bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient location strategy for airport surveillance using Mode-S multilateration systems
Authors: Mantilla-Gaviria Ivan A. , Leonardi Mauro , Galati Gaspare , Balbastre-Tejedor Juan V. , de Los Reyes Davó Elías
Published: February 2012

In this paper, the use of regularization methods to solve the location problem in multilateration systems, using Mode-S signals, is studied, evaluated, and developed. The Tikhonov method has been implemented as a first application to solve the classical system of hyperbolic equations in multilateration systems. Some simulations are obtained and the results are compared with those obtained by the well-established Taylor linearization and with the Cramér–Rao lower bound analysis. Significant improvements, for the accuracy, convergence, and the probability of location, are found for the application of the Tikhonov method.
Bottom dissipation of subinertial currents at the Atlantic zonal boundaries
Authors: Wright C. J. , Scott R. B. , Arbic B. K. , Furnival D. F.
Published: February 2012

Estimates of the dissipation of subinertial currents due to bottom boundary layer drag at the eastern and western boundaries of the North Atlantic ocean, between 15 N and 60 N, are computed using data from the world's largest archive of ocean current meter time series. We show from these data that a significant proportion of such loss in this region is due to dissipation at the western boundary ocean floor via quadratic bottom boundary layer drag, with an estimated 40–60% (31–47 GW) of the wind input power across the whole basin dissipated by this method. We further show that the majority of this dissipation occurs at shallow depths, <500 m; this has significant implications for the power available for abyssal mixing.
Stratospheric warmings and the geomagnetic lunar tide: 1958–2007
Authors: Yamazaki Y. , Richmond A. D. , Yumoto K.
Published: February 2012

A quantitative comparison of the geomagnetic lunar tide and lower stratospheric parameters (zonal mean air temperature T and zonal mean zonal wind U) is carried out for the period 1958–2007. The correlation between the amplitude of the geomagnetic lunar tide at an equatorial station, Addis Ababa, and the lower stratospheric parameters from the National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP‐NCAR) reanalysis is examined. It is found that the lunar tidal amplitude tends to be positively and negatively correlated with the stratospheric T and U, respectively, in high latitudes of the Northern Hemisphere during December and January. High correlations are observed in approximately 70% of stratospheric sudden warming (SSW) events. The results suggest that variability of the geomagnetic lunar tide during the northern winter is closely linked with dynamical changes in the lower stratospheric parameters associated with SSWs.
Circularly polarized plasmon modes in spheroidal nanoshells for applications to all-optical magnetic recording
Authors: Hung L. , Lang G. , McAvoy P. , Krafft C. , Mayergoyz I.
Published: February 2012

Circularly polarized plasmon modes in spheroidal nanoshells are studied. These plasmon modes are promising for all-optical magnetic recording. The formulas for the resonance wavelengths of these plasmon modes, their steady-state resonance amplitudes, and off-resonance excitations are derived. It is demonstrated that spheroidal nanoshells are superior to spherical nanoshells as far as the nanoscale focusing of circularly polarized light and the enhancement of its intensity are concerned.
L1 ordered phase formation in FePt, FePd, CoPt, and CoPd alloy thin films epitaxially grown on MgO(001) single-crystal substrates
Authors: Ohtake Mitsuru , Ouchi Shouhei , Kirino Fumiyoshi , Futamoto Masaaki
Published: February 2012

The FePt, FePd, CoPt, and CoPd epitaxial thin films are prepared on MgO(001) single-crystal substrates by ultrahigh vacuum RF magnetron sputtering. The effects of the magnetic material and the substrate temperature on the film growth, the film structure, and the magnetic properties are investigated. The L10 ordered phase formation is observed for FePt, FePd, and CoPt films prepared at temperatures higher than 200, 400, and 600 °C, respectively, whereas that is not recognized for CoPd films. The L10-FePd(001) single-crystal films with the c-axis normal to the substrate surface are formed, whereas the FePt and CoPt epitaxial films include L10(100) crystals whose c-axis is parallel to the substrate surface, in addition to the L10(001) crystals. Upon increasing the substrate temperature, the ordering degree increases. A higher ordering parameter is observed in the order of FePd > FePt > CoPt. The magnetic properties are influenced by the crystal structure, the crystallographic orientation of the L10 crystal, and the ordering degree.
Magnetic properties and microstructure of perpendicular FePt(B-Ag) granular films
Authors: Tsai J. L. , Huang J. C. , Tai H. W.
Published: February 2012

Multilayers [FePt(1 nm)/(BxAg1-x)(0.1 nm)]10 (x = 0 - 1) were alternately deposited on a glass substrate and subsequently annealed by a rapid thermal process (RTP) at 800 °C for 3 min. After RTP, FePt and immiscible (B, Ag) layers intermix to form (FePt)90(B-Ag)10 granular. The intermixed (B, Ag) atoms with high mobility diffuse among FePt grain boundaries to isolate and refine FePt grains uniformly with average grain size of 10 - 12 nm. The c-axis alignment in original multilayers remains unaltered during intermixing. With increasing Ag content in (BxAg1-x) (x = 0.3 - 0.7), c-axis orientation and grain-refinement are further improved. The optimal composition is (Fe0.48Pt0.52)90(B0.7Ag0.3)10.
Effect of pressure loading rate on the crystallographic texture of NdFeB nanocrystalline magnets
Authors: Rong Chuan-bing , Wu Y. Q. , Wang Dapeng , Zhang Ying , Poudyal Narayan , Kramer M. J. , Ping Liu J.
Published: February 2012

Plastic deformation of NdFeB nanocrystalline magnets has been performed at relatively low temperatures but high pressures compared to conventional hot deformation. The effect of deformation conditions on the crystallography texture of the anisotropic NdFeB magnets has been studied. It was observed that both deformation temperature and pressure loading rate significantly affect final crystallographic texture and thus magnetic properties. Energy product increases from 31 to 44 MGOe by simply reducing pressure loading rate from 300 MPa/min to 50 MPa/min. Microstructure observations confirm that better crystallographic texture has been obtained in the deformed magnets with a lower pressure loading rate.
Field weakening capability investigation of an axial flux permanent-magnet synchronous machine with radially sliding permanent magnets used for electric vehicles
Authors: Zhao Jing , Cheng Dansong , Zheng Ping , Liu Xiangdong , Tong Chengde , Song Zhiyi , Zhang Lu
Published: February 2012

Due to the advantage of high power density compared with the conventional radial flux machines, the axial flux permanent-magnet synchronous machines (PMSMs) are very suitable candidates for the power train of electric vehicles (EVs). In this paper, a new axial flux PMSM adopting radially sliding permanent magnets (PMs) to fulfill field-weakening control and to improve the operating speed range is investigated. The field-weakening structure and principle of the axial flux PMSM with radially sliding PMs are proposed and analyzed. The influence of radially sliding PMs on electromagnetic performances and parameters is analyzed based on FEM. The field-weakening method with radially sliding PMs, which is a mechanical method, is compared and combined with traditional electrical method. Due to the optimized combination of the two methods, the field-weakening capability of the machine is much improved and the maximum speed can reach up to six times of the base speed with constant power, which is very satisfying for EV drive application.
Investigation of magnetic properties of non-magnetic ion (Al, Ga, In) doped Ba2Mg0.5Co1.5Fe12O22
Authors: Lim Jung Tae , Kim Chin Mo , Lee Bo Wha , Kim Chul Sung
Published: February 2012

Ba2Mg0.5Co1.5Fe12O22 (non-doped) and non-magnetic ion (Al, Ga, In) doped Ba2Mg0.5Co1.5(Fe0.99M0.01)12O22 (M-doped) polycrystalline samples were prepared by the solid-state reaction method. The crystal structures and magnetic properties of samples were investigated with x-ray diffractometer (XRD), vibrating sample magnetometer (VSM), and Mössbauer spectroscopy. The crystal structures of non-doped and M-doped samples were determined as hexagonal structures with R-3m space group by the Rietveld refinement. The unit cell volume (Vu) of non-doped sample was Vu = 1298.0 Å3, while those of M-doped samples (M = Al, Ga, In) were Vu = 1295.7, 1296.7, and 1299.9 Å3, respectively. From the magnetic hysteresis curves at room temperature, the saturation magnetization (Ms) and coercivity (Hc) of non-doped sample were found to be Ms = 28.0 emu/g and Hc = 255.4 Oe, but those of M-doped samples (M = Al, Ga, In) were Ms = 24.7, 28.4, 28.6 emu/g, and Hc = 222.0, 215.9, 190.7 Oe, respectively. From the temperature dependence of magnetization curves under 100 Oe between 4.2 and 740 K, all samples showed magnetic structure transitions. In addition Mössbauer spectra of all samples were recorded at various temperatures ranging from 4.2 to 750 K. Based on the isomer shift (δ) values of all samples, the charge states were found to be Fe3+ state at 295 K.
Polycrystalline magnetic garnet films comprising weakly coupled crystallites for piezoelectrically-driven magneto-optic spatial light modulators
Authors: Mito S. , Sakurai H. , Takagi H. , Baryshev A. V. , Inoue M.
Published: February 2012

We have investigated the magnetization process of the polycrystalline magnetic garnet films in order to determine the most suitable composition of garnet films for piezoelectrically-driven magneto-optic spatial light modulators (MOSLMs). For experiment, the bismuth–dysprosium–aluminum-substituted yttrium iron (Bi1.3Dy0.7Y1.0Fe3.1Al1.9O12) garnet films were deposited by an RF magnetron sputter and annealed at 700 °C in air. The annealing time was varied in a range of several minutes to control the grain size. The saturation magnetization, the remanent magnetization and the composition of the fabricated garnet films slightly changed versus the annealing time. Experiments showed that the coercivity and the grain size increased at longer annealing; the coercivity was larger for films with bigger grains. This work shows that garnet films with smaller coercivity are most suitable for controlling the magnetization of garnet and, correspondingly, the magneto-optical rotation of MOSLM pixels driven by piezoelectrics.
Dust charging processes in the nonequilibrium dusty plasma with nonextensive power-law distribution
Authors: Gong Jingyu , Du Jiulin
Published: February 2012

The dust charging processes in the collections of electrons and ions in the nonequilibrium dusty plasma with power-law distributions are investigated on the basic of a new q-distribution function theory in nonextensive statistics. The electrons and ions in the plasma obey the power-law distributions and are with q-parameters different from each other. We derive generalized formulae for the dust charging currents in which the nonextensive effects play roles. Further we investigate the dust charging processes taking place in the homogeneous dusty plasma where only the particle velocities are power-law distributions and in the dust cloud plasma where the particle velocities and the particle densities are both power-law distributions. By numerical analyses we show that the nonextensive power-law distributions of electrons and ions have significant effects on the dust charging processes in the nonequilibrium dusty plasma.
Heat transfer and friction characteristics of solar air heater duct roughened by broken V-shape ribs combined with staggered rib piece
Authors: Patil Anil K. , Saini J. S. , Kumar K.
Published: February 2012

Thermal performance of solar air heater has been found to be substantially improved by the application of artificial roughness provided on underside of absorber surface. The present investigation was taken up to study the effect of broken V-rib roughness combined with staggered ribs on heat transfer and friction in a flow through artificially roughened solar air heater duct. This work covered a range of Reynolds number (Re) 3000–17 000, relative staggered rib pitch (p′/p) 0.2–0.8, relative staggered rib size (r/e) 1–2.5, relative gap position (s′/s) 0.2–0.8 for the fixed values of relative roughness pitch (p/e) of 10, relative roughness height (e/Dh) of 0.043, relative gap size (g/e) of 1, and angle of attack (α) of 60°. Experimental data pertinent to heat transfer and friction was generated and thermohydraulic performance was determined for different sets of roughness and flow parameters.
Detecting and tuning anisotropic mode splitting induced by birefringence in an InGaAs/GaAs/AlGaAs vertical-cavity surface-emitting laser
Authors: Yu J. L. , Chen Y. H. , Jiang C. Y. , Ye X. L. , Zhang H. Y.
Published: February 2012

The mode splitting induced by birefringence in an InGaAs/GaAs/AlGaAs vertical-cavity surface-emitting laser (VCSEL) has been studied by reflectance difference spectroscopy (RDS) at room temperature. The mode splitting, anisotropic broadening width, and the anisotropic integrated area of the cavity mode are determined. Uniaxial strain on the order of 10−4 is introduced to tune the mode splitting. The mode splitting can be linearly tuned by the uniaxial strain, which agrees very well with theoretical calculations using a Jones matrix approach. We demonstrate that the RDS is a powerful, nondestructive tool to study the cavity anisotropy of VCSELs.
A study of sub-terahertz and terahertz gyrotron oscillators
Authors: Kao S. H. , Chiu C. C. , Chu K. R.
Published: February 2012

We present a theoretical study on some of the key physics issues associated with over-moded, sub-terahertz, and terahertz (THz) gyrotron oscillators. Simulations of a large number of fundamental and second cyclotron harmonic modes yield a broad database for physics observations as well as a test of relevant scaling laws. Linear properties over a broad magnetic field range exhibit a number of interesting trends. Nonlinearly, despite the possibility of multimode excitation, each mode is found to exist as a dominant single mode in a narrow magnetic field range, and a significant fraction of these modes are due to second cyclotron harmonic interactions. The wall resistivity, while a relatively minor concern for sub-terahertz gyrotrons, is shown to play a radically different role in the THz regime. It affords a linear advantage to the harmonic modes while also significantly degrading their output efficiencies. These results are interpreted in terms of the nature of harmonic mode competition and the scaling laws for the cavity quality factors.
Chiral recognition of zinc phthalocyanine on Cu(100) surface
Authors: Chen Feng , Chen Xiu , Liu Lacheng , Song Xin , Liu Shuyi , Liu Juan , Ouyang Hongping , Cai Yingxiang , Liu Xiaoqing , Pan Haibing , Zhu Junfa , Wang Li
Published: February 2012

The windmill-like chiral nature of individual ZnPc molecules adsorbed on Cu(100) surface at room temperature has been revealed by scanning tunneling microscopy (STM) and the origin of such chirality is attributed to asymmetrical charge transfer between the molecules and the copper surface. Such chiral enantiomers do recognize each other in molecular level and spontaneously form second-level chiral supramolecular structures with the same chirality during thermally driven movements. The interactions between the ZnPc molecules during such chiral recognition process have been discussed based on the analysis of the sub-molecule-resolution STM images.
Sensitivity of nucleation phenomena on range of interaction potential
Authors: Singh Rakesh S. , Santra Mantu , Bagchi Biman
Published: February 2012

Theoretical and computational investigations of nucleation have been plagued by the sensitivity of the phase diagram to the range of the interaction potential. As the surface tension depends strongly on the range of interaction potential and as the classical nucleation theory (CNT) predicts the free energy barrier to be directly proportional to the cube of the surface tension, one expects a strong sensitivity of nucleation barrier to the range of the potential; however, CNT leaves many aspects unexplored. We find for gas-liquid nucleation in Lennard-Jones system that on increasing the range of interaction the kinetic spinodal (KS) (where the mechanism of nucleation changes from activated to barrierless) shifts deeper into the metastable region. Therefore the system remains metastable for larger value of supersaturation and this allows one to explore the high metastable region without encountering the KS. On increasing the range of interaction, both the critical cluster size and pre-critical minima in the free energy surface of kth largest cluster, at respective kinetic spinodals, shift towards smaller cluster size. In order to separate surface tension contribution to the increase in the barrier from other non-trivial factors, we introduce a new scaling form for surface tension and use it to capture both the temperature and the interaction range dependence of surface tension. Surprisingly, we find only a weak non-trivial contribution from other factors to the free energy barrier of nucleation.
Field-emission properties of individual GaN nanowires grown by chemical vapor deposition
Authors: Choi Yongho , Michan Mario , Johnson Jason L. , Naieni Ali Kashefian , Ural Ant , Nojeh Alireza
Published: February 2012

Single crystalline GaN nanowires were synthesized using chemical vapor deposition. Devices containing individual GaN nanowires were fabricated using contact printing. The local turn-on electric field at the tip of the GaN nanowires was compared to that of other nanomaterials. The quality of contact between GaN nanowires and metal electrodes was found to affect the field-emission behavior significantly. It was also observed that the field-emission behavior of individual GaN nanowires follows the conventional Fowler-Nordheim model in the range of applied electric fields.
Monte Carlo simulation study of positron generation in ultra-intense laser-solid interactions
Authors: Yan Yonghong , Wu Yuchi , Zhao Zongqing , Teng Jian , Yu Jinqing , Liu Dongxiao , Dong Kegong , Wei Lai , Fan Wei , Cao Leifeng , Yao Zeen , Gu Yuqiu
Published: February 2012

The Monte Carlo transport code Geant4 has been used to study positron production in the transport of laser-produced hot electrons in solid targets. The dependence of the positron yield on target parameters and the hot-electron temperature has been investigated in thick targets (mm-scale), where only the Bethe-Heitler process is considered. The results show that Au is the best target material, and an optimal target thickness exists for generating abundant positrons at a given hot-electron temperature. The positron angular distributions and energy spectra for different hot electron temperatures were studied without considering the sheath field on the back of the target. The effect of the target rear sheath field for positron acceleration was studied by numerical simulation while including an electrostatic field in the Monte Carlo model. It shows that the positron energy can be enhanced and quasi-monoenergetic positrons are observed owing to the effect of the sheath field.
Crystallization and surface texturing of amorphous-Si induced by UV laser for photovoltaic application
Authors: Hong Lei , Wang Xincai , Rusli  , Wang Hao , Zheng Hongyu , Yu Hongyu
Published: February 2012

The DPSS Nd:YVO4 UV laser is used to anneal amorphous silicon (a-Si) film to achieve crystallization and nano-dome surface texturing simultaneously in a one-step annealing process. With pulse energy of 380 mJ/cm2 and repetition rate of 20 kHz, the a-Si can be crystallized by the sequential lateral solidification process, which is evidenced by both SEM characterization and Raman spectra. In addition, the nano-dome like structure is confirmed by AFM characterization, which can lead to ∼200% boost in terms of light absorption as measured by UV-Visible - Near-infrared scanning spectrophotometer. This study highlights the great potential of Nd:YVO4 UV laser for its application in thin film Si solar cell industry to improve the film quality and light trapping capability.
Recoil frame photoelectron angular distributions of BF3: A sensitive probe of the shape resonance in the F 1s continuum
Authors: Mizuno T. , Adachi J. , Miyauchi N. , Kazama M. , Stener M. , Decleva P. , Yagishita A.
Published: February 2012

Recoil frame photoelectron angular distributions (RFPADs) of BF3 molecules are presented over the energy region of the shape resonance in the F 1s continuum. Time-dependent density functional theory calculations are also given to understand the shape resonance dynamics. The RFPADs have been compared with the theoretical calculations. It is found that the RFPADs calculated by the localized core-hole model are in better agreement with the experimental, compared with those by the delocalized core hole. Dipole matrix elements and dipole prepared continuum wavefunctions show that the shape resonance in the F 1s ionization continuum of BF3 is induced by p-partial waves as previously reported by Swanson et al. [J. Chem. Phys. 75, 619 (1981)10.1063/1.442078]. However, due to the couplings with the other partial waves the feature characteristic of the p-partial waves has not been observed in the RFPADs.
Memory switching properties of e-beam evaporated SiOx on N++ Si substrate
Authors: Wang Yanzhen , Chen Yen-Ting , Xue Fei , Zhou Fei , Chang Yao-Feng , Fowler Burt , Lee Jack C.
Published: February 2012

The resistive switching between high impedance (“off” state) and low impedance (“on” state) is demonstrated on e-beam evaporated SiOx/Si resistive random access memory devices in this paper. The set and reset voltages are independent of the device perimeters and oxide thicknesses after electroforming. A circuit model including filament conductance G is proposed to explain the measured “on” state capacitances under frequency ranges from 1 KHz to 1 MHz. The electrochemical redox process is adopted to explain the formation of Si filament during electroforming and switching. “On” and “off” currents were also measured at various operating temperatures. It is found that both set and reset voltages increase as temperature decreases and that no electroforming is exhibited at low temperature T = 77 K.
Improved dielectric functions in metallic films obtained via template stripping
Authors: Hyuk Park Jong , Nagpal Prashant , Oh Sang-Hyun , Norris David J.
Published: February 2012

We compare the dielectric functions of silver interfaces obtained via thermal evaporation with those obtained with template stripping. Ellipsometry measurements show that the smoother template-stripped surfaces exhibit effective dielectric functions with a more negative real component and a smaller imaginary component, implying higher conductivity and less energy loss, respectively. These results agree with the relation between dielectric function and surface roughness derived from combining the effective-medium model and the Drude-Lorentz model. The improvement in the effective dielectric properties shows that metallic films prepared via template stripping can be favorable for applications in electronics, nanophotonics, and plasmonics.
Communication: Fundamental measure theory for hard disks: Fluid and solid
Authors: Roth Roland , Mecke Klaus , Oettel Martin
Published: February 2012

Two-dimensional hard-particle systems are rather easy to simulate but surprisingly difficult to treat by theory. Despite their importance from both theoretical and experimental points of view, theoretical approaches are usually qualitative or at best semi-quantitative. Here, we present a density functional theory based on the ideas of fundamental measure theory for two-dimensional hard-disk mixtures, which allows for the first time an accurate description of the structure of the dense fluid and the equation of state for the solid phase within the framework of density functional theory. The properties of the solid phase are obtained by freely minimizing the functional.
Enhancement of ion generation in femtosecond ultraintense laser-foil interactions by defocusing
Authors: Xu M. H. , Li Y. T. , Carroll D. C. , Foster P. S. , Hawkes S. , Kar S. , Liu F. , Markey K. , McKenna P. , Streeter M. J. V. , Spindloe C. , Sheng Z. M. , Wahlström C.-G. , Zepf M. , Zheng J. , Zhang J. , Neely D.
Published: February 2012

A simple method to enhance ion generation with femtosecond ultraintense lasers is demonstrated experimentally by defocusing laser beams on target surface. When the laser is optimally defocused, we find that the population of medium and low energy protons from ultra-thin foils is increased significantly while the proton cutoff energy is almost unchanged. In this way, the total proton yield can be enhanced by more than 1 order, even though the peak laser intensity drops. The depression of the amplified spontaneous emission (ASE) effect and the population increase of moderate-energy electrons are believed to be the main reasons for the effective enhancement.
Dielectric responses and scaling behaviors in Aurivillius Bi6Ti3Fe2O18 multiferroic thin films
Authors: Bai W. , Chen G. , Zhu J. Y. , Yang J. , Lin T. , Meng X. J. , Tang X. D. , Duan C. G. , Chu J. H.
Published: February 2012

Dielectric responses and scaling behaviors of Aurivillius Bi6Ti3Fe2O18 (BTF2) multiferroic thin films were systemically detailed by the temperature-dependent dielectric/impedance spectroscopy. We clarified two dielectric relaxation processes presented in grain interior of the BTF2 films. One relaxation below ∼500 K was proposed to associate with the localized hopping process of carrier between Fe3+ and Fe2+ inside the grains. Another one above ∼500 K arose from the long-range movement of oxygen vacancies. The scaling behaviors implied that the distribution of relaxation times for oxygen vacancies was temperature independent while the dynamical processes for the hopping carriers presumably depended on temperature.
Optical observation of single-carrier charging in type-II quantum ring ensembles
Authors: Young R. J. , Smakman E. P. , Sanchez A. M. , Hodgson P. , Koenraad P. M. , Hayne M.
Published: February 2012

A high-purity GaSb/GaAs quantum ring system is introduced that provides both strong hole-confinement in the GaSb ring and electron confinement in its GaAs core. The latter is responsible for a reduced inhomogeous linewidth measured in photoluminescence, in comparison to the previous measurements made on nanostructures with differing morphology in this material system. This allows the resolution of multiple peaks in the photoluminescence due to discrete charging with holes, revealing the mechanism responsible for the excitation-power-induced blueshift.
85 °C error-free operation at 38 Gb/s of oxide-confined 980-nm vertical-cavity surface-emitting lasers
Authors: Moser P. , Wolf P. , Mutig A. , Larisch G. , Unrau W. , Hofmann W. , Bimberg D.
Published: February 2012

Extremely temperature stable oxide-confined high-speed 980-nm vertical-cavity surface-emitting lasers (VCSELs) for optical interconnects are presented. Error-free performance at 38 Gb/s and 40 Gb/s is demonstrated at temperatures as high as 85 °C and 75 °C, respectively. No adjustment of driving conditions was found to be necessary from room temperature up to 85 °C. In addition, energy-efficient 35 Gb/s operation at a very low pump current of only 4 mA is demonstrated with a low dissipated heat-to-bit rate ratio of 233 mW/Tbps. These are by far the highest bit rates reported for VCSELs at such temperatures.
Phase transition behaviors of PbZr1−xTixO3 single crystals as revealed by elastic anomalies and central peaks
Authors: Hyun Kim Tae , Ko Jae-Hyeon , Kojima Seiji , Bokov Alexei A. , Long Xifa , Ye Zuo-Guang
Published: February 2012

Two PbZr1−xTixO3 (PZT) single crystals with x≈ 0.45 and 0.42 near the morphotropic phase boundary were studied by Brillouin light scattering, giving rise to the first single-crystal elastic data which were discussed in terms of the correlation between the acoustic anomalies and the phase transition sequence. The ferroelectric phase transition of PZT with x≈ 0.45 was second order (or very close to the second order) which accompanied very large polarization fluctuations resulting in the formation of strong central peaks. A revised phase diagram of PZT was suggested including refinement of the tilt phase boundary and a possible existence of tricritical point.
Phosphorylation of syndapin I F-BAR domain at two helix-capping motifs regulates membrane tubulation
Authors: Quan Annie , Xue Jing , Wielens Jerome , Smillie Karen J. , Anggono Victor , Parker Michael W. , Cousin Michael A. , Graham Mark E. , Robinson Phillip J.
Published: February 2012

Syndapin I (PACSIN 1) is a synaptically enriched membrane tubulating protein that plays important roles in activity-dependent bulk endocytosis and neuronal morphogenesis. While syndapin I is an in vitro phosphoprotein, it is not known to be phosphorylated in neurons. Here, we report the identification of two phosphorylation sites, S76 and T181, of syndapin I from nerve terminals. Both residues are located at the N-terminal helix-capping motifs (N-Cap) of different α-helices in the F-BAR domain, important for F-BAR homodimer curvature and dimer-dimer filament assembly, respectively. Phospho-mimetic mutations of these residues regulate lipid-binding and tubulation both in vitro and in cells. Neither phosphosite regulated syndapin I function in activity-dependent bulk endocytosis. Rather, T181 phosphorylation was developmentally regulated and inhibited syndapin I function in neuronal morphogenesis. This suggests a novel mechanism for phosphorylation control of an F-BAR function through the regulation of α-helix interactions and stability within the folded F-BAR domain.
ATM kinase inhibition in glial cells activates the innate immune response and causes neurodegeneration inDrosophila
Authors: Petersen Andrew J. , Rimkus Stacey A. , Wassarman David A.
Published: February 2012

To investigate the mechanistic basis for central nervous system (CNS) neurodegeneration in the disease ataxia–telangiectasia (A-T), we analyzed flies mutant for the causative geneA-T mutated(ATM).ATMencodes a protein kinase that functions to monitor the genomic integrity of cells and control cell cycle, DNA repair, and apoptosis programs. Mutation of the C-terminal amino acid inDrosophilaATM inhibited the kinase activity and caused neuron and glial cell death in the adult brain and a reduction in mobility and longevity. These data indicate that reduced ATM kinase activity is sufficient to cause neurodegeneration in A-T. ATM kinase mutant flies also had elevated expression of innate immune response genes in glial cells.ATMknockdown in glial cells, but not neurons, was sufficient to cause neuron and glial cell death, a reduction in mobility and longevity, and elevated expression of innate immune response genes in glial cells, indicating that a non–cell-autonomous mechanism contributes to neurodegeneration in A-T. Taken together, these data suggest that early-onset CNS neurodegeneration in A-T is similar to late-onset CNS neurodegeneration in diseases such as Alzheimer's in which uncontrolled inflammatory response mediated by glial cells drives neurodegeneration.
Suppressing cascades of load in interdependent networks
Authors: Brummitt Charles D. , D’Souza Raissa M. , Leicht E. A.
Published: February 2012

Understanding how interdependence among systems affects cascading behaviors is increasingly important across many fields of science and engineering. Inspired by cascades of load shedding in coupled electric grids and other infrastructure, we study the Bak–Tang–Wiesenfeld sandpile model on modular random graphs and on graphs based on actual, interdependent power grids. Starting from two isolated networks, adding some connectivity between them is beneficial, for it suppresses the largest cascades in each system. Too much interconnectivity, however, becomes detrimental for two reasons. First, interconnections open pathways for neighboring networks to inflict large cascades. Second, as in real infrastructure, new interconnections increase capacity and total possible load, which fuels even larger cascades. Using a multitype branching process and simulations we show these effects and estimate the optimal level of interconnectivity that balances their trade-offs. Such equilibria could allow, for example, power grid owners to minimize the largest cascades in their grid. We also show that asymmetric capacity among interdependent networks affects the optimal connectivity that each prefers and may lead to an arms race for greater capacity. Our multitype branching process framework provides building blocks for better prediction of cascading processes on modular random graphs and on multitype networks in general.
The role of the small GTPase Rap in
Drosophila
R7 photoreceptor specification
Authors: Mavromatakis Yannis Emmanuel , Tomlinson Andrew
Published: February 2012

The
Drosophila
R7 photoreceptor provides an excellent model system with which to study how cells receive and “decode” signals that specify cell fate. R7 is specified by the combined actions of the receptor tyrosine kinase (RTK) and Notch (N) signaling pathways. These pathways interact in a complex manner that includes antagonistic effects on photoreceptor specification: RTK promotes the photoreceptor fate, whereas N inhibits. Although other photoreceptors are subject to only mild N activation, R7 experiences a high-level N signal. To counter this effect and to ensure that the cell is specified as a photoreceptor, a high RTK signal is transduced in the cell. Thus, there are two levels of RTK transduction in the photoreceptors: in R7 it is high, whereas in others it is low. Here, we address how this high-level RTK signal is transduced in R7 and find that, in addition to Ras, another small GTPase, Rap, is also engaged. Thus, when N activity is high, a robust RTK signal operates that uses both Ras and Rap, but when N activity is low, only a mild RTK signal is transduced and Ras alone suffices for the purpose.
Cyclin-dependent kinase 1 (Cdk1) is essential for cell division and suppression of DNA re-replication but not for liver regeneration
Authors: Diril M. Kasim , Ratnacaram Chandrahas Koumar , Padmakumar V. C. , Du Tiehua , Wasser Martin , Coppola Vincenzo , Tessarollo Lino , Kaldis Philipp
Published: February 2012

Cyclin-dependent kinase 1 (Cdk1) is an archetypical kinase and a central regulator that drives cells through G2 phase and mitosis. Knockouts of Cdk2, Cdk3, Cdk4, or Cdk6 have resulted in viable mice, but the in vivo functions of Cdk1 have not been fully explored in mammals. Here we have generated a conditional-knockout mouse model to study the functions of Cdk1 in vivo. Ablation of Cdk1 leads to arrest of embryonic development around the blastocyst stage. Interestingly, liver-specific deletion of Cdk1 is well tolerated, and liver regeneration after partial hepatectomy is not impaired, indicating that regeneration can be driven by cell growth without cell division. The loss of Cdk1 does not affect S phase progression but results in DNA re-replication because of an increase in Cdk2/cyclin A2 activity. Unlike other Cdks, loss of Cdk1 in the liver confers complete resistance against tumorigenesis induced by activated Ras and silencing of p53.
Robustness of topological order and formation of quantum well states in topological insulators exposed to ambient environment
Authors: Chen Chaoyu , He Shaolong , Weng Hongming , Zhang Wentao , Zhao Lin , Liu Haiyun , Jia Xiaowen , Mou Daixiang , Liu Shanyu , He Junfeng , Peng Yingying , Feng Ya , Xie Zhuojin , Liu Guodong , Dong Xiaoli , Zhang Jun , Wang Xiaoyang , Peng Qinjun , Wang Zhimin , Zhang Shenjin , Yang Feng , Chen Chuangtian , Xu Zuyan , Dai Xi , Fang Zhong , Zhou X. J.
Published: February 2012

The physical property investigation (like transport measurements) and ultimate application of the topological insulators usually involve surfaces that are exposed to ambient environment (1 atm and room temperature). One critical issue is how the topological surface state will behave under such ambient conditions. We report high resolution angle-resolved photoemission measurements to directly probe the surface state of the prototypical topological insulators, Bi
2
Se
3
and Bi
2
Te
3
, upon exposing to various environments. We find that the topological order is robust even when the surface is exposed to air at room temperature. However, the surface state is strongly modified after such an exposure. Particularly, we have observed the formation of two-dimensional quantum well states near the exposed surface of the topological insulators. These findings provide key information in understanding the surface properties of the topological insulators under ambient environment and in engineering the topological surface state for applications.
Structural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors
Authors: Osz Judit , Brélivet Yann , Peluso-Iltis Carole , Cura Vincent , Eiler Sylvia , Ruff Marc , Bourguet William , Rochel Natacha , Moras Dino
Published: February 2012

Transcription regulation by steroid hormones, vitamin derivatives, and metabolites is mediated by nuclear receptors (NRs), which play an important role in ligand-dependent gene expression and human health. NRs function as homodimers or heterodimers and are involved in a combinatorial, coordinated and sequentially orchestrated exchange between coregulators (corepressors, coactivators). The architecture of DNA-bound functional dimers positions the coregulators proteins. We previously demonstrated that retinoic acid (RAR-RXR) and vitamin D3 receptors (VDR-RXR) heterodimers recruit only one coactivator molecule asymmetrically without steric hindrance for the binding of a second cofactor. We now address the problem of homodimers for which the presence of two identical targets enhances the functional importance of the mode of binding. Using structural and biophysical methods and RAR as a model, we could dissect the molecular mechanism of coactivator recruitment to homodimers. Our study reveals an allosteric mechanism whereby binding of a coactivator promotes formation of nonsymmetrical RAR homodimers with a 2∶1 stoichiometry. Ligand conformation and the cofactor binding site of the unbound receptor are affected through the dimer interface. A similar control mechanism is observed with estrogen receptor (ER) thus validating the negative cooperativity model for an established functional homodimer. Correlation with published data on other NRs confirms the general character of this regulatory pathway.
Hypervariable loci in the human gut virome
Authors: Minot Samuel , Grunberg Stephanie , Wu Gary D. , Lewis James D. , Bushman Frederic D.
Published: February 2012

Genetic variation is critical in microbial immune evasion and drug resistance, but variation has rarely been studied in complex heterogeneous communities such as the human microbiome. To begin to study natural variation, we analyzed DNA viruses present in the lower gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA sequence. Viral genomes mostly showed low variation, but 51 loci of ∼100 bp showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data were in previously undescribed gene types, including genes encoding predicted Ig-superfamily proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade, which we find is the most abundant clade among gut viruses but only a minor component of bacterial RT populations. Hypervariation was targeted to 5′-AAY-3′ asparagine codons, which allows maximal chemical diversification of the encoded amino acids while avoiding formation of stop codons. These findings document widespread targeted hypervariation in the human gut virome, identify previously undescribed types of genes targeted for hypervariation, clarify association with RT gene clades, and motivate studies of hypervariation in the full human microbiome.
Overlapping functions between XLF repair protein and 53BP1 DNA damage response factor in end joining and lymphocyte development
Authors: Liu Xiangyu , Jiang Wenxia , Dubois Richard L. , Yamamoto Kenta , Wolner Zachary , Zha Shan
Published: February 2012

Nonhomologous end joining (NHEJ), a major pathway of DNA double-strand break (DSB) repair, is required during lymphocyte development to resolve the programmed DSBs generated during Variable, Diverse, and Joining [V(D)J] recombination. XRCC4-like factor (XLF) (also called Cernunnos or NHEJ1) is a unique component of the NHEJ pathway. Although germ-line mutations of other NHEJ factors abrogate lymphocyte development and lead to severe combined immunodeficiency (SCID), XLF mutations cause a progressive lymphocytopenia that is generally less severe than SCID. Accordingly, XLF-deficient murine lymphocytes show no measurable defects in V(D)J recombination. We reported earlier that ATM kinase and its substrate histone H2AX are both essential for V(D)J recombination in XLF-deficient lymphocytes, despite moderate role in V(D)J recombination in WT cells. p53-binding protein 1 (53BP1) is another substrate of ATM. 53BP1 deficiency led to small reduction of peripheral lymphocyte number by compromising both synapse and end-joining at modest level during V(D)J recombination. Here, we report that 53BP1/XLF double deficiency blocks lymphocyte development at early progenitor stages, owing to severe defects in end joining during chromosomal V(D)J recombination. The unrepaired DNA ends are rapidly degraded in 53BP1
−/−
XLF
−/−
cells, as reported for H2AX
−/−
XLF
−/−
cells, revealing an end protection role for 53BP1 reminiscent of H2AX. In contrast to the early embryonic lethality of H2AX
−/−
XLF
−/−
mice, 53BP1
−/−
XLF
−/−
mice are born alive and develop thymic lymphomas with translocations involving the T-cell receptor loci. Together, our findings identify a unique function for 53BP1 in end-joining and tumor suppression.
PK4, a eukaryotic initiation factor 2α(eIF2α) kinase, is essential for the development of the erythrocytic cycle of
Plasmodium
Authors: Zhang Min , Mishra Satish , Sakthivel Ramanavelan , Rojas Margarito , Ranjan Ravikant , Sullivan William J. , Fontoura Beatriz M. A. , Ménard Robert , Dever Thomas E. , Nussenzweig Victor
Published: February 2012

In response to environmental stresses, the mammalian serine threonine kinases PERK, GCN2, HRI, and PKR phosphorylate the regulatory serine 51 of the eukaryotic translation initiation factor 2α (eIF2α) to inhibit global protein synthesis.
Plasmodium
, the protozoan that causes malaria, expresses three eIF2α kinases: IK1, IK2, and PK4. Like GCN2, IK1 regulates stress response to amino acid starvation. IK2 inhibits development of malaria sporozoites present in the mosquito salivary glands. Here we show that the phosphorylation by PK4 of the regulatory serine 59 of
Plasmodium
eIF2α is essential for the completion of the parasite's erythrocytic cycle that causes disease in humans. PK4 activity leads to the arrest of global protein synthesis in schizonts, where ontogeny of daughter merozoites takes place, and in gametocytes that infect
Anopheles
mosquitoes. The implication of these findings is that drugs that reduce PK4 activity should alleviate disease and inhibit malaria transmission.
Rat brains also have a default mode network
Authors: Lu Hanbing , Zou Qihong , Gu Hong , Raichle Marcus E. , Stein Elliot A. , Yang Yihong
Published: February 2012

The default mode network (DMN) in humans has been suggested to support a variety of cognitive functions and has been implicated in an array of neuropsychological disorders. However, its function(s) remains poorly understood. We show that rats possess a DMN that is broadly similar to the DMNs of nonhuman primates and humans. Our data suggest that, despite the distinct evolutionary paths between rodent and primate brain, a well-organized, intrinsically coherent DMN appears to be a fundamental feature in the mammalian brain whose primary functions might be to integrate multimodal sensory and affective information to guide behavior in anticipation of changing environmental contingencies.
How Chinese people infer helpers’ ambiguous intentions: Helper effort and interpersonal relationships
Authors: Hu Yueqin , Gan Yiqun , Liu Yang
Published: February 2012

Previous researchers have tried to understand in what situations people feel gratitude and indebtedness in response to other people helping them, and have found that benefit value, helper effort, helper obligation, and helper intention were all important. However, helper intentions are not always clear. We gave Chinese participants helping vignettes and tested how they inferred helpers’ ambiguous intentions. Study 1 found that helper effort significantly influenced how they infer intentions, but benefit value and helper obligation did not. Study 2 replicated the effect of helper effort and found that more effort led participants to infer that the helper was more motivated by utilitarian interests. Study 3 focused on what type of relationship the helper had with the participants, and found that closeness led participants to infer more benevolent intentions and less utilitarian intentions.
Causal reasoning on biological networks: interpreting transcriptional changes
Authors: Chindelevitch Leonid , Ziemek Daniel , Enayetallah Ahmed , Randhawa Ranjit , Sidders Ben , Brockel Christoph , Huang Enoch S.
Published: February 2012

Motivation: The interpretation of high-throughput datasets has remained one of the central challenges of computational biology over the past decade. Furthermore, as the amount of biological knowledge increases, it becomes more and more difficult to integrate this large body of knowledge in a meaningful manner. In this article, we propose a particular solution to both of these challenges.

Methods: We integrate available biological knowledge by constructing a network of molecular interactions of a specific kind: causal interactions. The resulting causal graph can be queried to suggest molecular hypotheses that explain the variations observed in a high-throughput gene expression experiment. We show that a simple scoring function can discriminate between a large number of competing molecular hypotheses about the upstream cause of the changes observed in a gene expression profile. We then develop an analytical method for computing the statistical significance of each score. This analytical method also helps assess the effects of random or adversarial noise on the predictive power of our model.

Results: Our results show that the causal graph we constructed from known biological literature is extremely robust to random noise and to missing or spurious information. We demonstrate the power of our causal reasoning model on two specific examples, one from a cancer dataset and the other from a cardiac hypertrophy experiment. We conclude that causal reasoning models provide a valuable addition to the biologist's toolkit for the interpretation of gene expression data.

Availability and implementation: R source code for the method is available upon request.

Contact:  daniel.ziemek@pfizer.com

Supplementary information:  Supplementary data are available at Bioinformatics online.