bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of oxygen vacancies in TiO2-based resistive switches
Authors: Gu Tingkun
Published: January 2013

The effect of oxygen vacancies in TiO2 on the electronic properties of Pt/TiO2/Pt heterojunctions were investigated using first-principles methods. The arrangement of oxygen vacancies in TiO2 slabs is a crucial factor for conducting filament formation. Extended defect induced by the aligned neutral oxygen vacancies results in defect states being located at the Fermi level of the Pt electrodes in Pt/TiO2/Pt heterostructures, and produces a conducting filament connecting two Pt electrodes in the TiO2 film via the oxygen-deficient Ti ions. As oxygen vacancies in intrinsic state, the O-deficient Ti ions, which remain in a high valence state, like those in perfect TiO2, do not contribute to the conducting filament formation. Electronic structure analysis suggests that metallic filament formation in Pt/TiO2/Pt resistive switching cells might be closely related to the charge state and the arrangement of oxygen vacancies in TiO2 films.
Photoluminescence properties of (Ce3+, Mn2+)-codoped CaCO3 red phosphor
Authors: Nara Jun-ichi , Adachi Sadao
Published: January 2013

(Ce3+, Mn2+)-codoped CaCO3 phosphors are synthesized by the coprecipitation method, and their optical properties are investigated using diffuse reflectance, photoluminescence (PL) analysis, PL excitation spectroscopy, and PL lifetime measurements. The effects of Ce3+ doping on the Mn2+ emission band are studied in detail. The temperature-dependent PL properties are analyzed on the basis of the configurational-coordinate model. These analyses allow a better understanding of the PL properties of Mn2+ within the CaCO3 host. Remarkably, the red emission intensity of Mn2+ in the (Ce3+, Mn2+)-codoped phosphor is enhanced more than 200 times compared to the single Mn2+-doped phosphor, thereby suggesting the occurrence of an efficient resonant energy transfer between Ce3+ and Mn2+ ions.
Whispering gallery and Fabry–Pérot modes enhanced luminescence from individual ZnO micro mushroom
Authors: Wang B. , Jin X. , Wu H. Y. , Zheng Z. Q.
Published: January 2013

One kind of micro structures, ZnO mushrooms, have been synthesized by self-assembled method on single silicon substrates with Au catalyst assisted thermal evaporation of ZnO and active carbon powders. Cathodoluminescence for individual ZnO micro mushroom has been invested. The luminescence from the center region is attributed to the Fabry–Pérot mode enhanced emission, and the one from the hexagonal profiles is attributed to the whispering gallery mode enhanced emission when the individual ZnO micro mushroom is regarded as an optical resonator. The field-emission property of these ZnO micro mushrooms has been measured and the turn-on electric field is 5.9 V/μm.
Novel metal gates for high κ applications
Authors: Chang Mei , Chen Michael S. , David Anaïs , Gandikota Srinivas , Ganguli Seshadri , Hayden Brian E. , Hung Steven , Lu Xinliang , Mormiche Claire , Noori Atif , Smith Duncan C. A. , Vian Chris J. B.
Published: January 2013

The development of gate systems suitable for high κ dielectrics is critical to the advancement of complementary metal-oxide-semiconductor (CMOS) devices. Both the effective work function and material stability are key parameters to these systems. A systematic study of metal gates of the composition HfxSi1-x (0.25 ≤ x ≤ 1) is demonstrated here, including XPS, XRD and four point probe measurements. The effective work function of each material is evaluated and it is shown that it can be tuned from 4.5 to less than 4.0 eV. Suitable work functions for n-channel metal-oxide-semiconductor applications (4.05 ± 0.2 eV) were achieved using hafnium rich compositions; however, XPS and diffraction measurements confirmed that these materials demonstrated a high propensity to oxidise, causing the reduction of the underlying oxides, making them unsuitable for commercial application.
Constructal design of pedestrian evacuation from an area
Authors: Lui C. H. , Fong N. K. , Lorente S. , Bejan A. , Chow W. K.
Published: January 2013

Pedestrian movement occurs in evolutionary patterns the effect of which is to facilitate the access of people into and out of living spaces (areas, volumes). In this paper, we rely on the philosophy of Constructal design as applied physics, in order to uncover two fundamental features of evolutionary design for pedestrian evacuation from rectangular areas (e.g., lecture halls with seated occupants). First, the paper shows analytically that the aspect ratio of the floor area can be selected such that the total evacuation time is minimal. Second, the shape of the floor area of each aisle can be tapered such that the total evacuation time is decreased further. These two architectural features are confirmed by means of extensive and systematic numerical simulations of pedestrian evacuation, by using two numerical packages (Simulex and FDS + Evac).
Nitrogen-doped Ge3Te2 materials with self-restricted active region for low power phase-change memory
Authors: Peng Cheng , Yang Pingxiong , Wu Liangcai , Song Zhitang , Rao Feng , Song Sannian , Zhou Dong , Chu Junhao
Published: January 2013

In this paper, nitrogen-doped Ge3Te2 materials have been investigated for low power phase-change memory. Nitrogen incorporated in Ge3Te2 increases the crystallization temperature, electrical resistance, and band gap significantly. The introduced GeNx pile up at the grain-boundaries and suppress the crystal growth of Ge3Te2, which further leads to larger crystalline resistance and smaller active region. 10-year data retention of nitrogen-doped Ge3Te2 film reaches a peak value with a N2 flow of 2 sccm, while it decreases sharply as the N2 flow reaches 3 sccm. This is due to the formation of inhomogeneous nucleation sites at the GeNx-GeTe interface. Phase-change memory device based on nitrogen-doped Ge3Te2 film shows much lower RESET power consumption than that of pure Ge3Te2. It's considered that the self-restricted active region and effect of GeNx microheaters play an important role in cutting down the power consumption.
High excitation carrier density recombination dynamics of InGaN/GaN quantum well structures: Possible relevance to efficiency droop
Authors: Davies M. J. , Badcock T. J. , Dawson P. , Kappers M. J. , Oliver R. A. , Humphreys C. J.
Published: January 2013

We report on the optical properties of InGaN/GaN quantum well structures measured at 10 K as a function of excitation density. At high excitation power densities we observe a component in the spectra that decays more rapidly than the localised carrier emission observed for low excitation power densities. We attribute this component to recombination involving weakly localised or delocalised carriers. At the high excitation power densities there is a reduction in the recombination internal quantum efficiency, so called efficiency droop. These observations are compatible with the model whereby efficiency droop is explained in terms of the non radiative loss of delocalised carriers.
Spin lifetime measurements in GaAsBi thin films
Authors: Pursley Brennan , Luengo-Kovac M. , Vardar G. , Goldman R. S. , Sih V.
Published: January 2013

Photoluminescence spectroscopy and Hanle effect measurements are used to investigate carrier spin dephasing and recombination times in the semiconductor alloy GaAsBi as a function of temperature and excitation energy. Hanle effect measurements reveal the product of g-factor and effective spin dephasing time (gTs) ranges from 0.8 ns at 40 K to 0.1 ns at 120 K. The temperature dependence of gTs provides evidence for a thermally activated effect, which is attributed to hole localization at single Bi or Bi cluster sites below 40 K.
Towards liquid metal ion source chips: Indium liquid metal ion source with glass microcapillaries
Authors: Tajmar M. , Plesescu F.
Published: January 2013

A liquid-metal-ion-source with indium propellant using an uncoated fused quartz glass microcapillary was manufactured and tested. The extremely thin capillary enabled a very low ignition voltage of 1000 V and a high electrical impedance ideal for clustering. However, low bonding forces between indium and glass resulted in a rather short lifetime of little more than 10 min. The use of pure glass as emitter material may enable liquid ion source chips with high current densities in the future.
Effect of polarity on Ni/InN interfacial reactions
Authors: Kragh-Buetow K. C. , Weng X. , Readinger E. D. , Wraback M. , Mohney S. E.
Published: January 2013

Ni films on (0001) and (0001¯) InN exhibited different reaction kinetics upon annealing at 673K. Structural and chemical analysis using grazing incidence X-ray diffraction, transmission electron microscopy, and X-ray energy dispersive spectrometry indicated that an interfacial reaction did not occur between the Ni film and the In-polar (0001) InN layer. However, the N-polar face reacted with Ni to form the Ni3InNx ternary phase with an anti-perovskite structure. The difference in reactivity for Ni on In-face and N-face InN indicates that polarity alters the reaction and may also affect interactions between other metals and group III-nitride semiconductors.
Liquid-phase deposition of thin Si films by ballistic electro-reduction
Authors: Ohta T. , Gelloz B. , Kojima A. , Koshida N.
Published: January 2013

It is shown that the nanocryatalline silicon ballistic electron emitter operates in a SiCl4 solution without using any counter electrodes and that thin amorphous Si films are efficiently deposited on the emitting surface with no contaminations and by-products. Despite the large electrochemical window of the SiCl4 solution, electrons injected with sufficiently high energies preferentially reduce Si4+ ions at the interface. Using an emitter with patterned line emission windows, a Si-wires array can be formed in parallel. This low-temperature liquid-phase deposition technique provides an alternative clean process for power-effective fabrication of advanced thin Si film structures and devices.
Light-emitting devices based on erbium-doped TiO2/p+-Si heterostructures: Engineering of electroluminescence via aluminum co-doping
Authors: Yang Yang , Li Yunpeng , Jin Lu , Ma Xiangyang , Yang Deren
Published: January 2013

We have recently reported erbium (Er)-related visible and infrared (∼1540 nm) electroluminescence (EL) from the light-emitting device (LED) based on Er-doped TiO2 (TiO2:Er)/p+-Si heterostructure, triggered by the energy transferred from oxygen-vacancy-related self-trapped excitons (STEs) to Er3+ ions in anatase TiO2. Herein, we further co-dope aluminum (Al) into the TiO2:Er film, which is also used to form heterostructure with p+-Si. The LED based on such heterostructure features the Er-related EL with the substantially suppressed visible emissions and the remarkably enhanced ∼1540 nm emission. The Al co-doping is proved not to substantially affect the amounts of oxygen-vacancy-related STEs and Er3+ ions in anatase TiO2. In this context, the above-mentioned engineering of Er-related EL is tentatively ascribed to the modification of crystal field around the Er3+ ions in anatase TiO2 by the Al co-doping.
Random lasing and weak localization of light in transparent Nd+3 doped phosphate glass
Authors: Zhang Jingwen , Xu Long , Wang Hao , Huang Feng , Sun Xiudong , Zhao Hua , Chen Xuesheng
Published: January 2013

Random lasing action and weak localization of light were observed in multiple visible wavelengths with highly transparent, Nd+3 doped phosphate glass gain media, with strong energy redistribution between different frequencies under different pumping powers. A tentative model based on photoinduced scattering was proposed and verified with a He-Ne laser beam in probing the lasing zone. The remarkable coherency and intensity changes of the probing laser beam confirmed the local, random scattering behind the photoinduced random lasing and the localization of light.
Transparent and flexible amorphous In-Si-O films for flexible organic solar cells
Authors: Lee Hye-Min , Kang Sin-Bi , Chung Kwun-Bum , Kim Han-Ki
Published: January 2013

We report on transparent amorphous In-Si-O (ISO) electrodes for flexible organic solar cells (FOSCs). Effective Si doping into the In2O3 matrix led to a completely amorphous ISO film as well as a low sheet resistance of 51.91 Ω/sq and a high near-infrared optical transmittance of 81.51% (550 nm), and which are desirable electrode characteristics for FOSCs. In addition, the ISO film showed outstanding flexibility in outer and inner bending tests due to the stable amorphous structure. Based on x-ray absorption spectroscopy and high resolution transmission microscope examinations, detailed microstructure and electronic structure of amorphous ISO film were investigated. Furthermore, FOSCs with an amorphous ISO anode showed an open circuit voltage (0.578 V), short circuit current (7.641 mA/cm2), fill factor (62.96%), and power conversion efficiency (2.78%), indicating that ISO is a promising flexible amorphous transparent electrode for FOSCs.
Giant magnetocaloric effect in Ho12Co7 compound
Authors: Zheng X. Q. , Shao X. P. , Chen J. , Xu Z. Y. , Hu F. X. , Sun J. R. , Shen B. G.
Published: January 2013

Magnetic properties and magnetocaloric effects of Ho12Co7 compound are investigated by magnetization and heat capacity measurement. The Ho12Co7 compound undergoes antiferromagnetic (AFM)-AFM transition at T1 = 9 K, AFM-ferromagnetic (FM) transition at T2 = 17 K, and FM-paramagnetic transition at TC = 30 K, with temperature increasing. There are two peaks on the magnetic entropy change (ΔSM) versus temperature curves and the maximal value of –ΔSM is found to be 19.2 J/kg K with the refrigerant capacity value of 554.4 J/kg under a field change from 0 to 5 T. The shape of the ΔSM-T curves obtained from heat capacity measurement is in accordance with that from magnetization measurement. The excellent magnetocaloric performance indicates the applicability of Ho12Co7 as an appropriate candidate for magnetic refrigerant in low temperature ranges.
Gate traps inducing band-bending fluctuations on AlGaN/GaN heterojunction transistors
Authors: Pérez-Tomás A. , Fontserè A. , Sánchez S. , Jennings M. R. , Gammon P. M. , Cordier Y.
Published: January 2013

Here, using a frequency dependent conductance analysis, we map the parallel conductance vs gate bias/frequency and further analyze the slow and fast traps as a function of the Fermi level for different gate architectures of analogous AlGaN/GaN heterojunction transistors with Schottky and SiNx metal-insulator-semiconductor (MIS) gate. The density of interface traps (Dit)-MIS reducing Dit-, the characteristic trap constant and the variance of the band-bending (σs) have been investigated for slow and fast traps. Additional gate stress appears to have a notable effect on the MIS fast trap profile with σs increasing up to 2.5 kT/q.
Cavity piezooptomechanics: Piezoelectrically excited, optically transduced optomechanical resonators
Authors: Xiong Chi , Fan Linran , Sun Xiankai , Tang Hong X.
Published: January 2013

We present a monolithic integrated aluminum nitride (AlN) optomechanical resonator in which the mechanical motion is actuated by piezoelectric force and the displacement is transduced by a high-Q optical cavity. The AlN optomechanical resonator is excited from a radio-frequency electrode via a small air gap to eliminate resonator-to-electrode loss. We observe the electrically excited mechanical motion at 47.3 MHz, 1.04 GHz, and 3.12 GHz, corresponding to the 1st, 2nd, and 4th radial-contour mode of the wheel resonator, respectively. An equivalent circuit model is developed to describe the observed Fano-like resonance spectrum.
Study of beam optics and beam halo by integrated modeling of negative ion beams from plasma meniscus formation to beam acceleration
Authors: Miyamoto K. , Okuda S. , Hatayama A. , Hanada M. , Kojima A.
Published: January 2013

To understand the physical mechanism of the beam halo formation in negative ion beams, a two-dimensional particle-in-cell code for simulating the trajectories of negative ions created via surface production has been developed. The simulation code reproduces a beam halo observed in an actual negative ion beam. The negative ions extracted from the periphery of the plasma meniscus (an electro-static lens in a source plasma) are over-focused in the extractor due to large curvature of the meniscus.
d magnetism in semiconductors through confining delocalized atomic orbitals
Authors: Kan E. J. , Wu Fang , Wu Haiping , Xiao Chuanyun , Xiang Hongjun , Deng Kaiming
Published: January 2013

Although localized atomic 2p orbitals have been taken as the possible origin of d0 materials, the collective magnetic ordering is impeded by the low concentration of local magnetic moments. Using first-principles calculations with wurtzite GaN as a prototype material, we predict that the delocalized defect orbitals can induce local magnetic moments and form collective magnetic ordering through confinement. By applying external strain, the delocalized defect orbitals which are partially filled by anion-vacancy are well confined, leading to the spontaneous spin ordering.
Improving imaging resolution of shaking targets by Fourier-transform ghost diffraction
Authors: Zhang Cong , Gong Wenlin , Han Shensheng
Published: January 2013

For conventional imaging, shaking of the imaging system or the target leads to the degradation of imaging resolution. The influence of the target's shaking to Fourier-transform ghost diffraction (FGD) is investigated and phase-retrieval method is used to recover the target's imaging. The analytical results, which are backed up by numerical simulation and experiments, demonstrate that the quiver of target has no effect on the resolution of FGD and high-resolution imaging can be always achieved by phase-retrieval method from FGD patterns. This approach can be applied in high-precision imaging systems, to overcome the influence of the system's shaking to imaging resolution.
Influence of scandium concentration on power generation figure of merit of scandium aluminum nitride thin films
Authors: Akiyama Morito , Umeda Keiichi , Honda Atsushi , Nagase Toshimi
Published: January 2013

The authors have investigated the influence of scandium concentration on the power generation figure of merit (FOM) of scandium aluminum nitride (ScxAl1−xN) films prepared by cosputtering. The power generation FOM strongly depends on the scandium concentration. The FOM of Sc0.41Al0.59N film was 67 GPa, indicating that the FOM is five times larger than that of AlN. The FOM of Sc0.41Al0.59N film is higher than those of lead zirconate titanate and Pb(Mg1/3Nb2/3)O3-PbTiO3 films, which is the highest reported for any piezoelectric thin films. The high FOM of Sc0.41Al0.59N film is due to the high d31 and the low relative permittivity.
Influence of the dynamic lattice strain on the transport behavior of oxide heterojunctions
Authors: Wang J. , Hu F. X. , Chen L. , Zhao Y. Y. , Lu H. X. , Sun J. R. , Shen B. G.
Published: January 2013

All-perovskite oxide heterojunctions composed of electron-doped titanate LaxSr1 − xTiO3 (x = 0.1, 0.15) and hole-doped manganite La0.67Ca0.33MnO3 films were fabricated on piezoelectric substrate of (001)-0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 (PMN-PT). Taking advantage of the excellent converse piezoelectric effect of PMN-PT, we investigated the influence of the dynamic lattice strain on transport properties of the heterojunctions by applying external bias electric fields on the PMN-PT substrate. Photovoltaic experiments were carried out to characterize the interfacial barrier of the heterojunction. A linear reduction in the barrier height was observed with the increase of the bias field applied on PMN-PT. The value of the barrier height reduces from ∼1.55 (∼1.30) to 1.02 (1.08) eV as the bias field increases from 0 to 12 kV/cm for the junction of La0.10Sr0.9TiO3/La0.67Ca0.33MnO3 (La0.15Sr0.85TiO3/La0.67Ca0.33MnO3). The observed dependency of barrier height on external field can be ascribed to the increasing release of trapped carriers by strain modulation, which results in a suppression of the depletion layer and increases the opportunity for electron tunneling across the depletion area.
Multi-modal characterization of nanogram amounts of a photosensitive polymer
Authors: Kim Seonghwan , Lee Dongkyu , Yun Minhyuk , Jung Namchul , Jeon Sangmin , Thundat Thomas
Published: January 2013

Here, we demonstrate multi-modal approach of simultaneous characterization of poly(vinyl cinnamate) (PVCN) using a microcantilever sensor. We integrate nanomechanical thermal analysis with photothermal cantilever deflection spectroscopy for discerning ultraviolet (UV) exposure-induced variations in the thermodynamic and thermomechanical properties of the PVCN as a function of temperature and UV irradiation time. UV radiation-induced photo-cross-linking processes in the PVCN are verified with the increase of the Young's modulus and cantilever deflection as well as the decrease in the hysteresis of deflection and the intensity of C=C peak in the nanomechanical infrared spectrum as a function of UV irradiation time.
Design criteria for developing low-resource magnetic bead assays using surface tension valves
Authors: Adams Nicholas M. , Creecy Amy E. , Majors Catherine E. , Wariso Bathsheba A. , Short Philip A. , Wright David W. , Haselton Frederick R.
Published: January 2013

Many assays for biological sample processing and diagnostics are not suitable for use in settings that lack laboratory resources. We have recently described a simple, self-contained format based on magnetic beads for extracting infectious disease biomarkers from complex biological samples, which significantly reduces the time, expertise, and infrastructure required. This self-contained format has the potential to facilitate the application of other laboratory-based sample processing assays in low-resource settings. The technology is enabled by immiscible fluid barriers, or surface tension valves, which stably separate adjacent processing solutions within millimeter-diameter tubing and simultaneously permit the transit of magnetic beads across the interfaces. In this report, we identify the physical parameters of the materials that maximize fluid stability and bead transport and minimize solution carryover. We found that fluid stability is maximized with ≤0.8 mm i.d. tubing, valve fluids of similar density to the adjacent solutions, and tubing with ≤20 dyn/cm surface energy. Maximizing bead transport was achieved using ≥2.4 mm i.d. tubing, mineral oil valve fluid, and a mass of 1-3 mg beads. The amount of solution carryover across a surface tension valve was minimized using ≤0.2 mg of beads, tubing with ≤20 dyn/cm surface energy, and air separators. The most favorable parameter space for valve stability and bead transport was identified by combining our experimental results into a single plot using two dimensionless numbers. A strategy is presented for developing additional self-contained assays based on magnetic beads and surface tension valves for low-resource diagnostic applications.
Correlation between the microstructures and the deformation mechanisms of CuZr-based bulk metallic glass composites
Authors: Song K. K. , Pauly S. , Sun B. A. , Tan J. , Stoica M. , Kühn U. , Eckert J.
Published: January 2013

The variation of the transformation-mediated deformation behavior with microstructural changes in CuZr-based bulk metallic glass composites is investigated. With increasing crystalline volume fraction, the deformation mechanism gradually changes from a shear-banding dominated process as evidenced by a chaotic serrated flow behavior, to being governed by a martensitic transformation with a pronounced elastic-plastic stage, resulting in different plastic deformations evolving into a self-organized critical state characterized by the power-law distribution of shear avalanches. This is reflected in the stress-strain curves by a single-to-“double”-to-“triple”-double yielding transition and by different mechanical properties with different serrated flow characteristics, which are interpreted based on the microstructural evolutions and a fundamental energy theorem. Our results can assist in understanding deformation behaviors for high-performance metastable alloys.
Fast and low-temperature reduction of graphene oxide films using ammonia plasma
Authors: Kim Maeng Jun , Jeong Yonkil , Sohn SangHo , Lee Sung Yeup , Kim Yong Jae , Lee Kwanghee , Kahng Yung Ho , Jang Jae-Hyung
Published: January 2013

Reduced graphene oxide (rGO) has been produced using an ammonia (NH3) plasma reduction method. Simultaneous nitrogen doping during the reduction process enabled a rapid and low-temperature restoration of the electrical properties of the rGO. The chemical, structural, and electrical properties of the rGO films were analyzed using x-ray photoelectron spectroscopy, Raman spectroscopy, atomic force microscopy, and conductivity measurements. The oxygen functional groups were efficiently removed, and simultaneous nitrogen doping (6%) was carried out. In addition, the surface of the rGO film was flattened. Consequently, the rGO films exhibited electrical properties comparable to those prepared via other reduction methods.
Dissolving, trapping and detrapping mechanisms of hydrogen in bcc and fcc transition metals
Authors: You Yu-Wei , Kong Xiang-Shan , Wu Xue-Bang , Xu Yi-Chun , Fang Q. F. , Chen J. L. , Luo G.-N. , Liu C. S. , Pan B. C. , Wang Zhiguang
Published: January 2013

First-principles calculations are performed to investigate the dissolving, trapping and detrapping of H in six bcc (V, Nb, Ta, Cr, Mo, W) and six fcc (Ni, Pd, Pt, Cu, Ag, Au) metals. We find that the zero-point vibrations do not change the site-preference order of H at interstitial sites in these metals except Pt. One vacancy could trap a maximum of 4 H atoms in Au and Pt, 6 H atoms in V, Nb, Ta, Cr, Ni, Pd, Cu and Ag, and 12 H atoms in Mo and W. The zero-point vibrations never change the maximum number of H atoms trapped in a single vacancy in these metals. By calculating the formation energy of vacancy-H (Vac-Hn) complex, the superabundant vacancy in V, Nb, Ta, Pd and Ni is demonstrated to be much more easily formed than in the other metals, which has been found in many metals including Pd, Ni and Nb experimentally. Besides, we find that it is most energetically favorable to form Vac-H1 complex in Pt, Cu, Ag and Au, Vac-H4 in Cr, Mo and W, and Vac-H6 in V, Nb, Ta, Pd and Ni. At last, we examine the detrapping behaviors of H atoms in a single vacancy and find that with the heating rate of 10 K/min a vacancy could accommodate 4, 5 and 6 H atoms in Cr, Mo and W at room temperature, respectively. The detrapping temperatures of all H atoms in a single vacancy in V, Nb, Ta, Ni, Pd, Cu and Ag are below room temperature.
Percept—Percept Couplings
Authors: Epstein William
Published: January 2013

Relations among percepts in the organized perceptual world are called percept—percept couplings. If these couplings are assigned a causal interpretation they present a challenge to a theory of direct perception. Experimental evidence of percept-percept coupling is reviewed and the case for a causal interpretation of these relations is examined. It is concluded that the causal interpretation is plausible and that the facts of percept—percept couplings need to be addressed by advocates of a theory of direct perception.
Rate Coefficients for Intramolecular Homolytic Substitution of Oxyacyl Radicals at Sulfur
Authors: Aitken Heather M. , Horvat Sonia M. , Coote Michelle L. , Lin Ching Yeh , Schiesser Carl H.
Published: January 2013

It is predicted on the basis of ab initio and density functional calculations that intramolecular homolytic substitution of oxyacyl radicals at the sulfur atom in ω-alkylthio-substituted radicals do not involve hypervalent intermediates. With tert-butyl as the leaving radical, free energy barriers ΔG‡ (G3(MP2)-RAD) for these reactions range from 45.8 kJ mol–1 for the formation of the five-membered cyclic thiocarbonate (8) to 56.7 kJ mol–1 for the formation of the six-membered thiocarbonate (9). Rate coefficients in the order of 104–106 s–1 and 101–104 s–1 for the formation of 8 and 9, respectively, at 353.15 K in the gas phase are predicted at the G3(MP2)-RAD level of theory.
CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging
Authors: Baruch Kuti , Ron-Harel Noga , Gal Hilah , Deczkowska Aleksandra , Shifrut Eric , Ndifon Wilfred , Mirlas-Neisberg Nataly , Cardon Michal , Vaknin Ilan , Cahalon Liora , Berkutzki Tamara , Mattson Mark P. , Gomez-Pinilla Fernando , Friedman Nir , Schwartz Michal
Published: January 2013

The adaptive arm of the immune system has been suggested as an important factor in brain function. However, given the fact that interactions of neurons or glial cells with T lymphocytes rarely occur within the healthy CNS parenchyma, the underlying mechanism is still a mystery. Here we found that at the interface between the brain and blood circulation, the epithelial layers of the choroid plexus (CP) are constitutively populated with CD4
+
effector memory cells with a T-cell receptor repertoire specific to CNS antigens. With age, whereas CNS specificity in this compartment was largely maintained, the cytokine balance shifted in favor of the T helper type 2 (Th2) response; the Th2-derived cytokine IL-4 was elevated in the CP of old mice, relative to IFN-γ, which decreased. We found this local cytokine shift to critically affect the CP epithelium, triggering it to produce the chemokine CCL11 shown to be associated with cognitive dysfunction. Partial restoration of cognitive ability in aged mice, by lymphopenia-induced homeostasis-driven proliferation of memory T cells, was correlated with restoration of the IL-4:IFN-γ ratio at the CP and modulated the expression of plasticity-related genes at the hippocampus. Our data indicate that the cytokine milieu at the CP epithelium is affected by peripheral immunosenescence, with detrimental consequences to the aged brain. Amenable to immunomodulation, this interface is a unique target for arresting age-related cognitive decline.
Dynamics and biological relevance of DNA demethylation in
Arabidopsis
antibacterial defense
Authors: Yu Agnès , Lepère Gersende , Jay Florence , Wang Jingyu , Bapaume Laure , Wang Yu , Abraham Anne-Laure , Penterman Jon , Fischer Robert L. , Voinnet Olivier , Navarro Lionel
Published: January 2013

DNA methylation is an epigenetic mark that silences transposable elements (TEs) and repeats. Whereas the establishment and maintenance of DNA methylation are relatively well understood, little is known about their dynamics and biological relevance in plant and animal innate immunity. Here, we show that some TEs are demethylated and transcriptionally reactivated during antibacterial defense in
Arabidopsis
. This effect is correlated with the down-regulation of key transcriptional gene silencing factors and is partly dependent on an active demethylation process. DNA demethylation restricts multiplication and vascular propagation of the bacterial pathogen
Pseudomonas syringae
in leaves and, accordingly, some immune-response genes, containing repeats in their promoter regions, are negatively regulated by DNA methylation. This study provides evidence that DNA demethylation is part of a plant-induced immune response, potentially acting to prime transcriptional activation of some defense genes linked to TEs/repeats.
Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes
Authors: Arges Christopher G. , Ramani Vijay
Published: January 2013

Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability.
The Effect of Supercenter‐format Stores on the Healthfulness of Consumers' Grocery Purchases
Authors: Volpe Richard , Okrent Abigail , Leibtag Ephraim
Published: January 2013

We examine the effect of supercenter market share on consumers' food‐at‐home purchasing habits in the United States. We measure healthfulness several different ways to ensure robustness, but all measurements place a greater value on fresh fruits and vegetables and whole grains than on processed foods high in sugar and sodium. We find that from 1998–2006 consumers generally purchased less healthful foods at supercenters than they do at supermarkets. Moreover, a one‐percent increase in the local market share of supercenters results in a decrease in purchase healthfulness for groceries of 0.10 to 0.46 percent. This relationship is statistically significant and robust.
Improving the reuse of computational models through version control
Authors: Waltemath Dagmar , Henkel Ron , Hälke Robert , Scharm Martin , Wolkenhauer Olaf
Published: January 2013

Motivation: Only models that are accessible to researchers can be reused. As computational models evolve over time, a number of different but related versions of a model exist. Consequently, tools are required to manage not only well-curated models but also their associated versions.

Results: In this work, we discuss conceptual requirements for model version control. Focusing on XML formats such as Systems Biology Markup Language and CellML, we present methods for the identification and explanation of differences and for the justification of changes between model versions. In consequence, researchers can reflect on these changes, which in turn have considerable value for the development of new models. The implementation of model version control will therefore foster the exploration of published models and increase their reusability.

Availability: We have implemented the proposed methods in a software library called Biochemical Model Version Control System. It is freely available at http://sems.uni-rostock.de/bives/. Biochemical Model Version Control System is also integrated in the online application BudHat, which is available for testing at http://sems.uni-rostock.de/budhat/ (The version described in this publication is available from http://budhat-demo.sems.uni-rostock.de/).

Contact:  dagmar.waltemath@uni-rostock.de
Systematic inference of highways of horizontal gene transfer in prokaryotes
Authors: Bansal Mukul S. , Banay Guy , Harlow Timothy J. , Gogarten J. Peter , Shamir Ron
Published: January 2013

Motivation: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species (or linages) between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. Inferring such highways is crucial to understanding the evolution of prokaryotes and for inferring past symbiotic and ecological associations among different species.

Results: We present a new improved method for systematically detecting highways of gene sharing. As we demonstrate using a variety of simulated datasets, our method is highly accurate and efficient, and robust to noise and high rates of HGT. We further validate our method by applying it to a published dataset of >22 000 gene trees from 144 prokaryotic species. Our method makes it practical, for the first time, to perform accurate highway analysis quickly and easily even on large datasets with high rates of HGT.

Availability and implementation: An implementation of the method can be freely downloaded from: http://acgt.cs.tau.ac.il/hide.

Contact:  rshamir@tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
APoc: large-scale identification of similar protein pockets
Authors: Gao Mu , Skolnick Jeffrey
Published: January 2013

Motivation: Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes, or ‘pockets’, on the protein’s surface. An efficient method for comparing these pockets could greatly assist the classification of ligand-binding sites, prediction of protein molecular function and design of novel drug compounds.

Results: We introduce a computational method, APoc (Alignment of Pockets), for the large-scale, sequence order-independent, structural comparison of protein pockets. A scoring function, the Pocket Similarity Score (PS-score), is derived to measure the level of similarity between pockets. Statistical models are used to estimate the significance of the PS-score based on millions of comparisons of randomly related pockets. APoc is a general robust method that may be applied to pockets identified by various approaches, such as ligand-binding sites as observed in experimental complex structures, or predicted pockets identified by a pocket-detection method. Finally, we curate large benchmark datasets to evaluate the performance of APoc and present interesting examples to demonstrate the usefulness of the method. We also demonstrate that APoc has better performance than the geometric hashing-based method SiteEngine.

Availability and implementation: The APoc software package including the source code is freely available at http://cssb.biology.gatech.edu/APoc.

Contact:  skolnick@gatech.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction
Authors: Arunapuram Preeti , Edvardsson Ingolfur , Golden Michael , Anderson James W. J. , Novák Ádám , Sükösd Zsuzsanna , Hein Jotun
Published: January 2013

Motivation: Comparative modeling of RNA is known to be important for making accurate secondary structure predictions. RNA structure prediction tools such as PPfold or RNAalifold use an aligned set of sequences in predictions. Obtaining a multiple alignment from a set of sequences is quite a challenging problem itself, and the quality of the alignment can affect the quality of a prediction. By implementing RNA secondary structure prediction in a statistical alignment framework, and predicting structures from multiple alignment samples instead of a single fixed alignment, it may be possible to improve predictions.

Results: We have extended the program StatAlign to make use of RNA-specific features, which include RNA secondary structure prediction from multiple alignments using either a thermodynamic approach (RNAalifold) or a Stochastic Context-Free Grammars (SCFGs) approach (PPfold). We also provide the user with scores relating to the quality of a secondary structure prediction, such as information entropy values for the combined space of secondary structures and sampled alignments, and a reliability score that predicts the expected number of correctly predicted base pairs. Finally, we have created RNA secondary structure visualization plugins and automated the process of setting up Markov Chain Monte Carlo runs for RNA alignments in StatAlign.

Availability and implementation: The software is available from http://statalign.github.com/statalign/.

Contact: novak@stats.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
A coherent feedforward loop design principle to sustain robustness of biological networks
Authors: Le Duc-Hau , Kwon Yung-Keun
Published: January 2013

Motivation: Many studies have investigated the relationship between structural properties and dynamic behaviors in biological networks. In particular, feedback loop (FBL) and feedforward loop (FFL) structures have received a great deal of attention. One interesting and common property of FBL and FFL structures is their coherency of coupling. However, the role of coherent FFLs in relation to network robustness is not fully known, whereas that of coherent FBLs has been well established.

Results: To establish that coherent FFLs are abundant in biological networks, we examined gene regulatory and signaling networks and found that FFLs are ubiquitous, and are in a coherently coupled form. This result was also observed in the species-based signaling networks that are integrated from KEGG database. By using a random Boolean network model, we demonstrated that these coherent FFLs can improve network robustness against update-rule perturbations. In particular, we found that coherent FFLs increase robustness because these structures induce downstream nodes to be robust against update-rule perturbations. Therefore, coherent FFLs can be considered as a design principle of human signaling networks that improve network robustness against update-rule perturbations.

Contact:  kwonyk@ulsan.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
Authors: Li Tao , Li Qian-Zhong , Liu Shuai , Fan Guo-Liang , Zuo Yong-Chun , Peng Yong
Published: January 2013

Motivation: Protein–DNA interactions often take part in various crucial processes, which are essential for cellular function. The identification of DNA-binding sites in proteins is important for understanding the molecular mechanisms of protein–DNA interaction. Thus, we have developed an improved method to predict DNA-binding sites by integrating structural alignment algorithm and support vector machine–based methods.

Results: Evaluated on a new non-redundant protein set with 224 chains, the method has 80.7% sensitivity and 82.9% specificity in the 5-fold cross-validation test. In addition, it predicts DNA-binding sites with 85.1% sensitivity and 85.3% specificity when tested on a dataset with 62 protein–DNA complexes. Compared with a recently published method, BindN+, our method predicts DNA-binding sites with a 7% better area under the receiver operating characteristic curve value when tested on the same dataset. Many important problems in cell biology require the dense non-linear interactions between functional modules be considered. Thus, our prediction method will be useful in detecting such complex interactions.

Availability: The PreDNA webserver is freely available at: http://202.207.14.178/predna/index.aspx

Contact:  qzli@imu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online
Transport of misfolded endoplasmic reticulum proteins to the cell surface by MHC class II molecules
Authors: Jiang Yan , Arase Noriko , Kohyama Masako , Hirayasu Kouyuki , Suenaga Tadahiro , Jin Hui , Matsumoto Maki , Shida Kyoko , Lanier Lewis L. , Saito Takashi , Arase Hisashi
Published: January 2013

Nascent MHC class II molecules are associated with the invariant chain and are transported to the endolysosomal pathway, where MHC class II molecules acquire peptide antigens. On the other hand, misfolded endoplasmic reticulum (ER) proteins are generally degraded in the cells and are neither expressed on the cell surface nor secreted. Here, we found that MHC class II molecules associate with some misfolded ER proteins via the peptide-binding groove in competition with invariant chain. The misfolded proteins associated with MHC class II molecules are transported intact to the cell surface without processing to peptides. Furthermore, these complexes efficiently stimulate antigen-specific B cells. These findings reveal that MHC class II molecules function as a chaperone for the cell surface expression of misfolded ER proteins. In addition, we suggest that MHC class II molecules present not only peptides but also intact host-cell-derived proteins on the cell surface. These findings provide new insights into the function of MHC class II molecules.
Impact of Entropy Monitoring on Volatile Anesthetic Uptake
Authors: El Hor Tarek , Van Der Linden Philippe , De Hert Stephan , Mélot Christian , Bidgoli Javad
Published: January 2013

Background:

Electroencephalogram-derived monitoring to assess anesthetic depth may allow more accurate hypnotic drug administration, resulting in decreased anesthetic drug consumption. The authors hypothesized that the use of M-Entropy monitoring (Datex-Ohmeda, Helsinki, Finland) is associated with reduced sevoflurane uptake (primary outcome) in patients undergoing major abdominal surgery.

Methods:

A total of 50 patients with an American Society of Anesthesiology score of II–III, scheduled for elective laparoscopic rectosigmoidectomy were randomized into two groups in this randomized controlled trial. In the control group, the target expiratory fraction of sevoflurane was adapted according to standard clinical practice. In the study group, the target expiratory fraction of sevoflurane was adapted to maintain state entropy values between 40 and 60. State entropy values were continuously recorded in both groups but were not available to the anesthesiologist in the control group. In both groups, patients were ventilated using the auto-control mode of the Zeus® (Dräger, Lübeck, Germany) respirator, which allows precise measurements of sevoflurane uptake. Sufentanil was administered using a target-controlled infusion system.

Results:

Demographics did not differ between groups. During the anesthesia maintenance phase, state entropy values were lower in the control group than the study group (P < 0.0001). Sevoflurane uptake was higher in the control group than the study group (5.2 ± 1.4 ml/h vs. 3.8 ± 1.5 ml/h; P = 0.0012). Three patients in the control group developed intraoperative hypotension compared with none in the study group (P = 0.03).

Conclusions:

Monitoring the depth of anesthesia using M-Entropy was associated with a significant reduction in sevoflurane uptake.