bluuebunny/crossref_metadata_2025 huggingface dataset:
One-step aluminium-assisted crystallization of Ge epitaxy on Si by magnetron sputtering
Authors: Liu Ziheng , Hao Xiaojing , Ho-Baillie Anita , Green Martin A.
Published: February 2014

In this work, one-step aluminium-assisted crystallization of Ge on Si is achieved via magnetron sputtering by applying an in-situ low temperature (50 °C to 150 °C) heat treatment in between Al and Ge depositions. The effect of heat treatment on film properties and the growth mechanism of Ge epitaxy on Si are studied via X-ray diffraction, Raman and transmission electron microscopy analyses. Compared with the conventional two-step process, the one-step aluminium-assisted crystallization requires much lower thermal budget and results in pure Ge epitaxial layer, which may be suitable for use as a virtual substrate for the fabrication of III-V solar cells.
Tunnel barrier engineering of titanium oxide for high non-linearity of selector-less resistive random access memory
Authors: Lee Sangheon , Woo Jiyong , Lee Daeseok , Cha Euijun , Park Jaesung , Moon Kibong , Song Jeonghwan , Koo Yunmo , Hwang Hyunsang
Published: February 2014

In this study, the effect of the oxygen profile and thickness of multiple-layers TiOx on tunnel barrier characteristics was investigated to achieve high non-linearity in low-resistance state current (ILRS). To form the tunnel barrier in multiple-layer of TiOx, tunnel barrier engineering in terms of the thickness and oxygen profile was attempted using deposition and thermal oxidation times. It modified the defect distribution of the tunnel barrier for effective suppression of ILRS at off-state (½VRead). By inserting modified tunnel barrier in resistive random access memory, a high non-linear ILRS was exhibited with a significantly lowered ILRS for ½VRead.
Genetic algorithm applied to the optimization of quantum cascade lasers with second harmonic generation
Authors: Gajić A. , Radovanović J. , Milanović V. , Indjin D. , Ikonić Z.
Published: February 2014

A computational model for the optimization of the second order optical nonlinearities in GaInAs/AlInAs quantum cascade laser structures is presented. The set of structure parameters that lead to improved device performance was obtained through the implementation of the Genetic Algorithm. In the following step, the linear and second harmonic generation power were calculated by self-consistently solving the system of rate equations for carriers and photons. This rate equation system included both stimulated and simultaneous double photon absorption processes that occur between the levels relevant for second harmonic generation, and material-dependent effective mass, as well as band nonparabolicity, were taken into account. The developed method is general, in the sense that it can be applied to any higher order effect, which requires the photon density equation to be included. Specifically, we have addressed the optimization of the active region of a double quantum well In0.53Ga0.47As/Al0.48In0.52As structure and presented its output characteristics.
Polarization matching design of InGaN-based semi-polar quantum wells—A case study of (112¯2) orientation
Authors: Kozlowski Grzegorz , Schulz Stefan , Corbett Brian
Published: February 2014

We present a theoretical study of the polarization engineering in semi-polar III-nitrides heterostructures. As a case study, we investigate the influence of GaN, AlGaN, and AlInN barrier material on the performance of semi-polar (112¯2) InGaN-based quantum wells (QWs) for blue (450 nm) and yellow (560 nm) emission. We show that the magnitude of the total built-in electric field across the QW can be controlled by the barrier material. Our results indicate that AlInN is a promising candidate to achieve (i) reduced wavelength shifts with increasing currents and (ii) strongly increased electron-hole wave function overlap, important for reduced optical recombination times.
Propagation of nonlinearly generated harmonic spin waves in microscopic stripes
Authors: Rousseau O. , Yamada M. , Miura K. , Ogawa S. , Otani Y.
Published: February 2014

We report on the experimental study of the propagation of nonlinearly generated harmonic spin waves in microscopic CoFeB stripes. Using an all electrical technique with coplanar waveguides, we find that two kinds of spin waves can be generated by nonlinear frequency multiplication. One has a non-uniform spatial geometry and thus requires appropriate detector geometry to be identified. The other corresponds to the resonant fundamental propagative spin waves and can be efficiently excited by double- or triple-frequency harmonics with any geometry. Nonlinear excited spin waves are particularly efficient in providing an electrical signal arising from spin wave propagation.
Probing deeper by hard x-ray photoelectron spectroscopy
Authors: Risterucci P. , Renault O. , Martinez E. , Detlefs B. , Delaye V. , Zegenhagen J. , Gaumer C. , Grenet G. , Tougaard S.
Published: February 2014

We report an hard x-ray photoelectron spectroscopy method combining high excitation energy (15 keV) and improved modelling of the core-level energy loss features. It provides depth distribution of deeply buried layers with very high sensitivity. We show that a conventional approach relying on intensities of the core-level peaks is unreliable due to intense plasmon losses. We reliably determine the depth distribution of 1 ML La in a high-κ/metal gate stack capped with 50 nm a-Si. The method extends the sensitivity of photoelectron spectroscopy to depths beyond 50 nm.
Origin of the martensitic and austenitic phase transition in core-surface smart nanoparticles with size effects and hysteretic splitting
Authors: Yalçın Orhan , Erdem Rıza , Özüm Songül
Published: February 2014

Blume-Emery-Griffiths model is used to study the effects of the bilinear and biquadratic exchange interactions as well as crystal field interaction on the magnetic properties of core-surface smart nanoparticles. From the minimization of the free energy in pair approximation in Kikuchi version, a set of equations for the bond variables and magnetization are derived. Based on the numerical solutions of these equations, magnetization and hysteresis curves are obtained. Besides the first- and second-order phase transitions, martensitic and austenitic phase regions are observed in the phase diagrams of homogeneous and composite nanoparticles and the origin of martensitic transitions (MT)-austenitic transitions (AT) is investigated. It is found that MT-AT occurred for a nonzero biquadratic exchange parameter. On the other hand, nonzero single-ion anisotropy caused the hysteretic splitting in core-surface type nanoparticles. Martensitic and austenitic results of nanoparticles agree with the experimental results in literature.
Quantum-confinement effects on conduction band structure of rectangular cross-sectional GaAs nanowires
Authors: Tanaka H. , Morioka N. , Mori S. , Suda J. , Kimoto T.
Published: February 2014

The conduction band structure and electron effective mass of GaAs nanowires with various cross-sectional shapes and orientations were calculated by two methods, a tight-binding method and an effective mass equation taking the bulk full-band structure into account. The effective mass of nanowires increases as the cross-sectional size decreases, and this increase in effective mass depends on the orientations and substrate faces of nanowires. Among [001], [110], and [111]-oriented rectangular cross-sectional GaAs nanowires, [110]-oriented nanowires with wider width along the [001] direction showed the lightest effective mass. This dependence originates from the anisotropy of the Γ valley of bulk GaAs. The relationship between effective mass and bulk band structure is discussed.
Nanoscale patterning of graphene through femtosecond laser ablation
Authors: Sahin R. , Simsek E. , Akturk S.
Published: February 2014

We report on nanometer-scale patterning of single layer graphene on SiO2/Si substrate through femtosecond laser ablation. The pulse fluence is adjusted around the single-pulse ablation threshold of graphene. It is shown that, even though both SiO2 and Si have more absorption in the linear regime compared to graphene, the substrate can be kept intact during the process. This is achieved by scanning the sample under laser illumination at speeds yielding a few numbers of overlapping pulses at a certain point, thereby effectively shielding the substrate. By adjusting laser fluence and translation speed, 400 nm wide ablation channels could be achieved over 100 μm length. Raster scanning of the sample yields well-ordered periodic structures, provided that sufficient gap is left between channels. Nanoscale patterning of graphene without substrate damage is verified with Scanning Electron Microscope and Raman studies.
A water-processable organic electron-selective layer for solution-processed inverted organic solar cells
Authors: Chen Dongcheng , Zhou Hu , Cai Ping , Sun Shi , Ye Hua , Su Shi-Jian , Cao Yong
Published: February 2014

A triazine- and pyridinium-containing water-soluble material of 1,1′,1″-(4,4′,4″-(1,3,5-triazine-2,4,6-triyl)tris(benzene-4,1-diyl))tris(methylene)tripyridinium bromide (TzPyBr) was developed as an organic electron-selective layer in solution-processed inverted organic solar cells due to its strong anti-erosion capacity against non-polar organic solvents commonly used for the active layer. Ohmic-like contact with the adjacent active materials like fullerene derivatives is speculated to be formed, as confirmed by the work-function measurements with scanning Kelvin probe and ultraviolet photoelectron spectroscopy techniques. Besides, considering the deep highest occupied molecular orbital energy level of TzPyBr, excellent hole-blocking property of the electron-selective layer is also anticipated. The inverted organic photovoltaic devices based on the TzPyBr/ITO (indium tin oxide) bilayer cathode exhibit dramatically enhanced performance compared to the control devices with bare ITO as the cathode and even higher efficiency than the conventional type devices with ITO and Al as the electrodes.
Directional collimation of substrate emitting quantum cascade laser by nanopores arrays
Authors: Zhang Jin-Chuan , Yao Dan-Yang , Zhuo Ning , Yan Fang-Liang , Liu Feng-Qi , Wang Li-Jun , Liu Jun-Qi , Wang Zhan-Guo
Published: February 2014

We report a beam reshaping phenomena via nanopore array defined on the emission window of a substrate emitting quantum cascade lasers. A pronounced beam divergence reduction by a factor of 6 in the elongated beam direction is achieved. A collimated laser beam with small divergence (2.9° × 0.12°) is observed. These single-mode devices preserve good power and spectral performances at room temperature continuous wave operation. This beam reshaping design is simple to fabricate and able to be adapted for other wavelengths ranging from the visible to mid-infrared regimes, which would open up major opportunities for the control of beam divergence.
Capacitive micromachined ultrasonic transducer arrays as tunable acoustic metamaterials
Authors: Lani Shane W. , Wasequr Rashid M. , Hasler Jennifer , Sabra Karim G. , Levent Degertekin F.
Published: February 2014

Capacitive Micromachined Ultrasonic Transducers (CMUTs) operating in immersion support dispersive evanescent waves due to the subwavelength periodic structure of electrostatically actuated membranes in the array. Evanescent wave characteristics also depend on the membrane resonance which is modified by the externally applied bias voltage, offering a mechanism to tune the CMUT array as an acoustic metamaterial. The dispersion and tunability characteristics are examined using a computationally efficient, mutual radiation impedance based approach to model a finite-size array and realistic parameters of variation. The simulations are verified, and tunability is demonstrated by experiments on a linear CMUT array operating in 2-12 MHz range.
Efficiency enhancement of InGaN/GaN solar cells with nanostructures
Authors: Bai J. , Yang C. C. , Athanasiou M. , Wang T.
Published: February 2014

We demonstrate InGaN/GaN multi-quantum-well solar cells with nanostructures operating at a wavelength of 520 nm. Nanostructures with a periodic nanorod or nanohole array are fabricated by means of modified nanosphere lithography. Under 1 sun air-mass 1.5 global spectrum illumination, a fill factor of 50 and an open circuit voltage of 1.9 V are achieved in spite of very high indium content in InGaN alloys usually causing degradation of crystal quality. Both the nanorod array and the nanohole array significantly improve the performance of solar cells, while a larger enhancement is observed for the nanohole array, where the conversion efficiency is enhanced by 51%.
Identification of an isolated arsenic antisite defect in GaAsBi
Authors: Dagnelund D. , Puustinen J. , Guina M. , Chen W. M. , Buyanova I. A.
Published: February 2014

Optically detected magnetic resonance and photoluminescence spectroscopy are employed to study grown-in defects in GaAs0.985Bi0.015 epilayers grown by molecular beam epitaxy. The dominant paramagnetic defect is identified as an isolated arsenic antisite, AsGa, with an electron g-factor of 2.03 ± 0.01 and an isotropic hyperfine interaction constant A = (900 ± 20) × 10−4 cm−1. The defect is found to be preferably incorporated during the growth at the lowest growth temperature of 270 °C, but its formation can be suppressed upon increasing growth temperature to 315 °C. The AsGa concentration is also reduced after post-growth rapid thermal annealing at 600 °C.
FeCoSiBNbCu bulk metallic glass with large compressive deformability studied by time-resolved synchrotron X-ray diffraction
Authors: Stoica Mihai , Scudino Sergio , Bednarčik Jozef , Kaban Ivan , Eckert Jürgen
Published: February 2014

By adding 0.5 at. % Cu to the strong but brittle [(Fe0.5Co0.5)0.75Si0.05B0.20]96Nb4 bulk metallic glass, fully amorphous rods with diameters up to 2 mm were obtained. The monolithic samples with 1 mm diameter revealed a fracture strain of 3.80% and a maximum stress of 4143 MPa upon compression, together with a slight work-hardening behavior. SEM micrographs of fractured samples did neither reveal any shear bands on the lateral surface nor the typical vein patterns which characterize ductile fracture. However, some layers appear to have flowed and this phenomenon took place before the brittle final fracture. An estimate of the temperature rise ΔT in the shear plane gives 1039 K, which is large enough to melt a layer of 120 nm. The overall performance and the macroscopic plastic strain depend on the interaction between cleavage-like and viscous flow-like features. Mechanical tests performed in-situ under synchrotron radiation allowed the calculation of the strain tensor components, using the reciprocal-space data and analyzing the shift of the first (the main) and the second broad peak positions in the X-ray diffraction patterns. The results revealed that each atomic shell may have a different stiffness, which may explain the macroscopic compressive plastic deformation. Also, there were no signs of (nano) crystallization induced by the applied stress, but the samples preserve a monolithic amorphous structure until catastrophic failure occurs.
The role of a-axis grains in the transition to the normal state of YBa2Cu3O7−δ films and of 2G-coated conductors when induced by high electrical current densities
Authors: Bernstein P. , Ferro G. , Harnois C. , Mc Loughlin C. , Noudem J. , Osorio M. R. , Thimont Y. , Veira J. A. , Vidal D. , Vidal F.
Published: February 2014

The influence of surface defects, in particular of a-axis grains, on the transition to the normal state induced by high current densities in YBa2Cu3O7−δ (YBCO) thin films and in a commercial 2G-coated conductor is investigated. For that purpose, the surface of the samples is observed by scanning electron microscopy and isothermal current-voltage curves are measured at different temperatures with pulsed currents up to the quenching value I*. The results show that the ratio of I* to the critical current is large if a-axis grains are not visible at the surface of the YBCO films, while it is much lower if the surface includes a-axis grains as this is the case for the coated conductor. The connection between the transition onset and the vortex dynamics, as well as the role of the a-axis grains in this process are discussed. The relation between the I* values obtained from thermal calculations and those resulting from vortex dynamics considerations is also discussed, as well as the possible consequences suggested by this work for the different applications of the coated conductors.
Characteristic properties of Raman scattering and photoluminescence on ZnO crystals doped through phosphorous-ion implantation
Authors: Jeong T. S. , Yu J. H. , Mo H. S. , Kim T. S. , Lim K. Y. , Youn C. J. , Hong K. J.
Published: February 2014

P-doped ZnO was fabricated by means of the ion-implantation method. At the Raman measurement, the blue shift of the E2high mode and A1(LO) phonon of the inactive mode were observed after the P-ion implantation. It suggested to be caused by the compressive stress. Thus, Hall effect measurement indicates that the acceptor levels exists in P-doped ZnO while still maintaining n-type ZnO. From the X-ray photoelectron spectroscopy, the chemical bond formation of the P2p3/2 spectrum consisted of 2(P2O5) molecules. Therefore, the implanted P ions were substituted to the Zn site in ZnO. From the photoluminescence (PL) spectra, P-related PL peaks were observed in the energy ranges of 3.1 and 3.5 eV, and its origin was analyzed at PZn-2VZn complexes, acting as a shallow acceptor. With increasing temperatures, the neutral-acceptor bound-exciton emission, (A0, X), shows a tendency to quench the intensity and extend the emission linewidth. From the relations of the intensity and the linewidth as a function of temperature, the broadening of linewidth was believed to the result that the vibration mode of E2high participates in the broadening process of (A0, X) and the change of luminescent intensity was attributed to the partial dissociation of (A0, X). Consequently, these facts indicate that the acceptor levels existed in P-doped ZnO layer by the ion implantation.
Intrinsic relationship between electronic structures and phase transition of SrBi2−xNdxNb2O9 ceramics from ultraviolet ellipsometry at elevated temperatures
Authors: Duan Z. H. , Jiang K. , Xu L. P. , Li Y. W. , Hu Z. G. , Chu J. H.
Published: February 2014

The ferroelectric orthorhombic to paraelectric tetragonal phase transition of SrBi2−xNdxNb2O9 (x = 0, 0.05, 0.1, and 0.2) layer-structured ceramics has been investigated by temperature-dependent spectroscopic ellipsometry. Based on the analysis of dielectric functions from 0 to 500 °C with double Tauc-Lorentz dispersion model, the interband transitions located at ultraviolet region have shown an abrupt variation near the Curie temperature. The changes of dielectric functions are mainly due to the thermal-optical and/or photoelastic effect. Moreover, the characteristic alteration in interband transitions can be ascribed to distortion of NbO6 octahedron and variation of hybridization between Bi 6s and O 2p states during the structure transformation.
Antisymmetric magnetoresistance in SmCo5 amorphous films with imprinted in-plane magnetic anisotropy
Authors: Moubah R. , Magnus F. , Hjörvarsson B. , Andersson G.
Published: February 2014

We report on magnetoresistance measurements in SmCo5 amorphous films with a giant imprinted magnetic anisotropy. At low applied field parallel to the easy axis, the magnetoresistance exhibits a hysteretic, square, and antisymmetric shape. The antisymmetry in the magnetoresistance is a result of the non-uniform distribution of the magnetization direction over the sample in conjunction with the extraordinary Hall effect. Moreover, the combination of anisotropic magnetoresistance measurements and magnetic domain imaging demonstrates that the symmetry depends on the magnetization orientation with respect to the applied field.
Enhance the coercivity of the rhombohedral lattice L11 CoPt thin film on glass substrate
Authors: Sun An-Cheng , Huang Chuan-Fa , Huang S. H.
Published: February 2014

CoPt L11 thin films with different thicknesses of 2-50 nm were epitaxially grown on Pt(111) underlayer on amorphous glass substrates by magnetron sputtering. The results show that high out-of-plane coercivity (Hc⊥), good perpendicular magnetic anisotropy (PMA), large magnetocrystalline anisotropy constant (Ku), and negative nucleation field (Hn) were achieved simultaneously in the thinner CoPt films, indicating a high impedance in the domain wall motion. TEM cross-section images displayed a well developed epitaxy of CoPt L11(111) orientation starting from Pt(111) plane and extending into magnetic CoPt(111) film, inducing the PMA of CoPt films. Surface morphologies of CoPt/Pt/glass films confirmed that surface CoPt grain sizes are similar to their magnetic domain sizes found in magnetic force microscopy results, evidencing the grain boundary pinning effect on the enhancement of Hc⊥. When the thickness of CoPt film was reduced to 3 nm, higher PMA with Hc⊥ ∼ 1.8 kOe and Ku ∼ 1.9 × 107 erg/cm3 suggests that L11 CoPt thin film is a promising candidate in the design of advanced spintronic devices, magnetic sensors, and magnetic recording media.
Fabrication of dot pattern using magnetic phase change on Pt ion-implanted L1 FePtRh film with high magnetocrystalline anisotropy
Authors: Hasegawa T. , Yamazaki T. , Kondo Y. , Ishio S.
Published: February 2014

Phase change from ferromagnetic to nonmagnetic phase by ion implantation was investigated for bit patterning. An antiferromagnetic L10 FePt0.64Rh0.36 film was implanted with Pt ions at 6.0 × 1015 ions/cm2 in order to control its magnetic properties. The film changed to a ferromagnetic one, with the (001) crystalline texture being normal to the film plane and a magnetocrystalline anisotropy of 2.3 × 107 erg/cm3 in the perpendicular direction. Using this magnetic phase change, a planar dot pattern was fabricated. The average height between the dots and the spacing was 0.35 nm, and ferromagnetic dots 50 nm in diameter were observed.
Structural defects induced by Fe-ion implantation in TiO2
Authors: Leedahl B. , Zatsepin D. A. , Boukhvalov D. W. , Green R. J. , McLeod J. A. , Kim S. S. , Kurmaev E. Z. , Zhidkov I. S. , Gavrilov N. V. , Cholakh S. O. , Moewes A.
Published: February 2014

X-ray photoelectron spectroscopy and resonant x-ray emission spectroscopy measurements of pellet and thin film forms of TiO2 with implanted Fe ions are presented and discussed. The findings indicate that Fe-implantation in a TiO2 pellet sample induces heterovalent cation substitution (Fe2+ → Ti4+) beneath the surface region. But in thin film samples, the clustering of Fe atoms is primarily detected. In addition to this, significant amounts of secondary phases of Fe3+ are detected on the surface of all doped samples due to oxygen exposure. These experimental findings are compared with density functional theory calculations of formation energies for different configurations of structural defects in the implanted TiO2:Fe system. According to our calculations, the clustering of Fe-atoms in TiO2:Fe thin films can be attributed to the formation of combined substitutional and interstitial defects. Further, the differences due to Fe doping in pellet and thin film samples can ultimately be attributed to different surface to volume ratios.
Chemical post-treatment and thermoelectric properties of poly(3,4-ethylenedioxylthiophene):poly(styrenesulfonate) thin films
Authors: Luo Jinji , Billep Detlef , Blaudeck Thomas , Sheremet Evgeniya , Rodriguez Raul D. , Zahn Dietrich R. T. , Toader Marius , Hietschold Michael , Otto Thomas , Gessner Thomas
Published: February 2014

We report on the modification of the thermoelectric properties of poly(3,4-ethylenedioxylthiophene):poly(styrenesulfonate) (PEDOT:PSS) thin films by means of a simple post treatment of the solid thin films realized by drop-coating. We show that the organic polar solvents, dimethyl sulfoxide and ethylene glycol as secondary dopants for PEDOT:PSS, only affect the film morphology for which a high electrical conductivity is observed. In contrast, ethanolamine (MEA) and ammonia solutions are reduction agents that improve the density of PEDOT chains in the reduced forms (polaron and neutral states), resulting in the trade-off between Seebeck coefficient and electrical conductivity. Furthermore, we show that the nature of amines determines the reduction degree: the nitrogen lone pair electrons in MEA are easier to be donated than those in ammonia solution and will therefore neutralize the PEDOT chains.
Optimal preselection and postselection in weak measurements for observing photonic spin Hall effect
Authors: Zhou Xinxing , Li Xing , Luo Hailu , Wen Shuangchun
Published: February 2014

Photonic spin Hall effect (SHE) holds great potential applications in precision metrology. How to obtain a high measurement precision is an important issue to detect the photonic SHE. In this Letter, we propose using optimal preselection and postselection in weak measurements to enhance the measurement precision. We find that the maximum weak value and pointer shift can be obtained with an optimal overlap of preselection and postselection states. These findings offer the possibility for improving the precision of weak measurements and thereby have possible applications for accurately characterizing the parameters of nanostructures.
Investigation of high hole mobility In0.41Ga0.59Sb/Al0.91Ga0.09Sb quantum well structures grown by molecular beam epitaxy
Authors: Wang Juan , Xing Jun-Liang , Xiang Wei , Wang Guo-Wei , Xu Ying-Qiang , Ren Zheng-Wei , Niu Zhi-Chuan
Published: February 2014

Modulation-doped In0.41Ga0.59Sb/Al0.91Ga0.09Sb quantum-well (QW) structures were grown by molecular beam epitaxy. Cross-sectional transmission electron microscopy and atomic force microscopy studies show high crystalline quality and smooth surface morphology. X-ray diffraction investigations confirm 1.94% compressive strain within In0.41Ga0.59Sb channel. High room temperature hole mobility with high sheet density of 1000 cm2/Vs, 0.877 × 1012/cm2, and 965 cm2/Vs, 1.112 × 1012/cm2 were obtained with different doping concentrations. Temperature dependent Hall measurements show different scattering mechanisms on hole mobility at different temperature range. The sheet hole density keeps almost constantly from 300 K to 77 K. This study shows great potential of In0.41Ga0.59Sb/Al0.91Ga0.09Sb QW for high-hole-mobility device applications.
Note: Phase retrieval method for analyzing single-phase displacement interferometry data
Authors: Chen X. H. , Zeng X. L. , Fan D. , Liu Q. C. , Bie B. X. , Zhou X. M. , Luo S. N.
Published: February 2014

We present a phase retrieval method (PRM) for analyzing single-phase displacement interferometry measurements on rapidly changing velocity histories, including photon Doppler velocimetry (PDV). PRM identifies the peaks and valleys as well as zero-crossing points in a PDV time series, performs normalization and extracts point-by-point phase and thus velocity information. PRM does not require a wide time window as in sliding window Fourier transformation, and thus improves the effective temporal resolution. This method is implemented in analyzing PDV data obtained from gas gun experiments, and validated against simultaneous measurements with velocity interferometer system for any reflector.
Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations
Authors: Fang X. W. , Huang Li , Wang C. Z. , Ho K. M. , Ding Z. J.
Published: February 2014

Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints.
Secretion of a pneumococcal type II secretion system pilus correlates with DNA uptake during transformation
Authors: Balaban Murat , Bättig Patrick , Muschiol Sandra , Tirier Stephan M. , Wartha Florian , Normark Staffan , Henriques-Normark Birgitta
Published: February 2014

Significance

Streptococcus pneumoniae
is a naturally competent organism, which can take up extracellular DNA by natural transformation. However, the mechanism by which DNA traverses the capsule and cell well layer is not understood. Here we describe a pilus structure in
S. pneumoniae
that is initially assembled on the bacterial surface when competence is induced, but subsequently secreted into the medium. We propose a mechanism for DNA uptake whereby the assembling pilus locally disrupts the rigid cell wall, creating a channel upon its release, creating an entry port for exogenous DNA. As DNA uptake coincides with pilus secretion, we suggest that, rather than acting as a retractile apparatus dragging DNA inside, the pilus acts as a cell-wall channel “drilling device.”
Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2–V3 interaction and modulates neutralization sensitivity
Authors: Cimbro Raffaello , Gallant Thomas R. , Dolan Michael A. , Guzzo Christina , Zhang Peng , Lin Yin , Miao Huiyi , Van Ryk Donald , Arthos James , Gorshkova Inna , Brown Patrick H. , Hurt Darrell E. , Lusso Paolo
Published: February 2014

Significance

Despite intensive efforts, the structure of the native HIV-1 envelope trimer—the sole relevant target for vaccine design—has remained elusive. Our work identifies a key structural constraint that stabilizes the native envelope conformation and modulates its sensitivity to neutralization. We show that this constraint is established by previously unrecognized sulfated tyrosines within the second variable loop (V2) of the envelope glycoprotein subunit gp120, which mediate intramolecular interaction with the base of the third variable loop, V3. Strikingly, the V2 sulfotyrosines functionally mimic those present in the N terminus of the CCR5 coreceptor, which bind to the same V3 region. Our results shed light on the mechanisms adopted by HIV-1 to elude immunologic control and open new perspectives for vaccine design.
High-strength cellular ceramic composites with 3D microarchitecture
Authors: Bauer Jens , Hengsbach Stefan , Tesari Iwiza , Schwaiger Ruth , Kraft Oliver
Published: February 2014

Significance

It has been a long-standing effort to create materials with low density but high strength. Technical foams are very light, but compared with bulk materials, their strength is quite low because of their random structure. Natural lightweight materials, such as bone, are cellular solids with optimized architecture. They are structured hierarchically and actually consist of nanometer-size building blocks, providing a benefit from mechanical size effects. In this paper, we demonstrate that materials with a designed microarchitecture, which provides both structural advantages and size-dependent strengthening effects, may be fabricated. Using 3D laser lithography, we produced micro-truss and -shell structures from ceramic–polymer composites that exceed the strength-to-weight ratio of all engineering materials, with a density below 1,000 kg/m
3
.
Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression
Authors: Rogier Eric W. , Frantz Aubrey L. , Bruno Maria E. C. , Wedlund Leia , Cohen Donald A. , Stromberg Arnold J. , Kaetzel Charlotte S.
Published: February 2014

Significance

An experimental system was developed in mice to study the long-term benefits of early exposure to secretory antibodies of the IgA class (SIgA) in breast milk. We found that breast milk-derived SIgA promoted intestinal epithelial barrier function in suckling neonates, preventing systemic infection by potential pathogens. Long-term benefits of early exposure to SIgA included maintenance of a healthy gut microbiota and regulation of gene expression in intestinal epithelial cells. These findings suggest that maternal antibodies provide benefits to the intestinal immune system of the breast-fed infant, which persist into adulthood.
Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling
Authors: Kasperkiewicz Paulina , Poreba Marcin , Snipas Scott J. , Parker Heather , Winterbourn Christine C. , Salvesen Guy S. , Drag Marcin
Published: February 2014

Significance

The exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1–S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural amino acid sequences, and thus we termed it the Hybrid Combinatorial Substrate Library. Using this approach, we have designed an extremely active substrate of NE and subsequently converted it into an ultrasensitive activity-based probe for imaging active elastase during the process of neutrophil extracellular trap formation. Our study could have a substantial effect on the design of substrates, inhibitors, and probes for any endopeptidase.
Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign
Authors: Tran Karen , Poulsen Christian , Guenaga Javier , de Val Natalia , Wilson Richard , Sundling Christopher , Li Yuxing , Stanfield Robyn L. , Wilson Ian A. , Ward Andrew B. , Karlsson Hedestam Gunilla B. , Wyatt Richard T.
Published: February 2014

Significance

The development of broadly neutralizing antibodies (bNAbs) to HIV-1 is often thought to be a key component of a successful vaccine. A common target of bNAbs is the conserved CD4 binding site (CD4bs) on the HIV envelope glycoprotein (Env) trimeric spike. Although CD4bs-directed bNAbs have been isolated from infected individuals, elicitation of such bNAbs by Env vaccination has proven difficult. To help understand the limitations of current immunogens, we structurally characterized two vaccine-elicited, CD4bs-directed non-bNAbs from primates. We demonstrate that these vaccine-elicited Abs attempt a vertical approach to the CD4bs, thereby clashing with the variable region of the trimeric spike cap, whereas CD4bs-directed bNAbs adopt angles of approach that avoid such clashes. This analysis can inform future vaccine redesign.
Functional and genetic studies of isolated cells from parathyroid tumors reveal the complex pathogenesis of parathyroid neoplasia
Authors: Shi Yuhong , Hogue Joyce , Dixit Darshana , Koh James , Olson John A.
Published: February 2014

Significance

Parathyroid adenomas, the main cause of primary hyperparathyroidism (PHPT), are thought to result from clonal expansion of tumor cells and to be insensitive to normal calcium feedback due to the loss of the calcium-sensing receptor (CASR). Utilizing flow cytometric analysis to isolate and individually study oxyphil cells, chief cells, and lymphocytes from resected parathyroid tumors and glands, we now report previously unrecognized heterogeneity in these tissues with respect to calcium responsiveness, CASR expression, and clonal origin of parathyroid tumors. Such heterogeneity of parathyroid adenomas likely reflects the complex etiopathogenesis and clinical heterogeneity of PHPT.
BMP signaling requires retromer-dependent recycling of the type I receptor
Authors: Gleason Ryan J. , Akintobi Adenrele M. , Grant Barth D. , Padgett Richard W.
Published: February 2014

Significance

The mechanisms that mediate bone morphogenetic protein (BMP) receptor recycling, and the importance of such recycling for signaling in vivo, have remained poorly understood. We find that the retromer complex functions as a linchpin in the recycling of the BMP type I receptor SMA-6 (small-6). In the absence of retromer-dependent recycling, retromer mutants result in the missorting of SMA-6 to lysosomes and a loss of BMP-mediated signaling. Surprisingly, we find that the BMP type II receptor, DAF-4 (dauer formation-defective-4), recycles through a distinct recycling pathway. Taken together, our results indicate a mechanism that separates the type I and type II receptors during receptor recycling, potentially terminating signaling while preserving both receptors for further rounds of activation.
UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs
Authors: Pirooz Sara Dolatshahi , He Shanshan , Zhang Tian , Zhang Xiaowei , Zhao Zhen , Oh Soohwan , O’Connell Douglas , Khalilzadeh Payam , Amini-Bavil-Olyaee Samad , Farzan Michael , Liang Chengyu
Published: February 2014

Significance

Negative-strand RNA viruses are highly pathogenic and cause many severe diseases in humans and animals. These viruses generally use existing cellular pathways to enter cells, which involves intensive interaction with the endomembrane network, offering the endocytic pathway as an attractive scheme for therapeutic intervention. Molecular mechanisms governing virus entry remain incompletely understood. We found that UV-radiation resistance-associated gene, well known for regulating autophagy and intracellular trafficking, is a critical factor for virus entry through combinatorial interactions with a tether and endosomal SNAREs. Understanding the mechanism that allows the virus to interact with late endocytic organelles could identify the specific set of proteins that have a role in virus entry, which will help us to design specific therapeutic agents against endocytic virus entries.
Identification of the transforming
STRN-ALK
fusion as a potential therapeutic target in the aggressive forms of thyroid cancer
Authors: Kelly Lindsey M. , Barila Guillermo , Liu Pengyuan , Evdokimova Viktoria N. , Trivedi Sumita , Panebianco Federica , Gandhi Manoj , Carty Sally E. , Hodak Steven P. , Luo Jianhua , Dacic Sanja , Yu Yan P. , Nikiforova Marina N. , Ferris Robert L. , Altschuler Daniel L. , Nikiforov Yuri E.
Published: February 2014

Significance

Thyroid cancer is common and has an excellent outcome in many cases, although a proportion of these tumors have a progressive clinical course and high mortality. Using whole-transcriptome (RNA-sequencing) analysis, we discovered previously unknown genetic events, anaplastic lymphoma kinase (
ALK
) gene fusions, in thyroid cancer and demonstrate that they occur more often in aggressive cancers. The most common fusion identified in these tumors involved the striatin (
STRN
) gene, and we show that it is transforming and tumorigenic in vivo. Finally, we demonstrate that the kinase activity of STRN-ALK can be blocked by ALK inhibitors, raising a possibility that ALK fusions may be used as a therapeutic target for patients with the most aggressive and frequently lethal forms of thyroid cancer.
Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase
Authors: Sugishima Masakazu , Sato Hideaki , Higashimoto Yuichiro , Harada Jiro , Wada Kei , Fukuyama Keiichi , Noguchi Masato
Published: February 2014

Significance

Heme oxygenase (HO) is a key enzyme for heme degradation that is deeply involved in iron homeostasis, defensive reaction against oxidative stress, and signal transduction mediated by carbon monoxide. To complete a single HO reaction, seven electrons supplied from NADPH-cytochrome P450 reductase (CPR) are required. Based on crystallography, X-ray scattering, and NMR analyses of CPR, it has been proposed that CPR has a dynamic equilibrium of the “closed-open transition.” The crystal structure of the transient complex of CPR with heme-bound HO clearly demonstrated that it is the open form of CPR that can interact with and transfer electrons to heme-bound HO. Moreover, the complex structure provides a scaffold to research the protein–protein interactions between CPR and other redox partners.
Long-distance mechanism of neurotransmitter recycling mediated by glial network facilitates visual function in
Drosophila
Authors: Chaturvedi Ratna , Reddig Keith , Li Hong-Sheng
Published: February 2014

Significance

Neurons communicate at synapses through neurotransmitters. For sustained neuronal signaling, neurotransmitters are recycled after release from neuronal terminals. During this process, perisynaptic glial cells take in and convert neurotransmitters such as glutamate, GABA, and histamine into inactive metabolites for transport. It has been assumed that inactive metabolites are delivered directly into neighboring neuronal terminals for neurotransmitter regeneration. Our work in the fruit fly, however, demonstrates that a gap junction-dependent multicellular glial network transports metabolites of histamine between perisynaptic glia and cell bodies of photoreceptor neurons, and this is required for visual signal transmission and alert behavior. Thus, by mediating this novel, long-distance recycling of neurotransmitters, intercellular glial networks play an important role in the maintenance of neuronal functions.
IgH
class switching exploits a general property of two DNA breaks to be joined
in cis
over long chromosomal distances
Authors: Gostissa Monica , Schwer Bjoern , Chang Amelia , Dong Junchao , Meyers Robin M. , Marecki Gregory T. , Choi Vivian W. , Chiarle Roberto , Zarrin Ali A. , Alt Frederick W.
Published: February 2014

Significance

During an immune response, B lymphocytes generate different classes of antibodies better suited to protect against particular pathogens by making two chromosomal cuts that are joined to replace one type of antibody gene with a different one. These cuts happen in widely separated segments of the chromosome that must be physically adjacent to be joined. We have asked how this happens. The surprising answer is that genes and gene segments lying certain distances apart on any chromosome may actually be packaged such that both are frequently touching or nearly touching and, if broken, can be efficiently joined by general processes that repair breaks in all our genes. The joining mechanisms we describe also may contribute to genetic deletions in cancers.
Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification
Authors: Alekseyenko Artyom A. , Gorchakov Andrey A. , Kharchenko Peter V. , Kuroda Mitzi I.
Published: February 2014

Significance

The fidelity of gene expression is regulated by chromosome-associated protein complexes. A traditional approach to characterizing complexes bound to chromosomes requires their release from the DNA to solubilize them. Here we develop an alternative approach, BioTAP-XL, that allows identification of protein–protein interactions while complexes remain linked to the DNA. We focus on protein interactions and genome localization of human EZH2 and two of its relatively uncharacterized interactors, C10orf12 and C17orf96. Our results provide strong evidence for diversity in human Polycomb repressive complexes, which are composed of factors essential for gene silencing during development in higher organisms. We propose that BioTAP-XL is an effective general approach for investigating the composition and subunit diversity of chromosome-associated complexes.
Measuring analyticity and syntheticity in creoles
Authors: Siegel Jeff , Szmrecsanyi Benedikt , Kortmann Bernd
Published: February 2014

Creoles (here including expanded pidgins) are commonly viewed as being more analytic than their lexifiers and other languages in terms of grammatical marking. The purpose of the study reported in this article was to examine the validity of this view by measuring the frequency of analytic (and synthetic) markers in corpora of two different English-lexified creoles — Tok Pisin and Hawai‘i Creole — and comparing the quantitative results with those for other language varieties.

To measure token frequency, 1,000 randomly selected words in each creole corpus were tagged with regard to word class, and categorized as being analytic, synthetic, both analytic and synthetic, or purely lexical. On this basis, an Analyticity Index and a Syntheticity Index were calculated. These were first compared to indices for other languages and then to L1 varieties of English (e.g. standard British and American English and British dialects) and L2 varieties (e.g. Singapore English and Hong Kong English). Type frequency was determined by the size of the inventories of analytic and synthetic markers used in the corpora, and similar comparisons were made.

The results show that in terms of both token and type frequency of grammatical markers, the creoles are not more analytic than the other varieties. However, they are significantly less synthetic, resulting in much higher ratios of analytic to synthetic marking. An explanation for this finding relates to the particular strategy for grammatical expansion used by individuals when the creoles were developing.
On the origins of Chota Valley Spanish
Authors: Sessarego Sandro
Published: February 2014

Chota Valley Spanish (CVS) is an Afro-Hispanic dialect spoken in the provinces of Imbabura and Carchi, Ecuador. The structure of CVS is relatively similar to Spanish, even though the conditions that characterized colonial Chota Valley seem — at a first glance — to have been ideal for a creole language to develop: a low white/black ratio, harsh working conditions on sugarcane plantations, massive introduction of African-born workers, and minimal contact with the outside Spanish speaking world (Schwegler 1999: 240; McWhorter 2000: 10–11). Two main hypotheses have been proposed to account for this fact: (a) the Monogenesis Hypothesis (Schwegler 1999); (b) the Afrogenesis Hypothesis (McWhorter 2000).

In the present paper, the linguistic and sociohistorical evidence available for CVS is analyzed. Findings indicate that the long assumed creolizing conditions for CVS were not in place in colonial Chota Valley and therefore hypotheses (a) and (b) do not accurately explain the true nature and evolution of this language. The present study suggests that CVS can be better analyzed as the result of intermediate and advanced second language acquisition processes, which do not imply a previous creole stage.
Re-entry into quiescence protects hematopoietic stem cells from the killing effect of chronic exposure to type I interferons
Authors: Pietras Eric M. , Lakshminarasimhan Ranjani , Techner Jose-Marc , Fong Sarah , Flach Johanna , Binnewies Mikhail , Passegué Emmanuelle
Published: February 2014

Type I interferons (IFN-1s) are antiviral cytokines that suppress blood production while paradoxically inducing hematopoietic stem cell (HSC) proliferation. Here, we clarify the relationship between the proliferative and suppressive effects of IFN-1s on HSC function during acute and chronic IFN-1 exposure. We show that IFN-1–driven HSC proliferation is a transient event resulting from a brief relaxation of quiescence-enforcing mechanisms in response to acute IFN-1 exposure, which occurs exclusively in vivo. We find that this proliferative burst fails to exhaust the HSC pool, which rapidly returns to quiescence in response to chronic IFN-1 exposure. Moreover, we demonstrate that IFN-1–exposed HSCs with reestablished quiescence are largely protected from the killing effects of IFNs unless forced back into the cell cycle due to culture, transplantation, or myeloablative treatment, at which point they activate a p53-dependent proapoptotic gene program. Collectively, our results demonstrate that quiescence acts as a safeguard mechanism to ensure survival of the HSC pool during chronic IFN-1 exposure. We show that IFN-1s can poise HSCs for apoptosis but induce direct cell killing only upon active proliferation, thereby establishing a mechanism for the suppressive effects of IFN-1s on HSC function.