bluuebunny/crossref_metadata_2025 huggingface dataset:
Averaged variational principle for autoresonant Bernstein–Greene–Kruskal modes
Authors: Khain P. , Friedland L.
Published: October 2010

Whitham’s averaged variational principle is applied in studying dynamics of formation of autoresonant (continuously phase-locked) Bernstein–Greene–Kruskal (BGK) modes in a plasma driven by a chirped frequency ponderomotive wave. A flat-top electron velocity distribution is used as a model allowing a variational formulation within the water bag theory. The corresponding Lagrangian, averaged over the fast phase variable yields evolution equations for the slow field variables, allows uniform description of all stages of excitation of driven-chirped BGK modes, and predicts modulational stability of these nonlinear phase-space structures. Numerical solutions of the system of slow variational equations are in good agreement with Vlasov–Poisson simulations.
Simulation of discharging dust grains by laser excitation of neutral atoms
Authors: Robicheaux F. , Denney S. T. , Henry M. A.
Published: October 2010

We have simulated a method for changing the charge on dust grains in plasmas by exciting a small fraction of the neutral atoms into highly excited states. The atoms can be preferentially excited near a dust grain and quickly ionized by the hot electrons in the plasma. Because the neutral atom has low speed when it is excited, the resulting positive ion strikes the dust with nearly unit efficiency and the electron is repelled into the plasma. The rate for this process can be controlled by varying the state excited and/or the density of excited atoms. Thus, this mechanism gives a controllable method for varying the dust charge without substantially changing the other plasma properties.
Thermal effects on magnetization switching under radio frequency excitations
Authors: Wang Xiaobin , Ryan Patrick
Published: October 2010

Magnetization thermal switching dynamics under radio frequency (rf) excitations are studied based upon optimal reversal path and logarithmic susceptibility concepts. We characterize thermal magnetization switching under both rf magnetic field and spin torque excitations. For rf magnetic field induced thermal switching, magnetization thermal stability barrier dependence upon rf frequency is compared to zero temperature magnetization dynamic coercivity dependence upon rf frequency. The maximum thermal reversal barrier reduction happens near linearized small angle magnetization resonant frequency, quite different from zero temperature coercivity frequency response. For magnetic elements excited by rf spin torque current, we study adiabatic and nonadiabatic spin torque effects on thermal stability barrier frequency dependence. For cylindrical symmetric case, nonadiabatic term does not affect thermal reversal barrier reduction to leading order. For thin film element without cylindrical symmetry, nonadiabatic term affects frequency response of normalized logarithmic susceptibility significantly only when its magnitude is comparable to that of the adiabatic spin torque term.
Continuum models for the contact line problem
Authors: Ren Weiqing , Hu Dan , E Weinan
Published: October 2010

Continuum models are derived for the moving contact line problem through a combination of macroscopic and microscopic considerations. Macroscopic thermodynamic argument is used to place constraints on the form of the boundary conditions at the solid surface and the contact line. This information is then used to set up molecular dynamics to measure the detailed functional dependence of the boundary conditions. Long range molecular forces are taken into account in the form of a surface potential. This allows us to handle the case of complete wetting as well as the case of partial wetting. In particular, we obtain a new continuum model for both cases in a unified form. Two main parameters and different spreading regimes are identified from the analysis of the energy dissipations for the continuum model. Scaling laws in these different regimes are derived. The new continuum model also allows us to derive boundary conditions for the lubrication approximation. Numerical results are presented for the thin film model and the effect of the boundary condition is investigated.
Energy resolution of gamma-ray spectroscopy of JET plasmas with a LaBr3 scintillator detector and digital data acquisition
Authors: Nocente M. , Tardocchi M. , Chugunov I. , Pereira R. C. , Edlington T. , Fernandes A. M. , Gin D. , Grosso G. , Kiptily V. , Murari A. , Neto A. , Perelli Cippo E. , Pietropaolo A. , Proverbio I. , Shevelev A. , Sousa J. , Syme B. , Gorini G. ,   JET-EFDA Contributors
Published: October 2010

A new high efficiency, high resolution, fast γ-ray spectrometer was recently installed at the JET tokamak. The spectrometer is based on a LaBr3(Ce) scintillator coupled to a photomultiplier tube. A digital data acquisition system is used to allow spectrometry with event rates in excess of 1 MHz expected in future JET DT plasmas. However, at the lower rates typical of present day experiments, digitization can degrade the energy resolution of the system, depending on the algorithms used for extracting pulse height information from the digitized pulses. In this paper, the digital and analog spectrometry methods were compared for different experimental conditions. An algorithm based on pulse shape fitting was developed, providing energy resolution equivalent to the traditional analog spectrometry method.
The C12(H3e,pγ)N14 reaction cross section for γ-ray spectroscopy simulation of fusion plasmas
Authors: Proverbio I. , Nocente M. , Kiptily V. G. , Tardocchi M. , Gorini G. ,   JET-EFDA Contributors
Published: October 2010

High resolution γ-ray spectroscopy measurements were performed in JET (H3e)D plasmas with high energy ion populations driven by radio-frequency (RF) heating. One of the first reactions investigated was C12(H3e,pγ)N14, which was observed at low H3e concentrations. In order to interpret the measurements in this work, cross section data for the C12(H3e,pγ)N14 reaction are evaluated. Available data for the population of excited states in N14 up to the eighth level are assessed in the range E3He=0–5 MeV. Discrepancies and gaps in the database have been solved by means of interpolations and consistency analysis. The evaluated cross section data are used to predict the intensity ratio of characteristic 2.31 and 1.63 MeV γ-rays.
Upgrade of the lithium beam diagnostic at JET
Authors: Brix M. , Dodt D. , Korotkov A. , Morgan P. , Dunai D. , Fischer R. , Meigs A. , Nedzelskiy I. S. , Schweinzer J. , Vince J. , Zoletnik S. ,   JET-EFDA Contributors
Published: October 2010

A 60 kV neutral Li beam is injected into the edge plasma of JET to measure the electron density. The beam observation system has been improved by replacing a Czerny-Turner spectrometer with a high-resolution transmission-grating spectrometer and a fast back-illuminated frame-transfer camera. The larger throughput of the spectrometer, the increased sensitivity, and the faster readout of the new camera allow inter-ELM (edge localized mode) measurements (frame rate of 100 Hz). The calibration of the setup, as well as an improved spectral fitting technique in the presence of carbon background radiation, is discussed in detail. The density calculation is based on a statistical analysis method. Results are presented for different plasma scenarios.
Enhancement of JET’s mirror-link near-ultraviolet to near-infrared divertor spectroscopy system
Authors: Meigs A. , Stamp M. , Igreja R , Sanders S. , Heesterman P. ,   JET-EFDA Contributors
Published: October 2010

Since 1994, JET has had a mirror-link spectroscopy system with a poloidal view of 150 mm of the outer divertor split into three ranges: near-ultraviolet (near-UV) (∼300–450 nm), visible (450–750 nm), and near-infrared (near-IR) (750–1200 nm). The system consists of three Czerny–Turner/charge coupled device (CCD) pairs: 1 m focal length for the near-UV, 0.75 m focal length for the visible, and 0.5 m focal length for the near-IR. All were aligned along the same optical path to the divertor. As part of the JET ITER-like wall enhancements, the diagnostic system will be upgraded in five areas: (1) frame rate, (2) quantum efficiency (QE), (3) radial coverage, (4) optical throughput, and (5) for the near-UV, spectral resolution and survey capability. New CCDs for the near-UV and visible will have increased QE and allow three times frame rate. The near-UV will benefit from a 0.75 m imaging spectrometer with three gratings. The optics have been redesigned to allow ∼360 mm view and greater than two times throughput. This paper will look at the design and implementation as well as the new diagnostic capabilities of the system.
Gyrokinetic study of the role of β on electron particle transport in tokamaks
Authors: Hein T. , Angioni C. , Fable E. , Candy J.
Published: October 2010

Electromagnetic effects on the radial transport of electrons in the core of tokamak plasmas are studied by means of linear and nonlinear gyrokinetic simulations with the code GYRO [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] and by an analytical derivation. The impact of a finite β, that is, a finite ratio of the plasma pressure to the magnetic pressure, is considered on the fluctuations of the magnetic field through Ampére’s law, as well as on the geometrical modification of the vertical drift produced by the Shafranov shift in the magnetic equilibrium, which, for realistic descriptions, has to be included in both electrostatic and electromagnetic modeling. The condition of turbulent particle flux at the null, which allows the determination of stationary logarithmic density gradients when neoclassical transport and particle sources are negligible, is investigated for increasing values of β, in regimes of ion temperature gradient and trapped electron mode turbulence. The loss of adiabaticity of passing electrons produced by fluctuations in the magnetic vector potential produces an outward convection. When the magnetic equilibrium geometry is kept fixed, this induces a strong reduction of the stationary logarithmic density gradient with increasing β. This effect is partly compensated by the geometrical effect on the vertical drift. This compensation effect, however, is significantly weaker in nonlinear simulations as compared to quasilinear calculations. A detailed comparison between quasilinear and nonlinear results reveals that the predicted value of the logarithmic density gradient is highly sensitive on the assumptions on the wave number spectrum applied in the quasilinear model. The qualitative consistency of the theoretical predictions with the experimental results obtained so far on the dependence of density peaking on β is discussed by considering the additional impact, with increasing β, of a particle source delivered by neutral beam injection heating. (Some figures in this article are in color only in the electronic version.)
The electric dipole moment of iridium monofluoride, IrF
Authors: Zhuang Xiujuan , Steimle Timothy C. , Linton Colan
Published: October 2010

The P(5) branch features of the A Φ34←X Φ34 (1,0) band near 628.2 nm of a molecular beam of iridium monofluoride, I193rF, were recorded field free and in the presence of a static electric field. The I193r (I1=3/2) and F19 (I2=1/2) hyperfine interactions in the A Φ34 (υ=1) and X Φ34 (υ=0) states were analyzed. The permanent electric dipole moments, μ⃗el, for the A Φ34 (υ=1) and X Φ34 (υ=0) states were determined to be 1.88(5) and 2.82(6) D, respectively, from the analysis of the observed Stark shifts. A comparison of the electric dipole moments for IrC, IrN, and CoF is presented.
Mechanical response of GaN film and micropillar under nanoindentation and microcompression
Authors: Sung T. H. , Huang J. C. , Hsu J. H. , Jian S. R.
Published: October 2010

The mechanical properties of GaN are examined by microcompression. The Young’s modulus and compressive yield stress in microscale are directly measured to be ∼226 and 10 GPa, comparable to the modulus (∼272 GPa) and hardness (15 GPa) measured by nanoindentation. The Raman spectrum measurements and transmission electron microscopy observations reveal that the residual stress in deposited film can be largely released in the form of micropillar. Upon microcompression, the strain energy is basically stored by dislocation and defect accumulation, with minimum residual stress regeneration. The small bending of the c-axis of the GaN micropillar upon compression would affect its optical performance.
Highly photostable organic distributed feedback laser emitting at 573 nm
Authors: Navarro-Fuster Victor , Calzado Eva M. , Boj Pedro G. , Quintana José A. , Villalvilla José M. , Díaz-García María A. , Trabadelo Vera , Juarros Aritz , Retolaza Aritz , Merino Santos
Published: October 2010

An efficient, low-cost, and highly photostable second-order distributed feedback (DFB) laser, fabricated by thermal nanoimprint lithography and based on a polymer active film containing a perylenediimide derivative, is reported. It shows a photostability half-life of 3.1×105 pump pulses (>8 h), when pumped at the same spot of the film. This value is the highest reported to date for organic DFB lasers measured under ambient conditions. The device emits at 573 nm, matching the second low-loss transmission window of poly(methylmethacrylate) (460–590 nm), thus offering potential for applications in data communications based on polymer optical fibers.
Optical spin-filtering effect in charged InAs/GaAs quantum dots
Authors: Taylor M. W. , Harbord E. , Spencer P. , Clarke E. , Slavcheva G. , Murray R.
Published: October 2010

We present time resolved photoluminescence results using nonresonant polarized light which show that the electron spin-flip time is much longer than the recombination time for an ensemble of p-doped InAs/GaAs quantum dots. Under continuous wave excitation the degree of optical polarization of the ground state is found to be around 10%. However, the excited state polarization is twice this value. We attribute this effect to Pauli blocking of the injected spin population captured into the dots and show that the effect persists up to room temperature. For resonant excitation, values are nearly doubled in accordance with increased spin injection efficiency.
Bennett clocking of nanomagnetic logic using multiferroic single-domain nanomagnets
Authors: Atulasimha J. , Bandyopadhyay S.
Published: October 2010

The authors show that it is possible to rotate the magnetization of a multiferroic (strain-coupled two-layer magnetostrictive-piezoelectric) nanomagnet by a large angle with a small electrostatic potential. This can implement Bennett clocking [Int. J. Theor. Phys. 21, 905 (1982)] in nanomagnetic logic arrays resulting in unidirectional propagation of logic bits from one stage to another. This method is potentially more energy efficient than using spin-transfer torque for magnetization rotation. For realistic parameters, it is shown that a potential of ∼0.2 V applied to a multiferroic nanomagnet can rotate magnetization by nearly 90° to implement Bennett clocking.
Microwave power thin film resistors for high frequency and high power load applications
Authors: Jiang H. C. , Si X. , Zhang W. L. , Wang C. J. , Peng B. , Li Y. R.
Published: October 2010

The authors report a power-dividing-based microwave power thin film resistor (MPTFR) that exhibits high operating frequency and high power load. The MPTFR is comprised of substrate, ground electrodes, two TaN resistive films, power dividing circuit and signal input port. The experimental results show that the voltage standing wave ratio of the MPTFR is lower than 1.6 in the band of 3.4–7.4 GHz and 8.2–9.8 GHz. The power load of the MPTFR is 200 W. The experimental data are in good agreement with the electromagnetic simulations.
Charles Fenner and Early Landform Studies in South Australia
Authors: Twidale C. Rowland
Published: October 2010

Charles Albert Edward Fenner (1884?1955) was educated in Melbourne but spent the major part of his working life in South Australia, first as Superintendent of Technical Education and later as Director of Education, holding the latter post during the difficult years of the Second World War. He is best remembered for his role in the establishment of Geography as a university discipline and for his landform studies. He brought together earlier work on the tectonics of the Gulfs region of South Australia and introduced the term ?shatter belt' to describe the complex of horsts and sunken blocks. He noted evidence pointing to recent and continuing earth movements, and suggested that such earth movements were responsible for the westerly diversion of the River Murray at Chucka Bend. He also conceived a hypothesis of ?double planation' in explanation of the morphology of the Mt Lofty Ranges.
Alan Kenneth Head 1925 - 2010
Authors: Humble Peter
Published: October 2010

Alan Head had many scientific interests. He was a mathematical physicist but was so widely read that he could turn his hand to almost anything that had a scientific basis. His contributions ranged from a design for a giant radio telescope to writing a computer program to simulate the diffraction of electrons as they pass through a crystalline specimen containing defects on an atomic scale and to calculate the images produced by these defects; from the elastic properties of engineering materials to the aberrations in aplanatic, non-spherical lens systems; from the causes of fracture in solid state materials to the patented design for a refrigerator that obtains its cooling power by selectively radiating electromagnetic radiation through a ?window' in the earth's atmosphere to outer space; from Galois theory to quantum computers. Perhaps his greatest success was the theory of fatigue in aluminium alloys used in the construction of jet aeroplanes. Not only was he able to establish the micro-mechanisms involved, his analysis was such that the time that the processes would take to produce a complete failure could be estimated. Without this analysis, commercial aviation as we know it today would have been totally unsafe, whereas knowing the effective lifetime of components and replacing them before the end of their lifetime meant that, provided the relevant maintenance was carried out diligently, travel by air could be safe. The project that gave Alan most pleasure was his understanding of Galois theory and his being the first person to apply it to a practical case concerning the elastic anisotropy of crystalline materials. These two examples epitomise the value Alan put on ?theory'. Theory was only good if it led to a practical, useful result. Alan Head had a brilliant career but his feet were always firmly on the ground. He was modest, quietly spoken and very approachable. He was a friend and mentor to many. There are more than ten scientific topics (including those mentioned above) described in this memoir and he made significant contributions to all of them.
Inositol hexakisphosphate kinase-2 acts as an effector of the vertebrate Hedgehog pathway
Authors: Sarmah Bhaskarjyoti , Wente Susan R.
Published: October 2010

Inositol phosphate (IP) kinases constitute an emerging class of cellular kinases linked to multiple cellular activities. Here, we report a previously uncharacterized cellular function in Hedgehog (Hh) signaling for the IP kinase designated inositol hexakisphosphate kinase-2 (IP6K2) that produces diphosphoryl inositol phosphates (PP-IPs). In zebrafish embryos, IP6K2 activity was required for normal development of craniofacial structures, somites, and neural crest cells.
ip6k2
depletion in both zebrafish and mammalian cells also inhibited Hh target gene expression. Inhibiting IP
6
kinase activity using N(2)-(m-(trifluoromethy)lbenzyl) N(6)-(p-nitrobenzyl)purine (TNP) resulted in altered Hh signal transduction. In zebrafish, restoring IP6K2 levels with exogenous
ip6k2
mRNA reversed the effects of IP6K2 depletion. Furthermore, overexpression of
ip6k2
in mammalian cells enhanced the Hh pathway response, suggesting IP6K2 is a positive regulator of Hh signaling. Perturbations from IP6K2 depletion or TNP were reversed by overexpressing
smoM2
,
gli1
, or
ip6k2
. Moreover, the inhibitory effect of cyclopamine was reversed by overexpressing
ip6k2
. This identified roles for the inositol kinase pathway in early vertebrate development and tissue morphogenesis, and in Hh signaling. We propose that IP6K2 activity is required at the level or downstream of Smoothened but upstream of the transcription activator Gli1.
Electron transport coefficients in the mixtures of H2O with N2, O2, CO2 and dry air for the optimization of non-thermal atmospheric pressure plasmas
Authors: Ruíz-Vargas G , Yousfi M , de Urquijo J
Published: October 2010

This paper presents the simultaneous measurement and calculation of the electron drift velocity in binary and ternary mixtures of N2, O2, CO2 with H2O. The main aim of this study has been the generation of a self-consistent set of validated collision cross sections that explain thoroughly the dependence of the electron drift velocity in the above pure gases and their mixtures. In doing this, changes to the collision cross section set for H2O had to be made, while all other cross section sets remained unchanged. It is worth mentioning that only a few experiments had been performed before dealing with water mixtures. The electron drift velocities in the binary and ternary mixtures under study show the effects of negative differential conductivity, and this has been explained thoroughly in terms of the collision cross sections and electron distribution functions through a multi-term Boltzmann code. It is important to note that two-term codes fail to predict the dependence of the drift velocity at low water concentrations and low E/N values. Calculated values of longitudinal and transverse diffusion coefficients, mean energies and distribution functions are also given over the E/N range 0.1 Td–2 kTd (1 Td = 10−17 V cm2).
Damage, refractive index and near-field intensity profiles in a single-mode waveguide of LiNbO3 by 400 keV He ion implantation
Authors: Zhang S M , Liu X H , Qin X F , Wang K M , Liu X
Published: October 2010

We report on a single-mode waveguide in lithium niobate produced by 400 keV He ion implantation with a dose of 3 × 1016 ions cm−2 at liquid nitrogen temperature. Rutherford backscattering/channelling spectra have been measured in the waveguide before and after annealing and the damage profile has been extracted. The shape of the measured damage profile is similar to that of the ordinary refractive index by the intensity calculation method. The near-field intensity profile in a ridge waveguide is given and the propagation loss for the extraordinary index is estimated to be 1.9 dB cm−1.
Electrical and optical properties of Sb-doped BaSnO3 epitaxial films grown by pulsed laser deposition
Authors: Liu Qinzhuang , Dai Jianming , Liu Zhongliang , Zhang Xiaobo , Zhu Guangping , Ding Guohua
Published: October 2010

In this paper we report the structural, electrical and optical properties of epitaxial Ba(Sb
x
Sn1−x
)O3 (x = 0–0.30) (BSSO) films grown on SrTiO3(0 0 1) substrates by the pulsed laser deposition method. The investigation reveals that the transport and optical characteristics of BSSO films depend very sensitively on the Sb-doping content. Temperature-dependent resistivity measurements show that at low Sb contents (x = 0.03, 0.07) the metal–semiconductor transition occurs at 150 K and 80 K, respectively, and the semiconductor behaviour appears in high doped (x = 0.15, 0.30) films. The transmittance decreases significantly from about 80% to nearly zero in the visible region and the optical band gap shifts from 3.48 to 4.0 eV with increasing Sb content in the films. The lowest room-temperature resistivity of 2.43 mΩ cm with carrier density and mobility of 1.65 × 1021 cm−3 and 1.75 cm2 V−1 s−1 was obtained in the films with doping at x = 0.07. By employing them as bottom electrodes we have fabricated transparent Pb(Zr0.52Ti0.48)O3 ferroelectric capacitors showing square polarization–electric field hysteresis loops, indicating that these perovskite-type BSSO films at low doping can be potentially used in transparent devices especially based on all-perovskite heterostructures.
Suppressed magnetoelectric effect in epitaxially grown multiferroic Pb(Zr0.57Ti0.43)O3–Pb(Fe2/3W1/3)O3 solid-solution thin films
Authors: Lee D , Park Y-A , Yang S M , Song T K , Jo Y , Hur N , Jung J H , Noh T W
Published: October 2010

We report on the epitaxial growth of single-phase [Pb(Zr0.57Ti0.43)O3]0.8[Pb(Fe2/3W1/3)O3]0.2 (PZT–PFW) solid-solution thin films using pulsed laser deposition. X-ray diffraction measurements reveal that the films have a tetragonal structure. The films exhibit ferroelectric properties and weak ferromagnetic responses at room temperature. The magnetoelectric effects were investigated; the nonlinear magnetocapacitance coefficient, β33, was measured and found to be comparable to those of multiferroic hexagonal manganites, but at least two orders of magnitude smaller than that for polycrystalline PZT–PFW films.
Structural effects on the emission properties of Pr3+-doped Ba2NaNb5O15 crystals
Authors: Cavalli Enrico , Calestani Gianluca , Mezzadri Francesco , Faoro Raffaele , Tonelli Mauro , Boutinaud Philippe
Published: October 2010

Single crystals of Ba2NaNb5O15 doped with Pr3+ have been grown from sodium tetraborate flux. Their emission properties have been measured as a function of the doping level under different excitation and temperature conditions. The experimental observations have been accounted for by considering the effects of the crystal structure, of the doping mechanisms and of the interactions between host lattice and doping ions. The proposed conclusions have been verified by means of single crystal x-ray diffraction measurements and the resulting site occupancies of the active ions have been discussed in the light of the synthesis procedure.
Thermal annealing of nanocrystalline Fe3S4 films deposited on Si substrates by dc-magnetron sputtering at room temperature
Authors: Liu H F , Huang A , Chi D Z
Published: October 2010

Thermal annealing of nanocrystal Fe3S4 films are studied using x-ray diffraction (XRD), scanning-electron microscopy, micro-Raman scattering and vibrating sample magnetometry. The evolution of XRD patterns due to thermal annealing provides evidence for the conversion of Fe3S4 to Fe7S8 and Fe3O4 at low temperatures and an increase in the annealing temperature leads to a single phase of Fe3O4. Raman spectroscopy reveals a large electron–phonon coupling strength for the Fe3O4 nanocrystals, which also exhibits an apparent reduction with an increase in annealing temperature. This behaviour, together with the magnetization evolutions, most likely originates from the coalescence of Fe3O4 grains as well as the annihilation of crystal disorders/defects, such as antiphase boundaries, presented in the Fe3O4 nanocrystals.
Dielectric relaxation and magnetic properties of Cr doped GaFeO3
Authors: Bakr Mohamed M , Wang H , Fuess H
Published: October 2010

Polycrystalline GaFe1−x
Cr
x
O3 (x = 0.05, 0.1 and 0.15) samples were prepared by solid state reaction. The monophasic compounds crystallize in the orthorhombic space group Pc21
n and the unit cell volume decreases with increasing Cr content. The saturated magnetization and magnetic transition temperature of the ceramics decrease due to the dilution of the magnetic interaction with Cr concentration. The dielectric properties were investigated from 133 to 353 K at various frequencies (100–107 Hz). Whereas the dielectric constant decreases with Cr content an increase in dielectric loss tangent was observed. The activation energies of the compounds (calculated both from loss and modulus spectrum) are the same and have values ∼0.22 eV and 0.27 eV for Cr = 10% and 15%, respectively, and hence the relaxation process may be attributed to the same type of charge carrier. A separation of the grain and grain boundary properties has been achieved using an equivalent circuit model. The capacitance and resistances associated with the grain boundary were found to be higher than those associated with grain.
Temperature dependence of the photoluminescence from InP/GaAs type-II ultrathin quantum wells
Authors: Singh S D , Porwal S , Alexander K , Dixit V K , Srivastava A K , Oak S M
Published: October 2010

Temperature dependence of the photoluminescence (PL) spectra has been investigated for InP/GaAs type-II ultrathin quantum wells (QWs). Room temperature PL has been observed for 1.43 monolayer thick ultrathin QW. Fitting parameters of the Bose–Einstein empirical relation for ultrathin QWs show that the temperature dependence of PL peak energy is similar to the temperature dependence of the band gap for InP and GaAs materials. In addition, we have also determined the PL quenching mechanism from the Arrhenius-like plot of integrated PL intensity. Thermal escape of carriers from these ultrathin QWs into the GaAs barrier is mainly responsible for the PL quenching with temperature. This is also supported by the observation that the PL intensity related to the GaAs barrier increases with increasing temperature.
Zds2p Regulates Swe1p-dependent Polarized Cell Growth inSaccharomyces cerevisiaevia a Novel Cdc55p Interaction Domain
Authors: Yasutis Kimberly , Vignali Marissa , Ryder Matthew , Tameire Feven , Dighe Shubha A. , Fields Stanley , Kozminski Keith G.
Published: October 2010

Deletion of the paralogs ZDS1 and ZDS2 in the budding yeast Saccharomyces cerevisiae causes a mis-regulation of polarized cell growth. Here we show a function for these genes as regulators of the Swe1p (Wee1p) kinase–dependent G2/M checkpoint. We identified a conserved domain in the C-terminus of Zds2p consisting of amino acids 813–912 (hereafter referred to as ZH4 for Zds homology 4) that is required for regulation of Swe1p-dependent polarized bud growth. ZH4 is shown by protein affinity assays to be necessary and sufficient for interaction with Cdc55p, a regulatory subunit of protein phosphatase 2A (PP2A). We hypothesized that the Zds proteins are in a pathway that negatively regulates the Swe1p-dependent G2/M checkpoint via Cdc55p. Supporting this model, deletion of CDC55 rescues the aberrant bud morphology of a zds1Δzds2Δ strain. We also show that expression of ZDS1 or ZDS2 from a strong galactose-inducible promoter can induce mitosis even when the Swe1p-dependent G2/M checkpoint is activated by mis-organization of the actin cytoskeleton. This negative regulation requires the CDC55 gene. Together these data indicate that the Cdc55p/Zds2p module has a function in the regulation of the Swe1p-dependent G2/M checkpoint.
Polycystin-1 Surface Localization Is Stimulated by Polycystin-2 and Cleavage at the G Protein-coupled Receptor Proteolytic Site
Authors: Chapin Hannah C. , Rajendran Vanathy , Caplan Michael J.
Published: October 2010

Polycystin (PC)1 and PC2 are membrane proteins implicated in autosomal dominant polycystic kidney disease. A physiologically relevant cleavage at PC1's G protein-coupled receptor proteolytic site (GPS) occurs early in the secretory pathway. Our results suggest that PC2 increases both PC1 GPS cleavage and PC1's appearance at the plasma membrane. Mutations that prevent PC1's GPS cleavage prevent its plasma membrane localization. PC2 is a member of the trp family of cation channels and is an important PC1 binding partner. The effect of PC2 on PC1 localization is independent of PC2 channel activity, as tested using channel-inhibiting PC2 mutations. PC1 and PC2 can interact through their C-terminal tails, but removing the C-terminal tail of either protein has no effect on PC1 surface localization in human embryonic kidney 293 cells. Experiments in polarized LLC-PK cells show that apical and ciliary PC1 localization requires PC2 and that this delivery is sensitive to PC2 truncation. In sum, our work shows that PC2 expression is required for the movement of PC1 to the plasma and ciliary membranes. In fibroblast cells this localization effect is independent of PC2's channel activity or PC1 binding ability but involves a stimulation of PC1's GPS cleavage before the PC1 protein's surface delivery.
Optimized data fusion for K-means Laplacian clustering
Authors: Yu Shi , Liu Xinhai , Tranchevent Léon-Charles , Glänzel Wolfgang , Suykens Johan A. K. , De Moor Bart , Moreau Yves
Published: October 2010

Motivation: We propose a novel algorithm to combine multiple kernels and Laplacians for clustering analysis. The new algorithm is formulated on a Rayleigh quotient objective function and is solved as a bi-level alternating minimization procedure. Using the proposed algorithm, the coefficients of kernels and Laplacians can be optimized automatically.

Results: Three variants of the algorithm are proposed. The performance is systematically validated on two real-life data fusion applications. The proposed Optimized Kernel Laplacian Clustering (OKLC) algorithms perform significantly better than other methods. Moreover, the coefficients of kernels and Laplacians optimized by OKLC show some correlation with the rank of performance of individual data source. Though in our evaluation the K values are predefined, in practical studies, the optimal cluster number can be consistently estimated from the eigenspectrum of the combined kernel Laplacian matrix.

Availability: The MATLAB code of algorithms implemented in this paper is downloadable from http://homes.esat.kuleuven.be/~sistawww/bioi/syu/oklc.html.

Contact:  shiyu@uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Neostigmine/Glycopyrrolate Administered after Recovery from Neuromuscular Block Increases Upper Airway Collapsibility by Decreasing Genioglossus Muscle Activity in Response to Negative Pharyngeal Pressure
Authors: Herbstreit Frank , Zigrahn Daniela , Ochterbeck Christof , Peters Jürgen , Eikermann Matthias
Published: October 2010

Background

Reversal of residual neuromuscular blockade by acetylcholinesterase inhibitors (e.g., neostigmine) improves respiratory function. However, neostigmine may also impair muscle strength. We hypothesized that neostigmine administered after recovery of the train-of-four (TOF) ratio impairs upper airway integrity and genioglossus muscle function.

Methods

We measured, in 10 healthy male volunteers, epiglottic and nasal mask pressures, genioglossus electromyogram, air flow, respiratory timing, and changes in lung volume before, during (TOF ratio: 0.5), and after recovery of the TOF ratio to unity, and after administration of neostigmine 0.03 mg/kg IV (with glycopyrrolate 0.0075 mg/kg). Upper airway critical closing pressure (Pcrit) was calculated from flow-limited breaths during random pharyngeal negative pressure challenges.

Results

Pcrit increased significantly after administration of neostigmine/glycopyrrolate compared with both TOF recovery (mean ± SD, by 27 ± 21%; P = 0.02) and baseline (by 38 ± 17%; P = 0.002). In parallel, phasic genioglossus activity evoked by negative pharyngeal pressure decreased (by 37 ± 29%, P = 0.005) compared with recovery, almost to a level observed at a TOF ratio of 0.5. Lung volume, respiratory timing, tidal volume, and minute ventilation remained unchanged after neostigmine/glycopyrrolate injection.

Conclusion

Neostigmine/glycopyrrolate, when administered after recovery from neuromuscular block, increases upper airway collapsibility and impairs genioglossus muscle activation in response to negative pharyngeal pressure. Reversal with acetylcholinesterase inhibitors may be undesirable in the absence of neuromuscular blockade.
Electrical signalling of dominance in a wild population of electric fish
Authors: Fugère Vincent , Ortega Hernán , Krahe Rüdiger
Published: October 2010

Animals often use signals to communicate their dominance status and avoid the costs of combat. We investigated whether the frequency of the electric organ discharge (EOD) of the weakly electric fish,
Sternarchorhynchus
sp., signals the dominance status of individuals. We correlated EOD frequency with body size and found a strong positive relationship. We then performed a competition experiment in which we found that higher frequency individuals were dominant over lower frequency ones. Finally, we conducted an electrical playback experiment and found that subjects more readily approached and attacked the stimulus electrodes when they played low-frequency signals than high-frequency ones. We propose that EOD frequency communicates dominance status in this gymnotiform species.
Performance of human groups in social foraging: the role of communication in consensus decision making
Authors: King Andrew J. , Narraway Claire , Hodgson Lindsay , Weatherill Aidan , Sommer Volker , Sumner Seirian
Published: October 2010

Early hominids searched for dispersed food sources in a patchy, uncertain environment, and modern humans encounter equivalent spatial–temporal coordination problems on a daily basis. A fundamental, but untested assumption is that our evolved capacity for communication is integral to our success in such tasks, allowing information exchange and consensus decisions based on mutual consideration of pooled information. Here we examine whether communication enhances group performance in humans, and test the prediction that consensus decision-making underlies group success. We used bespoke radio-tagging methodology to monitor the incremental performance of communicating and non-communicating human groups (small group sizes of two to seven individuals), during a social foraging experiment. We found that communicating groups (
n
= 22) foraged more effectively than non-communicating groups (
n
= 21) and were able to reach consensus decisions (an ‘agreement’ on the most profitable foraging resource) significantly more often than non-communicating groups. Our data additionally suggest that gesticulations among group members played a vital role in the achievement of consensus decisions, and therefore highlight the importance of non-verbal signalling of intentions and desires for successful human cooperative behaviour.
Heritability of female extra-pair paternity rate in song sparrows (Melospiza melodia)
Authors: Reid Jane M. , Arcese Peter , Sardell Rebecca J. , Keller Lukas F.
Published: October 2010

The forces driving the evolution of extra-pair reproduction in socially monogamous animals remain widely debated and unresolved. One key hypothesis is that female extra-pair reproduction evolves through indirect genetic benefits, reflecting increased additive genetic value of extra-pair offspring. Such evolution requires that a female's propensity to produce offspring that are sired by an extra-pair male is heritable. However, additive genetic variance and heritability in female extra-pair paternity (EPP) rate have not been quantified, precluding accurate estimation of the force of indirect selection. Sixteen years of comprehensive paternity and pedigree data from socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia) showed significant additive genetic variance and heritability in the proportion of a female's offspring that was sired by an extra-pair male, constituting major components of the genetic architecture required for extra-pair reproduction to evolve through indirect additive genetic benefits. However, estimated heritabilities were moderately small (0.12 and 0.18 on the observed and underlying latent scales, respectively). The force of selection on extra-pair reproduction through indirect additive genetic benefits may consequently be relatively weak. However, the additive genetic variance and non-zero heritability observed in female EPP rate allow for multiple further genetic mechanisms to drive and constrain mating system evolution.
Chimpanzees help conspecifics obtain food and non-food items
Authors: Melis Alicia P. , Warneken Felix , Jensen Keith , Schneider Anna-Claire , Call Josep , Tomasello Michael
Published: October 2010

Chimpanzees (Pan troglodytes) sometimes help both humans and conspecifics in experimental situations in which immediate selfish benefits can be ruled out. However, in several experiments, chimpanzees have not provided food to a conspecific even when it would cost them nothing, leading to the hypothesis that prosociality in the food-provisioning context is a derived trait in humans. Here, we show that chimpanzees help conspecifics obtain both food and non-food items—given that the donor cannot get the food herself. Furthermore, we show that the key factor eliciting chimpanzees' targeted helping is the recipients' attempts to either get the food or get the attention of the potential donor. The current findings add to the accumulating body of evidence that humans and chimpanzees share the motivation and skills necessary to help others in situations in which they cannot selfishly benefit. Humans, however, show prosocial motives more readily and in a wider range of contexts.
Plant-ants feed their host plant, but above all a fungal symbiont to recycle nitrogen
Authors: Defossez Emmanuel , Djiéto-Lordon Champlain , McKey Doyle , Selosse Marc-André , Blatrix Rumsaïs
Published: October 2010

In ant–plant symbioses, plants provide symbiotic ants with food and specialized nesting cavities (called domatia). In many ant–plant symbioses, a fungal patch grows within each domatium. The symbiotic nature of the fungal association has been shown in the ant-plant
Leonardoxa africana
and its protective mutualist ant
Petalomyrmex phylax
. To decipher trophic fluxes among the three partners, food enriched in
13
C and
15
N was given to the ants and tracked in the different parts of the symbiosis up to 660 days later. The plant received a small, but significant, amount of nitrogen from the ants. However, the ants fed more intensively the fungus. The pattern of isotope enrichment in the system indicated an ant behaviour that functions specifically to feed the fungus. After 660 days, the introduced nitrogen was still present in the system and homogeneously distributed among ant, plant and fungal compartments, indicating efficient recycling within the symbiosis. Another experiment showed that the plant surface absorbed nutrients (in the form of simple molecules) whether or not it is coated by fungus. Our study provides arguments for a mutualistic status of the fungal associate and a framework for investigating the previously unsuspected complexity of food webs in ant–plant mutualisms.
Neural processing of imminent collision in humans
Authors: Billington Jac , Wilkie Richard M. , Field David T. , Wann John P.
Published: October 2010

Detecting a looming object and its imminent collision is imperative to survival. For most humans, it is a fundamental aspect of daily activities such as driving, road crossing and participating in sport, yet little is known about how the brain both detects and responds to such stimuli. Here we use functional magnetic resonance imaging to assess neural response to looming stimuli in comparison with receding stimuli and motion-controlled static stimuli. We demonstrate for the first time that, in the human, the superior colliculus and the pulvinar nucleus of the thalamus respond to looming in addition to cortical regions associated with motor preparation. We also implicate the anterior insula in making timing computations for collision events.
Sizing up your enemy: individual predation vulnerability predicts migratory probability
Authors: Skov Christian , Baktoft Henrik , Brodersen Jakob , Brönmark Christer , Chapman Ben B. , Hansson Lars-Anders , Nilsson P. Anders
Published: October 2010

Partial migration, in which a fraction of a population migrate and the rest remain resident, occurs in an extensive range of species and can have powerful ecological consequences. The question of what drives differences in individual migratory tendency is a contentious one. It has been shown that the timing of partial migration is based upon a trade-off between seasonal fluctuations in predation risk and growth potential. Phenotypic variation in either individual predation risk or growth potential should thus mediate the strength of the trade-off and ultimately predict patterns of partial migration at the individual level (i.e. which individuals migrate and which remain resident). We provide cross-population empirical support for the importance of one component of this model—individual predation risk—in predicting partial migration in wild populations of breamAbramis brama, a freshwater fish. Smaller, high-risk individuals migrate with a higher probability than larger, low-risk individuals, and we suggest that predation risk maintains size-dependent partial migration in this system.
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
Authors: Lunter Gerton , Goodson Martin
Published: October 2010

High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences (“reads”) resulting from a sequencing run are first “mapped” (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
Authors: Le Si Quang , Durbin Richard
Published: October 2010

Reductions in the cost of sequencing have enabled whole-genome sequencing to identify sequence variants segregating in a population. An efficient approach is to sequence many samples at low coverage, then to combine data across samples to detect shared variants. Here, we present methods to discover and genotype single-nucleotide polymorphism (SNP) sites from low-coverage sequencing data, making use of shared haplotype (linkage disequilibrium) information. For each population, we first collect SNP candidates based on independent sequence calls per site. We then use MARGARITA with genotype or phased haplotype data from the same samples to collect 20 ancestral recombination graphs (ARGs). We refine the posterior probability of SNP candidates by considering possible mutations at internal branches of the 40 marginal ancestral trees inferred from the 20 ARGs at the left and right flanking genotype sites. Using a population genetic prior distribution on tree-branch length and Bayesian inference, we determine a posterior probability of the SNP being real and also the most probable phased genotype call for each individual. We present experiments on both simulation data and real data from the 1000 Genomes Project to prove the applicability of the methods. We also explore the relative tradeoff between sequencing depth and the number of sequenced samples.
DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials
Authors: Vallotton Pascal , Sun Changming , Lovell David , Fazio Vincent J. , Newman Janet
Published: October 2010

The application of robotics to protein crystallization trials has resulted in the production of millions of images. Manual inspection of these images to find crystals and other interesting outcomes is a major rate-limiting step. As a result there has been intense activity in developing automated algorithms to analyse these images. The very first step for most systems that have been described in the literature is to delineate each droplet. Here, a novel approach that reaches over 97% success rate and subsecond processing times is presented. This will form the seed of a new high-throughput system to scrutinize massive crystallization campaigns automatically.