bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of laser interaction with ablative plasma and hydrodynamic behavior of laser supported plasma
Authors: Tong Huifeng , Yuan Hong , Tang Zhiping
Published: January 2013

When an intense laser beam irradiates on a solid target, ambient air ionizes and becomes plasma, while part of the target rises in temperature, melts, vaporizes, ionizes, and yet becomes plasma. A general Godunov finite difference scheme WENO (Weighted Essentially Non-Oscillatory Scheme) with fifth-order accuracy is used to simulate 2-dimensional axis symmetrical laser-supported plasma flow field in the process of laser ablation. The model of the calculation of ionization degree of plasma and the interaction between laser beam and plasma are considered in the simulation. The numerical simulations obtain the profiles of temperature, density, and velocity at different times which show the evolvement of the ablative plasma. The simulated results show that the laser energy is strongly absorbed by plasma on target surface and that the velocity of laser supported detonation (LSD) wave is half of the ideal LSD value derived from Chapman-Jouguet detonation theory.
Two-dimensional finite-element modeling of periodical interdigitated full organic solar cells
Authors: Granero P. , Balderrama V. S. , Ferré-Borrull J. , Pallarès J. , Marsal L. F.
Published: January 2013

By means of finite-element numerical modeling, we analyze the influence of the nanostructured dissociation interface geometry on the behavior of interdigitated heterojunction full organic solar cells. A systematic analysis of light absorption, exciton diffusion, and carrier transport, all in the same numerical framework, is carried out to obtain their dependence on the interface geometrical parameters: pillar diameter and height, and nanostructure period. Cells are constituted of poly(3-hexylthiophene) (P3HT) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61. Results show that light absorption is maximum for pillar heights of 80 nm and 230 nm. However, due to the short exciton diffusion length of organic materials, the analysis of the exciton diffusion process reveals that the 80 nm thickness gives rise to a higher photocurrent, except for the smaller pillar diameters. In terms of efficiency, it has been observed that the charge carrier transport is weakly dependent on the geometric parameters of the nanostructured interface if compared with the exciton diffusion process. The optimal cell is a device with a pillar height of 80 nm, a structure period of 25 nm, and a ratio of the nanopillar diameter to the period of 0.75, with an efficiency 3.6 times higher than the best planar bilayer reference device. This structure is such that it reaches a compromise between having a high proportion of P3HT to increase light absorption but preserving a small pillar diameter and interpillar distance to ensure an extended exciton dissociation interface.
Structural variants and the modified Slater-Pauling curve for transition-metal-based half-Heusler alloys
Authors: Shaughnessy M. , Damewood L. , Fong C. Y. , Yang L. H. , Felser C.
Published: January 2013

We compare the physical differences between two atomic configurations, found in the literature, of the half-Heusler alloys—XMnY, where X is a transition-metal element and Y is a nonmetallic element. The structural differences arise from the placement of the X and Y atoms and the vacancy within the full-Heusler (L21) structure. In one configuration, Y and Mn are nearest neighbors and the vacancy is at (1/4,3/4,1/4)a (4d) while in the other configuration, X and Mn are nearest neighbors and the vacancy is located at (0,0,1/2)a (4b), where a is the lattice constant of face-centered cube. We suggest that the important difference between the two configurations is the identity of the transition-metal element nearest to the non-metal element. Physical properties, in particular the bonding features, reflect this difference. The general validity of the modified Slater-Pauling curve, which gives successful zeroth-order prediction of the magnetic moments of many half-Heusler alloys including CrMnSb in the second configuration, is tested in the six XMnY alloys studied here. Their calculated moments obey the predictions by the modified Slater-Pauling curve for positive moments only. Exceptions appear for predictions with negative moments. A simple and plausible physical reason is provided. Furthermore, the possibility of a non-ferromagnetic phase is examined and the energetics between the ferromagnetic and non-ferromagnetic phases are compared.
Detection of defect states in low-k dielectrics using reflection electron energy loss spectroscopy
Authors: King S.W. , French B. , Mays E.
Published: January 2013

Reflection electron energy loss spectroscopy (REELS) has been utilized to measure the band gap (Eg) and energy position of sub-gap defect states for both non-porous and porous low dielectric constant (low-k) materials. We find the surface band gap for non-porous k = 2.8–3.3 a-SiOC:H dielectrics to be ≅ 8.2 eV and consistent with that measured for a-SiO2 (Eg = 8.8 eV). Ar+ sputtering of the non-porous low-k materials was found to create sub-gap defect states at ≈ 5.0 and 7.2 eV within the band gap. Based on comparisons to observations of similar defect states in crystalline and amorphous SiO2, we attribute these sub-gap defect states to surface oxygen vacancy centers. REELS measurements on a porous low-k a-SiOC:H dielectric with k = 2.3 showed a slightly smaller band gap (Eg = 7.8 eV) and a broad distribution of defects states ranging from 2 to 6 eV. These defect states are attributed to a combination of both oxygen vacancy defects created by the UV curing process and carbon residues left in the film by incomplete removal of the sacrificial porogen. Plasma etching and ashing of the porous low-k dielectric were observed to remove the broad defect states attributed to carbon residues, but the oxygen vacancy defects remained.
Enhanced microwave dielectric tunability of Ba0.5Sr0.5TiO3 thin films grown with reduced strain on DyScO3 substrates by three-step technique
Authors: Liu Hongrui , Avrutin Vitaliy , Zhu Congyong , Özgür Ümit , Yang Juan , Lu Changzhi , Morkoç Hadis
Published: January 2013

Tunable dielectric properties of epitaxial ferroelectric Ba0.5Sr0.5TiO3 (BST) thin films deposited on nearly lattice-matched DyScO3 substrates by radio frequency magnetron sputtering have been investigated at microwave frequencies and correlated with residual compressive strain. To reduce the residual strain of the BST films caused by substrate clamping and improve their microwave properties, a three-step deposition method was devised and employed. A high-temperature deposition at 1068 K of the nucleation layer was followed by a relatively low-temperature deposition (varied in the range of 673–873 K) of the BST interlayer and a high-temperature deposition at 1068 K of the top layer. Upon post-growth thermal treatment at 1298 K the films grown by the three-step method with the optimized interlayer deposition temperature of 873 K exhibited lower compressive strain compared to the control layer (−0.002 vs. −0.006). At 10 GHz, a high dielectric tunability of 47.9% at an applied electric field of 60 kV/cm was achieved for the optimized films. A large differential phase shift of 145°/cm and a figure of merit of 23°/dB were obtained using a simple coplanar waveguide phase shifter at 10 GHz. The low residual strain and improved dielectric properties of the films fabricated using the three-step deposition technique were attributed to reduced clamping of the BST films by the nearly lattice-matched substrate.
Relaxation of biofunctionalized magnetic nanoparticles in ultra-low magnetic fields
Authors: Yang H. C. , Chiu L. L. , Liao S. H. , Chen H. H. , Horng H. E. , Liu C. W. , Liu C. I. , Chen K. L. , Chen M. J. , Wang L. M.
Published: January 2013

In this work, the spin-spin relaxation rate, 1/T2, and spin-lattice relaxation rate, 1/T1, of protons’ spins induced by biofunctionalized magnetic nanoparticles and ferrofluids are investigated using a high-Tc superconducting quantum interference device-detected magnetometer in ultra-low fields. The biofunctionalized magnetic nanoparticles are the anti-human C-reactive protein (antiCRP) coated onto dextran-coated superparamagnetic iron oxides Fe3O4, which is labeled as Fe3O4-antiCRP. The ferrofluids are dextran-coated iron oxides. It was found that both 1/T2 and 1/T1 of protons in Fe3O4-antiCRP are enhanced by the presence of magnetic nanoparticles. Additionally, both the 1/T1 and 1/T2 of Fe3O4-antiCRP are close to that of ferrofluids, which are dextran-coated Fe3O4 dispersed in phosphate buffer saline. Characterizing the relaxation of Fe3O4-antiCRP can be useful for biomedical applications.
The failure models of Sn-based solder joints under coupling effects of electromigration and thermal cycling
Authors: Ma Limin , Zuo Yong , Liu Sihan , Guo Fu , Wang Xitao
Published: January 2013

Currently, the main concerns of Pb-free solder joints are focusing on electromigration (EM) and thermomechanical fatigue (TMF) problems. Many models have been established to understand the failure mechanisms of the joint under such single test conditions. Based on the fact that almost all microelectronic devices serve in combination conditions of fluctuated temperature and electric current stressing, the coupling effects of EM and TMF on evolution of microstructure and resistance of solder joint had been investigated. The failure models of binary SnBi alloy and ternary SnAgCu (SAC) solder under the coupling stressing were divided into four and three different stages, respectively. The failure mechanisms were dominant by the relationship of phase segregation, polarity effect, phase coarsening, and the coefficient of thermal expansion mismatch. Cracks tend to form and propagate along the interface between intermetallic compound layers and solder matrix in SAC solder. However, grain boundary was considered as the nucleation sites for microcracks in SnBi solder. High current density alleviates the deterioration of solder at the beginning stage of coupling stressing through Joule heating effect. An abrupt jump of resistance could be observed before the failure of the joint. The failure molds were determined by interactions of EM behaviors and TMF damages.
Design of half-metallic Heusler-based superlattices with vanishing net magnetization
Authors: Tırpancı Şaban , Şaşıoğlu E. , Galanakis I.
Published: January 2013

Employing first-principles electronic structure calculations, we show that it is possible to achieve half-metallic antiferromagnetism in artificial superlattices based on Heusler compounds. Suitable alternation of full-Heusler compounds with more and less than 24 valence electrons in the unit cell results in superlattices with zero total spin magnetic moment keeping the half-metallic character of the initial compounds. We demonstrate it considering superlattices made up from Mn2TiGe (Mn2VGa) and Co2TiGe (Co2VGa) compounds, which have 22 and 26 valence electrons, respectively. Moreover, these compounds posses similar lattice constants and have been already grown as thin films making them promising for spintronics devices.
Suppression of Auger-stimulated efficiency droop in nitride-based light emitting diodes
Authors: Vaxenburg R. , Lifshitz E. , Efros Al. L.
Published: January 2013

We calculate the rate of nonradiative Auger recombination in InGaN/GaN quantum wells with rectangular and smooth confining potentials. The calculations show that the rate of Auger recombination in rectangular quantum wells is sufficiently high to explain the efficiency droop in nitride-based light emitting diodes (LEDs). This rate, however, can be reduced by softening of the confining potential and a three-fold suppression is demonstrated in the studied quantum wells. The suppression of the Auger recombination rate improves LED radiative efficiency and reduces the droop effect, as we show using the standard recombination (ABC) model.
Simulation of an Ar/NH3 low pressure magnetized direct current discharge
Authors: Li Zhi , Zhao Zhen , Li Xuehui
Published: January 2013

A two-dimensional fluid model has been used to investigate the properties of plasma in an Ar/NH3 low pressure magnetized direct current discharge. We compared the simulation results with the theoretical and experimental results of the other gas discharge in which the magnetic field is considered. Results that obtained using this method are in good agreement with literature. The simulation results show that the positive ammonia ion density follows the positive argon ion density. The Ar2+ density is slightly higher than the Ar+ density at 100 mTorr. The largest ammonia ion is NH3+ ion, followed by NH2+, NH4+, and NH+ ions. The contribution of NH+ ions to the density of the positive ammonia ions is marginal. The influence of pressure on the plasma discharge has been studied by simulation, and the mechanisms have been discussed. The average plasma density increases as pressure increased. The plasma density appears to be more inhomogeneous than that at the lower pressure. The ratio of charge particles changed as pressure increased. The Ar+ density is slightly higher than the Ar2+ density as the pressure increased. It makes NH4+ ratio increase as pressure increased. It shows that the electron temperature drops with rising pressure by numerical calculation.
Effective mass of electron in monolayer graphene: Electron-phonon interaction
Authors: Tiras E. , Ardali S. , Tiras T. , Arslan E. , Cakmakyapan S. , Kazar O. , Hassan J. , Janzén E. , Ozbay E.
Published: January 2013

Shubnikov-de Haas (SdH) and Hall effect measurements performed in a temperature range between 1.8 and 275 K, at an electric field up to 35 kV m−1 and magnetic fields up to 11 T, have been used to investigate the electronic transport properties of monolayer graphene on SiC substrate. The number of layers was determined by the use of the Raman spectroscopy. The carrier density and in-plane effective mass of electrons have been obtained from the periods and temperature dependencies of the amplitude of the SdH oscillations, respectively. The effective mass is in good agreement with the current results in the literature. The two-dimensional (2D) electron energy relaxations in monolayer graphene were also investigated experimentally. The electron temperature (Te) of hot electrons was obtained from the lattice temperature (TL) and the applied electric field dependencies of the amplitude of SdH oscillations. The experimental results for the electron temperature dependence of power loss indicate that the energy relaxation of electrons is due to acoustic phonon emission via mixed unscreened piezoelectric interaction and deformation-potential scattering.
The incomplete plasma dispersion function: Properties and application to waves in bounded plasmas
Authors: Baalrud S. D.
Published: January 2013

The incomplete plasma dispersion function is a generalization of the plasma dispersion function in which the defining integral spans a semi-infinite, rather than infinite, domain. It is useful for describing the linear dielectric response and wave dispersion in non-Maxwellian plasmas when the distribution functions can be approximated as Maxwellian over finite, or semi-infinite, intervals in velocity phase-space. A ubiquitous example is the depleted Maxwellian electron distribution found near boundary sheaths or double layers, where the passing interval can be modeled as Maxwellian with a lower temperature than the trapped interval. The depleted Maxwellian is used as an example to demonstrate the utility of using the incomplete plasma dispersion function for calculating modifications to wave dispersion relations.
Detailed analysis of spin-dependent quantum interference effects in magnetic tunnel junctions with Fe quantum wells
Authors: Sheng P. , Bonell F. , Miwa S. , Nakamura T. , Shiota Y. , Murakami S. , Lam D. D. , Yoshida S. , Suzuki Y.
Published: January 2013

We investigated spin-dependent quantum interference effects in Cr(001)/wedge Fe(001)/MgO(001)/Fe(001) magnetic tunnel junctions by dI/dV measurements. dI/dV intensities were mapped two-dimensionally as a function of applied voltage and Fe thickness, indicating a clear signature of quantum well (QW) states in the ultrathin Fe (001) electrode. However, resonant positions of QW states were systematically shifted by one monolayer when compared with the first-principles calculation results. X-ray absorption spectroscopy and magnetic circular dichroism measurements were also performed. While Fe oxide presence at Fe/MgO interface was ruled out, Fe/Cr intermixing could not be excluded. Hence, controlling the Fe/Cr interface may affect QW state.
Silicon nanocrystals embedded in silicon carbide: Investigation of charge carrier transport and recombination
Authors: Löper Philipp , Canino Mariaconcetta , Qazzazie Dureid , Schnabel Manuel , Allegrezza Marco , Summonte Caterina , Glunz Stefan W. , Janz Stefan , Zacharias Margit
Published: January 2013

An illumination-dependent analysis of silicon nanocrystal p-i-n solar cells is presented within the framework of the constant field approximation. Silicon nanocrystals in silicon carbide were prepared by solid-phase crystallization and contacted with doped a-SixC1−x:H. This paper aims at determining the fundamental transport and recombination properties, i.e., the effective mobility lifetime product, of the nanocrystal layer at device level. Illumination-dependent current-voltage curves are modelled with a voltage-dependent collection function with only two free parameters, and excellent agreement is found between theory and experiment. An effective mobility lifetime product of 10−10 cm2/V is derived and confirmed independently from an alternative method.
Improved photovoltaic effects in InGaN-based multiple quantum well solar cell with graphene on indium tin oxide nanodot nodes for transparent and current spreading electrode
Authors: Hoon Seo Tae , Shim Jae-Phil , Jin Chae Seung , Shin GangU , Kyoung Kim Bo , Lee Dong-Seon , Hee Lee Young , Suh Eun-Kyung
Published: January 2013

We implemented graphene network on indium tin oxide (ITO) nanodots to a transparent and current-spreading electrode in InGaN-based solar cell to improve power conversion efficiency. The external quantum efficiency and short circuit current density (Jsc) of solar cells with graphene network on ITO nanodots were enhanced compared to those of solar cells with ITO and bare graphene film. The increase of the power conversion efficiency is attributed to the high transmittance, internal light-scattering effect, and effective carrier absorption of ITO nanodots.
Detecting the local transport properties and the dimensionality of transport of epitaxial graphene by a multi-point probe approach
Authors: Barreto Lucas , Perkins Edward , Johannsen Jens , Ulstrup Søren , Fromm Felix , Raidel Christian , Seyller Thomas , Hofmann Philip
Published: January 2013

The electronic transport properties of epitaxial monolayer graphene (MLG) and hydrogen-intercalated quasi free-standing bilayer graphene (QFBLG) on SiC(0001) are investigated by micro multi-point probes. Using a probe with 12 contacts, we perform four-point probe measurements with the possibility to effectively vary the contact spacing over more than one order of magnitude, allowing us to establish that the transport is purely two-dimensional. Combined with the carrier density obtained by angle-resolved photoemission spectroscopy, we find the room temperature mobility of MLG to be (870±120) cm2/V s. The transport in QFBLG is also found to be two-dimensional with a mobility of (1600±160) cm2/V s.
Asymmetry of localised states in a single quantum ring: Polarization dependence of excitons and biexcitons
Authors: Kim H. D. , Kyhm K. , Taylor R. A. , Nogues G. , Je K. C. , Lee E. H. , Song J. D.
Published: January 2013

We performed spectroscopic studies of a single GaAs quantum ring with an anisotropy in the rim height. The presence of an asymmetric localised state was suggested by the adiabatic potential. The asymmetry was investigated in terms of the polarization dependence of excitons and biexcitons, where a large energy difference (∼0.8 meV) in the exciton emission energy for perpendicular polarizations was observed and the oscillator strengths were also compared using the photoluminescence decay rate. For perpendicular polarizations, the biexciton exhibits twice the energy difference seen for the exciton, a fact that may be attributed to a possible change in the selection rules for the lowered symmetry.
Single-mode surface-emitting concentric-circular-grating terahertz quantum cascade lasers
Authors: Liang Guozhen , Liang Houkun , Zhang Ying , Khanna Suraj P. , Li Lianhe , Giles Davies A. , Linfield Edmund , Fatt Lim Dau , Seng Tan Chuan , Fung Yu Siu , Chun Liu Hui , Jie Wang Qi
Published: January 2013

We demonstrate single-mode surface-emitting terahertz frequency quantum cascade lasers utilising non-uniform second-order distributed feedback concentric-circular-gratings. The grating is designed for single-mode operation and surface emission for efficient and directional optical power out-coupling. The devices exhibit single-mode operation over the entire dynamic range with a side-mode-suppression-ratio of around 30 dB at 78 K, and a six-fold rotationally symmetric far-field pattern. In addition, the devices show a peak output power approximately three times higher than in ridge-waveguide lasers of similar size, whilst maintaining similar threshold current densities for the 3.8 THz emission and without remarkably sacrificing the maximum temperature operation performance. Owing to the high symmetry of the structure and the broad area light emission from surface, the devices are potentially very suitable for use as single-mode, high power emitters for integration into two-dimensional laser arrays.
Optical identification of oxygen vacancy types in SnO2 nanocrystals
Authors: Liu L. Z. , Xu J. Q. , Wu X. L. , Li T. H. , Shen J. C. , Chu Paul K.
Published: January 2013

The oxygen vacancies in spherical and cuboid SnO2 nanocrystals prepared by hydrothermal and laser ablation methods are investigated optically. Three oxygen-vacancy-related photoluminescence peaks at ∼430, ∼501, and ∼618 nm are observed, and Raman scattering and density functional calculation disclose that they originate from in-plane, sub-bridging, and bridging oxygen vacancies, respectively. This work reveals that the photoluminescence peaks together with the Raman modes can be used to identify the oxygen vacancy types in SnO2 nanostructures.
Edge-induced flattening in the fabrication of ultrathin freestanding crystalline silicon sheets
Authors: Gopalakrishnan Gokul , Czaplewski David A. , McElhinny Kyle M. , Holt Martin V. , Silva-Martínez Juan C. , Evans Paul G.
Published: January 2013

Silicon nanomembranes are suspended single-crystal sheets of silicon, tens of nanometers thick, with areas in the thousands of square micrometers. Challenges in fabrication arise from buckling due to strains of over 10−3 in the silicon-on-insulator starting material. In equilibrium, the distortion is distributed across the entire membrane, minimizing the elastic energy with a large radius of curvature. We show that flat nanomembranes can be created using an elastically metastable configuration driven by the silicon-water surface energy. Membranes as thin as 6 nm are fabricated with vertical deviations below 10 nm in a central 100 μm × 100 μm area.
Effect of embedding nanoparticles on the lattice thermal conductivity of bulk semiconductor crystals
Authors: Ezzahri Younès , Joulain Karl
Published: January 2013

We analyze the effect of embedding semiconductor nanoparticles as extrinsic phonon scattering centers on the steady-state κ(0) and dynamical κ(Ω) behaviors of the lattice thermal conductivity of bulk semiconductor (SC) alloy crystals. As an example, we consider the case of Ge nanoparticles embedded in a Si0.7Ge0.3 alloy crystal host matrix. The analysis includes the study of the effect of changing the size and concentration of the nanoparticles in combination with changing the ambient temperature while all other intrinsic properties of the SC alloy crystal host matrix are kept constant. Our calculations confirm the existence of an optimal nanoparticles size that minimizes κ(0). Depending on the ambient temperature, the optimal size either increases or decreases as a function of the nanoparticles concentration. Our calculations show also the cut-off frequency fC of κ(Ω) to be very sensitive to the size and concentration of the embedded nanoparticles. For a fixed ambient temperature and nanoparticles concentration, fC manifests a very interesting behavior as a function of the nanoparticles size. While embedding nanoparticles in SC alloy matrices reduces the steady-state κ(0), it however tends to increase fC of the dynamical κ(Ω) in comparison with intrinsic SC alloys. The study sheds light also on the fundamental role that normal processes have in treating phonon heat transfer phenomenon.
Neurophysiological Studies May Provide a Misleading Picture of How Perceptual-Motor Interactions are Coordinated
Authors: Mann David , Dicks Matt , Cañal-Bruland Rouwen , Van Der Kamp John
Published: January 2013

Neurophysiological measurement techniques like fMRI and TMS are increasingly being used to examine the perceptual-motor processes underpinning the ability to anticipate the actions of others. Crucially, these techniques invariably restrict the experimental task that can be used and consequently limit the degree to which the findings can be generalised. These limitations are discussed based on a recent paper by Tomeo et al. (2012) who sought to examine responses to fooling actions by using TMS on participants who passively observed spliced video clips where bodily information was, and was not, linked to the action outcome. We outline two particular concerns with this approach. First, spliced video clips that show physically impossible actions are unlikely to simulate a “fooling” action. Second, it is difficult to make meaningful inferences about perceptual-motor expertise from experiments where participants cannot move. Taken together, we argue that wider generalisations based on these findings may provide a misunderstanding of the phenomenon such a study is designed to explore.
Impaired epithelial differentiation of induced pluripotent stem cells from ectodermal dysplasia-related patients is rescued by the small compound APR-246/PRIMA-1
MET
Authors: Shalom-Feuerstein Ruby , Serror Laura , Aberdam Edith , Müller Franz-Josef , van Bokhoven Hans , Wiman Klas G. , Zhou Huiqing , Aberdam Daniel , Petit Isabelle
Published: January 2013

Ectodermal dysplasia is a group of congenital syndromes affecting a variety of ectodermal derivatives. Among them, ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome is caused by single point mutations in the
p63
gene, which controls epidermal development and homeostasis. Phenotypic defects of the EEC syndrome include skin defects and limbal stem-cell deficiency. In this study, we designed a unique cellular model that recapitulated major embryonic defects related to EEC. Fibroblasts from healthy donors and EEC patients carrying two different point mutations in the DNA binding domain of p63 were reprogrammed into induced pluripotent stem cell (iPSC) lines. EEC-iPSC from both patients showed early ectodermal commitment into K18
+
cells but failed to further differentiate into K14
+
cells (epidermis/limbus) or K3/K12
+
cells (corneal epithelium). APR-246 (PRIMA-1
MET
), a small compound that restores functionality of mutant p53 in human tumor cells, could revert corneal epithelial lineage commitment and reinstate a normal p63-related signaling pathway. This study illustrates the relevance of iPSC for p63 related disorders and paves the way for future therapy of EEC.
APR-246/PRIMA-1
MET
rescues epidermal differentiation in skin keratinocytes derived from EEC syndrome patients with
p63
mutations
Authors: Shen Jinfeng , van den Bogaard Ellen H. , Kouwenhoven Evelyn N. , Bykov Vladimir J. N. , Rinne Tuula , Zhang Qiang , Tjabringa Geuranne S. , Gilissen Christian , van Heeringen Simon J. , Schalkwijk Joost , van Bokhoven Hans , Wiman Klas G. , Zhou Huiqing
Published: January 2013

p53 and p63 share extensive sequence and structure homology.
p53
is frequently mutated in cancer, whereas mutations in
p63
cause developmental disorders manifested in ectodermal dysplasia, limb defects, and orofacial clefting. We have established primary adult skin keratinocytes from ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome patients with
p63
mutations as an in vitro human model to study the disease mechanism in the skin of EEC patients. We show that these patient keratinocytes cultured either in submerged 2D cultures or in 3D skin equivalents have impaired epidermal differentiation and stratification. Treatment of these patient keratinocytes with the mutant p53-targeting compound APR-246/PRIMA-1
MET
(p53 reactivation and induction of massive apoptosis) that has been successfully tested in a phase I/II clinical trial in cancer patients partially but consistently rescued morphological features and gene expression during epidermal stratification in both 2D and 3D models. This rescue coincides with restoration of p63 target-gene expression. Our data show that EEC patient keratinocytes with p63 mutations can be used for characterization of the abnormal molecular circuitry in patient skin and may open possibilities for the design of novel pharmacological treatment strategies for patients with mutant
p63
-associated developmental abnormalities.
Otolith Microstructure during the Early Life-History Stages of Brown Trout: Validation and Interpretation
Authors: Dodson Julian J. , Sirois Pascal , Daigle Gaétan , Gaudin Philippe , Bardonnet Agnès
Published: January 2013

We examined the extent to which otolith microstructure provides an accurate estimate of age, growth, and early life history transitions during the period between hatching and 1 week after emergence in Brown Trout Salmo trutta exposed to natural variations in ambient water temperature. All fry analyzed possessed a prominent check on the observed date of hatching. After hatching, daily growth increments were visible on sagittal otoliths. There was no evidence for the formation of an emergence check mark and no statistically significant evidence that emergence and daily temperature fluctuations interacted to form check marks. However, daily temperature fluctuations may influence the formation of check marks, largely based on an observed increase in the proportion of fish possessing checks on the days following the two largest temperature fluctuations observed during the experiment. There was no evidence that feeding or stressing emergent fish contributed to the formation of an emergence check mark. The observed proportionality of somatic and otolith growth in conjunction with daily growth increments and the formation of a prominent hatch mark provides the opportunity to back-calculate somatic length distributions and to document the hatching, dispersal, growth, and survival of the early life history stages of Brown Trout in nature.

Received May 3, 2012; accepted October 29, 2012
Cigarette Smoking and Measures of Impulsivity in a College Sample
Authors: Balevich Emily C. , Wein Naftali D. , Flory Janine D.
Published: January 2013

Background

An association between impulsivity and smoking has been consistently reported in the literature, but few studies have examined how distinct dimensions of impulsivity may relate differentially to smoking initiation versus persistent smoking. The aim of the current study was to examine the relationship between self-report and behavioral measures of impulsivity and smoking status in college students.

Methods

Participants ( N = 243) completed a self-report history of tobacco use, 2 self-report measures of impulsivity (the Barratt Impulsiveness Scale and Zuckerman Sensation-Seeking Scale), and 2 behavioral measures (the Delay Discounting Task and Iowa Gambling Task). All participants were classified as never-smokers, triers, or smokers based on their smoking history, and between-group differences on the 4 measures were examined.

Results

On the self-report measures, all 3 groups differed on sensation seeking, with the never-smokers reporting the lowest levels and the smokers reporting the highest. Furthermore, the smokers reported significantly higher disinhibitory impulsivity than the triers and never-smokers. The groups did not differ on the behavioral measures.

Conclusions

These results indicate that distinct dimensions of impulsivity characterize different smoking phenotypes. In particular, sensation seeking is associated with the initiation of smoking, whereas disinhibitory impulsivity is associated with the transition to more persistent and regular use of cigarettes.
Grappling with the Legacy of Modernity: Implications for the Sociology of Religion
Authors: Vásquez Manuel A.
Published: January 2013

This chapter shows how taken-for-granted assumptions about modernity are embedded in our understandings of religion, and what we learn about religion and modernity by bringing those taken-for-granted assumptions to the fore. After excavating the modernist biases that have vitiated the social sciences' approach to religion, it concludes by presenting a more embedded, relational, embodied, and polyvalent understanding of subjectivity that can help reorient the sociology of religion along more fruitful lines.
Graphlet-based measures are suitable for biological network comparison
Authors: Hayes Wayne , Sun Kai , Pržulj Nataša
Published: January 2013

Motivation: Large amounts of biological network data exist for many species. Analogous to sequence comparison, network comparison aims to provide biological insight. Graphlet-based methods are proving to be useful in this respect. Recently some doubt has arisen concerning the applicability of graphlet-based measures to low edge density networks—in particular that the methods are ‘unstable’—and further that no existing network model matches the structure found in real biological networks.

Results: We demonstrate that it is the model networks themselves that are ‘unstable’ at low edge density and that graphlet-based measures correctly reflect this instability. Furthermore, while model network topology is unstable at low edge density, biological network topology is stable. In particular, one must distinguish between average density and local density. While model networks of low average edge densities also have low local edge density, that is not the case with protein–protein interaction (PPI) networks: real PPI networks have low average edge density, but high local edge densities, and hence, they (and thus graphlet-based measures) are stable on these networks. Finally, we use a recently devised non-parametric statistical test to demonstrate that PPI networks of many species are well-fit by several models not previously tested. In addition, we model several viral PPI networks for the first time and demonstrate an exceptionally good fit between the data and theoretical models.

Contact: natasha@imperial.ac.uk
Bellman’s GAP—a language and compiler for dynamic programming in sequence analysis
Authors: Sauthoff Georg , Möhl Mathias , Janssen Stefan , Giegerich Robert
Published: January 2013

Motivation: Dynamic programming is ubiquitous in bioinformatics. Developing and implementing non-trivial dynamic programming algorithms is often error prone and tedious. Bellman’s GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique.

Results: In Bellman’s GAP, dynamic programming algorithms are described in a declarative style by tree grammars, evaluation algebras and products formed thereof. This bypasses the design of explicit dynamic programming recurrences and yields programs that are free of subscript errors, modular and easy to modify. The declarative modules are compiled into C++ code that is competitive to carefully hand-crafted implementations.

This article introduces the Bellman’s GAP system and its language, GAP-L. It then demonstrates the ease of development and the degree of re-use by creating variants of two common bioinformatics algorithms. Finally, it evaluates Bellman’s GAP as an implementation platform of ‘real-world’ bioinformatics tools.

Availability: Bellman’s GAP is available under GPL license from http://bibiserv.cebitec.uni-bielefeld.de/bellmansgap. This Web site includes a repository of re-usable modules for RNA folding based on thermodynamics.

Contact:  robert@techfak.uni-bielefeld.de

Supplementary information:  Supplementary data are available at Bioinformatics online
Effect of oral digoxin in high‐risk heart failure patients: a pre‐specified subgroup analysis of the DIG trial
Authors: Gheorghiade Mihai , Patel Kanan , Filippatos Gerasimos , Anker Stefan D. , van Veldhuisen Dirk J. , Cleland John G.F. , Metra Marco , Aban Inmaculada B. , Greene Stephen J. , Adams Kirkwood F. , McMurray John J.V. , Ahmed Ali
Published: January 2013

Aims

In the Digitalis Investigation Group (DIG) trial, digoxin reduced mortality or hospitalization due to heart failure (HF) in several pre‐specified high‐risk subgroups of HF patients, but data on protocol‐specified 2‐year outcomes were not presented. In the current study, we examined the effect of digoxin on HF death or HF hospitalization and all‐cause death or all‐cause hospitalization in high‐risk subgroups during the protocol‐specified 2 years of post‐randomization follow‐up.

Methods and results

In the DIG trial, 6800 ambulatory patients with chronic HF, normal sinus rhythm, and LVEF ≤45% (mean age 64 years, 26% women, 17% non‐whites) were randomized to receive digoxin or placebo. The three high‐risk groups were defined as NYHA class III–IV symptoms (n = 2223), LVEF <25% (n = 2256), and cardiothoracic ratio (CTR) >55% (n = 2345). In all three high‐risk subgroups, compared with patients in the placebo group, those in the digoxin group had a significant reduction in the risk of the 2‐year composite endpoint of HF mortality or HF hospitalization: NYHA III–IV [hazard ratio (HR) 0.65; 95% confidence interval (CI) 0.57–0.75; P < 0.001], LVEF <25% (HR 0.61; 95% CI 0.53–0.71; P < 0.001), and CTR >55% (HR 0.65; 95% CI 0.57–0.75; P < 0.001). Digoxin‐associated HRs (95% CI) for 2‐year all‐cause mortality or all‐cause hospitalization for subgroups with NYHA III–IV, LVEF <25%, and CTR >55% were 0.88 (0.80–0.97; P = 0.012), 0.84 (0.76–0.93; P = 0.001), and 0.85 (0.77–0.94; P = 0.002), respectively.

Conclusions

Digoxin improves outcomes in chronic HF patients with NYHA class III–IV, LVEF <25%, or CTR >55%, and should be considered in these patients.
Two decades of annual landed and discarded catches of three southern Gulf of St Lawrence skate species estimated under multiple sources of uncertainty
Authors: Benoît Hugues P.
Published: January 2013

Benoît, H. P. 2013. Two decades of annual landed and discarded catches of three southern Gulf of St Lawrence skate species estimated under multiple sources of uncertainty. – ICES Journal of Marine Science, 70: 554–563. Estimating fishery impacts on commercially unimportant species is often hindered by limited and possibly biased data for landed and discarded catch, and poor information on discard mortality. The three skate (family Rajidae) species occurring in southern Gulf of St Lawrence (Canada) exemplify this problem. Assessing the contribution of fishing to important declines in their adult abundance has been complicated by catch data that are not disaggregated by species, concerns about the reliability of discard amounts estimated from fisheries observer surveys, and unknown discard mortality rates. An approach is presented for producing annual estimates of landed and discarded catch, as well as discard mortality rates, for the three species for the period 1991–2011. The approach used data from landing statistics and from observer surveys, and models for disaggregating mixed fishery catches into their constituent species and for estimating minimum discard mortalities. Bootstrapping was used to propagate errors associated with different components of the estimation process. The estimation was partly validated by comparing recorded landings with landings estimated from fisheries observer surveys. This paper demonstrates how multiple sources of uncertainty in discard loss estimation can be addressed by dividing the estimation process into linked components that can be individually addressed and ideally validated.
Treatment with Carbon Monoxide-releasing Molecules and an HO-1 Inducer Enhances the Effects and Expression of µ-Opioid Receptors during Neuropathic Pain
Authors: Hervera Arnau , Leánez Sergi , Motterlini Roberto , Pol Olga
Published: January 2013

Background:

The administration of µ-opioid receptors (MOR) and δ-opioid receptors (DOR) as well as cannabinoid-2 receptor (CB2R) agonists attenuates neuropathic pain. We investigated if treatment with two carbon monoxide-releasing molecules (CORM-2 and CORM-3) or an inducible heme oxygenase inducer (cobalt protoporphyrin IX, CoPP) could modulate the local and systemic effects and expression of MOR, DOR, and CB2R during neuropathic pain.

Methods:

In C57BL/6 mice, at 10 days after the chronic constriction of sciatic nerve, we evaluated the effects of the intraperitoneal administration of 10 mg/kg of CORM-2, CORM-3, or CoPP on the antiallodynic and antihyperalgesic actions of a locally or systemically administered MOR (morphine), DOR ([d-Pen(2),d-Pen(5)]-enkephalin) or CB2R ((2-methyl-1-propyl-1H-indol-3-yl)-1-naphthalenylmethanone ) agonist. The effects of CORM-2 and CoPP treatments on the expression of MOR, DOR, CB2R, inducible and constitutive heme oxygenases, microglia activation marker (CD11b/c), and neuronal and inducible nitric oxide synthases were also assessed.

Results:

Treatments with CO-RMs and CoPP reduced the mechanical and thermal hypersensitivity induced by sciatic nerve injury, increased the local, but not systemic, antinociceptive effects of morphine, and decreased those produced by DPDPE and JWH-015. Both CORM-2 and CoPP treatments enhanced MOR and inducible heme oxygenase expression, unaltered DOR and constitutive heme oxygenase expression, and decreased the overexpression of CB2R, CD11b/c, and neuronal and inducible nitric oxide synthases induced by sciatic nerve injury.

Conclusions:

This study shows that CO-RMs and CoPP treatments increase the local antinociceptive effects of morphine through enhancing MOR peripheral expression and inhibiting spinal microglial activation and overexpression of neuronal/inducible nitric oxide synthases.
Paenisporosarcina

indica sp. nov., a psychrophilic bacterium from a glacier, and reclassification of

Sporosarcina antarctica

Yu et al., 2008 as

Paenisporosarcina

antarctica comb. nov. and emended description of the genus

Paenisporosarcina
Authors: Reddy G. S. N. , Manasa B. Poorna , Singh Sanjay K. , Shivaji S.
Published: January 2013

A Gram-stain-positive, aerobic, spore-forming, rod-shaped bacterium, PN2T, was isolated from a soil sample collected near the Pindari glacier. It contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7c alcohol as the predominant fatty acids, MK-7 as the major menaquinone and A4α type (l-Lys–d-Glu) peptidoglycan. Based on these characteristics, strain PN2T was assigned to the genus

Paenisporosarcina

. Phylogenetic analysis based on 16S rRNA gene sequence placed strain PN2T within the genus

Paenisporosarcina

and showed a sequence similarity of 98.5–99.0 % with members of this genus.

Paenisporosarcina macmurdoensis

CMS 21wT,

Paenisporosarcina quisquiliarum

SK 55T and

Sporosarcina antarctica

N-05T were identified as the most closely related species with 16S rRNA gene sequence similarities of 98.6 %, 99.0 % and 98.4 %, respectively. The values for DNA–DNA relatedness between strain PN2T and

P. macmurdoensis

,

P. quisquiliarum

and

S. antarctica

were below the 70 % threshold value (32.0 %, 42.0 % and 38.0 % respectively). In addition, strain PN2T exhibited a number of phenotypic differences from

P. macmurdoensis

,

P. quisquiliarum

and

S. antarctica

. Based on the cumulative differences, strain PN2T was identified as representing a novel species and the name

Paenisporosarcina

indica sp. nov. was proposed. The type strain of

Paenisporosarcina

indica sp. nov. is PN2T (LMG 23933T = JCM 15114T). Furthermore, based on the morphological and chemotaxonomic characteristics, the species

Sporosarcina antarctica

was reclassified as a species of the genus

Paenisporosarcina

and renamed

Paenisporosarcina

antarctica comb. nov. In addition, an emended description of the genus

Paenisporosarcina

is presented.
Martelella

endophytica sp. nov., an antifungal bacterium associated with a halophyte
Authors: Bibi Fehmida , Chung Eu Jin , Khan Ajmal , Jeon Che Ok , Chung Young Ryun
Published: January 2013

A Gram-staining-negative, non-spore-forming endophytic bacterium, designated strain YC6887T, was isolated from a root sample of a halophyte, Rosa rugosa, collected from a tidal flat area of Namhae Island, located at the southern end of Korea. Strain YC6887T was found to exhibit inhibitory activity against oomycete plant pathogens. The cells were non-motile and aerobic rods. The strain was able to grow at 4–40 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0–8.5). Strain YC6887T was able to grow at NaCl concentrations of 0–9 % (w/v) with optimum growth at 4–5 % (w/v) NaCl, but NaCl is not essential for growth. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus

Martelella

, a member of order

Rhizobiales

, exhibiting highest similarity with

Martelella mediterranea

(98.6 %). The DNA–DNA relatedness between strain YC6887T and

M. mediterranea

MACL11T was 19.8±6.8. Chemotaxonomically, strain YC6887T contained C19 : 0 cyclo ω8c (28.0 %) and C18 : 1ω7c (17.9 %) as predominant fatty acids, confirming the affiliation of strain YC6887T with the genus

Martelella

. The major respiratory quinone was Q-10 and the DNA G+C content was 62.1 mol%. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA–DNA hybridization data, strain YC6887T should be classified as representing a novel species of the genus

Martelella

, for which the name

Martelella

endophytica sp. nov. is proposed. The type strain is YC6887T ( = KCCM 43011T = NBRC 109149T).
Moniliella byzovii sp. nov., a chlamydospore-forming black yeast isolated from flowers
Authors: Thanh Vu Nguyen , Hien Dinh Duc , Thom Tran Thi
Published: January 2013

Yeasts of the genus Moniliella were isolated from 651 flower samples collected in Vietnam, using an enrichment medium containing 50 % glucose. Species of the genus Moniliella were found in 5 % of the samples and 54 strains were isolated. The strains were identified based on D1/D2 LSU rRNA gene sequences as M. megachiliensis (15 strains), M. dehoogii (14 strains), and M. mellis (2 strains). The remaining 23 strains could not be reliably placed under any known species. Among them, 12 strains isolated from flowers of Ipomoea pes-caprae and Calotropis gigantea were peculiar for the intensive formation of chlamydospores. These strains could be subdivided into pigmented and non-pigmented groups. Both groups were identical in PCR fingerprints generated with primer (GAC)5 and in D1/D2 and ITS sequences. The yeast was closely related to M. fonsecae but differed from the latter by 52 nt (or 10.3 % of divergence) in the D1/D2 sequence and 71 nt (or 16.9 % of divergence) in the ITS sequence. The name Moniliella byzovii sp. nov. is proposed for this novel species. The type strain is TBY 2041.7T = CBS 12757T = NRRL Y-63661T. The MycoBank number is MB 803186.
Isolation and characterization of Pigmentiphaga-like isolates from human clinical material
Authors: Bridger Natalie , Drews Steven , Burdz Tamara , Wiebe Deborah , Pacheco Ana Luisa , Ng Betty , Bernard Kathryn
Published: January 2013

Species in the genus Pigmentiphaga are Gram-negative, catalase- and oxidase-positive rods derived exclusively to date from environmental sources. Features of strains most like Pigmentiphaga
daeguensis or Pigmentiphaga kullae from a case of suppurative otitis media in a 6-year-old female post-transplant recipient and in a human stool sample are described.