bluuebunny/crossref_metadata_2025 huggingface dataset:
Current orientation and contact distance dependence of rapid voltage oscillations in the organic conductor β″-[bis(ethylenedithio)tetrathiafulvalene]3(HSO4)2
Authors: Wakita Hitoshi , Tamura Kozo , Ozawa Tatsuhiko , Bando Yoshimasa , Kawamoto Tadashi , Mori Takehiko
Published: December 2010

In an organic conductor β″-[bis(ethylenedithio)tetrathiafulvalene]3(HSO4)2, characteristic voltage oscillation is observed in the negative differential resistance region of the nonlinear conductivity below the metal–insulator transition at 125 K. The observed frequency f is 4–25 kHz and increases linearly with the collective current Jco. The oscillation appears in the two crystal directions of the conducting layer in agreement with the two-dimensional nonstripe charge order, where the anisotropy of the Jco/f slope is about two. The voltage oscillation disappears when the contact distance is larger than 0.02 cm, and at the same time the current-voltage characteristics loses a sharp negative resistance region. Since this critical length corresponds to the characteristic domain size of the charge order, the observed oscillation is interpreted by coherent transport of charge order which can move in different two directions.
Numeric description of space charge in polyethylene under ac electric fields
Authors: Zhao J. , Xu Z. , Chen G. , Lewin P. L.
Published: December 2010

Space charge in polyethylene-based insulation materials and its effect on the local electric field under a dc environment have been extensively examined over the last few decades while the behavior of space charge under ac stress has received less attention. Space charge phenomenon under ac electric fields becomes an important issue with increased operating field strength in many applications, such as next generation high voltage cables. In this paper, a bipolar charge transport model has been developed to simulate space charge in polymers under ac electric fields. Obtained simulation results show that there is a small quantity of phase-dependent bipolar charge accumulation in the vicinity of the electrodes that does not move into the bulk under ac stress. This causes a slight distortion of the local field in the bulk. However, at lower frequencies less than 1 Hz, there is increased charge accumulation and penetration. Comparison with available experimental data suggests that the model is capable of describing the underlying physics of charge behavior when a dielectric material is subjected to ac electric fields. Due to the weak charge movement in the bulk, the conduction current density is small and hence the displacement component dominates the total current density and this increases linearly with ac frequency.
A universal exponential factor in the dimensional crossover from graphene to graphite
Authors: Jiang Jin-Wu , Wang Jian-Sheng
Published: December 2010

A universal exponential factor, γc=π/2, is disclosed for the dimensional crossover of few-layer graphene (FLG) from two-dimensional graphene to three-dimensional graphite. γc is found by analyzing available experimental data on different properties of FLG with varying thickness. A theoretical study on the phonon spectrum of the vertical acoustic mode in FLG is carried out to further check this exponential factor γc. Interestingly, the same exponential factor appears in the dimensional crossover of the phonon mode. It turns out that the exponential factor γc is related to the homogeneous Helmholtz-like molal equation in the mass transfer with a first order chemical reaction. The finding should provide valuable information for experimentalists and theorists in the future investigation on thickness dependent properties of FLG.
Magnetic thermodynamics of fcc Ni from first-principles partition function approach
Authors: Shang Shun-Li , Saal James E. , Mei Zhi-Gang , Wang Yi , Liu Zi-Kui
Published: December 2010

Exploration of longstanding issues in magnetic materials, for example the nature of Curie/Néel temperature and the Schottky anomaly of heat capacity, appeals to reliable models at finite temperatures. Based on first-principles calculations and partition function approach with the microstates being the collinear magnetic configurations, the magnetic thermodynamics of fcc Ni, including the heat capacity and the pressure-dependent Curie temperature, is predicted well and compared with the results from experiments and mean-field approach. As demonstrated in fcc Ni, it is found that the magnetic thermodynamics containing anomalies stems from the magnetic configurational entropy caused by the competition of various magnetic states.
Surface plasmon resonances in silver Bowtie nanoantennas with varied bow angles
Authors: Ding Wei , Bachelot Renaud , Kostcheev Sergei , Royer Pascal , Espiau de Lamaestre Roch
Published: December 2010

Plasmon resonances in silver Bowtie nanoantennas have been numerically and experimentally investigated with varying the bow angle. Finite-difference time-domain simulation demonstrates one fundamental and two types of high-order resonances. With the increase in the bow angle, the peak of the fundamental resonance first blueshifts, and then redshifts. Two types of high-order resonances, which are prone to be excited at large bow angles, are assigned to the charge/current oscillations either between the corners or between the edges of the nanoprisms. Experimentally, far-field extinction measurement to lithogragphically fabricated Bowtie nanoantenna arrays corroborates our interpretation. As far as a 300 nm long, large angle silver Bowtie antenna is concerned, the resonances appear at the wavelengths of ∼830, ∼600, and ∼400 nm, respectively, in accordance with the simulation. The spectrally resolved multiple resonances illustrate the diversity of the excitation in optical nanoantennas and imply potential applications in nanophotonics.
A note on reductions of the dispersionless Toda hierarchy
Authors: Lee Niann-Chern , Shen Hsin-Fu , Tu Ming-Hsien
Published: December 2010

We investigate the algebraic structure of the dispersionless Hirota equations for the m + 1-variable reductions of the dispersionless Toda hierarchy which contains the special case for m = 1 considered by Kodama and Pierce. We demonstrate the m = 2 case to illustrate the obtained result.
Free-electronlike diffusive thermopower of indium tin oxide thin films
Authors: Wu Chih-Yuan , Thanh Tra Vu , Chen Yi-Fu , Lee Jui-Kan , Lin Juhn-Jong
Published: December 2010

We report our measurements of thermopower, S(T), on a series of indium tin oxide thin films from 300 down to 5 K to extract the carrier concentration n. The temperature behavior of S(T) below 300 K can be essentially described by a prevailing linear diffusive contribution. In this wide temperature interval, the phonon-drag thermopower is negligible relative to the diffusive thermopower. Therefore, the free-electronlike characteristic is clearly addressed. It should be stressed that linearity in Sd from liquid-helium temperatures all the way up to room temperatures is seldom seen even in simple metals.
Highly efficient orange emission in ZnO:Se nanorods
Authors: Sun Luwei , He Haiping , Liu Chao , Ye Zhizhen
Published: December 2010

The origin of the visible emissions in ZnO nanostructures is a long-standing issue. In this work, a strong orange emission around 2.1 eV in ZnO:Se nanorods is reported. Temperature-dependent photoluminescence (PL) and PL decay results indicate that radiative recombination dominates the overall decay process, leading to highly efficient orange emission at room temperature. It is proposed that Se acts as isoelectronic centers and no evidence of ZnO1−xSex alloy formation is found. Based on the PL excitation results, we propose a Se-induced impurity band model to describe the photophysics of the orange emission.
Photoexcited carrier relaxation dynamics and terahertz response of photoconductive antennas made on proton bombarded GaAs materials
Authors: Savard S. , Allard J.-F. , Bernier M. , Petersen J. C. , Dodge J. S. , Fournier P. , Morris D.
Published: December 2010

We present a model reproducing the instrumental response of a time-domain spectrometer that integrates photoconductive transmitter and receiver antennas made on identical proton-bombarded GaAs substrates. This model is used to determine the ultrafast capture time of the photoexcited carriers by the ion-bombardment-induced traps. A 0.5 ps capture time can be extracted for a low laser pump fluence of 0.66 μJ/cm2 per pulse. This carrier trapping time gets longer as the pump fluence increases. This behavior is explained by a gradual filling of the traps that are distributed over a 1 μm depth from the GaAs surface. This interpretation is supported by time-resolved measurements obtained on the same photoconductive material using both an 820 nm pump/terahertz-probe transmission experiment and a degenerate 760 nm pump/probe reflectivity experiment. The differential transmission and reflectivity dynamics are reproduced using a biexponential function which correctly describes the photoexcited carrier relaxation and transport dynamics in this material. The strong agreement observed between these different measurements reinforces the validity of the theoretical model used to reproduce the instrumental response of the terahertz setup.
High throughput optical readout of dense arrays of nanomechanical systems for sensing applications
Authors: Martínez N. F. , Kosaka P. M. , Tamayo J. , Ramírez J. , Ahumada O. , Mertens J. , Hien T. D. , Rijn C. V. , Calleja M.
Published: December 2010

We present an instrument based on the scanning of a laser beam and the measurement of the reflected beam deflection that enables the readout of arrays of nanomechanical systems without limitation in the geometry of the sample, with high sensitivity and a spatial resolution of few micrometers. The measurement of nanoscale deformations on surfaces of cm2 is performed automatically, with minimal need of user intervention for optical alignment. To exploit the capability of the instrument for high throughput biological and chemical sensing, we have designed and fabricated a two-dimensional array of 128 cantilevers. As a proof of concept, we measure the nanometer-scale bending of the 128 cantilevers, previously coated with a thin gold layer, induced by the adsorption and self-assembly on the gold surface of several self-assembled monolayers. The instrument is able to provide the static and dynamic responses of cantilevers with subnanometer resolution and at a rate of up to ten cantilevers per second. The instrumentation and the fabricated chip enable applications for the analysis of complex biological systems and for artificial olfaction.
Substituting fields within the action: Consistency issues and some applications
Authors: Pons Josep M.
Published: December 2010

In field theory, as well as in mechanics, the substitution of some fields in terms of other fields at the level of the action raises an issue of consistency with respect to the equations of motion. We discuss this issue and give an expression which neatly displays the difference between doing the substitution at the level of the Lagrangian or at the level of the equations of motion. Both operations do not commute in general. A very relevant exception is the case of auxiliary variables, which are discussed in detail together with some of their relevant applications. We discuss the conditions for the preservation of symmetries—Noether as well as non-Noether—under the reduction of degrees of freedom provided by the mechanism of substitution. We also examine how the gauge fixing procedures fit in our framework and give simple examples on the issue of consistency in this case.
Nanomechanical torque magnetometry of permalloy cantilevers
Authors: Losby Joseph , Burgess Jacob A. J. , Holt Chris M. B. , Westwood Jocelyn N. , Mitlin David , Hiebert Wayne K. , Freeman Mark R.
Published: December 2010

There is mounting interest in bridging the fields of nanomechanics and nanomagnetism. Metallic nanocantilevers, which are magnetic throughout their volume, were fabricated using permalloy in order to detect domain switching along the cantilever length through mechanical deflection driven by magnetic torque. A finite element model describing the interaction of the magnetization of the cantilever with an external driving field is discussed, and illustrated for the simple example of magnetization reversal via propagation of a straight domain wall. The interferometrically obtained cantilever deflection through the magnetic actuation of the fundamental mode exhibits magnetic hysteresis. The experimental results are also compared to the finite element mechanical transformation of the output from a Landau–Lifshitz–Gilbert based micromagnetic simulation of the hysteresis.
Blow-up solutions of the general b-equation
Authors: Lv Guangying , Wang Mingxin
Published: December 2010

In this short paper, we consider the b-equation. A new precise blow-up scenario is described and some new results are obtained for the blow-up phenomena.
Transient Raman response and soliton self-frequency shift in tellurite microstructured fiber
Authors: Yan Xin , Qin Guanshi , Liao Meisong , Suzuki Takenobu , Ohishi Yasutake
Published: December 2010

We report on the Raman response function and the soliton self-frequency shift in a tellurite microstructured fiber pumped at 1557 nm. The Raman response function in a tellurite fiber quantifies a contribution of the Raman fraction to the nonlinear optical response. Continuous soliton wavelength shift from 1582 to 1851 nm is observed in a tellurite microstructured optical fiber with the length of 6.5 cm. The experimental results strongly correlated with the numerical simulations based on a generalized nonlinear Schrödinger equation.
Micelles induced high coercivity in single domain cobalt-ferrite nanoparticles
Authors: Pal Debabrata , Mandal Madhuri , Chaudhuri Arka , Das Bipul , Sarkar Debasish , Mandal Kalyan
Published: December 2010

We have prepared CoFe2O4 nanoparticles in micellar medium by wet chemical technique and obtained very high coercivity value of 4.4 kOe at room temperature for particle size ∼16 nm. A large coercivity (∼20 kOe) is observed on cooling down to 2.5 K. We annealed the sample at different temperatures to check the role of micelles and particles size in the change in coercivity value. Here we observed micelles as capping agent playing an important role to enhance the coercivity, as after removal of micelles for the same particle size the coercivity drops from 4.4 kOe to small value ∼350 Oe. But the coercivity again increases due to the increase in particle size with increase in annealing temperature from 873 K and above. To obtain structural information and size of particles, we have taken x-ray diffraction spectra from the samples before and after annealing at different temperatures which confirm the spinel phase only.
Wavenumber spectrum of whistler turbulence: Particle-in-cell simulation
Authors: Saito S. , Gary S. Peter , Narita Y.
Published: December 2010

The forward cascade of decaying whistler turbulence is studied in low beta plasma to understand essential properties of the energy spectrum at electron scales, by using a two-dimensional electromagnetic particle-in-cell (PIC) simulation. This simulation demonstrates turbulence in which the energy cascade rate is greater than the dissipation rate at the electron inertial length. The PIC simulation shows that the magnetic energy spectrum of forward-cascaded whistler turbulence at electron inertial scales is anisotropic and develops a very steep power-law spectrum which is consistent with recent solar wind observations. A comparison of the simulated spectrum with that predicted by a phenomenological turbulence scaling model suggests that the energy cascade at the electron inertial scale depends on both magnetic fluctuations and electron velocity fluctuations, as well as on the whistler dispersion relation. Thus, not only kinetic Alfvén turbulence but also whistler turbulence may explain recent solar wind observations of very steep magnetic spectra at short scales.
Current distribution measurements inside an electromagnetic plasma gun operated in a gas-puff mode
Authors: Poehlmann Flavio R. , Cappelli Mark A. , Rieker Gregory B.
Published: December 2010

Measurements are presented of the time-dependent current distribution inside a coaxial electromagnetic plasma gun. The measurements are carried out using an array of six axially distributed dual-Rogowski coils in a balanced circuit configuration. The radial current distributions indicate that operation in the gas-puff mode, i.e., the mode in which the electrode voltage is applied before injection of the gas, results in a stationary ionization front consistent with the presence of a plasma deflagration. The effects of varying the bank capacitance, transmission line inductance, and applied electrode voltage were studied over the range from 14 to 112 μF, 50 to 200 nH, and 1 to 3 kV, respectively.
Relaxation of chemical reactions to stationary states in the chemical affinities space
Authors: Sonnino Giorgio
Published: December 2010

Using the mass balance equations for chemical reactions, we show how the system relaxes toward a steady-state in and out of the Onsager region. In the chemical affinities space, after fast transients, the relaxation process is a straight line when operating in the Onsager region, while out of this regime, the evolution of the system is such that the projections of the evolution equations for the forces and the shortest path on the flows coincide. For spatially extended systems, similar results are valid for the evolution of the thermodynamic mode (i.e., the mode with wave-number k = 0). These results allow us to obtain the expression for the affine connection of the space covered by the thermodynamic forces, close to the steady-states. Through the affine connection, the nonlinear closure equations are derived.
On the calculation of equilibrium thermodynamic properties and the establishment of statistical-thermodynamically-consistent finite bound-state partition functions in nonideal multicomponent plasma mixtures within the chemical model
Authors: Zaghloul Mofreh R.
Published: December 2010

The problem of the calculation of equilibrium thermodynamic properties and the establishment of statistical-thermodynamically consistent finite bound-state partition functions in nonideal multicomponent plasma systems is revised within the chemical picture. The present exploration accompanied by the introduction of a generalized consistent formulation, in terms of the solution of the inverse problem, clears ambiguities and gives a better understanding of the problem on top of pointing out weaknesses and inaccuracies/inconsistencies buried in widely used models in literature.
Whole blood pumping with a microthrottle pump
Authors: Davies M. J. , Johnston I. D. , Tan C. K. L. , Tracey M. C.
Published: December 2010

We have previously reported that microthrottle pumps (MTPs) display the capacity to pump solid phase suspensions such as polystyrene beads which prove challenging to most microfluidic pumps. In this paper we report employing a linear microthrottle pump (LMTP) to pump whole, undiluted, anticoagulated, human venous blood at 200 μl min−1 with minimal erythrocyte lysis and no observed pump blockage. LMTPs are particularly well suited to particle suspension transport by virtue of their relatively unimpeded internal flow-path. Micropumping of whole blood represents a rigorous real-world test of cell suspension transport given blood’s high cell content by volume and erythrocytes’ relative fragility. A modification of the standard Drabkin method and its validation to spectrophotometrically quantify low levels of erythrocyte lysis by hemoglobin release is also reported. Erythrocyte lysis rates resulting from transport via LMTP are determined to be below one cell in 500 at a pumping rate of 102 μl min−1.
Spatially autoresonant stimulated Raman scattering in inhomogeneous plasmas in the kinetic regime
Authors: Chapman T. , Hüller S. , Masson-Laborde P. E. , Rozmus W. , Pesme D.
Published: December 2010

The impact of spatial autoresonance on backward stimulated Raman scattering in inhomogeneous plasmas is investigated in the regime where the dominant nonlinear frequency shift of the Langmuir wave is due to kinetic effects. By numerically solving the coupled mode equations, the spatial growth of the Langmuir wave is observed to self-adjust so as to cancel the detuning from resonance due to inhomogeneity, giving rise to phase-locked solutions to the electron plasma wave equation. For a single resonant point in a linear density profile, the envelope of the electron plasma wave is characterized by a growth that begins at the resonant point and is proportional to the square of distance propagated. In the more physical case where the scattered light is seeded with a broadband noise, autoresonance may lead to a reflectivity well above the level predicted by the usual Rosenbluth gain factor [M. N. Rosenbluth, Phys. Rev. Lett. 29, 565 (1972)].
Dust ion-acoustic shock waves in charge varying dusty plasmas with electrons having vortexlike velocity distribution
Authors: Alinejad H. , Tribeche M.
Published: December 2010

A weakly nonlinear analysis is carried out to investigate the properties of dust ion-acoustic shock waves in a charge varying dusty plasma with vortexlike electron distribution. We use the ionization model, hot ions with equilibrium streaming speed and a trapped electron charging current derived from the well-known orbit limited motion theory. A new modified Burger equation is derived. Besides nonlinear trapping, this equation involves two kinds of dissipation (the anomalous one inherent to nonadiabatic dust charge fluctuation and the one due to the particle loss and ionization). These two kinds of dissipation can act concurrently. The traveling wave solution has been acquired by employing the modified extended tanh-function method. The shocklike solution is numerically analyzed based on the typical numerical data from laboratory dusty plasma devices. It is found that ion temperature, trapped particles, and weak dissipations significantly modify the shock structures.
Excitation of surface field cavity and coherence of electromagnetic field scattering on two-dimensional cylindrical lattice
Authors: Konoplev I. V. , Fisher L. , Cross A. W. , Phelps A. D. R. , Ronald K. , Thumm M.
Published: December 2010

The excitation of a surface field cavity based on a large area two-dimensional cylindrical lattice and surface field scattering within the cavity are investigated. It is shown that the interaction between surface and volume fields via distributed scatterers becomes coherent and the cavity excitation takes place only when it is irradiated with a near cut-off transverse-magnetic polarized field. The coherence of the radiation observed from the surface field scattering is investigated.
Characterization of tumors using high-Tc superconducting quantum interference device-detected nuclear magnetic resonance and imaging
Authors: Liao Shu-Hsien , Huang Kai-Wen , Yang Hong-Chang , Yen Chang-Te , Chen M. J. , Chen Hsin-Hsien , Horng Herng-Er , Yang Shieh Yueh
Published: December 2010

The characterization of cancerous livers in rats using nuclear magnetic resonance and magnetic resonance imaging (NMR/MRI) based on high-Tc superconducting quantum interference devices (SQUIDs) is presented. The T1−1 were observed to be 6.5±0.5 s−1 for controlled livers and 2.85±0.2 s−1 for cancerous livers, which indicate that the T1 can be used to distinguish the cancerous tissues from controlled liver tissues. The intensity ratio for tap water, cancerous tissue, and controlled tissue, respectively, is 1:1.15:0.56 at TBp=1 s. The SQUID-detected NMR/MRI exhibits potential applications in research and clinics.
Enhanced Ohmic contact via graphitization of polycrystalline silicon carbide
Authors: Liu F. , Hsia B. , Carraro C. , Pisano A. P. , Maboudian R.
Published: December 2010

Electrical contact to silicon carbide with low contact resistivity and high stability is a critical requirement for SiC-based microsystem and nanosystem technology for harsh environment applications. In this letter, nanocrystalline graphitic carbon is grown at the interface between SiC and Pt to lower the Ohmic contact resistivity and enhance the stability of Pt contacts to polycrystalline 3C-SiC operated at elevated temperatures. Analysis shows that reduced barrier height, oxide-free surface, reduced density of vacancy defects, and suppressed reactivity between Pt and SiC are likely responsible for the reduced Ohmic contact resistivity and high thermal stability of Pt contacts to graphitized SiC.
Experimental analysis of internal optical losses in polarization-insensitive semiconductor optical amplifiers
Authors: Tanaka Shinsuke , Morito Ken
Published: December 2010

We experimentally investigated the internal optical loss of a polarization-insensitive multiple quantum well semiconductor optical amplifier (SOA) over a wide injection current range. The precise fitting of noise figure spectra using gain spectra and transparent wavelengths enabled a direct estimation of internal optical loss inside gain bandwidth. The internal optical loss of the SOA exhibited large dependencies on injection current and the optical confinement factor of the active layer. A large difference in optical losses between polarization modes and operating wavelengths of the SOA indicates a strong influence of intervalence band absorption.
The effect of Ti and ITO adhesion layers on gold split-ring resonators
Authors: Jeppesen Claus , Mortensen Niels Asger , Kristensen Anders
Published: December 2010

Ultrathin adhesion layers serve a well-documented fabrication purpose while its influence on the optical properties of gold nanostructures is often neglected. Gold split-ring resonators are fabricated with two commonly used adhesion layers: titanium and indium tin oxide. When compared to all-gold reference samples, a spectral shift of the ground mode resonance is observed. For the titanium sample the spectral shift is accompanied by a resonance broadening, which is less profound for indium tin oxide. The mutual correlation between the shift and the broadening is shown to be qualitatively consistent with perturbative considerations.
Work function of single-wall silicon carbide nanotube
Authors: Zheng Fawei , Yang Yu , Zhang Ping
Published: December 2010

Using first-principles calculations, we study the work function of single-wall silicon carbide nanotube (SiCNT). The work function is found to be highly dependent on the tube chirality and diameter. It increases by decreasing the tube diameter. The work function of zigzag SiCNT is always larger than that of armchair SiCNT. We reveal that the difference between the work function of zigzag and armchair SiCNT comes from their different intrinsic electronic structures, for which the singly degenerate energy band above the Fermi level of zigzag SiCNT is specifically responsible. Our finding offers potential usages of SiCNT in field-emission devices.
Glycoprotein mucin molecular brush on cancer cell surface acting as mechanical barrier against drug delivery
Authors: Wang Xin , Shah Aalok A. , Campbell Robert B. , Wan Kai-tak
Published: December 2010

Uptake of cytotoxic drugs by typical tumor cells is limited by the dense dendritic network of oligosaccharide mucin chains that forms a mechanical barrier. Atomic force microscopy is used to directly measure the force needed to pierce the mucin layer to reach the cell surface. Measurements are analyzed by de Gennes’ steric reptation theory. Multidrug resistant ovarian tumor cells shows significantly larger penetration load compared to the wide type. A pool of pancreatic, lung, colorectal, and breast cells are also characterized. The chemotherapeutic agent, benzyl-α-GalNac, for inhibiting glycosylation is shown to be effective in reducing the mechanical barrier.
Secondary electron yield of multiwalled carbon nanotubes
Authors: Alam M. K. , Yaghoobi P. , Chang M. , Nojeh A.
Published: December 2010

Secondary electron yield from individual multiwalled carbon nanotubes is investigated for a wide range of primary beam energies (0.5–15 keV). By using a simple experimental procedure under an optical microscope, we make suspended nanotubes, which are free from interaction with the substrate during electron yield measurements. It is found that the secondary electron yield from isolated suspended nanotubes is less than unity and decreases as a function of primary electron energy.
Enhanced striatal cholinergic neuronal activity mediatesl-DOPA–induced dyskinesia in parkinsonian mice
Authors: Ding Yunmin , Won Lisa , Britt Jonathan P. , Lim Sean Austin O. , McGehee Daniel S. , Kang Un Jung
Published: December 2010

Treatment of Parkinson disease (PD) withl-3,4-dihydroxyphenylalanine (l-DOPA) dramatically relieves associated motor deficits, butl-DOPA–induced dyskinesias (LID) limit the therapeutic benefit over time. Previous investigations have noted changes in striatal medium spiny neurons, including abnormal activation of extracellular signal-regulated kinase1/2 (ERK). Using two PD models, the traditional 6-hydroxydopamine toxic lesion and a genetic model with nigrostriatal dopaminergic deficits, we found that acute dopamine challenge induces ERK activation in medium spiny neurons in denervated striatum. After repeatedl-DOPA treatment, however, ERK activation diminishes in medium spiny neurons and increases in striatal cholinergic interneurons. ERK activation leads to enhanced basal firing rate and stronger excitatory responses to dopamine in striatal cholinergic neurons. Pharmacological blockers of ERK activation inhibitl-DOPA–induced changes in ERK phosphorylation, neuronal excitability, and the behavioral manifestation of LID. In addition, a muscarinic receptor antagonist reduces LID. These data indicate that increased dopamine sensitivity of striatal cholinergic neurons contributes to the expression of LID, which suggests novel therapeutic targets for LID.
Statistical method for revealing form-function relations in biological networks
Authors: Mugler Andrew , Grinshpun Boris , Franks Riley , Wiggins Chris H.
Published: December 2010

Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions—lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively. The question “how does function follow form” is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed viahttp://formfunction.sourceforge.net.
Potassium (K
+
) gradients serve as a mobile energy source in plant vascular tissues
Authors: Gajdanowicz Pawel , Michard Erwan , Sandmann Michael , Rocha Marcio , Corrêa Luiz Gustavo Guedes , Ramírez-Aguilar Santiago J. , Gomez-Porras Judith L. , González Wendy , Thibaud Jean-Baptiste , van Dongen Joost T. , Dreyer Ingo
Published: December 2010

The essential mineral nutrient potassium (K
+
) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K
+
contributes to plant productivity. K
+
is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K
+
also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K
+
in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K
+
circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed
Arabidopsis
K
+
channel AKT2 taps this “potassium battery,” which then efficiently assists the plasma membrane H
+
-ATPase in energizing the transmembrane phloem (re)loading processes.
Stromal retinoic acid receptor β promotes mammary gland tumorigenesis
Authors: Liu Xingxing , Nugoli Mélanie , Laferrière Julie , Saleh Sadiq M. , Rodrigue-Gervais Ian G. , Saleh Maya , Park Morag , Hallett Michael T. , Muller William J. , Giguère Vincent
Published: December 2010

Retinoic acid is a potent differentiation and antiproliferative agent of breast cancer cells, and one of its receptors, retinoic acid receptor β (RARβ), has been proposed to act as a tumor suppressor. In contrast, we report herein that inactivation of
Rarb
in the mouse results in a protective effect against ErbB2-induced mammary gland tumorigenesis. Strikingly, tissue recombination experiments indicate that the presence of
Rarb
in the stromal compartment is essential for the growth of mammary carcinoma. Ablation of
Rarb
leads to a remodeling of the stroma during tumor progression that includes a decrease in angiogenesis, in the recruitment of inflammatory cells, and in the number myofibroblasts. In agreement with this finding, we observed that a markedly reduced expression of chemokine (C-X-C motif) ligand 12 (
Cxcl12
) in the stroma of
Rarb
-null mice is accompanied by a decrease in the CXCL12/chemokine C-X-C receptor 4 (CXCR4)/ErbB2 signaling axis in the tumors. Relevance to the human disease is underlined by the finding that gene-expression profiling of the
Rarb
-deficient mammary stromal compartment identified an ortholog RARβ signature in human microdissected breast tissues that differentiates tumor from normal stroma. Our study thus implicates RARβ in promoting tumorigenesis and suggests that retinoid-based approaches for the prevention and treatment of breast cancer should be redesigned.
Ancient watercourses and biogeography of the Sahara explain the peopling of the desert
Authors: Drake Nick A. , Blench Roger M. , Armitage Simon J. , Bristow Charlie S. , White Kevin H.
Published: December 2010

Evidence increasingly suggests that sub-Saharan Africa is at the center of human evolution and understanding routes of dispersal “out of Africa” is thus becoming increasingly important. The Sahara Desert is considered by many to be an obstacle to these dispersals and a Nile corridor route has been proposed to cross it. Here we provide evidence that the Sahara was not an effective barrier and indicate how both animals and humans populated it during past humid phases. Analysis of the zoogeography of the Sahara shows that more animals crossed via this route than used the Nile corridor. Furthermore, many of these species are aquatic. This dispersal was possible because during the Holocene humid period the region contained a series of linked lakes, rivers, and inland deltas comprising a large interlinked waterway, channeling water and animals into and across the Sahara, thus facilitating these dispersals. This system was last active in the early Holocene when many species appear to have occupied the entire Sahara. However, species that require deep water did not reach northern regions because of weak hydrological connections. Human dispersals were influenced by this distribution; Nilo-Saharan speakers hunting aquatic fauna with barbed bone points occupied the southern Sahara, while people hunting Savannah fauna with the bow and arrow spread southward. The dating of lacustrine sediments show that the “green Sahara” also existed during the last interglacial (∼125 ka) and provided green corridors that could have formed dispersal routes at a likely time for the migration of modern humans out of Africa.
Revisiting human natural killer cell subset function revealed cytolytic CD56
dim
CD16
+
NK cells as rapid producers of abundant IFN-γ on activation
Authors: De Maria Andrea , Bozzano Federica , Cantoni Claudia , Moretta Lorenzo
Published: December 2010

The two major functions of human natural killer (NK) cells are conventionally associated with distinct cell subsets. Thus, cytolytic activity is mostly confined to the CD56
dim
CD16
+
subset, whereas cytokine production is generally assigned to CD56
bright
CD16
+/−
cells. In this study, we reevaluated the functional capabilities of these NK subsets with regard to the production of IFN-γ at different time points after cell triggering via NKp46 and NKp30 activating receptors. Different from previous studies, cytokine production was also assessed at early intervals. We show that CD56
dim
NK cells produce IFN-γ already at 2 to 4 h, whereas no cytokine production is detected beyond 16 h. In contrast, CD56
bright
cells release IFN-γ only at late time intervals (>16 h after stimulation). The rapid IFN-γ production by CD56
dim
NK cells is in line with the presence of IFN-γ mRNA in freshly isolated cells. Rapid IFN-γ production was also induced by combinations of IL-2, IL-12, and IL-15. Our data indicate that not only cytolytic activity but also early IFN-γ production is a functional property of CD56
dim
NK cells. Thus, this subset can assure a rapid and comprehensive NK cell intervention during the early phases of innate responses.
Conserved endoplasmic reticulum-associated degradation system to eliminate mutated receptor-like kinases in
Arabidopsis
Authors: Su Wei , Liu Yidan , Xia Yang , Hong Zhi , Li Jianming
Published: December 2010

Endoplasmic reticulum (ER)-associated degradation (ERAD) is an integral part of the ER quality-control system that removes toxic misfolded proteins via ubiquitin/proteasome-mediated degradation. Most of our knowledge on ERAD comes from biochemical and genetic studies in yeast and mammalian cells. Although ERAD is known to operate in plant cells, little is known about its molecular components and its biochemical mechanism. A genetic screen for suppressors of the
Arabidopsis bri1-9
, a weak dwarf mutant caused by ER retention of a structurally defective yet biochemically competent brassinosteroid (BR) receptor BRI1, resulted in identification of the
EMS-mutagenized bri1 suppressor 5
(
EBS5
) gene that encodes an
Arabidopsis
homolog of the yeast Hrd3/mammlian Sel1L protein known to be involved in ERAD. Loss-of-function
ebs5
mutations block the ERAD of bri1-9 and bri1-5, another ER-retained BR receptor. We showed that EBS5 complemented the ERAD defect of the yeast
Δhrd3
mutant and interacted with the two mutated BR receptors in plant cells. Using a reverse genetic approach, we discovered that two
Arabidopsis
homologs of the yeast/mammalian Hrd1, an ER membrane-localized ubiquitin ligase, function redundantly in the ERAD of bri1-9. Together, our results revealed functional roles of two conserved ERAD components in degrading mutated/misfolded receptor-like kinases in
Arabidopsis
.
The noisy edge of traveling waves
Authors: Hallatschek Oskar
Published: December 2010

Traveling waves are ubiquitous in nature and control the speed of many important dynamical processes, including chemical reactions, epidemic outbreaks, and biological evolution. Despite their fundamental role in complex systems, traveling waves remain elusive because they are often dominated by rare fluctuations in the wave tip, which have defied any rigorous analysis so far. Here, we show that by adjusting nonlinear model details, noisy traveling waves can be solved exactly. The moment equations of these tuned models are closed and have a simple analytical structure resembling the deterministic approximation supplemented by a nonlocal cutoff term. The peculiar form of the cutoff shapes the noisy edge of traveling waves and is critical for the correct prediction of the wave speed and its fluctuations. Our approach is illustrated and benchmarked using the example of fitness waves arising in simple models of microbial evolution, which are highly sensitive to number fluctuations. We demonstrate explicitly how these models can be tuned to account for finite population sizes and determine how quickly populations adapt as a function of population size and mutation rates. More generally, our method is shown to apply to a broad class of models, in which number fluctuations are generated by branching processes. Because of this versatility, the method of model tuning may serve as a promising route toward unraveling universal properties of complex discrete particle systems.
Structural studies of ion permeation and Ca
2+
blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore
Authors: Derebe Mehabaw G. , Zeng Weizhong , Li Yang , Alam Amer , Jiang Youxing
Published: December 2010

Cyclic nucleotide-gated (CNG) channels play an essential role in the visual and olfactory sensory systems and are ubiquitous in eukaryotes. Details of their underlying ion selectivity properties are still not fully understood and are a matter of debate in the absence of high-resolution structures. To reveal the structural mechanism of ion selectivity in CNG channels, particularly their Ca
2+
blockage property, we engineered a set of mimics of CNG channel pores for both structural and functional analysis. The mimics faithfully represent the CNG channels they are modeled after, permeate Na
+
and K
+
equally well, and exhibit the same Ca
2+
blockage and permeation properties. Their high-resolution structures reveal a hitherto unseen selectivity filter architecture comprising three contiguous ion binding sites in which Na
+
and K
+
bind with different ion-ligand geometries. Our structural analysis reveals that the conserved acidic residue in the filter is essential for Ca
2+
binding but not through direct ion chelation as in the currently accepted view. Furthermore, structural insight from our CNG mimics allows us to pinpoint equivalent interactions in CNG channels through structure-based mutagenesis that have previously not been predicted using NaK or K
+
channel models.
RNA polymerase and transcription elongation factor Spt4/5 complex structure
Authors: Klein Brianna J. , Bose Daniel , Baker Kevin J. , Yusoff Zahirah M. , Zhang Xiaodong , Murakami Katsuhiko S.
Published: December 2010

Spt4/5 in archaea and eukaryote and its bacterial homolog NusG is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating RNA polymerase. Here, we present the crystal structure of Spt4/5 as well as the structure of RNA polymerase-Spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. The Spt4/5 binds in the middle of RNA polymerase claw and encloses the DNA, reminiscent of the DNA polymerase clamp and ring helicases. The transcription elongation complex model reveals that the Spt4/5 is an upstream DNA holder and contacts the nontemplate DNA in the transcription bubble. These structures reveal that the cellular RNA polymerases also use a strategy of encircling DNA to enhance its processivity as commonly observed for many nucleic acid processing enzymes including DNA polymerases and helicases.
Critical role of aquaporin-4 (AQP4) in astrocytic Ca
2+
signaling events elicited by cerebral edema
Authors: Thrane Alexander S. , Rappold Phillip M. , Fujita Takumi , Torres Arnulfo , Bekar Lane K. , Takano Takahiro , Peng Weiguo , Wang Fushun , Rangroo Thrane Vinita , Enger Rune , Haj-Yasein Nadia N. , Skare Øivind , Holen Torgeir , Klungland Arne , Ottersen Ole P. , Nedergaard Maiken , Nagelhus Erlend A.
Published: December 2010

Aquaporin-4 (AQP4) is a primary influx route for water during brain edema formation. Here, we provide evidence that brain swelling triggers Ca
2+
signaling in astrocytes and that deletion of the Aqp4 gene markedly interferes with these events. Using in vivo two-photon imaging, we show that hypoosmotic stress (20% reduction in osmolarity) initiates astrocytic Ca
2+
spikes and that deletion of
Aqp4
reduces these signals. The Ca
2+
signals are partly dependent on activation of P2 purinergic receptors, which was judged from the effects of appropriate antagonists applied to cortical slices. Supporting the involvement of purinergic signaling, osmotic stress was found to induce ATP release from cultured astrocytes in an AQP4-dependent manner. Our results suggest that AQP4 not only serves as an influx route for water but also is critical for initiating downstream signaling events that may affect and potentially exacerbate the pathological outcome in clinical conditions associated with brain edema.
Trk retrograde signaling requires persistent, Pincher-directed endosomes
Authors: Philippidou Polyxeni , Valdez Gregorio , Akmentin Wendy , Bowers William J. , Federoff Howard J. , Halegoua Simon
Published: December 2010

Target-derived neurotrophins use retrogradely transported Trk-signaling endosomes to promote survival and neuronal phenotype at the soma. Despite their critical role in neurotrophin signaling, the nature and molecular composition of these endosomes remain largely unknown, the result of an inability to specifically identify the retrograde signaling entity. Using EGF-bound nanoparticles and chimeric, EGF-binding TrkB receptors, we elucidate Trk-endosomal events involving their formation, processing, retrograde transport, and somal signaling in sympathetic neurons. By comparing retrograde endosomal signaling by Trk to the related but poorly neuromodulatory EGF-receptor, we find that Trk and EGF-receptor endosomes are formed and processed by distinct mechanisms. Surprisingly, Trk and EGF-receptors are both retrogradely transported to the soma in multivesicular bodies. However, only the Trk-multivesicular bodies rely on Pincher-dependent macroendocytosis and processing. Retrograde signaling through Pincher-generated Trk-multivesicular bodies is distinctively refractory to signal termination by lysosomal processing, resulting in sustained somal signaling and neuronal gene expression.
Phosphorylation of Grainy head by ERK is essential for wound-dependent regeneration but not for development of an epidermal barrier
Authors: Kim Myungjin , McGinnis William
Published: December 2010

Grainy head (GRH) is a key transcription factor responsible for epidermal barrier formation and repair, whose function is highly conserved across diverse animal species. However, it is not known how GRH function is reactivated to repair differentiated epidermal barriers after wounding. Here, we show that GRH is directly regulated by extracellular signal-regulated kinase (ERK) phosphorylation, which is required for wound-dependent expression of GRH target genes in epidermal cells. Serine 91 is the principal residue in GRH that is phosphorylated by ERK. Although mutations of the ERK phosphorylation sites in GRH do not impair its DNA binding function, the ERK sites in GRH are required to activate
Dopa decarboxylase (Ddc)
and
misshapen (msn)
epidermal wound enhancers as well as functional regeneration of an epidermal barrier upon wounding. This result indicates that the phosphorylation sites are essential for damaged epidermal barrier repair. However, GRH with mutant ERK phosphorylation sites can still promote barrier formation during embryonic epidermal development, suggesting that ERK sites are dispensable for the GRH function in establishing epidermal barrier integrity. These results provide mechanistic insight into how tissue repair can be initiated by posttranslational modification of a key transcription factor that normally mediates the developmental generation of that tissue.