bluuebunny/crossref_metadata_2025 huggingface dataset:
Time-dependent quantum transport and power-law decay of the transient current in a nano-relay and nano-oscillator
Authors: Cuansing Eduardo C. , Liang Gengchiau
Published: October 2011

Time-dependent nonequilibrium Green’s functions are used to study electron transport properties in a device consisting of two linear chain leads and a time-dependent interlead coupling that is switched on non-adiabatically. We derive a numerically exact expression for the particle current and examine its characteristics as it evolves in time from the transient regime to the long-time steady-state regime. We find that just after switch-on, the current initially overshoots the expected long-time steady-state value, oscillates and decays as a power law, and eventually settles to a steady-state value consistent with the value calculated using the Landauer formula. The power-law parameters depend on the values of the applied bias voltage, the strength of the couplings, and the speed of the switch-on. In particular, the oscillating transient current decays away longer for lower bias voltages. Furthermore, the power-law decay nature of the current suggests an equivalent series resistor-inductor-capacitor circuit wherein all of the components have time-dependent properties. Such dynamical resistive, inductive, and capacitive influences are generic in nano-circuits where dynamical switches are incorporated. We also examine the characteristics of the dynamical current in a nano-oscillator modeled by introducing a sinusoidally modulated interlead coupling between the two leads. We find that the current does not strictly follow the sinusoidal form of the coupling. In particular, the maximum current does not occur during times when the leads are exactly aligned. Instead, the times when the maximum current occurs depend on the values of the bias potential, nearest-neighbor coupling, and the interlead coupling.
Kelvin probe force gradient microscopy of charge dissipation in nano thin dielectric layers
Authors: Dunaevskiy M. S. , Alekseev P. A. , Girard P. , Lahderanta E. , Lashkul A. , Titkov A. N.
Published: October 2011

Application of Kelvin probe force gradient microscopy (KPFGM) to visualize the local charge dissipation in thin dielectric layers is considered. By this method, the local charge behavior in nano thin SiO2, Si3N4, and LaScO3 dielectric layers has been studied. Local charging of the layers has been performed at the point contact with a conductive probe. KPFGM potential images reveal variations of the surface potential in the locally charged areas, which makes it possible to detect the injected charge and to study its behavior. Special experiments on the SiO2 layers with embedded Si-nanocrystals, when lateral spreading of injected charge had been suppressed, permitted to demonstrate high (better than 20 nm) lateral resolution of KPFGM observations. A simple electrostatic model has been developed to estimate the total amount of injected charge. The obtained estimations made it possible to control charge retention in the dielectric layer and possible leaks into the substrate. The studied dielectric layers demonstrate a broadening of the charged area with time t, proportionally to t1/2, what indicates the domination of the diffusion mechanism in charge lateral spreading on the large time scale. These observations permitted to determine the diffusion coefficients, mobilities, and diffusion activation energies for charges in the studied dielectric layers. To obtain the correct information on the injected charge behavior, the parasitic charge dissipation through the surface film of adsorbed water should be reduced to a negligible level. It was achieved by working in moderate vacuum conditions with an additional sample heating.
Process driven oxygen redistribution and control in Si0.7Ge0.3/HfO2/TaN gate stack film systems
Authors: Lysaght Patrick S. , Woicik Joseph C. , Huang Jeff , Oh Jungwoo , Min Byoung-Gi , Kirsch Paul D.
Published: October 2011

Bulk and surface sensitive photoemission core line spectra have been acquired for Si and Ge following each step in the process sequence of Si0.7Ge0.3/2 nm HfO2/2.5 nm TaN/950 °C gate stack film systems. Extended x-ray absorption fine structure measurements have confirmed Ge segregation and pileup to form a Ge-rich layer at the SiGe surface during Si oxidation. Transmission electron micrograph cross-sections with electron energy loss element profiles have verified the effectiveness of plasma nitridation for restricting SiGe oxidation and achieving <1 nm equivalent oxide thickness with gate leakage current density equivalent to that of Si substrates without the necessity of a Si cap for oxidation control.
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
Authors: Wu Johnny , Zhen Xia , Shen Hujun , Li Guohui , Ren Pengyu
Published: October 2011

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
Laser-induced fluorescence studies of HfF+ produced by autoionization
Authors: Loh Huanqian , Wang Jia , Grau Matt , Yahn Tyler S. , Field Robert W. , Greene Chris H. , Cornell Eric A.
Published: October 2011

Autoionization of Rydberg states of HfF, prepared using the optical-optical double resonance technique, holds promise to create HfF+ in a particular Zeeman level of a rovibronic state for an electron electric dipole moment search. We characterize a vibronic band of Rydberg HfF at 54 cm−1 above the lowest ionization threshold and directly probe the state of the ions formed from this vibronic band by performing laser-induced fluorescence on the ions. The Rydberg HfF molecules show a propensity to decay into only a few ion rotational states of a given parity and are found to preserve their orientation qualitatively upon autoionization. We show empirically that we can create 30% of the total ion yield in a particular |J+, M+〉 state and present a simplified model describing autoionization from a given Rydberg state that assumes no angular dynamics.
Structural, electronic, optical, and magneto-optical properties of Bi12MO20 (M = Ti, Ge, Si) sillenite crystals from first principles calculations
Authors: Lima A. F. , Farias S. A. S. , Lalic M. V.
Published: October 2011

The structural, electronic, optical, and magneto-optical properties of the three Bi12MO20 sillenites (BMO; M = Ti, Ge, and Si) have been investigated on the basis of the first-principles calculations performed by the full potential augmented plane wave method. The BMO’s linear optical responses are found to be very similar, but their optical rotatory powers and Faraday ellipticities exhibit notable differences in both visible and ultraviolet parts of the spectra. These differences originate from the subtle differences within the BMO’s electronic structures, such as different band-gaps and different offsets of the valence band tops. The latter are found to be caused not by the influence of the M ion electronic states, but by particular behavior of the M–O and the Bi–O chemical bonds.
The S1/S2 exciton interaction in 2-pyridone·6-methyl-2-pyridone: Davydov splitting, vibronic coupling, and vibronic quenching
Authors: Heid Cornelia G. , Ottiger Philipp , Leist Roman , Leutwyler Samuel
Published: October 2011

The excitonic splitting between the S1 and S2 electronic states of the doubly hydrogen-bonded dimer 2-pyridone·6-methyl-2-pyridone (2PY·6M2PY) is studied in a supersonic jet, applying two-color resonant two-photon ionization (2C-R2PI), UV-UV depletion, and dispersed fluorescence spectroscopies. In contrast to the C2h symmetric (2-pyridone)2 homodimer, in which the S1 ← S0 transition is symmetry-forbidden but the S2 ← S0 transition is allowed, the symmetry-breaking by the additional methyl group in 2PY·6M2PY leads to the appearance of both the S1 and S2 origins, which are separated by Δexp = 154 cm−1. When combined with the separation of the S1 ← S0 excitations of 6M2PY and 2PY, which is δ = 102 cm−1, one obtains an S1/S2 exciton coupling matrix element of VAB, el = 57 cm−1 in a Frenkel-Davydov exciton model. The vibronic couplings in the S1/S2 ← S0 spectrum of 2PY·6M2PY are treated by the Fulton-Gouterman single-mode model. We consider independent couplings to the intramolecular 6a′ vibration and to the intermolecular σ′ stretch, and obtain a semi-quantitative fit to the observed spectrum. The dimensionless excitonic couplings are C(6a′) = 0.15 and C(σ′) = 0.05, which places this dimer in the weak-coupling limit. However, the S1/S2 state exciton splittings Δcalc calculated by the configuration interaction singles method (CIS), time-dependent Hartree-Fock (TD-HF), and approximate second-order coupled-cluster method (CC2) are between 1100 and 1450 cm−1, or seven to nine times larger than observed. These huge errors result from the neglect of the coupling to the optically active intra- and intermolecular vibrations of the dimer, which lead to vibronic quenching of the purely electronic excitonic splitting. For 2PY·6M2PY the electronic splitting is quenched by a factor of ∼30 (i.e., the vibronic quenching factor is Γexp = 0.035), which brings the calculated splittings into close agreement with the experimentally observed value. The 2C-R2PI and fluorescence spectra of the tautomeric species 2-hydroxypyridine·6-methyl-2-pyridone (2HP·6M2PY) are also observed and assigned.
Excitonic couplings and Stark effect in individual quantum dot molecules
Authors: Boyer de la Giroday A. , Sköld N. , Farrer I. , Ritchie D. A. , Shields A. J.
Published: October 2011

We present a comprehensive study of electric field effects upon the photoluminescence of individual quantum dot molecules. Using p-i-n diode structures, we are able to observe neutral, negatively and positively charged excitons, and biexcitons in a single device. Each molecule shows an extremely rich line structure which can be accurately described with a simple model. Moreover, reversing the doping sequence allows both electron and hole coupling between the dots to be investigated. High potential barriers cladding the quantum dot molecule allow the application of strong electric fields, resulting in a larger than expected quantum confined Stark effect.
Study of grain interactions in perpendicular magnetic recording media using first order reversal curve diagrams
Authors: Papusoi C. , Srinivasan K. , Acharya R.
Published: October 2011

It is demonstrated that, for perpendicular magnetic recording (PMR) media, first order reversal curve analysis can independently measure the grain coercive field distribution (or switching field distribution) and the strength of grain interactions, i.e., the demagnetization (mean-field) factor and the dispersion of grain interaction fields around the mean-field. The coercive field distribution is used to determine the intrinsic anisotropy field distribution of PMR media. The temperature dependence of the demagnetization factor shows that the strength of inter-granular exchange coupling is increasing with increasing medium thickness and it is decreasing with increasing temperature.
Vibrational contributions to cubic response functions from vibrational configuration interaction response theory
Authors: Hansen Mikkel Bo , Christiansen Ove
Published: October 2011

In continuation of our recent paper on vibrational quadratic response functions for vibrational configuration interaction wave functions, we present in this paper a derivation and implementation of the pure vibrational cubic response function for vibrational configuration interaction wave functions. In addition, we present combined electronic and vibrational cubic response functions derived from sum-over-states expressions in the Born-Oppenheimer framework and a discussion of complicating issues. The implementation enables analytic calculation of the pure vibrational cubic response function via response theory, which constitutes a part of the vibronic cubic response function.
Lateral dynamics of charged lipids and peripheral proteins in spatially heterogeneous membranes: Comparison of continuous and Monte Carlo approaches
Authors: Kiselev Vladimir Yu. , Leda Marcin , Lobanov Alexey I. , Marenduzzo Davide , Goryachev Andrew B.
Published: October 2011

Biological membranes are complex environments whose physico-chemical properties are of utmost importance for the understanding of many crucial biological processes. Much attention has been given in the literature to the description of membranes along the z-axis perpendicular to the membrane. Here, we instead consider the lateral dynamics of lipids and peripheral proteins due to their electrostatic interaction. Previously, we constructed a Monte Carlo automaton capable of simulating mutual diffusive dynamics of charged lipids and associated positively charged peptides. Here, we derive and numerically analyze a system of Poisson-Boltzmann-Nernst-Planck (PBNP) equations that provide a mean-field approximation compatible with our Monte Carlo model. The thorough comparison between the mean-field PBNP equations and Monte Carlo simulations demonstrates that both the approaches are in a good qualitative agreement in all tested scenarios. We find that the two methods quantitatively deviate when the local charge density is high, presumably because the Poisson-Boltzmann formalism is applicable in the so-called weak coupling limit, whose validity is restricted to low charge densities. Nevertheless, we conclude that the mean-field PBNP approach provides a good approximation for the considerably more detailed Monte Carlo model at only a fraction of the associated computational cost and allows simulation of the membrane lateral dynamics on the space and time scales relevant for the realistic biological problems.
Bioinspired ultraviolet reflective photonic structures derived from butterfly wings (Euploea)
Authors: Song Fang , Su Huilan , Chen Jianjun , Zhang Di , Moon Won-Jin
Published: October 2011

Butterfly wings have been demonstrated to have potential applications in various optical devices. For complementarily, we extend them to ultraviolet (UV) reflectors, inspired by the UV reflective photonic structures that have been evolved to satisfy UV communication systems of butterflies. UV reflective photonic structures of butterfly wings were replicated in multiscale, and thus endowed the resultant SnO2 materials with enhanced UV reflection. This biomimetic strategy provides us a universal way towards UV reflectors without changing the chemical compositions. Furthermore, the UV reflection could be potentially tuned by choosing different photonic structures of butterfly wings and other bio-species.
Doping of graphene adsorbed on the a-SiO2 surface
Authors: Miwa R. H. , Schmidt Tome M. , Scopel W. L. , Fazzio A.
Published: October 2011

We have performed an ab initio theoretical investigation of a graphene sheet adsorbed on amorphous SiO2 surface (G/a-SiO2). We find that graphene adsorbs on the a-SiO2 surface through van der Waals interactions. The inhomogeneous topology of the a-SiO2 clean surface promotes a total charge density displacement on the adsorbed graphene sheet, giving rise to electron-rich as well as hole-rich regions on the graphene. Furthermore, the adsorbed graphene sheet exhibits a net total charge density gain. In this case, the graphene sheet becomes n-type doped, however, no chemical bonds form at the graphene–SiO2 interface. The electronic charge transfer from a-SiO2 to the graphene sheet occurs upon the formation of a partially occupied level lying above the Dirac point. We find that this partially occupied level comes from the three-fold coordinated oxygen atoms in the a-SiO2 substrate.
Phase transitions of a single polyelectrolyte in a poor solvent with explicit counterions
Authors: Varghese Anoop , Vemparala Satyavani , Rajesh R.
Published: October 2011

Conformational properties of a single flexible polyelectrolyte chain in a poor solvent are studied using constant temperature molecular dynamics simulation. The effects of counterions are explicitly taken in to account. Structural properties of various phases and the transition between these phases are studied by tracking the values of asphericity, radius of gyration, fraction of condensed counterions, number of non-bonded neighbours, and Coulomb interaction energies. From our simulations, we find strong evidence for a first-order phase transition from extended to collapsed phase consistent with earlier theoretical predictions. We also identify a continuous phase transition associated with the condensation of counterions and estimate the critical exponents associated with the transition. Finally, we argue that previous suggestions of existence of an independent intermediate phase between extended and collapsed phases is only a finite size effect.
Strain-induced tuning of the emission wavelength of high quality GaAs/AlGaAs quantum dots in the spectral range of the 87Rb D2 lines
Authors: Kumar S. , Trotta R. , Zallo E. , Plumhof J. D. , Atkinson P. , Rastelli A. , Schmidt O. G.
Published: October 2011

Reversible biaxial strains are used for tuning the emission wavelengths of high quality GaAs/AlGaAs quantum dots (QDs) in the spectral range of the 87Rb D2 lines. The strain is transferred by integrating free standing (Al)GaAs nanomembranes, containing QDs, onto piezoelectric actuators. Narrow excitonic emission lines as sharp as 25 μeV are shown, and a tuning range larger than 5 nm is demonstrated. This range corresponds to an induced anisotropic biaxial strain of the order of 0.15%, as evaluated from the shift in the emission of the GaAs from the nanomembranes. The presented on-chip technology is potentially interesting for future quantum memories based on hybrid semiconductor-atomic interfaces.
The effect of narrow bandwidth infrared radiation on the growth of Escherichia coli
Authors: Tsai Shang-Ru , Huang Tsui-Chin , Liang Chia-Ming , Chang Hsin-Yi , Chang Yi-Tsung , Huang Hsuan-Cheng , Juan Hsueh-Fen , Lee Si-Chen
Published: October 2011

While broad band infrared has a number of biomedical applications, the effects with specific wavelengths on biomolecule remain unclear. In this study, narrow band infrared plasmonic thermal emitters with peak wavelengths from 3.0 to 5.0 μm were developed to irradiate Escherichia coli (E. coli) cultures for 24 h. It was found that with peak wavelengths at 4.0, 4.5, and 5.0 μm, they could promote the growth of cells. Systems biology analyses were performed to investigate the underlying molecular mechanisms. Furthermore, specific wavelengths (4.0-5.0 μm) induced the expression of transporters and enzymes involved in metabolism and respiration, thus stimulating the proliferation of E. coli.
Communication: Orbital instabilities and triplet states from time-dependent density functional theory and long-range corrected functionals
Authors: Sears John S. , Koerzdoerfer Thomas , Zhang Cai-Rong , Brédas Jean-Luc
Published: October 2011

Long-range corrected hybrids represent an increasingly popular class of functionals for density functional theory (DFT) that have proven to be very successful for a wide range of chemical applications. In this Communication, we examine the performance of these functionals for time-dependent (TD)DFT descriptions of triplet excited states. Our results reveal that the triplet energies are particularly sensitive to the range-separation parameter; this sensitivity can be traced back to triplet instabilities in the ground state coming from the large effective amounts of Hartree-Fock exchange included in these functionals. As such, the use of standard long-range corrected functionals for the description of triplet states at the TDDFT level is not recommended.
Unsteady MHD two-phase Couette flow of fluid-particle suspension in an annulus
Authors: Jha Basant K. , Apere Clement A.
Published: October 2011

The problem of two-phase unsteady MHD flow between two concentric cylinders of infinite length has been analysed when the outer cylinder is impulsively started. The system of partial differential equations describing the flow problem is formulated taking the viscosity of the particle phase into consideration. Unified closed form expressions are obtained for the velocities and the skin frictions for both cases of the applied magnetic field being fixed to either the fluid or the moving outer cylinder. The problem is solved using a combination of the Laplace transform technique, D’Alemberts and the Riemann-sum approximation methods. The solution obtained is validated by comparisons with the closed form solutions obtained for the steady states which has been derived separately. The governing equations are also solved using the implicit finite difference method to verify the present proposed method. The variation of the velocity and the skin friction with the dimensionless parameters occuring in the problem are illustrated graphically and discussed for both phases.
Accurate characterization of organic thin film transistors in the presence of gate leakage current
Authors: Singh Vinay K. , Mazhari Baquer
Published: October 2011

The presence of gate leakage through polymer dielectric in organic thin film transistors (OTFT) prevents accurate estimation of transistor characteristics especially in subthreshold regime. To mitigate the impact of gate leakage on transfer characteristics and allow accurate estimation of mobility, subthreshold slope and on/off current ratio, a measurement technique involving simultaneous sweep of both gate and drain voltages is proposed. Two dimensional numerical device simulation is used to illustrate the validity of the proposed technique. Experimental results obtained with Pentacene/PMMA OTFT with significant gate leakage show a low on/off current ratio of ∼ 102 and subthreshold is 10 V/decade obtained using conventional measurement technique. The proposed technique reveals that channel on/off current ratio is more than two orders of magnitude higher at ∼104 and subthreshold slope is 4.5 V/decade.
Minimising weight loss in new broiler hatchlings through early feeding of simple sugars
Authors: Bhuiyan M. M. , Gao F. , Chee S. H. , Iji P. A.
Published: October 2011

Two experiments were conducted to assess the effect of delayed access to feed after hatch and the potential of two carbohydrate oligomers, trehalose and palatinose, as supplements for early feeding of broiler chickens. A total of 360 and 252 straight run broiler chicks were used in Experiments 1 and 2, respectively, with each involving six treatments and six replicates. The diets were commercial in nature and supplemented with palatinose or trehalose (at 10 or 20 g/kg). Chicks were allowed to access feed within 8 h of hatch or 36 h. In Experiment 2, the supplements were fed at 10 or 20 g/kg diet; the commercial diets was also fed immediately or delayed. One of the diets contains zinc-bacitracin at 50 ppm and fed within 8 h of hatch. Delayed access to feed and water was found to reduce starting weight at placement whereas early access to feed generally improved it. Supplementation with trehalose, in particular led to higher (P < 0.001) 21-day weights than in the other groups although feed conversion ratio was not improved. The benefits of early feeding was demonstrated and trehalose may have some potential as an early feed supplement but further studies are required into how it can be applied at economic levels to minimise production costs down.
Effects of an organic acid mixture and methionine supplements on intestinal morphology, protein and nucleic acids content, microbial population and performance of broiler chickens
Authors: Saki A. A. , Eftekhari S. M. , Zamani P. , Aliarabi H. , Abbasinezhad M.
Published: October 2011

A study was carried out to investigate the effects of dietary supplementation of an organic acids mixture and two methionine supplements on intestinal morphology, protein and nucleic acids content, microbial population and performance of broiler chickens. Six hundred unsexed day-old Ross 308 broiler chicks were used in a factorial arrangement (3 × 2) based on a completely randomised design by four replicates with 25 chicks in each. Experimental diets consisted of: 0% organic acid mixture + DL-methionine (Treatment 1), 0% organic acid mixture + Alimet (Treatment 2), 0.5% organic acid mixture + DL-methionine (Treatment 3), 0.5% organic acid mixture + Alimet (Treatment 4), 1% organic acid mixture + DL-methionine (Treatment 5) and 1% organic acid mixture + Alimet (Treatment 6). A significant increase in jejunum mucosal DNA content was found by using 1% of organic acid mixture compared with those by other levels of organic acids at 21 days of age (P < 0.05). Also Treatments 5 and 6 had a higher mucosal DNA content than other treatments (P < 0.05) in a similar period. While at grower stage, the results have shown that protein content, protein/DNA and protein/RNA ratio by 0.5 and 1% of organic acids mixture significantly increased compared with those in the 0% level (P < 0.05). The addition of 1% level of organic acid mixture significantly increased villus height compared with 0 and 0.5% level of organic acid mixture at 21 days of age (P < 0.05). Highest and lowest villus heights were obtained by Treatments 1 and 6 (P < 0.05). Crypt depth increased by 0.5 and 1% of organic acid at 21 and 42 days of age (P < 0.05). Villus surface was significantly increased by 1% of organic acid mixture compared with that by 0% level at 21 days of age. The use of organic acid levels especially 1% resulted in an increase in lactic acid bacteria and decreased Enterobacteriaceae counts in the ileum of broiler chicken (P < 0.05). Better bodyweight and feed conversion ratio were obtained (P < 0.05) by 0.5 and 1% of organic acids mixture, although no response was found in feed intake and mortality in this respect (P > 0.05). The results of this study have shown improved reactions on intestinal morphometrical parameters and microflora atmosphors, by using 1% organic acid mixture. In contrast no differences were found between Alimet and DL-methionine in all tested parameters.
Condom use in China: prevalence, policies, issues and barriers
Authors: Zou Huachun , Xue Hui , Wang Xiaofang , Lu Damien
Published: October 2011

In this review, we describe condom use and its influencing factors in China, with a particular focus on the five populations that are at high risk for HIV/sexually transmissible infections (STI) infection: female sex workers, men who have sex with men, migrant workers, young people and sero-discordant couples. The risk for HIV/STI infection is high while condom use rates are low among these five populations. The 100% Condom Use Programme was successful in trial regions in increasing condom use and decreasing HIV/STI prevalence; however, long-term and routine condom promotion strategies should be in place to ensure better awareness of condom use, high availability of condoms and high rate of condom use among populations at high risk of HIV/STI infection in China. Realistic and vigorous condom-related policies and action plans should be developed and implemented to address the issues and barriers facing condom promotion in China.
Brief exploration of short and mid‐term timeout effects on basketball scoring according to situational variables
Authors: Sampaio Jaime , Lago‐Peñas Carlos , Gómez Miguel A.
Published: October 2011

The aim of this study was to identify the effects of timeouts on Basketball teams' performance differences, as measured by points scored by the team that calls a timeout and points scored by the opponent team according to game location, the quality of the opponent and the game quarter. Sixty games were analysed using the play‐by‐play game‐related statistics from the Asociación de Clubes de Baloncesto (ACB) League in Spain (2009–2010 season). For each timeout, the points scored in the previous and post 3, 5 and 10 ball possessions were registered for the teams that called the timeout and for the opponents (n=436 and n=427, n=322 and n=319, n=112 and n=110 for 3, 5 and 10 ball possessions, respectively). For the teams that called the timeout, the results reflected positive effects on points scored, with increases of 1.59, 2.10 and 2.29 points during the period within the third, fifth and tenth timeout ball possessions. For the teams that have not called the timeout, the results identified timeout negative effects in points scored, during the period within the third and fifth ball possessions (decreases in points scored of 1.59 and 1.77, respectively). Unexpectedly, the situational variables had little or no effects on points scored, which opens up this important topic for further studies and discussion.
Predicting residue–residue contacts using random forest models
Authors: Li Yunqi , Fang Yaping , Fang Jianwen
Published: October 2011

Motivation: Protein residue–residue contact prediction can be useful in predicting protein 3D structures. Current algorithms for such a purpose leave room for improvement.

Results: We develop ProC_S3, a set of Random Forest algorithm-based models, for predicting residue–residue contact maps. The models are constructed based on a collection of 1490 non–redundant, high-resolution protein structures using >1280 sequence-based features. A new amino acid residue contact propensity matrix and a new set of seven amino acid groups based on contact preference are developed and used in ProC_S3. ProC_S3 delivers a 3-fold cross-validated accuracy of 26.9% with coverage of 4.7% for top L/5 predictions (L is the number of residues in a protein) of long-range contacts (sequence separation ≥24). Further benchmark tests deliver an accuracy of 29.7% and coverage of 5.6% for an independent set of 329 proteins. In the recently completed Ninth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), ProC_S3 is ranked as No. 1, No. 3, and No. 2 accuracies in the top L/5, L/10 and best 5 predictions of long-range contacts, respectively, among 18 automatic prediction servers.

Availability:  http://www.abl.ku.edu/proc/proc_s3.html.

Contact:  jwfang@ku.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
PRINCIPLE: a tool for associating genes with diseases via network propagation
Authors: Gottlieb Assaf , Magger Oded , Berman Igor , Ruppin Eytan , Sharan Roded
Published: October 2011

Summary: PRINCIPLE is a Java application implemented as a Cytoscape plug-in, based on a previously published algorithm, PRINCE. Given a query disease, it prioritizes disease-related genes based on their closeness in a protein–protein interaction network to genes causing phenotypically similar disorders to the query disease.

Availability: Implemented in Java, PRINCIPLE runs over Cytoscape 2.7 or newer versions. Binaries, default input files and documentation are freely available at http://www.cs.tau.ac.il/~bnet/software/PrincePlugin/.

Contact:roded@tau.ac.il; assafgot@tau.ac.il
Molecular Mechanisms of Opioid Receptor-dependent Signaling and Behavior
Authors: Al-Hasani Ream , Bruchas Michael R.
Published: October 2011

Opioid receptors have been targeted for the treatment of pain and related disorders for thousands of years and remain the most widely used analgesics in the clinic. Mu (μ), kappa (κ), and delta (δ) opioid receptors represent the originally classified receptor subtypes, with opioid receptor like-1 (ORL1) being the least characterized. All four receptors are G-protein coupled and activate inhibitory G proteins. These receptors form homo- and heterodimeric complexes and signal to kinase cascades and scaffold a variety of proteins.The authors discuss classic mechanisms and developments in understanding opioid tolerance and opioid receptor signaling and highlight advances in opioid molecular pharmacology, behavioral pharmacology, and human genetics. The authors put into context how opioid receptor signaling leads to the modulation of behavior with the potential for therapeutic intervention. Finally, the authors conclude there is a continued need for more translational work on opioid receptors in vivo.
Arginyl‐Glutamine Dipeptide or Docosahexaenoic Acid Attenuates Hyperoxia‐induced Small Intestinal Injury in Neonatal Mice
Authors: Li Nan , Ma Liya , Liu Xueyan , Shaw Lynn , Calzi Sergio Li , Grant Maria B. , Neu Josef
Published: October 2011

Background and Objective:

Supplementation studies of glutamine, arginine, and docosahexaenoic acid (DHA) have established the safety of each of these nutrients in neonates; however, the potential for a more stable and soluble dipeptide, arginyl‐glutamine (Arg‐Gln) or DHA with anti‐inflammatory properties, to exert benefits on hyperoxia‐induced intestinal injury has not been investigated. Arg‐Gln dipeptide has been shown to prevent retinal damage in a rodent model of oxygen‐induced injury. The objective of the present study was to investigate whether Arg‐Gln dipeptide or DHA could also attenuate markers of injury and inflammation to the small intestine in this same model.

Methods:

Seven‐day‐old mouse pups were placed with their dams in 75% oxygen for 5 days. After 5 days of hyperoxic exposure (P7–P12), pups were removed from hyperoxia and allowed to recover in atmospheric conditions for 5 days (P12–P17). Mouse pups received Arg‐Gln (5 g · kg−1 · day−1) or DHA (5 g · kg−1 · day−1) or vehicle orally started on P12 through P17. Distal small intestine (DSI) histologic changes, myeloperoxidase (MPO), lactate dehydrogenase (LDH), inflammatory cytokines, and tissue apoptosis were evaluated.

Results:

Hyperoxic mice showed a greater distortion of overall villus structure and with higher injury score (P < 0.05). Arg‐Gln dipeptide and DHA supplementation groups were more similar to the room air control group. Supplementation of Arg‐Gln or DHA reduced hyperoxia‐induced MPO activity (P < 0.05). Supplementation of Arg‐Gln or DHA returned LDH activity to the levels of control. Hyperoxia induced apoptotic cell death in DSIs, and both Arg‐Gln and DHA reversed this effect (P < 0.05).

Conclusions:

Supplementation with either Arg‐Gln or DHA may limit some inflammatory and apoptotic processes involved in hyperoxic‐induced intestinal injury in neonatal mice.
Salmonella spp. survival strategies within the host gastrointestinal tract
Authors: Álvarez-Ordóñez Avelino , Begley Máire , Prieto Miguel , Messens Winy , López Mercedes , Bernardo Ana , Hill Colin
Published: October 2011

Human salmonellosis infections are usually acquired via the food chain as a result of the ability of Salmonella serovars to colonize and persist within the gastrointestinal tract of their hosts. In addition, after food ingestion and in order to cause foodborne disease in humans, Salmonella must be able to resist several deleterious stress conditions which are part of the host defence against infections. This review gives an overview of the main defensive mechanisms involved in the Salmonella response to the extreme acid conditions of the stomach, and the elevated concentrations of bile salts, osmolytes and commensal bacterial metabolites, and the low oxygen tension conditions of the mammalian and avian gastrointestinal tracts.
A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis
Authors: Castelló María José , Carrasco Jose Luis , Navarrete-Gómez Marisa , Daniel Jacques , Granot David , Vera Pablo
Published: October 2011

DNA-binding protein phosphatases (DBPs) have been identified as a novel class of plant-specific regulatory factors playing a role in plant-virus interactions. NtDBP1 from tobacco (Nicotiana tabacum) was shown to participate in transcriptional regulation of gene expression in response to virus infection in compatible interactions, and AtDBP1, its closest relative in the model plant Arabidopsis (Arabidopsis thaliana), has recently been found to mediate susceptibility to potyvirus, one of the most speciose taxa of plant viruses. Here, we report on the identification of a novel family of highly conserved small polypeptides that interact with DBP1 proteins both in tobacco and Arabidopsis, which we have designated DBP-interacting protein 2 (DIP2). The interaction of AtDIP2 with AtDBP1 was demonstrated in vivo by bimolecular fluorescence complementation, and AtDIP2 was shown to functionally interfere with AtDBP1 in yeast. Furthermore, reducing AtDIP2 gene expression leads to increased susceptibility to the potyvirus Plum pox virus and to a lesser extent also to Turnip mosaic virus, whereas overexpression results in enhanced resistance. Therefore, we describe a novel family of conserved small polypeptides in plants and identify AtDIP2 as a novel host factor contributing to resistance to potyvirus in Arabidopsis.
Identification of preneoplastic lesions as mucin‐depleted foci in patients with sporadic colorectal cancer
Authors: Sakai Eiji , Morioka Takamitsu , Yamada Eiji , Ohkubo Hidenori , Higurashi Takuma , Hosono Kunihiro , Endo Hiroki , Takahashi Hirokazu , Takamatsu Reika , Cui Changxu , Shiozawa Manabu , Akaike Makoto , Samura Hironori , Nishimaki Tadashi , Nakajima Atsushi , Yoshimi Naoki
Published: October 2011

In experimental models, mucin‐depleted foci (MDF), formed by dysplastic crypts devoid of mucin production have been recognized to be correlated with colorectal carcinogenesis and to serve as preneoplastic lesions of colorectal cancer (CRC). In humans, there is only one report of identification of MDF in patients with familial adenomatous polyposis and CRC; however, the histological characteristics of human MDF are not discussed extensively in the report. In the present study, colonic samples from 53 patients with sporadic CRC were stained with Alcian blue and examined for the presence of MDF. Subsequently, the samples were examined for the presence of aberrant crypt foci (ACF) by methylene blue staining. We classified MDF into two categories: flat‐MDF and protruded‐MDF (having the characteristics of both ACF and MDF). We found a total of 354, 41 and 19 colonic mucosal lesions with a mean multiplicity of 44, 38.9 and 66.9 crypts (ACF, flat‐MDF and protruded‐MDF, respectively). The density of MDF was 0.0082 lesions/cm2. The ACF identified in sporadic CRC patients corresponded to hyperplastic or non‐dysplasic lesions. However, MDF identified in these patients corresponded to low‐grade dysplasia. In addition, we found that Paneth cell metaplasia and inflammatory cell infiltration were specific histological features of MDF. These histological characteristics are reported to be associated with the development of CRC. Therefore, our results indicate that MDF might represent preneoplastic lesions in human colorectal carcinogenesis. (Cancer Sci 2012; 103: 144–149)
Review article: the effectiveness of standard triple therapy for Helicobacter pylori has not changed over the last decade, but it is not good enough
Authors: Gisbert J. P. , Calvet X.
Published: October 2011

Aliment Pharmacol Ther 2011; 34: 1255–1268

Background  A decrease in the Helicobacter pylori eradication rate after standard triple therapy has been suggested in recent years.

Aim  To assess the efficacy of standard triple therapy in the eradication of H. pylori through an epidemiological analysis of all published Spanish trials. A secondary aim was to review the prevalence of clarithromycin resistance in Spain.

Methods  Articles on H. pylori eradication in Spain published in peer‐reviewed journals were identified through MEDLINE searches. Studies that included a triple therapy consisting of any proton pump inhibitor with clarithromycin (500 mg b.d.) and amoxicillin (1 g b.d.) for up to 14 days were selected. Spanish studies evaluating the prevalence of clarithromycin resistance were also reviewed. Meta‐analysis was performed using the generic inverse variance method.

Results  The pooled eradication rates by year from Spanish studies evaluating the efficacy of the standard triple regimen revealed a relatively constant rate over the years. Overall, the analysis of the 32 studies (4727 patients) showed a mean H. pylori cure rate of 80% (95% CI = 77–82%) by intention‐to‐treat and 83% (81–86%) by per‐protocol. When only peptic ulcer disease or 7‐day regimens were considered, results were similar. Based on 13 studies (3293 patients), mean clarithromycin resistance rate was 8% (5–10%).

Conclusion  Although a decrease in the H. pylori eradication rate after triple therapy has been suggested in recent years, cure rates with this regimen did not change in Spain between 1997 and 2008. However, this by no means indicates that the efficacy of standard triple therapy in Spain is acceptable, as it has been calculated to be around only 80%. Therefore, it is evident that new strategies to improve first‐line treatment are urgently needed.
Thermal properties of sediments in southern Israel: a comprehensive data set for heat flow and geothermal energy studies
Authors: Schütz F. , Norden B. , Förster, DESIRE Group A.
Published: October 2011

To decipher the thermal structure of the sedimentary veneer in southern Israel, new values of thermal conductivity and porosity as well as of the radiogenic heat budget are provided. Thermal conductivity is measured for lithotypes and scaled up for geological formations. The new data are higher than most of the previously measured values, in particular for sandstones and siltstones, whose mean values are 5.0 and 2.9 W m−1 K−1. Mean values of the most abundant lithotypes, which are dolomites and limestones, are on the order of 4.1 and 2.7 W m−1 K−1, respectively. The total radiogenic heat production of the sedimentary cover varies slightly over southern Israel, due to variable lithology and total sediment thickness, yielding a maximum heat flow on the order of 4 mW m−2 where the sedimentary section is thickest (ca. 7 km). A temperature prognosis was made by calculating temperature profiles to the top of the crystalline basement at five well locations applying the new thermal‐conductivity data set and three scenarios of surface heat flow (50, 55 and 60 mW m−2). The calculated temperatures best match with measured drillstem‐test temperatures by using heat‐flow values close to the upper bound of range. Surface heat flow on the order of 55–60 mW m−2 is supported by a reevaluation of an existing temperature log and the application of thermal conductivity from this study. The temperature prediction for southern Israel shows values of 100–120°C at 3500–4500 m depth, indicating a geothermal potential that can be used for heating as well as electricity production.
Beyond behavioural observations: a deeper view through the sensory reactions of children with profound intellectual and multiple disabilities
Authors: Lima M. , Silva K. , Amaral I. , Magalhães A. , de Sousa L.
Published: October 2011

Background The present study was aimed at assessing the behavioural and physiological responsiveness of three children with profound intellectual and multiple disabilities to a set of sensory stimuli.

Methods Eighteen items, ‘believed’ by clinicians to be appropriate for routine interventions, were presented to the participants and responsiveness was assessed in terms of: (i) consistent behavioural and electrodermal reactions and (ii) biphasic changes in heart rate.

Results Results were twofold. First, all participants showed frequent consistent physiological reactions but rare consistent behavioural ones. Second, all participants showed biphasic changes in heart rate, pointing to the possibility of different appraisals (novelty and pleasantness) of most of the presented items.

Conclusions Data here presented may have implications for the development and the emotional well‐being of individuals with profound intellectual and multiple disabilities in that it suggests that reactions to, and potential appraisals of, sensory stimuli may occur despite the lack of consistent observable behaviours.
Changes within the thyroid axis after long‐term TSH‐suppressive levothyroxine therapy
Authors: Verburg Frederik A. , Smit Johannes W. A. , Grelle Inge , Visser Theo J. , Peeters Robin P. , Reiners Christoph
Published: October 2011

Objective  The effects of long‐term TSH‐suppressive levothyroxine (LT4) therapy on thyroid hormone metabolism in patients with differentiated thyroid carcinoma (DTC) are unknown. The aim of the study was to investigate the changes in thyroid hormone metabolism after long‐term TSH‐suppressive LT4 therapy in patients with DTC.

Patients and Methods  Sixty one patients with DTC were followed. For each patient, frozen remnant sera from two time points were selected: time1 (drawn within 1 year of I‐131 ablation; TSH on file <0·3 mIU/l; recruitment period 1999–2002) and time2 (last available sample with TSH on file <0·3 mIU/l; minimum of 3 years of continuous TSH‐suppressive LT4‐therapy on record). TSH, reverse triiodothyronine (rT3), total triiodothyronine (TT3) and total thyroxine (TT4) levels were measured at both time1 and time2, and relationships between these parameters were analysed.

Results  Total triiodothyronine, TT4 and TSH levels were significantly reduced at time2 (P < 0·001), whereas LT4 dose, bodyweight and rT3 levels remained constant between time1 and time2. There were no significant changes in the relationship between the dose of LT4/kg bodyweight and TT4 levels (P = 0·14). TT4/TT3 was increased at time2 (P < 0·001), whereas TT4/rT3 and TT3/rT3 were significantly decreased at time2. There appeared to be no relationship of the effects found and advancing age.

Conclusion  After long‐term TSH‐suppressive LT4 therapy for DTC, there are significant changes in thyroid hormone metabolism, which are best explained by a combined downregulation of deiodinases subtypes 1 and 2 and an upregulation of deiodinase subtype 3.
Post‐release mortality of angled golden perch Macquaria ambigua and Murray cod Maccullochella peelii
Authors: HALL K. C. , BROADHURST M. K. , BUTCHER P. A.
Published: October 2011

Abstract  Short‐term (≤4 days) post‐release mortalities of two large, culturally and ecologically important Australian freshwater teleosts golden perch Macquaria ambigua (Richardson) and Murray cod Maccullochella peelii (Mitchell) were investigated. There was no angler‐induced mortality among golden perch that were immediately released in winter and spring, but 24% of this species and 15% of Murray cod died after delayed release in summer. Significant predictors of mortality were limited to times caught and total length for golden perch, and restraint methods and recovery times for Murray cod, but other parameters were also implicated as cumulative influences. The estimated mortalities may be sufficient to produce population‐level impacts for these two long‐lived species but could be considerably reduced through revisions of tournament regulations.