bluuebunny/crossref_metadata_2025 huggingface dataset:
Chain bridging in a model of semicrystalline multiblock copolymers
Authors: Shah Manas , Ganesan Venkat
Published: February 2009

Recent experimental observations have suggested an intimate connection between the chain conformations and mechanical properties of semicrystalline multiblock copolymers. Motivated by these studies, we present a theoretical study evaluating the bridging/looping fractions in a model of semicrystalline multiblock copolymers. We model the noncrystalline block (A) as a flexible Gaussian chain and the crystalline block (B) as a semiflexible chain with a temperature dependent rigidity and interactions that favor the formation of parallel oriented bonds. Using self-consistent field theory, the bridging fractions of the various domains in different multiblock copolymers (ABA, BAB, ABABA, and BABAB) are evaluated and compared with their flexible counterparts. In general, we observe that for both triblock and pentablock copolymers, rendering one of the blocks crystallizable promotes bridging in that component while reducing the bridging in the other noncrystallizable component. Moreover, the bridging fractions in tri- and pentablock copolymers were seen to be quantitatively similar except insofar as being normalized by the volume fraction of bridgeable units.
Thermostat for high temperature and transient characterization of thin film thermoelectric materials
Authors: Singh Rajeev , Shakouri Ali
Published: February 2009

We have designed and fabricated a vacuum-insulated thermostat capable of measuring the thermoelectric properties of thin films from room temperature to 850 K. High speed Seebeck voltage transients are resolved to 200 ns with 63 dB dynamic range in order to directly measure thermoelectric device figure of merit. In-plane Seebeck coefficient probes measure voltage and temperature difference at identical locations with low parasitic contributions. In-plane electrical conductivity measurement is accomplished at high speed to avoid possible Seebeck voltage effect on van der Pauw measurements.
Coulomb-modified spin polarization in a four-terminal parallel double-quantum-dot structure
Authors: Gong Weijiang , Zheng Yisong
Published: February 2009

Electron transport through a parallel double-dot structure with four terminals is theoretically studied. Introduction of a local Rashba spin-orbit interaction results in a distinct spin polarization of the electrons being transported through the structure. More interestingly, we find that the intradot electron interaction can influence the spin-polarized electron transport spectrum in a nontrivial way. It can enhance or reverse the electron spin polarization, depending on the strengths of the electron interaction. The underlying quantum interference that gives rise to such results is clarified by the analysis of the phase relation among the electron transmission paths.
Carrier conduction mechanism for phosphorescent material doped organic semiconductor
Authors: Noh Seunguk , Suman C. K. , Hong Yongtaek , Lee Changhee
Published: February 2009

The mobility of charge carriers has been investigated in the pristine and phosphorescent material doped 4,4′,4″-tris(N-carbazolyl) triphenylamine (TCTA) using time-of-flight photoconductivity technique. Doping phosphorescent material fac-tris(2-phenylpyridine) iridium [Ir(ppy)3] increases the electron mobility whereas the hole mobility decreases to the order of 10−4–10−6 cm2/V s measured at room temperature with different bias voltages. The analysis of field and temperature dependences of the mobility agrees well with the Gaussian disorder model. The calculated positional disorders (Σ) for TCTA, Ir(ppy)3-doped TCTA, and tris(1-phenylisoquinoline) iridium [Ir(piq)3]-doped TCTA are 0.12, 2.05, and 1.62 for hole, respectively; 3.89 for electron in only Ir(ppy)3-doped TCTA. The ambipolar transport for holes and electrons is possible by doping TCTA with Ir(ppy)3 (green dopant) whereas only hole transport with reduced mobility is achieved for Ir(piq)3 (red dopant).
State and parameter estimation of spatiotemporally chaotic systems illustrated by an application to Rayleigh–Bénard convection
Authors: Cornick Matthew , Hunt Brian , Ott Edward , Kurtuldu Huseyin , Schatz Michael F.
Published: February 2009

Data assimilation refers to the process of estimating a system’s state from a time series of measurements (which may be noisy or incomplete) in conjunction with a model for the system’s time evolution. Here we demonstrate the applicability of a recently developed data assimilation method, the local ensemble transform Kalman filter, to nonlinear, high-dimensional, spatiotemporally chaotic flows in Rayleigh–Bénard convection experiments. Using this technique we are able to extract the full temperature and velocity fields from a time series of shadowgraph measurements. In addition, we describe extensions of the algorithm for estimating model parameters. Our results suggest the potential usefulness of our data assimilation technique to a broad class of experimental situations exhibiting spatiotemporal chaos.
A long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states
Authors: Rohrdanz Mary A. , Martins Katie M. , Herbert John M.
Published: February 2009

We introduce a hybrid density functional that asymptotically incorporates full Hartree–Fock exchange, based on the long-range-corrected exchange-hole model of Henderson et al. [J. Chem. Phys. 128, 194105 (2008)]. The performance of this functional, for ground-state properties and for vertical excitation energies within time-dependent density functional theory, is systematically evaluated, and optimal values are determined for the range-separation parameter, ω, and for the fraction of short-range Hartree–Fock exchange. We denote the new functional as LRC-ωPBEh, since it reduces to the standard PBEh hybrid functional (also known as PBE0 or PBE1PBE) for a certain choice of its two parameters. Upon optimization of these parameters against a set of ground- and excited-state benchmarks, the LRC-ωPBEh functional fulfills three important requirements: (i) It outperforms the PBEh hybrid functional for ground-state atomization energies and reaction barrier heights; (ii) it yields statistical errors comparable to PBEh for valence excitation energies in both small and medium-sized molecules; and (iii) its performance for charge-transfer excitations is comparable to its performance for valence excitations. LRC-ωPBEh, with the parameters determined herein, is the first density functional that satisfies all three criteria. Notably, short-range Hartree–Fock exchange appears to be necessary in order to obtain accurate ground-state properties and vertical excitation energies using the same value of ω.
Nonlinear electron magnetohydrodynamic physics. VII. Magnetic loop antenna in a field-free plasma
Authors: Stenzel R. L. , Urrutia J. M. , Strohmaier K. D.
Published: February 2009

Nonlinear whistler phenomena near a magnetic loop antenna in a field-free plasma have been investigated experimentally. The loop field oscillates at a frequency far below the electron plasma frequency, hence all linear electromagnetic modes are cut off. However, the peak antenna field is so large that the electrons become magnetized allowing whistler modes to exist in the near zone of the antenna. The shielding magnetic field propagates at a speed which increases with magnetic field strength and decays slower than the rf period, resulting in a remnant field when the antenna field vanishes. A field-reversed configuration (FRC) is produced when the antenna field reverses direction. The FRC expands into the magnetized plasma and produces self-consistent magnetic helicity consistent with that of whistler modes. Thus, the new field penetrates in the whistler mode in a background field left over from the previous half-cycle. The electrons become unmagnetized at large distances, and the field convection goes over into field diffusion. Observations of light emission indicate electron energization. Current-driven instabilities produce magnetic oscillations with frequencies much higher than the applied one. Small amplitude, high-frequency whistlers propagate in the large amplitude fields of the low-frequency whistler, but become absorbed at larger distances where the cyclotron frequency decreases below the wave frequency. The nonlinear phenomena observed may be relevant to inductively coupled plasma sources, laser-plasma interactions, plasma opening switches, and active experiments in space.
The generalized oscillator strengths of hydrogenlike ions in Debye plasmas
Authors: Qi Y. Y. , Wu Y. , Wang J. G. , Qu Y. Z.
Published: February 2009

Plasma screening effects on the high-energy electron-impact excitation of hydrogenlike ions are investigated under the first Born approximation. The screening interactions are described by the Debye–Hückel model, and the wave functions are calculated numerically in a symplectic scheme. The generalized oscillator strengths (GOS) for transitions between the principal quantum number n⩽3 bound states are presented, and as an example, the scaled differential cross sections and total cross sections for 1s→2s and 2p and 2s→2p transitions are also given. It is found that the plasma screening interactions reduce the GOS for transitions between the states with different n and increase the GOS between the states with same n. The differential and total cross sections are decreased as the screening interactions increase.
Closure of quantum hydrodynamic moment equations
Authors: Hughes Keith H. , Parry Steven M. , Burghardt Irene
Published: February 2009

The hydrodynamic formulation of mixed quantum states involves a hierarchy of coupled equations of motion for the momentum moments of the Wigner function. In this work a closure scheme for the hierarchy is developed. The closure scheme uses information contained in the lower known moments to expand the Wigner phase-space distribution function in a Gauss–Hermite orthonormal basis. The higher moment required to terminate the hierarchy is then easily obtained from the reconstructed approximate Wigner function by a straightforward integration over the momentum space. Application of the moment closure scheme is demonstrated for the dissipative and nondissipative dynamics of two different systems: (i) double-well potential, (ii) periodic potential.
The splash of a solid sphere impacting on a liquid surface: Numerical simulation of the influence of wetting
Authors: Do-Quang Minh , Amberg Gustav
Published: February 2009

The impact of a solid sphere on a liquid surface has challenged researchers for centuries and remains of interest today. Recently, Duez et al. [Nat. Phys. 3, 180 (2007)] published experimental results of the splash generated when a solid sphere enters water. Interestingly, the microscopic properties of the solid surface control the nature of the macroscopic behavior of the splash. So by a change in the surface chemistry of the solid sphere, a big splash can be turned into an inconspicuous disappearance and vice versa. This problem was investigated by numerical simulations based on the Navier–Stokes equations coupled with the Cahn–Hilliard equations. This system allows us to simulate the motion of an air-water interface as a solid sphere impacts the liquid pond. The inclusion of the surface energies of the solid surface in the formulation gives a reasonably quantitative description of the dynamic wetting. Numerical results with different wetting properties and impact speed are presented and directly compared with the recent experimental results from Duez et al.
On the lattice parameters of silicon carbide
Authors: Stockmeier M. , Müller R. , Sakwe S. A. , Wellmann P. J. , Magerl A.
Published: February 2009

The thermal expansion coefficients of the hexagonal SiC polytypes 4H and 6H and with Al and N dopants have been determined for temperatures between 300 and 1770 K. Further, a set of the room temperature lattice parameters in dependence on doping with N, Al, and B has been obtained. Data for the thermal expansion were taken on a triple axis diffractometer for high energy x rays with a photon energy of 60 keV, which allows the use of large single crystals with a volume of at least 6×6×6 mm3 without the need to consider absorption. The room temperature measurements for samples with different dopants have been performed on a four-circle diffractometer. The thermal expansion coefficients along the a- and c-directions, α11 and α33, increase from 3×10−6 K−1 at 300 K to 6×10−6 K−1 at 1750 K. It is found that α11 and α33 are isotropic within 107 K−1. At high temperatures both coefficients for doped samples are ∼0.2×10−6 and 0.3×10−6 K−1 lower than for the undoped material.
Squared eigenfunctions for the Sasa–Satsuma equation
Authors: Yang Jianke , Kaup D. J.
Published: February 2009

Squared eigenfunctions are quadratic combinations of Jost functions and adjoint Jost functions which satisfy the linearized equation of an integrable equation. They are needed for various studies related to integrable equations, such as the development of its soliton perturbation theory. In this article, squared eigenfunctions are derived for the Sasa–Satsuma equation whose spectral operator is a 3×3 system, while its linearized operator is a 2×2 system. It is shown that these squared eigenfunctions are sums of two terms, where each term is a product of a Jost function and an adjoint Jost function. The procedure of this derivation consists of two steps: First is to calculate the variations of the potentials via variations of the scattering data by the Riemann–Hilbert method. The second one is to calculate the variations of the scattering data via the variations of the potentials through elementary calculations. While this procedure has been used before on other integrable equations, it is shown here, for the first time, that for a general integrable equation, the functions appearing in these variation relations are precisely the squared eigenfunctions and adjoint squared eigenfunctions satisfying, respectively, the linearized equation and the adjoint linearized equation of the integrable system. This proof clarifies this procedure and provides a unified explanation for previous results of squared eigenfunctions on individual integrable equations. This procedure uses primarily the spectral operator of the Lax pair. Thus two equations in the same integrable hierarchy will share the same squared eigenfunctions (except for a time-dependent factor). In the Appendix, the squared eigenfunctions are presented for the Manakov equations whose spectral operator is closely related to that of the Sasa–Satsuma equation.
Experimental investigation of the Cs2 a Σ3u+ triplet ground state: Multiparameter Morse long range potential analysis and molecular constants
Authors: Xie F. , Sovkov V. B. , Lyyra A. M. , Li D. , Ingram S. , Bai J. , Ivanov V. S. , Magnier S. , Li Li
Published: February 2009

We have observed the vibrational levels v″=0–40 of the Cs2 a Σ3u+ state by perturbation facilitated infrared-infrared double resonance excitation and spectrally resolved fluorescence measurements, and derived a multiparameter Morse long range potential and molecular constants based on these data.
Guiding and confining fast electrons by transient electric and magnetic fields with a plasma inverse cone
Authors: Lei A. L. , Cao L. H. , Yang X. Q. , Tanaka K. A. , Kodama R. , He X. T. , Mima K. , Nakamura T. , Norimatsu T. , Yu W. , Zhang W. Y.
Published: February 2009

The fast electron propagation in an inverse cone target is investigated computationally and experimentally. Two-dimensional particle-in-cell simulation shows that fast electrons with substantial numbers are generated at the outer tip of an inverse cone target irradiated by a short intense laser pulse. These electrons are guided and confined to propagate along the inverse cone wall, forming a large surface current. The propagation induces strong transient electric and magnetic fields which guide and confine the surface electron current. The experiment qualitatively verifies the guiding and confinement of the strong electron current in the wall surface. The large surface current and induced strong fields are of importance for fast ignition related researches.
Force spectroscopy of a single artificial biomolecule bond: The Kramers’ high-barrier limit holds close to the critical force
Authors: Husson J. , Dogterom M. , Pincet F.
Published: February 2009

We use a minimal system with a single micron-size bead trapped with optical tweezers to investigate the kinetics of escape under force. Surprisingly, the exponential decay of the off rate with the barrier energy is still valid close to the critical force. Hence, the high viscosity approximation derived by Kramers in the case of a high energy barrier holds even for an energy barrier close to the thermal energy. Several recent models describe a single biomolecule bond by a smooth single-barrier energy profile. When this approach is accurate enough, our result justifies the use of Kramers’ approximation in the high-force regime, close to the critical force of the system, as done in recent single biomolecule bond studies.
Photoinduced resistivity change of electron-doped La0.8Te0.2MnO3 film
Authors: Gao G. M. , Chen C. L. , Han L. A. , Cao X. S.
Published: February 2009

In this paper, electron-doped La0.8Te0.2MnO3 film has been prepared on SrTiO3 (100) substrate by pulsed laser deposition method, and the photoinduced resistivity change and colossal magnetoresistance effect have been investigated. The results show that the film has a high metal-insulator transition temperature TMI of ∼283 K and the maximum magnetoresistance ratio is ∼24% at 0.7 T. Under laser irradiation, TMI varies from 283 to 243 K and resistivity increases below TMI, while it decreases above TMI. The maximum photoinduced resistivity change in resistivity (LR%) is 134.8%. The photoinduced relaxation character of the film indicates that the relaxation of photoinduced character relates to the excitation of small polarons.
Stable complementary inverters with organic field-effect transistors on Cytop fluoropolymer gate dielectric
Authors: Walser M. P. , Kalb W. L. , Mathis T. , Brenner T. J. , Batlogg B.
Published: February 2009

We present results on small-molecule p- and n-type organic semiconductors in combination with the highly water repellent fluoropolymer Cytop™ as the gate dielectric. Using pentacene and N,N′-ditridecylperylene-3,4,9,10-tetracarboxylicdiimide (PTCDI-C13), we fabricated complementary inverters of high electrical quality and stability that are almost unaffected by repeated gate bias stress. The combined p- and n-type field-effect transistors show nearly ideal characteristics, very small hysteresis, and similar saturation mobility (∼0.2 cm2/V s). Particularly PTCDI-C13 thin-film transistors exhibit a remarkable performance in the subthreshold regime if chromium is used as contact material for electron injection: a near zero onset and a subthreshold swing as low as 0.6 V/decade.
Thermally actuated tapping mode atomic force microscopy with polymer microcantilevers
Authors: Mitra Bhaskar , Gaitas Angelo
Published: February 2009

This paper demonstrates a thermally actuated tapping mode atomic force microscopy (AFM) with a polymer cantilever. The cantilever (350×250×3 μm3) is made from polyimide and includes an embedded resistive heater for thermal actuation. The oscillation of the cantilever is due to the stress gradient caused by alternating heating and cooling from the periodic ac excitation of the heater. The tip oscillation amplitude is 5–10 nm in air. The oscillation occurs at 2ω and is a linear function of the applied voltage. The maximum oscillation amplitude is seen at 0.8 Hz with a 3dB frequency of 26 Hz. The damping of the oscillation due to tip-sample interaction is used to image the sample without any optomechanical feedback. Scans with a 200 nm tall grating indicate a resolution comparable to deflection signal from the AFM in contact mode.
Localized growth of InAs quantum dots on nanopatterned InP(001) substrates
Authors: Turala Artur , Regreny Philippe , Rojo-Romeo Pedro , Gendry Michel
Published: February 2009

We present the method of site-controlled growth of InAs quantum dots on InP(001) by solid-source molecular beam epitaxy. InAs dots are positioned using nanopatterns realized by electron beam lithography and dry etching. We have obtained the localized InAs dots for InAs deposit thickness inferior to the critical thickness for the two-dimensional/three-dimensional growth mode transition measured on a flat InP surface, implying that the dots can be actively positioned at predefined nucleation sites. Photoluminescence results show the emission of localized InAs dots on patterns overgrown with a thin InP buffer layer, at a wavelength around 1.5 μm at room temperature.
Measuring the relative permittivity of polyetherimide/(Ba0.8Sr0.2)(Ti0.9Zr0.1)O3 composites from 10 kHz to 12 GHz
Authors: Yang Cheng-Fu , Wu Chia-Ching , Chen Ying-Chung , Su Chean-Cheng
Published: February 2009

The relative permittivity of polyetherimide-(Ba0.8Sr0.2)(Ti0.9Zr0.1)O3 (PEI-BSTZ) composites is measured from 10 kHz to 1 MHz using plate method. As the content of BSTZ filler is less than 18 vol %, the experimental values are fitted to the values predicted by Lichtenecker equation. As the content is more than 18 vol %, the measured relative permittivity of PEI-BSTZ composites is higher than the predicted values. The relative permittivity of PEI-BSTZ composites is measured at 1–12 GHz using “square cavity resonator” method. Measured at gigahertz, the relative permittivity of PEI-BSTZ composites is almost unchanged.
Magneto-optical waveguides made of cobalt ferrite nanoparticles embedded in silica/zirconia organic-inorganic matrix
Authors: Choueikani Fadi , Royer François , Jamon Damien , Siblini Ali , Rousseau Jean Jacques , Neveu Sophie , Charara Jamal
Published: February 2009

This paper describes a way to develop magneto-optical waveguides via sol-gel process. They are made of cobalt ferrite nanoparticles embedded in a silica/zirconia matrix. Thin films are coated on glass substrate using the dip-coating technique. Annealing and UV treatment are applied to finalize sample preparation. Therefore, planar waveguides combining magneto-optical properties with a low refractive index (≈1,5) are obtained. M-lines and free space ellipsometry measurements show a specific Faraday rotation of 250°/cm and a modal birefringence of 1×10−4 at 820 nm. Thus, the mode conversion efficiency can reach a maximum value around 56%.
Fast discharge speed in poly(vinylidene fluoride) graft copolymer dielectric films achieved by confined ferroelectricity
Authors: Guan Fangxiao , Yuan Zhongzhe , Shu Essay W. , Zhu Lei
Published: February 2009

Although a high electric energy density was recently reported for defect-modified poly(vinylidene fluoride) (PVDF) copolymers at millisecond discharge, they usually deliver less energy at a high pulse rate. In this letter, a low loss polystyrene (PS) was grafted as side chains onto the P(VDF-chlorotrifluoroethylene) main chain. After PVDF crystallization, dielectric PS side chains were segregated to the crystalline-amorphous interface, forming a finite confinement layer for ferroelectric PVDF crystals. We speculated that less space charge was induced during electric poling because of the nanoscale confinement effect. Consequently, a fast discharge speed and a relatively high energy density were achieved.
Air-stable n-channel single-crystal transistors with negligible threshold gate voltage
Authors: Yamagishi M. , Tominari Y. , Uemura T. , Takeya J.
Published: February 2009

Single-crystal transistors of highly electron-affine organic compounds were constructed on solid dielectrics to study intrinsic constraints for the n-channel field effect in ambient atmosphere. Tetracyanoquinodimethane field-effect devices reproducibly operate with a high mobility of 0.2–0.5 cm2/V s in the air. The threshold gate voltage is negligible unlike most other air-stable n-type organic transistors reported, including polycrystal film devices of the same compound. Together with the other example of less electron-affine semiconductor crystal showing air-stable field effect but with notable threshold voltage, the result suggests that crucial in air-stable n-channel field effect is sufficient electron-affinity of the organic semiconductors.
Quantitative strain-field measurement of 1:1 B-site cation ordered domains and antiphase boundaries in Pb(Sc1/2Ta1/2)O3 ceramics by high-resolution transmission electron microscopy
Authors: Tai Cheuk W. , Lereah Y.
Published: February 2009

Quantitative strain measurements of the 1:1 B-site cation ordered domains, antiphase boundaries, and dislocations in a highly ordered Pb(Sc1/2Ta1/2)O3 ceramic have been carried out by high-resolution transmission electron microscopy and geometric phase analysis. A phase shift of π between two adjacent ordered domains across an antiphase boundary is determined unambiguously. The maximum in-plane strain and lattice rotation induced by a dislocation are 9.5% and 5.4°, respectively. In a defect-free antiphase boundary, the maximum in-plane strain and lattice rotation are 1.8% and 0.9°, respectively. The strain mainly concentrates inside the antiphase boundary.
Experimental evidence of left handed transmission through arrays of ferromagnetic microwires
Authors: García-Miquel H. , Carbonell J. , Boria V. E. , Sánchez-Dehesa J.
Published: February 2009

Experimental evidence of left-handed transmission is demonstrated through an array of ferromagnetic microwires. We used amorphous magnetic microwires to take advantage of both electric and magnetic responses locally generating a double negative medium at microwave frequencies, where the ferromagnetic resonance effects take place. The dilution of the responses of the ferromagnetic material provided by the organization of the microstructure in the form of an array provides a means of synthesizing a tailored response to electromagnetic radiation. Finally, transmission characteristics of the analyzed array can be tuned as a function of the applied external magnetic field.
The cardiac glycoside binding site on the Na,K-ATPase α2 isoform plays a role in the dynamic regulation of active transport in skeletal muscle
Authors: Radzyukevich T. L. , Lingrel J. B , Heiny J. A.
Published: February 2009

The physiological significance of the cardiac glycoside-binding site on the Na,K-ATPase remains incompletely understood. This study used a gene-targeted mouse (α2
R/R
) which expresses a ouabain-insensitive α2 isoform of the Na,K-ATPase to investigate whether the cardiac glycoside-binding site plays any physiological role in active Na
+
/K
+
transport in skeletal muscles or in exercise performance. Skeletal muscles express the Na,K-ATPase α2 isoform at high abundance and regulate its transport over a wide dynamic range under control of muscle activity. Na,K-ATPase active transport in the isolated extensor digitorum longus (EDL) muscle of α2
R/R
mice was lower at rest and significantly enhanced after muscle contraction, compared with WT. During the first 60 s after a 30-s contraction, the EDL of α2
R/R
mice transported 70.0 nmol/g·min more
86
Rb than WT. Acute sequestration of endogenous ligand(s) in WT mice infused with Digibind to sequester endogenous cardiac glycoside(s) produced similar effects on both resting and contraction-induced
86
Rb transport. Additionally, the α2
R/R
mice exhibit an enhanced ability to perform physical exercise, showing a 2.1- to 2.8-fold lower failure rate than WT within minutes of the onset of moderate-intensity treadmill running. Their enhanced exercise performance is consistent with their enhanced contraction-induced Na,K-ATPase transport in the skeletal muscles. These results demonstrate that the Na,K-ATPase α2 isozyme in skeletal muscle is regulated dynamically by a mechanism that utilizes the cardiac glycoside-binding site and an endogenous ligand(s) and that its cardiac glycoside-binding site can play a physiological role in the dynamic adaptations to exercise.
TOX3 regulates calcium-dependent transcription in neurons
Authors: Yuan Shauna H. , Qiu Zilong , Ghosh Anirvan
Published: February 2009

We report the cloning and characterization of TOX3, a high mobility group box protein involved in mediating calcium-dependent transcription. TOX3 was identified as a calcium-dependent transactivator using the Transactivator Trap screen. We find that TOX3 interacts with both cAMP response element (CRE)-binding protein (CREB) and CREB-binding protein (CBP), and knockdown of the endogenous TOX3 by RNAi leads to significant reduction of calcium-induced c-fos expression and complete inhibition of calcium activation of the c-fos promoter. The effects of TOX3 on calcium-dependent transcription require the CRE elements. These observations identify TOX3 as an important regulator of calcium-dependent transcription and suggest that TOX3 exerts its effect on CRE-mediated transcription via its association with the CREB–CBP complex.
Reduction of scale invariance of activity fluctuations with aging and Alzheimer's disease: Involvement of the circadian pacemaker
Authors: Hu Kun , Van Someren Eus J. W. , Shea Steven A. , Scheer Frank A. J. L.
Published: February 2009

Human motor control systems orchestrate complex scale-invariant patterns of activity over a wide range of time scales (minutes to hours). The neural mechanisms underlying scale-invariance are unknown in humans. In rats, the master circadian pacemaker [suprachiasmatic nucleus (SCN)] is crucially involved in scale-invariant activity fluctuations over multiple time scales from minutes to 24 h. Aging and Alzheimer's disease (AD) are associated with progressive dysfunction of the SCN. Thus, if the SCN is responsible for the scale-invariant activity fluctuations in humans, we predict disturbances of scale-invariant activity fluctuations in elderly humans and even more pronounced disturbances in elderly humans with AD. To test these hypotheses, we studied spontaneous daytime activity patterns in 13 young adults (mean ± SD: 25.5 ± 6.1 y); 13 elderly people with early-stage AD (68.5 ± 6.1 y) matched with 13 elderly controls (68.6 ± 6.1 y); and 14 very old people with late-stage AD (83.9 ± 6.7 y) matched with 12 very old controls (80.8 ± 8.6 y). In young adults, activity exhibited robust scale-invariant correlations across all tested time scales (minutes to 8 h). The scale-invariant correlations at 1.5–8 h declined with age (
P
= 0.01) and were significantly reduced in the elderly (
P
= 0.04) and very old controls (
P
= 0.02). Remarkably, an age-independent AD effect further reduced the scale-invariant correlations at 1.5–8 h (
P
= 0.04), leading to the greatest reduction of the scale-invariant correlations in very old people with late-stage AD—resembling closely the loss of correlations at large time scales in SCN-lesioned animals. Thus, aging and AD significantly attenuate the scale invariance of activity fluctuations over multiple time scales. This attenuation may reflect functional changes of the SCN.
The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks
Authors: Shao Genze , Lilli Dana R. , Patterson-Fortin Jeffrey , Coleman Kara A. , Morrissey Devon E. , Greenberg Roger A.
Published: February 2009

DNA double strand breaks (DSBs) initiate reversible cellular checkpoint and repair activities. Whereas many of the activating events at DSBs have recently been elucidated, the mechanisms used to terminate responses at these sites are largely undefined. Here we report a pathway required to reverse RNF8-Ubc13 dependent ubiquitination events on chromatin flanking DSBs. Inhibition of the Rap80-BRCC36 de-ubiquitinating enzyme complex partially restored DSB-associated ubiquitin levels following RNF8 knockdown or proteasome inhibition. Similarly, BRCC36 knockdown or expression of a BRCC36 de-ubiquitinating enzyme-inactive mutant rescued both 53BP1 recruitment to DSBs and ionizing radiation-induced γH2AX ubiquitination following RNF8 depletion, and mitigated ionizing radiation sensitivity resulting from RNF8 deficiency. Thus, concomitant and opposing RNF8-Ubc13 ubiquitin ligase and Rap80-BRCC36 ubiquitin hydrolysis activities are responsible for determining steady-state ubiquitin levels at DNA DSBs. These findings reveal a Rap80-BRCC36 dependent pathway that is required for appropriate DSB recruitment and repair responses.
ARNT PAS-B has a fragile native state structure with an alternative β-sheet register nearby in sequence space
Authors: Evans Matthew R. , Card Paul B. , Gardner Kevin H.
Published: February 2009

The aryl hydrocarbon receptor nuclear translocator (ARNT) is a basic helix–loop–helix Period/ARNT/Single-minded (bHLH-PAS) protein that controls various biological pathways as part of dimeric transcriptional regulator complexes with other bHLH-PAS proteins. The two PAS domains within ARNT, PAS-A and PAS-B, are essential for the formation of these complexes because they mediate protein–protein interactions via residues located on their β-sheet surfaces. While investigating the importance of residues in ARNT PAS-B involved in these interactions, we uncovered a point mutation (Y456T) on the solvent-exposed β-sheet surface that allowed this domain to interconvert with a second, stable conformation. Although both conformations are present in equivalent quantities in the Y456T mutant, this can be shifted almost completely to either end point by additional mutations. A high-resolution solution structure of a mutant ARNT PAS-B domain stabilized in the new conformation revealed a 3-residue slip in register and accompanying inversion of the central Iβ-strand. We have demonstrated that the new conformation has >100-fold lower in vitro affinity for its heterodimerization partner, hypoxia-inducible factor 2α PAS-B. We speculate that the pliability in β-strand register is related to the flexibility required of ARNT to bind to several partners and, more broadly, to the abilities of some PAS domains to regulate their activities in response to small-molecule cofactors.
An oxygen-sensitive mechanism in regulation of epithelial sodium channel
Authors: Wang Su , Publicover Stephen , Gu Yuchun
Published: February 2009

Epithelial sodium channels (ENaCs) are of immense importance, controlling Na
+
transport across epithelia and thus playing a central role in all aspects of fluid clearance as well as numerous other functions. Regulation of these channels is critical. Here, we show that haem, a regulator of Na
+
transport, directly influences ENaC activity, decreasing channel-open probability (but not unitary conductance) in inside-out patches (but not outside-out). Conversely, exposure to the protein in the presence of NADPH and at normoxic O
2
tension (requirements for activity of hemeoxygenase) increases channel activity. CO, a product of hemeoxygenase activity, activated ENaC in a manner similar to that of haem plus NADPH. However, under hypoxic conditions, inhibition of ENaC by haem occurred even in the presence of NADPH. These data demonstrate a potent, O
2
-sensitive mechanism for regulation of ENaC, in which hemeoxygenase acts as the O
2
sensor, its substrate and product inhibiting and stimulating (respectively) the activity of ENaC.
Estrogen promotes the survival and pulmonary metastasis of tuberin-null cells
Authors: Yu Jane J. , Robb Victoria A. , Morrison Tasha A. , Ariazi Eric A. , Karbowniczek Magdalena , Astrinidis Aristotelis , Wang Chunrong , Hernandez-Cuebas Lisa , Seeholzer Laura F. , Nicolas Emmanuelle , Hensley Harvey , Jordan V. Craig , Walker Cheryl L. , Henske Elizabeth P.
Published: February 2009

Lymphangioleiomyomatosis (LAM) is an often fatal disease primarily affecting young women in which tuberin (TSC2)-null cells metastasize to the lungs. The mechanisms underlying the striking female predominance of LAM are unknown. We report here that 17-β-estradiol (E
2
) causes a 3- to 5-fold increase in pulmonary metastases in male and female mice, respectively, and a striking increase in circulating tumor cells in mice bearing tuberin-null xenograft tumors. E
2
-induced metastasis is associated with activation of p42/44 MAPK and is completely inhibited by treatment with the MEK1/2 inhibitor, CI-1040. In vitro, E
2
inhibits anoikis of tuberin-null cells. Finally, using a bioluminescence approach, we found that E
2
enhances the survival and lung colonization of intravenously injected tuberin-null cells by 3-fold, which is blocked by treatment with CI-1040. Taken together these results reveal a new model for LAM pathogenesis in which activation of MEK-dependent pathways by E
2
leads to pulmonary metastasis via enhanced survival of detached tuberin-null cells.
Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added
Authors: Avbelj Franc , Baldwin Robert L.
Published: February 2009

Recent calorimetric measurements of the solvation enthalpies of some dipeptide analogs confirm our earlier prediction that the principle of group additivity is not valid for the interaction of the peptide group with water. We examine the consequences for understanding the properties of peptide solvation. A major consequence is that the current value of the peptide-solvation enthalpy, which is a basic parameter in analyzing the energetics of protein folding, is seriously wrong. Electrostatic calculations of solvation-free energies provide an estimate of the size and nature of the error. Peptide hydrogen exchange rates provide an experimental approach for testing the accuracy of the solvation-free energies of peptide groups found by electrostatic calculations. These calculations emphasize that ignoring electrostatic interactions with neighboring NHCO groups should be a major source of error. Results in 1972 for peptide hydrogen exchange rates demonstrate that peptide-solvation-free energies are strongly affected by adjoining NHCO groups. In the past, the effect of adjoining peptide groups on the exchange rate of a peptide NH proton was treated as an inductive effect. The effect can be calculated, however, by an electrostatic model with fixed partial charges and a continuum solvent.
Identification of compounds that potentiate CREB signaling as possible enhancers of long-term memory
Authors: Xia Menghang , Huang Ruili , Guo Vicky , Southall Noel , Cho Ming-Hsuang , Inglese James , Austin Christopher P. , Nirenberg Marshall
Published: February 2009

Many studies have implicated the cAMP Response Element Binding (CREB) protein signaling pathway in long-term memory. To identify small molecule enhancers of CREB activation of gene expression, we screened ≈73,000 compounds, each at 7–15 concentrations in a quantitative high-throughput screening (qHTS) format, for activity in cells by assaying CREB mediated β-lactamase reporter gene expression. We identified 1,800 compounds that potentiated CREB mediated gene expression, with potencies as low as 16 nM, comprising 96 structural series. Mechanisms of action were systematically determined, and compounds that affect phosphodiesterase 4, protein kinase A, and cAMP production were identified, as well as compounds that affect CREB signaling via apparently unidentified mechanisms. qHTS folowed by interrogation of pathway targets is an efficient paradigm for lead generation for chemical genomics and drug development.
Enhanced sensitivity to DSS colitis caused by a hypomorphic
Mbtps1
mutation disrupting the ATF6-driven unfolded protein response
Authors: Brandl Katharina , Rutschmann Sophie , Li Xiaohong , Du Xin , Xiao Nengming , Schnabl Bernd , Brenner David A. , Beutler Bruce
Published: February 2009

Here, we describe an
N
-ethyl-
N
-nitrosourea (ENU)-induced missense error in the membrane-bound transcription factor peptidase site 1 (S1P)-encoding gene (
Mbtps1
) that causes enhanced susceptibility to dextran sodium sulfate (DSS)-induced colitis. S1P cleaves and activates cAMP response element binding protein/ATF transcription factors, the sterol regulatory element-binding proteins (SREBPs), and other proteins of both endogenous and viral origin. Because S1P has a nonredundant function in the ATF6-dependent unfolded protein response (UPR),
woodrat
mice show diminished levels of major endoplasmic reticulum chaperones GRP78 (BiP) and GRP94 in the colon upon DSS administration. Experiments with bone marrow chimeric mice reveal a requirement for S1P in nonhematopoietic cells, without which a diminished UPR and colitis develop.
The G protein-coupled receptor FSHR-1 is required for the
Caenorhabditis elegans
innate immune response
Authors: Powell Jennifer R. , Kim Dennis H. , Ausubel Frederick M.
Published: February 2009

Innate immunity is an ancient defense system used by both vertebrates and invertebrates. Previously characterized innate immune responses in plants and animals are triggered by detection of pathogens using specific receptors, which typically use a leucine-rich repeat (LRR) domain to bind molecular patterns associated with infection. The nematode
Caenorhabditis elegans
uses defense pathways conserved with vertebrates; however, the mechanism by which
C. elegans
detects pathogens is unknown. We screened all LRR-containing transmembrane receptors in
C. elegans
and identified the G protein-coupled receptor FSHR-1 as an important component of the
C. elegans
immune response to Gram-negative and Gram-positive bacterial pathogens. FSHR-1 acts in the
C. elegans
intestine, the primary site of exposure to ingested pathogens. FSHR-1 signals in parallel to the known p38 MAPK pathway but converges to regulate the transcriptional induction of an overlapping but nonidentical set of antimicrobial effectors. FSHR-1 may act generally to boost the nematode immune response, or it may function as a pathogen receptor.
Potassium softens vascular endothelium and increases nitric oxide release
Authors: Oberleithner H. , Callies C. , Kusche-Vihrog K. , Schillers H. , Shahin V. , Riethmüller C. , MacGregor G. A. , de Wardener H. E.
Published: February 2009

In the presence of aldosterone, plasma sodium in the high physiological range stiffens endothelial cells and reduces the release of nitric oxide. We now demonstrate effects of extracellular potassium on stiffness of individual cultured bovine aortic endothelial cells by using the tip of an atomic force microscope as a mechanical nanosensor. An acute increase of potassium in the physiological range swells and softens the endothelial cell and increases the release of nitric oxide. A high physiological sodium concentration, in the presence of aldosterone, prevents these changes. We propose that the potassium effects are caused by submembranous cortical fluidization because cortical actin depolymerization induced by cytochalasin D mimics the effect of high potassium. In contrast, a low dose of trypsin, known to activate sodium influx through epithelial sodium channels, stiffens the submembranous cell cortex. Obviously, the cortical actin cytoskeleton switches from gelation to solation depending on the ambient sodium and potassium concentrations, whereas the center of the cell is not involved. Such a mechanism would control endothelial deformability and nitric oxide release, and thus influence systemic blood pressure.
Micromagnetic selection of aptamers in microfluidic channels
Authors: Lou Xinhui , Qian Jiangrong , Xiao Yi , Viel Lisan , Gerdon Aren E. , Lagally Eric T. , Atzberger Paul , Tarasow Theodore M. , Heeger Alan J. , Soh H. Tom
Published: February 2009

Aptamers are nucleic acid molecules that have been selected in vitro to bind to their molecular targets with high affinity and specificity. Typically, the systematic evolution of ligands by exponential enrichment (SELEX) process is used for the isolation of specific, high-affinity aptamers. SELEX, however, is an iterative process requiring multiple rounds of selection and amplification that demand significant time and labor. Here, we describe an aptamer discovery system that is rapid, highly efficient, automatable, and applicable to a wide range of targets, based on the integration of magnetic bead-based SELEX process with microfluidics technology. Our microfluidic SELEX (M-SELEX) method exploits a number of unique phenomena that occur at the microscale and implements a design that enables it to manipulate small numbers of beads precisely and isolate high-affinity aptamers rapidly. As a model to demonstrate the efficiency of the M-SELEX process, we describe here the isolation of DNA aptamers that tightly bind to the light chain of recombinant
Botulinum
neurotoxin type A (with low-nanomolar dissociation constant) after a single round of selection.
Methylphenidate-induced dendritic spine formation and ΔFosB expression in nucleus accumbens
Authors: Kim Yong , Teylan Merilee A. , Baron Matthew , Sands Adam , Nairn Angus C. , Greengard Paul
Published: February 2009

Methylphenidate is the psychostimulant medication most commonly prescribed to treat attention deficit hyperactivity disorder (ADHD). Recent trends in the high usage of methylphenidate for both therapeutic and nontherapeutic purposes prompted us to investigate the long-term effects of exposure to the drug on neuronal adaptation. We compared the effects of chronic methylphenidate or cocaine (15 mg/kg, 14 days for both) exposure in mice on dendritic spine morphology and ΔFosB expression in medium-sized spiny neurons (MSN) from ventral and dorsal striatum. Chronic methylphenidate increased the density of dendritic spines in MSN-D1 (MSN-expressing dopamine D1 receptors) from the core and shell of nucleus accumbens (NAcc) as well as MSN-D2 (MSN-expressing dopamine D2 receptors) from the shell of NAcc. In contrast, cocaine increased the density of spines in both populations of MSN from all regions of striatum. In general, the effect of methylphenidate on the increase of shorter spines (class 2) was less than that of cocaine. Interestingly, the methylphenidate-induced increase in the density of relatively longer spines (class 3) in the shell of NAcc was bigger than that induced by cocaine. Furthermore, methylphenidate exposure increased expression of ΔFosB only in MSN-D1 from all areas of striatum, and surprisingly, the increase was greater than that induced by cocaine. Thus, our results show differential effects of methylphenidate and cocaine on neuronal adaptation in specific types of MSN in reward-related brain regions.
Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin
Authors: Wieland Brown Laura C. , Acker Michael G. , Clardy Jon , Walsh Christopher T. , Fischbach Michael A
Published: February 2009

The thiazolylpeptides are a family of >50 bactericidal antibiotics that block the initial steps of bacterial protein synthesis. Here, we report a biosynthetic gene cluster for thiocillin and establish that it, and by extension the whole class, is ribosomally synthesized. Remarkably, the C-terminal 14 residues of a 52-residue peptide precursor undergo 13 posttranslational modifications to give rise to thiocillin, making this antibiotic the most heavily posttranslationally-modified peptide known to date.
Marine science with global vision: creating a place for early career scientists. An introduction to selected articles from the 2007 Early Career Scientists Conference
Authors: North Elizabeth W. , Mueter Franz J.
Published: February 2009

North, E. W., and Mueter, F. J. 2009. Marine science with global vision: creating a place for early career scientists. An introduction to selected articles from the 2007 Early Career Scientists Conference. – ICES Journal of Marine Science, 66: 334–335.