bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry
Authors: Leader David P. , Burgess Karl , Creek Darren , Barrett Michael P.
Published: October 2011

This work describes a freely available web‐based facility which can be used to analyse raw or processed mass spectrometric data from metabolomics experiments and display the metabolites identified – and changes in their experimental abundance – in the context of the metabolic pathways in which they occur. The facility, Pathos (http://motif.gla.ac.uk/Pathos/), employs Java servlets and is underpinned by a relational database populated from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Input files can contain either raw m/z values from experiments conducted in different modes, or KEGG or MetaCyc IDs assigned by the user on the basis of the m/z values and other criteria. The textual output lists the KEGG pathways on an XHTML page according to the number of metabolites or potential metabolites that they contain. Filtering by organism is also available. For metabolic pathways of interest, the user is able to retrieve a pathway map with identified metabolites highlighted. A particular feature of Pathos is its ability to process relative quantification data for metabolites identified under different experimental conditions, and to present this in an easily comprehensible manner. Results are colour‐coded according to the degree of experimental change, and bar charts of the results can be generated interactively from either the text listings or the pathway maps. The visual presentation of the output from Pathos is designed to allow the rapid identification of metabolic areas of potential interest, after which particular results may be examined in detail. Copyright © 2011 John Wiley & Sons, Ltd.
Was kann und tut die Rehabilitationspsychologie?
Authors: Bengel Jürgen
Published: October 2011

Einleitung

Die Rehabilitationspsychologie ist eine der zentralen Disziplinen innerhalb der Rehabilitation und der Rehabilitationswissenschaften. Sie hat sich in Deutschland und auch weltweit von einer primär diagnostischen Aufgabenstellung und Funktion in den 70er Jahren zu einer Disziplin mit einem breiten Tätigkeitsprofil entwickelt. Zielsetzungen einer Psychologie in der Rehabilitation liegen in der Unterstützung bei der Krankheitsverarbeitung, der Reduktion von psychosozialen Belastungen und der Versorgung von psychischen Störungen bei den Rehabilitanden und den Angehörigen. Psychologische Maßnahmen zielen auf eine Stärkung der Veränderungsmotivation und geben Hilfen zur Änderung eines gesundheitlich risikoreichen Lebensstils.
Zielorientierung in der medizinischen Rehabilitation – weiterhin eine Herausforderung
Authors: Pohontsch Nadine , Meyer Thorsten
Published: October 2011

Einleitung

Es herrscht Einigkeit darüber, dass Ziele für die Rehabilitation essentiell sind. Das deutsche Rehabilitationsrecht formuliert als übergeordnetes Ziel rehabilitativer Leistungen die Förderung der Selbstbestimmung und Teilhabe. Die theoretischen Grundlagen der Zielvereinbarung in der Rehabilitation bedürfen jedoch weiterer Ausarbeitung. Auch die praktische Integration der Zielorientierung und der gemeinsamen Zielfestlegung in den gesamten Rehabilitationsprozess stellt eine noch lange nicht bewältigte Herausforderung dar.
Variability of Indian monsoonal rainfall over the past 100 ka and its implication for C3–C4vegetational change
Authors: Agrawal Shailesh , Sanyal Prasanta , Sarkar Anindya , Jaiswal Manoj Kumar , Dutta Koushik
Published: October 2011

Oxygen and carbon isotope ratios of soil carbonate and carbon isotope ratios of soil organic matter (SOM) separated from three cores, Kalpi, IITK and Firozpur, of the Ganga Plain, India are used to reconstruct past rainfall variations and their effect on ambient vegetation. The δ18O values of soil carbonate (δ18OSC) analyzed from the cores range from −8.2 to −4.1‰. Using these variations in δ18OSCvalues we are able, for the first time, to show periodic change in rainfall amount between 100 and 18 ka with three peaks of higher monsoon at about 100, 40 and 25 ka. The estimation of rainfall variations using δ18O value of rainwater-amount effect suggests maximum decrease in rainfall intensity (~ 20%) during the last glacial maximum. The δ13C values of soil carbonate (δ13CSC) and SOM (δ13CSOM) range from −6.3 to + 1.6‰ and −28.9 to −19.4‰, respectively, implying varying proportions of C3and C4vegetations over the Ganga Plain during the last 100 ka. The comparison between monsoonal rainfall and atmospheric CO2with vegetation for the time period 84 to 18 ka indicate that relative abundances of C3and C4vegetations were mainly driven by variations in monsoonal rainfall.
Development of unusual rock weathering features in the Cordillera Blanca, Peru
Authors: Rodbell Donald T. , Frey Holli M. , Manon Matthew R.F. , Smith Jacqueline A. , McTurk Nicholas A.
Published: October 2011

Mylonite textures in granodiorite boulders are responsible for higher rates of surface denudation of host rocks and the progressive development of unusual rock weathering features, termed weathering posts. These textures are characterized by smaller grain sizes, higher biotite content, and a higher biotite axial ratio in host rocks relative to weathering posts. Elemental concentrations do not show a significant difference between weathering posts and the host rocks in which they are found, and this reflects the absence of a weathering residue on the rock surfaces. Chemical weathering loosens the bonds between mineral grains through the expansion of biotite, and the loosened grains fall off or are blown off the boulder surface and continue their chemical alteration in the surrounding soil. The height of weathering posts on late Quaternary moraines increases at a linear rate of ~ 1.45±0.45 cm (1000 yr)– 1 until post heights reach the diameter of host rocks. Such a rate of boulder denudation, if unrecognized, would generate significant errors (> 20%) in cosmogenic exposure ages for Pleistocene moraines. Given the paucity of boulders with diameters that significantly exceed 1.5 m, the maximum age of utility of weathering posts as a numeric age indicator is ~ 100 ka.
Increased Plasma Levels of Nesfatin-1 in Patients with Newly Diagnosed Type 2 Diabetes Mellitus
Authors: Zhang Z. , Li L. , Yang M. , Liu H. , Boden G. , Yang G.
Published: October 2011

Nesfatin-1, which is derived from nucleobindin2 (NUCB2), has been recently identified as a novel satiety regulator. However, its pathophysiological role in humans remains unknown. The aim of the present study was to investigate plasma nesfatin-1 levels and the association between plasma nesfatin-1 levels and various metabolic parameters in humans.

74 subjects with newly diagnosed type 2 diabetes mellitus (nT2DM), 73 subjects with impaired glucose tolerance (IGT) and 73 subjects with normal glucose tolerance (NGT) were enrolled in this study. Plasma nesfatin-1 levels were measured by a commercially available enzyme- linked immunosorbent assay.

Plasma nesfatin-1 levels were elevated in subjects with both nT2DM and IGT compared to controls (1.91±0.79 and 1.80±0.80 vs. 1.41±0.58 μ g/L, P<0.05 or P<0.01 ). Simple regression analysis showed that in subjects with IGT and nT2DM, plasma nesfatin-1 correlated positively with body mass index (BMI), hemoglobin A1c (HbA1c), fasting blood glucose (FBG), 2 h blood glucose after a glucose load (2hPBG), fasting plasma insulin (FINS) and the homeostasis model assessment of insulin resistance (HOMA-IR). Multivariate logistic regression analysis revealed that plasma nesfatin-1 was significantly associated with IGT and nT2DM, even after controlling for differences in BMI.

Plasma nesfatin-1 concentrations were found to be elevated in subjects with both IGT and nT2DM and to be related with several clinical parameters known to be associated with insulin resistance.
A Novel PRKAR1A Mutation in Korean Carney Complex Family
Authors: Rhee S. , Kwon H. , Lee J. , Woo J.-T. , Kim M. , Lim Y. , Rhee B. , Koh S. , Lee S. , Lee M.-H. , Kim D. , Chon S. , Oh S. , Kim S. , Kim J.-W. , Kim Y. , Choi Y.
Published: October 2011

Carney complex (CNC) is an autosomal dominant hereditary or sporadic multiple neoplastic syndrome that shows variable clinical symptoms. Generally, CNC appears as skin pigmentation, cardiac or cutaneous myxomas, and multiple endocrine tumours. We performed an extensive evaluation of 9 individuals within 1 family in whom CNC was suspected. Among them, 5 had CNC with various clinical manifestations. We also performed mutational analysis of suspected genes in these patients. Although all patients were members of the same family, variable CNC-related manifestations were observed in each patient. An analysis showed a novel deletion mutation (c.537delA) in exon 6 of the PRKAR1A gene in the patients. Based on our results, the patients were determined to have CNC type I. This is the first such mutational report in Korea.
Treatment with Actovegin® Improves Sensory Nerve Function and Pathology in Streptozotocin-Diabetic Rats via Mechanisms Involving Inhibition of PARP Activation
Authors: Dieckmann A. , Kriebel M. , Andriambeloson E. , Ziegler D. , Elmlinger M.
Published: October 2011

Diabetic neuropathy is one of the most severe complications of diabetes, affecting approximately one-third of diabetic patients. We investigated the potential neuroprotective effect of Actovegin®, a deproteinized hemoderivative of calf blood, in an animal model of diabetic neuropathy.

A single intravenous injection of streptozotocin (STZ, 55 mg/kg) was used to induce experimental diabetes in male Sprague-Dawley rats. Actovegin® (200 or 600 mg/kg) was administered intraperitoneally from day 11 to day 40 post-STZ exposure. N-acetylcysteine (NAC) was used as a positive control and was added to drinking water (0.2 g/l) from day 2 until day 40. Measurements to assess efficacy included sensory nerve conduction velocity (SNCV), intraepidermal nerve fiber density (IENFD), and poly(ADP-ribose) content.

A decrease (35%) in sensory nerve conduction velocity (SNCV) was seen in STZ-induced diabetic rats from day 10 post-STZ administration and persisted at days 25 and 39. At study completion (day 41), a decrease (32%) in intraepidermal nerve fiber density (IENFD) was found in hind-paw skin biopsies from STZ-rats. Reduced SNCV and IENFD were significantly ameliorated by both doses of Actovegin®. More­over, 600 mg/kg Actovegin® markedly decreased poly(ADP-ribose) polymerase (PARP) activity in sciatic nerves from STZ-diabetic rats as assessed by poly(ADP-ribose) content.

Actovegin® improved several para­meters of experimental diabetic neuropathy via mechanisms involving suppression of PARP activation, providing a rationale for treatment of this disease in humans.
Velocity scaling for filament motion in scrape-off layer plasmas
Authors: Kube R. , Garcia O. E.
Published: October 2011

The velocity scaling for isolated plasma filaments in non-uniformly magnetized plasmas with respect to filament amplitude and cross-field size has been investigated by means of numerical simulations. The model includes electric currents due to magnetic gradient and curvature drifts, polarization drifts, and parallel currents through sheaths, where the magnetic field lines intersect material walls. In the ideal limit, the radial velocity of the filament increases with the square root of its size. When sheath currents dominate over polarization currents, the filament velocity is inversely proportional to the square of its size. In the presence of sheath currents, the velocity is maximum for an intermediate filament size determined by the balance between diamagnetic, polarization, and sheath currents. The parameter dependence of this filament size and velocity is elucidated. The results are discussed in the context of blob-like structures in basic laboratory plasma experiments and in the scrape-off layer of magnetically confined plasmas.
Quantification of impact energy dissipation capacity in metallic thin-walled hollow sphere foams using high speed photography
Authors: Li P. , Petrinic N. , Siviour C. R.
Published: October 2011

Quantification of energy dissipation capacity in metallic foams is required for their application in transport components subject to high velocity impact loads. In this study, in-situ high speed photography combined with in-house grid tracking codes was used to quantitatively investigate the impact behavior of electrodeposited nickel thin-walled hollow sphere foams in gas gun impact testing at an initial velocity of 60–140 m s−1. The energy dissipated by the foam varied almost linearly with the depth of impacted volume. The compressive plateau stress, which it is difficult to measure directly using conventional experiments, was then calculated for high impact loading velocity. It was found that both the energy dissipation capacity and average plateau strength increase with the initial impact velocity, which may suggest a rate dependency of the foam.
Mega-electron-volt proton irradiation on supported and suspended graphene: A Raman spectroscopic layer dependent study
Authors: Mathew S. , Chan T. K. , Zhan D. , Gopinadhan K. , Roy Barman A. , Breese M. B. H. , Dhar S. , Shen Z. X. , Venkatesan T. , Thong John T. L.
Published: October 2011

Graphene samples with 1, 2, and 4 layers and 1 + 1 folded bi-layers and graphite have been irradiated with 2 MeV protons at fluences ranging from 1 × 1015 to 6 × 1018 ions/cm2. The samples were characterized using visible and UV Raman spectroscopy and Raman microscopy. The ion-induced defects were found to decrease with increasing number of layers. Graphene samples suspended over etched holes in SiO2 have been fabricated and used to investigate the influence of the substrate SiO2 for defect creation in graphene. While Raman vibrational modes at 1460 cm−1 and 1555 cm−1 have been observed in the visible Raman spectra of substantially damaged graphene samples, these modes were absent in the irradiated-suspended monolayer graphene.
Diffusion of Ag and Co in ultrafine-grained α-Ti deformed by equal channel angular pressing
Authors: Fiebig Jochen , Divinski Sergiy , Rösner Harald , Estrin Yuri , Wilde Gerhard
Published: October 2011

Grain boundary diffusion of Co and Ag was investigated in coarse-grained and ultrafine-grained (UFG) α-Ti. Ultrafine grained Ti was produced by equal channel angular pressing (ECAP) and diffusion measurements were performed in a temperature interval where no significant grain growth occurred. Grain boundary diffusion of Co was found to be 1-2 orders of magnitude slower in UFG Ti, despite the attendant activation enthalpy being similar to that in coarse-grained α-Ti. By contrast, grain boundary diffusion of Ag occurred at a significantly higher rate in the ECAP-modified UFG Ti. This behaviour is associated with the specific diffusion mechanisms of Ag and Co: while Ag diffuses preferentially via substitutional sites, diffusion of Co is dominated by interstitial jumps. The existence of so-called non-equilibrium interfaces in UFG Ti, providing an increased density of traps for the interstitially diffusing Co and simultaneously enhancing substitutionally diffusion of Ag, is confirmed by the diffusion measurements.
Uniaxial tension-induced breaking in the gold nanowire with the influence of defects and temperatures
Authors: Wang Fenying , Chen Tiannan , Zhu Tiemin , Gao Yajun , Zhao Jianwei
Published: October 2011

Defects in metallic nanowires have raised concerns due to the influence on the properties of metallic nanowires in a nanoelectromechanical system. In this paper, the deformation and breaking of the [100] single-crystal gold nanowires containing vacancy defects are studied using molecular dynamics simulations at different temperatures. The statistical breaking position distributions show the deformation and breaking of the nanowires have a dependence on the applied temperature, and the sensitivity of the nanowire to vacancies is based on a competition between constructed vacancies and disordered crystalline structures induced by temperatures. At a low temperature of 100 K, a vacancy ratio of 25% has decided the breaking of the nanowire because microatomic fluctuation is in an equilibrium state. However, owing to acute atomic movements, the sensitivity of vacancies to breaking is not obvious before a vacancy ratio of 70% at a high temperature of 500 K.
Temperature dependence of current density and admittance in metal-insulator-semiconductor junctions with molecular insulator
Authors: Fadjie-Djomkam A. B. , Ababou-Girard S. , Hiremath R. , Herrier C. , Fabre B. , Solal F. , Godet C.
Published: October 2011

Electrical transport in ultrathin Metal-insulator-semiconductor (MIS) tunnel junctions is analyzed using the temperature dependence of current density and admittance characteristics, as illustrated by Hg//C12H25 – n Si junctions incorporating n-alkyl molecular layers (1.45 nm thick) covalently bonded to Si(111). The voltage partition is obtained from J(V, T) characteristics, over eight decades in current. In the low forward bias regime (0.2–0.4 V) governed by thermionic emission, the observed linear T-dependence of the effective barrier height, qΦEFF(T)=qΦB+(kT)β0dT, provides the tunnel barrier attenuation, exp(-β0dT), with β0= 0.93 Å−1 and the thermionic emission barrier height, ΦB=0.53 eV. In the high-forward-bias regime (0.5–2.0 V), the bias dependence of the tunnel barrier transparency, approximated by a modified Simmons model for a rectangular tunnel barrier, provides the tunnel barrier height, ΦT=0.5 eV; the fitted prefactor value, G0 = 10−10 Ω−1, is four decades smaller than the theoretical Simmons prefactor for MIM structures. The density distribution of defects localized at the C12H25 – n Si interface is deduced from admittance data (low-high frequency method) and from a simulation of the response time τR(V) using Gomila’s model for a non equilibrium tunnel junction. The low density of electrically active defects near mid-gap (DS < 2 × 1011 eV−1.cm−2) indicates a good passivation of dangling bonds at the dodecyl – n Si (111) interface.
1D modelling of nanosecond laser ablation of copper samples in argon at P = 1 atm with a wavelength of 532 nm
Authors: Clair Guillaume , L’Hermite Daniel
Published: October 2011

A one-dimensional model is developed for nanosecond laser ablation of a metal target (Cu) in a background gas (Ar) at any pressure. Simulations are performed with a 6 ns FWHM Gaussian laser pulse at 532 nm with a fluence of 11.3 J.cm−2. Heating, melting, evaporation, and condensation are considered to model the laser-target interaction. Expansion of the plume is investigated solving the Euler equations in a lagrangian formalism. Plasma formation is taken into account by computing the ionic species densities up to the second order of ionization in both the ablated material and the background gas. Such formation implies a strong laser-plasma interaction, assuming that the absorption phenomena are photoionization, electron-atom, and electron-ion inverse Bremsstrahlung. Radiative losses are supposed to be only described by electron-ion Bremsstrahlung. Preliminary results are presented and discussed.
A method for calculating plasma rotation velocity due to internal and external sources
Authors: Taguchi M.
Published: October 2011

A method for calculating the plasma rotation velocity caused by the effect of fluctuations due to instabilities and/or by externally imposed sources is presented for multiple ion species plasmas in a general toroidal magnetic field. The rotation velocity is shown to be obtained by solving generalized Spitzer equations, accompanied with the drift kinetic equations employing the pitch-angle-scattering and Krook collision terms. This method reduces to the moment equation approach in the conventional neoclassical transport theory when the source term can be approximated by a momentum source.
Investigation of turbulence in reversed field pinch plasma by using microwave imaging reflectometry
Authors: Shi Z. B. , Nagayama Y. , Yamaguchi S. , Hamada Y. , Hirano Y. , Kiyama S. , Koguchi H. , Michael C. A. , Sakakita H. , Yambe K.
Published: October 2011

Turbulence in the reversed field pinch (RFP) plasma has been investigated by using the microwave imaging reflectometry in the toroidal pinch experiment RX (TPE-RX). In conventional RFP plasma, the fluctuations are dominated by the intermittent blob-like structures. These structures are accompanied with the generation of magnetic field, the strong turbulence, and high nonlinear coupling among the high and low k modes. The pulsed poloidal current drive operation, which improves the plasma confinement significantly, suppresses the dynamo, the turbulence, and the blob-like structures.
Oblique propagation of nonlinear electrostatic waves in dense astrophysical magnetoplasmas
Authors: Masood W. , Rizvi H. , Siddiq M.
Published: October 2011

Nonlinear quantum ion-acoustic waves in dense dissipative as well as non-dissipative magnetized plasmas are investigated employing the quantum hydrodynamic model. In this regard, Zakharov Kuznetsov Burgers equation is derived in quantum plasmas, for the first time, using the small amplitude perturbation expansion method. The unique features of nonlinear electrostatic structures in pure electron-ion quantum magnetoplasma are highlighted and the parametric domain of the applicability of the model is unequivocally expressed. The present study may be useful to understand the nonlinear propagation characteristics of electrostatic shock and solitary structures in dense astrophysical systems where the quantum effects are expected to dominate.
Atomic lattice structure and continuum plate theories for the vibrational characteristics of graphenes
Authors: Arghavan S. , Singh A. V.
Published: October 2011

This paper is concerned with the equivalent extensional and flexural rigidities of a single layer graphene sheet by treating it as a plane lattice structure made of tightly packed carbon atoms into an array of honeycomb-shaped cells. Each carbon atom is modeled as a node with concentrated atomic mass and prescribed six degrees of freedom. The covalent bond between adjacent carbon atoms provides axial, bending, and torsional stiffness. Using the Poisson’s ratio of 0.16 and thickness of 3.4 Å, the equivalent Young’s moduli are found to be approximately 0.112 TPa for bending and in the range of 1.03–1.04 TPa for in-plane modes. Subsequently, the graphene structure is simulated by a classical plate with prescribed geometric and mechanical properties. The in-plane and out-of-plane free vibration analyses of the rectangular plate provide the natural frequencies and associated mode shapes. Results are compared with eigen analyses of the lattice structure model for different sizes of graphene. Examples are considered to show close agreement in the results from these two methods. Mode shapes reveal that the lattice structure model shows symmetry about the horizontal and vertical axes and also about the diagonals.
Non-resistance-based cell-state metric for phase-change memory
Authors: Sebastian Abu , Papandreou Nikolaos , Pantazi Angeliki , Pozidis Haralampos , Eleftheriou Evangelos
Published: October 2011

In phase-change memory (PCM), low-field electrical resistance is typically used to quantify the programmed cell state. However, this metric has several disadvantages. First, it exhibits temporal drift, which is a significant challenge for realizing multilevel PCM. Moreover, because of cell-geometry effects, this metric saturates after a certain point and thus masks the fact that the amorphous size increases with increasing input power. Finally, the resistance is typically measured as the current for a fixed bias voltage, which adversely affects the signal-to-noise ratio at high resistance values. A new metric for the programmed state in a PCM cell is proposed that has significant advantages over the resistance metric in all these aspects and is more representative of the fundamental programmed entity, which is the amorphous/crystalline phase configuration in the PCM cell. Analytical and experimental results are presented that demonstrate the efficacy of the proposed metric.
Unexpected size effect in the thermopower of thin-film stripes
Authors: Sun Weiqiang , Liu Haixiao , Gong Weiwei , Peng Lian-Mao , Xu Sheng-Yong
Published: October 2011

For low-dimensional materials, size effect of a physical property is usually expected to occur when one (or more) of the dimension sizes decreases to that comparable to or smaller than one of the intrinsic characteristic lengths, e.g., the mean free path. We report here an unexpected size effect, that in centimeter-long stripes of 100-nm-thick metallic thin films, a reduction of the absolute value of thermopower occurs when the stripe width is in the order of 30-50 μm, which is 100–1000 times larger than the intrinsic mean free path of the material. When the stripe width is reduced to 1.5 μm, a relative reduction of thermopower up to 35% is measured in some metals. We suggest that the sidewall scattering due to rough edges of these stripes may be the origin of this unexpected phenomenon. The results may be applied to construct novel thermoelectric devices, such as thermocouples made from a single metal film.
Influence of low pressure on laser inducing leaky Lamb wave and Scholte wave at air–solid interface
Authors: Yan Zhao , Zhonghua Shen , Jian Lu , Xiaowu Ni , Yiping Cui
Published: October 2011

A setup with Q-switched Nd:YAG laser inducing acoustic wave at air–solid interface and air-coupled optical deflection sensor was developed to research the influences of low air pressure on laser inducing leaky Lamb and Scholte waves at air–solid interface. The solid plate is settled in an airtight vessel abounded with standard air and its pressure can be adjusted by a vacuum pump. By experiments, the waveforms of laser induced interface acoustic waves, leaky Lamb and Scholte waves, under air pressures from 0.02 to 0.08 MPa with 0.01 MPa interval were first measured comprehensively. From the waveforms, we find that with increasing air pressure, the leaky energy of Lamb waves increase linearly and the amplitude of Scholte waves increase exponentially, but the velocity of Scholte waves decreases obviously.
Two-color InGaN/GaN microfacet multiple-quantum well structures grown on Si substrate
Authors: Zhang Liyang , Cheng Kai , Leys M. , Favia P. , Bender H. , Borghs G.
Published: October 2011

Two-color InGaN/GaN micro-facet multiple-quantum well (MQW) samples grown on 4 in. Si (111) substrate were systematically characterized. The micro-facet structure was achieved by epitaxial lateral overgrowth on SiO2 masked GaN surfaces with stripes along the 〈11¯00〉 direction and composed of (0001) and (112¯2) facets. Two different emission peaks stemming from (0001) and (112¯2) oriented MQWs are observed by photoluminescence. The relative intensities of the two peaks can be tuned by controlling the structure’s geometry and the experimentally derived growth rates on the different facets. For each facet, we have also determined the MQWs’ optical properties, the polarization, the internal quantum efficiency, and the light extraction efficiency. In addition, we analyzed the blue shift for differently oriented MQWs as function of temperature and excitation power.
Carrier-induced modulation of radiation by a gated graphene
Authors: Strikha M. V. , Vasko F. T.
Published: October 2011

The modulation of the transmitted (reflected) radiation due to change of interband transitions under variation of carriers concentration by the gate voltage is studied theoretically. The calculations were performed for strongly doped graphene on high-κ (Al2O3, HfO2, AlN, and ZrO2) or SiO2 substrates under normal propagation of radiation. We have obtained the modulation depth above 10% depending on wavelength, gate voltage (i.e., carriers concentration), and parameters of substrate. The graphene—dielectric substrate—doped Si (as gate) structures can be used as an effective electrooptical modulator of near-IR and mid-IR radiation for the cases of high-κ and SiO2 substrates, respectively.
Large reversible magnetocaloric effect in HoTiO3 single crystal
Authors: Su Yantao , Sui Yu , Cheng Jinguang , Wang Xianjie , Wang Yang , Liu Wanfa , Liu Xiaoyang
Published: October 2011

Large magnetocaloric effect has been observed in perovskite-type HoTiO3 single crystal accompanied by a second-order magnetic phase transition at TC ≈ 53 K. The values of maximum magnetic entropy change are about 5.96 and 11.56 J kg−1 K−1 under the magnetic field change of 2 and 5 T, respectively, without any detectable thermal and magnetic hysteresis loss. The large magnetic entropy change is attributed to the sharp magnetization jump, related to anomalies of the lattice parameters just at the Curie temperature. Such a large reversible magnetocaloric effect makes the perovskite HoTiO3 attractive for pursuing new materials for magnetic refrigeration.
Near-infrared quantum cutting in Ce3+, Er3+, and Yb3+ doped yttrium silicate powders prepared by combustion synthesis
Authors: Rakov Nikifor , Maciel Glauco S.
Published: October 2011

Yttrium silicate (YS) powders doped with Ce3+, Er3+, and Yb3+ were prepared by combustion synthesis. The material was investigated for use as energy downconverters to reduce thermalization losses in crystalline Si solar cells. The powders were excited by UV light (355 nm), and near-infrared emission around 1 μm was observed corresponding to a quantum cutting (QC) effect. The QC process occurs via cooperative energy transfer from Ce3+ (sensitizer) to Yb3+ (activator) in Ce3+:Yb3+ co-doped YS powders. QC was also observed in Er3+:Yb3+ co-doped YS powder via sequential energy transfer. The idea of synergy by use of Ce3+:Er3+:Yb3+ triply doped system to enhance the QC efficiency was investigated. We observed that the QC performance of Ce3+:Er3+:Yb3+ triply doped YS powder is not superior to that of Ce3+:Yb3+ co-doped YS powder due to near-infrared luminescence quenching induced by energy back-transfer from Yb3+ to Er3+.
Optimization of Co/Pt multilayers for applications of current-driven domain wall propagation
Authors: Wang K. , Wu M-C. , Lepadatu S. , Claydon J. S. , Marrows C. H. , Bending S. J.
Published: October 2011

A series of Co/Pt multilayers with perpendicular magnetic anisotropy has been grown by magnetron sputtering and characterized using magneto-optical Kerr effect measurements with a view to optimizing samples for current-driven domain motion applications. The influence of the thickness of both Co and Pt layers on the coercivity and switching behavior has been systematically investigated. The coercivity was found to depend strongly on the thickness of the Co layer and clear perpendicular magnetic anisotropy was observed in multilayer stacks with Co thickness ranging from 3 to 7 Å. Upon increasing the Co thickness further the magnetization reverts to the in-plane direction and both the coercivity and the remanence drop rapidly, with the former becoming dominated by shape anisotropy. Increasing the thickness of the Pt buffer layer leads to improved perpendicular magnetic anisotropy with higher coercive fields. In contrast, the thickness of the Pt capping layers does not appear to have any systematic influence on the anisotropy in the range of 22–62 Å. The coercivity can be further affected by the number of repeat Co layers in the stack due to exchange and magnetic coupling between adjacent Co layers. Upon increasing the thickness of the intermediate Pt spacer layer beyond 27 Å, a transition from a coherent single-unit-like reversal to a sequential layer-by-layer reversal was observed. Structures with sharp switching fields and medium coercivity (50–150 Oe) have Co thickness fractions in the range 5 ∼ 7% of the total stack height and should be well optimized for studying current-driven domain motion at low current densities.
Domain size engineering in tetragonal Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 crystals
Authors: Lin Dabin , Zhang Shujun , Li Zhenrong , Li Fei , Xu Zhuo , Wada Satoshi , Luo Jun , Shrout Thomas R.
Published: October 2011

The effect of domain size on the dielectric and piezoelectric properties of [111]-oriented tetragonal Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 crystals was investigated. The dielectric permittivity (ɛ33 T/ɛ0) and piezoelectric coefficient (d33) were found to be on the order of 13 800 and 1630 pC/N, respectively, for samples with domain size of ∼500 nm, a 3-fold increase to crystals with domain size of ∼50 μm. Rayleigh analysis revealed that the extrinsic contribution to the piezoelectric response increased from ∼8% to 30% with decreasing domain size, due to the increased domain wall density and associated irreversible domain wall motion. The enhanced properties were thought to relate to the fine domain structures, however, showing a poor electric field and temperature stabilities with domain size of 500 nm. Of particular significance is that samples with domain size being on the order of 5 μm exhibit field and temperature stabilities, with yet high piezoelectric properties, make it potential for transducer applications.
BioPAX support in CellDesigner
Authors: Mi Huaiyu , Muruganujan Anushya , Demir Emek , Matsuoka Yukiko , Funahashi Akira , Kitano Hiroaki , Thomas Paul D.
Published: October 2011

Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.

Availability: The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/

Contact:  huaiyumi@usc.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
TCDD Disrupts Hypural Skeletogenesis during Medaka Embryonic Development
Authors: Dong Wu , Hinton David E. , Kullman Seth W.
Published: October 2011

Defective bone and cartilage development account for a large number of human birth defects annually. Normal skeletogenesis involves cartilage development in early morphogenesis through a highly coordinated and orchestrated series of events involving commitment and differentiation of mesenchymal cells to chondrocytes followed by a highly programmed process of structural maturation. Recent developmental studies with laboratory model fish demonstrate that exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) results in cartilage and skeletal abnormalities. In this study, we exposed embryonic medaka to TCDD to induce developmental modification(s) of both cartilage and bone formation. Emphasis is placed on cell-rich hyaline cartilage of the hypural plate where both chondrogenesis and osteogenesis are impaired by TCDD exposure. In this model, TCDD exposure results in a concentration-dependent impairment of mesenchymal cell recruitment, chondrocyte cell proliferation, differentiation, and progression to hypertrophy. Gene expression of ColA2, a marker of chondrocyte terminal differentiation in hypural structures, is markedly attenuated consistent with hypural dysmorphogenesis. Assessment of hypural structure using a transgenic medaka expressing mCherry under control of the osterix promoter illustrated significant attenuation in expression of the osteoblast gene marker and lack of formation of a calcified perichondral sheath surrounding hypural anlage. Overall, these studies illustrate that TCDD impacts terminal differentiation and growth of cartilage and bone in axial structures not likely derived from neural crest progenitors in medaka hypurals.
Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant
Authors: Bibi Fehmida , Chung Eu Jin , Khan Ajmal , Jeon Che Ok , Chung Young Ryun
Published: October 2011

During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root ofRosa rugosacollected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881Tgrew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881Twas catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881Tbelonged to the genusRhizobiumand showed the highest 16S rRNA gene sequence similarity of 96.9 % toRhizobium rosettiformans, followed byRhizobium borbori(96.3 %),Rhizobium radiobacter(96.1 %),Rhizobium daejeonense(95.9 %),Rhizobium larrymoorei(95.6 %) andRhizobium giardinii(95.4 %). Phylogenetic analysis of strain YC6881TbyrecA,atpD,glnIIand 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881Twas a symbiotic bacterium that nodulatedVigna unguiculataandPisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c(53.7 %), C19 : 0cyclo ω8c(12.6 %) and C12 : 0(8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genesrecA,atpDandglnII, and fatty acid composition could be used to discriminate strain YC6881Tfrom other species of the genusRhizobiumin the same sublineage. Based on the results obtained in this study, strain YC6881Tis considered to represent a novel species of the genusRhizobium, for which the nameRhizobium halophytocolasp. nov. is proposed. The type strain is YC6881T( = KACC 13775T = DSM 21600T).
Cryptococcus thermophilus sp. nov., isolated from cassava sourdough
Authors: Vogelmann Stephanie A. , Chaves Sandra , Hertel Christian
Published: October 2011

A novel anamorphic yeast, strain LTH 6662T, was isolated from cassava sourdough. The isolate supposedly originated from cassava flour or was a contaminant thereof. Sequencing of the D1/D2 domain of the 26S rRNA gene indicated that strain LTH 6662T represents a novel species. Its closest relatives were members of the Cryptococcus humicola complex. The novel strain had several physiological characteristics that differed from those of related species: the ability to assimilate raffinose and cadaverine; the inability to assimilate soluble starch, xylitol, galactitol, butane-2,3-diol, sodium nitrite and lysine; the ability to grow without vitamins and at 42 °C; and the inability to produce starch-like substances. Its major ubiquinone was Q-10. In addition, buds were formed on small neck-like structures. In liquid medium, green or blue fluorescent substances were produced. The name Cryptococcus thermophilus sp. nov. is proposed, with LTH 6662T ( = DSM 19443T = CBS 10687T) as the type strain.
Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of

Flavobacterium hercynium

,

Flavobacterium resistens

and

Flavobacterium johnsoniae
Authors: Kim Joong-Jae , Kanaya Eiko , Weon Hang-Yeon , Koga Yuichi , Takano Kazufumi , Dunfield Peter F. , Kwon Soon-Wo , Kanaya Shigenori
Published: October 2011

A strictly aerobic, Gram-negative, yellow-pigmented, non-spore-forming rod, designated 15C3T, was isolated from aerobic leaf-and-branch compost at EXPO Park in Osaka, Japan. Growth was observed at 9–33 °C (optimum 25 °C) and pH 5.6–7.9 (optimum pH 6.1–7.0). No growth occurred with >2 % (w/v) NaCl. Strain 15C3T reduced nitrate to nitrogen and showed catalase activity but not oxidase activity. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The isolate contained phosphatidylethanolamine as the major polar lipid and menaquinone-6 as the major respiratory quinone. The G+C content of the genomic DNA of strain 15C3T was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15C3T belonged to the genus

Flavobacterium

and was most closely related to

Flavobacterium hercynium

WB 4.2-33T (96.9 % sequence similarity). On the basis of phenotypic and phylogenetic distinctiveness, strain 15C3T is considered to represent a novel species in the genus

Flavobacterium

, for which the name Flavobacterium compostarboris sp. nov. is proposed. The type strain is 15C3T ( = KACC 14224T  = JCM 16527T). Emended descriptions of

F. hercynium

,

Flavobacterium resistens

and

Flavobacterium johnsoniae

are also given.
Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)
Authors: Volokhov Dmitriy V. , Amselle Megan , Beck Brian J. , Popham David L. , Whittaker Paul , Wang Hua , Kerrigan Elizabeth , Chizhikov Vladimir E.
Published: October 2011

Three strains of lactic acid bacteria (LAB) were isolated from the faeces of apparently healthy wild Canada geese (Branta canadensis) in 2010 by cultivating faecal LAB on Rogosa SL agar under aerobic conditions. These three isolates were found to share 99.9 % gene sequence similarity of their 16S rRNA, their 16S–23S intergenic transcribed spacer region (ITS), partial 23S rRNA, rpoB, rpoC, rpoA and pheS gene sequences. However, the three strains exhibited lower levels of sequence similarity of these genetic targets to all known LAB, and the phylogenetically closest species to the geese strains were

Lactobacillus casei

,

Lactobacillus paracasei

,

Lactobacillus rhamnosus

and

Lactobacillus saniviri

. In comparison to

L. casei

ATCC 393T,

L. paracasei

ATCC 25302T,

L. rhamnosus

ATCC 7469T and

L. saniviri

DSM 24301T, the novel isolates reacted uniquely in tests for cellobiose, galactose, mannitol, citric acid, aesculin and dextrin, and gave negative results in tests for l-proline arylamidase and l-pyrrolydonyl-arylamidase, and in the Voges-Proskauer test. Biochemical tests for cellobiose, aesculin, galactose, gentiobiose, mannitol, melezitose, ribose, salicin, sucrose, trehalose, raffinose, turanose, amygdalin and arbutin could be used for differentiation between

L. saniviri

and the novel strains. On the basis of phenotypic and genotypic characteristics, and phylogenetic data, the three isolates represent a novel species of the genus

Lactobacillus

, for which the name Lactobacillus brantae sp. nov. is proposed. The type strain is SL1108T ( = ATCC BAA-2142T = LMG 26001T = DSM 23927T) and two additional strains are SL1170 and SL60106.
Erythrobacter marinus sp. nov., isolated from seawater
Authors: Jung Yong-Taek , Park Sooyeon , Oh Tae-Kwang , Yoon Jung-Hoon
Published: October 2011

A Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated strain HWDM-33T, was isolated from seawater of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HWDM-33T grew optimally at pH 7–8, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HWDM-33T clustered with

Erythrobacter gangjinensis

K7-2T, with which it shared 96.9 % sequence similarity. Strain HWDM-33T exhibited 94.2–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized species of the genus

Erythrobacter

. Strain HWDM-33T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, C17 : 1ω6c, and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HWDM-33T was 66.1 mol%. Differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain HWDM-33T was separate from

E. gangjinensis

and other recognized species of the genus

Erythrobacter

. On the basis of the data presented here, strain HWDM-33T represents a novel species of the genus

Erythrobacter

, for which the name Erythrobacter marinus sp. nov. is proposed. The type strain is HWDM-33T ( = KCTC 23554T  = CCUG 60528T).
Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.)
Authors: Hong Sung Wook , Park Jung Min , Kim Soo-Jin , Chung Kun Sub
Published: October 2011

A swarming and moderately halotolerant bacterium, designated strain A1-2T, was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2T belonged to the genus

Bacillus

and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with

Bacillus drentensis

LMG 21831T,

B. horneckiae

PT-45T,

B. niacini

BAC 1015,

B. infantis

SMC 4352-1T and

B. shackletonii

LMG 18435T, respectively. DNA–DNA relatedness values between the isolate and the reference strains were ≤38.3 %. The DNA G+C content of strain A1-2T was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0 (51.5 %) and anteiso-C15 : 0 (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2T represents a novel species of the genus

Bacillus

, for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2T ( = KCCM 90092T = JCM 16993T).
Lutibaculum baratangense gen. nov., sp. nov., a proteobacterium isolated from a mud volcano
Authors: Kumar P. Anil , Srinivas T. N. R. , Manasa P. , Madhu S. , Shivaji S.
Published: October 2011

A novel Gram-negative, oval to rod-shaped, motile bacterium, strain AMV1T, was isolated from a soil sample collected from a mud volcano of Baratang Island, Andamans, India. The predominant fatty acids were C16 : 0 (5.7 %), C18 : 1ω7c (78.6 %) and C19 : 0 cyclo ω8c (6.3 %). Strain AMV1T contained ubiquinone 10 (Q-10) as the major respiratory quinone and minor quantities of ubiquinone 9 (Q-9). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids, one unidentified phospholipid and one unidentified aminolipid. 16S rRNA gene sequence analysis indicated that strain AMV1T was related most closely to the type strains of

Tepidamorphus gemmatus

,

Bauldia consociata

,

Afifella pfennigii

and

Amorphus coralli

, four members of the order

Rhizobiales

(class

Alphaproteobacteria

), with pairwise sequence similarities of 95.0, 94.5, 94.4 and 94.0 %, respectively; it shared <94 % 16S rRNA gene sequence similarity with all the other members of the order

Rhizobiales

. Phylogenetic analyses indicated that strain AMV1T clustered with

Tepidamorphus gemmatus

and with species of the genera

Amorphus

,

Rhodobium

and

Afifella

. Phenotypic and phylogenetic characteristics thus suggest that strain AMV1T is a representative of a novel species of a new genus, for which the name Lutibaculum baratangense gen. nov., sp. nov. is proposed. The type strain of Lutibaculum baratangense is AMV1T ( = KCTC 22669T = NBRC 105799T = CCUG 58046T).