bluuebunny/crossref_metadata_2025 huggingface dataset:
Femtosecond-laser-driven photoelectron-gun for time-resolved cathodoluminescence measurement of GaN
Authors: Onuma T. , Kagamitani Y. , Hazu K. , Ishiguro T. , Fukuda T. , Chichibu S. F.
Published: April 2012

A rear-excitation femtosecond-laser-driven photoelectron gun (PE-gun) is developed for measuring time-resolved cathodoluminescence (TRCL) spectrum of wide bandgap materials and structures such as semiconductors and phosphors. The maximum quantum efficiency of a 20-nm-thick Au photocathode excited using a frequency-tripled Al2O3:Ti laser under a rear-excitation configuration is 3.6×10−6, which is a reasonable value for a PE-gun. When the distance between the front edge of the PE-gun and the observation point is 10 mm, the narrowest electron-beam (e-beam) diameter is 19 μm, which corresponds to one tenth of the laser-beam diameter and is comparable to the initial e-beam diameter of a typical W hair-pin filament of thermionic electron-gun. From the results of TRCL measurements on the freestanding GaN grown by the ammonothermal method and a GaN homoepitaxial film grown by metalorganic vapor phase epitaxy, overall response time for the present TRCL system is estimated to be 8 ps. The value is the same as that of time-resolved photoluminescence measurement using the same excitation laser pulses, meaning that the time-resolution is simply limited by the streak-camera, not by the PE-gun performance. The result of numerical simulation on the temporal e-beam broadening caused by the space-charge-effect suggests that the present PE-gun can be used as a pulsed e-beam source for spatio-time-resolved cathodoluminescence, when equipped in a scanning electron microscope.
Spin state transition and giant dielectric constant in Pr0.987Na0.013CoO3
Authors: Wang Heng , Li Guangshe , Zhao Minglei , Li Liping
Published: April 2012

Pr0.987Na0.013CoO3 exhibits an anomaly in magnetic susceptibility and transport behavior around 200 K, which is associated with a thermally excited spin transition of Co3+. We show that introduction of Na+ in PrCoO3 induced a variable range hopping (VRH) conduction. At the transition temperature, the density of state near Fermi level increased, while the hopping distance and hopping energy decreased. Extrinsic electrode polarization was also observed at low frequency, leading to a giant dielectric constant. Both conductivity and dielectric relaxation frequency in bulk follow a simple temperature dependence, T−1/4, indicating a close relationship between VRH conduction and dielectric relaxation.
Sensitivity test of a blue-detuned dipole trap designed for parity non-conservation measurements in Fr
Authors: Sheng D. , Zhang J. , Orozco L. A.
Published: April 2012

A dynamic blue-detuned optical dipole trap with stable 87Rb atoms produces a differential ac Stark shift of 18 Hz in the ground state hyperfine transition, and it preserves the ground state hyperfine superpositions for a long coherence time of 180 ms. The trapped atoms undergoing microwave Rabi oscillations are sensitive to a small signal, artificially generated with a second microwave source, phase locked to the first allowing a simple and effective method for determining signal-to-noise ratio limits through interference techniques. This provides an excellent means of calibrating sensitivity in experiments such as our ongoing Fr parity non-conservation measurement.
Influence of collision energy and reagent rotation on the cross sections and product polarizations of the reaction F+ HCl
Authors: Duan Zhi Xin , Li Wen Liang , Qiu Ming Hui
Published: April 2012

Quasiclassical trajectory calculations have been carried out for the F+HCl reaction in three dimensions on a recent DHSN PES of the ground 12A′ electronic state [M. P. Deskevich, M. Y. Hayes, K. Takahashi, R. T. Skodje, and D. J. Nesbitt, J. Chem. Phys. 124, 224303 (2006)]. The effects of the collision energy and the reagent initial rotational excitation on the cross sections and product polarization are studied for the v = 0 and j ⩽ 10 states of HCl over a wide collision energy range. It has been found that either the collision energy or the HCl rotational excitation increase remarkably reaction cross sections. The QCT-calculated integral cross sections are in good agreement with previous QM results. A detailed study on product polarization for the title reaction is also performed. The calculated results show that the product rotational angular momentum j′ is not only aligned, but also oriented along the direction perpendicular to the scattering plane. The orientation of the HF product rotational angular momentum vector j′ depends very sensitively on the collision energy and also affected by the reagent rotation. The theoretical findings and especially the roles of the collision energy and initial rotational momentum on the product polarization are discussed and reasonably explained by the HLH mass combination, the property of the PES, as well as the reactive mechanism.
Multidimensional lower bounds for the eigenvalues of Stokes and Dirichlet Laplacian operators
Authors: Yolcu Selma Yıldırım , Yolcu Türkay
Published: April 2012

This article is concerned with the improvements of certain eigenvalue inequalities of Stokes operator and Dirichlet Laplacian related to the Berezin-Li-Yau type inequalities. The formulas proved extend the earlier works of Melas [“A lower bound for sums of eigenvalues of the Laplacian,” Proc. Am. Math. Soc. 131(2), 631–636 (2002)]10.1090/S0002-9939-02-06834-X on Dirichlet Laplacian and of Ilyin [“Lower bounds for the spectrum of the Laplace and Stokes operators,” Discrete. Contin. Dyn. Syst. 28(1), 131–146 (2010)]10.3934/dcds.2010.28.131 on Stokes operator for any dimension d ⩾ 2 and they are asymptotically sharp as are the earlier inequalities of Berezin-Li-Yau, Melas, and Ilyin.
Stochastic stability of genetic regulatory networks with a finite set delay characterization
Authors: Zhang Wenbing , Tang Yang , Fang Jian-an , Wu Xiaotai
Published: April 2012

In this paper, the delay-distribution-dependent stability is derived for the stochastic genetic regulatory networks (GRNs) with a finite set delay characterization and interval parameter uncertainties. One important feature of the obtained results here is that the time-varying delays are assumed to be random and the sum of the occurrence probabilities of the delays is assumed to be 1. By employing a new Lyapunov-Krasovskii functional dependent on auxiliary delay parameters which allow the time-varying delays to be not differentiable, less conservative mean-square stochastic stability criteria are obtained. Finally, two examples are given to illustrate the effectiveness and superiority of the derived results.
Dust-driven and plasma-driven currents in the inner magnetosphere of Saturn
Authors: Olson J. , Brenning N.
Published: April 2012

General equations for dust-driven currents and current systems JD in magnetized plasmas are derived and, as a concrete example, applied to the E ring of Saturn at radial distances 3RS<R<5RS. An azimuthal ring current JD,ϕ acts as a current generator and is coupled to two secondary dust-driven current systems down to the ionosphere of Saturn, both rotating with the magnetospheric plasma. One of these closes across the polar cap, and the other over a limited range in latitude. These dust-driven current systems are embedded in three systems of plasma-driven currents Jp: a ring current, a cross-polar-cap current system, and an ion pickup current system. Both the JD and the Jp current systems have been quantitatively assessed from a data set for the E ring of Saturn in which the unknown distribution of small dust is treated by a power law extrapolation from the known distribution of larger dust. From data on the magnetic perturbations during a crossing of the equatorial plane, an approximate constraint on the fraction of the electrons that can be trapped on the dust is derived. For this amount of electron capture, it is demonstrated that all three types of dust-driven currents are, within somewhat more than an order of magnitude, of the same strength as the corresponding types of plasma-driven currents. Considering also that both plasma and dust densities vary with the geyser activity at the south pole of Enceladus, it is concluded that both the dust-driven and the plasma-driven contributions to the current system associated with the E ring need to be retained for a complete description.
Quantum mechanics on Laakso spaces
Authors: Kauffman Christopher J. , Kesler Robert M. , Parshall Amanda G. , Stamey Evelyn A. , Steinhurst Benjamin A.
Published: April 2012

We first review the spectrum of the Laplacian operator on a general Laakso space before considering modified Hamiltonians for the infinite square well, parabola, and Coulomb potentials. Additionally, we compute the spectrum for the Laplacian and its multiplicities when certain regions of a Laakso space are compressed or stretched and calculate the Casimir force experienced by two uncharged conducting plates by imposing physically relevant boundary conditions and then analytically regularizing the resulting zeta function. Lastly, we derive a general formula for the spectral zeta function and its derivative for Laakso spaces with strict self-similar structure before listing explicit spectral values for some special cases
A phonon scattering assisted injection and extraction based terahertz quantum cascade laser
Authors: Dupont E. , Fathololoumi S. , Wasilewski Z. R. , Aers G. , Laframboise S. R. , Lindskog M. , Razavipour S. G. , Wacker A. , Ban D. , Liu H. C.
Published: April 2012

A lasing scheme for terahertz quantum cascade lasers, based on consecutive phonon-photon-phonon emissions per module, is proposed and experimentally demonstrated. The charge transport of the proposed structure is modeled using a rate equation formalism. An optimization code based on a genetic algorithm was developed to find a four-well design in the GaAs/Al0.25Ga0.75As material system that maximizes the product of population inversion and oscillator strength at 150 K. The fabricated devices using Au double-metal waveguides show lasing at 3.2 THz up to 138 K. The electrical characteristics display no sign of differential resistance drop at lasing threshold, which, in conjunction with the low optical power of the device, suggest—thanks to the rate equation model—a slow depopulation rate of the lower lasing state, a hypothesis confirmed by non-equilibrium Green’s function calculations.
First principles study of the oxygen vacancy formation and the induced defect states in hafnium silicates
Authors: Chen Tsung-Ju , Kuo Chin-Lung
Published: April 2012

Using first-principles density functional theory calculations, we have investigated the O vacancy formation and the relevant induced defect states in hafnium silicates over a wide range of compositions. The PBE0 hybrid density functional was employed for the analysis of the electronic properties and the charge transition levels of the O vacancy in crystalline HfSiO4 and in amorphous Hf-silicates, respectively. Based on the generated structure models, eight typical kinds of O coordination structures were identified in amorphous Hf-silicates. Our calculated results show that the positions of the induced defect energy levels in the band gap and the formation energies of O vacancy are largely determined by the local structures of the vacancy sites, which appear to be nearly independent of the composition of amorphous Hf-silicates. Our calculations also show that O vacancy can possess the negative-U behavior in crystalline HfSiO4 but not in amorphous Hf-silicates, where most of the O vacancies can simply exhibit the negative-U behavior as in the positive charge states. Given the measured band offset of 3.40 eV between Si and amorphous Hf-silicates, a considerable number of O vacancies were found to prefer to stay in the charge neutral state as the Fermi level lies within the band gap region of Si. Furthermore, due to its relatively higher formation energy, the concentration of O vacancy in Hf-silicates can be much lower than that in m-HfO2 when the Fermi level lies below the midgap region of Si. Accordingly, a significantly reduced flat band voltage shift and less transient threshold voltage instability can be found in Hf-silicates as compared with m-HfO2, which are in good agreement with the recent experimental findings.
Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording
Authors: Borzenets I. V. , Yoon I. , Prior M. W. , Donald B. R. , Mooney R. D. , Finkelstein G.
Published: April 2012

This paper discusses several methods for manufacturing ultra-sharp probes, with applications geared toward, but not limited to, scanning microscopy (STM, AFM) and intra-cellular recordings of neural signals. We present recipes for making tungsten, platinum/iridium alloy, and nanotube fibril tips. Electrical isolation methods using Parylene-C or PMMA are described.
Free-suspended graphene synthesis via carbon diffusion through platinum-based metal
Authors: Zenasni Aziz , Delamoreanu Alexandru , Rabot Caroline
Published: April 2012

Some advances in chemical vapor deposition process have provided noteworthy results toward the growth of large scale graphene. However, in contact with a neighboring material, graphene performances are usually reduced. Decoupling graphene from the substrate by suspension or intercalation is foreseen to recover its intrinsic properties. This work reports an original way for graphene suspension which occurs during its growth on platinum metal. This suspension arises above platinum silicide clusters which form during the annealing and induce the metal dewetting. The stretched graphene is highly corrugated because the clusterization of silicides structures induces additional stress.
Atmospheric pressure dielectric barrier microplasmas inside hollow-core optical fibers
Authors: Ji Longfei , Liu Dongping , Song Ying , Niu Jinhai
Published: April 2012

An atmospheric glow microplasma is generated in the hollow core of microns-thick optical fibers (>1 m long) when the sinusoidal voltage with a peak voltage of 5 kV and a frequency of 5.0 kHz is applied to these microelectrodes along the outside of optical fibers. Measurements show that the atmospheric glow microdischarge consists of current pulses with amplitudes of tens of amperes and pulse widths of several microseconds. Atmospheric surface barrier discharges are formed along the inner surface of hollow optical fibers between adjacent microelectrodes, which results in the pulsed glow microdischarges. By flowing octafluorocyclobutane (c-C4F8)/helium (He) mixtures through the hollow-core optical fiber, fluorocarbon polymer (FCP) coatings are deposited on the inner surface of the > 1 m long optical fiber. Analysis indicates that the glow microdischarge contributes to the uniform deposition of FCP coatings on the inner surface of hollow fibers. The in situ optical emission measurements show that various carbon-containing species, such as CF2, CN, and C2 are generated in the visually uniform microplasmas. The discharge mechanism is discussed based on the I-V and optical emission measurements and FCP coating characterizations.
Improved electron mobility in InSb epilayers and quantum wells on off-axis Ge (001) substrates
Authors: Debnath M. C. , Mishima T. D. , Santos M. B. , Hossain K. , Holland O. W.
Published: April 2012

Two types of InSb structures, epilayers and quantum wells (QWs), have been grown on on-axis and 6°-off-axis Ge (001) substrates and examined by reflection high-energy electron diffraction, transmission electron microscopy, X-ray diffraction, atomic force microscopy, and the van der Pauw and Hall effect techniques. Anti-phase domain defects, which prevail in these InSb structures when grown on on-axis Ge (001) substrates, are significantly decreased by the use of 6° off-axis Ge (001) substrates. Such off-axis substrates also lead to reductions in the densities of micro-twins and threading dislocations. Room-temperature electron mobilities in 4.0-μm-thick InSb epilayers and 25-nm-thick InSb QWs grown on 6°-off-axis Ge (001) substrates are 59 000 and 14 000 cm2/(V s), respectively, which are ∼1.5 times higher than their counterparts grown on on-axis Ge (001) substrates. These improved mobilities are the highest among the reported values for each type of structure grown on Ge (001) substrates.
Epitaxial ferromagnetic nanoislands of cubic GdN in hexagonal GaN
Authors: Kent T. F. , Yang J. , Yang L. , Mills M. J. , Myers R. C.
Published: April 2012

Periodic structures of GdN particles encapsulated in a single crystalline GaN matrix were prepared by plasma assisted molecular beam epitaxy. High resolution x-ray diffractometery shows that GdN islands, with rock salt structure are epitaxially oriented to the wurtzite GaN matrix. Scanning transmission electron microscopy combined with in situ reflection high energy electron diffraction allows for the study of island formation dynamics, which occurs after 1.2 monolayers of GdN coverage. Magnetometry reveals two ferromagnetic phases, one due to GdN particles with Curie temperature of 70 K and a second, anomalous above room temperature phase.
Isotropic to smectic-C phase transition in liquid-crystalline elastomers
Authors: Mukherjee Prabir K.
Published: April 2012

A phenomenological model is developed to describe the isotropic-smectic-C phase transition in liquid-crystalline side-chain elastomers. We analyze the influence of external mechanical stress on the isotropic-smectic-C phase transition. While this phase transition is first order in low-molecular-weight materials, we show here that the order of this transition does not change in liquid-crystalline elastomers. The temperature dependence of the heat capacity and the nonlinear dielectric effect in the isotropic phase above the isotropic-smectic-C phase transition in liquid crystalline elastomers are calculated. The theoretical results are found to be in good agreement with experiment.
Nonlinear excitation of a rotational mode in a piezoelectrically excited square-extensional mode resonator
Authors: Lipiäinen Lauri , Jaakkola Antti , Kokkonen Kimmo , Kaivola Matti
Published: April 2012

We present an experimental study of the nonlinear behavior of a square-extensional (SE) mode microelectromechanical resonator, actuated with a piezoelectric AlN thin film. The acoustic vibration fields of the device are characterized using laser probing. A nonlinear vibration behavior of the SE mode is observed above a drive power level of −10 dBm such that the vibration amplitude of the SE mode saturates and a rotational in-plane vibration mode is excited at a significantly lower frequency (0.725 MHz) than the SE mode (16.670 MHz). Interestingly, the measured ∼10 nm saturation amplitude of the SE mode is more than a decade below the amplitude value at which mechanical or electromechanical nonlinearities are estimated to become significant.
Timing performance of 30-nm-wide superconducting nanowire avalanche photodetectors
Authors: Najafi F. , Marsili F. , Dauler E. , Molnar R. J. , Berggren K. K.
Published: April 2012

We investigated the timing jitter of superconducting nanowire avalanche photodetectors (SNAPs, also referred to as cascade-switching superconducting single-photon detectors) based on 30-nm-wide nanowires. At bias currents (IB) near the switching current, SNAPs showed sub-35-ps FWHM Gaussian jitter similar to standard 100-nm-wide superconducting nanowire single-photon detectors. At lower values of IB, the instrument response function (IRF) of the detectors became wider, more asymmetric, and shifted to longer time delays. We could reproduce the experimentally observed IRF time-shift in simulations based on an electrothermal model and explain the effect with a simple physical picture.
Optical trapping force reduction and manipulation of nanoporous beads
Authors: Wang Tao , Jiang Fan , Oehrlein Stefan , Zeng Erliang , Kershner Ryan , Cerrina Franco
Published: April 2012

We studied the interaction of infrared optical traps with controlled-pore glass (CPG) beads in aqueous medium. The lateral optical trapping force and stiffness were experimentally found considerably smaller than those of their solid counterparts. The simulation using an average refractive index revealed significant losses of effective trapping efficiency, which quantitatively agreed well with experimentally fitted curves. This effect was ascribed to the reduced relative refractive index of medium-filled CPG beads with respect to the medium. Combining optical trapping with mechanical confinements, we demonstrated a microfluidic platform allowing for the synthesis of multiple DNA oligonucleotide sequences on individual beads of interest.
Prediction of the nutritional composition of the crop contents of free-living scarlet macaw chicks by near-infrared reflectance spectroscopy
Authors: Cornejo Juan , Taylor Ryan , Sliffe Thomas , Bailey Christopher A. , Brightsmith Donald J.
Published: April 2012

Context
It is difficult to determine with accuracy the nutrition of bird diets through observation and analysis of dietary items. Collection of the ingested material from the birds provides an alternative but it is often limited by the small sizes of samples that can be obtained.

Aims
We tested the efficacy of near-infrared reflectance spectroscopy (NIRS) to assess the nutritional composition of very small samples of growing-parrot crop content.

Methods
We used 30 samples of the crop content of free-living scarlet macaw (Ara macao) chicks. Samples were scanned with a near-infrared reflectance analyser, and later analysed by traditional wet laboratory methods for crude protein/N, fat, ash, neutral detergent fibre, P, K, Ca, Mg, Cu, Zn and S. A calibration model was developed using principal components analysis.

Key results
Coefficients of determination in the calibration (R2) and standard errors of cross-validation (SECV) for most of the nutrients showed a good performance (mean R2 of 0.91 ± 0.11 s.d., n = 10) when excluding Zn (R2 of 0.15, SECV = 25.37).

Conclusions
The present results established NIRS as a valid technique for the non-destructive, low-cost prediction of a variety of nutritional attributes of avian crop contents as small as 0.5-g dry weight.

Implications
The use of NIRS expands the possibilities of wild-animal nutrition research.
The Europeanization process and Kurdish nationalism in Turkey: the case of the Democratic Society Party
Authors: Saylan İbrahim
Published: April 2012

This study aims at analyzing the impact of the European integration process on Kurdish nationalism in Turkey by focusing on the Democratic Society Party (Demokratik Toplum Partisi, DTP) as the major pro-Kurdish political party in Turkey between 2005 and 2009. It argues that the Europeanization process in Turkey, which accelerated in the post-Helsinki period, has brought about some important consequences concerning the recognition and expression of Kurdish identity. The study examines Europe's impact on the DTP through analysis of party documents and interviews with party representatives, in order to investigate the meaning and use of the European integration process in the DTP's sub-state nationalist ideology. This analysis shows that, although the Europeanization process in Turkey has somewhat broadened opportunity structures for Kurdish sub-state nationalist politics, overall the EU's impact on the DTP's nationalist politics has remained indirect and limited.
Scheduling observational and physical practice: Influence on the coding of simple motor sequences
Authors: Ellenbuerger Thomas , Boutin Arnaud , Blandin Yannick , Shea Charles H. , Panzer Stefan
Published: April 2012

The main purpose of the present experiment was to determine the coordinate system used in the development of movement codes when observational and physical practice are scheduled across practice sessions. The task was to reproduce a 1,300-ms spatial–temporal pattern of elbow flexions and extensions. An intermanual transfer paradigm with a retention test and two effector (contralateral limb) transfer tests was used. The mirror effector transfer test required the same pattern of homologous muscle activation and sequence of limb joint angles as that performed or observed during practice, and the nonmirror effector transfer test required the same spatial pattern movements as that performed or observed. The test results following the first acquisition session replicated the findings of Gruetzmacher, Panzer, Blandin, and Shea (2011). The results following the second acquisition session indicated a strong advantage for participants who received physical practice in both practice sessions or received observational practice followed by physical practice. This advantage was found on both the retention and the mirror transfer tests compared to the nonmirror transfer test. These results demonstrate that codes based in motor coordinates can be developed relatively quickly and effectively for a simple spatial–temporal movement sequence when participants are provided with physical practice or observation followed by physical practice, but physical practice followed by observational practice or observational practice alone limits the development of codes based in motor coordinates.
Bound context features are integrated at encoding
Authors: Boywitt C.Dennis , Meiser Thorsten
Published: April 2012

In the present research, we tested the predictions of different accounts of context binding in “remember” judgements. Context binding, defined as the stochastically dependent retrieval of two different context features, has previously been suggested to be due to mechanisms operating at retrieval either by cueing among context features (Meiser & Bröder, 2002) or by cueing between item and context features (Starns & Hicks, 2008). These accounts, however, do not make specific assumptions regarding the underlying memory representation supporting context binding. By contrast, here we propose that a binding process at encoding integrates item and context information into a coherent memory representation. Varying the presentation of the context features during encoding either with both context features presented simultaneously or with features spread over two encoding episodes, data from two experiments corroborate the notion that binding is produced at encoding. This result suggests that a binding process integrating the context features at encoding is necessary for stochastically dependent retrieval of context features.
Preparation and ferroelectric properties of freestanding Pb(Zr,Ti)O3 thin membranes
Authors: Zuo Zhenghu , Chen Bin , Zhan Qing-feng , Liu Yiwei , Yang Huali , Li Zhixiang , Xu Gaojie , Li Run-Wei
Published: April 2012

Freestanding Pb(Zr,Ti)O3 (PZT) thin membranes were fabricated by pulsed laser deposition on 200 nm-thick Pt foils which were obtained by etching the platinized Si substrates with HF solutions. X-ray diffraction patterns and Raman spectra show that the crystal lattice distortion of the PZT membranes is relaxed after removing the rigid substrates. Compared with the substrate-clamped PZT films, the saturation polarization and the remanent polarization of the freestanding PZT membranes are increased by about 18% and 21%, respectively. In addition, the freestanding PZT thin membranes possess higher dielectric tunability and larger domain size. The novel facile fabrication method is important for developing flexible ferroelectric devices and also for studying the strain effects on the physical properties of flexible functional membranes.
Brauer-Siegel for arithmetic tori and lower bounds for Galois orbits of special points
Authors: Tsimerman Jacob
Published: April 2012

Shyr derived an analogue of Dirichlet’s class number formula for arithmetic tori. We use this formula to derive a Brauer-Siegel formula for tori, relating the discriminant of a torus to the product of its regulator and class number. We apply this formula to derive asymptotics and lower bounds for Galois orbits of CM points in the Siegel modular variety

A

g
,
1

A_{g,1}

. Specifically, we ask that the sizes of these orbits grow like a power of the discriminant of the underlying endomorphism algebra. We prove this unconditionally in the case

g
≤
6

g\leq 6

, and for all

g
g

under the Generalized Riemann Hypothesis for CM fields. Along the way we derive a general transfer principle for torsion in ideal class groups of number fields.
APC and Smad7 link TGFβ type I receptors to the microtubule system to promote cell migration
Authors: Ekman Maria , Mu Yabing , Lee So Young , Edlund Sofia , Kozakai Takaharu , Thakur Noopur , Tran Hoanh , Qian Jiang , Groeden Joanna , Heldin Carl-Henrik , Landström Maréne
Published: April 2012

Cell migration occurs by activation of complex regulatory pathways that are spatially and temporally integrated in response to extracellular cues. Binding of adenomatous polyposis coli (APC) to the microtubule plus ends in polarized cells is regulated by glycogen synthase kinase 3β (GSK-3β). This event is crucial for establishment of cell polarity during directional migration. However, the role of APC for cellular extension in response to extracellular signals is less clear. Smad7 is a direct target gene for transforming growth factor-β (TGFβ) and is known to inhibit various TGFβ-induced responses. Here we report a new function for Smad7. We show that Smad7 and p38 mitogen–activated protein kinase together regulate the expression of APC and cell migration in prostate cancer cells in response to TGFβ stimulation. In addition, Smad7 forms a complex with APC and acts as an adaptor protein for p38 and GSK-3β kinases to facilitate local TGFβ/p38–dependent inactivation of GSK-3β, accumulation of β-catenin, and recruitment of APC to the microtubule plus end in the leading edge of migrating prostate cancer cells. Moreover, the Smad7–APC complex links the TGFβ type I receptor to the microtubule system to regulate directed cellular extension and migratory responses evoked by TGFβ.
Measuring Inefficiency in Long‐term Care Commissioning: Evidence from English Local Authorities
Authors: D'Amico Francesco , Fernandez Jose‐Luis
Published: April 2012

Using a stochastic frontier approach, this paper explores efficiency in the commissioning of publicly funded social services among 148 English Councils through a six‐year panel database (2002‐2007), covering institutional and community care. Our estimates provide key policy evidence in a context in which optimization is critical both for social and financial purposes. Results suggest a slight decrease in the average inefficiency score, moving from 1.080 in the first year to 1.076 in the last year. Cost‐output elasticity of institutional care is greater than those of community care services. Greater savings are obtained when the market is open to independent providers.
GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis
Authors: Pejaver Vikas R. , An Jaehyun , Rhee SungMin , Bhan Ankita , Choi Jeong-Hyeon , Liu Boshu , Lee Heewook , Brown Pamela J. , Kysela David , Brun Yves V. , Kim Sun
Published: April 2012

Motivation: Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community.

Results: We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.

Availability:  http://biohealth.snu.ac.kr/GeneclusterViz/; http://microbial.informatics.indiana.edu/GeneclusterViz/

Contact:  sunkim.bioinfo@snu.ac.kr; ybrun@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Development of a reverse-genetics system for murine norovirus 3: long-term persistence occurs in the caecum and colon
Authors: Arias Armando , Bailey Dalan , Chaudhry Yasmin , Goodfellow Ian
Published: April 2012

Human noroviruses (HuNoV) are a major cause of viral gastroenteritis worldwide, yet, due to the inability to propagate HuNoV in cell culture, murine norovirus (MNV) is typically used as a surrogate to study norovirus biology. MNV-3 represents an attractive strain to study norovirus infections in vivo because it establishes persistence in wild-type mice, yet causes symptoms resembling gastroenteritis in immune-compromised STAT1−/− mice. The lack of reverse-genetics approaches to recover genetically defined MNV-3 has limited further studies on the identification of viral sequences that contribute to persistence. Here we report the establishment of a combined DNA-based reverse-genetics and mouse-model system to study persistent MNV-3 infections in wild-type (C57BL/6) mice. Viral RNA and infectious virus were detected in faeces for at least 56 days after inoculation. Strikingly, the highest concentrations of viral RNA during persistence were detected in the caecum and colon, suggesting that viral persistence is maintained in these tissues. Possible adaptive changes arising during persistence in vivo appeared to accumulate in the minor capsid protein (VP2) and the viral polymerase (NS7), in contrast with adaptive mutations selected during cell-culture passages in RAW264.7 cells that appeared in the major capsid protein (VP1) and non-structural protein NS4. This system provides an attractive model that can be readily used to identify viral sequences that contribute to persistence in an immunocompetent host and to more acute infection in an immunocompromised host, providing new insights into the biology of norovirus infections.
ALEX1 suppresses colony formation ability of human colorectal carcinoma cell lines
Authors: Iseki Hiroyoshi , Takeda Akihiko , Andoh Toshiwo , Kuwabara Koki , Takahashi Norio , Kurochkin Igor V. , Ishida Hideyuki , Okazaki Yasushi , Koyama Isamu
Published: April 2012

Arm protein lost in epithelial cancers, on chromosome X (ALEX; also known as armadillo repeat containing, X‐linked [ARMCX]) is a novel subgroup within the armadillo (ARM) family, which has several ARM repeat domains. The biological function of classical ARM family members such as β‐catenin is well understood, but that of the ALEX/ARMCX family members is largely unknown. Here we evaluate the effects of ALEX1 overexpression on in vitro colony formation ability and expression of ALEX1 mRNA in human colorectal tumor. Overexpression of ALEX1 suppressed the anchorage‐dependent and ‐independent colony formation of human colorectal carcinoma cell lines by the study of stable clones of HCT116 cells expressing ALEX1 protein. Bisulfite genomic sequencing revealed that the promoter region of ALEX1 gene was highly methylated in both HCT116 and SW480 cells in comparison with PANC‐1 and MCF‐7 cells, which express endogenous ALEX1 mRNA, indicating the capability of promoter methylation to silence ALEX1 gene in HCT116 and SW480 cells. Our current findings suggest that overexpression of ALEX1 play a negative role in human colorectal tumorigenesis. (Cancer Sci 2012; 103: 1267–1271)
Insulin‐like growth factor binding protein‐3 suppresses vascular endothelial growth factor expression and tumor angiogenesis in head and neck squamous cell carcinoma
Authors: Oh Seung‐Hyun , Kim Woo‐Young , Lee Ok‐Hee , Kang Ju‐Hee , Woo Jong‐Kyu , Kim Jai‐Hyun , Glisson Bonnie , Lee Ho‐Young
Published: April 2012

Angiogenesis, the process by which new blood vessels are recruited to existing ones, is essential for tumor development. Insulin‐like growth factor (IGF) binding protein‐3 (IGFBP‐3), which modulates bioavailability of IGF, has been studied for its potential role in angiogenesis during tissue regeneration and cancer development. In this study, we assessed the role of IGFBP‐3 in tumor angiogenesis in head and neck squamous cell carcinoma (HNSCC) and human umbilical vein endothelial cells (HUVECs) using adenoviral (Ad‐BP3) and recombinant (rBP3) IGFBP‐3. Using an in vivo orthotopic tongue tumor model, we confirmed that both Ad‐BP3 and rBP3 suppress the growth of UMSCC38 HNSCC cells in vivo. Ad‐BP3 inhibited vascularization in tongue tumors and chorio‐allantoic membrane, and suppressed angiogenesis‐stimulating activities in UMSCC38 cells. In HUVECs, Ad‐BP3 decreased migration, invasion, and tube formation. rBP3 also suppressed production of vascular endothelial growth factor (VEGF) in HUVECs and UMSCC38 cells. IGFBP‐3‐GGG, a mutant IGFBP‐3 with loss of IGF binding capacity, suppressed VEGF production. In addition, we found that IGFBP‐3 suppressed VEGF expression, even in mouse embryonic fibroblasts from an IGF‐1R‐null mouse. Finally, we demonstrated that IGFBP‐3‐GGG inhibits tumor angiogenesis and growth to the same degree as wild‐type IGFBP‐3. Taken together, these results support the hypothesis that IGFBP‐3 has anti‐angiogenic activity in HNSCC, at least in part due to IGF‐independent suppression of VEGF production from vascular endothelial cells and cancer cells. (Cancer Sci 2012; 103: 1259–1266)
NIH3T3 cells overexpressing CD98 heavy chain resist early G1 arrest and apoptosis induced by serum starvation
Authors: Hara Kaori , Ueda Shiho , Ohno Yoshiya , Tanaka Toshiyuki , Yagi Hideki , Okazaki Shogo , Kawahara Rieko , Masayuki Takechi , Enomoto Takemi , Hashimoto Yoshiyuki , Masuko Kazue , Masuko Takashi
Published: April 2012

CD98 is a heterodimeric glycoprotein of 125‐kDa, which consists of a 90‐kDa heavy chain (hc) subunit and 35‐kDa to 55‐kDa light chain (lc) subunits. It is strongly expressed on the surface of proliferating normal cells and almost all tumor cells. To investigate the participation of CD98 in cellular proliferation and malignant transformation, we analyzed cell‐cycle progression of NIH3T3 clones transfected with cDNA of human CD98hc. Although NIH3T3 and control transfectant cells grown to the subconfluent state were arrested in the G0/G1 phase by serum starvation, considerable portions of CD98hc‐transfected cells resided at S and G2/M phases. Under serum‐starved and confluent conditions, significant fractions (20–25%) of NIH3T3 and control transfectant cells contained less than 2n content DNA, indicating occurrence of apoptosis, whereas no apoptotic cells were detected in CD98hc‐transfectant cells. Under serum‐starved conditions, a marked increase in the levels of cyclin D1 and cyclin E and a decrease in p16 were observed in CD98hc‐transfectant cells. The reverse was true for NIH3T3 and control transfectant cells. Our results suggest that resistance to G1 arrest and apoptosis by CD98 overexpression are associated with high G1‐cyclins and low p16 levels. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02304.x, 2012)
Cross‐sectional content analysis of clinically applied circumferences
Authors: Tresignie Jonathan , Scafoglieri Aldo , Cattrysse Erik , Clarys Jan Pieter
Published: April 2012

Eur J Clin Invest 2012; 42 (9): 961–966

Background  The contours of a human body are determined by the volumes of the underlying tissues [adipose tissue (AT), muscle, bone and viscera]. Conceptually, they are assumed to be used as a concentric set of cylinders. Determination of these clinically applied circumferences in terms of relative tissue proportions has led to conflicting results. As it remains unclear what a circumference really measures or represents and how it relates to body composition (BC), the aim of this study was to determine the content of the circumferences and whether these perimeters can be used to assess segmental or whole body tissue components.

Design  Subsequent to an anthropometric protocol, the five white Caucasian cadavers were fractionated into slices of 3 cm and segmental and whole BC was determined at the anatomical tissue‐system level by direct dissection.

Results  Only two circumferences correlated significantly with their dominating component [upper arm circumference (r = 0·98; P < 0·01) and waist circumference (WC) (r = 0·90; P < 0·05) with AT]. Two circumferences were related to a segmental tissue component [WC (r = 1·00; P < 0·001) with muscle mass of the trunk and wrist circumference (WrC) (r = 0·90; P < 0·05) with bone mass of the upper limb]. Two circumferences were related to a whole body tissue component [chest circumference (r = 0·90; P < 0·05) with whole body AT mass and WrC (r = 0·90; P < 0·05) with whole body bone mass].

Conclusion  The clinically applied circumferences do not measure what they pretend to measure. Of all the studied circumferences, only 2 circumferences (WC and WrC) can be used to assess segmental or whole body tissue components.
Biomass partitioning and root morphology of savanna trees across a water gradient
Authors: Tomlinson Kyle W. , Sterck Frank J. , Bongers Frans , da Silva Dulce A. , Barbosa Eduardo R. M. , Ward David , Bakker Freek T. , van Kaauwen Martijn , Prins Herbert H. T. , de Bie Steven , van Langevelde Frank
Published: April 2012

1. Plant organ biomass partitioning has been hypothesized to be driven by resources, such that species from drier environments allocate more biomass to roots than species from wetter environments to access water at greater soil depths. In savanna systems, fire may select for greater allocation to root biomass, especially in humid environments where fire is more frequent. Therefore, species from drier environments may have been under selection pressure to reach deeper soil water more effectively than species from humid environments, through faster root extension, more efficient depth penetration, and faster plant growth rates to respond rapidly to variable rainfall events.

2. We compared biomass partitioning, root morphology traits [root extension rate, RER; specific taproot length (STRL)] and relative growth rate (RGR) of seedlings of 51 savanna tree species, sampled from three continents (Africa, Australia and South America) in a greenhouse experiment. We used phylogenetically corrected and uncorrected analyses to compare the traits of the groups. We conducted a permanova on the combined traits to establish whether species could be distinguished on the basis of their combined traits.

3. On average, species from humid environments allocated more biomass to roots and less to stems than species from semi‐arid environments, consistent with the expectation that fire pressure selects for greater allocation to roots in humid environments. However, some species from humid environments had fast growth rates instead of high allocation to roots. Both RER and STRL were greater among species of semi‐arid environments than among species of humid environments, and also differed between continents. Differences between strategies under each climate type appear to be associated with leaf habit.

4. Synthesis. Plant biomass partitioning has been selected by defoliation pressure and the effects of this selection pressure can supersede any selection in response to local water constraints. Root morphological adaptations, but not plant growth rate, of tree seedlings, have been selected in response to water deficits.
Microscopy beyond the diffraction limit using actively controlled single molecules
Authors: MOERNER W.E.
Published: April 2012

In this short review, the general principles are described for obtaining microscopic images with resolution beyond the optical diffraction limit with single molecules. Although it has been known for several decades that single‐molecule emitters can blink or turn on and off, in recent work the addition of on/off control of molecular emission to maintain concentrations at very low levels in each imaging frame combined with sequential imaging of sparse subsets has enabled the reconstruction of images with resolution far below the optical diffraction limit. Single‐molecule active control microscopy provides a powerful window into information about nanoscale structures that was previously unavailable.
Thyroid Hormone Accelerates the Differentiation of Adult Hippocampal Progenitors
Authors: Kapoor R. , Desouza L. A. , Nanavaty I. N. , Kernie S. G. , Vaidya V. A.
Published: April 2012

Disrupted thyroid hormone function evokes severe physiological consequences in the immature brain. In adulthood, although clinical reports document an effect of thyroid hormone status on mood and cognition, the molecular and cellular changes underlying these behavioural effects are poorly understood. More recently, the subtle effects of thyroid hormone on structural plasticity in the mature brain, in particular on adult hippocampal neurogenesis, have come to be appreciated. However, the specific stages of adult hippocampal progenitor development that are sensitive to thyroid hormone are not defined. Using nestin‐green fluorescent protein reporter mice, we demonstrate that thyroid hormone mediates its effects on hippocampal neurogenesis by influencing Type 2b and Type 3 progenitors, although it does not alter proliferation of either the Type 1 quiescent progenitor or the Type 2a amplifying neural progenitor. Thyroid hormone increases the number of doublecortin (DCX)‐positive Type 3 progenitors, and accelerates neuronal differentiation into both DCX‐positive immature neurones and neuronal nuclei‐positive granule cell neurones. Furthermore, we show that this increase in neuronal differentiation is accompanied by a significant induction of specific transcription factors involved in hippocampal progenitor differentiation. In vitro studies using the neurosphere assay support a direct effect of thyroid hormone on progenitor development because neurospheres treated with thyroid hormone are shifted to a more differentiated state. Taken together, our results indicate that thyroid hormone mediates its neurogenic effects via targeting Type 2b and Type 3 hippocampal progenitors, and suggests a role for proneural transcription factors in contributing to the effects of thyroid hormone on neuronal differentiation of adult hippocampal progenitors.
Weekend catch‐up sleep is associated with decreased risk of being overweight among fifth‐grade students with short sleep duration
Authors: KIM CHAN‐WON , CHOI MIN‐KYU , IM HYOUNG‐JUNE , KIM OK‐HYUN , LEE HYE‐JA , SONG JIHYUN , KANG JAE‐HEON , PARK KYUNG‐HEE
Published: April 2012

Previous studies have reported a relationship between short sleep duration and childhood overweight. Although school‐aged children tend to compensate for weekday sleep deficit by increasing weekend sleep duration, the association between weekend catch‐up sleep and childhood overweight remains unclear. This study aimed to examine the relationship between weekend catch‐up sleep and being overweight in children. A total of 936 school children (48.2% boys) aged 10 or 11 years participated in this school‐based cohort study. Anthropometric measurements including height and body weight were carried out. We obtained data on sleep patterns, lifestyle and parent characteristics using questionnaires. The main outcome measure was childhood overweight. After adjusting for the relevant confounding variables (age, sex, breakfast eating, screen time and parental obesity), longer sleep on weekdays and weekends was associated with decreased odds of childhood overweight (OR: 0.68; 95% CI: 0.54–0.86; OR: 0.64; 95% CI: 0.53–0.77, respectively). Participants with increased catch‐up sleep duration during weekends also had decreased odds of being overweight (OR: 0.67; 95% CI: 0.53–0.85). There was an interaction between weekday sleep duration and weekend catch‐up sleep in relation to childhood overweight, and this effect of weekend catch‐up sleep on being overweight was stronger as the participants slept less on weekdays (P = 0.024). These results indicate that weekend catch‐up sleep is independently associated with decreased risk of being overweight in fifth‐grade students, and this effect can be varied by the weekday sleep duration. A prospective study is required to confirm this observation.