bluuebunny/crossref_metadata_2025 huggingface dataset:
Isoflurane Strongly Affects the Diffusion of Intracellular Metabolites, as Shown by 1H Nuclear Magnetic Resonance Spectroscopy of the Monkey Brain
Authors: Valette Julien , Guillermier Martine , Besret Laurent , Hantraye Philippe , Bloch Gilles , Lebon Vincent
Published: June 2006

Isoflurane is a volatile anesthetic commonly used for animal studies. In particular, diffusion nuclear magnetic resonance (NMR) spectroscopy is frequently performed under isoflurane anesthesia. However, isoflurane is known to affect the phase transition of lipid bilayer, possibly resulting in increased permeability to metabolites. Resulting decreased restriction may affect metabolite apparent diffusion coefficient (ADC). In the present work, the effect of isoflurane dose on metabolite ADC is evaluated using diffusion tensor spectroscopy in the monkey brain. For the five detected intracellular metabolites, the ADC exhibits a significant increase when isoflurane dose varies from 1% to 2%: 13%±8% for myo-inositol, 14%±13% for total N-acetyl-aspartate, 20%±18% for glutamate, 27%±7% for total creatine and 53%±17% for total choline. Detailed analysis of ADC changes experienced by the five different metabolites argues in favor of facilitated metabolite exchange between subcellular structures at high isoflurane dose. This work strongly supports the idea of metabolite diffusion in vivo being significantly restricted in subcellular structures at long diffusion time, and provides new insights for interpreting ADC values as measured by diffusion NMR spectroscopy.
Enhancement of photoelectrical properties in polymer nanocomposites containing modified single-walled carbon nanotubes by conducting dendrimer
Authors: Valentini L. , Mengoni F. , Armentano I. , Kenny J. M. , Ricco L. , Alongi J. , Trentini M. , Russo S. , Mariani A.
Published: June 2006

We report the photoinduced conductivity changes measured on a system composed of single-wall carbon nanotubes (SWNTs) modified by a semiconducting poly(amidoamine) dendrimer (PAMAMC) characterized by highly aromatic end groups. Under illumination hole injection into SWNTs prevails over the photoinjection of electrons from PAMAMC to SWNT holes, and film photoconductivity is observed. This system was incorporated as an electroactive component within a conducting polymer [poly(3-octylthiophene)], providing improvements in the photoelectrical properties of the composite. Such supramolecular structures consisting of dendrimer-functionalized carbon nanotubes provide the means for an approach toward the preparation of photoactive materials of high current interest.
Interdependence between stress, preferred orientation, and surface morphology of nanocrystalline TiN thin films deposited by dual ion beam sputtering
Authors: Abadias G. , Tse Y. Y. , Guérin Ph. , Pelosin V.
Published: June 2006

To clarify the underlying mechanisms that cause the preferred orientation in TiN films, we investigated the evolution with the thickness of the texture, surface morphology, and residual stress in TiN thin films deposited by dual ion beam sputtering. The films, with thickness h ranging from 50to300nm, were grown on oxidized Si substrates using a primary Ar ion beam accelerated under 1.2kV and different voltages Va of the (Ar+N2) assistance beam: 25, 50, and 150V. The influence of temperature was also investigated by varying the substrate temperature Ts (25–300°C) during growth or by performing a postdeposition annealing. X-ray diffraction (XRD) as well as transmission electron microscopy were used to study the microstructure and changes of texture with thickness h, while x-ray reflectivity and atomic force microscopy measurements were performed to determine the surface roughness. Residual stresses were measured by XRD and analyzed using a triaxial stress model. The crystallite group method was used for a strain determination of crystallites having different fiber axis directions, i.e., when a mixed texture exists. The surface roughness is found to increase with Va and Ts due to the resputtering effect of the film surface. XRD reveals that for a small thickness (h∼50nm) the TiN films exhibit a strong (002) texture independent of Va. For a larger thickness (100<h<300nm), the development of a (111) preferred orientation is observed together with a grain size increase, except at Ts=300°C, where the predominant texture remains (002). A minor (220) texture is also found, but its contribution strongly decreases with Va and Ts. The residual stresses are highly compressive, ranging from −8to−5GPa, depending on the deposition conditions. When a mixed texture exists, the analysis reveals that (111)-oriented grains sustain stresses that are about 20% more compressive than those sustained by (002)-oriented grains. The present results suggest that the change in the preferred orientation from (002) to (111) is not correlated with a strain energy minimization or with a systematic increase in surface morphology. Rather, kinetically driven mechanisms occurring during growth and linked to anisotropies in surface diffusivities, adatom mobilities, and collisional cascades effects are likely to control the texture development in TiN thin films produced with energetic ionic species. This interpretation is supported by in situ temperature XRD measurements.
An analytical model of self-starting thermoacoustic engines
Authors: Benavides Efrén Moreno
Published: June 2006

This paper presents a theoretical model of thermoacoustic engines. It aims for a better physical understanding of the power production of these devices. The main idea that supports the work is that the power output emerges from a thermodynamic cycle. The fluid near the heat exchangers is assumed to follow a thermodynamic cycle such as in a closed chamber of a Stirling reciprocating engine. This analogy between thermoacoustic engines and Stirling reciprocating engines introduces a lumped element in the model as the closed chamber of the Stirling engine. In the analogy, the boundaries of this lumped element are the pistons of the chamber, and the kinematical mechanism of the reciprocating engine is the acoustic process in the pipes. The position of the pistons is fixed by studying the longitudinal heat transfer process and the mass conservation. The set of equations obtained can be solved by using the mathematical limit that represents the actual small movement of the pistons. The result is four linear algebraic equations that can be easily solved in several practical cases. One outcome of this approach is the selection of a few dimensionless design parameters useful for any configuration of the engine. Another outcome is a simplified method of calculating the initial power around a self-starting point of a thermoacoustic engine. Finally, the threshold of several thermoacoustic devices is calculated with the present model and compared with the experimental results reported in the scientific literature.
Ti
O
2
and HfO2 in electrolyte-oxide-silicon configuration for applications in bioelectronics
Authors: Wallrapp Frank , Fromherz Peter
Published: June 2006

We study the electrical properties of thin TiO2 films made by atomic layer deposition (ALD) on p-doped silicon in an electrolyte-oxide-silicon (EOS) configuration. The electrolyte contact of the TiO2∕Si heterostructure allows measurements of the differential capacitance for a wide range of bias voltages as they cannot be performed in a metal-oxide-silicon structure because of extensive leakage currents. In the accumulation region of p-silicon, we find a saturation of capacitance that decreases with oxide thickness, indicating an insulator with a dielectric constant of 34. In the inversion region of p-silicon, the capacitance increases in two steps far beyond the saturation capacitance. We assign this effect to the presence of electrons in TiO2 which is controlled by the bias voltage and by immobile positive charges at the TiO2∕Si interface: When the Fermi energy in p-silicon is raised to the level of the low lying conduction band of TiO2, electrons accumulate in two layers near the TiO2∕Si interface and at the electrolyte/TiO2 interface with a concomitantly enhanced differential capacitance. As a control, we study HfO2 films also made by ALD. We obtain a dielectric constant of 15 from the capacitance in the accumulation region of p-silicon. For HfO2 with a high lying conduction band, the capacitance decreases as expected in the inversion region for the high-frequency limit of silicon. The electrical characterization of TiO2 and HfO2 in EOS junctions opens future applications of high-κ materials in bioelectronics for efficient capacitive interaction of silicon chips and living cells.
Micromanipulation of high and low indices microparticles using a microfabricated double axicon
Authors: Ahluwalia B. P. S. , Yuan X.-C. , Tao S. H. , Cheong W. C. , Zhang L. S. , Wang H.
Published: June 2006

The technique of transferring the momentum of optical potential landscapes to control the kinetics of the microscopic particles has recently gained considerable interest. In this paper, we report the optical micromanipulations of high and low indices particles using an optical trapping system integrated with a micron-sized double axicon. A double axicon is used to generate a self-imaged bottle beam, a propagation invariant beam. The transverse intensity profile of the self-imaged bottle beam oscillates along the propagation axis embedding three-dimensional intensity-null points, which are unique to conventional beams used in tweezers-like Gaussian, Laguerre-Gaussian, and Bessel beams. By imaging different portions of a self-imaged bottle beam, the same tweezers system can easily be modified for trapping applications of high and low indices microparticles. Furthermore, the self-reconstruction property of a self-imaged bottle beam is numerically studied and the minimum self-reconstruction distance of an obstructed self-imaged bottle beam is determined.
Formation process of β-FeSi2∕Si heterostructure in high-dose Fe ion implanted Si
Authors: Ishimaru Manabu , Omae Keisuke , Bae In-Tae , Naito Muneyuki , Hirotsu Yoshihiko , Valdez James A. , Sickafus Kurt E.
Published: June 2006

We have performed high-dose iron (Fe) ion implantation into a single crystalline silicon (Si) substrate in order to synthesize a β-FeSi2∕Si heterostructure. Si(001) substrates were implanted with 120keV Fe ions at 623K to a fluence of 4×1017∕cm2, followed by thermal annealing at temperatures ranging from 773to1073K. Implantation-induced microstructures as well as annealing-induced ones were examined by means of x-ray diffraction (XRD) and transmission electron microscopy (TEM) in combination with energy-dispersive x-ray spectroscopy. Grazing-incidence XRD and cross-sectional TEM observations indicated that a continuous iron silicide layer consisting of ε-FeSi and β-FeSi2 is formed in as-implanted samples. With increasing annealing temperature the ε-FeSi phase transformed into the β-FeSi2 one, and finally a continuous β-FeSi2 polycrystalline layer was formed on the topmost layer of the Si substrate. Pole figure XRD measurements revealed that the β-FeSi2 crystallites are not randomly oriented but possess a preferred orientation. We discussed structural evolution upon thermal annealing as well as the damage recovery processes in high-dose Fe ion implanted Si.
Optical properties of aligned carbon nanotube mats for photonic applications
Authors: Zhao G. L. , Bagayoko D. , Yang L.
Published: June 2006

We studied the optical properties of the aligned carbon nanotube (16, 0), (10, 0), and (8, 4) mats for photonic device applications. We employed ab initio density functional potentials and utlized the linear combination of atomic orbital formalism. We calculated the electronic structure of the carbon nanotube mats and the real and imaginary parts of the dielectric functions as functions of the photon energy. The calculated dielectric functions of the aligned carbon nanotube mats show a strong anisotropy when the electric field of the light is parallel or perpendicular to the tube axes. Especially, there are strong peaks in the imaginary part of the dielectric function near the absorption edges, when the electric field of the light is parallel to the carbon nanotube axes. The unusual optical properties of the semiconducting carbon nanotube mats present an opportunity for applications in electro-optical devices in the infrared energy region.
Can true space-charge-limited currents be observed in π-conjugated polymers?
Authors: Gregg Brian A. , Gledhill Sophie E. , Scott Brian
Published: June 2006

The observation of space-charge-limited (SCL) currents in hole conductors requires that the hole density injected at the electrode, pinj, overwhelm the bulk free hole density pf. It also requires that any mobile ion density nion be insignificant. SCL currents are often claimed in amorphous films of π-conjugated polymers. However, we estimate pf in poly(p-phenylene-vinylene) derivatives from the conductivities and carrier mobilities as 1017–1019cm−3 and show that even if nion=0, the currents in π-conjugated polymers are often better described as Poole-Frenkel (PF) currents. When nion>0, even the PF model is an oversimplification.
Spectroscopic ellipsometry and absorption study of Zn1−xMnxO∕Al2O3 (0⩽x⩽0.08) thin films
Authors: Lee Ghil Soo , Lee Ho Suk , Kang Tae Dong , Lee Hosun , Liu C. , Xiao B. , Özgür Ü. , Morkoç H.
Published: June 2006

We grow Zn1−xMnxO∕Al2O3 (0⩽x⩽0.08) thin films on sapphire (0001) using radio-frequency sputtering deposition method with Ar and various N2 flow rates. We examine the effect of N2 codoping on the band gap and Mn-related midgap absorption of (Zn,Mn)O. Using spectroscopic ellipsometry, we measure pseudodielectric functions in the spectral range between 1 and 4.5eV. Using the model of Holden et al. [T. Holden et al., Phys. Rev. B 56, 4037 (1997)], we determine the uniaxial (Zn,Mn)O dielectric function and the E0 band-gap energy. The fitted band gap does not change appreciably with increasing Mn composition up to 2%. We find a very large broadening of both the E0 band gap and its exciton partner E0x peaks even for less than 2% of optically determined Mn composition. In ellipsometric spectra, we also find Mn-related 3eV optical structure. In particular, optical absorption spectra with varying N2 gas flow rate show that the Mn-related peak intensity decreases with increasing N2 flux. The decrease of the 3eV Mn-related peak intensity is attributed to increasing N2 flow rate and Mn–N hybridization.
Tetragonal I41∕amd crystal structure of Li3BN2 from dehydrogenated Li–B–N–H
Authors: Pinkerton F. E. , Herbst J. F.
Published: June 2006

We have determined the crystal structure of Li3BN2 formed by dehydrogenation of LiB0.33N0.67H2.67 from powder x-ray diffraction (XRD) data using the Rietveld method. XRD measurements indicate unambiguously that this Li3BN2 polymorph is distinct from any of the previously reported Li3BN2 phases. We find a body-centered tetragonal I41∕amd structure (space group No. 141 in the International Tables for X-ray Crystallography) with a=6.60Å and c=10.35Å. We also describe the results of first principles theoretical modeling of the body-centered tetragonal Li3BN2 polymorph as well as the tetragonal P42212 and monoclinic P21∕c Li3BN2 structures previously reported. We obtained excellent agreement between the theoretically calculated I41∕amd Li3BN2 lattice constants and atomic positions and those obtained experimentally from XRD. The approximate enthalpy of formation of the I41∕amd Li3BN2 phase is ΔH=−495kJ∕molef.u..
Comparison of overlap-based models for approximating the exchange-repulsion energy
Authors: Söderhjelm Pär , Karlström Gunnar , Ryde Ulf
Published: June 2006

Different ways of approximating the exchange-repulsion energy with a classical potential function have been investigated by fitting various expressions to the exact exchange-repulsion energy for a large set of molecular dimers. The expressions involve either the orbital overlap or the electron-density overlap. For comparison, the parameter-free exchange-repulsion model of the effective fragment potential (EFP) is also evaluated. The results show that exchange-repulsion energy is nearly proportional to both the orbital overlap and the density overlap. For accurate results, a distance-dependent correction is needed in both cases. If few parameters are desired, orbital overlap is superior to density overlap, but the fit to density overlap can be significantly improved by introducing more parameters. The EFP performs well, except for delocalized π systems. However, an overlap expression with a few parameters seems to be slightly more accurate and considerably easier to approximate.
Capillary force lithography with impermeable molds
Authors: Yoon Hyunsik , Kim Tae-il , Choi Sejin , Suh Kahp Y. , Kim M. Joon , Lee Hong H.
Published: June 2006

Capillary force lithography (CFL) with impermeable mold is presented. For the CFL to be operative over large area, either the mold or the substrate has to be flexible. With a silicon wafer mold and a flexible substrate, a repeated line and space pattern with a spacing of 30nm is shown to be well patterned. With a flexible mold and a hard substrate, a similar pattern with a spacing of 60nm is demonstrated by CFL. The flexibility is needed for the intimate contact that is required between the mold and the substrate for the capillarity to take hold over large area. The forte of CFL with impermeable mold lies in the fact that the driving force for the patterning, which is capillary force, increases with decreasing pattern size.
Mechanism of Hf-silicide formation at interface between poly-Si electrode and HfO2∕Si gate stacks studied by photoemission and x-ray absorption spectroscopy
Authors: Takahashi H. , Okabayashi J. , Toyoda S. , Kumigashira H. , Oshima M. , Ikeda K. , Liu G. L. , Liu Z. , Usuda K.
Published: June 2006

We have investigated the mechanism for silicidation by chemical reactions at polycrystalline-Si (poly-Si)∕HfO2∕Si gate stacks by annealing in ultrahigh vacuum using photoemission spectroscopy and x-ray absorption spectroscopy. Si 2p, Hf 4f, and O 1s high-resolution photoemission spectra have revealed that a Hf-silicide formation starts at as low temperature as 700°C and that a Hf silicate is also formed at the interface between poly-Si electrodes and HfO2. The metallic Hf silicide is formed at the interface between HfO2 and Si substrates, which changes the band offsets on Si substrates. We have found that poly-Si electrodes promote the interfacial reaction between HfO2 and Si substrates, while the crystallization in a HfO2 layer is independent of the silicide formation. The silicidation mechanism based on photoemission spectra is also confirmed from the thermodynamical analysis considering the Gibbs’ free energy.
Prediction among different spectroscopic properties for aqueous systems
Authors: Zhu Xiao , Yao Jia , Li Haoran , Han Shijun
Published: June 2006

Spectroscopic properties obtained by NMR and vibrational spectra both reflect the microscopic environment of solutions, and the local composition (LC) theory can be used to study environmental effects on spectroscopic properties. Based on the LC model, the relationship between NMR and vibrational spectra, including infrared (IR) spectroscopy and Raman, were investigated. For the aqueous systems—water+N, N-dimethylformamide, water+acetone, water+methanol, and water+ethanol, we performed prediction between concentration-dependent peak positions of IR and Raman, as well as between concentration-dependent vibrational properties and H1 NMR chemical shifts. The results showed that reliable prediction could be achieved with the help of the LC model. This suggests that H1 NMR chemical shifts and vibrational spectroscopic properties may tell us the same story about the local environment encountered in solution.
Rotationally resolved S1←S electronic spectra of fluorene, carbazole, and dibenzofuran: Evidence for Herzberg-Teller coupling with the S2 state
Authors: Yi John T. , Alvarez-Valtierra Leonardo , Pratt David W.
Published: June 2006

Rotationally resolved fluorescence excitation spectra of the S1←S0 origin bands and higher vibronic bands of fluorene (FLU), carbazole (CAR), and dibenzofuran (DBF) have been observed and assigned. Analyses of these data show that replacement of the CH2 group in FLU with a NH group in CAR and an O atom in DBF produces only localized changes in structure, in the ground state. But the three molecules exhibit different changes in geometry when they are excited by light. The S1 states of the three molecules also are electronically very different. The S1←S0 transition moments of CAR and DBF are parallel to the C2 symmetry axis whereas the corresponding transition moment in FLU is perpendicular to this axis. Herzberg-Teller coupling involving the S2 state also has been observed in the spectra of higher vibronic bands of CAR and DBF. Possible reasons for these behaviors are discussed.
Ultrafast photoluminescence in silicon nanocrystals studied by femtosecond up-conversion technique
Authors: Trojánek F. , Neudert K. , Malý P. , Dohnalová K. , Pelant I.
Published: June 2006

Photoluminescence dynamics in silicon nanocrystals measured by a femtosecond up-conversion technique are reported. The samples were prepared by embedding porous silicon grains in a sol-gel derived SiO2 matrix. Efficient initial relaxation of the excess energy of photoexcited carriers with the effective rate ⩾3.8eV∕ps was observed. A fast decay component (400fs) of the photoluminescence signal was found and interpreted in terms of quenching the interior exciton radiative recombination by carrier trapping on the nanocrystal surface. The ultrafast photoluminescence dynamics are followed by a microsecond decay of the stretched-exponential type.
Vibrational predissociation of H5+
Authors: Špirko Vladimír , Amano Takayoshi , Kraemer Wolfgang P.
Published: June 2006

The full nine-dimensional vibrational Hamiltonian for H5+ described in the literature [Kraemer et al., J. Mol. Spectrosc. 164, 500 (1994)] is adopted here for an approximate evaluation of the spectral linewidths of the observed H–H stretching modes of the H5+ ion and the corresponding modes of its D5+ isotopomer. In this approximation the high dimensionality of the original Hamiltonian is reduced to a three-dimensional model Hamiltonian which takes only the H–H stretching modes and the molecular dissociation mode into consideration assuming that they are adiabatically separable from the remaining modes. To make the calculations numerically feasible, the molecular degenerate (“skeletal”) vibrations are assumed to take place in harmonic potentials, and the effect of the internal propeller rotation is completely disregarded. The linewidths calculated in this approximation are too small to explain the broad shapes of the observed spectral transitions. It can thus be argued that the failure to resolve rotational structure in the observed bands is mainly due to spectral congestion and only partly due to predissociation of the H5+ cluster.
A speculative study of 2∕3-order fractional Laplacian modeling of turbulence: Some thoughts and conjectures
Authors: Chen Wen
Published: June 2006

This study makes the first attempt to use the 2∕3-order fractional Laplacian modeling of Kolmogorov −5∕3 scaling of fully developed turbulence and enhanced diffusing movements of random turbulent particles. Nonlinear inertial interactions and molecular Brownian diffusivity are considered to be the bifractal mechanism behind multifractal scaling of moderate Reynolds number turbulence. Accordingly, a stochastic equation is proposed to describe turbulence intermittency. The 2∕3-order fractional Laplacian representation is also used to model nonlinear interactions of fluctuating velocity components, and then we conjecture a fractional Reynolds equation, underlying fractal spacetime structures of Lévy 2∕3 stable distribution and the Kolmogorov scaling at inertial scales. The new perspective of this study is that the fractional calculus is an effective approach to modeling the chaotic fractal phenomena induced by nonlinear interactions.
Point interactions in acoustics: One-dimensional models
Authors: Cacciapuoti C. , Figari R. , Posilicano A.
Published: June 2006

A one-dimensional system made up of a compressible fluid and several mechanical oscillators, coupled to the acoustic field in the fluid, is analyzed for different settings of the oscillator array. The dynamical models are formulated in terms of singular perturbations of the decoupled dynamics of the acoustic field and the mechanical oscillators. Detailed spectral properties of the generators of the dynamics are given for each model we consider. In the case of a periodic array of mechanical oscillators it is shown that the energy spectrum presents a band structure.
On the E to H and H to E transition mechanisms in inductively coupled plasma
Authors: Lee Min-Hyong , Chung Chin-Wook
Published: June 2006

Inductively coupled plasmas (ICP) exhibit two mode operations of capacitive coupling (E mode) and inductive coupling (H mode), and the density jump and hysteresis have been reported during the transition between these modes. In this study, the total power transferred to the plasma by capacitive and inductive coupling is calculated from Maxwell’s equations and global model, and from this, conditions required for stable E and H mode operations are obtained. The E to H and the H to E transitions occur when the system reaches critical electron densities. Analytical criterion for stable H mode operation that the skin depth should be smaller than 23R at low pressure, and 23(ω∕ν)R at high pressure is derived from the calculation. The dependence of transition electron densities and powers of E to H and H to E transitions on the pressure and discharge dimension is also discussed.
Extraction of large-scale coherent structure from plasma turbulence using rake probe and wavelet analysis in a tokamak
Authors: Xu G. S. , Wan B. N. , Zhang W.
Published: June 2006

In fusion plasmas, intermittently occurring large-scale coherent structures in electrostatic turbulence sometimes contribute more than 50% of total transport, so the investigation on these coherent structures is important for understanding plasma confinement. New experimental techniques are required to extract these coherent structures from fluctuating signals. In this work a 12-tip poloidal rake probe was used on the HT-7 superconducting tokamak to measure plasma turbulence in the plasma edge region. Several signal analysis methods based on a biorthogonal wavelet were developed and applied to the probe data. Since the structure of the selected wavelet is every similar to that of the turbulence wave packet, information about large-scale coherent structures can be selectively extracted from the ambient turbulence. The spatiotemporal patterns of the large-scale coherent structures were reconstructed using the selected wavelets as well as those of small-scale details. These wavelet-based techniques can be applied to all kinds of plasma fluctuation diagnostics, so they possibly present a new opportunity for uncovering the mechanism underlying plasma turbulent transport.
Improving confinement in quasi-axisymmetric stellarators
Authors: Mynick H. E. , Boozer A. H. , Ku L. P.
Published: June 2006

The confinement characteristics of some related quasi-axisymmetric stellarator (QA) designs are compared to gain more physical understanding of what causes the differences in their transport. From this, some general rules are found for features of QA magnetic geometries that are deleterious or helpful for confinement.
Initial measurement of the kinetic dust temperature of a weakly coupled dusty plasma
Authors: Williams Jeremiah D. , Thomas Edward
Published: June 2006

Measurements of the velocity space distribution function of 2.9μm diameter silica particles in an argon dc glow discharge dusty plasma are made through the use of stereoscopic particle image velocimetry (stereo-PIV). These distribution functions are then used to determine the kinetic temperature of the dust component. These measurements show that the kinetic temperature of the dust component is significantly larger than the other plasma components (electrons, ions, and background neutrals).
Infrared intensity in small ammonia and water clusters
Authors: Slipchenko Mikhail N. , Kuyanov Kirill E. , Sartakov Boris G. , Vilesov Andrey F.
Published: June 2006

Helium droplet technique has been used in order to measure the strength of the infrared absorption in small ammonia and water clusters as a function of size. Hydrogen bonding in ammonia and water dimers causes an enhancement of the intensity of the hydrogen stretching bands by a factor of four and three, respectively. Two types of the hydrogen bonded clusters show different size dependence of the infrared intensity per hydrogen bond. In ammonia (NH3)2 and (NH3)3 it is close to the crystal value. In water clusters, it increases monotonically with cluster size being in tetramers, a factor of two smaller than in the ice. The measured infrared intensity in water clusters is found to be a factor of two to three smaller as compared to the results of numerical calculations.
Regulation of large dense-core vesicle volume and neurotransmitter content mediated by adaptor protein 3
Authors: Grabner Chad P. , Price Steven D. , Lysakowski Anna , Cahill Anne L. , Fox Aaron P.
Published: June 2006

Adaptor protein 3 (AP-3) is a vesicle-coat protein that forms a heterotetrameric complex. Two types of AP-3 subunits are found in mammalian cells. Ubiquitous AP-3 subunits are expressed in all tissues of the body, including the brain. In addition, there are neuronal AP-3 subunits that are thought to serve neuron-specific functions such as neurotransmitter release. In this study, we show that overexpression of neuronal AP-3 in mouse chromaffin cells results in a striking decrease in the neurotransmitter content of individual vesicles (quantal size), whereas deletion of all AP-3 produces a dramatic increase in quantal size; these changes were correlated with alterations in dense-core vesicle size. AP-3 appears to localize in the trans-Golgi network and possibly immature secretory vesicles, where it may be involved in the formation of neurosecretory vesicles.
The consensus mechanics of cultured mammalian cells
Authors: Hoffman Brenton D. , Massiera Gladys , Van Citters Kathleen M. , Crocker John C.
Published: June 2006

Although understanding cells' responses to mechanical stimuli is seen as increasingly important for understanding cell biology, how to best measure, interpret, and model cells' mechanical properties remains unclear. We determine the frequency-dependent shear modulus of cultured mammalian cells by using four different methods, both unique and well established. This approach clarifies the effects of cytoskeletal heterogeneity, ATP-dependent processes, and cell regional variations on the interpretation of such measurements. Our results clearly indicate two qualitatively similar, but distinct, mechanical responses, corresponding to the cortical and intracellular networks, each having an unusual, weak power-law form at low frequency. The two frequency-dependent responses we observe are remarkably similar to those reported for a variety of cultured mammalian cells measured with different techniques, suggesting it is a useful consensus description. Finally, we discuss possible physical explanations for the observed mechanical response.
Recruitment of mRNA cleavage/polyadenylation machinery by the yeast chromatin protein Sin1p/Spt2p
Authors: Hershkovits Gitit , Bangio Haim , Cohen Ronit , Katcoff Don J.
Published: June 2006

The yeast chromatin protein Sin1p/Spt2p has long been studied, but the understanding of its function has remained elusive. The protein has sequence similarity to HMG1, specifically binds crossing DNA structures, and serves as a negative transcriptional regulator of a small family of genes that are activated by the SWI/SNF chromatin-remodeling complex. Recently, it has been implicated in maintaining the integrity of chromatin during transcription elongation. Here we present experiments whose results indicate that Sin1p/Spt2 is required for, and is directly involved in, the efficient recruitment of the mRNA cleavage/polyadenylation complex. This conclusion is based on the following findings: Sin1p/Spt2 frequently binds specifically downstream of many ORFs but almost always upstream of the first polyadenylation site. It directly interacts with Fir1p, a component of the cleavage/polyadenylation complex. Disruption of Sin1p/Spt2p results in foreshortened poly(A) tracts on mRNA. It is synthetically lethal with Cdc73p, which is involved in the recruitment of the complex. This report shows that a chromatin component is involved in 3′ end processing of RNA.
Allosteric mechanism in AMPA receptors: A FRET-based investigation of conformational changes
Authors: Ramanoudjame Gomathi , Du Mei , Mankiewicz Kimberly A. , Jayaraman Vasanthi
Published: June 2006

α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are the primary mediators of fast excitatory synaptic transmission in the mammalian CNS. Structures of the extracellular ligand-binding domain suggest that the extent of cleft closure in the ligand-binding domain controls the extent of activation of the receptor. Here we have developed a fluorescence resonance energy transfer-based probe that allows us to study the extent of cleft closure in the isolated ligand-binding domain in solution. These investigations show that the wild-type protein exhibits a graded cleft closure that correlates to the extent of activation, which is in qualitative agreement with the crystal structures. However, the changes in extent of cleft closure between the apo and agonist-bound states are smaller than that observed in the crystal structures. We have also used this method to study the L650T mutant and show that in solution the α-amino-5-methyl-3-hydroxy-4-isoxazole propionate-bound form of this mutant exists primarily in a conformation that is more closed than predicted based on the activity, indicating that the degree of cleft closure alone cannot be used as a measure of extent of activation of the receptor, and there are possibly other mechanisms in addition to cleft closure that mediate the subtleties in extent of activation by a given agonist.
Cleaver: software for identifying taxon specific restriction endonuclease recognition sites
Authors: Jarman Simon N.
Published: June 2006

Summary: Cleaver is an application for identifying restriction endonuclease recognition sites that occur in some taxa but not in others. Differences in DNA fragment restriction patterns among taxa are the basis for many diagnostic assays for taxonomic identification and are used in procedures for removing the DNA of some taxa from pools of DNA from mixed sources. Cleaver analyses restriction digestion of groups of orthologous DNA sequences simultaneously to allow identification of differences in restriction pattern among the fragments derived from different taxa.

Availability: Cleaver is freely available without registration from its website () and can be copied, modified and re-distributed under the terms of the GNU general public licence version2 (). The program can be run as a script for computers that have Python 2.3 and necessary extra modules installed. This allows it to run on Gnu/Linux, Unix, MacOSX and Windows platforms. Stand-alone executable versions for Windows and MacOSX operating systems are available.

Contact:  simon.jarman@aad.gov.au
DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance
Authors: Brézellec Pierre , Hoebeke Mark , Hiet Marie-Sophie , Pasek Sophie , Ferat Jean-Luc
Published: June 2006

Motivation: The Dam methyltransferase (DamMT) activity, broadly distributed in association with restriction endonucleases, as part of the restriction-modification defense systems, has evolved to become intimately associated with essential biological functions in a few organisms. In Escherichia coli, DamMT is involved in multiple aspects of DNA maintenance, replication initiation, daughter chromosome segregation, DNA mismatch repair, gene expression control, etc.

The participation of DamMT in such a diverse set of functions required that other genes adapted, or emerged through evolution, in response to the DamMT-induced modification of the genomic environment. One example is SeqA, a protein that senses the methylation status of the origin of replication of the chromosome to control the timing of replication initiation.

Interestingly, seqA is only present in a few DamMT-specifying proteobacteria. This observation led us to hypothesize that other genes, specifying related functions, might also be found in these organisms. To test this hypothesis, we implemented a large-scale comparative genomic screen meant to identify genes specifying DNA methylation sensing domains, probably involved in DNA maintenance functions.

Results: We carried out a phylogenetic analysis of DamMT, identifying two contrasting behaviors of the protein. Based on this phylogeny, we defined precisely a set of genomes, in which the protein activity is likely to be involved in DNA maintenance functions, the ‘resident’ dam genomes. We defined a second set of genomes, in which DamMT is not resident. We developped a new tool, ‘DomainSieve’, in order to screen these two sets for protein domains that are strictly associated with ‘resident’ dam genomes.

This approach was rewarding and generated a list of genes, among which some, at least, specify activities with clear linkage to DamMT-dependent DNA methylation and DNA maintenance.

Availability: DomainSieve is implemented as a web resource and is accessible at

Contact:  ferat@cgm.cnrs-gif.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
An analytical model for the energetics of quantum dots: beyond the small slope assumption
Authors: Gill S.P.A , Cocks A.C.F
Published: June 2006

Analytical models for strained heteroepitaxial quantum dot systems have invariably assumed that the dots have a low-aspect ratio (small slopes) and that the elastic properties of the dot and the substrate are identical. In this paper, a three-dimensional analytical model for the energetics of an array of axisymmetric quantum dots is developed from physical principles. This is valid for high-aspect ratio dots (such as GeSi and InGaAs) and allows the dot and substrate to have different elastic properties. It is shown that these features are very important in determining the strain energy of both isolated dots and arrays of interacting dots. Both the elastic relaxation energy (per unit volume) of a single dot and the elastic interaction energy (per unit volume) between multiple dots are found to be greatest for tall, steep dots and for dots which are stiffer than the substrate. The equilibrium of two-facet dots is investigated and shape transition phase diagrams for small slope monoelastic theory, GeSi and InGaAs are compared. Different features of the bimodal dot size distributions in these systems are explained.
Vertical jumping performance of bonobo (Pan paniscus) suggests superior muscle properties
Authors: Scholz Melanie N , D'Août Kristiaan , Bobbert Maarten F , Aerts Peter
Published: June 2006

Vertical jumping was used to assess muscle mechanical output in bonobos and comparisons were drawn to human jumping. Jump height, defined as the vertical displacement of the body centre of mass during the airborne phase, was determined for three bonobos of varying age and sex. All bonobos reached jump heights above 0.7 m, which greatly exceeds typical human maximal performance (0.3–0.4 m). Jumps by one male bonobo (34 kg) and one human male (61.5 kg) were analysed using an inverse dynamics approach. Despite the difference in size, the mechanical output delivered by the bonobo and the human jumper during the push-off was similar: about 450 J, with a peak power output close to 3000 W. In the bonobo, most of the mechanical output was generated at the hips. To account for the mechanical output, the muscles actuating the bonobo's hips (directly and indirectly) must deliver muscle-mass-specific power and work output of 615 W kg−1and 92 J kg−1, respectively. This was twice the output expected on the basis of muscle mass specific work and power in other jumping animals but seems physiologically possible. We suggest that the difference is due to a higher specific force (force per unit of cross-sectional area) in the bonobo.
Sexual segregation of seasonal foraging habitats in a non-migratory marine mammal
Authors: Breed Greg A , Bowen W.D , McMillan J.I , Leonard M.L
Published: June 2006

Many animal species segregate by sex. Such segregation may be social in nature, or ecological, or both. Grey seals (Halichoerus grypus), like many large mammals, are sexually size dimorphic. In size dimorphic species, allometric differences in morphology, metabolic rate and reproductive costs are likely. Such differences may require the sexes to use different foraging strategies or different habitats. To investigate sexual segregation of habitat in grey seals, we used satellite tracks from 95 (male 46; female 49) adults breeding at Sable Island, Nova Scotia (44 °N, 60 °W) collected from 1995 to 2005. Location estimates were made from satellite fixes using a state-space movement model to estimate true locations and regularize them in time. Location estimates were used to calculate home range kernels of male and female habitat use each month. Month by sex kernel home ranges revealed striking differences and dynamics in habitat use between males and females on spatial scales broader than most terrestrial examples and at temporal and spatial resolutions rarely available for marine species. Differences were most pronounced just before (October–December) and immediately after breeding (February–March). During both periods, males primarily used areas along the continental shelf break, while females mainly used mid-shelf regions. Coupled with previously identified sex-specific seasonal patterns of energy storage, diving and diet, our findings suggest that males and females differ profoundly in their spatial foraging strategies. These differences may serve to maximize fitness by reducing intersexual competition during key foraging periods.
Experimental demonstration of the antiherbivore effects of silica in grasses: impacts on foliage digestibility and vole growth rates
Authors: Massey Fergus P , Hartley Sue E
Published: June 2006

The impact of plant-based factors on the population dynamics of mammalian herbivores has been the subject of much debate in ecology, but the role of antiherbivore defences in grasses has received relatively little attention. Silica has been proposed as the primary defence in grasses and is thought to lead to increased abrasiveness of foliage so deterring feeding, as well as reducing foliage digestibility and herbivore performance. However, at present there is little direct experimental evidence to support these ideas. In this study, we tested the effects of manipulating silica levels on the abrasiveness of grasses and on the feeding preference and growth performance of field voles, specialist grass-feeding herbivores. Elevated silica levels did increase the abrasiveness of grasses and deterred feeding by voles. We also demonstrated, for the first time, that silica reduced the growth rates of both juvenile and mature female voles by reducing the nitrogen they could absorb from the foliage. Furthermore, we found that vole feeding leads to increased levels of silica in leaves, suggesting a dynamic feedback between grasses and their herbivores. We propose that silica induction due to vole grazing reduces vole performance and hence could contribute to cyclic dynamics in vole populations.
FeminizingWolbachiainZyginidia pullula(Insecta, Hemiptera), a leafhopper with an XX/X0 sex-determination system
Authors: Negri I , Pellecchia M , Mazzoglio P.J , Patetta A , Alma A
Published: June 2006

Zyginidia pullulais a grass-dwelling leafhopper characterized by a bisexual reproduction mode. In this species, some females collected in Northern Italy, when mated with males, gave origin to an exclusively female brood. Here, we demonstrated that in these lineages an infection by a new strain ofWolbachia pipientis—designated aswZygpul—was detected by amplifying and sequencing thewspand 16S rRNA genes. About half of the female progeny were characterized by intersexual phenotypes, i.e. showing upper pygofer appendages, a typical male secondary sexual feature. The karyological analysis proved that while phenotypically normal females had a female genotype, those with upper pygofer appendages had a male genotype and were thus feminized males.

The complete removal ofW. pipientisafter tetracycline treatment of morphologically normal females, and the consequent re-appearance of males in the brood, permitted us to connect the feminizing effect with the presence of the bacterium. This is the first case of feminization byW. pipientisin an XX/X0 sex-determination system, and is the second case reported in insects.
Modulation of appetite by gonadal steroid hormones
Authors: Asarian Lori , Geary Nori
Published: June 2006

Several sex differences in eating, their control by gonadal steroid hormones and their peripheral and central mediating mechanisms are reviewed. Adult female rats and mice as well as women eat less during the peri-ovulatory phase of the ovarian cycle (estrus in rats and mice) than other phases, an effect under the control of cyclic changes in estradiol secretion. Women also appear to eat more sweets during the luteal phase of the cycle than other phases, possibly due to simultaneous increases in estradiol and progesterone. In rats and mice, gonadectomy reveals further sex differences: orchiectomy decreases food intake by decreasing meal frequency and ovariectomy increases food intake by increasing meal size. These changes are reversed by testosterone and estradiol treatment, respectively. A variety of peripheral feedback controls of eating, including ghrelin, cholecystokinin (CCK), glucagon, hepatic fatty acid oxidation, insulin and leptin, has been shown to be estradiol-sensitive under at least some conditions and may mediate the estrogenic inhibition of eating. Of these, most progress has been made in the case of CCK. Neurons expressing estrogen receptor-α in the nucleus tractus solitarius of the brainstem appear to increase their sensitivity to CCK-induced vagal afferent input so as to lead to an increase in the satiating potency of CCK, and consequently decreased food intake, during the peri-ovulatory period in rats. Central serotonergic mechanisms also appear to be part of the effect of estradiol on eating. The physiological roles of other peripheral feedback controls of eating and their central mediators remain to be established.