bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross sections for the formation of H(n = 2) atom via superexcited states in photoexcitation of methane and ammonia
Authors: Kumagai Yoshiaki , Odagiri Takeshi , Nakano Motoyoshi , Tanabe Takehiko , Suzuki Isao H. , Hosaka Kouichi , Kitajima Masashi , Kouchi Noriyuki
Published: October 2013

The absolute cross sections for the formation of the H(2s) and H(2p) atoms, σ2s and σ2p, respectively, in photoexcitation of CH4 and NH3 were measured in the range of the incident photon energy 15–48 eV for studying superexcited states of the molecules. The same superexcited states were found to contribute to the σ2s and σ2p cross sections. It was concluded that the non-adiabatic transitions play a significant role during the dissociation of the superexcited states and ionic states.
Structural transition of zinc oxide cluster cations: Smallest tube like structure at (ZnO)6+
Authors: Koyasu Kiichirou , Komatsu Kunihiko , Misaizu Fuminori
Published: October 2013

Zinc oxide cluster cations have been analyzed by ion mobility spectrometry using a home-made drift cell combined with a time-of-flight reflectron mass spectrometer. Structural changes from cyclic to tube like structures were observed around n = 8, corresponding to predictions by theoretical calculations. The structures were assigned by comparing with the arrival time simulation using MOBCAL software. We have also observed ion-injection energy dependence of the structures of (ZnO)n+. The smallest tube structure of (ZnO)6+ has predominantly been observed at an injection energy of 200 eV. The extraordinary stability of the compact structure at this size has been observed for the first time.
A simple mechanism for emergent chirality in achiral hard particle assembly
Authors: Carmichael Scott P. , Shell M. Scott
Published: October 2013

For centuries, chirality has been appreciated as a key component in understanding how matter orders. While intuitively chiral particles can self-assemble into chiral superstructures, it is often less obvious how achiral particles can do the same. Here we show that there is a potentially general, packing-based mechanism that explains why many simple, two-dimensional achiral particles assemble into chiral materials. Namely, we use simulations of hard, regular polygons to show that the subtle shape modification of corner rounding surprisingly can induce chiral symmetry breaking by deforming the underlying close-packed lattice. The mechanism quantitatively explains recent experimental results reporting chiral symmetry breaking in the hard triangle system. Moreover, it predicts similar symmetry breaking in the rounded hard rectangle system, which we verify through simulations. Because effective corner rounding is easily realized by modulating repulsive interactions in real systems, this simple mechanism suggests tremendous potential for creating dynamically tunable chiral surfaces with a variety of applications.
Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization
Authors: Khavrutskii Ilja V. , Smith Jason B. , Wallqvist Anders
Published: October 2013

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM/molecular mechanical (QM/MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP/6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP/6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal/mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM/MM studies of reaction mechanisms.
Non-polynomial extensions of solvable potentials à la Abraham-Moses
Authors: Odake Satoru , Sasaki Ryu
Published: October 2013

Abraham-Moses transformations, besides Darboux transformations, are well-known procedures to generate extensions of solvable potentials in one-dimensional quantum mechanics. Here we present the explicit forms of infinitely many seed solutions for adding eigenstates at arbitrary real energy through the Abraham-Moses transformations for typical solvable potentials, e.g., the radial oscillator, the Darboux-Pöschl-Teller, and some others. These seed solutions are simple generalisations of the virtual state wavefunctions, which are obtained from the eigenfunctions by discrete symmetries of the potentials. The virtual state wavefunctions have been an essential ingredient for constructing multi-indexed Laguerre and Jacobi polynomials through multiple Darboux-Crum transformations. In contrast to the Darboux transformations, the virtual state wavefunctions generate non-polynomial extensions of solvable potentials through the Abraham-Moses transformations.
A verification of the gyrokinetic microstability codes GEM, GYRO, and GS2
Authors: Bravenec R. V. , Chen Y. , Candy J. , Wan W. , Parker S.
Published: October 2013

A previous publication [R. V. Bravenec et al., Phys. Plasmas 18, 122505 (2011)] presented favorable comparisons of linear frequencies and nonlinear fluxes from the Eulerian gyrokinetic codes gyro [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] and gs2 [W. Dorland et al., Phys. Rev. Lett. 85, 5579 (2000)]. The motivation was to verify the codes, i.e., demonstrate that they correctly solve the gyrokinetic-Maxwell equations. The premise was that it is highly unlikely for both codes to yield the same incorrect results. In this work, we add the Lagrangian particle-in-cell code gem [Y. Chen and S. Parker, J. Comput. Phys. 220, 839 (2007)] to the comparisons, not simply to add another code, but also to demonstrate that the codes' algorithms do not matter. We find good agreement of gem with gyro and gs2 for the plasma conditions considered earlier, thus establishing confidence that the codes are verified and that ongoing validation efforts for these plasma parameters are warranted.
General approach on chemistry and stress coupling effects during oxidation
Authors: Suo Yaohong , Shen Shengping
Published: October 2013

In this paper, the mechanism of growth strain is discussed based on the irreversible evolving equations by considering the coupling effects of stress and chemical reaction during isothermal oxidation, and a simple model relating the growth strain and the oxide thickness is developed. If the effect of the stress on the chemical reaction is not taken into account, the model reduces to the Clarke assumption. The expression of Dox is exhibited, and its value can be determined by experiments. The stress evolving equations are derived, where the viscoplastic strain of the oxide and metal and the growth strain of the oxide are considered. Numerical results are given and compared with results from experiments and the existing model. There is good agreement between the proposed model and the experimental data.
Sono-activated ultrasound localization microscopy
Authors: Desailly Yann , Couture Olivier , Fink Mathias , Tanter Mickael
Published: October 2013

Scanned at very high ultrasound frame rates, injectable microbubbles can be activated sequentially as isolated punctual sources of acoustic echoes. These signals can thus be localized far beyond the diffraction limit. The resolution improvement granted by Sono-Activated Ultrasound Localization Microscopy (SAULM) was demonstrated within microfluidic channels 20 times smaller than the imaging wavelength (λ = 870 μm). The width of the channels mapped with SAULM was 13 times smaller than as they appeared under conventional ultrasound imaging. Two channels separated by λ/4.5 could be distinguished. Implementing SAULM in-vivo could lead to a complete reconstruction of the vascular tree down to the smallest capillaries at several centimeter depth.
The effect of a transverse magnetic field on 1/f noise in graphene
Authors: Rumyantsev S. L. , Coquillat D. , Ribeiro R. , Goiran M. , Knap W. , Shur M. S. , Balandin A. A. , Levinshtein M. E.
Published: October 2013

The low frequency 1/f noise in graphene devices was studied in a transverse magnetic field of up to B = 14 T at temperatures T = 80 K and T = 285 K. The examined devices revealed a large physical magnetoresistance typical for graphene. At low magnetic fields (B < 2 T), the level of 1/f noise decreases with the magnetic field at both temperatures. The details of the 1/f noise response to the magnetic field depend on the gate voltage. However, in the high magnetic fields (B > 2 T), a strong increase of the noise level was observed for all gate biases.
Generation of broadband frequency-entangled photons using plasmon nanoantenna
Authors: Oka Hisaki
Published: October 2013

A scheme for the generation of frequency-entangled photons using a plasmon nanoantenna system is proposed. The nanoantenna system consists of two large metallic nanostructures confined in a one-sided microcavity with high spontaneous emission factor. Two input photons are converted into an entangled photon pair via the saturation effect of the nanoantenna. The degree of entanglement of the resultant entangled photons is evaluated using the entropy of entanglement, E. We show that broadband frequency-entangled photons with E up to ≈0.45 are generated owing to rapid plasmon radiative decay.
Highly effective and isotropic pinning in epitaxial Fe(Se,Te) thin films grown on CaF2 substrates
Authors: Braccini V. , Kawale S. , Reich E. , Bellingeri E. , Pellegrino L. , Sala A. , Putti M. , Higashikawa K. , Kiss T. , Holzapfel B. , Ferdeghini C.
Published: October 2013

We report on the isotropic pinning obtained in epitaxial Fe(Se,Te) thin films grown on CaF2(001) substrate. High critical current density values – larger than 1 MA/cm2 in self field and liquid helium – are reached together with a very weak dependence on the magnetic field and a complete isotropy. Analysis through transmission electron microscopy evidences the presence of defects looking like lattice disorder at a very small scale, between 5 and 20 nm, which are thought to be responsible for such isotropic behavior in contrast to what was observed on SrTiO3, where defects parallel to the c-axis enhance pinning in that direction.
Mono-bi-monolayer graphene junction introduced quantum transport channels
Authors: Yin Demin , Liu Weihua , Li Xin , Geng Li , Wang Xiaoli , Huai Pu
Published: October 2013

Quantum transport properties of mono-bi-monolayer graphene junctions (MBMGJs) are investigated via first principle calculation. The simulation results show that the MBMGJs introduce more effective quantum transport channels in comparing with a full monolayer graphene nanoribbon channel and result in significantly increased on-state current. An overlapping-MBMGJ channel with one overlapping zigzag carbon chain shows a larger current even than a full bilayer graphene channel. The robustness of the effective quantum transport channel introduced by the overlapping-MBMGJ against the variation of the length of the bilayer region is also verified.
Observation of salt effects on hydration water of lysozyme in aqueous solution using terahertz time-domain spectroscopy
Authors: Aoki Katsuyoshi , Shiraki Kentaro , Hattori Toshiaki
Published: October 2013

Terahertz time-domain spectroscopy was used to investigate the salt effect of ammonium sulfate on the dynamics of hydration water of lysozyme in aqueous solution. The absorption coefficient of lysozyme aqueous solutions containing salt was subtracted by that of the water and ammonium sulfate contained in the lysozyme solution. The results revealed that ammonium sulfate increases the absorption coefficient of the hydration water, which indicates that the dynamics of the hydration water becomes faster and/or the number of hydration water molecules decreases with increasing ammonium sulfate concentration.
Guided neuronal growth on arrays of biofunctionalized GaAs/InGaAs semiconductor microtubes
Authors: Bausch Cornelius S. , Koitmäe Aune , Stava Eric , Price Amanda , Resto Pedro J. , Huang Yu , Sonnenberg David , Stark Yuliya , Heyn Christian , Williams Justin C. , Dent Erik W. , Blick Robert H.
Published: October 2013

We demonstrate embedded growth of cortical mouse neurons in dense arrays of semiconductor microtubes. The microtubes, fabricated from a strained GaAs/InGaAs heterostructure, guide axon growth through them and potentially enable electrical and optical probing of propagating action potentials. The coaxial nature of the microtubes—similar to myelin—is expected to enhance the signal transduction along the axon. We present a technique of suppressing arsenic toxicity and prove the success of this technique by overgrowing neuronal mouse cells.
Charge transport and electroluminescence of silicon nanocrystals/SiO2 superlattices
Authors: López-Vidrier J. , Berencén Y. , Hernández S. , Blázquez O. , Gutsch S. , Laube J. , Hiller D. , Löper P. , Schnabel M. , Janz S. , Zacharias M. , Garrido B.
Published: October 2013

Charge transport and electroluminescence mechanisms in Si-rich Si oxynitride/silicon oxide (SRON/SiO2) superlattices deposited on p-type Si substrate are reported. The superlattice structures were deposited by plasma-enhanced chemical-vapor deposition and subsequently annealed at 1150 °C to precipitate and crystallize the Si excess into Si nanocrystals. The dependence of the electrical conduction on the applied voltage and temperature was found to be well described by a Poole-Frenkel transport mechanism over a wide voltage range. On the other hand, the observed dependence of the electroluminescence on the SRON layer thickness is a clear proof of quantum confinement and was attributed to an excitonic radiative recombination taking place in the confined states within the Si quantum dots. A model is proposed based on thermal hopping of electrons between the quantum dots acting as trap states (Poole-Frenkel). A correlation between carrier transport and electroluminescence has been established considering impact ionization of high-kinetic energy electrons on the Si quantum dots.
Si-adatom kinetics in defect mediated growth of multilayer epitaxial graphene films on 6H-SiC
Authors: Shetu Shamaita S. , Omar S. U. , Daniels K. M. , Daas B. , Andrews J. , Ma S. , Sudarshan T. S. , Chandrashekhar M. V. S.
Published: October 2013

We present a quantitative study on the growth of multilayer epitaxial graphene (EG) by solid-state decomposition of SiC on polar (c-plane Si and C-face) and non-polar (a and m planes) 6H-SiC faces, with distinctly different defect profiles. The growth rates are slower than expected from a mechanism that involves Si loss from an open and free surface, and much faster than expected for the nucleation of a defect-free EG layer, implying that defects in the EG play a critical role in determining the growth kinetics. We show that a Deal-Grove growth model, which assumes vertical diffusion of Si through these defects as the limiting factor for EG growth, is unsuitable for describing multilayer growth. Instead, we introduce a lateral “adatom” diffusion mechanism for Si out-diffusion, based on a modified Burton, Cabrera, and Frank model. In this model, defects in epitaxial graphene serve as sinks for Si desorption loss, taking the place of reactive sites, such as step edges for nucleation and growth of crystals produced with external precursors. This analysis shows that the surface diffusion of Si atoms to the grain boundaries of EG limits the growth on c-plane C-face and non-polar faces, rather than the purely vertical diffusion of Si through the grain boundaries described in the Deal-Grove model. However, for Si-face c-plane growth, diffusion of Si to the defects, as well as desorption of Si at the grain boundaries are both relevant, leading to a different temperature trend compared with the other faces. This distinct qualitative difference is ascribed to point-defects in Si-face growth, as contrasted with line defects/grain boundaries on the other faces. The size of the EG grains correlates with the surface diffusion length extracted from this model. The longer a Si adatom diffuses, the higher the quality of the grown EG film, an insight that provides valuable information on Si adatom kinetics for optimizing EG growth. We discuss the applicability of this model to growth of multilayer EG in an argon ambient at atmospheric pressure.
Precipitation of hydrides in high purity niobium after different treatments
Authors: Barkov F. , Romanenko A. , Trenikhina Y. , Grassellino A.
Published: October 2013

Precipitation of lossy non-superconducting niobium hydrides represents a known problem for high purity niobium in superconducting applications. Using cryogenic optical and laser confocal scanning microscopy, we have directly observed surface precipitation and evolution of niobium hydrides in samples after different treatments used for superconducting RF cavities for particle acceleration. Precipitation is shown to occur throughout the sample volume, and the growth of hydrides is well described by the fast diffusion-controlled process in which almost all hydrogen is precipitated at T = 140 K within ∼30 min. 120 °C baking and mechanical deformation are found to affect hydride precipitation through their influence on the number of nucleation and trapping centers.
Local characterization of the optical properties of annealed Au films on glass substrates
Authors: Bernardo-Gavito R. , Serrano A. , García M. A. , Miranda R. , Granados D.
Published: October 2013

We present scanning near field microscopy and local spectroscopic characterisation of gold nanoparticles fabricated on glass sodalime cover slides. The nanoislands are fabricated by the thermal annealing of gold thin films. Results are presented for samples annealed at 300 °C, 400 °C, and 500 °C. We study the spectral dependence of the transmittance at the nanoscale level with respect to the nanoislands size, shape, and interparticle distance employing a Scanning Near-field Optical Microscopy.
Anisotropic magnetocaloric effect in gadolinium thin films: Magnetization measurements and acoustic detection
Authors: Mansanares A. M. , Gandra F. C. G. , Soffner M. E. , Guimarães A. O. , da Silva E. C. , Vargas H. , Marin E.
Published: October 2013

In this letter, it is demonstrated the ability of the magnetoacoustic technique in detecting the magnetocaloric effect in gadolinium thin films (1.0 μm and 3.0 μm thick), which is not accessible through conventional temperature sensors because of the reduced mass of the samples. The method, which detects the direct effect of the sample temperature variation, proved to be sensitive to the anisotropy of the films, making possible for the investigation of the anisotropic magnetocaloric effect. Magnetization measurements were also carried out, and from these measurements both the adiabatic temperature and the isothermal entropy variations were calculated. The acoustically detected magnetocaloric effect shows very good agreement with these calculations.
First-principles studies on infrared properties of semiconducting graphene monoxide
Authors: Pu H. H. , Mattson E. C. , Rhim S. H. , Gajdardziksa-Josifovska M. , Hirschmugl C. J. , Weinert M. , Chen J. H.
Published: October 2013

Graphene monoxide (GMO), a recently proposed 2D crystalline material in the graphene family, is attractive for next-generation nanoelectronics because of its predicted tunable band gap. As a guide to GMO experimental characterization, we calculate the vibrational properties and obtain three infrared active vibration modes (B1u, B2u, and B3u) and six Raman active modes (B1g, B2g, 2B3g, and 2Ag) for intrinsic GMO. The frequencies of the infrared active modes depend on both local structural deformations and interactions between adjacent GMO layers. These results are consistent with experimental observations and provide a means of estimating the number of layers in intrinsic GMO.
A study of electrically active traps in AlGaN/GaN high electron mobility transistor
Authors: Yang Jie , Cui Sharon , Ma T. P. , Hung Ting-Hsiang , Nath Digbijoy , Krishnamoorthy Sriram , Rajan Siddharth
Published: October 2013

We have studied electron conduction mechanisms and the associated roles of the electrically active traps in the AlGaN layer of an AlGaN/GaN high electron mobility transistor structure. By fitting the temperature dependent I-V (Current-Voltage) curves to the Frenkel-Poole theory, we have identified two discrete trap energy levels. Multiple traces of I-V measurements and constant-current injection experiment all confirm that the main role of the traps in the AlGaN layer is to enhance the current flowing through the AlGaN barrier by trap-assisted electron conduction without causing electron trapping.
Linearity of graphene field-effect transistors
Authors: Jenkins K. A. , Farmer D. B. , Han S.-J. , Dimitrakopoulos C. , Oida S. , Valdes-Garcia A.
Published: October 2013

The linearity of the radio frequency response of graphene field-effect transistors has been measured as a function of gate bias using the two-tone method. Two kinds of transistors, which differ in both the graphene source material and the device structure, have been compared. Both devices show high linearity compared to contemporary silicon transistors. The physical origins of this behavior are analyzed and discussed.
High piezoelectricity due to multiphase coexistence in low-temperature sintered (Ba,Ca)(Ti,Sn)O3–CuOx ceramics
Authors: Zhou Peng-Fei , Zhang Bo-Ping , Zhao Lei , Zhao Xiao-Kun , Zhu Li-Feng , Cheng Li-Qian , Li Jing-Feng
Published: October 2013

Ultrahigh piezoelectric constant (d33 = 683 pC/N) and converse piezoelectric coefficient (dS/dE = 1257 pm/V) were observed in CuO-doped lead-free (Ba,Ca)(Ti,Sn)O3 ceramics at an optimal composition fabricated by a conventional sintering method at a low temperature 1250 °C. Since all samples showed a pure perovskite structure with coexisting multiphases including cubic, tetragonal, orthorhombic, and rhombohedral phases around two converged triple points, a good compositional stability of high piezoelectricity along with a high d33 and dS/dE over 600 pC/N and 1000 pm/V was achieved within a wide compositional region (1.0 ≤ x ≤ 3.0) regardless of the CuO content (x).
Spacecraft charging analysis with the implicit particle-in-cell code iPic3D
Authors: Deca J. , Lapenta G. , Marchand R. , Markidis S.
Published: October 2013

We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation results with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.
Note: Vibrationally mediated photodissociation of carbon dioxide cation
Authors: Mao Rui , Zhang Qun , Chen Min , He Chao , Zhou Dan-na , Bai Xi-lin , Zhang Limin , Chen Yang
Published: October 2013

The photodissociation dynamics of carbon dioxide cation, ${\rm CO}_{\rm 2}^ +$ CO 2+, mediated by its different $\tilde A{}^{\rm 2}\Pi _{u,1/2} (\upsilon _1,\upsilon _2,0)$ÃΠu,1/22(υ1,υ2,0) vibronic states has been investigated by means of time-sliced velocity map imaging. Through analysis of the recorded translational energy release spectra of photofragment CO+, we found that the photodissociation of ${\rm CO}_{\rm 2}^ +$ CO 2+ exhibits drastic change in a rather narrow energy region. A conformational barrier in the ${\rm CO}_{\rm 2}^ + ( {\tilde A{}^{\rm 2}A_1 } )$ CO 2+(ÃA12) state is suggested to be ∼5600 cm−1 relative to the ${\rm CO}_{\rm 2}^ + ( {\tilde A{}^{\rm 2}\Pi _{u,1/2} ( {0,0,0} )})$ CO 2+(ÃΠu,1/22(0,0,0)) state, in reasonable agreement with previous prediction.
Talbot-Lau based Moiré deflectometry with non-coherent sources as potential High Energy Density plasma diagnostic
Authors: Valdivia M. P. , Stutman D. , Finkenthal M.
Published: October 2013

X-ray phase-contrast radiography could better characterize highly localized density gradients expected in High Energy Density (HED) plasma experiments than conventional attenuation radiography. In particular, the Talbot-Lau (TL) grating interferometer, which works with extended and polychromatic x-ray sources, is a potentially attractive HED diagnostic due to its high sensitivity. For HED characterization the TL setup and imaging techniques must be changed from the recently studied medical system. The object magnification must be increased greatly in order to resolve μm scale gradients while the Talbot magnification must be increased in order to keep the gratings away from the plasma. Additionally, techniques for retrieving the density profile from a single plasma image must be developed. We thus study the performance of high magnification TL interferometers, in conjunction with Moiré fringe deflectometry for single image phase retrieval. The results show a very good interferometer contrast (≤30%) at high magnification. The Moiré technique enables measuring both sharp and mild density gradients with good accuracy and spatial resolution. Both the laboratory and simulation studies indicate that the TL based Moiré deflectometry is more sensitive than the propagation phase-contrast method when utilizing an extended x-ray source (∼80 μm). In HED experiments this would allow for less demanding X-ray backlighters than those used at present.
Surface InP/In0.48Ga0.52P quantum dots: Carrier recombination dynamics and their interaction with fluorescent dyes
Authors: Hestroffer Karine , Braun Robert , Ugur Asli , Tomm Jens W. , Hackbarth Steffen , Röder Beate , Hatami Fariba
Published: October 2013

We describe the properties and carrier dynamics of surface InP quantum dots (QDs) on In0.48Ga0.52P, lattice-matched to GaAs (100). The structures were grown using gas-source molecular beam epitaxy. The average height and lateral size of the dots are in the range of 2–6 and 30–50 nm, respectively. The photoluminescence of the surface dots peaks between 750 and 830 nm, depending on the growth conditions, and is red-shifted compared to the emission of the capped QDs grown under similar conditions. The integrated photoluminescence intensity is comparable to that of the capped QDs. The decay time of both surface and capped QDs is around 1 ns at 15 K. The strong luminescence of surface QDs is explained by the effect of acting vacuum/air as an effective barrier and saturated surface states. Enhancement of the QDs luminescence is observed for the samples coated with a fluorescent dye.
Image reconstruction enables high resolution imaging at large penetration depths in fluorescence microscopy
Authors: Dilipkumar Shilpa , Montalescot Sandra , Mondal Partha Pratim
Published: October 2013

Imaging thick specimen at a large penetration depth is a challenge in biophysics and material science. Refractive index mismatch results in spherical aberration that is responsible for streaking artifacts, while Poissonian nature of photon emission and scattering introduces noise in the acquired three-dimensional image. To overcome these unwanted artifacts, we introduced a two-fold approach: first, point-spread function modeling with correction for spherical aberration and second, employing maximum-likelihood reconstruction technique to eliminate noise. Experimental results on fluorescent nano-beads and fluorescently coated yeast cells (encaged in Agarose gel) shows substantial minimization of artifacts. The noise is substantially suppressed, whereas the side-lobes (generated by streaking effect) drops by 48.6% as compared to raw data at a depth of 150 μm. Proposed imaging technique can be integrated to sophisticated fluorescence imaging techniques for rendering high resolution beyond 150 μm mark.
Structural heterogeneity induced plasticity in bulk metallic glasses: From well-relaxed fragile glass to metal-like behavior
Authors: Li Weidong , Bei H. , Tong Y. , Dmowski W. , Gao Y. F.
Published: October 2013

To reveal the structural origin responsible for the sharp change of the fracture mode on the as-cast and thermally-relaxed status, we use nanomechanical testing to measure the stresses for the onset of plasticity of a metallic glass and develop a stochastic statistical model, which can be used to characterize structural heterogeneity (defect density and strength) inside the metallic glass. Our experiments and calculations found that, with increasing the structural relaxation, the defect density drops by two orders of magnitude. Correspondingly, the fracture of metallic glasses changes from a significantly plastic (metal-like) mode to an extremely brittle (fragile glass) one.
Angular-stable and polarization-independent frequency selective structure with high selectivity
Authors: Li Bo , Shen Zhongxiang
Published: October 2013

We present a three-dimensional bandpass frequency selective structure (FSS) with high selectivity and wide out-of-band rejection. Furthermore, the structure is insensitive to the variation of incident angle and polarization of a striking plane electromagnetic wave. By studying the electric fields and currents excited in the proposed structure, it is revealed that four resonators are constructed to produce the desired filtering response. Experiments show that the fabricated FSS has a 3 dB fractional bandwidth of 18.75% for the passband and a bandwidth of 268.25% for the upper out-of-band rejection better than 20 dB under the normal incidence.
Universal geometric classification of armchair honeycomb nanoribbons by their properties in a staggered sublattice potential
Authors: O'Brien T. E. , Zhang C. , Wright A. R.
Published: October 2013

We demonstrate the topological band-gap dependence of armchair honeycomb nanoribbons in a staggered sublattice potential. A scaling law is presented to quantify the band gap variation with potential strength. All armchair nanoribbons are described by one of three distinct classes depending on their width, consistent with previous classifications, namely, the well known massless Dirac condition, potentially gapless, and gapless-superlattice. The ability to tune and, in all cases close, the band-gap via external probes makes our classification particularly relevant experimentally. We propose several systems in which these results should shed considerable light, which have all already been experimentally realized.
Vision after 53 Years of Blindness
Authors: Šikl Radovan , Šimeček Michal , Porubanová-Norquist Michaela , Bezdíček Ondřej , Kremláček Jan , Stodůlka Pavel , Fine Ione , Ostrovsky Yuri
Published: October 2013

Several studies have shown that visual recovery after blindness that occurs early in life is never complete. The current study investigated whether an extremely long period of blindness might also cause a permanent impairment of visual performance, even in a case of adult-onset blindness. We examined KP, a 71-year-old man who underwent a successful sight-restoring operation after 53 years of blindness. A set of psychophysical tests designed to assess KP's face perception, object recognition, and visual space perception abilities were conducted six months and eight months after the surgery. The results demonstrate that regardless of a lengthy period of normal vision and rich pre-accident perceptual experience, KP did not fully integrate this experience, and his visual performance remained greatly compromised. This was particularly evident when the tasks targeted finer levels of perceptual processing. In addition to the decreased robustness of his memory representations, which was hypothesized as the main factor determining visual impairment, other factors that may have affected KP's performance were considered, including compromised visual functions, problems with perceptual organization, deficits in the simultaneous processing of visual information, and reduced cognitive abilities.
How to Test Molyneux's Question Empirically
Authors: Connolly Kevin
Published: October 2013

In a recent i-Perception article, Schwenkler (2012) criticizes a 2011 experiment by R. Held and colleagues purporting to answer Molyneux's question. Schwenkler proposes two ways to re-run the original experiment, either by allowing subjects to move around the stimuli, or by simplifying the stimuli to planar objects rather than three-dimensional ones. In Schwenkler (2013), he expands on and defends the former. I argue that this way of re-running the experiment is flawed, since it relies on a questionable assumption that newly sighted subjects will be able to appreciate depth cues. I then argue that the second way of re-running the experiment is successful both in avoiding the flaw of original Held experiment, and in avoiding the problem with the first way of re-running the experiment.
MicroRNA-directed program of cytotoxic CD8
+
T-cell differentiation
Authors: Trifari Sara , Pipkin Matthew E. , Bandukwala Hozefa S. , Äijö Tarmo , Bassein Jed , Chen Runqiang , Martinez Gustavo J. , Rao Anjana
Published: October 2013

Significance

Development of cytotoxic T lymphocytes (CTLs) from activated CD8
+
T cells is a key step of the antiviral immune response and is marked by the up-regulation of lytic molecules (perforin, granzymes). How this process is regulated at the posttranscriptional level is still largely unknown. Here we report that Dicer and microRNAs (miRNAs) restrict the expression of lytic molecules in mouse and human CTLs, and describe a unique signaling network that controls the expression of perforin, eomesodermin, and the IL-2Rα chain (CD25) downstream of IL-2 and inflammatory signals through miR-139 and miR-150 in differentiating CTLs.
Tourism Policy as a Tool for Rural Development
Authors: Hyytiä Nina , Kola Jukka
Published: October 2013

This paper studies whether tourism policies enhance regional development, and how such effects are distributed by the rural‐urban sphere in two structurally different rural regions in Finland. The overall GDP and employment effects were positive in both examined regions whether the main beneficiary was a rural or urban area. The tourism policies generated comparatively uniform gains in the diversified economic region in which the natural environment was the main tourist attraction. However, in the region where the food cluster was at the core of the economy, the gains were smaller and tended to accumulate in the urban area.
Anatomical entity mention recognition at literature scale
Authors: Pyysalo Sampo , Ananiadou Sophia
Published: October 2013

Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced.

Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database.

Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger.

Contact:  sophia.ananiadou@manchester.ac.uk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer
Authors: Li Gong-Hua , Huang Jing-Fei
Published: October 2013

Motivation: The discovery of therapeutic targets is important for cancer treatment. Although dozens of targets have been used in cancer therapies, cancer remains a serious disease with a high mortality rate. Owing to the expansion of cancer-related data, we now have the opportunity to infer therapeutic targets using computational biology methods.

Results: Here, we describe a method, termed anticancer activity enrichment analysis, used to determine genes that could be used as therapeutic targets. The results show that these genes have high likelihoods of being developed into clinical targets (>60%). Combined with gene expression data, we predicted 50 candidate targets for lung cancer, of which 19 of the top 20 genes are targeted by approved drugs or drugs used in clinical trials. A hexokinase family member, hexokinase domain-containing protein 1 (HKDC1), is the only one of the top 20 genes that has not been targeted by either an approved drug or one being used in clinical trials. Further investigations indicate that HKDC1 is a novel potential therapeutic target for lung cancer.

Conclusion: We developed a protocol to identify potential therapeutic targets from heterogeneous data. We suggest that HKDC1 is a novel potential therapeutic target for lung cancer.

Contact:  huangjf@mail.kiz.ac.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Protter: interactive protein feature visualization and integration with experimental proteomic data
Authors: Omasits Ulrich , Ahrens Christian H. , Müller Sebastian , Wollscheid Bernd
Published: October 2013

Summary: The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Here we present Protter, a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins. A built-in export function produces publication-quality customized protein illustrations, also for large datasets. Visualizations of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics.

Availability and implementation: The Protter web application is available at http://wlab.ethz.ch/protter. Source code and installation instructions are available at http://ulo.github.io/Protter/.

Contact: wbernd@ethz.ch

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A pathway-based data integration framework for prediction of disease progression
Authors: Seoane José A. , Day Ian N. M. , Gaunt Tom R. , Campbell Colin
Published: October 2013

Motivation: Within medical research there is an increasing trend toward deriving multiple types of data from the same individual. The most effective prognostic prediction methods should use all available data, as this maximizes the amount of information used. In this article, we consider a variety of learning strategies to boost prediction performance based on the use of all available data.

Implementation: We consider data integration via the use of multiple kernel learning supervised learning methods. We propose a scheme in which feature selection by statistical score is performed separately per data type and by pathway membership. We further consider the introduction of a confidence measure for the class assignment, both to remove some ambiguously labeled datapoints from the training data and to implement a cautious classifier that only makes predictions when the associated confidence is high.

Results: We use the METABRIC dataset for breast cancer, with prediction of survival at 2000 days from diagnosis. Predictive accuracy is improved by using kernels that exclusively use those genes, as features, which are known members of particular pathways. We show that yet further improvements can be made by using a range of additional kernels based on clinical covariates such as Estrogen Receptor (ER) status. Using this range of measures to improve prediction performance, we show that the test accuracy on new instances is nearly 80%, though predictions are only made on 69.2% of the patient cohort.

Availability:  https://github.com/jseoane/FSMKL

Contact:  J.Seoane@bristol.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Perturbations induced by a molecular cloud on the young stellar disc in the Galactic Centre
Authors: Mapelli Michela , Gualandris Alessia , Hayfield Tristen
Published: October 2013

The Galactic Centre (GC) is a crowded environment: observations have revealed the presence of (molecular, atomic and ionized) gas, a cusp of late-type stars and ∼100 early-type stars, about half of which are lying in one or possibly two discs. In this paper, we study the perturbations exerted on a thin stellar disc (with outer radius ∼0.4 pc) by a molecular cloud that falls towards the GC and is disrupted by the supermassive black hole (SMBH). The initial conditions for the stellar disc were drawn from the results of previous simulations of molecular cloud infall and disruption in the SMBH potential. We find that most of the gas from the disrupted molecular cloud settles into a dense and irregular disc surrounding the SMBH. If the gas disc and the stellar disc are slightly misaligned (∼5°–20°), the precession of the stellar orbits induced by the gas disc significantly increases the inclinations of the stellar orbits (by a factor of ∼3–5 in 1.5 Myr) with respect to the normal vector to the disc. Furthermore, the distribution of orbit inclinations becomes significantly broader. These results might be the clue to explain the broad distribution of observed inclinations of the early-type stars with respect to the normal vector of the main disc. We discuss the implications for the possibility that fresh gas was accreted by the GC after the formation of the disc(s) of early-type stars.
The Global Decline of the Labor Share*
Authors: Karabarbounis Loukas , Neiman Brent
Published: October 2013

The stability of the labor share of income is a key foundation in macroeconomic models. We document, however, that the global labor share has significantly declined since the early 1980s, with the decline occurring within the large majority of countries and industries. We show that the decrease in the relative price of investment goods, often attributed to advances in information technology and the computer age, induced firms to shift away from labor and toward capital. The lower price of investment goods explains roughly half of the observed decline in the labor share, even when we allow for other mechanisms influencing factor shares, such as increasing profits, capital-augmenting technology growth, and the changing skill composition of the labor force. We highlight the implications of this explanation for welfare and macroeconomic dynamics.
Apoptosis-like death in Leishmania donovani promastigotes induced by eugenol-rich oil of Syzygium aromaticum
Authors: Islamuddin Mohammad , Sahal Dinkar , Afrin Farhat
Published: October 2013

Leishmaniasis consists of a complex spectrum of infectious diseases with worldwide distribution of which visceral leishmaniasis or kala-azar caused by Leishmania donovani is the most devastating. In the absence of vaccines, chemotherapy remains the mainstay for the control of leishmaniasis. The drugs of choice are expensive and associated with multiple adverse side effects. Because of these limitations, the development of new antileishmanial compounds is imperative and plants offer prospects in this regard. The present work was conducted to study the antileishmanial potential of oil from Syzygium aromaticum flower buds (clove). The S. aromaticum oil was characterized by gas chromatography and GC-MS and eugenol as well as eugenyl acetate were found to be the most abundant compounds, composing 59.75 % and 29.24 %, respectively of the oil. Our findings have shown that eugenol-rich essential oil from S. aromaticum (EROSA) possesses significant activity against L. donovani, with 50 % inhibitory concentration of 21±0.16 µg ml−1 and 15.24±0.14 µg ml−1, respectively, against promastigotes and intracellular amastigotes. Alterations in cellular morphology and growth reversibility assay substantiated the leishmanicidal activity of EROSA. The leishmanicidal effect was mediated via apoptosis as confirmed by externalization of phosphatidylserine, DNA nicking by TdT-mediated dUTP nick-end labelling (TUNEL) assay, dyskinetoplastidy, cell cycle arrest at sub-G0–G1 phase, loss of mitochondrial membrane potential and reactive oxygen species generation. EROSA presented no adverse cytotoxic effects against murine macrophages even at 200 µg ml−1. Our studies authenticate the promising antileishmanial activity of EROSA, which is mediated by programmed cell death, and, accordingly, EROSA may be a source of novel agents for the treatment of leishmaniasis.