bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerating flat-histogram methods for potential of mean force calculations
Authors: Janosi Lorant , Doxastakis Manolis
Published: August 2009

Potential of mean force calculations along a reaction coordinate (RC) demand exhaustive sampling, which often leads to prohibitively long computational times. The expanded ensemble density of states (EXEDOS) [E. B. Kim, R. Faller, Q. Yan et al., J. Chem. Phys. 117, 7781 (2002)] is a simple flat-histogram Monte Carlo method based on the density of states algorithm proposed by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)]. EXEDOS offers the advantage of continuous uniform sampling of the RC with no a priori knowledge of the free energy profile. However, the method is not certain to converge within accessible simulation time. Furthermore, the strongly asymmetric distribution of tunneling times inherent in flat-histogram sampling imposes additional limitations. We propose several improvements that accelerate the EXEDOS method and can be generally applicable in free energy calculations. First, we propose an asynchronous parallel implementation of the density of states algorithm in a multiple-walkers multiple-windows scheme and extend the algorithm in an expanded ensemble [(MW)2-XDOS] for PMF calculations as the original EXEDOS. Despite the nonideal scaling over a number of processors this technique overcomes limitations by extreme values of tunneling times and allows consistent evaluations of performance. The second set of improvements addresses the dependence of convergence times on system size, density, and sampling rate of the RC. At low densities, the coupling of (MW)2-XDOS with the rejection-free geometric cluster move provides impressive performance that overshadows any other technique. However, the limited applicability of cluster moves at high densities requires an alternative approach. We propose the coupling of (MW)2-XDOS with preferential sampling methods. In the systems studied, single displacements in the proximity of particles defining the RC accelerate calculations significantly and render the simulation nearly size-independent. A further modification of preferential sampling involves collective displacements of particles performed in a “smart Monte Carlo” scheme. This “local Brownian dynamics” algorithm can be generally applicable to many free energy simulation methods and would be particularly beneficial at high densities and molecular systems with strong intramolecular potentials.
A flow cell for in situ synchrotron x-ray diffraction studies of scale formation under Bayer processing conditions
Authors: Webster Nathan A. S. , Madsen Ian C. , Loan Melissa J. , Scarlett Nicola V. Y. , Wallwork Kia S.
Published: August 2009

The design, construction, and commissioning of a stainless steel flow cell for in situ synchrotron x-ray diffraction studies of scale formation under Bayer processing conditions is described. The use of the cell is demonstrated by a study of Al(OH)3 scale formation on a mild steel substrate from synthetic Bayer liquor at 70 °C. The cell design allows for interchangeable parts and substrates and would be suitable for the study of scale formation in other industrial processes.
Plasma parameters of pulsed-dc discharges in methane used to deposit diamondlike carbon films
Authors: Corbella C. , Rubio-Roy M. , Bertran E. , Andújar J. L.
Published: August 2009

Here we approximate the plasma kinetics responsible for diamondlike carbon (DLC) depositions that result from pulsed-dc discharges. The DLC films were deposited at room temperature by plasma-enhanced chemical vapor deposition (PECVD) in a methane (CH4) atmosphere at 10 Pa. We compared the plasma characteristics of asymmetric bipolar pulsed-dc discharges at 100 kHz to those produced by a radio frequency (rf) source. The electrical discharges were monitored by a computer-controlled Langmuir probe operating in time-resolved mode. The acquisition system provided the intensity-voltage (I-V) characteristics with a time resolution of 1 μs. This facilitated the discussion of the variation in plasma parameters within a pulse cycle as a function of the pulse waveform and the peak voltage. The electron distribution was clearly divided into high- and low-energy Maxwellian populations of electrons (a bi-Maxwellian population) at the beginning of the negative voltage region of the pulse. We ascribe this to intense stochastic heating due to the rapid advancing of the sheath edge. The hot population had an electron temperature Tehot of over 10 eV and an initial low density nehot which decreased to zero. Cold electrons of temperature Tecold∼1 eV represented the majority of each discharge. The density of cold electrons necold showed a monotonic increase over time within the negative pulse, peaking at almost 7×1010 cm−3, corresponding to the cooling of the hot electrons. The plasma potential Vp of ∼30 V underwent a smooth increase during the pulse and fell at the end of the negative region. Different rates of CH4 conversion were calculated from the DLC deposition rate. These were explained in terms of the specific activation energy Ea and the conversion factor xdep associated with the plasma processes. The work deepens our understanding of the advantages of using pulsed power supplies for the PECVD of hard metallic and protective coatings for industrial applications (optics, biomedicine, and electronics).
The fractional Stokes–Einstein equation: Application to Lennard-Jones, molecular, and ionic liquids
Authors: Harris Kenneth R.
Published: August 2009

The fractional Stokes–Einstein (FSE) relation, (D/T)∝η−t, is shown to well correlate the molecular dynamics results of Meier et al. [J. Chem. Phys. 121, 3671 (2004); Meier et al.J. Chem. Phys. 121, 9526 (2004)] for the viscosity (η) and self-diffusion coefficient (D) of the Lennard-Jones fluid in the liquid and dense supercritical states, with the exponent t=(0.921±0.003). The Stokes–Einstein number n is viscosity dependent: ln n=const+(t−1)ln η. Molecular and ionic liquids for which high-pressure transport property data are available in the literature are shown to exhibit the same behavior with 0.79<t<1. Water is also shown to fit the FSE at atmospheric pressure, with a change in exponent t from 0.94 to 0.67 at about 258 K (265 K for D2O), but the FSE holds only approximately at high pressures. It sometimes argued that FSE in supercooled liquids near the glass transition is a diagnostic for dynamic heterogeneity, but this work shows that the FSE holds in normal liquids far from the glass transition. This result may provide a reference for complex liquids such as viscous glass formers that show a transition (dynamic crossover) in the temperature dependence of the viscosity and network-bonded liquids such as water.
Effect of radio frequency discharge power on dusty plasma parameters
Authors: Sheridan T. E.
Published: August 2009

The parameters of a two-dimensional dusty plasma consisting of six, 9 μm diameter particles trapped inside a radio frequency (rf) plasma sheath have been measured as a function of rf power in a 13.5 mtorr (1.8 Pa) argon discharge. The center-of-mass and breathing frequencies are found by projecting the cluster’s Brownian motion onto the associated normal mode. The center-of-mass frequency (i.e., radial confinement) is insensitive to rf power. The Debye shielding parameter κ, as found from the breathing frequency, increases from ≈0.5 to 2 as the square root of rf power. The Debye length decreases from ≈2.7 to 0.7 mm as the inverse of the square root of rf power. The average particle charge q≈−17 000e is effectively independent of rf power. These results are consistent with an electron temperature that is independent of rf power and an ion density that is directly proportional to rf power, where the Debye length is determined by the ion density in combination with the electron temperature.
Crucial role of doping dynamics on transport properties of Sb-doped SnO2 nanowires
Authors: Klamchuen Annop , Yanagida Takeshi , Nagashima Kazuki , Seki Shu , Oka Keisuke , Taniguchi Masateru , Kawai Tomoji
Published: August 2009

Impurity doping on semiconductor nanowires grown by vapor-liquid-solid (VLS) mechanism remains an important challenge. Here we demonstrate the importance of doping dynamics to control the transport properties of Sb-doped SnO2 nanowires. Sb doping decreased the resistivity of SnO2 nanowires down to 10−3 Ω cm range, while there was the lower bound of resistivity even increasing further the dopant concentration from supplied source. We found that the doping limitation is related to the re-evaporation events of dopant through vapor-solid growth process rather than VLS process. Thus understanding the dopant incorporation dynamics is essential to control the transport properties of SnO2 nanowires by impurity doping.
On the universality of the long-/short-range separation in multiconfigurational density-functional theory. II. Investigating f actinide species
Authors: Fromager Emmanuel , Réal Florent , Wåhlin Pernilla , Wahlgren Ulf , Jensen Hans Jørgen Aa.
Published: August 2009

In a previous paper [Fromager et al., J. Chem. Phys. 126, 074111 (2007)], some of the authors proposed a recipe for choosing the optimal value of the μ parameter that controls the long-range/short-range separation of the two-electron interaction in hybrid multiconfigurational self-consistent field short-range density-functional theory (MC-srDFT) methods. For general modeling with MC-srDFT methods, it is clearly desirable that the same universal value of μ can be used for any molecule. Their calculations on neutral light element compounds all yielded μopt=0.4 a.u. In this work the authors investigate the universality of this value by considering “extreme” study cases, namely, neutral and charged isoelectronic f0 actinide compounds (ThO2, PaO2+, UO22+, UN2, CUO, and NpO23+). We find for these compounds that μopt=0.3 a.u. but show that 0.4 a.u. is still acceptable. This is a promising result in the investigation of a universal range separation. The accuracy of the currently best MC-srDFT (μ=0.3 a.u.) approach has also been tested for equilibrium geometries. Though it performs as well as wave function theory and DFT for static-correlation-free systems, it fails in describing the neptunyl (VII) ion NpO23+ where static correlation is significant; bending is preferred at the MC-srDFT (μ=0.3 a.u.) level, whereas the molecule is known to be linear. This clearly shows the need for better short-range functionals, especially for the description of the short-range exchange. It also suggests that the bending tendencies observed in DFT for NpO23+ cannot be fully explained by the bad description of static correlation effects by standard functionals. A better description of the exchange seems to be essential too.
Current scaling in an atmospheric pressure capillary dielectric barrier discharge
Authors: Sands Brian L. , Huang Shih K. , Ganguly Biswa N.
Published: August 2009

Current scaling in an atmospheric pressure capillary dielectric barrier discharge, comprising a structured rare gas flow that extends into ambient air, is characterized by electrical and optical measurements. In the transient glow mode, two current scaling regimes were identified that are separated by the static free shear flow boundary. The peak current was sensitive to cathode placement relative to this flow structure and could be scaled from ∼300 mA to over 5 A. Applying a Boltzmann equation solver, it was found that ∼1% air entrainment into the flow and an E/N≲5×10−16 V cm−2 could account for the observed trends.
Temporal evolution of the laser-induced plasma generated by IR CO2 pulsed laser on carbon targets
Authors: Camacho J. J. , Díaz L. , Santos M. , Juan L. J. , Poyato J. M. L.
Published: August 2009

Time-resolved optical emission analysis was carried out for the plasma plume, produced by high-power tunable IR CO2 pulsed laser ablation of graphite, at λ=10.591 μm and in a regime of relatively high laser fluences (123–402 J/cm2). Wavelength-dispersed spectra of the plasma plume, at medium-vacuum conditions (4 Pa) and at 9.0 mm from the target, show ionized species (C+, C2+, C3+, C4+, N2+ , N+, and O+), neutral atoms (C, H, N, and O), and neutral diatomic molecules (C2, CN, OH, CH, and N2). In this work, we focus our attention on the temporal evolution of different atomic/ionic and molecular species over a broad spectral range from 190 to 1000 nm. The results show a faster decay for ionic fragments than for neutral atomic and molecular species. The velocity and kinetic energy distributions for different species were obtained from time-of-flight measurements using time-resolved optical emission spectroscopy. Possible mechanisms for the production of these distributions are discussed. Excitation temperature, electron density, and vibrational temperature in the laser-induced plasma were estimated from the analysis of spectral data at various times from the laser pulse incidence.
A compact surface decontamination system for surface-sensitive magnetic imaging
Authors: Konoto M. , Akoh H. , Tokura Y.
Published: August 2009

A surface decontamination system for application in surface sensitive magnetic imaging tools, such as a spin-polarized scanning electron microscope, is described. Adsorbed contaminant is chemically decomposed with the use of active oxygen in a compact vacuum chamber mounted in a microscope. The present method is especially suitable for fragile magnetic surfaces of complex oxide materials to which the conventional physical etching widely used for magnetic metals could cause serious structural damage. We have succeeded in detecting magnetic signals from a decontaminated oxide surface and visualizing domain images with sufficient magnetic contrast to analyze detailed domain structures.
Direct observation of the gas-surface interaction kinetics in nanowires through pulsed self-heating assisted conductometric measurements
Authors: Prades J. D. , Jimenez-Diaz R. , Hernandez-Ramirez F. , Pan J. , Romano-Rodriguez A. , Mathur S. , Morante J. R.
Published: August 2009

Dynamics of gas-surface interactions determine the limits of the fastest response times of sensors based on metal oxides. Here, the kinetics of adsorption and desorption of gaseous molecules onto the surface of metal oxide nanowires was analyzed through pulsed self-heating assisted conductometric measurements. This approach overcomes gas diffusion, which is typical of conventional porous film based devices, and provides thermal response times fast enough to evaluate the fundamental gas-surface reactions kinetics. Experimental response and recovery times of individual SnO2 nanowires toward oxidizing and reducing gases obtained with the here-proposed methodology were related to the reaction barriers predicted by theoretical models and other experimental techniques.
Electron injection via pentacene thin films for efficient inverted organic light-emitting diodes
Authors: Yun Changhun , Cho Hyunsu , Kang Hyeseung , Lee Young Mi , Park Yongsup , Yoo Seunghyup
Published: August 2009

We report on the fabrication of efficient inverted organic light-emitting diodes (IOLEDs) using pentacene films as an electron injection/transport layer between Al and Alq3 layers. These IOLED devices turn on at 4.7 V and exhibit a luminous efficiency of 9.5 cd/A without any dopants or reactive metals. Analysis using space-charge-limited characteristics of electron-only devices and ultraviolet photoelectron spectroscopy measurement of metal/organic interfaces indicates that the efficient IOLED characteristics can be attributed partly to the electron mobility of pentacene that is 102–104 times larger than that of Alq3 and to the effective reduction in injection barrier at contacts.
Pull-in control due to Casimir forces using external magnetic fields
Authors: Esquivel-Sirvent R. , Palomino-Ovando M. A. , Cocoletzi G. H.
Published: August 2009

We present a theoretical calculation of the pull-in control in capacitive microswitches actuated by Casimir forces using external magnetic fields. The external magnetic fields induce an optical anisotropy due to the excitation of magnetoplasmons that reduces the Casimir force. The calculations are performed in the Voigt configuration and the results show that as the magnetic field increases the system becomes more stable. The detachment length for a cantilever is also calculated for a cantilever, showing that it increases with increasing magnetic field. At the pull-in separation, the stiffness of the system decreases with the increasing magnetic field.
Fermion Monte Carlo without fixed nodes: A game of life, death, and annihilation in Slater determinant space
Authors: Booth George H. , Thom Alex J. W. , Alavi Ali
Published: August 2009

We have developed a new quantum Monte Carlo method for the simulation of correlated many-electron systems in full configuration-interaction (Slater determinant) spaces. The new method is a population dynamics of a set of walkers, and is designed to simulate the underlying imaginary-time Schrödinger equation of the interacting Hamiltonian. The walkers (which carry a positive or negative sign) inhabit Slater determinant space, and evolve according to a simple set of rules which include spawning, death and annihilation processes. We show that this method is capable of converging onto the full configuration-interaction (FCI) energy and wave function of the problem, without any a priori information regarding the nodal structure of the wave function being provided. Walker annihilation is shown to play a key role. The pattern of walker growth exhibits a characteristic plateau once a critical (system-dependent) number of walkers has been reached. At this point, the correlation energy can be measured using two independent methods—a projection formula and a energy shift; agreement between these provides a strong measure of confidence in the accuracy of the computed correlation energies. We have verified the method by performing calculations on systems for which FCI calculations already exist. In addition, we report on a number of new systems, including CO, O2, CH4, and NaH—with FCI spaces ranging from 109 to 1014, whose FCI energies we compute using modest computational resources.
A restricted quantum reaction path Hamiltonian: Theory, discrete variable representation propagation algorithm, and applications
Authors: González Javier , Giménez Xavier , Bofill Josep Maria
Published: August 2009

A derivation of a quantum reaction path Hamiltonian is proposed, which is based on a reformulation of the classical version of González et al. [J. Phys. Chem. A 105, 5022 (2001)], and the resulting equations are solved by means of a discrete variable representation approach, leading to a well-suited algorithm for the calculation of quantum dynamics of chemical reactions involving polyatomic molecules. General expressions for any type of reaction path are presented with special interest in the intrinsic reaction coordinate, which have been used to study selected cases, including a one-dimensional Eckart barrier, for which results are shown to be exact, two bidimensional systems, namely, a Müller–Brown potential energy surface, which is characteristic of polyatomic isomerization processes, and the collinear H+H2 chemical reaction, and finally the tridimensional, J=0, F+H2 reaction. Results for the specific chemical systems are shown to be in quite good agreement with exact two- and three-dimensional quantum calculations concerning autocorrelation functions as well as transmission factors as a function of total energy.
Motion of a vortex ring in a simple shear flow
Authors: Cheng M. , Lou J. , Lim T. T.
Published: August 2009

The motion and deformation of a vortex ring in a linear or simple shear flow have been simulated numerically by using the lattice Boltzmann method with multiple relaxation times. The study is motivated by a recent experiment [T. T. Lim, K. B. Lua, and K. Thet, Phys. Fluids 20, 051701 (2008)], which shows that a vortex ring propagating in a uniform cross flow does not experience Kutta lift and undergo tilting and deformation. The focus of the present study is to examine the effect of a simple shear in a cross flow on the motion of a vortex ring. Numerical approach is adopted here because a truly simple shear flow is difficult to generate experimentally. Our computation shows that a vortex ring tilts and deforms in a simple shear flow, and the tilting can be attributed to the modification of the vorticity distribution of the vortex ring as a result of the entrainment of background vorticity by the vortex core. It is further shown that although the shear in the flow has the tendency to elongate the vortex ring, the tilting angle of the ring increases with the shear ratio.
Monoclinic MB phase and phase instability in [110] field cooled Pb(Zn1/3Nb2/3)O3–4.5%PbTiO3 single crystals
Authors: Yao Jianjun , Cao Hu , Ge Wenwei , Li Jiefang , Viehland D.
Published: August 2009

We report the finding of a monoclinic MB phase in Pb(Zn1/3Nb2/3)O3–4.5%PbTiO3 single crystals. High precision x-ray diffraction investigations of [110] field cooled crystals have shown a transformation sequence of cubic(C)→tetragonal(T)→orthorhombic(O)→monoclinic(MB), which is different from that previously reported [A.-E. Renault et al., J. Appl. Phys. 97, 044105 (2005)]. Beginning in the zero-field-cooled condition at 383 K, a rhombohedral (R)→MB→O sequence was observed with increasing field. Coexisting MB and O phases were then found upon removal of field, which fully transformed to MB on cooling to room temperature.
The impact of wheat stubble on evaporation from a sandy soil
Authors: Ward P. R. , Whisson K. , Micin S. F. , Zeelenberg D. , Milroy S. P.
Published: August 2009

In Mediterranean-type climates, dryland soil water storage and evaporation during the hot and dry summer are poorly understood, particularly for sandy-textured soils. Continued evaporation during summer, and any effects of crop stubble management, could have a significant impact on annual components of the water balance and crop yield. In this research, the effect of wheat stubble management on summer evaporation and soil water storage was investigated for a sandy soil in south-western Australia, during the summers of 2005–06 and 2006–07. Treatments comprised: retained standing stubble; retained flattened stubble; removed stubble; and removed stubble followed by burying the crowns with topsoil from an adjacent area. Under ‘dry’ conditions, evaporation continued at ~0.2 mm/day. In contrast to previous results for finer textured soil types, stubble retention did not decrease the rate of evaporation, but marginally (10–30%) increased evaporation on 7 out of 14 days when measurements were taken. Significant differences due to stubble management were observed in two successive summers, but only for relatively dry soil conditions. There were no significant differences observed for several days after irrigation or rainfall. Under dry conditions in the absence of rainfall, total decrease in water storage during a 90-day summer period could be ~20 mm, but differences attributable to stubble management are likely to be a few mm.
Potential to improve on-farm wheat yield and WUE in Australia
Authors: Hochman Z. , Holzworth D. , Hunt J. R.
Published: August 2009

Water-use efficiency (WUE) is defined here as the ratio of grain yield (kg/ha) to crop water use by evapotranspiration (mm). Much of the WUE literature has focussed on either the determination of the boundary of attainable WUE for any amount of available water, or on the practicalities of measurement of the WUE of a crop. While these are important issues for defining the gap between the attained and the potential WUE, little progress has been reported on clarifying the components that contribute to this gap or on how it can be bridged. To address these questions, we analysed 334 wheat fields for which we had the data necessary to both calculate WUE and to simulate crop growth and water use. Simulations were conducted through Yield Prophet®, an on-line version of the APSIM systems model. For this dataset, evapotranspiration accounted for 69% of observed yield variation, although the more commonly used growing-season (April–October) rainfall accounted for 50%. Considering that evapotranspiration efficiency does not account for a wide range of potentially yield-limiting factors including soil and fertiliser nitrogen supply, crop phenology, and sowing dates, or rainfall distribution, these results reinforce the importance of evapotranspiration efficiency as a yield determinant for well managed crops in water-limited environments. WUE attained over the whole dataset was 15.2 kg grain/ha.mm (x-intercept = 67 mm), although this value contained data subsets with important differences in WUE based on soil water-holding capacity and regional diversity. Yield Prophet® simulated commercial wheat yields with RMSDs of 0.80 t/ha (r2 = 0.71), with some systematic error between observed and simulated yields. Simulated crops achieved a higher WUE (16.9 kg grain/ha.mm; x-intercept = 72 mm) than the observed crops, probably because APSIM does not account for effects of factors such as weeds, pests and diseases and impacts of severe weather. Simulated ‘what-if’ analysis suggested that further improvement in WUE may be achieved with an early sowing strategy or a higher nitrogen input strategy. A ‘yield maximising’ strategy that included an optimal plant density, early sowing date, and higher nitrogen inputs resulted in an average WUE (21.4 kg grain/ha.mm; x-intercept = 80 mm) that is close to the previously reported (French-Schultz) boundary of WUE. This outcome suggests a great deal of scope for Australian wheat growers to adopt strategies that improve their WUE. Yield Prophet® farmers have already demonstrated significant improvement in on-farm WUE compared with previous studies. However, additional improvements will only be partially realised due to considerations of the cost: benefit ratio and risk in a highly variable climate, and the operational feasibility of these strategies with current technologies.
Ipsilateral cortical fMRI responses after peripheral nerve damage in rats reflect increased interneuron activity
Authors: Pelled Galit , Bergstrom Debra A. , Tierney Patrick L. , Conroy Richard S. , Chuang Kai-Hsiang , Yu David , Leopold David A. , Walters Judith R. , Koretsky Alan P.
Published: August 2009

In the weeks following unilateral peripheral nerve injury, the deprived primary somatosensory cortex (SI) responds to stimulation of the ipsilateral intact limb as demonstrated by functional magnetic resonance imaging (fMRI) responses. The neuronal basis of these responses was studied by using high-resolution fMRI, in vivo electrophysiological recordings, and juxtacellular neuronal labeling in rats that underwent an excision of the forepaw radial, median, and ulnar nerves. These nerves were exposed but not severed in control rats. Significant bilateral increases of fMRI responses in SI were observed in denervated rats. In the healthy SI of the denervated rats, increases in fMRI responses were concordant with increases in local field potential (LFP) amplitude and an increased incidence of single units responding compared with control rats. In contrast, in the deprived SI, increases in fMRI responses were associated with a minimal change in LFP amplitude but with increased incidence of single units responding. Based on action potential duration, juxtacellular labeling, and immunostaining results, neurons responding to intact forepaw stimulation in the deprived cortex were identified as interneurons. These results suggest that the increases in fMRI responses in the deprived cortex reflect increased interneuron activity.
Inferring species interactions in tropical forests
Authors: Volkov Igor , Banavar Jayanth R. , Hubbell Stephen P. , Maritan Amos
Published: August 2009

We present 2 distinct and independent approaches to deduce the effective interaction strengths between species and apply it to the 20 most abundant species in the long-term 50-ha plot on Barro Colorado Island, Panama. The first approach employs the principle of maximum entropy, and the second uses a stochastic birth–death model. Both approaches yield very similar answers and show that the collective effects of the pairwise interspecific interaction strengths are weak compared with the intraspecific interactions. Our approaches can be applied to other ecological communities in steady state to evaluate the extent to which interactions need to be incorporated into theoretical explanations for their structure and dynamics.
Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif
Authors: Seo Young-Kyo , Chong Hansook Kim , Infante Aniello M. , Im Seung-Soon , Xie Xiaohui , Osborne Timothy F.
Published: August 2009

Lipid homeostasis in vertebrates is regulated by 3 sterol regulatory element binding protein (SREBP) isoforms. Here, we identify targets of SREBP-1 in mammalian liver using chromatin immunoprecipitation–high-throughput DNA sequencing. Antisera to SREBP-1 were used with liver chromatin from mice fed a high-carbohydrate diet after a fast, which leads to superinduction of hepatic SREBP-1c expression. SREBP-1–DNA complexes were subjected to massive parallel DNA sequencing using the Illumina Genome Analyzer II, resulting in 5.7 million sequence reads. Mapping these reads to the mouse reference genome identified 426 peaks of SREBP-1 binding vs. a control antibody. These binding peaks show a striking enrichment in proximal promoter regions, with 52% located within 1 kb upstream of a transcription start site. A previously undescribed sequence motif (5′-ACTACANNTCCC-3′) was present in 76% of the total peaks, and we show that it is a functional SREBP-1 response element. Our analysis also reveals that an Sp1 consensus site is present as a “coregulatory” motif in 50% of the SREBP-1 binding peaks, consistent with previous functional studies. SREBP-1 bound not only to many well-characterized SREBP-1 target genes but to several other previously unknown targets in lipid and carbohydrate metabolism as well as many putative target genes in other diverse biological pathways.
Presynaptic NR2A-containing NMDA receptors implement a high-pass filter synaptic plasticity rule
Authors: Bidoret Céline , Ayon Annick , Barbour Boris , Casado Mariano
Published: August 2009

The detailed characterization of synaptic plasticity has led to the replacement of simple Hebbian rules by more complex rules depending on the order of presynaptic and postsynaptic action potentials. Here, we describe a mechanism endowing a plasticity rule with additional computational complexity—a dependence on the pattern of presynaptic action potentials. The classical Hebbian rule is based on detection of conjunctive presynaptic and postsynaptic activity by postsynaptic NMDA receptors, but there is also accumulating evidence for the existence of presynaptic NMDA receptors in several brain structures. Here, we examine the role of presynaptic NMDA receptors in defining the temporal structure of the plasticity rule governing induction of long-term depression (LTD) at the cerebellar parallel fiber-Purkinje cell synapse. We show that multiple presynaptic action potentials at frequencies between 40 Hz and 1 kHz are necessary for LTD induction. We characterize the subtype, kinetics, and role of presynaptic NMDA receptors involved in the induction of LTD, showing how the kinetics of the NR2A subunits expressed by parallel fibers implement a high-pass filter plasticity rule that will selectively attenuate synapses undergoing high-frequency bursts of activity. Depending on the type of NMDA receptor subunit expressed, high-pass filters of different corner frequencies could be implemented at other synapses expressing NMDA autoreceptors.
Cell-type-specific isolation of ribosome-associated mRNA from complex tissues
Authors: Sanz Elisenda , Yang Linghai , Su Thomas , Morris David R. , McKnight G. Stanley , Amieux Paul S.
Published: August 2009

Gene profiling techniques allow the assay of transcripts from organs, tissues, and cells with an unprecedented level of coverage. However, most of these approaches are still limited by the fact that organs and tissues are composed of multiple cell types that are each unique in their patterns of gene expression. To identify the transcriptome from a single cell type in a complex tissue, investigators have relied upon physical methods to separate cell types or in situ hybridization and immunohistochemistry. Here, we describe a strategy to rapidly and efficiently isolate ribosome-associated mRNA transcripts from any cell type in vivo. We have created a mouse line, called RiboTag, which carries an
Rpl22
allele with a floxed wild-type C-terminal exon followed by an identical C-terminal exon that has three copies of the hemagglutinin (HA) epitope inserted before the stop codon. When the RiboTag mouse is crossed to a cell-type-specific Cre recombinase-expressing mouse, Cre recombinase activates the expression of epitope-tagged ribosomal protein RPL22

ha

, which is incorporated into actively translating polyribosomes. Immunoprecipitation of polysomes with a monoclonal antibody against HA yields ribosome-associated mRNA transcripts from specific cell types. We demonstrate the application of this technique in brain using neuron-specific Cre recombinase-expressing mice and in testis using a Sertoli cell Cre recombinase-expressing mouse.
Sources of fluctuation in article choice in English and German by Syrian Arabic and Japanese native speakers
Authors: Jaensch Carol , Sarko Ghisseh
Published: August 2009

Recent work by Tania Ionin and colleagues (Ionin et al. 2004a; Ionin et al. 2008) has suggested that native speakers of article-less languages may fluctuate between selecting articles based on definiteness and selecting them based on specificity. This was termed the Fluctuation Hypothesis (Ionin et al. 2004a). The Fluctuation Hypothesis assumes learners to have full access to Universal Grammar (UG) properties, including those which are not instantiated in their L1 grammars. This contrasts with the Failed Functional Features Hypothesis (Hawkins and Chan 1997), now termed the Representational Deficit Hypothesis (Hawkins and Franceschina 2004; Hawkins et al. 2006). This proposes that learners will fail to acquire uninterpretable features, if these are not present in their L1. The current study tests the Fluctuation Hypothesis with two new groups of speakers acquiring languages with definite and indefinite articles which are marked for definiteness, whilst still allowing a semantic distinction between [+specific] and [–specific]. The languages acquired are German, by native speakers of Japanese, a language without articles; and English, by native speakers of Syrian Arabic, a language with an overt marker for definiteness, but not for indefiniteness. Although the initial results seem to indicate that fluctuation may be responsible for optionality amongst these learners, further analysis shows that this variation may be due to other factors.
Autocatalytic Processing of m-AAA Protease Subunits in Mitochondria
Authors: Koppen Mirko , Bonn Florian , Ehses Sarah , Langer Thomas
Published: August 2009

m-AAA proteases are ATP-dependent proteolytic machines in the inner membrane of mitochondria which are crucial for the maintenance of mitochondrial activities. Conserved nuclear-encoded subunits, termed paraplegin, Afg3l1, and Afg3l2, form various isoenzymes differing in their subunit composition in mammalian mitochondria. Mutations in different m-AAA protease subunits are associated with distinct neuronal disorders in human. However, the biogenesis of m-AAA protease complexes or of individual subunits is only poorly understood. Here, we have examined the processing of nuclear-encoded m-AAA protease subunits upon import into mitochondria and demonstrate autocatalytic processing of Afg3l1 and Afg3l2. The mitochondrial processing peptidase MPP generates an intermediate form of Afg3l2 that is matured autocatalytically. Afg3l1 or Afg3l2 are also required for maturation of newly imported paraplegin subunits after their cleavage by MPP. Our results establish that mammalian m-AAA proteases can act as processing enzymes in vivo and reveal overlapping activities of Afg3l1 and Afg3l2. These findings might be of relevance for the pathogenesis of neurodegenerative disorders associated with mutations in different m-AAA protease subunits.
PubMed-EX: a web browser extension to enhance PubMed search with text mining features
Authors: Tsai Richard Tzong-Han , Dai Hong-Jie , Lai Po-Ting , Huang Chi-Hsin
Published: August 2009

Summary: PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources.

Availability: PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

Contact:  thtsai@saturn.yzu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrating spatial and temporal mortality from herring on capelin larvae: a study in the Barents Sea
Authors: Pedersen O. P. , Pedersen T. , Tande K. S. , Slagstad D.
Published: August 2009

Pedersen, O. P., Pedersen, T., Tande, K. S., and Slagstad, D. 2009. Integrating spatial and temporal mortality from herring on capelin larvae: a study in the Barents Sea. – ICES Journal of Marine Science, 66: 2183–2194. Barents Sea herring and capelin are commercially very important fish stocks. We investigate the spatial and temporal mortality rate of capelin larvae in 2001 as a function of herring predation. Our methods are based on Lagrangian modelling, field surveys, and experimental data. The impact of juvenile herring predation on capelin recruitment is corroborated, in particular the importance of the integrated spatio-temporal overlap between the two stocks. Capelin larvae were reduced to 20–50% in two weeks in accordance with different simulation scenarios. Hamre advanced a hypothesis in 1994 that juvenile herring are important predators of capelin larvae and a main cause of poor capelin recruitment in years when herring are very abundant in the Barents Sea. This hypothesis is supported through the results of this work.
Structural and Functional Diversity of CLAVATA3/ESR (CLE)-Like Genes from the Potato Cyst Nematode Globodera rostochiensis
Authors: Lu Shun-Wen , Chen Shiyan , Wang Jianying , Yu Hang , Chronis Demosthenis , Mitchum Melissa G. , Wang Xiaohong
Published: August 2009

Plant CLAVATA3/ESR-related (CLE) peptides have diverse roles in plant growth and development. Here, we report the isolation and functional characterization of five new CLE genes from the potato cyst nematode Globodera rostochiensis. Unlike typical plant CLE peptides that contain a single CLE motif, four of the five Gr-CLE genes encode CLE proteins with multiple CLE motifs. These Gr-CLE genes were found to be specifically expressed within the dorsal esophageal gland cell of nematode parasitic stages, suggesting a role for their encoded proteins in plant parasitism. Overexpression phenotypes of Gr-CLE genes in Arabidopsis mimicked those of plant CLE genes, and Gr-CLE proteins could rescue the Arabidopsis clv3-2 mutant phenotype when expressed within meristems. A short root phenotype was observed when synthetic GrCLE peptides were exogenously applied to roots of Arabidopsis or potato similar to the overexpression of Gr-CLE genes in Arabidopsis and potato hairy roots. These results reveal that G. rostochiensis CLE proteins with either single or multiple CLE motifs function similarly to plant CLE proteins and that CLE signaling components are conserved in both Arabidopsis and potato roots. Furthermore, our results provide evidence to suggest that the evolution of multiple CLE motifs may be an important mechanism for generating functional diversity in nematode CLE proteins to facilitate parasitism.
Expression Analysis of the First Arbuscular Mycorrhizal Fungi Aquaporin Described Reveals Concerted Gene Expression Between Salt-Stressed and Nonstressed Mycelium
Authors: Aroca Ricardo , Bago Alberto , Sutka Moira , Paz José Antonio , Cano Custodia , Amodeo Gabriela , Ruiz-Lozano Juan Manuel
Published: August 2009

Roots of most plants in nature are colonized by arbuscular mycorrhizal (AM) fungi. Among the beneficial effects of this symbiosis to the host plant is the transport of water by the AM mycelium from inaccessible soil water resources to host roots. Here, an aquaporin (water channel) gene from an AM fungus (Glomus intraradices), which was named GintAQP1, is reported for the first time. From experiments in different colonized host roots growing under several environmental conditions, it seems that GintAQP1 gene expression is regulated in a compensatory way regarding host root aquaporin expression. At the same time, from in vitro experiments, it was shown that a signaling communication between NaCl-treated mycelium and untreated mycelium took place in order to regulate gene expression of both GintAQP1 and host root aquaporins. This communication could be involved in the transport of water from osmotically favorable growing mycelium or host roots to salt-stressed tissues.
Constitutive modelling of passive myocardium: a structurally based framework for material characterization
Authors: Holzapfel Gerhard A. , Ogden Ray W.
Published: August 2009

In this paper, we first of all review the morphology and structure of the myocardium and discuss the main features of the mechanical response of passive myocardium tissue, which is an orthotropic material. Locally within the architecture of the myocardium three mutually orthogonal directions can be identified, forming planes with distinct material responses. We treat the left ventricular myocardium as a non-homogeneous, thick-walled, nonlinearly elastic and incompressible material and develop a general theoretical framework based on invariants associated with the three directions. Within this framework we review existing constitutive models and then develop a structurally based model that accounts for the muscle fibre direction and the myocyte sheet structure. The model is applied to simple shear and biaxial deformations and a specific form fitted to the existing (and somewhat limited) experimental data, emphasizing the orthotropy and the limitations of biaxial tests. The need for additional data is highlighted. A brief discussion of issues of convexity of the model and related matters concludes the paper.
Simulation of the contractile response of cells on an array of micro-posts
Authors: McGarry J. P. , Fu J. , Yang M. T. , Chen C. S. , McMeeking R. M. , Evans A. G. , Deshpande V. S.
Published: August 2009

A bio-chemo-mechanical model has been used to predict the contractile responses of smooth cells on a bed of micro-posts. Predictions obtained for smooth muscle cells reveal that, by converging onto a single set of parameters, the model captures all of the following responses in a self-consistent manner: (i) the scaling of the force exerted by the cells with the number of posts; (ii) actin distributions within the cells, including the rings of actin around the micro-posts; (iii) the curvature of the cell boundaries between the posts; and (iv) the higher post forces towards the cell periphery. Similar correspondences between predictions and measurements have been demonstrated for fibroblasts and mesenchymal stem cells once the maximum stress exerted by the stress fibre bundles has been recalibrated. Consistent with measurements, the model predicts that the forces exerted by the cells will increase with both increasing post stiffness and cell area (or equivalently, post spacing). In conjunction with previous assessments, these findings suggest that this framework represents an important step towards a complete model for the coupled bio-chemo-mechanical responses of cells.
Evaluation of fundamental hypotheses underlying constrained mixture models of arterial growth and remodelling
Authors: Valentín A. , Humphrey J. D.
Published: August 2009

Evolving constituent composition and organization are important determinants of the biomechanical behaviour of soft tissues. In arteries, vascular smooth muscle cells and fibroblasts continually produce and degrade matrix constituents in preferred modes and at altered rates in response to changing mechanical stimuli. Smooth muscle cells similarly exhibit vasoactive changes that contribute to the control of overall structure, function and mechanical behaviour. Constrained mixture models provide a useful framework in which to quantify arterial growth and remodelling for they can account for cell-mediated changes in individual structurally significant constituents. Our simulations show that the combined effects of changing mass density turnover and vasoactivity, as well as the prestretch at which constituents are incorporated within extant matrix, are essential to capture salient features of bounded arterial growth and remodelling. These findings emphasize the importance of formulating biologically motivated constitutive relations in any theory of growth and remodelling and distinct advantages of the constrained mixture approach, in particular.
Differential growth and residual stress in cylindrical elastic structures
Authors: Vandiver Rebecca , Goriely Alain
Published: August 2009

Cylindrical forms are among one of Nature’s fundamental building blocks. They serve many different purposes, from sustaining body weight to carrying flows. Their mechanical properties are generated through the often complex arrangements of the walls. In particular, in many structures that have elastic responses, such as stems and arteries, the walls are in a state of tension generated by differential growth. Here, the effect of differential growth and residual stress on the overall mechanical response of the cylindrical structure is studied within the framework of morpho-elasticity.
Ca2+ Regulates Reactive Oxygen Species Production and pH during Mechanosensing inArabidopsisRoots
Authors: Monshausen Gabriele B. , Bibikova Tatiana N. , Weisenseel Manfred H. , Gilroy Simon
Published: August 2009

Mechanical stimulation of plants triggers a cytoplasmic Ca2+ increase that is thought to link the touch stimulus to appropriate growth responses. We found that in roots of Arabidopsis thaliana, external and endogenously generated mechanical forces consistently trigger rapid and transient increases in cytosolic Ca2+ and that the signatures of these Ca2+ transients are stimulus specific. Mechanical stimulation likewise elicited an apoplastic alkalinization and cytoplasmic acidification as well as apoplastic reactive oxygen species (ROS) production. These responses showed the same kinetics as mechanically induced Ca2+ transients and could be elicited in the absence of a mechanical stimulus by artificially increasing Ca2+ concentrations. Both pH changes and ROS production were inhibited by pretreatment with a Ca2+ channel blocker, which also inhibited mechanically induced elevations in cytosolic Ca2+. In trichoblasts of the Arabidopsis root hair defective2 mutant, which lacks a functional NADPH oxidase RBOH C, touch stimulation still triggered pH changes but not the local increase in ROS production seen in wild-type plants. Thus, mechanical stimulation likely elicits Ca2+-dependent activation of RBOH C, resulting in ROS production to the cell wall. This ROS production appears to be coordinated with intra- and extracellular pH changes through the same mechanically induced cytosolic Ca2+ transient.