bluuebunny/crossref_metadata_2025 huggingface dataset:
Laminar streaks with spanwise wall forcing
Authors: Ricco Pierre
Published: June 2011

The influence of steady sinusoidal oscillations of spanwise wall velocity on the Klebanoff modes, i.e. unsteady streaky fluctuations induced by free-stream turbulence in the pre-transitional Blasius boundary layer, is investigated numerically. The wall motion induces a spanwise boundary layer which grows downstream as x1/6 and has an asymptotic analytical solution at large downstream distances. While the forcing has no effect on the initial growth of the streaks, their intensity eventually increases or decreases substantially depending on the relative magnitude between the forcing wavelength and the characteristic length scales of the streaks. The wall actuation enhances the streak intensity if the streak spanwise length scale is much larger than the Blasius boundary layer thickness. The streak energy is instead attenuated when the spanwise viscous diffusion effects play a key role. Wall pressure fluctuations may also be significantly damped in this case. The Klebanoff modes generated by full-spectrum free-stream turbulence are predicted to be attenuated by the wall motion. The asymptotic scaling analysis reveals that there exists an optimal forcing wavelength for full-spectrum streak attenuation as long as the spanwise length scales of the dominant streaks are as large as or smaller than the Blasius boundary layer thickness, a common scenario encountered in experiments. The optimal forcing wavelength is found to be comparable with the streak streamwise length scale. As the amplitude of the wall forcing increases, the reduction of streak intensity grows monotonically. The streaks are completely suppressed in the limit of large amplitude.
Geometrical effects on spin injection: 3D spin drift diffusion model
Authors: Thingna Juzar , Wang Jian-Sheng
Published: June 2011

We discuss a three-dimensional (3D) spin drift diffusion (SDD) model to inject spin from a ferromagnet (FM) to a normal metal (N) or semiconductor (SC). Using this model we investigate the problem of spin injection into isotropic materials like GaAs and study the effect of FM contact area and SC thickness on spin injection. We find that in order to achieve detectable spin injection a small contact area or thick SC samples are essential for direct contact spin injection devices. We investigate the use of thin metal films (Cu) proposed by Kumar et al. [Appl. Phys. Lett. 91, 142110 (2007)] and show that they are an excellent substitute for tunneling barriers (TB) in the regime of small contact area. Since most tunneling barriers are prone to pinhole defects, we study the effect of pinholes in AlO tunneling barriers and show that the reduction in the spin-injection ratio (γ) is solely due to the effective area of the pinholes and there is no correlation between the number of pinholes and the spin-injection ratio.
Abnormal temperature dependent photoluminescence of excited states of InAs/GaAs quantum dots: Carrier exchange between excited states and ground states
Authors: Zhou X. L. , Chen Y. H. , Ye X. L. , Xu Bo , Wang Z. G.
Published: June 2011

This paper presents detailed studies on the temperature dependent photoluminescence (PL) of excited states (ES) of self-assembled InAs/GaAs quantum dots. Two abnormal temperature dependent characteristics of ES have been observed: first is the strong broadening of PL linewidth with increasing temperature from 15 to 300 K. Second, the intensity ratio of ES to ground states (GS) increases with raising temperature under all measured excitation powers. Such peculiarities could be well explained by the thermal carrier exchange between GS and ES. Taking into account the GS-ES carrier exchange, an improved carrier equation model is adopted to describe the temperature dependence of intensity ratio of ES to GS. The temperature dependent carrier population of ES is further discussed based on the simulation results.
Dark current mechanisms in quantum dot laser structures
Authors: Hasbullah N. F. , David J. P. R. , Mowbray D. J.
Published: June 2011

Current-voltage measurements have been performed on InAs/InGaAs/GaAs quantum dot structures with varying growth and design parameters. These measurements show that the forward and reverse bias dark currents decrease with increasing spacer growth temperature, however, they are relatively insensitive to the number of periods of the quantum dot layers. Temperature dependent current-voltage measurements show that the mechanism that governs the reverse bias leakage current is due to generation-recombination via mid-band traps assisted by the Frenkel-Poole emission of carriers from these traps.
Edge plasma boundary layer generated by kink modes in tokamaks
Authors: Zakharov Leonid E.
Published: June 2011

This paper describes the structure of the electric current generated by external wall touching and free boundary kink modes at the plasma edge using the ideally conducting plasma model. Both kinds of modes generate δ-functional surface current at the plasma edge. Free boundary kink modes also perturb the core plasma current, which in the plasma edge compensates the difference between the δ-functional surface currents of free boundary and wall touching kink modes. In addition, the resolution of an apparent paradox with the pressure balance across the plasma boundary in the presence of the surface currents is provided.
Minority-carrier diffusion length, minority-carrier lifetime, and photoresponsivity of β-FeSi2 layers grown by molecular-beam epitaxy
Authors: Akutsu Keiichi , Kawakami Hideki , Suzuno Mitsushi , Yaguchi Takashi , Jiptner Karolin , Chen Jun , Sekiguchi Takashi , Ootsuka Teruhisa , Suemasu Takashi
Published: June 2011

We have epitaxially grown undoped β-FeSi2 films on Si(111) substrates via atomic-hydrogen-assisted molecular-beam epitaxy. β-FeSi2 films grown without atomic hydrogen exhibited p-type conduction with a hole density of over 1019 cm−3 at room temperature (RT). In contrast, those prepared with atomic hydrogen showed n-type conduction and had a residual electron density that was more than two orders of magnitude lower than the hole density of films grown without atomic hydrogen (of the order of 1016 cm−3 at RT). The minority-carrier diffusion length was estimated to be approximately 16 μm using an electron-beam-induced current technique; this value is twice as large as that for β-FeSi2 prepared without atomic hydrogen. This result could be well explained in terms of the minority-carrier lifetimes measured by a microwave photoconductance decay technique. The 1/e decay time using a 904 nm laser pulse was approximately 17 μs, which is much longer than that for β-FeSi2 prepared without atomic hydrogen (3 μs). The photoresponsivity reached 13 mA/W at 1.31 μm, which is the highest value ever reported for β-FeSi2 films.
Interfacial nanolayers and permittivity of ferroelectric superlattices
Authors: Pertsev N. A. , Tyunina M.
Published: June 2011

In ferroelectric superlattices (SLs), the short-range interactions and intermixing between contacting dissimilar materials can lead to the formation of interfacial nanolayers with physical properties different from those of both constituents. We demonstrate theoretically that such nanolayers can give rise to a sizable dependence of the SL permittivity on the period even in the paraelectric regime. The results of dielectric measurements performed for coherent Ba0.8Sr0.2TiO3–Ba0.4Sr0.6TiO3 SLs are qualitatively consistent with the theoretical predictions. At the same time, the experimental data indicate that other factors also contribute to the variation of the permittivity with the period in ferroelectric superlattices and multilayers.
Electronic structure and transport properties of single and double filled CoSb3 with atoms Ba, Yb and In
Authors: Zhou An , Liu Lisheng , Zhai Pengcheng , Zhao Wenyu , Zhang Qingjie
Published: June 2011

We report an investigation of the electronic structures and electrical transport properties of the single-filled and double-filled CoSb3 skutterudites with Ba, Yb and In atoms by density functional calculations and Boltzmann transport theory. The band structure and the density of states of single and double filled CoSb3 are calculated and discussed. Based on the results of the band structure, the temperature dependence of Seebeck coefficients, the electrical conductivity, the power factor and the carrier concentration are computed, which are generally in good agreement with the experimental data. The results indicate that the combination of (Ba, In) could greatly improve the thermoelectric properties while the combination of (In, Yb) and (Ba, Yb) would have negative effect on the power factors, due to the fact that the interaction of Yb atoms with CoSb3 would result in a reduction of the electron mobility.
Femtosecond broadband fluorescence upconversion spectroscopy: Improved setup and photometric correction
Authors: Zhang X.-X. , Würth C. , Zhao L. , Resch-Genger U. , Ernsting N. P. , Sajadi M.
Published: June 2011

A setup for fluorescence upconversion spectroscopy (FLUPS) is described which has 80 fs temporal response (fwhm) for emission in the spectral range 425–750 nm. Broadband phase matching is achieved with tilted gate pulses at 1340 nm. Background from harmonics of the gate pulse is removed and sensitivity increased compared to previous designs. Photometric calibration of the upconversion process is performed with a set of fluorescent dyes. For Coumarin 153 in methanol the peak position, bandwidth, and asymmetry depending on delay time are reported.
Polarization switching and discharging behaviors in serially connected ferroelectric Pt/Pb(Zr,Ti)O3/Pt and paraelectric capacitors
Authors: Lee Hyun Ju , Park Min Hyuk , Kim Gun Hwan , Seok Jun Yeong , Kim Yu Jin , Hwang Cheol Seong , Jiang An Quan
Published: June 2011

The polarization switching behavior in serially connected ferroelectric Pt/Pb(Zr,Ti)O3/Pt and paraelectric capacitors with various capacitances was examined using transient switching current measurements. Provided that a high enough voltage to switch the ferroelectric capacitor was applied to the series capacitor, stable polarization switching was maintained before the applied voltage approached zero, irrespective of the capacitance of the paraelectric capacitor. For the series capacitor containing a small paraelectric capacitance, the voltage across the paraelectric capacitor was much higher than the coercive voltage of the PZT capacitor, which acted as a field depolarizing PZT capacitor resulting in back-switching when the applied voltage was removed. In contrast, no back-switching occurred in the series capacitor containing a sufficiently large paraelectric capacitance because the voltage across the paraelectric capacitor was smaller than the coercive voltage of the ferroelectric capacitor. The effects of the measurement set-up and their implications for various suggested applications are also discussed in detail. This result improves the understanding on the role of passive interfacial layers in metal-ferroelectric-metal capacitors.
The onset of double diffusive reaction-convection in an anisotropic porous layer
Authors: Malashetty M. S. , Biradar Bharati S.
Published: June 2011

The onset of double diffusive reaction-convection in a horizontal anisotropic porous layer saturated with binary mixture, which is heated and salted from below and subjected to chemical equilibrium on the boundaries, is studied analytically using both linear and nonlinear stability analyses. A linear stability analysis is performed to investigate how the dissolution or precipitation of reactive component affects the onset of convection. The Darcy model is employed as momentum equation. The effect of mechanical and thermal anisotropy parameters, reaction rate, Lewis number, solute Rayleigh number, and normalized porosity on the stability of the system is investigated. We find that the chemical reaction may be stabilizing or destabilizing and that the anisotropic parameters have significant influence on the stability criterion. The effect of various parameters on the stationary, oscillatory, and finite amplitude convection is shown graphically. A weak nonlinear theory based on the truncated representation of Fourier series method is used to find the finite amplitude Rayleigh number and heat and mass transfer.
Self-sustained processes in the logarithmic layer of turbulent channel flows
Authors: Hwang Yongyun , Cossu Carlo
Published: June 2011

It has recently been shown that large-scale and very-large-scale motions can self-sustain in turbulent channel flows even in the absence of input from motions at smaller scales. Here we show that also motions at intermediate scales, mainly located in the logarithmic layer, survive when motions at smaller scales are artificially quenched. These elementary self-sustained motions involve the bursting and regeneration of sinuous streaks. This is a further indication that a full range of autonomous self-sustained processes exists in turbulent channel flows with scales ranging from those of the buffer layer streaks to those of the large scale motions in the outer layer.
Statistical thermodynamics of fluids with both dipole and quadrupole moments
Authors: Benavides Ana L. , García Delgado Francisco J. , Gámez Francisco , Lago Santiago , Garzón Benito
Published: June 2011

New Gibbs ensemble simulation data for a polar fluid modeled by a square-well potential plus dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions are presented. This simulation data is used in order to assess the applicability of the multipolar square-well perturbation theory [A. L. Benavides, Y. Guevara, and F. del Río, Physica A 202, 420 (1994)10.1016/0378-4371(94)90469-3] to systems where more than one term in the multipole expansion is relevant. It is found that this theory is able to reproduce qualitatively well the vapor-liquid phase diagram for different multipolar moment strengths, corresponding to typical values of real molecules, except in the critical region. Hence, this theory is used to model the behavior of substances with multiple chemical bonds such as carbon monoxide and nitrous oxide and we found that with a suitable choice of the values of the intermolecular parameters, the vapor-liquid equilibrium of these species is adequately estimated.
Spectromicroscopy of tantalum oxide memristors
Authors: Strachan John Paul , Medeiros-Ribeiro Gilberto , Yang J. Joshua , Zhang M.-X. , Miao Feng , Goldfarb Ilan , Holt Martin , Rose Volker , Williams R. Stanley
Published: June 2011

We report experiments to measure material changes in tantalum oxide-based memristive devices. The high endurance and low power demonstrated in this material system suggests a unique mechanism for the switching, which we investigated using x-ray based spectromicroscopy and nanospectroscopy. Our study nondestructively identified a localized (<150nm diameter) Ta-rich phase surrounded by nano- or polycrystalline Ta2O5.
Linewidth roughness in nanowire-mask-based graphene nanoribbons
Authors: Xu Guangyu , Torres Carlos M. , Bai Jingwei , Tang Jianshi , Yu Tao , Huang Yu , Duan Xiangfeng , Zhang Yuegang , Wang Kang L.
Published: June 2011

We present the analysis of linewidth roughness (LWR) in nanowire-mask-based graphene nanoribbons (GNRs) and evaluate its impact on the device performance. The data show that the LWR amplitude decreases with the GNR width, possibly due to the etching undercut near the edge of a nanowire-mask. We further discuss the large variation in GNR devices in the presence of LWR by analyzing the measured transport properties and on/off ratios.
Mach 5 bow shock control by a nanosecond pulse surface dielectric barrier discharge
Authors: Nishihara M. , Takashima K. , Rich J. W. , Adamovich I. V.
Published: June 2011

Bow shock perturbations in a Mach 5 air flow, produced by low-temperature, nanosecond pulse, and surface dielectric barrier discharge (DBD), are detected by phase-locked schlieren imaging. A diffuse nanosecond pulse discharge is generated in a DBD plasma actuator on a surface of a cylinder model placed in air flow in a small scale blow-down supersonic wind tunnel. Discharge energy coupled to the actuator is 7.3–7.8 mJ/pulse. Plasma temperature inferred from nitrogen emission spectra is a few tens of degrees higher than flow stagnation temperature, T = 340 ± 30 K. Phase-locked Schlieren images are used to detect compression waves generated by individual nanosecond discharge pulses near the actuator surface. The compression wave propagates upstream toward the baseline bow shock standing in front of the cylinder model. Interaction of the compression wave and the bow shock causes its displacement in the upstream direction, increasing shock stand-off distance by up to 25%. The compression wave speed behind the bow shock and the perturbed bow shock velocity are inferred from the Schlieren images. The effect of compression waves generated by nanosecond discharge pulses on shock stand-off distance is demonstrated in a single-pulse regime (at pulse repetition rates of a few hundred Hz) and in a quasi-continuous mode (using a two-pulse sequence at a pulse repetition rate of 100 kHz). The results demonstrate feasibility of hypersonic flow control by low-temperature, repetitive nanosecond pulse discharges.
Biaxially textured cobalt-doped BaFe2As2 films with high critical current density over 1 MA/cm2 on MgO-buffered metal-tape flexible substrates
Authors: Katase Takayoshi , Hiramatsu Hidenori , Matias Vladimir , Sheehan Chris , Ishimaru Yoshihiro , Kamiya Toshio , Tanabe Keiichi , Hosono Hideo
Published: June 2011

High critical current densities (Jc)>1 MA/cm2 were realized in cobalt-doped BaFe2As2 (BaFe2As2:Co) films on flexible metal substrates with biaxially textured MgO base-layers fabricated by an ion-beam assisted deposition technique. The BaFe2As2:Co films showed small in-plane crystalline misorientations (ΔϕBaFe2As2:Co) of ∼3° regardless of twice larger misorientations of the MgO base-layers (ΔϕMgO=7.3°), and exhibited high self-field Jc up to 3.5 MA/cm2 at 2 K. These values are comparable to that on MgO single crystals and the highest Jc among iron pnictide superconducting tapes and wires ever reported. High in-field Jc suggests the existence of c-axis correlated vortex pinning centers.
Ferroelectric properties and dynamic scaling of ⟨100⟩ oriented (K0.5Na0.5)NbO3 single crystals
Authors: Gupta Shashaank , Priya Shashank
Published: June 2011

In this letter, we report the dielectric and ferroelectric (FE) characteristics of potassium sodium niobate (K0.5Na0.5NbO3) single crystals grown by flux method. Orientation analysis of as-grown cubical-shaped crystals was conducted by electron backscattered diffraction technique revealing the ⟨100⟩ crystallographic orientation of two opposing major faces. Annealed crystals were found to exhibit FE orthorhombic to FE tetragonal transition temperature of 200 °C and Curie temperature of 407 °C. Poled ⟨100⟩ oriented crystals had longitudinal piezoelectric constant of 148 pC/N. Dielectric measurement as a function of temperature was conducted to determine the second order parameter in Gibbs free energy expansion. Dynamic hysteresis analysis on these crystals showed the power law relations to be of the form ⟨A⟩∝f0.47Eo−0.85Eo1.45f0.14 and ⟨A⟩∝f0.04Eo below and above the coercive field.
Origins of low resistivity in Al ion-implanted ZnO bulk single crystals
Authors: Oga T. , Izawa Y. , Kuriyama K. , Kushida K. , Kinomura A.
Published: June 2011

The origins of low resistivity in Al ion-implanted ZnO bulk single crystals are studied by combining Rutherford backscattering spectroscopy (RBS), nuclear reaction analysis (NRA), photoluminescence (PL), and Van der Pauw methods. The Al-ion implantation (peak concentration: 2.6 × 1020cm−3) into ZnO is performed using a multiple-step energy. The resistivity decreases from ∼104 Ω cm for un-implanted ZnO to 1.4 × 10−1 Ω cm for as-implanted, and reaches 6.0 × 10−4 Ω cm for samples annealed at 1000 °C. RBS and NRA measurements for as-implanted ZnO suggest the existence of the lattice displacement of Zn (Zni) and O (Oi), respectively. After annealing at 1000 °C, the Zni related defects remain and the Oi related defects disappear. The origin of the low resistivity in the as-implanted sample is attributed to the Zni (∼30 meV [Look et al., Phys. Rev. Lett. 82, 2552 (1999)]). In contrast, the origin of the low resistivity in the sample annealed at 1000 °C is assigned to both of the Zni related defects and the electrically activated Al donor. A new PL emission appears at around 3.32 eV after annealing at 1000 °C, suggesting electrically activated Al donors.
Secondary ions mass spectroscopy measurements of dopant impurities in highly stressed InGaN laser diodes
Authors: Marona L. , Perlin P. , Czernecki R. , Leszczyński M. , Boćkowski M. , Jakiela R. , Suski T. , Najda S. P.
Published: June 2011

We performed a systematic secondary ions mass spectroscopy (SIMS) study of dopant impurities in life-time stressed InGaN laser devices in order to investigate the main degradation mechanism that is observed in nitride laser diodes. A continuous wave (cw) current density of 3 kA/cm2 was applied to InGaN laser diodes over an extended period of time and we observed the characteristic square root degradation of optical power. We compared the SIMS profiles of Mg, H, and Si impurities in the aged devices and observe that the impurities are remarkably stable over 10 000 h of cw operation. Nor is there any SIMS evidence of p-contact metals penetrating into the semiconductor material. Thus our SIMS results are contrary to what one would expect for impurity diffusion causing the observed square root degradation characteristic.
Correlated electrical breakdown in arrays of high density aligned carbon nanotubes
Authors: Shekhar Shashank , Erementchouk Mikhail , Leuenberger Michael N. , Khondaker Saiful I.
Published: June 2011

We demonstrate that in a densely packed aligned array of single walled carbon nanotubes, the electrical breakdown of one nanotube leads to a highly correlated electrical breakdown of neighboring nanotubes, thereby producing a nanofissure. We show that the origin of the correlation is the electrostatic field of the broken nanotubes that produces locally inhomogeneous current and Joule heating distributions in the neighboring intact nanotubes triggering their breakdowns in the vicinity of the broken nanotubes. Our results suggest that the densely aligned arrays behave like a correlated solid.
Nitrided SrTiO3 as charge-trapping layer for nonvolatile memory applications
Authors: Huang X. D. , Lai P. T. , Liu L. , Xu J. P.
Published: June 2011

Charge-trapping characteristics of SrTiO3 with and without nitrogen incorporation were investigated based on Al/Al2O3/SrTiO3/SiO2/Si (MONOS) capacitors. A Ti-silicate interlayer at the SrTiO3/SiO2 interface was confirmed by x-ray photoelectron spectroscopy and transmission electron microscopy. Compared with the MONOS capacitor with SrTiO3 as charge-trapping layer (CTL), the one with nitrided SrTiO3 showed a larger memory window (8.4 V at ±10 V sweeping voltage), higher P/E speeds (1.8 V at 1 ms +8 V) and better retention properties (charge loss of 38% after 104 s), due to the nitrided SrTiO3 film exhibiting higher dielectric constant, higher deep-level traps induced by nitrogen incorporation, and suppressed formation of Ti silicate between the CTL and SiO2 by nitrogen passivation.
Structure-based prediction reveals capping motifs that inhibit β-helix aggregation
Authors: Bryan Allen W. , Starner-Kreinbrink Jennifer L. , Hosur Raghavendra , Clark Patricia L. , Berger Bonnie
Published: June 2011

The parallel β-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and some vertebrates. β-helix structure has been observed in monomeric units of some aggregated amyloid fibers. In contrast, soluble β-helices, both right- and left-handed, are usually “capped” on each end by one or more secondary structures. Here, an in-depth classification of the diverse range of β-helix cap structures reveals subtle commonalities in structural components and in interactions with the β-helix core. Based on these uncovered commonalities, a toolkit of automated predictors was developed for the two distinct types of cap structures. In vitro deletion of the toolkit-predicted C-terminal cap from the pertactin β-helix resulted in increased aggregation and the formation of soluble oligomeric species. These results suggest that β-helix cap motifs can prevent specific, β-sheet-mediated oligomeric interactions, similar to those observed in amyloid formation.
Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes
Authors: Lim Kian Huat , Ferraris Luciana , Filloux Madeleine E. , Raphael Benjamin J. , Fairbrother William G.
Published: June 2011

We present an intuitive strategy for predicting the effect of sequence variation on splicing. In contrast to transcriptional elements, splicing elements appear to be strongly position dependent. We demonstrated that exonic binding of the normally intronic splicing factor, U2AF65, inhibits splicing. Reasoning that the positional distribution of a splicing element is a signature of its function, we developed a method for organizing all possible sequence motifs into clusters based on the genomic profile of their positional distribution around splice sites. Binding sites for serine/arginine rich (SR) proteins tended to be exonic whereas heterogeneous ribonucleoprotein (hnRNP) recognition elements were mostly intronic. In addition to the known elements, novel motifs were returned and validated. This method was also predictive of splicing mutations. A mutation in a motif creates a new motif that sometimes has a similar distribution shape to the original motif and sometimes has a different distribution. We created an intraallelic distance measure to capture this property and found that mutations that created large intraallelic distances disrupted splicing in vivo whereas mutations with small distances did not alter splicing. Analyzing the dataset of human disease alleles revealed known splicing mutants to have high intraallelic distances and suggested that 22% of disease alleles that were originally classified as missense mutations may also affect splicing. This category together with mutations in the canonical splicing signals suggest that approximately one third of all disease-causing mutations alter pre-mRNA splicing.
Temporal and Geographic Genetic Divergence: Characterizing Sockeye Salmon Populations in the Chignik Watershed, Alaska, Using Single‐Nucleotide Polymorphisms
Authors: Creelman Elisabeth K. , Hauser Lorenz , Simmons Ryan K. , Templin William D. , Seeb Lisa W.
Published: June 2011

The high fidelity of Pacific salmon Oncorhynchus spp. to their natal spawning habitat often results in genetically divergent populations. Management and conservation of the natural variation within species is critical for maintaining robust populations. The Chignik watershed, Alaska, supports highly productive populations of sockeye salmon Oncorhynchus nerka that vary in return timing and spawning locations among breeding populations, presenting challenges to the management of commercially exploited stocks. We describe the genetic structure of the sockeye salmon populations spawning in the Chignik watershed using 45 single‐nucleotide polymorphisms from 2,013 individuals representing 19 collections of spawning adults. From these data we estimated within‐population statistics and among‐population divergence, detected loci in linkage disequilibrium and loci that are FST outliers, and tested loci for potential use in mixed‐stock assessments. The results indicate significant genetic structure among the sockeye salmon populations in the Chignik watershed at both spatial and temporal scales. This structuring can be largely explained by putative evidence of selection at two markers and the differences in spawn timing between populations. Genetic structure determined at geographic and temporal levels provides a basis for application in the conservation of this resource and the management of commercial and subsistence fisheries.
Does Lower Crab Creek in the Eastern Washington Desert Have a Native Population of Chinook Salmon?
Authors: Small Maureen P. , Burgess Dave , Dean Cheryl , Warheit Kenneth I.
Published: June 2011

Lower Crab Creek (LCC) in eastern Washington is a groundwater‐fed tributary to the Columbia River at river kilometer 661. The creek traverses agriculturally modified desert habitat, and in several reaches the water quality is poor, summer water temperatures are lethal to fish, and stream habitat is degraded. The creek was thought to be unsuitable for salmonids, yet fall‐run Chinook salmon Oncorhynchus tshawytscha spawn and rear in it. The origin of these fish is uncertain since it is unclear whether LCC was a perennial creek prior to the hydrologic changes in the Columbia River basin stemming from the Columbia Basin Irrigation Project in the 1950s. We used genetic analyses to examine the hypotheses that these fish are (1) random strays, (2) a population founded since the 1950s (by wild or hatchery strays), or (3) an established native population. Chinook salmon juveniles and adults were collected in LCC and genetically characterized with the Chinook salmon microsatellite DNA locus suite in the Genetic Analysis of Pacific Salmonids database. The LCC population of Chinook salmon was found to be significantly different from interior Columbia River basin hatchery and wild populations and to have alleles that are absent from proximal populations. Lower Crab Creek Chinook salmon showed no evidence of recent founding and had genetic diversity, allelic richness, and effective population size similar to those of other Columbia River basin Chinook salmon. The data suggest that a genetically distinct, native population of Chinook salmon inhabits LCC that has adapted to the rigorous environment.
Single‐Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed‐Stock Analyses of Sockeye Salmon from the Copper River, Alaska
Authors: Ackerman Michael W. , Habicht Christopher , Seeb Lisa W.
Published: June 2011

Genetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single‐nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single‐nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south‐central Alaska. We evaluated the information content of the four nonneutral loci for use in genetic stock identification and assessed their ability to improve the accuracy and precision of composition estimates. The average measure of informativeness for assignment (In) for neutral loci was 0.019, and the average In for nonneutral loci was 0.064. A simulation‐based approach indicated that the addition of the nonneutral SNP loci to a neutral marker panel provided significantly higher resolution in the assignment of individuals to their populations of origin than would have been accomplished by adding an equal number of neutral loci. Nonneutral SNP loci improved the ability to identify the origin of individual fish and to estimate the composition of Pacific salmon populations in mixed fisheries.
The KdV curve and Schrödinger-Airy curve
Authors: Song Chong
Published: June 2011

Among other things, we introduce the notion of KdV curves and Schrödinger-Airy curves. These curves are stable solutions to the geometric KdV-Airy flow equation and Schrödinger-Airy flow equation respectively, which were recently proposed by Sun and Wang. We demonstrate that the KdV curves can be regarded as a 3rd-order analogue of geodesics. Other interesting properties of these curves will be addressed. Explicit examples of these curves will be provided. In addition, we will consider a perturbed KdV curve system and show the existence of multiple solutions to this system on the torus.
Refining Opportunity Cost Estimates of Not Adopting GM Cotton: An Application in Seven Sub‐Saharan African Countries
Authors: Bouët Antoine , Gruère Guillaume P.
Published: June 2011

A computable general equilibrium model is applied to evaluate the opportunity costs of not adopting Bt cotton, a genetically‐modified (GM) insect resistant cotton, in Benin, Burkina‐Faso, Mali, Senegal, Togo, Tanzania, and Uganda when it is adopted in other countries. Our model uniquely employs country‐specific partial adoption rates and factor‐biased productivity shocks in the cotton and oilseed sectors of all adopting regions. Assuming a 50% adoption rate, the opportunity cost of not adopting Bt cotton in the seven surveyed countries amounts to $41 million per year, which is a significant but lower cost than that suggested by the results of previous studies. Trade liberalization only marginally increases this estimate.
Methyl-Analyzer—whole genome DNA methylation profiling
Authors: Xin Yurong , Ge Yongchao , Haghighi Fatemeh G.
Published: June 2011

Summary: Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution.

Availability and implementation: Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html.

Contact:  fgh3@columbia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integration of gene normalization stages and co-reference resolution using a Markov logic network
Authors: Dai Hong-Jie , Chang Yen−Ching , Tsai Richard Tzong-Han , Hsu Wen−Lian
Published: June 2011

Motivation: Gene normalization (GN) is the task of normalizing a textual gene mention to a unique gene database ID. Traditional top performing GN systems usually need to consider several constraints to make decisions in the normalization process, including filtering out false positives, or disambiguating an ambiguous gene mention, to improve system performance. However, these constraints are usually executed in several separate stages and cannot use each other's input/output interactively. In this article, we propose a novel approach that employs a Markov logic network (MLN) to model the constraints used in the GN task. Firstly, we show how various constraints can be formulated and combined in an MLN. Secondly, we are the first to apply the two main concepts of co-reference resolution—discourse salience in centering theory and transitivity—to GN models. Furthermore, to make our results more relevant to developers of information extraction applications, we adopt the instance-based precision/recall/F-measure (PRF) in addition to the article-wide PRF to assess system performance.

Results: Experimental results show that our system outperforms baseline and state-of-the-art systems under two evaluation schemes. Through further analysis, we have found several unexplored challenges in the GN task.

Contact:  hongjie@iis.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genomic data integration using guided clustering
Authors: Maneck Matthias , Schrader Alexandra , Kube Dieter , Spang Rainer
Published: June 2011

Motivation: In biomedical research transcriptomic, proteomic or metabolomic profiles of patient samples are often combined with genomic profiles from experiments in cell lines or animal models. Integrating experimental data with patient data is still a challenging task due to the lack of tailored statistical tools.

Results: Here we introduce guided clustering, a new data integration strategy that combines experimental and clinical high-throughput data. Guided clustering identifies sets of genes that stand out in experimental data while at the same time display coherent expression in clinical data. We report on two potential applications: The integration of clinical microarray data with (i) genome-wide chromatin immunoprecipitation assays and (ii) with cell perturbation assays. Unlike other analysis strategies, guided clustering does not analyze the two datasets sequentially but instead in a single joint analysis. In a simulation study and in several biological applications, guided clustering performs favorably when compared with sequential analysis approaches.

Availability:  Guided clustering is available as a R-package from http://compdiag.uni-regensburg.de/software/guidedClustering.shtml. Documented R code of all our analysis is included in the Supplementary Materials. All newly generated data are available at the GEO database (GSE29700).

Contact:  rainer.spang@klinik.uni-regensburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploring Potential Noninvasive Biomarkers in Eosinophilic Esophagitis in Children
Authors: Subbarao Girish , Rosenman Marc B. , Ohnuki Lyo , Georgelas Ann , Davis Miriam , Fitzgerald Joseph F. , Molleston Jean P. , Croffie Joseph M. , Pfefferkorn Marian D. , Corkins Mark R. , Lim Joel R. , Steiner Steven J. , Schaefer Elizabeth , Gleich Gerald J. , Gupta Sandeep K.
Published: June 2011

Background and Aims:

Eosinophilic esophagitis (EE) continues to present clinical challenges, including a need for noninvasive tools to manage the disease. To identify a marker able to assess disease status in lieu of repeated endoscopies, we examined 3 noninvasive biomarkers, serum interleukin (IL)‐5, serum eosinophil‐derived neurotoxin (EDN), and stool EDN, and examined possible correlations of these with disease phenotype and activity (symptoms and histology) in a longitudinal study of children with EE.

Subjects and Methods:

Children with EE were studied for up to 24 weeks (12 weeks on 1 of 2 corticosteroid therapies and 12 weeks off therapy). Twenty children with normal esophagogastroduodenoscopies with biopsies were enrolled as controls. Serum IL‐5, serum EDN, and stool EDN were measured at weeks 0, 4, 12, 18, and 24 in children with EE, and at baseline alone for controls. Primary and secondary statistical analyses (excluding and including outlier values of the biomarkers, respectively) were performed.

Results:

Sixty subjects with EE (46 [75%] boys, mean age 7.5 ± 4.4 years) and 20 normal controls (10 [50%] boys, mean age 6.7 ± 4.1 years) were included. Significant changes in serum EDN (significant decrease from baseline to week 4, and then rebound from week 4 to week 12) occurred. Serum EDN levels were stable after week 12. Serum IL‐5 and stool EDN levels in subjects with EE were not statistically different from those of the control subjects when each time point for the cases was compared with the controls’ 1‐time measurement.

Conclusions:

Serum EDN levels were significantly higher in subjects with EE than in controls, and the results suggest a possible role, after additional future studies, for serum EDN in establishing EE diagnosis, assessing response to therapy, and/or monitoring for relapse or quiescence.
Acute on Chronic Liver Disease in Children From the Developing World
Authors: Jagadisan Barath , Srivastava Anshu , Yachha Surender Kumar , Poddar Ujjal
Published: June 2011

Objectives:

A subset of children with chronic liver disease (CLD) decompensate following an acute insult; however, data for children are not readily available. The present study aims to characterize the clinical presentation, etiology, outcome, and determinants of short‐term mortality in children with an acute hepatic insult superimposed over CLD.

Patients and Methods:

Children of acute on chronic liver disease (ACLD) were grouped as acute on chronic liver failure (ACLF) and non‐ACLF. ACLF was defined as per the definition proposed by Asian Pacific Association for the Study of Liver. The acute insult, etiology of CLD, and clinical and laboratory parameters at admission along with 3‐month outcome were assessed. Receiver operating curve (ROC) was plotted to measure the performance of pediatric end‐stage liver disease (PELD) score in predicting the 3‐month mortality.

Results:

Of the 36 children with ACLD (median age 9.5; range 3–15 years), 17 fulfilled ACLF criteria and 19 non‐ACLF. CLD was diagnosed for the first time in 86% children during their presentation with a superimposed acute insult. Wilson disease and autoimmune liver disease were the most common underlying etiology. Acute insult was caused by hepatitis E virus (HEV) in 27 (75%) children and hepatitis A virus (HAV) in 10 (28%). The 3‐month mortality of ACLF group was significantly higher than that of non‐ACLF group (59% vs 11%, P = 0.001). PELD score of >25.5 predicted death, with a sensitivity of 100% and specificity of 83.3%.

Conclusions:

Superinfection with hepatotropic viruses on CLD in children manifests as ACLD: ACLF and non‐ACLF. Hepatitis E virus is the most common superinfection in the population studied. The mortality in ACLF is 5 times higher than that in the non‐ACLF group. PELD score is useful in differentiating likely survivors and nonsurvivors.
Fluid–body interactions: clashing, skimming, bouncing
Authors: Smith Frank T. , Wilson Phillip L.
Published: June 2011

Solid–solid and solid–fluid impacts and bouncing are the concern here. A theoretical study is presented on fluid–body interaction in which the motion of the body and the fluid influence each other nonlinearly. There could also be many bodies involved. The clashing refers to solid–solid impacts arising from fluid–body interaction in a channel, while the skimming refers to another area where a thin body impacts obliquely upon a fluid surface. Bouncing usually then follows in both areas. The main new contribution concerns the influences of thickness and camber which lead to a different and more general form of clashing and hence bouncing.
Lentibacter algarum gen. nov., sp. nov., isolated from coastal water during a massive green algae bloom
Authors: Li Zhao , Qu Zhe , Zhang Xiuming , Zhang Xiao-Hua
Published: June 2011

Two novel Gram-stain-negative, aerobic strains (ZXM100T and ZXM098) were isolated from seawater in the coastal region of Qingdao (36.027° N 120.184° E), China, during a massive green algae bloom. Cells were ovoid to irregular short rods and lacked flagella. Poly-β-hydroxybutyrate was accumulated. Cells did not contain bacteriochlorophyll a. The isolates grew at NaCl concentrations of 3–9 % and 22–28 °C. C18 : 1ω7c, C18 : 0 and C16 : 0 were the major fatty acid components. The polar lipids of ZXM100T were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, a single lipid and an unidentified aminolipid. The predominant isoprenoid quinone of ZXM100T was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains belonged to the family

Rhodobacteraceae

. Based on the results obtained in this study, strain ZXM100T was considered to represent a novel species in a new genus, for which the name Lentibacter algarum gen. nov., sp. nov. is proposed. The type strain is ZXM100T ( = LMG 24861T = CGMCC 1.10234T); the DNA G+C content of the type strain is 54.6 mol%.
Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake
Authors: Makhdoumi-Kakhki A. , Amoozegar M. A. , Bagheri M. , Ramezani M. , Ventosa A.
Published: June 2011

Strain EB21T was isolated from a brine sample from Aran-Bidgol salt lake, a saline playa in Iran. Strain EB21T was an orange–red-pigmented, motile rod and required at least 2 M NaCl but not MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.2 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C, while it was able to grow at pH 6.0–8.0 and 25–55 °C. Analysis of the 16S rRNA gene sequence revealed that strain EB21T is a member of the family

Halobacteriaceae

, showing low levels of similarity to other members of the family. The highest sequence similarities, 91.8, 91.7 and 91.5 %, were obtained with the 16S rRNA gene sequences of the type strains of

Halobiforma lacisalsi

,

Haloterrigena thermotolerans

and

Halalkalicoccus tibetensis

, respectively. Polar lipid analyses revealed that strain EB21T contains phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Three unidentified glycolipids and one minor phospholipid were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 67.7 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain EB21T is thus considered to represent a novel species in a new genus within the family

Halobacteriaceae

, order

Halobacteriales

, for which the name Haloarchaeobius iranensis gen. nov., sp. nov. is proposed. The type strain of Haloarchaeobius iranensis is EB21T ( = IBRC-M 10013T  = KCTC 4048T).
Actinomadura rupiterrae sp. nov., isolated from cliff soil
Authors: Lee Soon Dong
Published: June 2011

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16 : 0, C18 : 1ω9c and iso-C16 : 0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA–DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T  = KCTC 19559T  = DSM 45251T).