bluuebunny/crossref_metadata_2025 huggingface dataset:
An isomerization-induced cage-breaking process in a molecular glass former below Tg
Authors: Teboul V. , Saiddine M. , Nunzi J.-M. , Accary J.-B.
Published: March 2011

A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials.
Perpendicular-bias-field-dependent vortex-gyration eigenfrequency
Authors: Yoo Myoung-Woo , Lee Ki-Suk , Han Dong-Soo , Kim Sang-Koog
Published: March 2011

We found that the angular frequency ω0 of vortex-core gyrations is controllable by the application of static perpendicular bias fields Hp as studied by micromagnetic simulations and Thiele’s-approach-based quantitative interpretation. The observed linear dependence of ω0 on Hp could be explained in terms of the dynamic variables of the vortex, the gyrovector constant G, and the potential stiffness constant κ, for cases of negligible damping. Here we calculated the values of G and κ as a function of Hp directly from the simulation numerical data using Thiele’s equivalent force equations, providing a more correct understanding of the remarkable change of ω0 with Hp. This micromagnetic-simulation-based quantitative analysis is a straightforward, accurate, and effective means of understanding vortex dynamics in nanoscale magnetic elements.
Dispersion interaction in hydrogen-chain models
Authors: Liu Ru-Fen , Ángyán János G. , Dobson John F.
Published: March 2011

We have investigated the dispersion interaction in hydrogen chain models via density functional theory-based symmetry-adapted perturbation theory using the asymptotically corrected PBE0 energy functional. The quasimetallic and the insulating prototype systems were chosen to be hydrogen chains with equally and alternately spaced H2 units, respectively. The dependence of the dispersion energy on the chain length for quasimetallic and insulating cases has been determined for two chains arranged either in pointing or in parallel geometries. The results are compared with those previously calculated from a continuum coupled-plasmon approach [Phys. Rev. B 77, 075436 (2008)]. The interaction energy has also been modeled by pairwise summations over short fragments of the chains, demonstrating the failure of the additivity principle for the quasimetallic case, while confirming that the additivity is a qualitatively reasonable hypothesis for the insulating case.
Bond alternation, polarizability, and resonance detuning in methine dyes
Authors: Olsen Seth , McKenzie Ross H.
Published: March 2011

We derive structure–property relationships for methine (“Brooker”) dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J. R. Platt, J. Chem. Phys. 25, 80 (1956)] can also be distinguished by their single–double bond alternation and by their charge localization character. These assumptions are independent of the primary constraint that defines the diabatic states in the Platt model-–specifically, the Brooker deviation rule for methine dyes [L. G. S. Brooker, Rev. Mod. Phys. 14, 275 (1942)]. Taking these assumptions, we show that the Platt model offers an alternate route to known structure–property relationships between the bond length alternation and the quadratic nonlinear polarizability β. We show also that the Platt model can be parameterized without the need for synthesis of the symmetric parents of a given dye, using the dipole data obtained through spectroscopic measurements. This suggests that the Platt model parameters may be used as independent variables in free-energy relationships for chromophores whose symmetric parents cannot be synthesized or chromophores strongly bound to biomolecular environments. The latter category includes several recently characterized biomolecular probe constructs. We illustrate these concepts by an analysis of previously reported electroabsorption and second-harmonic generation experiments on green fluorescent proteins.
Phase transitions of two-dimensional dipolar fluids in external fields
Authors: Schmidle Heiko , Klapp Sabine H. L.
Published: March 2011

In this work, we study condensation phase transitions of two-dimensional Stockmayer fluids under additional external fields using Monte-Carlo (MC) simulations in the grand-canonical ensemble. We employ two recently developed methods to determine phase transitions in fluids, namely Wang–Landau (WL) MC simulations and successive-umbrella (SU) sampling. Considering first systems in zero field (and dipolar coupling strengths μ2/εσ3 ⩽ 6), we demonstrate that the two techniques yield essentially consistent results but display pronounced differences in terms of efficiency. Indeed, comparing the computation times for these systems on a qualitative level, the SU sampling turns out to be significantly faster. In the presence of homogeneous external fields, however, the SU method becomes plagued by pronounced sampling difficulties, yielding the calculation of coexistence lines essentially impossible. Employing the WL scheme, on the other hand, we find phase coexistence even for strongly field-aligned systems. The corresponding critical temperatures are significantly shifted relative to the zero-field case.
A multicolor microfluidic droplet dye laser with single mode emission
Authors: Aubry G. , Kou Q. , Soto-Velasco J. , Wang C. , Meance S. , He J. J. , Haghiri-Gosnet A. M.
Published: March 2011

A digital microfluidic dye laser that integrates a Fabry–Perot cavity with two fiber-based mirrors is shown to exhibit a single mode emission. In addition, fast switching is achieved via the alternation of droplet streams that contain two different dyes. Single-longitudinal-mode emission is observed for each dye wavelength (at 565 and 586 nm) with a linewidth narrower than 0.12 nm. This system appears thus well suited for on-chip spectroscopy and flow cytometry.
Liquid structure of 1-alkyl-3-methylimidazolium-hexafluorophosphates by wide angle x-ray and neutron scattering and molecular dynamics
Authors: Macchiagodena Marina , Gontrani Lorenzo , Ramondo Fabio , Triolo Alessandro , Caminiti Ruggero
Published: March 2011

We report for the first time joined energy dispersed x-ray and neutron diffraction experiments on a series of (both protiated and selectively deuteriated) 1-alkyl-3-methylimidazolium hexafluorophosphate salts (alkyl = butyl, hexyl, octyl) at ambient conditions. The x-ray experimental data are used to optimize the interaction potential used for running molecular dynamics simulations on these systems. Such a potential leads to a good description of neutron scattering data from the samples without additional refinement, thus further validating the potential definition. The molecular dynamics simulations were used to access microscopic information on the morphology of the proposed systems, thus probing the role played by alkyl chain length on the structure. The comparison of x-ray weighted and neutron-weighted computed diffraction patterns allows the rationalization of several diffraction features. Further insight into cation–anion coordination and alkyl chain conformational equilibrium is provided on the basis of the MD-derived snapshots, confirming and extending previously obtained results on these issues.
Quantum decoherence in finite size exciton–phonon systems
Authors: Pouthier Vincent
Published: March 2011

Based on the operatorial formulation of the perturbation theory, the properties of a confined exciton coupled with phonons in thermal equilibrium is revisited. Within this method, the dynamics is governed by an effective Hamiltonian which accounts for exciton–phonon entanglement. The exciton is dressed by a virtual phonon cloud whereas the phonons are clothed by virtual excitonic transitions. Special attention is thus paid for describing the time evolution of the excitonic coherences at finite temperature. As in an infinite lattice, temperature-enhanced quantum decoherence takes place. However, it is shown that the confinement softens the decoherence. The coherences are very sensitive to the excitonic states so that the closer to the band center the state is located, the slower the coherence decays. In particular, for odd lattice sizes, the coherence between the vacuum state and the one-exciton state exactly located at the band center survives over an extremely long time scale. A superimposition involving the vacuum and this specific one-exciton state behaves as an ideal qubit insensitive to its environment.
Fluid simulations of frequency effects on nonlinear harmonics in inductively coupled plasma
Authors: Si Xue-Jiao , Zhao Shu-Xia , Xu Xiang , Bogaerts A. , Wang You-Nian
Published: March 2011

A fluid model is self-consistently established to investigate the harmonic effects in an inductively coupled plasma, where the electromagnetic field is solved by the finite difference time domain technique. The spatiotemporal distribution of harmonic current density, harmonic potential, and other plasma quantities, such as radio frequency power deposition, plasma density, and electron temperature, have been investigated. Distinct differences in current density have been observed when calculated with and without Lorentz force, which indicates that the nonlinear Lorentz force plays an important role in the harmonic effects, especially at low frequencies. Moreover, the even harmonics are larger than the odd harmonics both in the current density and the potential. Finally, the dependence of various plasma quantities with and without the Lorentz force on various driving frequencies is also examined. It is shown that the deposited power density decreases and the depth of penetration increases slightly because of the Lorentz force. The electron density increases distinctly while the electron temperature remains almost the same when the Lorentz force is taken into account.
[1 + 1] photodissociation of ${\rm CS}_{\rm 2}^ + (\tilde X{}^{\rm 2}\Pi _g)$CS2+(X̃2Πg) via the vibrationally mediated $\tilde B^{\rm 2} \Sigma _u^ +$B̃2Σu+ state: Multichannels exhibiting and mode specific dynamics
Authors: Li Jialin , Zhang Cuimei , Zhang Qun , Chen Yang , Huang Cunshun , Yang Xueming
Published: March 2011

Dissociation dynamics of ${\rm CS}_{\rm 2}^ +$ CS 2+ vibrationally mediated via its $\tilde B{}^2\Sigma _u^ +$B̃2Σu+ state, was studied using the time-sliced velocity map imaging technique. The parent ${\rm CS}_{\rm 2}^ +$ CS 2+ cation was prepared in its $\tilde X{}^2\Pi _g$X̃2Πg ground state through a [3 + 1] resonance enhanced multiphoton ionization process, via the 4pσ3Πu intermediate Rydberg state of neutral CS2 molecule at 483.14 nm. ${\rm CS}_{\rm 2}^ +$ CS 2+($\tilde X{}^2\Pi _g$X̃2Πg) was dissociated by a [1 + 1] photoexcitation mediated via the vibrationally selected $\tilde B$B̃ state over a wavelength range of 267–283 nm. At these wavelengths the $\tilde C{}^2\Sigma _g^ +$C̃2Σg+ and $\tilde D{}^2\Sigma _u^ +$D̃2Σu+ states are excited, followed by numerous S+ and CS+ dissociation channels. The S+ channels specified as three distinct regions were shown with vibrationally resolved structures, in contrast to the less-resolved structures being presented in the CS+ channels. The average translational energy releases were obtained, and the S+/CS+ branching ratios with mode specificity were measured. Two types of dissociation mechanisms are proposed. One mechanism is the direct coupling of the $\tilde C$C̃ and $\tilde D$D̃ states with the repulsive satellite states leading to the fast photofragmentation. The other mechanism is the internal conversion of the $\tilde C$C̃ and $\tilde D$D̃ states to the $\tilde B$B̃ state, followed by the slow fragmentation occurred via the coupling with the repulsive satellite states.
A regularity criterion for the three-dimensional nematic liquid crystal flow in terms of one directional derivative of the velocity
Authors: Liu Qiao , Zhao Jihong , Cui Shangbin
Published: March 2011

In this paper we provide a sufficient condition for regularity of solutions to the 3D nematic liquid crystal flow in the entire space in terms of one directional derivative of the velocity field. More precisely, we prove that if ∂3u belongs to \documentclass[12pt]{minimal}\begin{document}$L^{\beta }(0,T;L^{\alpha }(\mathbb {R}^{3}))$\end{document}Lβ(0,T;Lα(R3)) with \documentclass[12pt]{minimal}\begin{document}$\frac{3}{\alpha }+\frac{2}{\beta }\le 1$\end{document}3α+2β≤1 and α > 3, then the solution (u, d) is regular.
Quantum vibrational analysis and infrared spectra of microhydrated sodium ions using an ab initio potential
Authors: Kamarchik Eugene , Wang Yimin , Bowman Joel M.
Published: March 2011

We present a full-dimensional potential energy surface and a dipole moment surface (DMS) for hydrated sodium ion. These surfaces are based on an n-body expansion for both the potential energy and the dipole moment, truncated at the two-body level for the H2O–Na+ interaction and also for the DMS. The water–water interaction is truncated at the three-body level. The new full-dimensional two-body H2O–Na+ potential is a fit to roughly 20 000 coupled-cluster single double (triple)/aug-cc-pVTZ energies. Properties of this two-body potential and the potential describing (H2O)nNa+ clusters, with n up to 4 are given. We then report anharmonic, coupled vibrational calculations with the “local-monomer model” to obtain infrared spectra and also 0 K radial distribution functions for these clusters. Some comparisons are made with the recent infrared predissociation spectroscopy experiments of Miller and Lisy [J. Am. Chem. Soc. 130, 15381 (2008).]
First principles predictions of thermophysical properties of refrigerant mixtures
Authors: Oakley Mark T. , Do Hainam , Hirst Jonathan D. , Wheatley Richard J.
Published: March 2011

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.
A non-Abelian SO(8) monopole as generalization of Dirac-Yang monopoles for a 9-dimensional space
Authors: Le Van-Hoang , Nguyen Thanh-Son
Published: March 2011

We establish an explicit form of a non-Abelian SO(8) monopole in a 9-dimensional space and show that it is indeed a direct generalization of Dirac and Yang monopoles. Using the generalized Hurwitz transformation, we have found a connection between a 16-dimensional harmonic oscillator and a 9-dimensional hydrogenlike atom in the field of the SO(8) monopole (MICZ-Kepler problem). Using the built connection the group of dynamical symmetry of the 9-dimensional MICZ-Kepler problem is found as SO(10, 2).
Colloidal quantum dot photodetectors enhanced by self-assembled plasmonic nanoparticles
Authors: Huang Ludan , Tu Chang-Ching , Lin Lih Y.
Published: March 2011

Self-assembled colloidal plasmonic silver nanoparticles monolayers were integrated into solution-processed colloidal quantum dot (QD) photodetectors. We observed plasmon enhancement of photodetector responsivity over a board spectrum range (400–600 nm), with a 1.2–1.6 fold enhancement for a 440-nm-thick QD film device and a 2.4–3.3 fold enhancement for a 100-nm-thick QD device. The enhancement behavior was wavelength dependent with higher enhancement factor at longer wavelengths. The origins of responsivity enhancement were discussed.
Plasmonic concentrators for enhanced light absorption in ultrathin film organic photovoltaics
Authors: Ostfeld A. E. , Pacifici D.
Published: March 2011

We report on experimental absorption enhancement in 24 and 150-nm-thick bulk heterojunctions of the conducting polymer poly(3-hexylthiophene) and the fullerene (6,6)-phenyl C61 butyric acid methyl ester. By using periodic and quasiperiodic hole arrays as nanoengineered plasmonic concentrators milled in a silver film, a spectrally broad, omnidirectional, and polarization-insensitive absorption enhancement is observed over that of a reference layer deposited on a flat film. As the result of increased absorption, an enhancement in the polymer fluorescence intensity is also observed. This demonstrates the potential of plasmonic concentrators for improved energy harvesting in ultrathin film solar cells.
Low temperature tunneling current enhancement in silicide/Si Schottky contacts with nanoscale barrier width
Authors: Reckinger Nicolas , Tang Xiaohui , Dubois Emmanuel , Larrieu Guilhem , Flandre Denis , Raskin Jean-Pierre , Afzalian Aryan
Published: March 2011

The low temperature electrical behavior of adjacent silicide/Si Schottky contacts with or without dopant segregation is investigated. The electrical characteristics are very well modeled by thermionic-field emission for nonsegregated contacts separated by micrometer-sized gaps. Still, an excess of current occurs at low temperature for short contact separations or dopant-segregated contacts when the voltage applied to the device is sufficiently high. From two-dimensional self-consistent nonequilibrium Green’s function simulations, the dependence of the Schottky barrier profile on the applied voltage, unaccounted for in usual thermionic-field emission models, is found to be the source of this deviation.
Magnetoresistive switching and highly polarized electroluminescence from semimagnetic semiconductor bicrystals Zn1−xMnxTe
Authors: Van Khoi Le , Gałązka R. R.
Published: March 2011

The Zn1−xMnxTe bicrystals grown by the high-pressure Bridgman method exhibit magnetic-field-sensitive current-voltage characteristics. The threshold voltage of avalanche breakdown decreases by 40% as the magnetic field increases from 0 to 14 T. In the postbreakdown regime, the Zn1−xMnxTe bicrystals emit an intense red and green electroluminescence. Under magnetic field, the green emission exhibits a high degree of circular polarization which reaches 0.95 and 0.78 at 1.8 K and 4.2 K, respectively. The relation between the photon energy of the green emission and the threshold voltage has been studied.
Synthesis and physical properties of ZnO/CdTe core shell nanowires grown by low-cost deposition methods
Authors: Consonni V. , Rey G. , Bonaimé J. , Karst N. , Doisneau B. , Roussel H. , Renet S. , Bellet D.
Published: March 2011

Vertically aligned ZnO/CdTe core/shell nanowire arrays have been grown by low-cost deposition techniques. ZnO nanowires have a wurtzite structure and are c-axis oriented. The CdTe shell completely covers ZnO nanowires and consists of nanograins, which are slightly oriented along the ⟨111⟩ direction owing to a grain growth process driven by surface energy minimization. Their nucleation follows the Volmer–Weber growth mechanism: in particular, island coalescence results in the generation of high tensile stress, which significantly reduces the CdTe optical band gap. Furthermore, both ZnO and CdTe exhibit excitonic emission bands around 3.36 eV and 1.56 eV, respectively.
First principle study of the thermal conductance in graphene nanoribbon with vacancy and substitutional silicon defects
Authors: Jiang Jin-Wu , Wang Bing-Shen , Wang Jian-Sheng
Published: March 2011

The thermal conductance in graphene nanoribbon with a vacancy or silicon point defect is investigated by nonequilibrium Green’s function (NEGF) formalism combined with first-principles calculations of density-functional theory with local density approximation. The thermal conductance is very sensitive to the position of the vacancy defect, while insensitive to the position of silicon defect. A vacancy defect situated at the center of the nanoribbon generates a saddlelike surface, which greatly reduces the thermal conductance by strong scattering to all phonon modes; while an edge vacancy defect only results in a further reconstruction of the edge and slightly reduces the thermal conductance.
Low resistance Ti/Au contacts to amorphous gallium indium zinc oxides
Authors: Kim Hyunsoo , Kim Kyoung-Kook , Lee Sung-Nam , Ryou Jae-Hyun , Dupuis Russell D.
Published: March 2011

We report on low-resistance Ti (50 nm)/Au (80 nm) contacts to amorphous gallium indium zinc oxides (a-GIZO). The specific contact resistances obtained using the transmission line method were as low as 2.85×10−5 Ω cm2 when annealed at 500 °C for 1 min in N2 ambient. This could be attributed to the combined effects of structural relaxation of a-GIZO films at elevated temperatures, causing drastic increases in both electron concentration and Hall mobility, and to interfacial reactions between Ti/Au and a-GIZO layers producing oxygen vacancies near the surface.
Strong-field plasmonic electron acceleration with few-cycle, phase-stabilized laser pulses
Authors: Rácz P. , Irvine S. E. , Lenner M. , Mitrofanov A. , Baltuška A. , Elezzabi A. Y. , Dombi P.
Published: March 2011

We carried out experimental investigations on surface plasmon enhanced electron acceleration with few-cycle, carrier-envelope phase (CEP) stabilized laser pulses. We determined the spectrum of electrons accelerated in the plasmonic field and found that signatures of the phase stabilized optical waveform driving the individual electron trajectories are washed out in the electron spectra. We attribute this effect to nanoscale surface roughness of the metallic samples, as supported by extensive numerical simulations. This finding explains the previously observed, low CEP sensitivity of photoemission processes from metallic films and enables the development of femtosecond electron sources for ultrafast time-resolved applications.
Transport mechanisms in MgO/GaAs(001) delta-doped junctions
Authors: Le Gall S. , Lépine B. , Delhaye G. , Jézéquel G. , Turban P. , Schieffer P.
Published: March 2011

The transport mechanisms through MgO ultrathin layers (0.5–1.2 nm) deposited on n-type doped GaAs(001) layers have been studied. In order to favor field emission (FE) across the junctions, a high doping concentration layer in vicinity of the semiconductor surfaces has been included. Varying doping concentration of the underlying GaAs layer we find that the dominant transport mechanism is either the variable-range hopping mechanism or a thermionic emission-like process instead of the FE process. The observation of such mechanisms can be explained by the fact that during the MgO deposition, defect states are introduced in the semiconductor band gap.
Incorporation of potassium at CuPc/C60 interface for photovoltaic application
Authors: Shih Chuan-Feng , Hung Kuang-Teng , Chen Hui-Ju , Hsiao Chu-Yun , Huang Kuan-Ta , Chen Szu-Hung
Published: March 2011

This letter demonstrates the effect of potassium (K) doping at the donor–acceptor interface of CuPc/C60-based organic solar cells. Power conversion efficient (PCE) doubled when a little K was doped into the CuPc/C60 interface and the device was postannealed (75 °C, 10 min). Changes in binding energies, depletion capacitance, and mobilities of electrons and holes were investigated. The marked improvement of PCE arose mostly from the increase in short-circuit current, owing to the modified charge transfer process.
Field emission from GeSe2 nanowalls
Authors: Zhang Yanjun , Li Hui , Jiang Li , Liu Huibiao , Shu Chunying , Li Yuliang , Wang Chunru
Published: March 2011

Single-crystalline GeSe2 nanowalls were prepared via a chemical vapor deposition process. Field-emission (FE) properties of as-prepared GeSe2 nanowalls were investigated. The FE properties could be observed in the GeSe2 nanowalls. The electron emission process from GeSe2 nanowalls is a quantum tunneling process, which follows the Fowler–Nordheim behavior. Their turn-on fields and current densities are comparable to those of many other semiconductor nanomaterials. The field enhancement factor for a single GeSe2 nanowall is estimated to be as high as 527 and 1054 with the average spacing between the electrodes is 100 μm and 200 μm, respectively. These results indicate that GeSe2 nanostructures are promising candidates for applications in field emitter.
Observation of continuous and reversible bcc–fcc phase transformation in Ag/V multilayers
Authors: Wei Q. M. , Liu X.-Y. , Misra A.
Published: March 2011

A continuous and reversible bcc–fcc phase transformation via a rotation of bcc{110} or fcc{111} planes is observed in the Bain orientation relationship in a sputter deposited V/Ag multilayers using high resolution transmission electron microscopy and analyzed using molecular dynamics simulations. As a result of the continuous phase transformation, an intermediate bct phase connecting the bcc and fcc phases coexists, giving rise to the Bain path. The periodic displacement of atoms occurs in every two adjacent Ag and V layers. The alternating shear stress created by misfit strain is responsible for generating such transformation.
Size distribution of folded chain crystal nuclei of polyethylene on active centers
Authors: Kožíšek Zdeněk , Hikosaka Masamichi , Okada Kiyoka , Demo Pavel
Published: March 2011

Kinetic equations describing temporal evolution of the size distribution of crystalline nuclei of folded chain polyethylene on active centers are solved numerically. Basic characteristics of nucleation processes (the total number of supercritical nuclei and the size distribution of nuclei) are determined and compared with the experimental data. It is shown that even though the total number of supercritical nuclei coincides with the experimental data, the size distribution prediction fails. This is caused by the fact that the total number of nuclei (usually used in analysis of the experimental data), in contrast to the size distribution of nuclei, represents an integral quantity. Using the experimental data of the steady state size distribution of nuclei enables us to determine thermodynamic parameters (especially interfacial energies) of the studied system more precisely and consequently to correct kinetic parameters to get coincidence of kinetic model with the experimental data in both, the total number of supercritical nuclei and also the size distribution of nuclei.
The canine oocyte: uncommon features of in vivo and in vitro maturation
Authors: Chastant-Maillard Sylvie , Viaris de Lesegno Christine , Chebrout Martine , Thoumire Sandra , Meylheuc Thierry , Fontbonne Alain , Chodkiewicz Marc , Saint-Dizier Marie , Reynaud Karine
Published: March 2011

The biology of the canine oocyte is unusual compared with that of other mammalian females. The present paper reviews both in vivo and in vitro specificities of canine oocytes. Final follicular growth in the bitch is characterised by an early appearance of LH binding sites in the granulosa, a high proportion of polyovular follicles and a preovulatory luteinisation, starting at the time of the LH surge. Through follicular fluid, preovulatory oocytes are thus exposed to high levels of progesterone, as high as 1000-fold plasma concentrations. The composition of the follicular fluid is affected by the size of the female. The more specific aspect of oocyte biology in the bitch is ovulation: oocytes are expelled immature, at the Prophase I stage. Ovulatory follicles are 6–8 mm in diameter, releasing oocytes from 110 µm, with dark cytoplasm. Resumption of meiosis occurs from 48 h postovulation, MII stages appearing 48–54 h after ovulation. The mechanisms controlling such a late meiotic resumption are still unknown. Granulosa cells seem to play a central role as in other mammalian species, but not with cAMP as the principal mediator. The importance of a transient reactivation of oocyte transcription a few hours before meiotic resumption is to be explored. These specific features may contribute to the low efficiency of IVM. Only 10–20% oocytes reach the metaphase stage and suffer from a poor cytoplasmic maturation. Moreover, in vitro culture of canine oocytes is associated with a high proportion of degeneration. To date, IVM of the oocytes is the main limiting factor for the development of assisted reproductive techniques in the canine. A better knowledge of the basic physiology of folliculogenesis and the molecular mechanisms controlling oocyte meiosis resumption in this species may allow us to overcome this obstacle.
Expression of functional melatonin MT1 receptors in equine luteal cells: in vitro effects of melatonin on progesterone secretion
Authors: Pedreros Marcos , Ratto Marcelo , Guerra Montserrat
Published: March 2011

In the present study, we analysed the molecular mechanism(s) by which melatonin directly affects ovarian function in the mare. In Experiment 1, follicles and corpora lutea (CL) were collected from slaughterhouse ovaries and analysed for melatonin (MT1) receptor mRNA and protein. In Experiment 2, CL were collected from slaughterhouse ovaries and cultured in Dulbecco’s modified Eagle’s medium-F12 medium (control medium) supplemented with 50 ng mL–1 equine chorionic gonadotrophin (eCG), 1 nM–1 μM melatonin, 1 μM forskolin or 1 μM luzindole. Explants were cultured for 3 h in the presence of these drugs. Conditioned media were analysed for progesterone production; luteal cells were analysed for cholesterol side-chain cleavage enzyme (P450scc), a steroidogenic enzyme that converts cholesterol into pregnenolone. Both MT1 receptor mRNA and protein were expressed in follicles and CL. Melatonin inhibited both the eCG- and forskolin-stimulated production of progesterone, as well as the forskolin-stimulated expression of P450scc, in equine luteal cells and the effect was dose-dependent. The inhibitory effect of melatonin was blocked by luzindole, a non-selective melatonin MT1 and MT2 receptor antagonist. The data support the presence of functional melatonin receptors in luteal cells and a regulatory role for melatonin in the endocrine function of the equine CL.
Unsuspected pathway of the allosteric transition in hemoglobin
Authors: Fischer Stefan , Olsen Kenneth W. , Nam Kwangho , Karplus Martin
Published: March 2011

Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin.
Nature
228:726–734], the subunit motions do not follow the textbook description of a simple rotation of one αβ-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 μs) as well as a slow (20 μs) component and provide a testable model for single molecule FRET experiments.
Biology-oriented synthesis of a natural-product inspired oxepane collection yields a small-molecule activator of the Wnt-pathway
Authors: Basu Sudipta , Ellinger Bernhard , Rizzo Stefano , Deraeve Céline , Schürmann Markus , Preut Hans , Arndt Hans-Dieter , Waldmann Herbert
Published: March 2011

In Biology Oriented Synthesis the scaffolds of biologically relevant compound classes inspire the synthesis of focused compound collections enriched in bioactivity. This criterion is met by the structurally complex scaffolds of natural products (NPs) selected in evolution. The synthesis of NP-inspired compound collections approaching the complexity of NPs calls for the development of efficient synthetic methods. We have developed a one pot 4–7 step synthesis of mono-, bi-, and tricyclic oxepanes that resemble the core scaffolds of numerous NPs with diverse bioactivities. This sequence entails a ring-closing ene-yne metathesis reaction as key step and makes productive use of polymer-immobilized scavenger reagents. Biological profiling of a corresponding focused compound collection in a reporter gene assay monitoring for Wnt-signaling modulation revealed active Wntepanes. This unique class of small-molecule activators of the Wnt pathway modulates the van-Gogh-like receptor proteins (Vangl), which were previously identified in noncanonical Wnt signaling, and acts in synergy with the canonical activator protein (Wnt-3a).
Ectopic B-cell clusters that infiltrate transplanted human kidneys are clonal
Authors: Cheng Julong , Torkamani Ali , Grover Rajesh K. , Jones Teresa M. , Ruiz Diana I. , Schork Nicholas J. , Quigley Michael M. , Hall F. Wesley , Salomon Daniel R. , Lerner Richard A.
Published: March 2011

B cells and their immunoglobulin products participate in allograft rejection of transplanted human kidneys in which an interesting feature is the presence of a germinal center like B-cell clusters in the allograft. We report here that the immunoglobulin repertoires of these infiltrating B cells are highly restricted and the B cells within a cluster are clonal. Antibody libraries made from the infiltrating B cells of individual patients unexpectedly revealed that each patient utilizes a particular set of dominant germ line genes as well as dominant complementarity determining region 3. Comparison of kidney and peripheral blood from the same patient showed that the immunoglobulin genes from both compartments had dominant clones, but they differed. The lymphocytes that infiltrate the kidneys express the immunoglobulin gene somatic recombination machinery usually restricted to highly activated lymphocytes in germinal centers and lymphomas. An analogy can be made between the inescapable antigenic drive in chronic infection versus that in an allograft, both of which may lead to emergence of dominant B-cell clones and even lymphoid malignancy.
High genetic diversity in a world-wide collection ofLathyrus sativusL. revealed by isozymatic analysis
Authors: Gutiérrez-Marcos José Francisco , Vaquero Francisca , Sáenz de Miera Luis Enrique , Vences Francisco Javier
Published: March 2011

Grasspea (Lathyrus sativusL.) is an annual, herbaceous, drought-resistant legume and staple crop in Asian and African countries. Little is known about the nature and the amount of genetic diversity present in existing grasspea seed collections, yet this information is pivotal for future breeding programmes, such as those striving to reduce high neurotoxin levels present in seeds. Here we report on the level of genetic diversity within a world-wide collection ofL. sativus, determined by isozymatic analysis. Although grasspea is generally considered a predominantly self-pollinating species, we found that the population genetic structure of these accessions showed a considerable outcrossing rate of 36%. The identification of a mixed mating system inL. sativushas significant implications for collecting and multiplying genetic resources for conservation and for future breeding purposes. In addition, we determined the genetic closeness of grasspea accessions from different geographical regions around the world. While we noticed an allelic richness in this species that was conserved across the regions, we did not find any evidence of high genetic identity between accessions, even when originating from the same geographical location. Instead, we found that greater genetic variability existed at the intra-regional level than at the inter-regional level.
A DNA fingerprinting-based taxonomic allocation of Kamut wheat
Authors: Khlestkina Elena K. , Röder Marion S. , Grausgruber Heinrich , Börner Andreas
Published: March 2011

Kamut wheat, said to have been derived from seed found in the Egyptian pyramids, appeared on the market about 25 years ago. We have investigated its taxonomic placement using microsatellite genotyping. In all, 89 accessions of 13 tetraploid wheat species, along with samples of Kamut wheat, were genotyped using two A and B genome wheat microsatellite markers per chromosome, generating 453 alleles (8–33 alleles per locus), and a mean allelic polymorphic information content (PIC) of 0.80. A diversity analysis showed that nine major accession groups could be defined, and these were inconsistent with formal taxonomic classifications of about 10% of the material. Most of these misclassifications are due to either species introgression or seed admixture. Some accessions appear to be duplicates. The Kamut wheats grouped together in a cluster containing three accessions ofTriticum polonicumand three ofT. durum, originating from Turkey, Iraq, Iran and Israel. We suggest that Kamut perhaps derived from a natural hybrid betweenT. durumandT. polonicum, which occurred in the Fertile Crescent.
AFLP marker diversity in water yam (Dioscorea alataL.)
Authors: Egesi C. N. , Asiedu R. , Ude G. , Ogunyemi S. , Egunjobi J. K.
Published: March 2011

Amplified fragment length polymorphism (AFLP) markers were employed to assess intraspecific variability in water yam (Dioscorea alataL.). Fifty-three accessions of diverse geographic origins in West and Central Africa (Benin, Côte d'Ivoire, Ghana, Nigeria and Chad) and Puerto Rico were analysed using three AFLP primer combinations. Of the 342 amplification products generated, a mean of 53.4% were polymorphic. Genetic similarity coefficients ranged from 0.29 to 0.95. The accessions could be clustered into three major genetic groups with one outlier. Each group was a mixture of accessions of different geographical origin indicating that geography has not played a major role in the differentiation of the species. A few accessions clustered very tightly suggesting that there may be duplicate accessions in the collection. The wide genetic variation observed constitutes a good basis for genetic improvement of yam.
Addenda and corrigenda to “The Minkowski question mark function: explicit series for the dyadic period function and moments”
Authors: Alkauskas Giedrius
Published: March 2011

In this supplement we fully complete the proofs of the statements which were left out or only briefly sketched in the main paper.
Structure-based de novo prediction of zinc-binding sites in proteins of unknown function
Authors: Zhao Wei , Xu Meng , Liang Zhi , Ding Bo , Niu Liwen , Liu Haiyan , Teng Maikun
Published: March 2011

Motivation: Zinc-binding proteins are the most abundant metallo-proteins in Protein Data Bank (PDB). Accurate prediction of zinc-binding sites in proteins of unknown function may provide important clues for the inference of protein function. As zinc binding is often associated with characteristic 3D arrangements of zinc ligand residues, its prediction may benefit from using not only the sequence information but also the structure information of proteins.

Results: In this work, we present a structure-based method, TEMSP (3D TEmplate-based Metal Site Prediction), to predict zinc-binding sites. TEMSP significantly improves over previously reported best methods in predicting as many as possible true ligand residues for zinc with minimum overpredictions: if only those results in which all zinc ligand residues have been correctly predicted are defined as true positives, our method improves sensitivity from less than 30% to above 60%, and selectivity from around 25% to 80%. These results are for predictions based on apo state structures. In addition, the method can predict the zinc-bound local structures reliably, generating predictions useful for function inference. We applied TEMSP to 1888 protein structures of the ‘Unknown Function’ class in the PDB database. A number of zinc-binding sites have been discovered de novo, i.e. based solely on the protein structures. Using the predicted local structures of these sites, possible functional roles were analyzed.

Availability: TEMSP is freely available from http://netalign.ustc.edu.cn/temsp/.

Contact:  hyliu@ustc.edu.cn; mkteng@ustc.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A wholly defined Agilent microarray spike-in dataset
Authors: Zhu Qianqian , Miecznikowski Jeffrey C. , Halfon Marc S.
Published: March 2011

Motivation: Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms.

Results: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this ‘Ag Spike’ dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.

Availability: The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).

Contact:  qzhu@buffalo.edu; mshalfon@buffalo.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Nonspecific Proctitis: Association with Human Immunodeficiency Virus Infection in Homosexual Men
Authors: Law Carmella L. H. , Qassim Mohammed , Cunningham Anthony L. , Mulhall Brian , Grierson Jean M.
Published: March 2011

In a cross-sectional study of 140 homosexual men attending a sexually transmissible diseases clinic, the association between the presence of antibody to the human immunodeficiency virus (HIV) and the presence of proctitis, as determined by histologic examination, as well as past or present exposure to other pathogens and details of sexual practices was analyzed. Significant associations with HIV seropositivity were found with the number of lifetime partners, positive treponemal serology, and evidence of previous infection with herpes simplex virus. However the major and unique finding was the strong and independent association between proctitis diagnosed by histologic criteria and seropositivity for HIV. Whether this is cause or effect awaits further elucidation.
Roles of the spiA gene from Salmonella enteritidis in biofilm formation and virulence
Authors: Dong Hongyan , Peng Daxin , Jiao Xinan , Zhang Xiaorong , Geng Shizhong , Liu Xiufan
Published: March 2011

Salmonella enteritidis has emerged as one of the most important food-borne pathogens for humans, and the formation of biofilms by this species may improve its resistance to disadvantageous conditions. The spiA gene of Salmonella typhimurium is essential for its virulence in host cells. However, the roles of the spiA gene in biofilm formation and virulence of S. enteritidis remain unclear. In this study we constructed a spiA gene mutant with a suicide plasmid. Phenotypic and biological analysis revealed that the mutant was similar to the wild-type strain in growth rate, morphology, and adherence to and invasion of epithelial cells. However, the mutant showed reduced biofilm formation in a quantitative microtitre assay and by scanning electron microscopy, and significantly decreased curli production and intracellular proliferation of macrophages during the biofilm phase. In addition, the spiA mutant was attenuated in a mouse model in both the exponential growth and biofilm phases. These data indicate that the spiA gene is involved in both biofilm formation and virulence of S. enteritidis.
Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries
Authors: Matsumoto Takashi , Tanaka Tsuyoshi , Sakai Hiroaki , Amano Naoki , Kanamori Hiroyuki , Kurita Kanako , Kikuta Ari , Kamiya Kozue , Yamamoto Mayu , Ikawa Hiroshi , Fujii Nobuyuki , Hori Kiyosumi , Itoh Takeshi , Sato Kazuhiro
Published: March 2011

Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare ‘Haruna Nijo’) under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
Defining intra‐operative hypotension – a pilot comparison of blood pressure during sleep and general anaesthesia*
Authors: Soo J. C. L. , Lacey S. , Kluger R. , Silbert B. S.
Published: March 2011

The scientific justification for particular values of intra‐operative hypotension is poorly substantiated. To provide a rationale for appropriate values we recorded blood pressure measurements at home for 24 h using an automated non‐invasive ambulatory blood pressure measurement device. These blood pressures were compared with blood pressure measured before and during general anaesthesia in 18 subjects undergoing elective day surgery. We confirmed that a pre‐operative reading taken upon admission to hospital is significantly elevated compared to a usual daytime blood pressure in the same patient. The median (IQR [range]) increases in systolic and mean arterial pressures were 10 (2–15 [−5 to 59]) mmHg, p = 0.003 and 10 (5–14 [−5 to 35]) mmHg, p = 0.002, respectively. When using this admission blood pressure measurement as a ‘baseline’, systolic and mean arterial pressures decreased during sleep by 41 (30–46 [6–83]) mmHg and 34 (26–36 [6–58]) mmHg, respectively (p = 0.001). This decreased even further intra‐operatively: systolic blood pressure by 49 (36–64 [15–96]) mmHg and mean arterial pressure by 36 (26–46 [8–66]) mmHg (p = 0.001).