bluuebunny/crossref_metadata_2025 huggingface dataset:
Ab initio charge analysis of pure and hydrogenated perovskites
Authors: Bork N. , Bonanos N. , Rossmeisl J. , Vegge T.
Published: February 2011

We present a density functional theory based Bader analysis of the charge distribution in pure and hydrogenated SrTiO3. We find that the hydrogen defect carries a +0.56e charge and the OH defect carries a +0.50e charge compared to the host oxygen. Calculations on BaNbO3, CaTiO3, and SrZrO3 support these findings. The distribution of the remaining electronic density decays exponentially with distance to the hydrogen defect. Diffusional paths are calculated wherein the hydrogenic species retain a charge between +0.57 and +0.54e showing that hydrogen permeation should not be viewed as consisting of virtually independent protonic and electronic transport processes.
Equilibrium equation of state of a hard sphere binary mixture at very large densities using replica exchange Monte Carlo simulations
Authors: Odriozola Gerardo , Berthier Ludovic
Published: February 2011

We use replica exchange Monte Carlo simulations to measure the equilibrium equation of state of the disordered fluid state for a binary hard sphere mixture up to very large densities where standard Monte Carlo simulations do not easily reach thermal equilibrium. For the moderate system sizes we use (up to N = 100), we find no sign of a pressure discontinuity near the location of dynamic glass singularities extrapolated using either algebraic or simple exponential divergences, suggesting they do not correspond to genuine thermodynamic glass transitions. Several scenarios are proposed for the fate of the fluid state in the thermodynamic limit.
Time-optimal control of spin 1/2 particles in the presence of radiation damping and relaxation
Authors: Zhang Y. , Lapert M. , Sugny D. , Braun M. , Glaser S. J.
Published: February 2011

We consider the time-optimal control of an ensemble of uncoupled spin 1/2 particles in the presence of relaxation and radiation damping effects, whose dynamics is governed by nonlinear equations generalizing the standard linear Bloch equations. For a single spin, the optimal control strategy can be fully characterized analytically. However, in order to take into account the inhomogeneity of the static magnetic field, an ensemble of isochromats at different frequencies must be considered. For this case, numerically optimized pulse sequences are computed and the dynamics under the corresponding optimal field is experimentally demonstrated using nuclear magnetic resonance techniques.
Electron paramagnetic resonance studies on Mn doped GaSb
Authors: Ganesan K. , Rao S. S. , Bhat S. V. , Bhat H. L.
Published: February 2011

We report on the X-band (∼9.43 GHz) electron paramagnetic resonance (EPR) investigations carried out on polycrystalline Ga1−xMnxSb (x=0.02). A strong EPR signal with an effective g factor (geff) close to 2.00 was observed, suggesting that the ionic state of Mn which replaces Ga ion in the lattice, is Mn2+ attributable to ΔM=1 transition of the ionized Mn acceptor A−, Mn(3d5). The apparent absence of EPR signal, typical for neutral Mn acceptor at g=2.7 suggests either no such centers are present or the signal broadens beyond detection limit. The temperature dependent EPR studies combined with dc magnetization data suggest the possible coexistence of antiferromagnetic and ferromagnetic phases at very low temperatures.
Magnetization asymmetry of type-II superconductors in high magnetic fields
Authors: Gokhfeld D. M. , Balaev D. A. , Petrov M. I. , Popkov S. I. , Shaykhutdinov K. A. , Val’kov V. V.
Published: February 2011

Inhomogeneous distribution of the pinning force in superconductor results in a magnetization asymmetry. A model considering the field distribution in superconductor was developed and symmetric and asymmetric magnetization loops of porous and textured Bi1.8Pb0.3Sr1.9Ca2Cu3Ox were fitted. It is found that the thermal equilibrium magnetization realizes in crystals smaller than some size depending on temperature and magnetic field.
Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons
Authors: Alizadeh Elahe , Gschliesser David , Bartl Peter , Hager Michaela , Edtbauer Achim , Vizcaino Violaine , Mauracher Andreas , Probst Michael , Märk Tilmann D. , Ptasińska Sylwia , Mason Nigel J. , Denifl Stephan , Scheier Paul
Published: February 2011

Dissociative electron attachment to dialanine and alanine anhydride has been studied in the gas phase utilizing a double focusing two sector field mass spectrometer. We show that low-energy electrons (i.e., electrons with kinetic energies from near zero up to 13 eV) attach to these molecules and subsequently dissociate to form a number of anionic fragments. Anion efficiency curves are recorded for the most abundant anions by measuring the ion yield as a function of the incident electron energy. The present experiments show that as for single amino acids (M), e.g., glycine, alanine, valine, and proline, the dehydrogenated closed shell anion (M–H)− is the most dominant reaction product. The interpretation of the experiments is aided by quantum chemical calculations based on density functional theory, by which the electrostatic potential and molecular orbitals are calculated and the initial electron attachment process prior to dissociation is investigated.
Magnetoelectric effect in crystallographically textured BaTiO3 films deposited on ferromagnetic metallic glass foils
Authors: Wang Zhiguang , Yan Li , Yang Yaodong , Li Jie-Fang , Das Jaydip , Geiler Anton L. , Yang Aria , Chen Yajie , Harris V. G. , Viehland D.
Published: February 2011

We demonstrate a significant control of the polarization response under an applied magnetic field for a magnetoelectric (ME) heterostructure. This structure was comprised of a 2 μm thick ferroelectric BaTiO3 (BTO) film deposited on flexible ferromagnetic metallic glass foil (25 μm thick). Au was used as a buffer layer to control BTO growth orientation, and to protect the metallic glass from oxidation. x-ray diffraction and scanning electron microscopy demonstrated the successful growth of well-crystallized BTO films with a high degree of (111) orientation on the amorphous metallic glass foils. Well-defined polarization (P-E) and magnetization (M-H) hysteresis loops confirmed the coexistence of ferroelectric and ferromagnetic properties. A ME voltage coefficient of about ∼60 mV/cm Oe was measured.
High pressure, mechanical, and optical properties of ZrW2O8
Authors: Ramzan M. , Luo W. , Ahuja R.
Published: February 2011

In this paper, we present the high pressure studies of well known negative thermal expansion material ZrW2O8 on the basis of our density functional theory calculations. We reproduce the experimental α and γ crystal structures of ZrW2O8. We calculate the transition pressure (from α to γ) of this material to be ≈26 kbar. Our calculated positional and axial parameters are in an excellent agreement with the available experimental values for the both α and γ phases of this material. Then we study the mechanical properties of this material. We calculate the elastic constants, bulk, shear and Young’s moduli, Poisson’s ratio, and Debye temperature of α-ZrW2O8. In our study, we find that the generalized gradient approximation method fails to obtain the correct values while the local density approximation (LDA) method successfully reproduces the experimental bulk modulus of ZrW2O8. Our calculated values of the shear and Young’s moduli, Poisson’s ratio, and Debye temperature of α-ZrW2O8 with LDA method are also in good agreement with the experimental results. Finally, we predict and analyze the optical properties of this material.
Maximum likelihood-based analysis of single-molecule photon arrival trajectories
Authors: Hajdziona Marta , Molski Andrzej
Published: February 2011

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.
Phase diagram of magnetic multilayers with tilted dual spin torques
Authors: Wang Ri-Xing , He Peng-Bin , Li Zai-Dong , Pan An-Lian , Liu Quan-Hui
Published: February 2011

A theoretic study is presented on the magnetization dynamics in magnetic multilayers with two tilted spin polarizers. Magnetic phase diagrams are established under the control of the magnitude and direction of dual spin torques. Different magnetic states, including parallel and antiparallel orientations, out-of-plane orientations, in-plane, and out-of-plane precessions, bistable states, can be distinguished in the phase diagrams. For the bistable states, there exists hysteretic switching between static and dynamic states. Selecting different pinned-layer configurations, the reversal between parallel and antiparallel orientation and the switching from stable states to precessional ones can be realized by increasing current. In addition, the dynamic evolutions of magnetic states are demonstrated.
Escorted free energy simulations
Authors: Vaikuntanathan Suriyanarayanan , Jarzynski Christopher
Published: February 2011

We describe a strategy to improve the efficiency of free energy estimates by reducing dissipation in nonequilibrium Monte Carlo simulations. This strategy generalizes the targeted free energy perturbation approach [C. Jarzynski, Phys. Rev. E 65, 046122 (2002)] to nonequilibrium switching simulations, and involves generating artificial, “escorted” trajectories by coupling the evolution of the system to updates in external work parameter. Our central results are: (1) a generalized fluctuation theorem for the escorted trajectories, and (2) estimators for the free energy difference ΔF in terms of these trajectories. We illustrate the method and its effectiveness on model systems.
Stiffness detection and reduction in discrete stochastic simulation of biochemical systems
Authors: Pu Yang , Watson Layne T. , Cao Yang
Published: February 2011

Typical multiscale biochemical models contain fast-scale and slow-scale reactions, where “fast” reactions fire much more frequently than “slow” ones. This feature often causes stiffness in discrete stochastic simulation methods such as Gillespie's algorithm and the Tau-Leaping method leading to inefficient simulation. This paper proposes a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. Numerical results on a stiff decaying dimerization model and a heat shock protein regulation model demonstrate the efficiency and accuracy of the proposed methods for multiscale biochemical systems.
High-speed electret charging using vacuum UV photoionization
Authors: Honzumi Makoto , Hagiwara Kei , Iguchi Yoshinori , Suzuki Yuji
Published: February 2011

We propose a high-speed charging method of electrets using vacuum ultraviolet irradiation. Due to a large amount of the ionization current at reduced pressure, it takes only a few seconds to charge 15-μm-thick polymer electret film to the surface potential of −900 V. This charging rate is two orders of magnitudes larger than corona/soft-x-ray charging methods. The purity of N2 gas depends on the charging rate since the O2 quenching mechanisms of exited N2 molecule would exist. No charge decay is observed for 3000 h, which indicates charged electrets are as stable as those by other charging methods.
Contacting graphene
Authors: Robinson Joshua A. , LaBella Michael , Zhu Mike , Hollander Matt , Kasarda Richard , Hughes Zachary , Trumbull Kathleen , Cavalero Randal , Snyder David
Published: February 2011

We present a robust method for forming high quality ohmic contacts to graphene, which improves the contact resistance by nearly 6000 times compared to untreated metal/graphene interfaces. The optimal specific contact resistance for treated Ti/Au contacts is found to average <10−7 Ω cm2. Additionally, we examine Al/Au, Ti/Au, Ni/Au, Cu/Au, Pt/Au, and Pd/Au contact metallizations and find that most metallizations result in similar specific contact resistances in this work regardless of the work function difference between graphene and the metal overlayer. The results presented in this work serve as a foundation for achieving ultralow resistance ohmic contacts to graphene for high speed electronic and optoelectronic applications.
Epitaxial SrO interfacial layers for HfO2–Si gate stack scaling
Authors: Marchiori C. , Frank M. M. , Bruley J. , Narayanan V. , Fompeyrine J.
Published: February 2011

We discuss the structural and electrical properties of scaled 2 nm HfO2/SrO gate stacks. Thin SrO layers are deposited by molecular beam epitaxy onto (001) p-Si substrates as alternative passivating interfacial layers (ILs) to SiO2. X-ray photoelectron spectroscopy and transmission electron microscopy show that, despite some HfO2–SrO intermixing, the SrO IL acts as a barrier against HfxSiy and SiO2 formation during high-κ deposition. Electrical measurements on metal-oxide-semiconductor capacitors with TiN metal gates integrated in a low-temperature process flow reveal an equivalent oxide thickness of 5 Å with competitive leakage current and hysteresis and a negative flat band voltage shift, suitable for n-channel transistors.
Charge transfer dynamics of model charge transfer centers of a multicenter water splitting dye complex on rutile TiO2(110)
Authors: Weston Matthew , Britton Andrew J. , O’Shea James N.
Published: February 2011

Charge transfer dynamics between an adsorbed molecule and a rutile TiO2(110) surface have been investigated in three organometallic dyes related to multicenter water splitting dye complexes: Ru 535 (cis-bis(isothiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato)-ruthenium(II)), Ru 455 (cis-bis(2,2′-bipyridyl)-(2,2′-bipyridyl-4,4′-dicarboxylic acid)-ruthenium(II)), and Ru 470 (tris(2,2′-bipyridyl-4,4′-dicarboxylic acid)-ruthenium(II)). The adsorption of the dye molecules on the rutile TiO2(110) surface has been studied using core-level and valence photoemission. Dye molecules were deposited in situ using ultrahigh vacuum electrospray deposition. Core-level photoemission spectra reveal that each complex bonds to the surface via deprotonation of two carboxylic groups. All three dye complexes show evidence of ultrafast charge transfer to the TiO2 substrate using the core-hole clock implementation of resonant photoemission spectroscopy.
Stacked GeO/SrTiOx Resistive Memory with Ultralow Resistance Currents
Authors: Cheng C. H. , Chin Albert , Yeh F. S.
Published: February 2011

We report a high performance and low-power operated resistive memory. Using stacked covalent-bond-dielectric GeOx on metal-oxide SrTiOx to form the cost-effective Ni/GeOx/SrTiOx/TaN resistive random access memory, ultralow set power of small 1 μW (0.9 μA at 1.2 V), reset power of 13 pW (0.13 nA at 0.1 V), fast 50 ns switching time and good 106 cycling endurance are realized.
Correlation between saturation magnetization and surface morphological features in Zn1−xCrxO thin films
Authors: Hu Y. M. , Li S. S. , Chia C. H.
Published: February 2011

The effect of chromium doping on the defect-induced ferromagnetism of Zn1−xCrxO films was investigated in this study. X-ray diffraction and x-ray photoelectron results confirm Cr substitution at Zn sites in the ZnO host lattice. A parabolic dependence of the saturation magnetization on the stoichiometric variable x was observed. Photoluminescence and magnetic results indicate that magnetic moments in Zn1−xCrxO films stem from Zn vacancies on the film surface or at grain boundaries. As the variation in saturation magnetization is consistent with that in surface morphology, the ferromagnetism in Zn1−xCrxO films is sensitive to the morphological modification caused by Cr doping.
Catalytic activity of Pd ensembles over Au(111) surface for CO oxidation: A first-principles study
Authors: Yuan D. W. , Liu Z. R. , Chen J. H.
Published: February 2011

Employing the first-principles pseudopotential plane-wave methods and nudged-elastic-band simulations, we studied the reaction of CO oxidation on Pd-decorated Au(111) surface. We found that the contiguous Pd ensembles are required for the CO + O2 reaction. Interestingly, Pd dimer is an active site for the two-step reaction of \documentclass[12pt]{minimal}\begin{document}${\rm CO+O_{2} \longrightarrow OOCO \longrightarrow CO_{2}+O}$\end{document} CO +O2→ OOCO → CO 2+O, and a low energy barrier (0.29 eV) is found for the formation of the intermediate metastable state (OOCO) compared to the barrier of 0.69 eV on Pd trimer. Furthermore, the residual atomic O in the CO + O2 reaction can be removed by another CO on Pd dimer with the barrier of 0.56 eV close to the value of 0.52 eV on Pd monomer via Langmuir–Hinshelwood mechanism. The higher energy barriers (0.96 and 0.64 eV) are also found for the CO + O reaction on Pd trimers. The calculated results indicate Pd dimer is highly reactive for CO oxidation by O2 via association mechanism on Pd-decorated Au(111) surface.
Penetration and screening of perpendicularly launched electromagnetic waves through bounded supercritical plasma confined in multicusp magnetic field
Authors: Dey Indranuj , Bhattacharjee Sudeep
Published: February 2011

The question of electromagnetic wave penetration and screening by a bounded supercritical (ωp>ω with ωp and ω being the electron-plasma and wave frequencies, respectively) plasma confined in a minimum B multicusp field, for waves launched in the k⊥Bo mode, is addressed through experiments and numerical simulations. The scale length of radial plasma nonuniformity (|ne/(∂ne/∂r)|) and magnetostatic field (Bo) inhomogeneity (|Bo/(∂Bo/∂r)|) are much smaller than the free space (λo) and guided wavelengths (λg). Contrary to predictions of plane wave dispersion theory and the Clemow–Mullaly–Allis (CMA) diagram, for a bounded plasma a finite propagation occurs through the central plasma regions where αp2=ωp2/ω2≥1 and βc2=ωce2/ω2⪡1(∼10−4), with ωce being the electron cyclotron frequency. Wave screening, as predicted by the plane wave model, does not remain valid due to phase mixing and superposition of reflected waves from the conducting boundary, leading to the formation of electromagnetic standing wave modes. The waves are found to satisfy a modified upper hybrid resonance (UHR) relation in the minimum B field and are damped at the local electron cyclotron resonance (ECR) location.
Magnetic field effect on stimulated Raman scattering of electromagnetic waves from nanoparticle lattice
Authors: Chakhmachi A. , Maraghechi B.
Published: February 2011

The influence of a static magnetic field on the Raman scattering of a millimeter pump wave propagating through periodic nanoparticles is studied. Formulas for the growth rate of the scattered electromagnetic wave and the electrostatic wave are derived and analyzed. It is found that the growth rate for the backscattering case is larger than that of forward scattering and the growth rate is increased by the static magnetic field. A resonance in the dispersion relation of the electromagnetic wave is found as a combination of the cyclotron and plasma frequency. However, no instability was found for this lower branch of the dispersion curve.
Electronic and transport properties of a nanometer-scale Au/AlN(0001)/Au junction from first-principles
Authors: Lu T.-H. , Tsai M.-H.
Published: February 2011

A nanometer-scale Au/Al(0001)/Au junction has been studied by first-principles calculation methods. The calculated current density-voltage curve shows Ohmic behavior, switching effect, and negative differential conductance in various bias ranges. The electronic structure shows the existence of an intrinsic band tilt due to the polar nature of the AlN film, which gives rise to the presence of hole states at the N-surface side and interface states at the Al-surface side of the AlN film. The bias induced changes of hole and interface states and the states of the Al and N ions in central layers determine the transport property.
Vibrational properties of graphene fluoride and graphane
Authors: Peelaers H. , Hernández-Nieves A. D. , Leenaerts O. , Partoens B. , Peeters F. M.
Published: February 2011

The vibrational properties of graphene fluoride and graphane are studied using ab initio calculations. We find that both sp3 bonded derivatives of graphene have different phonon dispersion relations and phonon densities of states as expected from the different masses associated with the attached atoms of fluorine and hydrogen, respectively. These differences manifest themselves in the predicted temperature behavior of the constant-volume specific heat of both compounds.
p23
H
implicated as
cis/trans
regulator of AlaXp-directed editing for mammalian cell homeostasis
Authors: Nawaz Mir Hussain , Merriman Eve , Yang Xiang-Lei , Schimmel Paul
Published: February 2011

The toxicity of mistranslation of serine for alanine appears to be universal, and is prevented in part by the editing activities of alanyl-tRNA synthetases (AlaRSs), which remove serine from mischarged tRNA
Ala
. The problem of serine mistranslation is so acute that free-standing, genome-encoded fragments of the editing domain of AlaRSs are found throughout evolution. These AlaXps are thought to provide functional redundancy of editing. Indeed, archaeal versions rescue the conditional lethality of bacterial cells harboring an editing-inactive AlaRS. In mammals, AlaXps are encoded by a gene that fuses coding sequences of a homolog of the HSP90 cochaperone p23 (p23
H
) to those of AlaXp, to create p23
H
AlaXp. Not known is whether this fusion protein, or various potential splice variants, are expressed as editing-proficient proteins in mammalian cells. Here we show that both p23
H
AlaXp and AlaXp alternative splice variants can be detected as proteins in mammalian cells. The variant that ablated p23
H
and encoded just AlaXp was active in vitro. In contrast, neither the p23
H
AlaXp fusion protein, nor the mixture of free p23
H
with AlaXp, was active. Further experiments in a mammalian cell-based system showed that RNAi-directed suppression of sequences encoding AlaXp led to a serine-sensitive increase in the accumulation of misfolded proteins. The results demonstrate the dependence of mammalian cell homeostasis on AlaXp, and implicate p23
H
as a
cis
- and
trans
-acting regulator of its activity.
Measurement of electron energy band structure in the valence band of MgO thin film with and without a sprayed functional layer by secondary electron emission from Auger neutralization
Authors: Choi Joon Ho , Son Chang Gil , Hong Young June , Park Byoung Choo , Uhm Han Sup , Choi Eun Ha
Published: February 2011

We have investigated the electron energy band structure of MgO thin film with and without a sprayed functional layer (FL), based on the Auger neutralization theory by a gamma-focused ion beam (γ-FIB) system. We have measured the secondary electron emission characteristics of MgO thin film with and without the sprayed FL, and from which their respective energy band structure f

e
(α) functions have also been investigated by using an He ion beam with ionization energy 24.58 eV through Fast Fourier Transform (FFT) and inverse-Fast Fourier Transform (IFFT).
A new platform for RFID research in Vietnam
Authors: Tran Ai Nhan , Nguyen Son Dat , Thai Pham Duc Hoang , Nguyen Thuat Tran , Dang Chien Mau , Fribourg-Blanc Eric
Published: February 2011

Radio-Frequency IDentification (RFID) is a technology that has been emerging for less than a decade as the primary choice to exchange information between objects and their environment. Most of the challenges arise due to the passive nature of the tags placed on objects. The absence of a local power source implies that power management is critical for efficient work of the data exchange link. This paper presents the platform under development at the Laboratory for Nanotechnology to study these challenges. The primary goal of the platform is to implement the complete chain from design and simulation of tags to antenna measurements and field tests of tags through fabrication of real tags on flexible substrates. This structure allows for fundamental and practical studies of new concepts in sensing and wireless networks based on passive tags. A description of the actual achievements is also included.
Calling at a cost: elevated nestling calling attracts predators to active nests
Authors: Haff Tonya M. , Magrath Robert D.
Published: February 2011

Begging by nestling birds has been used to test evolutionary models of signalling but theory has outstripped evidence. Eavesdropping predators potentially impose a cost on begging that ensures signal honesty, yet little experimental evidence exists for such a cost at active nests because the use of artificial nests, long playback bouts and absence of parents may have exaggerated costs. We broadcast short periods (1 h) of either nestling vocalizations or background noise at active white-browed scrubwren,
Sericornis frontalis
, nests. Nestlings called naturally during both treatments, allowing us to test whether elevated calling increases risk, a key but rarely tested assumption of evolutionary models. Predators visited nests exclusively during periods of elevated calling. Furthermore, playbacks affected neither adult visits nor nestling activity, suggesting that calling alone attracted predators. Adults gave alarm calls and nestlings usually called less when predators approached nests. Predation risk to broods is, therefore, likely to fluctuate substantially over short periods of time, depending on nestling hunger and whether adults or young have detected predators. This study confirms a present-day cost of nestling begging, demonstrates that this cost can be incurred over short periods and supports the importance of parent–offspring antipredator strategies in reducing predation risk.
Orientation angle and the adhesion of single gecko setae
Authors: Hill Ginel C. , Soto Daniel R. , Peattie Anne M. , Full Robert J. , Kenny T. W.
Published: February 2011

We investigated the effects of orientation angle on the adhesion of single gecko setae using dual-axis microelectromechanical systems force sensors to simultaneously detect normal and shear force components. Adhesion was highly sensitive to the pitch angle between the substrate and the seta's stalk. Maximum lateral adhesive force was observed with the stalk parallel to the substrate, and adhesion decreased smoothly with increasing pitch. The roll orientation angle only needed to be roughly correct with the spatular tuft of the seta oriented grossly towards the substrate for high adhesion. Also, detailed measurements were made to control for the effect of normal preload forces. Higher normal preload forces caused modest enhancement of the observed lateral adhesive force, provided that adequate contact was made between the seta and the substrate. These results should be useful in the design and manufacture of gecko-inspired synthetic adhesives with anisotropic properties, an area of substantial recent research efforts.
Resonant oscillations of an inhomogeneous gas between concentric spheres
Authors: Seymour Brian R. , Mortell Michael P. , Amundsen David E.
Published: February 2011

We investigate the effects of nonlinearity, geometry and stratification on the resonant motion of a gas contained between two concentric spheres. The emphasis is on whether the motion is continuous, and on how the inhomogeneity, geometry or nonlinearity can move the motion to a shocked state. Linear undamped theory yields a standing wave of arbitrary amplitude and an eigenvalue equation in which the higher eigenvalues are not integer multiples of the fundamental; the system is said to be dissonant. Higher modes, generated by the nonlinearity, are not resonant and consequently shocks may not form. When the output is shockless, the amplitude is two orders of magnitude greater than that of the input. When the eigenvalues for a homogeneous gas are not sufficiently dissonant and shocks form, the introduction of a stratification in the gas can restore dissonance and allow a continuous output. Similarly, the introduction of an inhomogeneity can change a continuous motion to a shocked one, as can an increase in the input Mach number, or an increase in the geometrical parameter. Various limits of the eigenvalue equation are considered and previous results for simpler geometries are recovered; e.g. a full sphere, a cone and a straight tube.
Oldest cingulate skulls provide congruence between morphological and molecular scenarios of armadillo evolution
Authors: Billet Guillaume , Hautier Lionel , de Muizon Christian , Valentin Xavier
Published: February 2011

The cingulates of the mammalian order Xenarthra present a typical case of disagreement between molecular and morphological phylogenetic studies. We report here the discovery of two new skulls from the Late Oligocene Salla Beds of Bolivia (approx. 26 Ma), which are the oldest known well-preserved cranial remains of the group. A new taxon is described:Kuntinaru boliviensisgen. et sp. nov. A phylogenetic analysis clustersK. boliviensistogether with the armadillo subfamily Tolypeutinae. These skulls document an early spotty occurrence for the Tolypeutinae at 26 Ma, in agreement with the temporal predictions of previous molecular studies. The fossil record of tolypeutines is now characterized by a unique occurrence in the Late Oligocene, and a subsequent 12 Myr lack in the fossil record. It is noteworthy that the tolypeutines remain decidedly marginal in the Late Palaeogene and Early Neogene deposits, whereas other cingulate groups diversify. Also, the anatomical phylogenetic analysis herein, which includesK. boliviensis, is congruent with recent molecular phylogenetic analyses.Kuntinaru boliviensisis the oldest confident calibration point available for the whole Cingulata.
Variation in hippocampal morphology along an environmental gradient: controlling for the effects of day length
Authors: Roth Timothy C. , LaDage Lara D. , Pravosudov Vladimir V.
Published: February 2011

Environmental conditions may create increased demands for memory, which in turn may affect specific brain regions responsible for memory function. This may occur either via phenotypic plasticity or selection for individuals with enhanced cognitive abilities. For food-caching animals, in particular, spatial memory appears to be important because it may have a direct effect on fitness via their ability to accurately retrieve food caches. Our previous studies have shown that caching animals living in more harsh environments (characterized by low temperatures, high snow cover and short day lengths) possess more neurons within a larger hippocampus (Hp), a part of the brain involved in spatial memory. However, the relative role of each of these environmental features in the relationship is unknown. Here, we dissociate the effects of one theoretically important factor (day length) within the environmental severity/Hp relationship by examining food-caching birds (black-capped chickadee,
Poecile atricapillus
) selected at locations along the same latitude, but with very different climatic regimes. There was a significant difference in Hp attributes among populations along the same latitude with very different climatic features. Birds from the climatically mild location had significantly smaller Hp volumes and fewer Hp neurons than birds from the more harsh populations, even though all populations experienced similar day lengths. These results suggest that variables such as temperature and snow cover seem to be important even without the compounding effect of reduced day length at higher latitudes and suggest that low temperature and snow cover alone may be sufficient to generate high demands for memory and the hippocampus. Our data further confirmed that the association between harsh environment and the hippocampus in food-caching animals is robust across a large geographical area and across years.
Constrained mate choice in social monogamy and the stress of having an unattractive partner
Authors: Griffith Simon C. , Pryke Sarah R. , Buttemer William A.
Published: February 2011

In socially monogamous animals, mate choice is constrained by the availability of unpaired individuals in the local population. Here, we experimentally investigate the physiological stress endured by a female (the choosy sex) when pairing with a non-preferred social partner. In two experimental contexts, female Gouldian finches (Erythrura gouldiae) socially paired with poor-quality mates had levels of circulating corticosterone that were three to four times higher than those observed in females that were paired with preferred mates. The elevated level of this stress hormone in response to partner quality was observed within 12 h of the experimental introduction and maintained over a period of several weeks. Our findings demonstrate the extent of intra-individual conflict that occurs when individuals are forced to make mate-choice decisions that are not perfectly aligned with mate-choice preferences. The elevated level of corticosterone also suggests a mechanistic route through which females might adaptively manage their responses to intersexual conflict over reproductive investment.
Modelling the impact of local reactive school closures on critical care provision during an influenza pandemic
Authors: House Thomas , Baguelin Marc , Van Hoek Albert Jan , White Peter J. , Sadique Zia , Eames Ken , Read Jonathan M. , Hens Niel , Melegaro Alessia , Edmunds W. John , Keeling Matt J.
Published: February 2011

Despite the fact that the 2009 H1N1 pandemic influenza strain was less severe than had been feared, both seasonal epidemics of influenza-like-illness and future influenza pandemics have the potential to place a serious burden on health services. The closure of schools has been postulated as a means of reducing transmission between children and hence reducing the number of cases at the peak of an epidemic; this is supported by the marked reduction in cases during school holidays observed across the world during the 2009 pandemic. However, a national policy of long-duration school closures could have severe economic costs. Reactive short-duration closure of schools in regions where health services are close to capacity offers a potential compromise, but it is unclear over what spatial scale and time frame closures would need to be made to be effective. Here, using detailed geographical information for England, we assess how localized school closures could alleviate the burden on hospital intensive care units (ICUs) that are reaching capacity. We show that, for a range of epidemiologically plausible assumptions, considerable local coordination of school closures is needed to achieve a substantial reduction in the number of hospitals where capacity is exceeded at the peak of the epidemic. The heterogeneity in demand per hospital ICU bed means that even widespread school closures are unlikely to have an impact on whether demand will exceed capacity for many hospitals. These results support the UK decision not to use localized school closures as a control mechanism, but have far wider international public-health implications. The spatial heterogeneities in both population density and hospital capacity that give rise to our results exist in many developed countries, while our model assumptions are sufficiently general to cover a wide range of pathogens. This leads us to believe that when a pandemic has severe implications for ICU capacity, only widespread school closures (with their associated costs and organizational challenges) are sufficient to mitigate the burden on the worst-affected hospitals.
Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrane release of its kinase inhibitor
Authors: Jaillais Yvon , Hothorn Michael , Belkhadir Youssef , Dabi Tsegaye , Nimchuk Zachary L. , Meyerowitz Elliot M. , Chory Joanne
Published: February 2011

Receptor tyrosine kinases control many critical processes in metazoans, but these enzymes appear to be absent in plants. Recently, two Arabidopsis receptor kinases—BRASSINOSTEROID INSENSITIVE 1 (BRI1) and BRI1-ASSOCIATED KINASE1 (BAK1), the receptor and coreceptor for brassinosteroids—were shown to autophosphorylate on tyrosines. However, the cellular roles for tyrosine phosphorylation in plants remain poorly understood. Here, we report that the BRI1 KINASE INHIBITOR 1 (BKI1) is tyrosine phosphorylated in response to brassinosteroid perception. Phosphorylation occurs within a reiterated [KR][KR] membrane targeting motif, releasing BKI1 into the cytosol and enabling formation of an active signaling complex. Our work reveals that tyrosine phosphorylation is a conserved mechanism controlling protein localization in all higher organisms.
Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
Authors: Feber Andrew , Wilson Gareth A. , Zhang Lu , Presneau Nadege , Idowu Bernadine , Down Thomas A. , Rakyan Vardhman K. , Noon Luke A. , Lloyd Alison C. , Stupka Elia , Schiza Vassia , Teschendorff Andrew E. , Schroth Gary P. , Flanagan Adrienne , Beck Stephan
Published: February 2011

Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. By using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumors (MPNSTs), benign neurofibromas, and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. In contrast to what has been reported for other tumor types, no significant global hypomethylation was observed in MPNSTs using methylome analysis by MeDIP-seq. However, a highly significant (P < 10−100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNSTs. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLα) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P < 10−60), non–CGI-associated promoters (P < 10−4) and hypomethylated cDMRs in SINE repeats (P < 10−100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyze cancer methylomes.
The R2R3 MYB Transcription Factor DUO1 Activates a Male Germline-Specific Regulon Essential for Sperm Cell Differentiation inArabidopsis
Authors: Borg Michael , Brownfield Lynette , Khatab Hoda , Sidorova Anna , Lingaya Melanie , Twell David
Published: February 2011

The male germline in flowering plants arises through asymmetric division of a haploid microspore. The resulting germ cell undergoes mitotic division and specialization to produce the two sperm cells required for double fertilization. The male germline-specific R2R3 MYB transcription factor DUO1 POLLEN1 (DUO1) plays an essential role in sperm cell specification by activating a germline-specific differentiation program. Here, we show that ectopic expression of DUO1 upregulates a significant number (~63) of germline-specific or enriched genes, including those required for fertilization. We validated 14 previously unknown DUO1 target genes by demonstrating DUO1-dependent promoter activity in the male germline. DUO1 is shown to directly regulate its target promoters through binding to canonical MYB sites, suggesting that the DUO1 target genes validated thus far are likely to be direct targets. This work advances knowledge of the DUO1 regulon that encompasses genes with a range of cellular functions, including transcription, protein fate, signaling, and transport. Thus, the DUO1 regulon has a major role in shaping the germline transcriptome and functions to commit progenitor germ cells to sperm cell differentiation.
Effects of training on functional variables of muscles in reared Atlantic salmon Salmo salar smolts: connection to downstream migration pattern
Authors: Anttila K. , Jokikokko E. , Erkinaro J. , Järvilehto M. , Mänttäri S.
Published: February 2011

The relative amount of muscle contraction regulating dihydropyridine and ryanodine receptors in the swimming muscles of trained reared Atlantic salmon Salmo salar smolts was compared with those of untrained and wild smolts. After an optimized 2 week training period, i.e. swimming with a velocity of 1·5 body lengths per second for 6 h per day, the level of both receptors was significantly higher in the muscles of trained S. salar than in the untrained ones before they were released into the natural environment. This difference persisted after downstream migration in the river. The highest level of receptors was observed in wild S. salar. Swimming performance was also higher in trained fish compared to untrained ones. Furthermore, swimming performance was positively associated with the level of receptors in both red and white muscle types. Downstream migration after release into the wild was significantly slower in trained smolts than in untrained fish. This indicates that trained smolts were most probably swimming harder against the current in the river than untrained smolts. The possible advantages for a slower migration in the river are discussed. This study shows that the prerequisites for effective contraction of the swimming muscles are better met in trained S. salar compared to untrained fish, and the muscles of trained smolts more closely resemble those of wild smolts. The results also imply that the capacity of untrained, reared smolts to swim against the current is not equal to that of their trained or wild counterparts which affects the downstream migration pattern of S. salar smolts.
Prolonged feed deprivation does not permanently compromise digestive function in migrating European glass eels Anguilla anguilla
Authors: Gisbert E. , Fernández I. , Alvarez‐González C. A.
Published: February 2011

The effects of prolonged feed deprivation (40 days at 18° C) and re‐feeding (30 days) on body mass, growth and the activity of selected pancreatic and intestinal enzymes were evaluated in migrating European glass eels Anguilla anguilla by comparison with a control group fed to satiation with hake Merluccius merluccius roe for the duration of the experiment. Feed deprivation resulted in mass loss and a reduction in digestive function, as revealed by a decrease in the total and specific activities of pancreatic (trypsin and α‐amylase) and intestinal brush border (alkaline phosphatase and leucine aminopeptidase) enzymes. The total activity of intestinal brush border enzymes diminished after 5 days of feed deprivation, whereas that of pancreatic enzymes did not decrease until 10 days, indicating that the intestine is more sensitive to feed deprivation than the pancreas. Re‐feeding A. anguilla that were starved for 40 days resulted in compensatory growth, with specific growth rates that were 2·6 times higher than the control group. This compensatory growth was associated with the recovery of trypsin and intestinal brush border enzyme activities, which were restored to control levels within 5 days of re‐feeding. The ability to maintain pancreatic enzyme activity during 40 days of feed deprivation, and rapidly recover capacity for protein digestion upon re‐feeding, would enable A. anguilla at this glass eel stage to withstand periods without food but rapidly provide amino acids for protein synthesis and growth when suitable food was available.
Increased exposure to predators increases both exploration and activity level in Brachyrhaphis episcopi
Authors: Archard G. A. , Braithwaite V. A.
Published: February 2011

Two temperament traits, tendency to explore and activity level, were measured in a tropical poeciliid fish, the Panamanian bishop Brachyrhaphis episcopi. Open‐field arena tests were used to quantify how predation pressure shapes activity levels and exploratory behaviours. Fish behaviour differed between high and low‐predation populations. Fish that experienced higher levels of predation were both more explorative and more active. There were also some individual differences within populations; fish varied in their levels of exploration and activity in a novel open arena, but these differences were not related to sex or size. Together with previous studies on this species, these results indicate that there is a behavioural syndrome associated with predation pressure. Fish from high‐predation populations are bolder, more explorative and more active than those from low‐predation populations.
Bufalin and cinobufagin induce apoptosis of human hepatocellular carcinoma cells via Fas‐ and mitochondria‐mediated pathways
Authors: Qi Fanghua , Inagaki Yoshinori , Gao Bo , Cui Xiaoyan , Xu Huanli , Kokudo Norihiro , Li Anyuan , Tang Wei
Published: February 2011

Bufadienolides bufalin and cinobufagin are cardiotonic steroids isolated from the skin and parotid venom glands of the toad Bufo bufo gargarizans Cantor. They have been shown to induce a wide spectrum of cancer cell apoptosis. However, the detailed molecular mechanisms of inducing apoptosis in hepatocellular carcinoma (HCC) are still unclear. In the present study, the apoptosis‐inducing effect of bufalin and cinobufagin on HCC cell line HepG2 was investigated. We found bufalin and cinobufagin induced marked changes in apoptotic morphology and significantly increased the proportion of apoptotic cells. This apoptotic induction was associated with an increase in Fas, Bax and Bid expression, a decrease in Bcl‐2 expression, disruption of the mitochondrial membrane potential, release of cytochrome c, activation of caspase‐3, ‐8, ‐9 and ‐10, and the cleavage of poly(ADP‐ribose)polymerase (PARP), which indicated that bufalin and cinobufagin induced apoptosis through both Fas‐ and mitochondria‐mediated pathways. In addition, caspase activation during bufalin‐ and cinobufagin‐induced apoptosis was further confirmed by caspase‐3 inhibitor Z‐DEVD‐FMK, caspase‐8 inhibitor Z‐IETD‐FMK, caspase‐9 inhibitor Z‐LEHD‐FMK and caspase‐10 inhibitor Z‐AEVD‐FMK. The results showed that bufalin‐ and cinobufagin‐induced apoptosis was blocked by these inhibitors and particularly by caspase‐10 inhibitor. Taken together, bufalin and cinobufagin induce apoptosis of HepG2 cells via both Fas‐ and mitochondria‐mediated pathways, and a Fas‐mediated caspase‐10‐dependent pathway might play a crucial role. (Cancer Sci 2011; 102: 951–958)