bluuebunny/crossref_metadata_2025 huggingface dataset:
Electromagnetic-wave absorption properties of FeCo nanocapsules and coral-like aggregates self-assembled by the nanocapsules
Authors: Liu X. G. , Geng D. Y. , Ma S. , Meng H. , Tong M. , Kang D. J. , Zhang Z. D.
Published: September 2008

FeCo nanocapsules with FeCo alloy as core and amorphous Al2O3 as shell have been synthesized by a modified arc-discharge technique. Three-dimensional coral-like aggregates are self-assembled by the nanocapsules in the arc-discharge process. The FeCo nanocapsules are ferromagnetic at room temperature. The electromagnetic-wave absorption properties of FeCo nanocapsules were investigated in the frequency range from 2 to 18 GHz. A reflection loss exceeding −20 dB was obtained in the frequency range of 5.2–15.9 GHz for absorber thicknesses of 2–4 mm. An optimal reflection loss of −44.8 dB was reached at 12.8 GHz for an absorber thickness of 3 mm. As a result, these FeCo nanocapsules may be applied in high-frequency electromagnetic-wave absorption.
Interaction of low-energy nitrogen ions with GaAs surfaces
Authors: Majlinger Z. , Bozanic A. , Petravic M. , Kim K.-J. , Kim B. , Yang Y.-W.
Published: September 2008

We have studied the interaction of low-energy nitrogen ions (0.3–2 keV N2+) with GaAs (100) surfaces by photoemission spectroscopy (PES) around N 1s and Ga 3d core levels and near-edge x-ray absorption fine structure (NEXAFS) around the N K edge. At the lowest bombardment energy, nitrogen forms bonds with both Ga and As, while Ga-N bonds form preferentially at higher energies. Thermal annealing at temperatures above 350 °C promotes the formation of GaN on the surface, but it is insufficient to remove the disorder introduced by ion implantation. Nitrogen interstitials and antisites have been identified in NEXAFS spectra, while interstitial molecular nitrogen provides a clear signature in both PES and NEXAFS.
Symmetry unbreaking in the shapes of perfect projectiles
Authors: Roper Marcus , Squires Todd M. , Brenner Michael P.
Published: September 2008

We study the shapes of perfect projectiles: Bodies of prescribed volume that are designed to suffer minimum fluid drag in steady flight. Perfect projectiles have a surprising property: Although the flow of fluid around the body of the projectile is fore-aft asymmetric at moderate flow speeds, the shape of the body that minimizes drag is nonetheless highly symmetrical. We show that perfect projectiles are weakly asymmetric and that their asymmetry grows with the cube of the projectile size for sufficiently small projectiles. The persistence of apparent fore-aft symmetry is speculated to be a signature of the linearity and reciprocity of the drag-determining features of the flow around the projectile.
The Lorentz group and its finite field analogs: Local isomorphism and approximation
Authors: Foldes Stephan
Published: September 2008

Finite Lorentz groups acting on four-dimensional vector spaces coordinatized by finite fields with a prime number of elements are represented as homomorphic images of countable, rational subgroups of the Lorentz group acting on real four-dimensional space-time. Bounded subsets of the real Lorentz group are retractable with arbitrary precision to finite subsets of such rational subgroups. These finite retracts correspond, via local isomorphisms, to well-behaved subsets of Lorentz groups over finite fields. This establishes a relationship of approximation between the real Lorentz group and Lorentz groups over very large finite fields.
Breaching the work output limitation of ferromagnetic shape memory alloys
Authors: Ganor Yaniv , Shilo Doron , Shield Thomas W. , James Richard D.
Published: September 2008

One important parameter that quantifies the performance of ferromagnetic shape memory alloys is the blocking stress. To date, the low blocking levels (<5 MPa) impede the utilization of these alloys in applications where high work output is required. In this paper, we demonstrate an increase in the blocking stress by more than 100% by reducing the actuator size. A new theoretical model shows that smaller specimens have increased values of the blocking stress due to an enhancement in the energy barrier to magnetization rotation and indicates on a fundamental relationship among the specimen size, its microstructure, and its physical properties.
Good performance of the M06 family of hybrid meta generalized gradient approximation density functionals on a difficult case: CO adsorption on MgO(001)
Authors: Valero Rosendo , Gomes José R. B. , Truhlar Donald G. , Illas Francesc
Published: September 2008

The adsorption of CO on Mg(001) constitutes a challenge for current density functional approximations because of its weak interaction character. In the present work we show that the M06-2X and M06-HF exchange-correlation functionals are the first ones to provide a simultaneously satisfactory description of adsorbate geometry, vibrational frequency shift, and adsorption energy of CO on MgO(001). For a sufficiently large embedded cluster model, the three functionals of the M06 family—which contain a nonzero percentage of Hartree–Fock exchange (M06, M06-2X, and M06-HF)—all predict positive C–O vibrational shifts, in agreement with the experimental findings, while the local M06-L functional gives large negative shifts. Moreover, the shifts computed with the M06-2X and M06-HF potentials are in good agreement with the experimental shift of +14 cm−1. The interaction energy (De) calculated with M06-2X and M06-HF is ∼6.0 kcal/mol, which agrees well with the De value (∼4 kcal/mol) deduced from the D0 obtained in thermal desorption measurements on single-crystal surfaces.
Resistive edge mode instability in stellarator and tokamak geometries
Authors: Mahmood M. Ansar , Rafiq T. , Persson M. , Weiland J.
Published: September 2008

Geometrical effects on linear stability of electrostatic resistive edge modes are investigated in the three-dimensional Wendelstein 7-X stellarator [G. Grieger et al., Plasma Physics and Controlled Nuclear Fusion Research 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525] and the International Thermonuclear Experimental Reactor [Progress in the ITER Physics Basis, Nucl. Fusion 7, S1, S285 (2007)]-like equilibria. An advanced fluid model is used for the ions together with the reduced Braghinskii equations for the electrons. Using the ballooning mode representation, the drift wave problem is set as an eigenvalue equation along a field line and is solved numerically using a standard shooting technique. A significantly larger magnetic shear and a less unfavorable normal curvature in the tokamak equilibrium are found to give a stronger finite-Larmor radius stabilization and a more narrow mode spectrum than in the stellarator. The effect of negative global magnetic shear in the tokamak is found to be stabilizing. The growth rate on a tokamak magnetic flux surface is found to be comparable to that on a stellarator surface with the same global magnetic shear but the eigenfunction in the tokamak is broader than in the stellarator due to the presence of large negative local magnetic shear (LMS) on the tokamak surface. A large absolute value of the LMS in a region of unfavorable normal curvature is found to be stabilizing in the stellarator, while in the tokamak case, negative LMS is found to be stabilizing and positive LMS destabilizing.
Development of a simple 2.45 GHz microwave plasma with a repulsive double hexapole configuration
Authors: Arciaga Marko , Tumlos Roy , Ulano April , Lee Henry , Lledo Rumar , Ramos Henry
Published: September 2008

A simple and inexpensive 2.45 GHz microwave plasma source with a repulsive double hexapole configuration is described and characterized. In this work, the operation of the source is shown to be flexible in terms of electron density, electron temperature, and plasma uniformity even at low-pressures (approximately millitorr). It allows for easy control of the electron temperature (2–3.8 eV) and density (∼109–1010 cm−3) by removing either of the two hexapoles or by varying the separation distance between the two hexapoles. Characterization was done via information gathered from the usual Langmuir probe measurements for electron temperature and density. The source makes a resonant surface with its repulsive double hexapole magnetic configuration providing an additional longitudinal confinement near the walls midway between the two hexapoles. Magnetic field maps are presented for varying double hexapole distances. Power delivery for various settings is also presented.
Ultralow power consumption gas sensors based on self-heated individual nanowires
Authors: Prades J. D. , Jimenez-Diaz R. , Hernandez-Ramirez F. , Barth S. , Cirera A. , Romano-Rodriguez A. , Mathur S. , Morante J. R.
Published: September 2008

Dissipated power in metal oxide nanowires (rNW<45 nm) often causes important self-heating effects and as a result, undesired aging and failure of the devices. Nevertheless, this effect can be used to optimize the sensing conditions for the detection of various gaseous species, avoiding the requirement of external heaters. In this letter, the sensing capabilities of self-heated individual SnO2 nanowires toward NO2 are presented. These proof-of-concept systems exhibited responses nearly identical to those obtained with integrated microheaters, demonstrating the feasibility of taking advantage of self-heating in nanowires to develop ultralow power consumption integrated devices.
An electrical switch based on Ag-tetracyanoquinodimethane sandwiched by crossed carbon nanotube electrodes
Authors: Zhou Wei , Ren Liang , Lin Feng , Jiao Liying , Xue Teng , Xian Xiaojun , Liu Zhongfan
Published: September 2008

We report herein a method to fabricate an electrical switch device in which two crossed carbon nanotubes (CNTs) serve as electrode contacts and Ag-tetracyanoquinodimethane (AgTCNQ) is embedded into the crossed point functions as the electrical bistable medium. To fabricate this device, an electrodeposition method is used to grow AgTCNQ particles along a CNT, and then the top CNT is placed intersectionally over the former tube wrapped with AgTCNQ. The device shows typical switching performance with an on/off ratio up to 103. The excellent electrical properties and nanoscale diameter of CNTs of this device show promising applications in the integrations of CNT nanoelectronics.
Thermal bending of nanojets: Molecular dynamics simulations of an asymmetrically heated nozzle
Authors: Kang Wei , Landman Uzi , Glezer Ari
Published: September 2008

A method for deflecting high velocity liquid nanojets through nonuniform asymmetric heating of a cylindrical nozzle is described using molecular dynamics simulations of liquid propane. The deflection originates mainly from a strong, highly nonisotropic evaporation flux from the liquid near the exit, resulting in overall cooling and a force that bends the nanojet in the lower temperature direction. Also discussed is the formation of a self-convergent virtual nozzle in the injector-confined liquid with an exit radius smaller than that of the injector, portraying the temperature and density profiles in the heated liquid and resulting in a nanojet of reduced dimensions.
Observation of coupled-cavity structures in metamaterials
Authors: Caglayan Humeyra , Bulu Irfan , Loncar Marko , Ozbay Ekmel
Published: September 2008

In this letter, we investigated the transmission properties of metamaterial based coupled-cavity structures. We first calculated the effective parameters of a split-ring resonator (SRR) and composite metamaterial (CMM) structures. Subsequently, we introduced coupled-cavity structures and presented the transmission spectrum of SRR and CMM based coupled-cavity structures. The splitting of eigenmodes was observed due to the interaction between the localized electromagnetic cavity modes. Finally, the dispersion relation and normalized group velocity of the coupled-cavity structures were calculated. The maximum group velocity was found to be 100 times smaller than the speed of light in vacuum.
Laser activation of dopants for nanowire devices on glass and plastic
Authors: Misra Nipun , Grigoropoulos Costas P. , Stumbo David P. , Miller Jeffrey N.
Published: September 2008

We report postgrowth doping of silicon nanowires (SiNWs) through ion implantation and subsequent annealing with nanosecond pulsed laser light. The green laser annealing process allows for polarization selective localized heating and enables highly efficient activation of implanted boron and arsenic in the SiNWs as revealed by electrical resistivity measurements. Transistor devices fabricated by this technique show reduced parasitic series resistance and higher drive currents making the process suitable for fabrication of high-performance NW based electronics on glass and plastics.
Experimental study of the thermoelectric power factor enhancement in composites
Authors: Heremans J. P. , Jaworski C. M.
Published: September 2008

D. J. Bergman and L. J. Fel [J. Appl. Phys. 85, 8205 (1999)] calculated that in composites the thermoelectric power factor, the product of the square of the thermopower and the electrical conductivity, can be enhanced over that of the individual constituents, but the figure of merit cannot. This is demonstrated here experimentally in the elemental bismuth-silver system, and ascribed to the fact that inclusions of a highly electrically conducting material (Ag) in a matrix of a material with a high thermopower (Bi) enhance the conductivity of the composite more than they reduce its thermopower. The power factor is technologically important in transient thermoelectric cooling.
Spectral effects of gain saturation in the β-phase of poly(9,9-dioctylfluorene)
Authors: Anni M. , Alemanno M.
Published: September 2008

We investigated the amplified spontaneous emission (ASE) properties of the β-phase of poly(9,9-dioctylfluorene) at T=5 K. We observe ASE at about 478 nm with a threshold as low as 50 μJ cm−2. For excitation density higher than 350 μJ cm−2 a clear spectral rebroadening and a progressive ASE intensity saturation, ascribed to gain saturation, are observed. The gain saturation at 478 nm leads to ASE from the 470 nm vibronic band, with a threshold of about 3.0 mJ cm−2. We show that these effects are due to the break down, at high excitation density, of the four level amplifier scheme, typically applied to conjugated polymer films.
Silicon nanowire detectors showing phototransistive gain
Authors: Zhang Arthur , You Sifang , Soci Cesare , Liu Yisi , Wang Deli , Lo Yu-Hwa
Published: September 2008

Nanowire photodetectors are shown to function as phototransistors with high sensitivity. Due to small lateral dimensions, a nanowire detector can have low dark current while showing large phototransistive gain. Planar and vertical silicon nanowire photodetectors fabricated in a top-down approach using an etching process show a phototransistive gain above 35 000 at low light intensities. Simulations show that incident light can be waveguided into vertical nanowires resulting in up to 40 times greater external quantum efficiency above their physical fill factor. Vertical silicon nanowire phototransistors formed by etching are attractive for low light level detection and for integration with silicon electronics.
Dislocation density reduction in multicrystalline silicon solar cell material by high temperature annealing
Authors: Hartman Katy , Bertoni Mariana , Serdy James , Buonassisi Tonio
Published: September 2008

We propose and demonstrate a method to remove performance-limiting dislocations from multicrystalline silicon (mc-Si) solar cell material, appropriate for wafers or bricks. Dislocation density reductions of >95% are achieved in commercial mc-Si via high temperature annealing with an impurity diffusion barrier, with controlled ambient and time-temperature profiles. The dislocation density reduction follows temperature-dependent models developed by Kuhlmann [Proc. Phys. Soc., London, Sect. A 64, 140 (1951)] and Nes [Acta Metall. Mater. 43, 2189 (1995)]. It is believed that higher annealing temperatures (>1170 °C) allow dislocation movement unconstrained by crystallographic glide planes, leading to dislocation annihilation within minutes.
Resonantly enhanced reflection of quadrupole polaritons in Cu2O
Authors: Jang J. I. , Sun Y. , Mani S. , Ketterson J. B.
Published: September 2008

Using resonant two-photon excitation, we create a coherently propagating polariton wave packet and measure its reflectance (R) and transmittance (T) at the boundary opposite to the incoming surface. We find an enhanced reflection of polaritons from sample surfaces such that the ratio T/R deviates significantly from the present theory. This anomalous boundary effect most likely arises from the quadrupole excitonic component of polaritons.
Imaging the antiparallel magnetic alignment of adjacent Fe and MnAs thin films
Authors: Breitwieser R. , Marangolo M. , Lüning J. , Jaouen N. , Joly L. , Eddrief M. , Etgens V. H. , Sacchi M.
Published: September 2008

The magnetic coupling between iron and α-MnAs in the epitaxial system Fe/MnAs/GaAs(001) has been studied at the submicron scale, using element-selective x-ray photoemission electron microscopy. At room temperature, MnAs layers display ridges and grooves, alternating α (magnetic) and β (nonmagnetic) phases. The self-organized microstructure of MnAs and the stray fields that it generates govern the local alignment between the Fe and α-MnAs magnetization directions, which is mostly antiparallel with a marked dependence upon the magnetic domain size.
Dichromatic color tuning with InGaN-based light-emitting diodes
Authors: Fellows Natalie N. , Sato Hitoshi , Lin You-da , Chung Roy B. , DenBaars Steven P. , Nakamura Shuji
Published: September 2008

Color tuning GaN based light-emitting diodes (LEDs) both electrically and optically was investigated. Color mixing of two LED dies, one nonpolar (λp=467 nm) and one semipolar (λp=574 nm), produced white light. Electrically, the correct current was supplied to each die in order to change its correlated color temperature and Commission Internationale de l’Eclairage (CIE) chromaticity coordinates from 3287 K and (0.425, 0.413) to 7242 K and (0.303, 0.315). The optical polarization anisotropy inherent in nonpolar and semipolar wurtzite GaN allowed color tuning optically with the use of a polarizer. Several regions of the CIE diagram were explored using this method and are discussed.
Electron emission from Pd-carbon compound film on carbon nanoislands
Authors: Zhu Dan , Li Dejie , Wang Jian
Published: September 2008

Electron emission from Pd-carbon compound thin film based on carbon nanoislands is reported. The carbon nanoislands, which are formed by etching uniform carbon film in oxygen plasma using Bi nanoislands as the mask, introduce local heating of Pd-carbon thin film on it and help in forming the electron emission area. Electron emission with good stability and uniformity is reproducibly obtained with the emission efficiency up to 0.9% when an anode voltage of 3 kV is applied with a distance of 2 mm.
Role of fluorine in plasma nitridated ZrO2 thin films under irradiation
Authors: Huang A. P. , Xiao Z. S. , Liu X. Y. , Wang L. , Chu Paul K.
Published: September 2008

The role of fluorine in plasma-nitridated ZrO2 thin films under electron irradiation is investigated in situ by real-time high-resolution transmission electron microscopy. Fluorine and nitrogen codoping can suppress the microstructure evolution during electron beam bombardment and the corresponding origin is probed and verified. The results obtained by irradiation with an ultraviolet laser show that plasma fluorination can effectively remove the dissociative N or O particles in the ZrO2 thin films which can escape from the interstitial sites under electron irradiation. The mechanism of the irradiation stability of the F and N codoped ZrO2 thin film is also discussed.
Magnetotransport of manganite superlattices: Investigating the role of a magnetic insulating spacer
Authors: Niebieskikwiat D. , Hueso L. E. , Mathur N. D. , Salamon M. B.
Published: September 2008

Magnetotransport data are presented for a set of manganite superlattices comprising La2∕3Sr1∕3MnO3 as the ferromagnetic (FM) metallic layers (thickness 11.9nm) and Pr2∕3Ca1∕3MnO3 as the antiferromagnetic insulating spacer (IS) with thicknesses tIS between 0.8 and 7.6nm. Previous studies on this system showed the presence of FM inclusions within the IS, with a notable magnetization peak at tIS∼3nm. Now, we show that this peak is also accompanied by a maximum in the magnetoresistance (MR). Moreover, the MR data of all the samples scale in a single curve, MR∝MIS2, where MIS is the magnetization of the IS. These results provide a quantitative demonstration of the feasibility to improve the response of engineered MR devices by including magnetically active IS instead of the usual nonmagnetic compounds.
Determination of free carrier density in the low doping regime of 4H-SiC by Raman scattering
Authors: Nakashima S. , Kitamura T. , Kato T. , Kojima K. , Kosugi R. , Okumura H. , Tsuchida H. , Ito M.
Published: September 2008

The free carrier concentration of n-4H-SiC was deduced by Raman spectroscopy using LO phonon plasmon coupled (LOPC) modes as a monitor band. We could determine the free carrier concentration from the reading of the peak frequency of the LOPC mode in the concentration range from 1019 down to 1016cm−3. The damping of LO phonons was evaluated as a function of the carrier concentration. Line shape analysis of the LOPC mode revealed that the damping of the LO phonon deduced from this analysis is sensitive to charged defects including ionized impurities.
Band alignment of InN∕GaAs heterojunction determined by x-ray photoelectron spectroscopy
Authors: Zhang Riqing , Guo Yan , Song Huaping , Liu Xianglin , Yang Shaoyan , Wei Hongyuan , Zhu Qinsheng , Wang Zhanguo
Published: September 2008

The valence band offset (VBO) of the InN∕GaAs heterojunction is directly determined by x-ray photoelectron spectroscopy to be 0.94±0.23eV. The conduction band offset is deduced from the known VBO value to be 1.66±0.23eV, and a type-II band alignment forms at the InN∕GaAs heterojunction.
Mitochondrial potassium channel Kv1.3 mediates Bax-induced apoptosis in lymphocytes
Authors: Szabó Ildikò , Bock Jürgen , Grassmé Heike , Soddemann Matthias , Wilker Barbara , Lang Florian , Zoratti Mario , Gulbins Erich
Published: September 2008

The potassium channel Kv1.3 has recently been located to the inner mitochondrial membrane of lymphocytes. Here, we show that mouse and human cells that are genetically deficient in either Kv1.3 or transfected with siRNA to suppress Kv1.3-expression resisted apoptosis induced by several stimuli, including Bax over-expression. Retransfection of either Kv1.3 or a mitochondrial-targeted Kv1.3 restored cell death. Bax interacted with and functionally inhibited mitochondrial Kv1.3. Incubation of isolated Kv1.3-positive mitochondria with recombinant Bax, t-Bid, or toxins that bind to and inhibit Kv1.3 successively triggered hyperpolarization, formation of reactive oxygen species, release of cytochrome
c
, and marked depolarization. Kv1.3-deficient mitochondria were resistant to Bax, t-Bid, and the toxins. Mutation of Bax at K128, which corresponds to a conserved lysine in Kv1.3-inhibiting toxins, abrogated its effects on both Kv1.3 and mitochondria. These findings suggest that Bax mediates cytochrome
c
release and mitochondrial depolarization in lymphocytes, at least in part, via its interaction with mitochondrial Kv1.3.
S4-based voltage sensors have three major conformations
Authors: Villalba-Galea Carlos A. , Sandtner Walter , Starace Dorine M. , Bezanilla Francisco
Published: September 2008

Voltage sensors containing the charged S4 membrane segment display a gating charge vs. voltage (
Q–V
) curve that depends on the initial voltage. The voltage-dependent phosphatase (Ci-VSP), which does not have a conducting pore, shows the same phenomenon and the
Q–V
recorded with a depolarized initial voltage is more stable by at least 3
RT
. The leftward shift of the
Q–V
curve under prolonged depolarization was studied in the Ci-VSP by using electrophysiological and site-directed fluorescence measurements. The fluorescence shows two components: one that traces the time course of the charge movement between the resting and active states and a slower component that traces the transition between the active state and a more stable state we call the relaxed state. Temperature dependence shows a large negative enthalpic change when going from the active to the relaxed state that is almost compensated by a large negative entropic change. The
Q–V
curve midpoint measured for pulses that move the sensor between the resting and active states, but not long enough to evolve into the relaxed states, show a periodicity of 120°, indicating a 3
10
secondary structure of the S4 segment when determined under histidine scanning. We hypothesize that the S4 segment moves as a 3
10
helix between the resting and active states and that it converts to an α-helix when evolving into the relaxed state, which is most likely to be the state captured in the crystal structures.
Advanced impedance matching system for ICRF heating using innovative twin stub tuner and frequency variation
Authors: Kumazawa R. , Saito K. , Kasahara H. , Seki T. , Mutoh T. , Shimpo F. , Nomura G. , Kato A. , Okada H. , Zhao Y. , Kwak J.G. , Yoon J.S.
Published: September 2008

Ion cyclotron range of frequency (ICRF) heating has been a reliable tool for steady-state plasma heating with high RF power of several tens of megawatts. However, a sudden increase in the reflected RF power during ICRF heating experiments with ELMy H-mode plasmas is an issue which must be solved for future fusion experimental devices or fusion reactors. This paper describes an innovative ICRF heating system using a frequency feedback control to reduce the reflected power in response to the rapid change in the plasma impedance in the ELMy H-mode plasma. A twin stub tuner has been newly invented for this purpose. The feasibility of keeping the reflected RF power fraction at a low level, e.g. 1%, is demonstrated even with a large change in plasma resistance, e.g. 2 ∼ 8Ω. Calculated and experimental results are presented for the conventional double stub tuner impedance matching system equipped with the twin stub tuner.
Heat pulse propagation studies around magnetic islands induced by the Dynamic Ergodic Divertor in TEXTOR
Authors: Spakman G.W. , Hogeweij G.M.D. , Jaspers R.J.E. , Schüller F.C. , Westerhof E. , Boom J.E. , Classen I.G.J. , Delabie E. , Domier C. , Donné A.J.H. , Kantor M.Yu. , Krämer-Flecken A. , Liang Y. , Luhmann N.C. , Park H.K. , van de Pol M.J. , Schmitz O. , Oosterbeek J.W.
Published: September 2008

Since the efficiency of the tearing mode suppression by heating depends on the electron heat diffusivity it is important to know if the electron heat transport coefficients inside the island are reduced compared with the ambient plasma. With that aim, modulated ECRH has been employed for heat pulse propagation studies in and around magnetic islands at the TEXTOR tokamak. The combination of its special hardware tools of the Dynamic Ergodic Divertor to generate tearing modes, the ECRH system for producing heat pulses and the electron cyclotron emission imaging (ECE-Imaging) diagnostic for its analysis offered a direct view of the perturbed two-dimensional heat flow in around the magnetic island. Inside m/n = 2/1 and m/n = 3/1 islands with a flattened temperature profile, the electron heat transport is shown to be strongly reduced with respect to the surrounding plasma. Inside the islands a heat pulse diffusion coefficients χe ∼ 0.4 m2 s−1 was derived, while outside the island it is an order of magnitude larger χe > 3 m2 s−1. In contrast, power balance calculations of strongly heated islands show that the electron transport is similar to the surrounding plasma. These results suggest that the heat transport inside a magnetic island is also governed by a critical gradient-like behaviour, similar to the bulk plasma.
Edge Te and ne profiles during type-I ELM mitigation experiments with perturbation fields on JET
Authors: Alfier A. , Beurskens M. , Giovannozzi E. , Kempenaars M. , Koslowski H.R. , Liang Y. , McKenna C. , Pasqualotto R. , Saarelma S. , Walsh M. , De La Luna E.
Published: September 2008

Edge localized mode (ELM) mitigation experiments have been carried out at JET in type-I ELMy H-mode plasmas. ELM mitigation was achieved through a stochastic edge induced by the ex-vessel error field correction coils system and was found to be independent of the distance of the plasma edge to the JET wall. In all cases the detrimental effect of the ELM on pedestal confinement was considerably reduced during the stochastization phase. The new high resolution Thomson scattering (HRTS) diagnostic, which has recently become operational at JET, is used to study the behaviour of electron temperature, density and pressure pedestal profiles during the mitigation phase. The pedestal properties are monitored in a consistent way by applying a hyperbolic tangent fit to the HRTS measurements. Stability modelling with the ELITE code using the fits to the spatially resolved pedestal profile measurements suggests that the observed ELM mitigation can be understood in terms of the peeling–ballooning model. The mitigation correlates with a reduction of the edge pressure gradient (due to both a reduced height and an increased width of the edge pressure transport barrier) which is consistent with the linear ELM stability theory. It is observed that in the case of an n = 1 external field, the barrier position and height are correlated with the toroidal direction of the applied perturbation. Agreement is found between the barrier position measured by HRTS and obtained from plasma equilibrium reconstruction. The external perturbation induces a deformation of the plasma column that is primarily toroidally symmetric with a secondary component that is toroidally asymmetric
Bayesian learning of biological pathways on genomic data assimilation
Authors: Yoshida Ryo , Nagasaki Masao , Yamaguchi Rui , Imoto Seiya , Miyano Satoru , Higuchi Tomoyuki
Published: September 2008

Motivation: Mathematical modeling and simulation, based on biochemical rate equations, provide us a rigorous tool for unraveling complex mechanisms of biological pathways. To proceed to simulation experiments, it is an essential first step to find effective values of model parameters, which are difficult to measure from in vivo and in vitro experiments. Furthermore, once a set of hypothetical models has been created, any statistical criterion is needed to test the ability of the constructed models and to proceed to model revision.

Results: The aim of our research is to present a new statistical technology towards data-driven construction of in silico biological pathways. The method starts with a knowledge-based modeling with hybrid functional Petri net. It then proceeds to the Bayesian learning of model parameters for which experimental data are available. This process exploits quantitative measurements of evolving biochemical reactions, e.g. gene expression data. Another important issue that we consider is statistical evaluation and comparison of the constructed hypothetical pathways. For this purpose, we have developed a new Bayesian information–theoretic measure that assesses the predictability and the biological robustness of in silico pathways.

Availability: The FORTRAN source codes are available at the URL http://daweb.ism.ac.jp/~yoshidar/GDA/

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  yoshidar@ism.ac.jp
Searching protein structure databases with DaliLite v.3
Authors: Holm L. , Kääriäinen S. , Rosenström P. , Schenkel A.
Published: September 2008

The Red Queen said, ‘It takes all the running you can do, to keep in the same place.’ Lewis Carrol

Motivation: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive—thorough but slow—search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC.

Availability: The Dali server for protein structure database searching at http://ekhidna.biocenter.helsinki.fi/dali_server is running DaliLite v.3. The software can be downloaded for academic use from http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3.

Contact:  liisa.holm@helsinki.fi
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
Authors: Ferná;ndez Elmer A. , Girotti María R. , del Olmo Juan A. López , Llera Andrea S. , Podhajcer Osvaldo L. , Cantet Rodolfo J. C. , Balzarini Mónica
Published: September 2008

Motivation: Difference in-gel electrophoresis (DIGE)-based protein expression analysis allows assessing the relative expression of proteins in two biological samples differently labeled (Cy5, Cy3 CyDyes). In the same gel, a reference sample is also used (Cy2 CyDye) for spot matching during image analysis and volume normalization. The standard statistical techniques to identify differentially expressed (DE) proteins are the calculation of fold-changes and the comparison of treatment means by the t-test. The analyses rarely accounts for other experimental effects, such as CyDye and gel effects, which could be important sources of noise while detecting treatment effects.

Results: We propose to identify DIGE DE proteins using a two-stage linear mixed model. The proposal consists of splitting the overall model for the measured intensity into two interconnected models. First, we fit a normalization model that accounts for the general experimental effects, such as gel and CyDye effects as well as for the features of the associated random term distributions. Second, we fit a model that uses the residuals from the first step to account for differences between treatments in protein-by-protein basis. The modeling strategy was evaluated using data from a melanoma cell study. We found that a heteroskedastic model in the first stage, which also account for CyDye and gel effects, best normalized the data, while allowing for an efficient estimation of the treatment effects. The Cy2 reference channel was used as a covariate in the normalization model to avoid skewness of the residual distribution. Its inclusion improved the detection of DE proteins in the second stage.

Contact:  elmer.fernandez@ucc.edu.ar

Supplementary information: R and SAS codes to analyze DIGE data with the proposed approach are available at http://www.uccor.edu.ar/modelo.php?param=3.8.5.15.2
Predation increases acoustic complexity in primate alarm calls
Authors: Stephan Claudia , Zuberbühler Klaus
Published: September 2008

According to most accounts, alarm calling in non-human primates is a biologically hardwired behaviour with signallers having little control over the acoustic structure of their calls. In this study, we compared the alarm calling behaviour of two adjacent populations of Diana monkeys at Taï forest (Ivory Coast) and Tiwai Island (Sierra Leone), which differ significantly in predation pressure. At Taï, monkeys regularly interact with two major predators, crowned eagles and leopards, while at Tiwai, monkeys are only hunted by crowned eagles. We monitored the alarm call responses of adult male Diana monkeys to acoustic predator models. We found no site-specific differences in the types of calls given to eagles, leopards and general disturbances, but there were consistent differences in how callers assembled calls into sequences. At Tiwai, males responded to leopards and general disturbances in the same way, while at Taï, males discriminated by giving call sequences that differed in the number of component calls. Responses to eagles were identical at both sites. We concluded that Diana monkeys are predisposed to use their repertoire in context-specific ways, but that ontogenetic experience determines how individual calls are assembled into meaningful sequences.
Should we believe model predictions of future climate change?
Authors: Knutti Reto
Published: September 2008

Predictions of future climate are based on elaborate numerical computer models. As computational capacity increases and better observations become available, one would expect the model predictions to become more reliable. However, are they really improving, and how do we know? This paper discusses how current climate models are evaluated, why and where scientists have confidence in their models, how uncertainty in predictions can be quantified, and why models often tend to converge on what we observe but not on what we predict. Furthermore, it outlines some strategies on how the climate modelling community may overcome some of the current deficiencies in the attempt to provide useful information to the public and policy-makers.
Facing future climate change: is the past relevant?
Authors: Skinner Luke
Published: September 2008

From a socio-economic perspective, the ‘sharp end’ of climate research is very much about looking forward in time. As far as possible, we need to know what to expect and approximately when to expect it. However, it is argued here that our approach to climate change (including its scientific basis and its policy implications) is firmly linked to our understanding of the past. This is mainly due to the role played by palaeoclimate reconstructions in shaping our expectations of the climate system, in particular via their ability to test the accuracy of our climate models. Importantly, this includes the intuitive models that each of us carries around in our mind, as well as the more complex numerical models hiding inside supercomputers. It is through such models that palaeoclimate insights may affect the scientific and political judgements that we must make in the face of persistent and ultimately irreducible predictive uncertainty. Already we can demonstrate a great deal of confidence in our current understanding of the global climate system based specifically on insights from the geological record. If further advances are to be made effectively, climate models should take advantage of both past and present constraints on their behaviour, and should be given added credence to the extent that they are compatible with an increasingly rich tapestry of past climatic phenomena. Furthermore, palaeoclimate data should be accompanied by clearly defined uncertainties, and organized in arrays that are capable of speaking directly to numerical models, and their limitations in particular.
Validation of Kalmia buxifolia (Bergius) Gift & Kron and Kalmia procumbens (L.) Gift & Kron
Authors: Kron K. A. , Judd W. S. , Anderberg A. A.
Published: September 2008

The basionyms for Kalmia buxifolia and K. procumbens are cited in order to make the previously published new combinations valid.
Faecal microbiota profile of Crohn’s disease determined by terminal restriction fragment length polymorphism analysis
Authors: ANDOH A. , TSUJIKAWA T. , SASAKI M. , MITSUYAMA K. , SUZUKI Y. , MATSUI T. , MATSUMOTO T. , BENNO Y. , FUJIYAMA Y.
Published: September 2008

Background  Terminal restriction fragment length polymorphism (T‐RFLP) analyses are powerful tools to assess the diversity of complex microbiota. T‐RFLPs permit rapid comparisons of microbiota from many samples.

Aim  To perform T‐RFLP analyses of faecal microbiota in Crohn’s disease (CD) patients to investigate potential alterations in faecal microbial communities and furthermore to analyse the effects of elemental diet on faecal microbiota profiles.

Methods  Thirty‐four patients with CD and 30 healthy individuals were enrolled in the study. DNA was extracted from stool samples and 16S rRNA genes were amplified by PCR. PCR products were digested with BslI restriction enzymes and T‐RF lengths were determined.

Results  Faecal microbial communities were classified into seven clusters. Almost all healthy individuals (28/30) were included in cluster I, II and III, but the majority of CD patients (25/34) could be divided into another four clusters (cluster IV–VII). Prediction of bacteria based on the BslI‐digested T‐RFLP database showed a significant decrease in Clostridium cluster IV, Clostridium cluster XI and subcluster XIVa in CD patients. In contrast, Bacteroides significantly increased in CD patients. Significant increases in Enterobacteriales were also observed in CD patients. Furthermore, elemental diets modulated faecal bacterial communities in CD patients.

Conclusions  Terminal restriction fragment length polymorphism analyses showed that the diversity of faecal microbiota in patients with CD differed from that of healthy individuals. Furthermore, elemental diets modulated faecal microbiota composition, and this effect may be involved in mechanisms of clinical effects of elemental diet.
Nursing emotion work and interprofessional collaboration in general internal medicine wards: a qualitative study
Authors: Miller Karen‐Lee , Reeves Scott , Zwarenstein Merrick , Beales Jennifer D. , Kenaszchuk Chris , Conn Lesley Gotlib
Published: September 2008

Title.  Nursing emotion work and interprofessional collaboration in general internal medicine wards: a qualitative study

Aim.  This paper is a report of a study to examine nursing emotion work and interprofessional collaboration in order to understand and improve collaborative nursing practice.

Background.  Nursing standards identify collaborative practice as necessary for quality patient care yet many nurses are often reluctant to participate in interprofessional teams. Strategies intended to improve participation often fail which suggests that the factors underpinning nurses’ disinclination towards interprofessional collaboration have yet to be understood. The concept of emotion work has not been applied to nursing interprofessionalism, and holds the potential to improve collaborative practice. Nursing emotion work is defined as the management of the emotions of self and others in order to improve patient care.

Methods.  Qualitative data were collected in 2006 using non‐participant observation, shadowing and semi‐structured interviews with nursing, medical and allied professionals in the general internal medicine wards of three hospitals in urban Canada.

Findings.  Nurses’ collaborations with other professionals are influenced by emotion work considerations. The establishment and maintenance of a nursing esprit de corps, corridor conflicts with physicians, and the failure of the interdisciplinary team to acknowledge the importance of nursing’s core caring values are important factors underpinning nurses’ interprofessional disengagement.

Conclusion.  Longstanding emotion work issues must be addressed before nurses will engage collaboratively. We suggest improving nursing collaboration through the refining of holistic nursing information, and reflections on practice by all interprofessional team members.
Making robust decisions for conservation with restricted money and knowledge
Authors: McDonald‐Madden Eve , Baxter Peter W.J. , Possingham Hugh P.
Published: September 2008

In conservation decision‐making, we operate within the confines of limited funding. Furthermore, we often assume particular relationships between management impact and our investment in management. The structure of these relationships, however, is rarely known with certainty – there is model uncertainty. We investigate how these two fundamentally limiting factors in conservation management, money and knowledge, impact optimal decision‐making.

We use information‐gap decision theory to find strategies for maximizing the number of extant subpopulations of a threatened species that are most immune to failure due to model uncertainty. We thus find a robust framework for exploring optimal decision‐making.

The performance of every strategy decreases as model uncertainty increases.

The strategy most robust to model uncertainty depends not only on what performance is perceived to be acceptable but also on available funding and the time horizon over which extinction is considered.

Synthesis and applications. We investigate the impact of model uncertainty on robust decision‐making in conservation and how this is affected by available conservation funding. We show that subpopulation triage can be a natural consequence of robust decision‐making. We highlight the need for managers to consider triage not as merely giving up, but as a tool for ensuring species persistence in light of the urgency of most conservation requirements, uncertainty and the poor state of conservation funding. We illustrate this theory by a specific application to allocation of funding to reduce poaching impact on the Sumatran tiger Panthera tigris sumatrae in Kerinci Seblat National Park.
The nodule inception‐like protein 7 modulates nitrate sensing and metabolism in Arabidopsis
Authors: Castaings Loren , Camargo Antonio , Pocholle Delphine , Gaudon Virginie , Texier Yves , Boutet‐Mercey Stéphanie , Taconnat Ludivine , Renou Jean‐Pierre , Daniel‐Vedele Françoise , Fernandez Emilio , Meyer Christian , Krapp Anne
Published: September 2008

Nitrate is an essential nutrient, and is involved in many adaptive responses of plants, such as localized proliferation of roots, flowering or stomatal movements. How such nitrate‐specific mechanisms are regulated at the molecular level is poorly understood. Although the Arabidopsis ANR1 transcription factor appears to control stimulation of lateral root elongation in response to nitrate, no regulators of nitrate assimilation have so far been identified in higher plants. Legume‐specific symbiotic nitrogen fixation is under the control of the putative transcription factor, NIN, in Lotus japonicus. Recently, the algal homologue NIT2 was found to regulate nitrate assimilation. Here we report that Arabidopsis thaliana NIN‐like protein 7 (NLP7) knockout mutants constitutively show several features of nitrogen‐starved plants, and that they are tolerant to drought stress. We show that nlp7 mutants are impaired in transduction of the nitrate signal, and that the NLP7 expression pattern is consistent with a function of NLP7 in the sensing of nitrogen. Translational fusions with GFP showed a nuclear localization for the NLP7 putative transcription factor. We propose NLP7 as an important element of the nitrate signal transduction pathway and as a new regulatory protein specific for nitrogen assimilation in non‐nodulating plants.