bluuebunny/crossref_metadata_2025 huggingface dataset:
Laser heating of finite two-dimensional dust clusters: B. Simulations
Authors: Thomsen Hauke , Kählert Hanno , Bonitz Michael , Schablinski Jan , Block Dietmar , Piel Alexander , Melzer André
Published: February 2012

Laser heating of monolayer dusty plasmas is investigated theoretically by Langevin dynamics simulations. The laser radiation pressure is used to externally control the dust temperature without changing the plasma properties. We show that the laser scanning pattern has a major influence on both the velocity distribution function and the stationary structure of the cluster. Furthermore, the heating effect is found to be enhanced when the laser spots move with slightly higher frequencies than the trap frequency. The simulations confirm that a proper thermodynamic excitation of the dust particles is possible.
Deep traps and enhanced photoluminescence efficiency in nonpolar a-GaN/InGaN quantum well structures
Authors: Polyakov A. Y. , Jang Lee-Woon , Jo Dong-Seob , Lee In-Hwan , Smirnov N. B. , Govorkov A. V. , Kozhukhova E. A. , Hyeon Baik Kwang , Hwang Sung-Min
Published: February 2012

Nonpolar (11-20) a-GaN/InGaN quantum well (QW) structures were grown by metalorganic chemical vapor deposition on r-plane (1-102) sapphire substrate using a two-stage growth procedure. Our studies demonstrate that, in contrast to polar QWs, these structures show the presence of deep electron traps with activation energy of 0.41 eV in admittance spectra and 1 eV electron traps in capacitance transient spectra. These traps are suspected to be nonradiative recombination centers, decreasing the nonpolar QW photoluminescence (PL) efficiency in our structures compared to polar structures. The PL efficiency of nonpolar QWs is shown to be greatly enhanced by coupling to localized surface plasmons formed by Ag nanoparticles.
Effect of nickel contamination on high carrier lifetime n-type crystalline silicon
Authors: Yoon Yohan , Paudyal Bijaya , Kim Jinwoo , Ok Young-Woo , Kulshreshtha Prashant , Johnston Steve , Rozgonyi George
Published: February 2012

The injection-dependent lifetimes of different levels of Ni-contaminated n-type Czochralski (CZ) silicon wafers were investigated using resonant-coupled photoconductance decay (RCPCD) and quasi-steady-state photoconductance technique (QSSPC). The lifetime degradation of the most heavily contaminated samples was caused by Ni silicide precipitates at the surface of the wafers. The impact on lifetime was determined by surface recombination velocities (SRV). SRV values from RCPCD were comparable to those extracted by the QSSPC technique. A direct correlation between minority carrier lifetime and the concentration of electrically active substitutional Ni and Ni silicide precipitate traps measured using deep level transient spectroscopy was established.
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol
Authors: Allison Jane R. , Riniker Sereina , van Gunsteren Wilfred F.
Published: February 2012

The time- and length-scale accessible to molecular dynamics simulations of biomolecular systems using atomic-level (AL) models is most limited by the calculation of the solvent-solvent interactions, which comprise the majority of the interactions and yet are seldom of specific interest. Coarse-graining (CG), in which multiple solvent molecules are subsumed into a single bead, provides a means of overcoming this limitation without resorting to implicit solvation models, which basically misrepresent the hydrophobic effect. Most existing CG models, however, do not explicitly include electrostatic interactions, and thus fail to reproduce important properties of the solvent such as dielectric screening. Moreover, CG models for one type of solvent molecule are seldom compatible with those for other solvents. Here, we develop polarizable CG models for the solvents dimethyl sulfoxide, chloroform, and methanol that are compatible with an existing CG model for water. The inclusion of polarizability greatly improves the reproduction of thermodynamic data measured experimentally and calculated from AL simulations for both the pure liquids and binary mixtures.
Correlations between the thermal vibrations of two cantilevers: Validation of deterministic analysis via the fluctuation-dissipation theorem
Authors: Honig Christopher D. F. , Radiom Milad , Robbins Brian A. , Walz John Y. , Paul Mark R. , Ducker William A.
Published: February 2012

We validate a theoretical approach for analyzing correlations in the fluctuations of two cantilevers in terms of a deterministic model, using the fluctuation-dissipation theorem [M. R. Paul and M. C. Cross, Phys. Rev. Lett. 92, 235501 (2004)]. The validation has been made possible through measurement of the correlations between the thermally stimulated vibrations of two closely spaced micrometer-scale cantilevers in fluid. Validation of the theory enables development of a method for characterizing fluids, which we call correlation force spectrometry.
Temperature dependent dynamics of ZnO nanoparticles probed by Raman scattering: A big divergence in the functional areas of nanoparticles and bulk materials
Authors: Kumar Yadav Harish , Katiyar R. S. , Gupta Vinay
Published: February 2012

Temperature dependent Raman scattering of the E2(low) and E2(high) modes of ZnO nanoparticle powder samples has been investigated. The dynamics exhibited by the ZnO nanoparticles, the E2 modes, follow single crystal like behavior but with strong cubic or/and quadratic anharmonicity by supporting additional channels for immediate lattice relaxation. The strong anharmonic character associated with the E2 modes reflects enhanced thermal conductivity of the ZnO nanoparticles. An anomalous variation in linewidth of the E2(low) mode is observed and is attributed to the superposition of the large displacement field, associated with the surface atoms of the nanoparticles and the lattice mode.
Nuclear signatures on the molecular harmonic emission and the attosecond pulse generation
Authors: Feng Liqiang , Chu Tianshu
Published: February 2012

In this paper, we theoretically investigate the nuclear signatures effects, i.e., the initial vibrational state and the isotopic effects on the generations of the molecular high-order harmonics and the attosecond pulses when the model H2+/D2+ ions are exposed to a 5 fs/800 nm chirp pulse. The numerical solution of the time-dependent Schrödinger equation for these vibrating molecule ions shows that the intensities of the harmonic spectra are reinforced with the enhancement of the initial vibrational state. Moreover, through the investigation of the isotopic effect, we find that more intense harmonics are generated in the lighter nucleus. Furthermore, by optimizing the chirp pulse under the optimal initial vibrational state, an intense ultrabroad supercontinuum with a 325 eV bandwidth can be obtained. By properly superposing the harmonic spectrum, an attosecond pulse as short as 57 as (16 as) is generated without (with) phase compensation.
Role of deep and shallow donor levels on n-type conductivity of hydrothermal ZnO
Authors: Brochen S. , Granier C. , Feuillet G. , Pernot J.
Published: February 2012

The residual n-type conductivity of O-polar hydrothermally grown ZnO single crystals and the role of annealing on the transport properties are assessed by temperature dependent Hall measurements on a wide 20–800 K temperature range. A deep level lying 250 meV below the conduction band is responsible for the residual n-type conductivity of unannealed samples. After annealing, a shallow donor level with 25 meV ionization energy becomes responsible for the sample conductivity in the room temperature range. Thanks to high temperature Hall measurement, the coexistence of the deep and the shallow level has been demonstrated in the case of annealed sample.
Characteristics of thickness-shear modes excited by two-layer piezoelectric film in acoustic sensors
Authors: Zhang Hui , Zhang Shu-yi , Fan Li , Wang Yu-ran
Published: February 2012

The thickness-shear mode (TSM) excited by two-layer, (112¯0)-textured, hexagonal piezoelectric film is studied to improve the performances of the acoustic sensors. The corresponding theoretical model is presented by the acoustic wave propagation theory in multi-layer structure combined with the excitation of TSM in two-layer piezoelectric film with opposite polarization direction. The model considers the effects of the acoustic attenuations in the Akheiser regime and Landau-Rumer regime. The calculated results manifest that, when the phase variation of two-layer piezoelectric film with opposite polarization direction is the same and equals to π, an enhanced second TSM can be excited and the corresponding first TSM is suppressed. The enhanced second TSM has higher resonant frequency and higher quality factor than the first TSM excited by a single- or two-layer piezoelectric film with identical polarization direction, which can be used for improving the mass sensitivity and sensitive resolution of the acoustic sensors in a liquid medium.
Investigation of the structural, electronic, and magnetic properties of Ni-based Heusler alloys from first principles
Authors: Qawasmeh Yasmeen , Hamad Bothina
Published: February 2012

Density functional theory (DFT) calculations are performed to investigate the structural, electronic, magnetic, and elastic properties of Ni2MnZ (Z = B, Al, Ga, In) and Ni2FeZ (Z = Al, Ga) full Heusler alloys. The alloys are found to be metallic ferromagnets with total magnetic moments of about 4μB/f.u. and 3μB/f.u for Ni2MnZ and Ni2FeZ alloys, respectively. The Ni2MnAl and Ni2MnIn alloys are found to be stable at L21 phase, while the other alloys are more stable in the tetragonal phase with c/a ratios of 1.38 and 1.27 for Ni2MnB and Ni2MnGa, respectively and 1.35 for both Ni2FeAl and Ni2FeGa. The Ni2MnB alloy exhibits the highest electron spin polarization in its tetragonal phase, which is about 88% greater than that of L21 structure. However, the Ni2MnGa, Ni2FeAl, and Ni2FeGa alloys exhibit lower spin polarizations in their tetragonal phase than those at the L21. The most contribution of the total magnetic moments comes from Mn or Fe atoms, whereas Ni atoms exhibit much smaller magnetic moments. However, Z atoms have small induced magnetic moments, which are coupled antiferromagnetically with Ni, Mn and Fe.
Valence band dependence on thermal treatment of gold doped glasses and glass ceramics
Authors: Radu T. , Benea D. , Ciceo-Lucacel R. , Ponta O. , Simon S.
Published: February 2012

This paper reports x-ray photoemission spectroscopy results regarding the nucleation and growing process of gold nanoparticles (AuNPs) in CaO-SiO2-P2O5 bioactive glasses heat treated at different temperatures. The analysis of the valence band (VB) spectra is discussed in terms of the AuNPs’ shape, size, and distribution at the sample surface at different temperatures. Moreover, the theoretical VB photoemission spectra of the investigated samples are presented, and their agreement with experimentally obtained spectra is discussed in detail.
Standoff detection via single-beam spectral notch filtered pulses
Authors: Natan Adi , Levitt Jonathan M. , Graham Leigh , Katz Ori , Silberberg Yaron
Published: February 2012

We demonstrate single-beam coherent anti-Stokes Raman spectroscopy (CARS), for detecting and identifying traces of solids, including minute amounts of explosives, from a standoff distance (>50 m) using intense femtosecond pulses. Until now, single-beam CARS methods relied on pulse-shapers in order to obtain vibrational spectra. Here, we present a simple and easy-to-implement detection scheme, using a commercially available notch filter that does not require the use of a pulse-shaper.
Angular distribution of field emitted electrons from vertically aligned carbon nanotube arrays
Authors: Iacobucci S. , Fratini M. , Rizzo A. , Scarinci F. , Zhang Y. , Mann M. , Li C. , Milne W. I. , El Gomati M. M. , Lagomarsino S. , Stefani G.
Published: February 2012

Angular field emission (FE) properties of vertically aligned carbon nanotube arrays have been measured on samples grown by plasma enhanced chemical vapor deposition and characterized by scanning electron microscope and I-V measurements. These properties determine the angular divergence of electron beams, a crucial parameter in order to obtain high brilliance FE based cathodes. From angular distributions of the electron beam transmitted through extraction grids of different mesh size and by using ray-tracing simulations, the maximum emission angle from carbon nanotube tips has been determined to be about ± 30° around the tube main axis.
Note: Rotational compliance and instantaneous center of rotation in segmented and V-shaped notch hinges
Authors: Tseytlin Yakov
Published: February 2012

This note shows a technique for the calculation of rotational compliance (stiffness) and develops a generalized mathematical model for the virtual center of rotation position in concave, segmented, and V-shaped notch hinges using Chebyshev's polynomials. The calculational results are in a good agreement with experimental data and finite element model verified output with estimated differences of less than 10%. This agreement shows that our tractable model is a general one for rotational compliance and the evaluation of a virtual center of rotation position in any type of concave flexure notch hinges.
Investigation of proximity effects in electron microscopy and lithography
Authors: Walz M.-M. , Vollnhals F. , Rietzler F. , Schirmer M. , Steinrück H.-P. , Marbach H.
Published: February 2012

A fundamental challenge in lithographic and microscopic techniques employing focused electron beams are so-called proximity effects due to unintended electron emission and scattering in the sample. Herein, we apply a method that allows for visualizing electron induced surface modifications on a SiN substrate covered with a thin native oxide layer by means of iron deposits. Conventional wisdom holds that by using thin membranes proximity effects can be effectively reduced. We demonstrate that, contrary to the expectation, these can be indeed larger on a 200 nm SiN-membrane than on the respective bulk substrate due to charging effects.
Negative differential spin conductance in doped zigzag graphene nanoribbons
Authors: Wu Ting-Ting , Wang Xue-Feng , Zhai Ming-Xing , Liu Hua , Zhou Liping , Jiang Yong-Jin
Published: February 2012

The spin dependent charge transport in zigzag graphene nanoribbons (ZGNRs) has been investigated by the nonequilibrium Green’s function method combined with the density functional theory at the local spin density approximation. The current versus voltage curve shows distinguished behaviors for symmetric and asymmetric ZGNRs, and the doping on the ZGNR edges can manipulate the spin transport. In special cases that a Be atom is substitutionally doped on one edge of the symmetric ZGNRs, one spin current shows negative differential resistance, whereas the other increases monotonically with the bias. This property might be used to design spin oscillators or other devices for spintronics.
Dipolar ordering of random two-dimensional spin ensemble
Authors: Panov Andrey V.
Published: February 2012

We theoretically study the randomly positioned two-dimensional system of interacting magnetic dipoles representing the monolayer arrays of single-domain particles. It is showed the onset of the dipolar in-plane superferromagnetic ordering of Ising spins at the surface concentrations of nanoparticles above 0.24. The critical concentration of particles with random easy axis arrangement at zero temperature is 0.65. It is demonstrated that the ensemble with Ising arrangement of spins is ordered at high temperatures close to a particle Curie point.
Anisotropy and extremely high coercivity in weak ferromagnetic LuFeO3
Authors: Zhu Wenka , Pi Li , Tan Shun , Zhang Yuheng
Published: February 2012

The temperature dependence of the structural anisotropy of weak ferromagnetic LuFeO3 is investigated through the XRD spectra at different temperatures. The structural anisotropy decreases with heating, which is in agreement with the magnetization-temperature measurement. The magnetic hysteresis loops reveal exceptionally high coercivity and saturation field. Its high energy of magnetocrystalline anisotropy may be responsible for the peculiar phenomenon. Thus, LuFeO3 is a super hard magnetic material. The magnetized LuFeO3 can steadily provide weak permanent magnetic field, which can be considered as a kind of useful application.
Cation stoichiometry optimization of SrTiO3 (110) thin films with atomic precision in homogeneous molecular beam epitaxy
Authors: Wang Zhiming , Feng Jiagui , Yang Yang , Yao Yuan , Gu Lin , Yang Fang , Guo Qinlin , Guo Jiandong
Published: February 2012

We study the evolution of surface reconstructions on SrTiO3 (110) determined by cation concentration ratio and find it detectable by high energy electron diffraction (RHEED) even at high temperature up to 800 °C. The evaporation rate of Sr and Ti sources can be calibrated precisely by monitoring RHEED patterns in situ and in real time during the extended homogeneous oxide molecule beam epitaxy growth of SrTiO3 (110) film. High quality film is obtained with deviation of cation stoichiometry less than 0.5%.
Improvement of coercivity and thermal stability of anisotropic Nd13Fe79.4B7Nb0.3Ga0.3 powders by diffusion of Pr-Cu alloys
Authors: Lin Zhong , Han Jingzhi , Xing Meiying , Liu Shunquan , Wu Rui , Wang Changsheng , Zhang Yan , Yang Yingchang , Yang Jinbo
Published: February 2012

Highly anisotropic Nd13Fe79.4B7Nb0.3Ga0.3 powders from a self-organized rod-like disproportionation microstructure and room temperature magnetic properties of μ0Mr = 1.4 T, iHc = 13 kOe, and (BH)max = 41 MGOe are obtained by optimizing hydrogenation disproportionation desorption recombination (HDDR) process. Diffusion of Pr68Cu32 alloy into the HDDR powders further increases the coercivity of the powders to 18 kOe. This enhancement in coercivity is mainly attributed to the modification of grain boundaries including the decrease of Fe content and the increase of boundary thickness. The modified boundaries can work as effective pinning layers for domain walls. The thermal stability of magnetic properties of HDDR powders is also improved after the diffusion treatment.
Dielectric function spectra and critical-point energies of Cu2ZnSnSe4 from 0.5 to 9.0 eV
Authors: Choi S. G. , Zhao H. Y. , Persson C. , Perkins C. L. , Donohue A. L. , To B. , Norman A. G. , Li J. , Repins I. L.
Published: February 2012

We present dielectric function ɛ = ɛ1 + iɛ2 spectra and critical-point energies of Cu2ZnSnSe4 determined by spectroscopic ellipsometry from 0.5 to 9.0 eV. We reduce artifacts from surface overlayers to the maximum extent possible by performing chemical-mechanical polishing and wet-chemical etching of the surface of a Cu2ZnSnSe4 thin film. Ellipsometric data are analyzed by the multilayer model and the ɛ spectra are extracted. The data exhibit numerous spectral features associated with critical points, whose energies are obtained by fitting standard lineshapes to second energy derivatives of the data. The experimental results are in good agreement with the ɛ spectra calculated within the GW quasi-particle approximation, and possible origins of the pronounced critical-point structures are identified.
Re-examining the logarithmic dependence of the mean velocity distribution in polymer drag reduced wall-bounded flow
Authors: White C. M. , Dubief Y. , Klewicki J.
Published: February 2012

A re-examination of the logarithmic dependence of the mean velocity distribution in polymer drag reduced flows shows that drag reducing polymers modify the von Kármán coefficient and, in channel flow, eradicate the log-layer at high drag reductions. It is also found that the “ultimate profile,” corresponding to the state of maximum drag reduction is not logarithmic.
Compact cryogenic source of periodic hydrogen and argon droplet beams for relativistic laser-plasma generation
Authors: Fraga R. A. Costa , Kalinin A. , Kühnel M. , Hochhaus D. C. , Schottelius A. , Polz J. , Kaluza M. C. , Neumayer P. , Grisenti R. E.
Published: February 2012

We present a cryogenic source of periodic streams of micrometer-sized hydrogen and argon droplets as ideal mass-limited target systems for fundamental intense laser-driven plasma applications. The highly compact design combined with a high temporal and spatial droplet stability makes our injector ideally suited for experiments using state-of-the-art high-power lasers in which a precise synchronization between the laser pulses and the droplets is mandatory. We show this by irradiating argon droplets with multi-terawatt pulses.
Multiferroic phase competitions in perovskite manganite thin films
Authors: Qin M. H. , Tao Y. M. , Zeng M. , Gao X. S. , Wu S. J. , Dong S. , Liu J.-M.
Published: February 2012

Based on the Mochizuki-Furukawa model, the cycloidal spin structures of orthorhombic RMnO3 manganite thin films on various magnetic substrates are simulated using Monte Carlo method. It is revealed that the long range cycloidal spin order can be modulated by the film thickness and substrate spin structure. In particular, the ferromagnetic and antiferromagnetic spin orders of the substrate in different orientations have different pinning effects on the cycloidal spin order of the thin film. The simulated results are discussed in terms of the competition between the single-ion anisotropy and spin-orbit coupling.
Tuning the interlayer exchange coupling between single perpendicularly magnetized CoFeB layers
Authors: Lavrijsen R. , Fernández-Pacheco A. , Petit D. , Mansell R. , Lee J. H. , Cowburn R. P.
Published: February 2012

We experimentally study the tunability of the Ruderman-Kittel-Kasuya-Yosida (RKKY) interlayer exchange coupling (IEC) in Pt/CoFeB/Pt/Ru/Pt/CoFeB/Pt stacks with perpendicular magnetic anisotropy (PMA). The perpendicular magnetization of a single Pt/Co60Fe20B20/Pt (at. %) shows full remanence and square hysteresis loops for a CoFeB thickness range of 0.60–1.0 nm. By inserting a Pt layer between the Ru and CoFeB, the PMA of the ultrathin CoFeB layers is stabilized and the IEC can be tuned. In particular, we show that the IEC versus Pt thickness exhibits a simple exponential decay with a decay length of 0.16 nm.
The effect of growth temperature of GaAs nucleation layer on InAs/GaAs quantum dots monolithically grown on Ge substrates
Authors: Wang T. , Lee A. , Tutu F. , Seeds A. , Liu H. , Jiang Q. , Groom K. , Hogg R.
Published: February 2012

The effect of the growth temperature of the GaAs nucleation layer on the properties of 1.3-μm InAs/GaAs quantum dots (QDs) monolithically grown on a Ge substrate is investigated by using transmission electron microscopy, etch pit density, and photoluminescence (PL) measurements. The photoluminescence intensity for Ge-based InAs/GaAs quantum dots is very sensitive to the initial GaAs nucleation temperature with the strongest room-temperature emission at 380 °C, due to the lower density of defects generated at the GaAs/Ge interface and prorogating into the III-V layers at this temperature. Furthermore, lasing operation up to 100 °C was achieved for Ge-based 1.3-μm InAs/GaAs quantum-dot diodes with the initial GaAs layer nucleated at 380 °C.
Deep traps in nonpolar m-plane GaN grown by ammonia-based molecular beam epitaxy
Authors: Zhang Z. , Hurni C. A. , Arehart A. R. , Yang J. , Myers R. C. , Speck J. S. , Ringel S. A.
Published: February 2012

Deep level defects in nonpolar m-plane GaN grown by ammonia-based molecular beam epitaxy were characterized using deep level transient spectroscopy (DLTS) and deep level optical spectroscopy (DLOS) and compared with polar c-plane GaN that was grown simultaneously in the same growth run. Significant differences in both the levels present and their concentrations were observed upon comparison of both growth orientations. DLTS revealed electron traps with activation energies of 0.14 eV, 0.20 eV, and 0.66 eV in the m-plane material, with concentrations that were ∼10−50 × higher than traps of similar activation energies in the c-plane material. Likewise, DLOS measurements showed ∼20 × higher concentrations of both a CN acceptor-like state at EC − 3.26 eV, which correlates with a high background carbon concentration observed by secondary ion mass spectroscopy for the m-plane material [A. Armstrong, A. R. Arehart, B. Moran, S. P. DenBaars, U. K. Mishra, J. S. Speck, and S. A. Ringel, Appl. Phys. Lett. 84, 374 (2004)], and the VGa-related state level at EC − 2.49 eV, which is consistent with an enhanced yellow luminescence observed by photoluminescence. The findings suggest a strong impact of growth dynamics on the incorporation of impurities and electrically active native point defects as a function of GaN growth plane polarity.
A transparent 90° polarization rotator by combining chirality and electromagnetic wave tunneling
Authors: Mutlu Mehmet , Ozbay Ekmel
Published: February 2012

A three-layer chiral metamaterial is constructed by using two layers of four mutually rotated resonators and a subwavelength mesh sandwiched symmetrically between these layers. The resulting structure is an ultrathin, transparent, and polarization angle independent 90° polarization rotator. Due to the electromagnetic tunneling effect exerted by the negative permittivity mesh, a cross-polarization conversion efficiency of 99% and 93% is achieved numerically and experimentally. The structure is modeled using the effective medium theory and then the transfer matrix method is applied to demonstrate the existence of the tunneling resonance theoretically.
Structure of saposin A lipoprotein discs
Authors: Popovic Konstantin , Holyoake John , Pomès Régis , Privé Gilbert G.
Published: February 2012

The saposins are small, membrane-active proteins that exist in both soluble and lipid-bound states. Saposin A has roles in sphingolipid catabolism and transport and is required for the breakdown of galactosylceramide by β-galactosylceramidase. In the absence of lipid, saposin A adopts a closed monomeric apo conformation typical of this family. To study a lipid-bound state of this protein, we determined the crystal structure of saposin A in the presence of detergent to 1.9 Å resolution. The structure reveals two chains of saposin A in an open conformation encapsulating 40 internally bound detergent molecules organized in a highly ordered bilayer-like hydrophobic core. The complex provides a high-resolution view of a discoidal lipoprotein particle in which all of the internalized acyl chains are resolved. Saposin A lipoprotein discs exhibit limited selectivity with respect to the incorporated lipid, and can solubilize phospholipids, sphingolipids, and cholesterol into discrete, monodisperse particles with mass of approximately 27 kDa. These discs may be the smallest possible lipoprotein structures that are stabilized by lipid self-assembly.
Control of target gene specificity during metamorphosis by the steroid response gene
E93
Authors: Mou Xiaochun , Duncan Dianne M. , Baehrecke Eric H. , Duncan Ian
Published: February 2012

Hormonal control of sexual maturation is a common feature in animal development. A particularly dramatic example is the metamorphosis of insects, in which pulses of the steroid hormone ecdysone drive the wholesale transformation of the larva into an adult. The mechanisms responsible for this transformation are not well understood. Work in
Drosophila
indicates that the larval and adult forms are patterned by the same underlying sets of developmental regulators, but it is not understood how the same regulators pattern two distinct forms. Recent studies indicate that this ability is facilitated by a global change in the responsiveness of target genes during metamorphosis. Here we show that this shift is controlled in part by the ecdysone-induced transcription factor E93. Although long considered a dedicated regulator of larval cell death, we find that E93 is expressed widely in adult cells at the pupal stage and is required for many patterning processes at this time. To understand the role of E93 in adult patterning, we focused on a simple E93-dependent process, the induction of the
Dll
gene within bract cells of the pupal leg by EGF receptor signaling. In this system, we show that E93 functions to cause
Dll
to become responsive to EGF receptor signaling. We demonstrate that E93 is both necessary and sufficient for directing this switch. E93 likely controls the responsiveness of many other target genes because it is required broadly for patterning during metamorphosis. The wide conservation of E93 orthologs suggests that similar mechanisms control life-cycle transitions in other organisms, including vertebrates.
Growth and development.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter covers the anatomy and morphology (plant habit, leaves, roots, and flowers and inflorescences) of the highbush (Vaccinium corymbosum) and rabbiteye (V. ashei) blueberry are discussed, along with vegetative and reproductive growth and development (vegetative and floral growth, root growth, pollination and fruit set, and fruit development). Environmental factors affecting growth and development (temperature and photoperiod) are presented.
Light, photosynthesis, quality and yield in blueberries.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter describes the physiology (functioning) of a blueberry (Vaccinium sp.) plant with regard to the generation and distribution of carbohydrates. Factors that are involved in dry matter production and partitioning among the various plant organs, and the effect of several environmental variables and management practices on dry matter partitioning to vegetative and reproductive organs are discussed.
Nutrition.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter focuses on the mineral nutrition of blueberries (Vaccinium spp.), the factors that affect the availability of nutrients, and the methods to establish (through plant analysis and foliar diagnosis) and supply (through soil application and foliar application of organic and inorganic fertilizers) the nutrients (N, P, K, Ca, Mg, S, Al, Fe, Mn, B, Zn and Cu) to satisfy crop demands. The N cycle, soil pH requirements of blueberries, and role of mycorrhizal fungi in blueberry nutrition are also covered.
Blueberry pests, their management and cultivar resistance.
Authors: Hancock J. , Retamales J.
Published: February 2012

This chapter presents the most relevant pests, diseases and weeds that attack blueberries (Vaccinium spp.). The most common weeds, pests (insects, mites and nematodes) and diseases (fungal, bacterial, viral and phytoplasma-induced diseases) of highbush (V. corymbosum) and rabbiteye (V. ashei) blueberries are specifically covered. The control of these organisms, and the role of cultivar resistance in pest, weed and disease management are discussed.
Modeling Habitat Selection of a Top Predator: Considering Growth and Physical Environments in a Spatial Context
Authors: May Cassandra J. , Aday D. Derek , Hale R. Scott , Denlinger Jonathan C. S. , Marschall Elizabeth A.
Published: February 2012

Mechanisms associated with habitat selection by fishes are often unknown and require both physical habitat and growth environment considerations. We used spatially explicit prey biomass estimates, predator growth rate potential (GRP), bottom slope, predator distance from shore, and substrate data to predict habitat use of the saugeye (walleye Sander vitreus × sauger S. canadensis), a popular sport fish that is stocked throughout the central United States. We used telemetry to determine saugeye locations, acoustics to estimate prey biomass and distributions, and a bioenergetics model to aid in calculation of GRP. Akaike's information criterion was used to determine which habitat variables were most important in explaining saugeye location. Models that included both physical habitat and either GRP or prey density performed better than models that considered only one of these parameter types. The resulting models provided the data to create location suitability maps. In general, saugeyes favored steep slopes over hard substrates in nearshore areas with high biomass of gizzard shad Dorosoma cepedianum or high GRP. This comprehensive analysis suggests that the consideration of both spatial habitat suitability and temporal prey availability may improve fisheries management and conservation through a quantitative appreciation of available resources.
Decomposing the interaction between retention interval and study/test practice: The role of retrievability
Authors: Jang Yoonhee , Wixted John T. , Pecher Diane , Zeelenberg René , Huber David E.
Published: February 2012

Even without feedback, test practice enhances delayed performance compared to study practice, but the size of the effect is variable across studies. We investigated the benefit of testing, separating initially retrievable items from initially nonretrievable items. In two experiments, an initial test determined item retrievability. Retrievable or nonretrievable items were subsequently presented for repeated study or test practice. Collapsing across items, in Experiment 1, we obtained the typical cross-over interaction between retention interval and practice type. For retrievable items, however, the cross-over interaction was quantitatively different, with a small study benefit for an immediate test and a larger testing benefit after a delay. For nonretrievable items, there was a large study benefit for an immediate test, but one week later there was no difference between the study and test practice conditions. In Experiment 2, initially nonretrievable items were given additional study followed by either an immediate test or even more additional study, and one week later performance did not differ between the two conditions. These results indicate that the effect size of study/test practice is due to the relative contribution of retrievable and nonretrievable items.
Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples
Authors: Turchin Michael C. , Hirschhorn Joel N.
Published: February 2012

Summary: Meta-analysis across genome-wide association studies is a common approach for discovering genetic associations. However, in some meta-analysis efforts, individual-level data cannot be broadly shared by study investigators due to privacy and Institutional Review Board concerns. In such cases, researchers cannot confirm that each study represents a unique group of people, leading to potentially inflated test statistics and false positives. To resolve this problem, we created a software tool, Gencrypt, which utilizes a security protocol known as one-way cryptographic hashes to allow overlapping participants to be identified without sharing individual-level data.

Availability: Gencrypt is freely available under the GNU general public license v3 at http://www.broadinstitute.org/software/gencrypt/

Contact:  joelh@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Predicting kinase substrates using conservation of local motif density
Authors: Lai Andy C. W. , Nguyen Ba Alex N. , Moses Alan M.
Published: February 2012

Motivation: Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates.

Results: This study introduces a new method to predict kinase substrates by extracting evolutionary information from multiple sequence alignments in a manner that is tolerant to degenerate motif positioning. Given a known consensus, the new method (ConDens) compares the observed density of matches to a null model of evolution and does not require labeled training data. We confirmed that ConDens has improved performance compared with several existing methods in the field. Further, we show that it is generalizable and can predict interesting substrates for several important eukaryotic kinases where training data is not available.

Availability and implementation: ConDens can be found at http://www.moseslab.csb.utoronto.ca/andyl/.

Contact:  alan.moses@utoronto.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
pymzML—Python module for high-throughput bioinformatics on mass spectrometry data
Authors: Bald Till , Barth Johannes , Niehues Anna , Specht Michael , Hippler Michael , Fufezan Christian
Published: February 2012

Summary: pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra.

Availability and implementation: pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed.

Contact:  christian@fufezan.net
Use of procalcitonin for the diagnosis of pneumonia in patients presenting with a chief complaint of dyspnoea: results from the BACH (Biomarkers in Acute Heart Failure) trial
Authors: Maisel Alan , Neath Sean‐Xavier , Landsberg Judd , Mueller Christian , Nowak Richard M. , Peacock W. Frank , Ponikowski Piotr , Möckel Martin , Hogan Christopher , Wu Alan H.B. , Richards Mark , Clopton Paul , Filippatos Gerasimos S. , Di Somma Salvatore , Anand Inder , Ng Leong L. , Daniels Lori B. , Christenson Robert H. , Potocki Mihael , McCord James , Terracciano Garret , Hartmann Oliver , Bergmann Andreas , Morgenthaler Nils G. , Anker Stefan D.
Published: February 2012

Aims

Biomarkers have proven their ability in the evaluation of cardiopulmonary diseases. We investigated the utility of concentrations of the biomarker procalcitonin (PCT) alone and with clinical variables for the diagnosis of pneumonia in patients presenting to emergency departments (EDs) with a chief complaint of shortness of breath.

Methods and results

The BACH trial was a prospective, international, study of 1641 patients presenting to EDs with dyspnoea. Blood samples were analysed for PCT and other biomarkers. Relevant clinical data were also captured. Patient outcomes were assessed at 90 days. The diagnosis of pneumonia was made using strictly validated guidelines. A model using PCT was more accurate [area under the curve (AUC) 72.3%] than any other individual clinical variable for the diagnosis of pneumonia in all patients, in those with obstructive lung disease, and in those with acute heart failure (AHF). Combining physician estimates of the probability of pneumonia with PCT values increased the accuracy to >86% for the diagnosis of pneumonia in all patients. Patients with a diagnosis of AHF and an elevated PCT concentration (>0.21 ng/mL) had a worse outcome if not treated with antibiotics (P = 0.046), while patients with low PCT values (<0.05 ng/mL) had a better outcome if they did not receive antibiotic therapy (P = 0.049).

Conclusion

Procalcitonin may aid in the diagnosis of pneumonia, particularly in cases with high diagnostic uncertainty. Importantly, PCT may aid in the decision to administer antibiotic therapy to patients presenting with AHF in which clinical uncertainty exists regarding a superimposed bacterial infection.

Trial registration: NCT00537628
Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
Authors: Liu Xiling , Somel Mehmet , Tang Lin , Yan Zheng , Jiang Xi , Guo Song , Yuan Yuan , He Liu , Oleksiak Anna , Zhang Yan , Li Na , Hu Yuhui , Chen Wei , Qiu Zilong , Pääbo Svante , Khaitovich Philipp
Published: February 2012

Over the course of ontogenesis, the human brain and human cognitive abilities develop in parallel, resulting in a phenotype strikingly distinct from that of other primates. Here, we used microarrays and RNA-sequencing to examine human-specific gene expression changes taking place during postnatal brain development in the prefrontal cortex and cerebellum of humans, chimpanzees, and rhesus macaques. We show that the most prominent human-specific expression change affects genes associated with synaptic functions and represents an extreme shift in the timing of synaptic development in the prefrontal cortex, but not the cerebellum. Consequently, peak expression of synaptic genes in the prefrontal cortex is shifted from <1 yr in chimpanzees and macaques to 5 yr in humans. This result was supported by protein expression profiles of synaptic density markers and by direct observation of synaptic density by electron microscopy. Mechanistically, the human-specific change in timing of synaptic development involves the MEF2A-mediated activity-dependent regulatory pathway. Evolutionarily, this change may have taken place after the split of the human and the Neanderthal lineages.
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Authors: Koboldt Daniel C. , Zhang Qunyuan , Larson David E. , Shen Dong , McLellan Michael D. , Lin Ling , Miller Christopher A. , Mardis Elaine R. , Ding Li , Wilson Richard K.
Published: February 2012

Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of tumors. Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor–normal pairs. Unlike most current approaches, our algorithm reads data from both samples simultaneously; a heuristic and statistical algorithm detects sequence variants and classifies them by somatic status (germline, somatic, or LOH); while a comparison of normalized read depth delineates relative copy number changes. We apply these methods to the analysis of exome sequence data from 151 high-grade ovarian tumors characterized as part of the Cancer Genome Atlas (TCGA). We validated some 7790 somatic coding mutations, achieving 93% sensitivity and 85% precision for single nucleotide variant (SNV) detection. Exome-based CNA analysis identified 29 large-scale alterations and 619 focal events per tumor on average. As in our previous analysis of these data, we observed frequent amplification of oncogenes (e.g., CCNE1, MYC) and deletion of tumor suppressors (NF1, PTEN, and CDKN2A). We searched for additional recurrent focal CNAs using the correlation matrix diagonal segmentation (CMDS) algorithm, which identified 424 significant events affecting 582 genes. Taken together, our results demonstrate the robust performance of VarScan 2 for somatic mutation and CNA detection and shed new light on the landscape of genetic alterations in ovarian cancer.
Close link between development and function of gamma−delta T cells
Authors: Shibata Kensuke
Published: February 2012

Murine γδ T cells develop as the first T‐cell lineage within the fetal thymus and disproportionately localize in mucosal tissues such as lung, skin, uterus, and intestine of adult mice. These unique developmental features and distribution patterns of γδ T cells enable rapid functioning against various insults from pathogens. γδ T cells are also able to respond to local inflammation and consequently regulate the pathogenesis of autoimmune disorders and development of tumors in mice and humans. Hence, it is clinically important to understand the mechanisms that regulate γδ T cell functions. Recent evidence has shown that generations of effector γδ T cell subsets producing IFN‐γ, IL‐4, and IL‐17 are programmed in the murine thymus before their migration to peripheral tissues. This review outlines our current understanding of the development and function of γδ T cells as they influence both innate and acquired immunity.
Bronchial and alveolar nitric oxide in exercise‐induced bronchoconstriction in asthmatic children
Authors: Chinellato I. , Piazza M. , Peroni D. , Sandri M. , Chiorazzo F. , Boner A. L. , Piacentini G.
Published: February 2012

Background

Epidemiological studies have shown an association between the severity of exercise‐induced bronchoconstriction (EIB) and fractional exhaled nitric oxide at the flow of 50 mL/s (FeNO50). However, no study has assessed the correlation between alveolar production (Calv) and bronchial flux (JNO) of nitric oxide (NO) and EIB in asthmatic children.

Objective

To identify the relationship between severity of EIB and bronchial or alveolar nitric oxide.

Methods

Our group included 36 allergic children with intermittent asthma. The EIB was determined by a standard exercise challenge and the severity was expressed as the maximum change in percentage from the baseline value of lung function (ΔFEV1%, ΔFEF25–75%) after exercising. A chemiluminescence analyser at multiple flows was used to calculate FeNO50, JNO and Calv, which reflect large airways, JNO and alveolar concentration of NO respectively.

Results

Sixteen (44.4%) children presented a ∆FEV1 ≥ 10%, eight (22.2%) had ∆FEV1 ≥ 15% and nine (25%) children had a ∆FEF25–75 ≥ 26%. A significant correlation was observed between severity of EIB and FeNO50, JNO and Calv. EIB was significantly more severe in children sensitive to indoor allergens compared with outdoor allergens only (P = 0.014); those children showed also higher levels of Calv (P = 0.003) and of JNO (P = 0.044).

Conclusions and Clinical Relevance

Our results suggest that inflammation is present in the central and peripheral airways and that it is associated with the severity of EIB.

Clinicaltrials.gov NCT00952835.
Altered frequency and phenotype of CD4+ forkhead box protein 3+ T cells and its association with autoantibody production in human immunodeficiency virus-infected paediatric patients
Authors: Argüello R J , Balbaryski J , Barboni G , Candi M , Gaddi E , Laucella S
Published: February 2012

The association between immune dysfunction and the development of autoimmune pathology in patients with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) is not clear. The frequency and phenotype of regulatory T cells, as well as the presence of autoantibodies, were evaluated in a paediatric cohort of HIV-infected patients without clinical evidence of autoimmune disease. Lower absolute counts but higher percentages of total CD4+ forkhead box protein 3 (FoxP3)+ T cells were recorded in children with severe immunosuppression than in those without evidence of immunosuppression. The frequencies of classical CD4+CD25+FoxP3+ regulatory T cells were not altered, whereas CD4+FoxP3+CD25- T cells were found increased significantly in patients with severe immunosuppression. Like classical regulatory T cells, CD4+FoxP3+CD25- T cells display higher cytotoxic T-lymphocyte antigen 4 (CTLA-4) but lower CD127 expression compared with CD4+FoxP3–CD25+ T cells. An improvement in CD4+ T cell counts, along with a decrease in viral load, was associated with a decrease in CD4+FoxP3+CD25- T cells. The majority of the patients with severe immunosuppression were positive for at least one out of seven autoantibodies tested and displayed hypergammaglobulinaemia. Conversely, HIV-infected children without evidence of immunosuppression had lower levels of autoantibodies and total immunoglobulins. A decline in CD4+FoxP3+ T cell numbers or a variation in their phenotype may induce a raise in antigen exposure with polyclonal B cell activation, probably contributing to the generation of autoantibodies in the absence of clinical autoimmune disease.