bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual Search Facilitation in Repeated Displays Depends on Visuospatial Working Memory
Authors: Manginelli Angela A. , Geringswald Franziska , Pollmann Stefan
Published: July 2011

When distractor configurations are repeated over time, visual search becomes more efficient, even if participants are unaware of the repetition. This contextual cueing is a form of incidental, implicit learning. One might therefore expect that contextual cueing does not (or only minimally) rely on working memory resources. This, however, is debated in the literature. We investigated contextual cueing under either a visuospatial or a nonspatial (color) visual working memory load. We found that contextual cueing was disrupted by the concurrent visuospatial, but not by the color working memory load. A control experiment ruled out that unspecific attentional factors of the dual-task situation disrupted contextual cueing. Visuospatial working memory may be needed to match current display items with long-term memory traces of previously learned displays.
Tidally driven multiscale pore water flow in a creek‐marsh system
Authors: Xin Pei , Yuan Li‐Rong , Li Ling , Barry D. A.
Published: July 2011

Intertidal wetlands are complex hydrological systems characterized by strong, dynamic interactions between coastal surface water and groundwater, driven particularly by tides. We simulated such interactions with a focus on three‐dimensional, variably saturated pore water flow in a creek‐marsh system that bordered a tidally dominated main channel. Simulated intratidal groundwater dynamics exhibited significant flow asymmetry with nonzero mean flow velocities over the tidal period. The tidally averaged flow led to pore water circulation with three dimensionality linked strongly to the marsh topography, over a range of spatial scales: near the creek bank, around the creek meander, and over long marsh sections inclined toward the main channel. Particle tracking revealed that time scales associated with these circulations differed by orders of magnitude. Under the simulated conditions, the creek served as the main outlet of the pore water circulation paths, especially those linked with infiltration into the upper marsh surface areas away from the main channel. Local net efflux, influenced by the creek channel curvature, varied along the creek but produced a total discharge largely proportional to the creek length. Water infiltrating the soil in the lower marsh surface areas away from the creek tended to discharge directly to the main channel. However, the total discharge to the main channel was much less than that into the creek. This study highlights the hydrological complexity of intertidal marshes and the need for further research on interactions among marsh morphology, hydrology, and ecology, which underpin the functionalities of these wetland systems.
Copula‐based daily rainfall disaggregation model
Authors: Gyasi‐Agyei Yeboah
Published: July 2011

A daily rainfall disaggregation model, which uses a copula to model the dependence structure between total depth, total duration of wet periods, and the maximum proportional depth of a wet period, is presented. The wet(1)‐dry(0) binary sequence is modeled by the nonrandomized Bartlett‐Lewis model with diurnal effect incorporated before superimposing the AR(1) depth process submodel. Unlike previous studies, the model is structured such that all wet day data available are considered in the analysis, without the need to discard any good quality daily data embedded in a month having some missing data. This increased the data size, thus improving the modeling process. Further, the daily data are classified according to the total duration of wet periods duration within the day. In this way a large proportion of the model parameters become seasonal invariant, the overriding factor being the total duration of wet periods. The potential of the developed model has been demonstrated by disaggregating both the data set used in developing the model parameters and also a 12 year continuous rainfall data set not used in the model parameterization. Gross rainfall statistics of several aggregation levels down to 6 min have been very well reproduced by the disaggregation model. The copula dependence structure and the variation of the depth process submodel parameters with the total duration of wet periods are also very well captured by the presented model.
Group IVA phospholipase A2 regulates testosterone biosynthesis by murine Leydig cells and is required for timely sexual maturation
Authors: Kurusu Shiro , Sapirstein Adam , Sawada Harumi , Kawaminami Mitsumori , Bonventre Joseph V.
Published: July 2011

In the present paper, we report that PLA2G4A (Group IVA phospholipase A2) is important in the development and function of rodent testes. Interstitial cells of rat testes had high PLA2 (phospholipase A2) activity that was very sensitive to the PLA2G4A-preferential inhibitor AACOCF3 (arachidonyl trifluoromethyl ketone). PLA2G4A protein was expressed primarily in the interstitial cells of wild-type mouse testes throughout maturation. Although Pla2g4a knockout (Pla2g4a−/−) male mice are fertile, their sexual maturation was delayed, as indicated by cauda epididymal sperm count and seminal vesicle development. Delayed function of Pla2g4a−/− mice testes was associated with histological abnormalities including disorganized architecture, swollen appearance and fewer interstitial cells. Basal secretion of testosterone was attenuated significantly and steroidogenic response to hCG (human chorionic gonadotropin) treatment was reduced in Pla2g4a−/− mice compared with their Pla2g4a+/+ littermates during the sexual maturation period. Chemical inhibition of PLA2G4A activity by AACOCF3 or pyrrophenone significantly reduced hCG-stimulated testosterone production in cultured rat interstitial cells. AACOCF3 inhibited forskolin- and cAMP analogue-stimulated testosterone production. These results provide the first evidence that PLA2G4A plays a role in male testes physiology and development. These results may have implications for the potential clinical use of PLA2G4A inhibitors.
Sphingolipid-based drugs selectively kill cancer cells by down-regulating nutrient transporter proteins
Authors: Romero Rosales Kimberly , Singh Gurpreet , Wu Kevin , Chen Jie , Janes Matthew R. , Lilly Michael B. , Peralta Eigen R. , Siskind Leah J. , Bennett Michael J. , Fruman David A. , Edinger Aimee L.
Published: July 2011

Cancer cells are hypersensitive to nutrient limitation because oncogenes constitutively drive glycolytic and TCA (tricarboxylic acid) cycle intermediates into biosynthetic pathways. As the anaplerotic reactions that replace these intermediates are fueled by imported nutrients, the cancer cell's ability to generate ATP becomes compromised under nutrient-limiting conditions. In addition, most cancer cells have defects in autophagy, the catabolic process that provides nutrients from internal sources when external nutrients are unavailable. Normal cells, in contrast, can adapt to the nutrient stress that kills cancer cells by becoming quiescent and catabolic. In the present study we show that FTY720, a water-soluble sphingolipid drug that is effective in many animal cancer models, selectively starves cancer cells to death by down-regulating nutrient transporter proteins. Consistent with a bioenergetic mechanism of action, FTY720 induced homoeostatic autophagy. Cells were protected from FTY720 by cell-permeant nutrients or by reducing nutrient demand, but blocking apoptosis was ineffective. Importantly, AAL-149, a FTY720 analogue that lacks FTY720's dose-limiting toxicity, also triggered transporter loss and killed patient-derived leukaemias while sparing cells isolated from normal donors. As they target the metabolic profile of cancer cells rather than specific oncogenic mutations, FTY720 analogues such as AAL-149 should be effective against many different tumour types, particularly in combination with drugs that inhibit autophagy.
EHD2 mediates trafficking from the plasma membrane by modulating Rac1 activity
Authors: Benjamin Sigi , Weidberg Hilla , Rapaport Debora , Pekar Olga , Nudelman Marina , Segal Daniel , Hirschberg Koret , Katzav Shulamit , Ehrlich Marcelo , Horowitz Mia
Published: July 2011

EHDs [EH (Eps15 homology)-domain-containing proteins] participate in different stages of endocytosis. EHD2 is a plasma-membrane-associated EHD which regulates trafficking from the plasma membrane and recycling. EHD2 has a role in nucleotide-dependent membrane remodelling and its ATP-binding domain is involved in dimerization, which creates a membrane-binding region. Nucleotide binding is important for association of EHD2 with the plasma membrane, since a nucleotide-free mutant (EHD2 T72A) failed to associate. To elucidate the possible function of EHD2 during endocytic trafficking, we attempted to unravel proteins that interact with EHD2, using the yeast two-hybrid system. A novel interaction was found between EHD2 and Nek3 [NIMA (never in mitosis in Aspergillus nidulans)-related kinase 3], a serine/threonine kinase. EHD2 was also found in association with Vav1, a Nek3-regulated GEF (guanine-nucleotide-exchange factor) for Rho GTPases. Since Vav1 regulates Rac1 activity and promotes actin polymerization, the impact of overexpression of EHD2 on Rac1 activity was tested. The results indicated that wt (wild-type) EHD2, but not its P-loop mutants, reduced Rac1 activity. The inhibitory effect of EHD2 overexpression was partially rescued by co-expression of Rac1 as measured using a cholera toxin trafficking assay. The results of the present study strongly indicate that EHD2 regulates trafficking from the plasma membrane by controlling Rac1 activity.
Carrier transport mechanism in the SnO2:F/p-type a-Si:H heterojunction
Authors: Cannella G. , Principato F. , Foti M. , Di Marco S. , Grasso A. , Lombardo S.
Published: July 2011

We characterize SnO2:F/p-type a-Si:H/Mo structures by current-voltage (I-V) and capacitance-voltage (C-V) measurements at different temperatures to determine the transport mechanism in the SnO2:F/p-type a-Si:H heterojunction. The experimental I-V curves of these structures, almost symmetric around the origin, are ohmic for |V|<0.1V and have a super-linear behavior (power law) for |V|<0.1V. The structure can be modeled as two diodes back to back connected so that the main current transport mechanisms are due to the reverse current of the diodes. To explain the measured C-V curves, the capacitance of the heterostructure is modeled as the series connection of the depletion capacitances of the two back to back connected SnO2:F/p-type a-Si:H and Mo/p-type a-Si:H junctions. We simulated the reverse I-V curves of the SnO2:F/p-type a-Si:H heterojunction at different temperatures by using the simulation software SCAPS 2.9.03. In the model the main transport mechanism is generation of holes enhanced by tunneling by acceptor-type interface defects with a trap energy of 0.4 eV above the valence bandedge of the p-type a-Si:H layer and with a density of 4.0 × 1013 cm−2. By using I-V simulations and the proposed C-V model the built-in potential (Vbi) of the SnO2:F/p-type a-Si:H (0.16 V) and p-type a-Si:H/Mo (0.14 V) heterojunctions are extracted and a band diagram of the characterized structure is proposed.
Design evaluation of graphene nanoribbon nanoelectromechanical devices
Authors: Lam Kai-Tak , Stephen Leo Marie , Lee Chengkuo , Liang Gengchiau
Published: July 2011

Computational studies on nanoelectromechanical switches based on bilayer graphene nanoribbons (BGNRs) with different designs are presented in this work. By varying the interlayer distance via electrostatic means, the conductance of the BGNR can be changed in order to achieve ON-states and OFF-states, thereby mimicking the function of a switch. Two actuator designs based on the modified capacitive parallel plate (CPP) model and the electrostatic repulsive force (ERF) model are discussed for different applications. Although the CPP design provides a simple electrostatic approach to changing the interlayer distance of the BGNR, their switching gate bias VTH strongly depends on the gate area, which poses a limitation on the size of the device. In addition, there exists a risk of device failure due to static fraction between the mobile and fixed electrodes. In contrast, the ERF design can circumvent both issues with a more complex structure. Finally, optimizations of the devices are carried out in order to provide insights into the design considerations of these nanoelectromechanical switches.
Hyperbolic-cosine waveguide tapers and oversize rectangular waveguide for reduced broadband insertion loss in W-band electron paramagnetic resonance spectroscopy
Authors: Mett R. R. , Sidabras J. W. , Anderson J. R. , Hyde J. S.
Published: July 2011

The two-way insertion loss of a 1 m length of waveguide was reduced by nearly 5 dB over a 4% bandwidth at W-band (94 GHz) for an electron paramagnetic resonance (EPR) spectrometer relative to WR10 waveguide. The waveguide has an oversize section of commercially available rectangular WR28 and a novel pair of tapers that vary in cross section with axial position according to a hyperbolic-cosine (HC) function. The tapers connect conventional rectangular WR10 waveguide to the WR28. For minimum loss, the main mode electric field is parallel to the long side of the WR28. Using mode coupling theory, the position of maximum flare (inflection point) in the taper was optimized with respect to the coupling to higher order modes and the reflection of the main mode. The optimum inflection point position is about one-tenth of the taper length from the small end of the taper. Reflection and coupling were reduced by about 20 dB relative to a pyramidal (linear) taper of the same length. Comb-like dips in the transmission coefficient produced by resonances of the higher order modes in the oversize section were about 0.03 dB. Specially designed high-precision, adjustable WR28 flanges with alignment to about 5 μm were required to keep higher order mode amplitudes arising from the flanges comparable to those from the HC tapers. Minimum return loss was about 30 dB. This paper provides a foundation for further optimization, if needed. Methods are not specific to EPR or the microwave frequency band.
Potential order-of-magnitude enhancement of wind farm power density via counter-rotating vertical-axis wind turbine arrays
Authors: Dabiri John O.
Published: July 2011

Modern wind farms comprised of horizontal-axis wind turbines (HAWTs) require significant land resources to separate each wind turbine from the adjacent turbine wakes. This aerodynamic constraint limits the amount of power that can be extracted from a given wind farm footprint. The resulting inefficiency of HAWT farms is currently compensated by using taller wind turbines to access greater wind resources at high altitudes, but this solution comes at the expense of higher engineering costs and greater visual, acoustic, radar, and environmental impacts. We investigated the use of counter-rotating vertical-axis wind turbines (VAWTs) in order to achieve higher power output per unit land area than existing wind farms consisting of HAWTs. Full-scale field tests of 10-m tall VAWTs in various counter-rotating configurations were conducted under natural wind conditions during summer 2010. Whereas modern wind farms consisting of HAWTs produce 2–3 W of power per square meter of land area, these field tests indicate that power densities an order of magnitude greater can potentially be achieved by arranging VAWTs in layouts that enable them to extract energy from adjacent wakes and from above the wind farm. Moreover, this improved performance does not require higher individual wind turbine efficiency, only closer wind turbine spacing and a sufficient vertical flux of turbulence kinetic energy from the atmospheric surface layer. The results suggest an alternative approach to wind farming that has the potential to concurrently reduce the cost, size, and environmental impacts of wind farms.
Integrated data analysis at TJ-II: The density profile
Authors: van Milligen B. Ph. , Estrada T. , Ascasíbar E. , Tafalla D. , López-Bruna D. , Fraguas A. López , Jiménez J. A. , García-Cortés I. , Dinklage A. , Fischer R.
Published: July 2011

An integrated data analysis system based on Bayesian inference has been developed for the TJ-II stellarator. It reconstructs the electron density profile at a single time point, using data from interferometry, reflectometry, Thomson scattering, and the Helium beam, while providing a detailed error analysis. In this work, we present a novel analysis of the ambiguity inherent in profile reconstruction from reflectometry and show how the integrated data analysis approach elegantly resolves it. Several examples of the application of the technique are provided, in both low-density discharges with and without electrode biasing, and in high-density discharges with an (L-H) confinement transition.
Ab initio calculations on the excited states of Na3 cluster to explore beyond Born-Oppenheimer theories: Adiabatic to diabatic potential energy surfaces and nuclear dynamics
Authors: Paul Amit Kumar , Ray Somrita , Mukhopadhyay Debasis , Adhikari Satrajit
Published: July 2011

We perform ab initio calculation using quantum chemistry package (MOLPRO) on the excited states of Na3 cluster and present the adiabatic PESs for the electronic states 22E′ and \documentclass[12pt]{minimal}\begin{document}$1^2A_1^{\prime }$\end{document}12A1′, and the non-adiabatic coupling (NAC) terms among those states. Since the ab initio calculated NAC elements for the states 22E′ and \documentclass[12pt]{minimal}\begin{document}$1^2A_1^\prime$\end{document}12A1′ demonstrate the numerical validity of so called “Curl Condition,” such states closely form a sub-Hilbert space. For this subspace, we employ the NAC terms to solve the “adiabatic-diabatic transformation (ADT)” equations to obtain the functional form of the transformation angles and pave the way to construct the continuous and single valued diabatic potential energy surface matrix by exploiting the existing first principle based theoretical means on beyond Born-Oppenheimer treatment. Nuclear dynamics has been carried out on those diabatic surfaces to reproduce the experimental spectrum for system B of Na3 cluster and thereby, to explore the numerical validity of the theoretical development on beyond Born-Oppenheimer approach for adiabatic to diabatic transformation.
Development of x-ray laminography under an x-ray microscopic condition
Authors: Hoshino Masato , Uesugi Kentaro , Takeuchi Akihisa , Suzuki Yoshio , Yagi Naoto
Published: July 2011

An x-ray laminography system under an x-ray microscopic condition was developed to obtain a three-dimensional structure of laterally-extended planar objects which were difficult to observe by x-ray tomography. An x-ray laminography technique was introduced to an x-ray transmission microscope with zone plate optics. Three prototype sample holders were evaluated for x-ray imaging laminography. Layered copper grid sheets were imaged as a laminated sample. Diatomite powder on a silicon nitride membrane was measured to confirm the applicability of this method to non-planar micro-specimens placed on the membrane. The three-dimensional information of diatom shells on the membrane was obtained at a spatial resolution of sub-micron. Images of biological cells on the membrane were also obtained by using a Zernike phase contrast technique.
Sound dispersion and attenuation in concentrated H2SO4 by visible and ultraviolet Brillouin spectroscopy
Authors: Benassi P. , Nardone M. , Giugni A.
Published: July 2011

The acoustic properties of highly concentrated H2SO4 are investigated performing visible and ultraviolet Brillouin scattering measurements. We analyzed the isotropic and anisotropic spectra of this molecular liquid in a wide temperature and exchanged wavector range in order to study the evolution of its sound velocity and viscosity. This allows us to extract the parameters required to describe its viscoelastic relaxation behavior. We found that the behavior of the hydrodynamic parameters of this molecular liquid shares some similarities with that of water indicating a rather high increase of sound velocity if compared to that measured by ultrasonics.
Efficient quantum trajectory representation of wavefunctions evolving in imaginary time
Authors: Garashchuk Sophya , Mazzuca James , Vazhappilly Tijo
Published: July 2011

The Boltzmann evolution of a wavefunction can be recast as imaginary-time dynamics of the quantum trajectory ensemble. The quantum effects arise from the momentum-dependent quantum potential – computed approximately to be practical in high-dimensional systems – influencing the trajectories in addition to the external classical potential [S. Garashchuk, J. Chem. Phys. 132, 014112 (2010)]. For a nodeless wavefunction represented as ψ(x, t) = exp ( − S(x, t)/ℏ) with the trajectory momenta defined by ∇S(x, t), analysis of the Lagrangian and Eulerian evolution shows that for bound potentials the former is more accurate while the latter is more practical because the Lagrangian quantum trajectories diverge with time. Introduction of stationary and time-dependent components into the wavefunction representation generates new Lagrangian-type dynamics where the trajectory spreading is controlled improving efficiency of the trajectory description. As an illustration, different types of dynamics are used to compute zero-point energy of a strongly anharmonic well and low-lying eigenstates of a high-dimensional coupled harmonic system.
Configuration of heat sources or sinks in a finite volume
Authors: Jung J. , Lorente S. , Anderson R. , Bejan A.
Published: July 2011

This work documents the design method of allocating channels that serve as heat sources or heat sinks in a conducting body. First, we develop a numerical model to find the optimum channel spacing for specified properties of the surrounding medium, the time scale of the heat transfer process, and the dimensions of the configuration. Second, we show with scale analysis that the optimal spacing (S/D) must equal τ1/2 in an order of magnitude sense, where τ is the dimensionless time scale of the process. This conclusion holds for the two heat transfer histories that were considered, exponential and top hat. We extend the method to a packing of channels of two sizes (diameters and heat source strengths). The optimal spacings and packing density obey the scaling rule determined for packing sources of a single size.
A compact physical model for morphology induced intrinsic degradation of organic bulk heterojunction solar cell
Authors: Ray Biswajit , Alam Muhammad A.
Published: July 2011

The gradual loss of efficiency during field operation poses a fundamental challenge for economic viability of any solar cell technology. Well known examples include light-induced degradation in Si-based cell (Staebler-Wronski effect), Cu diffusion in thin film (copper indium gallium selenide) cell, hot-spot degradation in series connected modules, etc. Here we develop a compact model for an intrinsic degradation concern for bulk heterojunction type organic photovoltaic (BH-OPV) cells that involve continued (thermal) phase segregation of the donor-acceptor molecules leading to characteristic loss of efficiency and performance. Our approach interprets a number of BH-OPV device degradation measurements within a common framework and suggests/rationalizes intuitive routes for lifetime improvement for such technologies.
A novel vacuum ultra violet lamp for metastable rare gas experiments
Authors: Daerr Heiner , Kohler Markus , Sahling Peter , Tippenhauer Sandra , Arabi-Hashemi Ariyan , Becker Christoph , Sengstock Klaus , Kalinowski Martin B.
Published: July 2011

We report on a new design of a vacuum ultra violet (VUV) lamp for direct optical excitation of high laying atomic states, e.g., for excitation of metastable rare gas atoms. The lamp can be directly mounted to ultra-high vacuum vessels (p ⩽ 10−10mbar). It is driven by a 2.45 GHz microwave source. For optimum operation, it requires powers of ∼20 W. The VUV light is transmitted through a magnesium fluoride window, which is known to have a decreasing transmittance for VUV photons with time. In our special setup, after a run-time of the VUV lamp of 550 h the detected signal continuously decreased to 25% of its initial value. This corresponds to a lifetime increase of two orders of magnitude compared to previous setups or commercial lamps.
Synthesis of copper/copper oxide nanoparticles by solution plasma
Authors: Saito Genki , Hosokai Sou , Tsubota Masakatsu , Akiyama Tomohiro
Published: July 2011

This paper describes the synthesis of copper/copper oxide nanoparticles via a solution plasma, in which the effect of the electrolyte and electrolysis time on the morphology of the products was mainly examined. In the experiments, a copper wire as a cathode was immersed in an electrolysis solution of a K2CO3 with the concentration from 0.001 to 0.50 M or a citrate buffer (pH = 4.8), and was melted by the local-concentration of current. The results demonstrated that by using the K2CO3 solution, we obtained CuO nanoflowers with many sharp nanorods, the size of which decreased with decreasing the concentration of the solution. Spherical particles of copper with/without pores formed when the citrate buffer was used. The pores in the copper nanoparticles appeared when the applied voltage changed from 105 V to 130 V, due to the dissolution of Cu2O.
Stability enhancement in organic photovoltaic device by using polymerized fluorocarbon anode buffer layer
Authors: Lo M. F. , Ng T. W. , Lai S. L. , Fung M. K. , Lee S. T. , Lee C. S.
Published: July 2011

We show that by introducing a polymerized fluorocarbon film (CFx) on indium tin oxide (ITO), stability of CuPc/C60 organic photovoltaic device can be improved. While the efficiency of a standard device decreases from 1.5% to 0.7% after 2000 h of storage and intermittent operation, a CFx-buffered device shows negligible changes (1.6% throughout 2000 h). We found that C60 is influenced by the ITO substrate. X-ray photoemission studies show that reactive −O• species on the ITO surface were minimized after CFx polymerization. Reduction of such species from organic layers is considered a major cause for the stability enhancement in the CFx-buffered device.
Optimal sizing of distributed resources in micro grid with loss of power supply probability technology by using breeding particle swarm optimization
Authors: Moghaddas-Tafreshi S. M. , Zamani H. A. , Hakimi S. M.
Published: July 2011

The deregulated energy environment, among other effects, has favored a gradual transition from centralized power generation to distributed generation sources connected at the medium voltage or low voltage side of the distribution network. Interconnection of small, modular generations and energy storages of low or medium voltage distribution systems forms a new type of power system, which called the micro grid (MG). This paper has developed a methodology of performing the optimal unit sizing for distributed energy resources in MG. The methodology aims at finding the configuration, among a set of systems components, which meets the desired system reliability requirements, with the minimum cost of energy (COE). Other than solar and wind energies, in this study the biogas power plant and the use of urban waste for producing electricity power are considered. The size of biogas power plant is calculated according to available municipal waste. The micro grid system is connected to the utility and can sale its extra produced power to utility. In first step, accurate mathematical models for characterizing standalone photovoltaic module, wind generator, biogas plant, and battery bank are proposed. In second step, based on a breeding particle swarm optimization algorithm, one optimal sizing method is developed to calculate the optimum system configuration that can achieve the customers required loss of power supply probability with a minimum COE. By this methodology, we can analyze MG
Low current density spin-transfer torque effect assisted by in-plane microwave field
Authors: Wang Jianbo , Mu Congpu , Wang Weiwei , Zhang Bin , Xia Haiyan , Liu Qingfang , Xue Desheng
Published: July 2011

A strategy is presented to greatly reduce both the critical spin polarized current density and the magnetization switching time in elliptical magnetic spin valve. This method is a combination of microwave field and spin polarized current. The numerical simulation at zero temperature shows that the critical current density and the magnetization switching time are sensitive to the frequency and the amplitude of microwave magnetic field. A 75% reduction in critical current density is observed when the frequency of microwave coincides with the natural ferromagnetic resonance frequency of free layer.
Surface plasmon effects on carbon nanotube field effect transistors
Authors: Isoniemi T. , Johansson A. , Hakala T. K. , Rinkiö M. , Törmä P. , Toppari J. J. , Kunttu H.
Published: July 2011

Herein, we experimentally demonstrate surface plasmon polariton (SPP) induced changes in the conductivity of a carbon nanotube field effect transistor (CNT FET). SPP excitation is done via Kretschmann configuration while the measured CNT FET is situated on the opposite side of the metal layer away from the laser, but within reach of the launched SPPs. We observe a shift of ∼0.4 V in effective gate voltage. SPP-intermediated desorption of physisorbed oxygen from the device is discussed as a likely explanation of the observed effect. This effect is visible even at low SPP intensities and within a near-infrared range.
Auger recombination in GaInN/GaN quantum well laser structures
Authors: Brendel M. , Kruse A. , Jönen H. , Hoffmann L. , Bremers H. , Rossow U. , Hangleiter A.
Published: July 2011

Nonradiative loss processes are a major concern in nitride-based light emitting devices. Utilizing optical gain measurements on GaInN/GaN/AlGaN laser structures, we have studied the dependence of the total recombination rate on excess carrier density, up to rather high densities. From a detailed quantitative analysis, we find a room-temperature Auger recombination coefficient of 1.8 ± 0.2 × 10−31 cm6/s in the bandgap range 2.5 − 3.1 eV, considerably lower than previous experimental estimates. Thus, Auger recombination is expected to be significant for laser diodes, while it is not likely to be a major factor for the droop observed in light-emitting diodes.
Quantum-Chemical Ab Initio Calculations on Borabenzene (C5H5B) and its Adducts with Ne, Ar, Kr, and N2. Could Free Borabenzene be Observed in Rare Gas Matrices?
Authors: Raabe Gerhard , Baldofski Matthias
Published: July 2011

Quantum-chemical calculations employing different theoretical methods and basis sets have been performed on borabenzene (C5H5B) as well as on its adducts to dinitrogen (N2) and the rare gases Ne, Ar, and Kr. In agreement with previous calculations, the ground state of borabenzene was found to be a planar singlet with six electrons in molecular orbitals of π symmetry and a wide C-B-C bond angle (142.2°). Depending on the method (PUMP2, SAC-CI, CASPT2(8,8)), the lowest triplet state was found to be 28 to 46 kcal mol–1 (1 kcal mol–1 = 4.186 kJ mol–1) higher in energy. The energies associated with the formation of the adducts with N2, Ne, Ar, and Kr were calculated as –14.9, –0.5, –1.4, and –3.5 kcal mol–1 respectively. Our calculated spectrum of the normal modes as well as the electronic excitation spectrum of the N2 adduct reproduce qualitatively the characteristic features of the IR and the UV-vis spectra described by experimentalists. The corresponding calculated spectra (normal modes, UV-vis) of the rare gas adducts were found to be very similar to those of free borabenzene.
Micrometer-Scale 2D Mapping of the Composition and Homogeneity of Polymer Inclusion Membranes
Authors: St John Alexander M. , Best Stephen P. , Wang Yaodong , Tobin Mark J. , Puskar Ljiljana , Siegele Rainer , Cattrall Robert W. , Kolev Spas D.
Published: July 2011

A new method for determining variations in composition at the micrometer level of polymer inclusion membranes (PIMs) using synchrotron-based Fourier-transform infrared (FTIR) microspectrometry is described and used to investigate the relationship between PIM composition and the reproducibility of formation of optically clear, ‘homogeneous’ polymer membranes. Membranes based on Aliquat 336 and poly(vinyl chloride) (PVC), di(2-ethylhexyl) phosphoric acid and PVC, and Aliquat 336 and cellulose triacetate give highly reproducible PIMs with excellent optical properties which are chemically homogeneous on the micrometer scale. The close relationship between the spatial distribution of the extractant in the PIM and the extracted species was demonstrated by proton-induced X-ray emission microspectrometry (µ-PIXE) examination of chemically homogeneous membranes loaded with uranium. There is a high correlation between the homogeneity of the distributions of extracted uranium, polymer, and extractant, both on the surface of the PIM and over its cross-section. This approach provides a quantitative basis for the evaluation and optimization of PIMs and similar composite materials.
Molecular Simulations to Rationalize Humanized Ab2/3H6 Activity
Authors: de Ruiter Anita , Mader Alexander , Kunert Renate , Oostenbrink Chris
Published: July 2011

The murine anti-idiotypic antibody 3H6 (Ab2/3H6) is directed against the human 2F5 antibody, which is capable of neutralizing HIV-1. Recently, four humanized Ab2/3H6 models have been developed in order to reduce the risk of human anti-mouse antibody (HAMA) responses in case of administration to humans. In this study, molecular dynamics simulations were performed on these models as well as on the murine Ab2/3H6 in solution and bound to 2F5, in order to rationalize the differences in binding affinities of the models towards 2F5. Analysis of these simulations suggested that the orientation and dynamics of the residues TYR54 and TYR103 of the heavy chain of Ab2/3H6 play an important role in these differences. Subsequently, the contribution of these residues to the binding affinity was quantified by applying free energy calculations.
Theoretical Investigations into the Role of Aryl Nitrenium Ions' Stability on Their Mutagenic Potential
Authors: Kim Eun J. , Matuszek Anna M. , Yu Bo , Reynisson Jóhannes
Published: July 2011

By using Mulliken and Natural Bond Orbital (NBO) methods based on the density functional theory (DFT), partial charges of exocyclic nitrogen atoms were calculated for nitrenium ions formed from 201 known drugs and 50 Ames positive (mutagenic) compounds containing aryl amine and nitro moieties. The statistical difference of the partial charges was analysed based on the hypothesis that the mutagens have a more negative charge on their exocyclic nitrogen atom resulting in stable nitrenium ions, and thus a longer lifetime to react selectively with DNA; whereas known drugs are not in general mutagenic and therefore have a relatively more positive partial charge. The nitrenium ions with 1° amine parent compounds did not show a statistical difference between drugs and mutagens based on the Mulliken charges. A slight difference was observed in the NBO data where the drugs have more negative partial charge on their exocyclic nitrogen atoms compared with the mutagens. Interestingly, nitrenium ions with aryl nitro drugs as their parent compounds have more negative charge on the exocyclic nitrogen compared with the other drug classes. Aryl nitro drugs are relatively scarce and are often linked to genotoxicity, which fits with the hypotheses proposed. These results indicate that other physical properties besides the stability of the nitrenium ions are important to determine the mutagenic potential of aryl amine and nitro containing compounds.
Peptide Isomerization Induced by pH Change Regulates the S1 Binding Site in Ficolins
Authors: Yang Lifeng , Zhang Jing , Ding Jeak Ling
Published: July 2011

Infection-inflammation mediated interactions between human ficolin and the pathogen GlcNAc is associated with local acidosis, leading to antimicrobial action. Therefore, revealing the precise molecular conformation induced by pH-shift is crucial in understanding the immune response. Here, we performed constant-pH molecular dynamics simulations on the L-ficolin fibrinogen-like domain over pH 4.5–9. An unusual cis-Asn244-Cys245 peptide bond prevailed over the pH range in the S1 binding site. Analysis of the hydrogen-bond network at S1 suggested Asn244 to be indispensible for maintaining the cis form of Asn244-Cys245, and the absence of the hydroxyl group on Phe262 accounts for the lack of GlcNAc binding.
Investigation into the Extension of the Non-Nucleoside Reverse Transcriptase Binding Pocket
Authors: Dupree Tom B. , Keller Paul A. , Griffith Renate
Published: July 2011

Superimposition of 125 non-nucleoside inhibitors from human immunodeficiency virus reverse transcriptase structures reveals a novel binding space deeper into the enzyme for some of these inhibitors, allowing access to the polymerase active site. This may enable us to design new inhibitors of this enzyme with better mutation resistance profiles. We have analysed this new binding space and have docked our in-house scaffolds into this region, highlighting the possibility of the formation of new hydrogen bonds with residues of the active site.
Marie Curie – A Pioneer of Radiochemistry and Dual Nobel Prize Laureate
Authors: Hardy Clarence
Published: July 2011

Marie Skłodowska Curie (1867–1934) was born in Warsaw. She was a pioneer in the field of radiochemistry and coined the word ‘radioactivity’ in 1898 as a result of her early research work in Paris. She discovered two new radioactive elements, polonium and radium, in 1898. She received two Nobel Prizes, the first in 1903 in Physics, jointly with Henri Becquerel and Pierre Curie, and the second in 1911 in Chemistry. These Prizes ensured her recognition as an outstanding scientist not only by the French government, who appointed her as the first woman professor in the University of Paris, but also by the wider international public. She showed great creativity and perseverance throughout her life and is recognized as one of the great women of science. It is fitting that her second Nobel Prize in Chemistry in 1911 and her outstanding career have been recognized by the United Nations by its declaration of 2011 as the International Year of Chemistry, and by IUPAC devoting a special issue of ‘Chemistry International’ (Vol. 33, No. 1) to her memory.
The History and Development of Radiation Chemistry
Authors: Cooper Ronald
Published: July 2011

Stemming from the discovery and isolation of radioactive elements by the Curies came observations of chemical and physical changes produced by ‘emanations’. From ~1900 AD, observations were sporadic and spread across a range of chemical systems. Several conflicting results from irradiated water were reported – one recording no decomposition, whereas another study observed hydrogen and hydrogen peroxide formation. The field progressed slowly while the only practical source of radiation was X-rays. After the mid-1940s, the isotope output from nuclear reactors gave chemists high-activity radiation sources with which to conduct experiments. Particle accelerators were utilized and led to the pulsed radiolysis technique, which unlocked the door to the study of ultrafast solution reactions of free radicals and excited states. The radiation chemistry of water is now a qualitative and quantitative basis for the initiation and study of a wide range of chemical and physical processes. Polymeric systems, solid-state dosimeters, and gaseous plasmas are active areas of research. The radiological use of radiation has an active radiobiology field developing new biochemical processes involving DNA stability.
Deletion of mouse
Porcn
blocks Wnt ligand secretion and reveals an ectodermal etiology of human focal dermal hypoplasia/Goltz syndrome
Authors: Barrott Jared J. , Cash Gabriela M. , Smith Aaron P. , Barrow Jeffery R. , Murtaugh L. Charles
Published: July 2011

The
Drosophila porcupine
gene is required for secretion of wingless and other Wnt proteins, and sporadic mutations in its unique human ortholog,
PORCN
, cause a pleiotropic X-linked dominant disorder, focal dermal hypoplasia (FDH, also known as Goltz syndrome). We generated a conditional allele of the X-linked mouse
Porcn
gene and analyzed its requirement in Wnt signaling and embryonic development. We find that
Porcn
-deficient cells exhibit a cell-autonomous defect in Wnt ligand secretion but remain responsive to exogenous Wnts. Consistent with the female-specific inheritance pattern of FDH,
Porcn
hemizygous male embryos arrest during early embryogenesis and fail to generate mesoderm, a phenotype previously associated with loss of Wnt activity. Heterozygous
Porcn
mutant females exhibit a spectrum of limb, skin, and body patterning abnormalities resembling those observed in human patients with FDH. Many of these defects are recapitulated by ectoderm-specific deletion of
Porcn
, substantiating a long-standing hypothesis regarding the etiology of human FDH and extending previous studies that have focused on downstream elements of Wnt signaling, such as β-catenin. Conditional deletion of
Porcn
thus provides an experimental model of FDH, as well as a valuable tool to probe Wnt ligand function in vivo.
Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments
Authors: Beauchamp Kyle A. , Ensign Daniel L. , Das Rhiju , Pande Vijay S.
Published: July 2011

As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet–triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet–triplet energy transfer experiments on HP35.
Symmetries in stimulus statistics shape the form of visual motion estimators
Authors: Fitzgerald James E. , Katsov Alexander Y. , Clandinin Thomas R. , Schnitzer Mark J.
Published: July 2011

The estimation of visual motion has long been studied as a paradigmatic neural computation, and multiple models have been advanced to explain behavioral and neural responses to motion signals. A broad class of models, originating with the Reichardt correlator model, proposes that animals estimate motion by computing a temporal cross-correlation of light intensities from two neighboring points in visual space. These models provide a good description of experimental data in specific contexts but cannot explain motion percepts in stimuli lacking pairwise correlations. Here, we develop a theoretical formalism that can accommodate diverse stimuli and behavioral goals. To achieve this, we treat motion estimation as a problem of Bayesian inference. Pairwise models emerge as one component of the generalized strategy for motion estimation. However, correlation functions beyond second order enable more accurate motion estimation. Prior expectations that are asymmetric with respect to bright and dark contrast use correlations of both even and odd orders, and we show that psychophysical experiments using visual stimuli with symmetric probability distributions for contrast cannot reveal whether the subject uses odd-order correlators for motion estimation. This result highlights a gap in previous experiments, which have largely relied on symmetric contrast distributions. Our theoretical treatment provides a natural interpretation of many visual motion percepts, indicates that motion estimation should be revisited using a broader class of stimuli, demonstrates how correlation-based motion estimation is related to stimulus statistics, and provides multiple experimentally testable predictions.
Siva1 suppresses epithelial–mesenchymal transition and metastasis of tumor cells by inhibiting stathmin and stabilizing microtubules
Authors: Li Nan , Jiang Peng , Du Wenjing , Wu Zhengsheng , Li Cong , Qiao Mengran , Yang Xiaolu , Wu Mian
Published: July 2011

Epithelial–mesenchymal transition (EMT) enables epithelial cells to acquire motility and invasiveness that are characteristic of mesenchymal cells. It plays an important role in development and tumor cell metastasis. However, the mechanisms of EMT and their dysfunction in cancer cells are still not well understood. Here we report that Siva1 interacts with stathmin, a microtubule destabilizer. Siva1 inhibits stathmin's activity directly as well as indirectly through Ca2+/calmodulin-dependent protein kinase II-mediated phosphorylation of stathmin at Ser16. Via the inhibition of stathmin, Siva1 enhances the formation of microtubules and impedes focal adhesion assembly, cell migration, and EMT. Low levels of Siva1 and Ser16-phosphorylated stathmin correlate with high metastatic states of human breast cancer cells. In mouse models, knockdown of Siva1 promotes cancer dissemination, whereas overexpression of Siva1 inhibits it. These results suggest that microtubule dynamics are critical for EMT. Furthermore, they reveal an important role for Siva1 in suppressing cell migration and EMT and indicate that down-regulation of Siva1 may contribute to tumor cell metastasis.
Dual role of Brg chromatin remodeling factor in Sonic hedgehog signaling during neural development
Authors: Zhan Xiaoming , Shi Xuanming , Zhang Zilai , Chen Yu , Wu Jiang I.
Published: July 2011

Sonic hedgehog (Shh) signaling plays diverse roles during animal development and adult tissue homeostasis through differential regulation of Gli family transcription factors. Dysregulated Shh signaling activities have been linked to birth defects and tumorigenesis. Here we report that Brg, an ATP-dependent chromatin remodeling factor, has dual functions in regulating Shh target gene expression. Using a Brg conditional deletion in Shh-responding neural progenitors and fibroblasts, we demonstrate that Brg is required both for repression of the basal expression and for the activation of signal-induced transcription of Shh target genes. In developing telencephalons deficient for Brg, Shh target genes were derepressed, whereas Brg-deleted cerebellar granule neuron precursors failed to respond to Shh to increase their proliferation. The repressor function of Brg was mediated through Gli3 and both the repressor and activator functions of Brg appeared to be independent of its ATPase activity. Furthermore, Brg facilitates Gli coactivator histone deacetylase (HDAC) binding to the regulatory regions of Shh target genes, providing a possible mechanism for its positive role in Shh signaling. Our results thus reveal that a complex chromatin regulation mechanism underlies the precise transcription outcomes of Shh signaling and its diverse roles during development.