ageing structures from fish of known-ages, or specimens whose ages are appropriate for bomb carbon validation. Often such specimens are extremely difficult or impossible to acquire so researchers have sought alternatives to validation. The alternative to age validation is age corroboration. Corroboration of a fish ageing method occurs when fish ages are found to be consistent with some ancillary information when comparisons are made in an unbiased manner. The question pursued in this study is how desirable are such comparisons from a scientific viewpoint. Information is presented that corroborates otolith ages for walleye pollock (Theragra chalcogramma), one of the largest groundfish fisheries in the world. Walleye pollock ages were corroborated using marginal increment analysis, ages following the strong 1978 year class in the eastern Bering Sea, and a comparison of ages read from otoliths with ages read from vertebrae. A new statistical method is suggested for comparing otolith and vertebra age readings. The walleye pollock example demonstrated that corroborating evidence can improve confidence in fish ages and ageing techniques.
Reply to the comment by Crook and Koster (2006) 'Temporal change in fish assemblages in the lower Goulburn River, south-eastern Australia'
Authors: Pollino Carmel A. , Feehan Pat , Grace Michael R. , Hart Barry T.
Published: May 2006

In an earlier paper, multivariate statistics were used on historic fisheries data sets to show spatial differences between fish communities in the Goulburn Catchment (Victoria, Australia). In this reply paper, some further statistical analyses are presented to provide evidence for the assertion that fish communities at each site were stable over the temporal scale of the data was valid. Indeed, evidence for the stabilisation and persistence of fish communities after a major disturbance has also been recognised in other studies. Furthermore, in making judgements about the stability and persistence of fish communities, the scale of a study is an important factor, with patterns at the catchment scale often not being the same as those at smaller spatial scales.
Molecular systematics of Australian Calotis (Asteraceae: Astereae)
Authors: Watanabe K. , Kosuge K. , Shimamura R. , Konishi N. , Taniguchi K.
Published: May 2006

The intra-generic relationships of the Australian genus Calotis, with various chromosome base numbers from x = 8 to x = 4, were examined by the comparison of nucleotide sequences of the complete ITS region of nuclear rDNA and of the matK gene of chloroplast DNA. Within a monophyletic Calotis, four lineages were identified. Reconstruction of ancestral states suggests that the chromosome base number for Calotis is x = 8. Dysploidal reductions in chromosome base number from x = 8 to x = 7 and from x = 8 to x = 5 or 4 have occurred independently at least three times. Lower base numbers of x = 7, 5, and 4 are found predominantly in the arid and semi-arid zone species of Central and Western Australia. Total karyotypic length (genome size) is greater in perennials than in annuals within the genus Calotis. The elaborated pappus and surface structures of cypsela, and life form of species seem to be homoplasous with multiple origins in the evolutionary history of the lineage.
A review of Planchonia (Lecythidaceae) in Australia
Authors: Barrett Russell L.
Published: May 2006

The genus Planchonia Blume is reviewed for Australia with two species recognised. Planchonia rupestris R.L. Barrett is described as a new species apparently endemic to the sandstone plateaux of the Kimberley region of Western Australia. Lectotypes are designated for Cumbia australis Britten, Planchonia crenata Miers and Planchonia arborea var. australis Benth., each of which are synonyms of Planchonia careya (F.Muell.) Kunth. Illustrations, distribution maps and a key to the Australian species are presented.
Transcription regulatory elements are punctuation marks for DNA replication
Authors: Mirkin Ekaterina V. , Castro Roa Daniel , Nudler Evgeny , Mirkin Sergei M.
Published: May 2006

Collisions between DNA replication and transcription significantly affect genome organization, regulation, and stability. Previous studies have described collisions between replication forks and elongating RNA polymerases. Although replication collisions with the transcription-initiation or -termination complexes are potentially even more important because most genes are not actively transcribed during DNA replication, their existence and mechanisms remained unproven. To address this matter, we have designed a bacterial promoter that binds RNA polymerase and maintains it in the initiating mode by precluding the transition into the elongation mode. By using electrophoretic analysis of replication intermediates, we have found that this steadfast transcription-initiation complex inhibits replication fork progression in an orientation-dependent manner during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, codirectional orientation. Thus, transcription regulatory signals may serve as “punctuation marks” for DNA replication
in vivo
.
Na
+
/monocarboxylate transport (SMCT) protein expression correlates with survival in colon cancer: Molecular characterization of SMCT
Authors: Paroder Viktoriya , Spencer Shelly R. , Paroder Monika , Arango Diego , Schwartz Simo , Mariadason John M. , Augenlicht Leonard H. , Eskandari Sepehr , Carrasco Nancy
Published: May 2006

We report an extensive characterization of the Na
+
/monocarboxylate transporter (SMCT), a plasma membrane protein that mediates active transport of monocarboxylates such as propionate and nicotinate, and we show that SMCT may play a role in colorectal cancer diagnosis. SMCT, the product of the
SLC5A8
gene, is 70% similar to the Na
+
/I
−
symporter, the protein that mediates active I
−
uptake in the basolateral surface of thyrocytes and other cells. SMCT was reported in the apical surface of thyrocytes and formerly proposed also to transport I
−
and was called the apical I
−
transporter. However, it is now clear that SMCT does not transport I
−
. Here we demonstrate a high-affinity Na
+
-dependent monocarboxylate transport system in thyroid cells, which is likely to be SMCT. We show that, whereas thyroidal Na
+
/I
−
symporter expression is thyroid-stimulating hormone (TSH)-dependent and basolateral, SMCT expression is TSH-independent and apical not only in the thyroid but also in kidney and colon epithelial cells and in polarized Madin–Darby canine kidney cells. We determine the kinetic parameters of SMCT activity and show its inhibition by ibuprofen (
K
i
= 73 ± 9 μM) in
Xenopus laevis
oocytes. SMCT was proposed to be a tumor suppressor in colon cancer [Li, H.,
et al.
(2003)
Proc. Natl. Acad. Sci. USA
100, 8412–8417]. Significantly, we show that higher expression of SMCT in colon samples from 113 colorectal cancer patients correlates with longer disease-free survival, suggesting that SMCT expression may be a favorable indicator of colorectal cancer prognosis.
Percutaneous balloon kyphoplasty in the treatment of pathological vertebral body fracture and deformity in multiple myeloma: a one-year follow-up
Authors: Pflugmacher R. , Kandziora F. , Schroeder R. -J. , Melcher I. , Haas N. P. , Klostermann C. K.
Published: May 2006

Purpose: To evaluate the clinical and radiographic outcomes of balloon kyphoplasty in patients with fractures of the thoracic and lumbar spine caused by multiple myeloma.

Material and Methods: Vertebral fractures due to multiple myeloma were treated by balloon kyphoplasty (20 patients, 48 vertebral bodies). Symptomatic levels were identified by clinical presentation, magnetic resonance imaging (MRI), radiographs, and computed tomography (CT). During the following year, visual analog scale (VAS) and Oswestry disability score were documented. Radiographs were taken pre- and postoperatively at 3, 6, and 12 months. Vertebral height and kyphotic deformity were measured to assess restoration of the sagittal alignment.

Results: The median pain scores (VAS) decreased significantly from pre- to post-treatment, as did the Oswestry disability score ( p<0.05). Clinically asymptomatic cement leakage occurred at 5 fracture levels (10.4%). During 1-year follow-up, this surgical technique demonstrated restoration and stabilization of the height of the vertebral body.

Conclusion: Balloon kyphoplasty is an effective minimally invasive procedure for stabilizing pathological vertebral fractures caused by multiple myeloma and leading to a statistically significant reduction of pain status. Balloon kyphoplasty stabilizes the vertebral body height, but is only partially able to prevent further kyphotic deformities.
Value of fat-suppressed proton-density-weighted turbo spin-echo sequences in detecting meniscal lesions: comparison with arthroscopy
Authors: Schäfer F. K. W. , Schäfer P. J. , Brossmann J. , Frahm C. , Hilgert R.-E. , Heller M. , Jahnke T.
Published: May 2006

Purpose: To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging (MRI) compared to arthroscopy in the detection of meniscal lesions.

Material and Methods: In a prospective study, 31 knee joints were imaged on a 1.5T MR scanner before arthroscopy using the following sequences: (a) coronal and sagittal FS-PDw TSE (TR/TE: 4009/15 ms); (b) coronal T1w SE (TR/TE: 722/20 ms), and sagittal PDw TSE (TR/TE: 3800/15 ms). Other imaging parameters were: slice thickness 3 mm, FOV 160 mm, matrix 256×256. A total of 186 meniscal regions (62 menisci; anterior horn, body, posterior horn) were evaluated. Standard of reference was arthroscopy. Sensitivity, specificity, negative predictive value (npv), positive predictive value (ppv), and accuracy were calculated.

Results: Arthroscopically, meniscal lesions were detected in 55/186 segments (35 medial and 20 lateral meniscal lesions). Sensitivity, specificity, npv, ppv, and accuracy for combination of coronal and sagittal FS PDw TSE were 91.4%, 98.3%, 95%, 97%, and 93.5% for the medial meniscus, and 90%, 98.6%, 97.3%, 94.7%, and 96.8% for the lateral. The results were comparable to the combination of coronal T1w SE and sagittal PDw TSE for the medial (88.6%, 98.3%, 93.4%, 96.9%, 91.4%) and the lateral (90%, 95.9%, 97.2%, 85.7%, 92.5%) meniscus.

Conclusion: FS PDw TSE-MR sequences are an excellent alternative for the detection of meniscal lesions in comparison with diagnostic arthroscopy.
Imaging findings in symptomatic patients with femoral diaphyseal stress injuries
Authors: Theodorou S. J. , Theodorou D. J. , Resnick D.
Published: May 2006

Purpose: To assess the imaging findings seen in symptomatic patients with stress injuries of the femoral diaphysis.

Material and Methods: Seven patients (5 F, 2 M, age range 16 to 56 years, mean 38 years) underwent imaging evaluation of the symptomatic lower extremity due to an insidious onset of thigh or groin pain unrelated to trauma. Imaging studies included radiography and magnetic resonance imaging (MRI) in seven patients, bone scintigraphy in five, and computed tomography (CT) in three.

Results: Radiographs depicted three frank fractures in two patients, and revealed findings of stress injury in six patients. Available scintigraphic and CT findings were abnormal. On MR images, a solitary fracture was seen in two patients; two patients presented with bilateral stress fractures of the femoral diaphysis; and all seven patients had the imaging features of stress injury. Femoral diaphyseal stress fractures ( n = 6) appeared as linear regions of T1- and T2-weighted low signal intensity, surrounded by diffuse bone marrow edema. Three of the six frank fractures, with an evident fracture line, were longitudinal and parallel to the cortical surface.

Conclusion: Femoral diaphyseal stress fractures are often inconspicuous with conventional radiography. MRI depicts the changes of stress injury in the femoral diaphysis, and is particularly useful in documenting the presence, morphology, and extent of fracture(s), information valuable for definitive diagnosis and appropriate management.