bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing capability indices for one-sided processes with measurement errors
Authors: Grau D.
Published: November 2013

In the manufacturing industry, many product characteristics are of one-sided tolerances. The process capability indices
Cpu (u, v) and
Cpl (u, v) can be used to measure process performance. Most research work related to capability indices assumes no gauge measurement errors. This assumption insufficiently reflects real situations even when advanced measuring instruments are used. In this paper we show that using a critical value without taking into account these errors, severely underestimates the α-risk which causes a less accurate testing capacity. In order to improve the results we suggest the use of an adjusted critical value, and we give a Maple program to get it. An example in a polymer granulates manufactory is presented to illustrate this approach.
Quasi-optical theory of relativistic surface-wave oscillators with one-dimensional and two-dimensional periodic planar structures
Authors: Ginzburg N. S. , Malkin A. M. , Sergeev A. S. , Zaslavsky V. Yu.
Published: November 2013

Within the framework of a quasi-optical approach, we develop 2D and 3D self-consistent theory of relativistic surface-wave oscillators. Presenting the radiation field as a sum of two counter-propagating wavebeams coupled on a shallow corrugated surface, we describe formation of an evanescent slow wave. Dispersion characteristics of the evanescent wave following from this method are in good compliance with those found from the direct cst simulations. Considering excitation of the slow wave by a sheet electron beam, we simulate linear and nonlinear stages of interaction, which allows us to determine oscillation threshold conditions, electron efficiency, and output coupling. The transition from the model of surface-wave oscillator operating in the π-mode regime to the canonical model of relativistic backward wave oscillator is considered. We also described a modified scheme of planar relativistic surface-wave oscillators exploiting two-dimensional periodic gratings. Additional transverse propagating waves emerging on these gratings synchronize the emission from a wide sheet rectilinear electron beam allowing realization of a Cherenkov millimeter-wave oscillators with subgigawatt output power level.
Experiments with biased side electrodes in electron cyclotron resonance ion sources
Authors: Drentje A. G. , Kitagawa A. , Uchida T. , Rácz R. , Biri S.
Published: November 2013

The output of highly charged ions from an electron cyclotron resonance ion source (ECRIS) consists of ionic losses from a highly confined plasma. Therefore, an increase of the output of the ions of interest always is a compromise between an increase in the confinement and an increase of the losses. One route towards a solution consists of attacking the losses in directions – i.e., radial directions – that do not contribute to the required output. This was demonstrated in an experiment (using the Kei ECRIS at NIRS, Japan) where radial losses were electrostatically reduced by positively biasing one set of six “side” electrodes surrounding the plasma in side-ward directions attached (insulated) to the cylindrical wall of the plasma chamber. Recently new studies were performed in two laboratories using two essentially different ion sources. At the BioNano ECRIS (Toyo University, Japan) various sets of electrodes were used; each of the electrodes could be biased individually. At the Atomki ECRIS (Hungary), one movable, off-axis side electrode was applied in technically two versions. The measurements show indeed a decrease of ionic losses but different effectivities as compared to the biased disk.
Structure formation in perfluoropentacene:diindenoperylene blends and its impact on transient effects in the optical properties studied in real-time during growth
Authors: Broch K. , Gerlach A. , Lorch C. , Dieterle J. , Novák J. , Hinderhofer A. , Schreiber F.
Published: November 2013

We discuss the result of the competing effects of favourable intermolecular interactions and steric incompatibilities due to the size mismatch of perfluoropentacene (PFP) and diindenoperylene (DIP) on the structure formation and associated optical properties in mixed films. Using real-time grazing incidence X-ray diffraction we investigate the size of coherently scattering islands ls as a function of film thickness and mixing ratio. We find that for PFP:DIP 1:2 blends ls is by a factor of ∼4 smaller than in pure DIP films, while ls of the PFP:DIP 2:1 blends is not significantly reduced compared with pure PFP. Yet, we observe an increase in ls with film thickness for all of the samples, independent on the mixing ratio. In parallel with the structural characterization we investigate the evolution of the absorption spectra in the visible spectral range and its dependence on ls in situ during film growth using differential reflectance spectroscopy. We observe a surprisingly strong effect of changes in the structural order on the shape of ε2, xy(E), evident by a pronounced evolution of characteristic peaks in the thickness range from 1.6 nm to 9.6 nm. The combined results of the real-time experiments allow to identify the thickness dependent crystal grain size as the origin of the observed transient effects in the absorption spectra.
Cascaded emission of linearly polarized single photons from positioned InP/GaInP quantum dots
Authors: Braun T. , Unsleber S. , Baumann V. , Gschrey M. , Rodt S. , Reitzenstein S. , Schneider C. , Höfling S. , Kamp M.
Published: November 2013

We report on the optical characterization of site-controlled InP/GaInP quantum dots (QDs). Spatially resolved low temperature cathodoluminescence proves the long-range ordering of the buried emitters, revealing a yield of ∼90% of optically active, positioned QDs and a strong suppression of emitters on interstitial positions. The emission of single QDs shows a pronounced degree of linear polarization along the [0,−1,1] crystal axis with an average degree of polarization of 94%. Photon correlation measurements of the emission from a single QD indicate the single-photon character of the exciton and biexciton emission lines as well as the cascaded nature of the photon pair.
Development of electron cyclotron emission imaging system on the HL-2A tokamak
Authors: Jiang M. , Shi Z. B. , Che S. , Domier C. W. , Luhmann N. C. , Hu X. , Spear A. , Liu Z. T. , Ding X. T. , Li J. , Zhong W. L. , Chen W. , Che Y. L. , Fu B. Z. , Cui Z. Y. , Sun P. , Liu Y. , Yang Q. W. , Duan X. R.
Published: November 2013

A 2D electron cyclotron emission imaging (ECEI) system has been developed for measurement of electron temperature fluctuations in the HL-2A tokamak. It is comprised of a front-end 24 channel heterodyne imaging array with a tunable RF range spanning 75–110 GHz, and a set of back-end ECEI electronics that together generate 24 × 8 = 192 channel images of the 2nd harmonic X-mode electron cyclotron emission from the HL-2A plasma. The simulated performance of the local oscillator (LO) optics and radio frequency (RF) optics is presented, together with the laboratory characterization results. The Gaussian beams from the LO optics are observed to properly cover the entire detector array. The ECE signals from the plasma are mixed with the LO signal in the array box, then delivered to the electronics system by low-loss microwave cables, and finally to the digitizers. The ECEI system can achieve temporal resolutions of ∼μs, and spatial resolutions of 1 cm (radially) and 2 cm (poloidally).
Thermal transpiration through single walled carbon nanotubes and graphene channels
Authors: Thekkethala Joe Francis , Sathian Sarith P.
Published: November 2013

Thermal transpiration through carbon nanotubes (CNTs) and graphene channels is studied using molecular dynamics (MD) simulations. The system consists of two reservoirs connected by a CNT. It is observed that a flow is developed inside the CNT from the low temperature reservoir to the high temperature reservoir when the two reservoirs are maintained at different temperatures. The influence of channel size and temperature gradient on the mean velocity is analysed by varying the CNT diameter and the temperature of one of the reservoirs. Larger flow rate is observed in the smaller diameter CNTs showing an increase in the mean velocity with increase in the temperature gradient. For the flow developed inside the CNTs, slip boundaries occur and the slip length is calculated using the velocity profile. We examine the effect of fluid-wall interaction strength (εfw), diffusivity (D), and viscosity of the fluid (μ) on the temperature induced fluid transport through the CNTs. Similar investigations are also carried out by replacing the CNT with a graphene channel. Results show that the mean velocity of the fluid atoms in the graphene channel is lower than that through the CNTs. This can be attributed to the higher degree of confinement observed in the CNTs.
Correlation between structural and opto-electronic characteristics of crystalline Si microhole arrays for photonic light management
Authors: Sontheimer Tobias , Preidel Veit , Lockau Daniel , Back Franziska , Rudigier-Voigt Eveline , Löchel Bernd , Erko Alexei , Schmidt Frank , Schnegg Alexander , Lips Klaus , Becker Christiane , Rech Bernd
Published: November 2013

By employing electron paramagnetic resonance spectroscopy, transmission electron microscopy, and optical measurements, we systematically correlate the structural and optical properties with the deep-level defect characteristics of various tailored periodic Si microhole arrays, which are manufactured in an easily scalable and versatile process on nanoimprinted sol-gel coated glass. While tapered microhole arrays in a structured base layer are characterized by partly nanocrystalline features, poor electronic quality with a defect concentration of 1017 cm−3 and a high optical sub-band gap absorption, planar polycrystalline Si layers perforated with periodic arrays of tapered microholes are composed of a compact crystalline structure and a defect concentration in the low 1016 cm−3 regime. The low defect concentration is equivalent to the one in planar state-of-the-art solid phase crystallized Si films and correlates with a low optical sub-band gap absorption. By complementing the experimental characterization with 3-dimensional finite element simulations, we provide the basis for a computer-aided approach for the low-cost fabrication of novel high-quality structures on large areas featuring tailored opto-electronic properties.
Comment on “Optimization of power and efficiency of thermoelectric devices with asymmetric thermal contacts” [J. Appl. Phys. 111, 024509 (2012)]
Authors: Lin Bihong
Published: November 2013

Yazawa and Shakouri [J. Appl. Phys. 111, 024509 (2012)] calculated the maximum power output of a thermoelectric power generation with asymmetric thermal contacts. However, the main results obtained are not identical with those given in textbooks, and consequently, some problems deserve some attention.
Radio frequency plasma power dependence of the moisture permeation barrier characteristics of Al2O3 films deposited by remote plasma atomic layer deposition
Authors: Jung Hyunsoo , Choi Hagyoung , Jeon Heeyoung , Lee Sanghun , Jeon Hyeongtag
Published: November 2013

In the present study, we investigated the gas and moisture permeation barrier properties of Al2O3 films deposited on polyethersulfone films (PES) by capacitively coupled plasma (CCP) type Remote Plasma Atomic Layer Deposition (RPALD) at Radio Frequency (RF) plasma powers ranging from 100 W to 400 W in 100 W increments using Trimethylaluminum [TMA, Al(CH3)3] as the Al source and O2 plasma as the reactant. To study the gas and moisture permeation barrier properties of 100-nm-thick Al2O3 at various plasma powers, the Water Vapor Transmission Rate (WVTR) was measured using an electrical Ca degradation test. WVTR decreased as plasma power increased with WVTR values for 400 W and 100 W of 2.6 × 10−4 gm−2day−1 and 1.2 × 10−3 gm−2day−1, respectively. The trends for life time, Al-O and O-H bond, density, and stoichiometry were similar to that of WVTR with improvement associated with increasing plasma power. Further, among plasma power ranging from 100 W to 400 W, the highest power of 400 W resulted in the best moisture permeation barrier properties. This result was attributed to differences in volume and amount of ion and radical fluxes, to join the ALD process, generated by O2 plasma as the plasma power changed during ALD process, which was determined using a plasma diagnosis technique called the Floating Harmonic Method (FHM). Plasma diagnosis by FHM revealed an increase in ion flux with increasing plasma power. With respect to the ALD process, our results indicated that higher plasma power generated increased ion and radical flux compared with lower plasma power. Thus, a higher plasma power provides the best gas and moisture permeation barrier properties.
Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules
Authors: Krasnoshchekov Sergey V. , Stepanov Nikolay F.
Published: November 2013

In the theory of anharmonic vibrations of a polyatomic molecule, mixing the zero-order vibrational states due to cubic, quartic and higher-order terms in the potential energy expansion leads to the appearance of more-or-less isolated blocks of states (also called polyads), connected through multiple resonances. Such polyads of states can be characterized by a common secondary integer quantum number. This polyad quantum number is defined as a linear combination of the zero-order vibrational quantum numbers, attributed to normal modes, multiplied by non-negative integer polyad coefficients, which are subject to definition for any particular molecule. According to Kellman's method [J. Chem. Phys. 93, 6630 (1990)], the corresponding formalism can be conveniently described using vector algebra. In the present work, a systematic consideration of polyad quantum numbers is given in the framework of the canonical Van Vleck perturbation theory (CVPT) and its numerical-analytic operator implementation for reducing the Hamiltonian to the quasi-diagonal form, earlier developed by the authors. It is shown that CVPT provides a convenient method for the systematic identification of essential resonances and the definition of a polyad quantum number. The method presented is generally suitable for molecules of significant size and complexity, as illustrated by several examples of molecules up to six atoms. The polyad quantum number technique is very useful for assembling comprehensive basis sets for the matrix representation of the Hamiltonian after removal of all non-resonance terms by CVPT. In addition, the classification of anharmonic energy levels according to their polyad quantum numbers provides an additional means for the interpretation of observed vibrational spectra.
In situ growth of p and n-type graphene thin films and diodes by pulsed laser deposition
Authors: Sarath Kumar S. R. , Nayak Pradipta K. , Hedhili M. N. , Khan M. A. , Alshareef H. N.
Published: November 2013

We report the in situ growth of p and n-type graphene thin films by ultraviolet pulsed laser deposition in the presence of argon and nitrogen, respectively. Electron microscopy and Raman studies confirmed the growth, while temperature dependent electrical conductivity and Seebeck coefficient studies confirmed the polarity type of graphene films. Nitrogen doping at different sites of the honeycomb structure, responsible for n-type conduction, is identified using X-ray photoelectron spectroscopy, for films grown in nitrogen. A diode-like rectifying behavior is exhibited by p-n junction diodes fabricated using the graphene films.
All-optical signal processing at 10 GHz using a photonic crystal molecule
Authors: Combrié Sylvain , Lehoucq Gaëlle , Junay Alexandra , Malaguti Stefania , Bellanca Gaetano , Trillo Stefano , Ménager Loic , Peter Reithmaier Johann , De Rossi Alfredo
Published: November 2013

We report on 10 GHz operation of an all-optical gate based on an Indium Phosphide Photonic Crystal Molecule. Wavelength conversion and all-optical mixing of microwave signals are demonstrated using the 2 mW output of a mode locked diode laser. The spectral separation of the optical pump and signal is crucial in suppressing optical cross-talk.
Phase-change radiative thermal diode
Authors: Ben-Abdallah Philippe , Biehs Svend-Age
Published: November 2013

A thermal diode transports heat mainly in one preferential direction rather than in the opposite direction. This behavior is generally due to the non-linear dependence of certain physical properties with respect to the temperature. Here we introduce a radiative thermal diode which rectifies heat transport thanks to the phase transitions of materials. Rectification coefficients greater than 70% and up to 90% are shown, even for small temperature differences. This result could have important applications in the development of future contactless thermal circuits or in the conception of radiative coatings for thermal management.
Controllable strain-induced uniaxial anisotropy of Fe81Ga19 films deposited on flexible bowed-substrates
Authors: Dai Guohong , Zhan Qingfeng , Yang Huali , Liu Yiwei , Zhang Xiaoshan , Zuo Zhenghu , Chen Bin , Li Run-Wei
Published: November 2013

We propose a convenient method to induce a uniaxial anisotropy in magnetostrictive Fe81Ga19 films grown on flexible polyethylene terephthalate (PET) substrates by bending the substrate prior to deposition. A tensile/compressive stress is induced in the Fe81Ga19 films when PET substrates are shaped from concave/convex to flat after deposition. The stressed Fe81Ga19 films exhibit a significant uniaxial magnetic anisotropy due to the internal stress arising from changes in shape of PET substrates. The easy axis is along the tensile stress direction and the coercive field along easy axis is increased with increasing the internal tensile stress. The remanence of hard axis is decreased with increasing the compressive stress, while the coercive field is almost unchanged. A modified Stoner-Wohlfarth model with considering the distribution of easy axes in polycrystalline films is used to account for the magnetic properties tuned by the strain-controlled magnetoelastic anisotropy in flexible Fe81Ga19 films. Our investigations provide a convenient way to induce uniaxial magnetic anisotropy, which is particularly important for fabricating flexible magnetoelectronic devices.
Effect of carrier density and valence states on superconductivity of oxygen annealed Fe1.06Te0.6Se0.4 single crystals
Authors: Su T. S. , Yin Y. W. , Teng M. L. , Gong Z. Z. , Zhang M. J. , Li X. G.
Published: November 2013

The variations of carrier density and valence states in oxygen annealed Fe1.06Te0.6Se0.4 single crystals were studied systematically. It was found that the carrier density nH increases after oxygen annealing by Hall coefficient measurements. The X-ray photoelectron spectroscopy experiments reveal that the oxygen annealing changes Fe0 and Te0 states to Fe2+/3+ and Te4+, respectively, while the valence variation of Se is negligible. Our results indicate that the improvement of superconductivity, such as the zero resistance transition temperature Tczero, shielding and Meissner fraction value 4πχ and upper critical field Hc2, could be closely related to the proper manipulation of nH and the valence states by oxygen annealing in the system.
Low-pressure plasma-etching of bulk polymer materials using gas mixture of CF4 and O2
Authors: Nabesawa Hirofumi , Hiruma Takaharu , Hitobo Takeshi , Wakabayashi Suguru , Asaji Toyohisa , Abe Takashi , Seki Minoru
Published: November 2013

In this study, we have proposed a low-pressure reactive ion etching of bulk polymer materials with a gas mixture of CF4 and O2, and have achieved precise fabrication of poly(methyl methacrylate) (PMMA) and perfluoroalkoxy (PFA) bulk polymer plates with high-aspect-ratio and narrow gap array structures, such as, pillar, frustum, or cone, on a nano/micro scale. The effects of the etching conditions on the shape and size of each pillar were evaluated by changing etching duration and the size/material of etching mask. The fabricated PMMA array structures indicate possibilities of optical waveguide and nanofiber array. PFA cone array structures showed super-hydrophobicity without any chemical treatments. Also, polystyrene-coated silica spheres were used as an etching mask for the pillar array structure formation to control the gap between pillars.
Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates
Authors: Arfin Najmul , Yadav Avinash Chand , Bohidar H. B.
Published: November 2013

The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ∼ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.
Construction of Vinyl Polymer and Polyester or Polyamide Units in a Single Polymer Chain via Metal-catalyzed Simultaneous Chain- and Step-growth Radical Polymerization of Various Monomers
Authors: Mizutani Masato , Satoh Kotaro , Kamigaito Masami
Published: November 2013

Metal-catalyzed simultaneous chain- and step-growth radical polymerization was examined to combine common conjugated vinyl monomers, such as various acrylates and styrene, as chain-growth monomers and various ester- or amide-linked monomers bearing both an unconjugated C=C bond and an active C–Cl bond as step-growth monomers. The CuCl/1,1,4,7,10,10-hexamethyltriethylenetetramine-catalyzed copolymerization of alkyl acrylates and various step-growth monomers at a 1 : 1-monomer feed ratio resulted in almost linear random copolymers that consisted of vinyl polymer and polyester units. Additional functional groups, such as oxyethylene and disulfide units, can be introduced into the main chain using a step-growth monomer that possesses the functional units between the unconjugated C=C bond and the active C–Cl bond. Copolymerization at a higher feed ratio of chain-growth monomers, such as alkyl acrylates and styrene, can provide multiblock vinyl polymers connected to the functionalized step-growth monomer units.
Evaluation of predator-exclusion cages used in turtle conservation: cost analysis and effects on nest environment and proxies of hatchling fitness
Authors: Riley J. L. , Litzgus J. D.
Published: November 2013

Context A main goal of conservation is to mitigate anthropogenic impacts on natural ecosystems, thus conservation tools themselves should not negatively affect target species. Predator-exclusion cages are effectively used to reduce predation of turtle nests; however, their effects on nest environment and developing hatchlings have not been examined. Aims Our study had the following four goals: (1) to examine effects of cages on the nest environment, (2) determine whether nest caging affects proxies for hatchling fitness, (3) evaluate whether nest predators preferentially interact with certain cage types, and (4) assess the cost-effectiveness of different nest caging designs. Methods In 2010 and 2011 in Algonquin Provincial Park, Ontario, painted turtle (Chrysemys picta; n = 93) and snapping turtle (Chelydra serpentina; n = 91) nests were assigned to one of three treatments (wooden-sided cages, above- and below-ground wire cages) or a control (no nest cage) and outfitted with a data logger to record incubation temperature. After emergence, hatching success and proxies of hatchling fitness were measured. Key results Nest temperature, hatching success, frequency of hatchling deformities and locomotor performance did not differ among cage treatments. However, hatchling body condition differed among treatments; wooden-sided and below-ground cages had the most positive influence on body condition in painted and snapping turtles, respectively. Predator interactions did not differ among treatments, and wooden-sided cages were the most inexpensive to construct. Conclusions Nest cages did not alter the nest environment from natural conditions but did alter hatchling body condition, and nest caging affected species differently. Implications Nest cages are known to reduce nest depredation, and our data indicated that, in general, nest cages also do not affect the nest environment or proxies for hatchling fitness. Thus, our findings indicated that cages are effective conservation tools that do not present secondary deleterious effects on potential recruitment.
Interaction of ganglioside GD3 with an EGF receptor sustains the self-renewal ability of mouse neural stem cells in vitro
Authors: Wang Jing , Yu Robert K.
Published: November 2013

Significance

Gangliosides are abundantly expressed in the nervous system and are known to play important roles in neurodevelopment. We previously demonstrated that GD3 is a predominant ganglioside species (>80% of the total gangliosides) in mouse neural stem cells (NSCs). To investigate its biological function, we found that GD3 is colocalized and interacts with the mitogen receptor EGFR in the microdomain structure of the plasma membrane. Such an interaction preserves the EGFR via an endosomal-plasma membrane recycling pathway after endocytosis of EGF and facilitates the EGF-mediated signaling responsible for regulating NSC cell-fate determination. This is an example of how a specific ganglioside can mediate the reuse of a mitogen receptor for promoting efficient cellular proliferation.
Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious
Authors: Wagner Allon , Zarecki Raphy , Reshef Leah , Gochev Camelia , Sorek Rotem , Gophna Uri , Ruppin Eytan
Published: November 2013

Significance

Biologists frequently overexpress genes to learn about their cellular functions, and biotechnologists do so to construct novel metabolic pathways that produce valuable chemical compounds. However, gene overexpression often leads to deleterious consequences whose cause is unclear. Here, we present a computational method named Expression-Dependent Gene Effects (EDGE) that can successfully predict the deleterious effects resulting from overexpression of either native or foreign (originating in another species) metabolic genes. EDGE relies on genome-scale metabolic models, an emerging computational paradigm for studying metabolism in silico. Beyond its biotechnological significance, gene overexpression also plays an important role in human disease. We show EDGE’s applicability in the latter case by demonstrating its ability to detect toxic genes whose expression tends to be suppressed in cancer cells.
Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochromecoxidase
Authors: Goyal Puja , Lu Jianxun , Yang Shuo , Gunner M. R. , Cui Qiang
Published: November 2013

Significance

Cytochromecoxidase is an important proton pump that utilizes the chemical energy released by oxygen reduction to generate the transmembrane proton concentration gradient. A conserved glutamate residue has been proposed to play a key role in proton pumping, although factors that control the timing and destination of proton transfers by this residue remain poorly understood. By integrating results from multiple computational methodologies, we propose a mechanism in which changes in local hydration and electrostatic interactions regulate the proton affinity of this key residue and, as a result, proton transfer activities. The results highlight the functional significance of local protein motions and hydration state of internal cavities.
Filopodial retraction force is generated by cortical actin dynamics and controlled by reversible tethering at the tip
Authors: Bornschlögl Thomas , Romero Stéphane , Vestergaard Christian L. , Joanny Jean-François , Van Nhieu Guy Tran , Bassereau Patricia
Published: November 2013

Significance

Cells can sense their environment by using hair-like structures called filopodia that often exert pulling forces upon adhesive tip contact. We show, using optical tweezers and confocal microscopy, that the retraction force is generated by the dynamics of the cortical actin cytoskeleton, constantly pulling on the filopodial base. The weakest point of force transduction is at the tip between the actin shaft and the membrane. This allows tip-bound filopodia to apply controlled forces and to use a “load-and-fail” sensing process.
Phronetic expertise in evidence use: a new perspective on how research can aid educational policy development
Authors: Brown Chris
Published: November 2013

The notion of evidence-informed policy making and the arguments in its favour are well established. At the same time, however, regular evidence use is yet to become a routine way of life for educational policy makers, particularly within the UK. This paper engages with the notion of expertise in evidence use, and with Flyvbjerg’s idea of phronesis. It also details how the phronetic approach can be adopted by policy makers and the potential implications for the policy development process. Given the issues that abound with current attempts to embed and enact evidence-informed policy making, the phronetic approach presents an alternative and viable way of both perceiving how evidence is currently used and also establishing enhanced levels of evidence use. In particular, the paper spotlights a need for current thought in this area to move away from rational and linear perspectives to encourage policy makers continuously to incorporate the most recent evidence into their thinking, and to make well-rounded decisions. The mechanisms required to facilitate phronetic expertise are examined as are the cultural issues that need to be addressed.
Strengthening the Influence of Advertised Reference Prices through Information Priming
Authors: Kan Christina , Lichtenstein Donald R. , Grant Susan Jung , Janiszewski Chris
Published: November 2013

The use of advertised reference price promotions, such as “regularly $119.99, sale price $39.99,” is ubiquitous in the marketplace. Thirty years of research supports the conclusion that advertised reference prices (e.g., $119.99) exert an influence on consumers' responses to offer prices (e.g., $39.99) via their assimilative influence on consumers' internal reference prices. The present research provides an enriched account of this assimilation process. Specifically, three studies show that increasing the overlap in information made accessible by the advertised reference price and information made accessible by the offer price increases the influence of the information primed by the advertised reference price on the construction of the internal reference price. Consequently, the offer price is considered more attractive. The identification of this process provides insight into additional variables that moderate the influence of advertised reference prices on downstream deal evaluations. Implications for theory, practice, and public policy are discussed.
Fission yeast tropomyosin specifies directed transport of myosin-V along actin cables
Authors: Clayton Joseph E. , Pollard Luther W. , Sckolnick Maria , Bookwalter Carol S. , Hodges Alex R. , Trybus Kathleen M. , Lord Matthew
Published: November 2013

A hallmark of class-V myosins is their processivity—the ability to take multiple steps along actin filaments without dissociating. Our previous work suggested, however, that the fission yeast myosin-V (Myo52p) is a nonprocessive motor whose activity is enhanced by tropomyosin (Cdc8p). Here we investigate the molecular mechanism and physiological relevance of tropomyosin-mediated regulation of Myo52p transport, using a combination of in vitro and in vivo approaches. Single molecules of Myo52p, visualized by total internal reflection fluorescence microscopy, moved processively only when Cdc8p was present on actin filaments. Small ensembles of Myo52p bound to a quantum dot, mimicking the number of motors bound to physiological cargo, also required Cdc8p for continuous motion. Although a truncated form of Myo52p that lacked a cargo-binding domain failed to support function in vivo, it still underwent actin-dependent movement to polarized growth sites. This result suggests that truncated Myo52p lacking cargo, or single molecules of wild-type Myo52p with small cargoes, can undergo processive movement along actin-Cdc8p cables in vivo. Our findings outline a mechanism by which tropomyosin facilitates sorting of transport to specific actin tracks within the cell by switching on myosin processivity.
A SUMO-targeted ubiquitin ligase is involved in the degradation of the nuclear pool of the SUMO E3 ligase Siz1
Authors: Westerbeck Jason W. , Pasupala Nagesh , Guillotte Mark , Szymanski Eva , Matson Brooke C. , Esteban Cecilia , Kerscher Oliver
Published: November 2013

The Slx5/Slx8 heterodimer constitutes a SUMO-targeted ubiquitin ligase (STUbL) with an important role in SUMO-targeted degradation and SUMO-dependent signaling. This STUbL relies on SUMO-interacting motifs in Slx5 to aid in substrate targeting and carboxy-terminal RING domains in both Slx5 and Slx8 for substrate ubiquitylation. In budding yeast cells, Slx5 resides in the nucleus, forms distinct foci, and can associate with double-stranded DNA breaks. However, it remains unclear how STUbLs interact with other proteins and their substrates. To examine the targeting and functions of the Slx5/Slx8 STUbL, we constructed and analyzed truncations of the Slx5 protein. Our structure–function analysis reveals a domain of Slx5 involved in nuclear localization and in the interaction with Slx5, SUMO, Slx8, and a novel interactor, the SUMO E3 ligase Siz1. We further analyzed the functional interaction of Slx5 and Siz1 in vitro and in vivo. We found that a recombinant Siz1 fragment is an in vitro ubiquitylation target of the Slx5/Slx8 STUbL. Furthermore, slx5∆ cells accumulate phosphorylated and sumoylated adducts of Siz1 in vivo. Specifically, we show that Siz1 can be ubiquitylated in vivo and is degraded in an Slx5-dependent manner when its nuclear egress is prevented in mitosis. In conclusion, our data provide a first look into the STUbL-mediated regulation of a SUMO E3 ligase.
PREDDIMER: a web server for prediction of transmembrane helical dimers
Authors: Polyansky Anton A. , Chugunov Anton O. , Volynsky Pavel E. , Krylov Nikolay A. , Nolde Dmitry E. , Efremov Roman G.
Published: November 2013

Summary: Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps.

Results: We implemented online the original PREDDIMER algorithm and benchmarked the server on 11 TM sequences, whose 3D dimer conformations were obtained previously by nuclear magnetic resonance spectroscopy. In the most of tested cases backbone root-mean-square deviations of closest predicted conformations from the experimental reference are below 3 Å. A randomization test displays good anticorrelation (−0.82) between values of the scoring function and statistical significance of the prediction ‘by chance’. Going beyond a single dimer conformation, our web tool predicts an ensemble of possible conformations, which may be useful for explanation of a functioning of bitopic membrane proteins, e.g. receptor tyrosine kinases.

Availability and implementation: PREDDIMER can be accessed for free on the web at http://model.nmr.ru/preddimer/

Contact: newant@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Allelic heterogeneity contributes to variability in ocular dysgenesis, myopathy and brain malformations caused by Col4a1 and Col4a2 mutations
Authors: Kuo Debbie S. , Labelle-Dumais Cassandre , Mao Mao , Jeanne Marion , Kauffman William B. , Allen Jennifer , Favor Jack , Gould Douglas B.
Published: November 2013

Collagen type IV alpha 1 and 2 (COL4A1 and COL4A2) are present in nearly all basement membranes. COL4A1 and COL4A2 mutations are pleiotropic, affecting multiple organ systems to differing degrees, and both genetic-context and environmental factors influence this variable expressivity. Here, we report important phenotypic and molecular differences in an allelic series of Col4a1 and Col4a2 mutant mice that are on a uniform genetic background. We evaluated three organs commonly affected by COL4A1 and COL4A2 mutations and discovered allelic heterogeneity in the penetrance and severity of ocular dysgenesis, myopathy and brain malformations. Similarly, we show allelic heterogeneity in COL4A1 and COL4A2 biosynthesis. While most mutations that we examined caused increased intracellular and decreased extracellular COL4A1 and COL4A2, we identified three mutations with distinct biosynthetic signatures. Reduced temperature or presence of 4-phenylbutyrate ameliorated biosynthetic defects in primary cell lines derived from mutant mice. Together, our data demonstrate the effects and clinical implications of allelic heterogeneity in Col4a1- and Col4a2-related diseases. Understanding allelic differences will be valuable for increasing prognostic accuracy and for the development of therapeutic interventions that consider the nature of the molecular cause in patients with COL4A1 and COL4A2 mutations.
The significant contribution of minor mergers to the cosmic star formation budget
Authors: Kaviraj Sugata
Published: November 2013

We estimate an empirical lower limit for the fraction of cosmic star formation that is triggered by minor mergers in the local Universe. Splitting the star formation budget by galaxy morphology, we find that early-type galaxies (ETGs) host ∼14 per cent of the budget, while Sb/Sc galaxies host the bulk (∼53 per cent) of the local star formation activity. Recent work indicates that star formation in nearby ETGs is driven by minor mergers, implying that at least ∼14 per cent of local star formation is triggered by this process. A more accurate estimate can be derived by noting that an infalling satellite likely induces a larger starburst in a galaxy of ‘later’ morphological type, both due to higher availability of gas in the accreting galaxy and also because a bigger bulge better stabilizes the disc against star formation. This enables us to use the star formation in ETGs to estimate a lower limit for the fraction of star formation in late-type galaxies (LTGs) that is minor-merger-driven. Using a subsample of ETGs that is mass- and environment-matched to the LTGs (implying a similar infalling satellite population), we estimate this limit to be ∼24 per cent. Thus, a lower limit for the fraction of cosmic star formation that is induced by minor mergers is ∼35 per cent [14 per cent (ETGs) + 0.24 × 86 per cent (LTGs)]. The observed positive correlation between black hole and galaxy mass further implies that a similar fraction of black hole accretion may also be triggered by minor mergers. Detailed studies of minor-merger remnants are therefore essential, to quantify the role of this important process in driving stellar mass and black hole growth in the local Universe.
Effects of Rice Flour Blends on Bread Texture and Staling
Authors: Sasaki Tomoko , Kohyama Kaoru , Miyashita Kanae , Okunishi Tomoya
Published: November 2013

The effects of blending rice flour with wheat flour on bread texture and staling were investigated with three rice varieties with different amylose contents. For the texture analysis of bread crumb, the compression test, puncture test, and tensile test were performed. A flour blend containing rice flour suppressed the recovery of the crumb after compression. For the puncture test, blends with rice flour increased the distance to penetrate the crumb. The rupture strain measured with the puncture test decreased with staling of the bread crumb for all samples tested. The fresh bread crumb sample containing waxy rice flour had much greater extensibility in the tensile test than the other samples tested, but it was dramatically decreased after one day of storage. Endothermic enthalpies corresponding to retrograded amylopectin, which is part of the staling process, were also measured. The enthalpy of bread crumb from the blended flour was lower than that of wheat flour bread up to three days but was higher on day 4. A blend of rice flour thus reduced amylopectin retrogradation during early storage, but it was accelerated later. Bread blended with waxy rice flour showed the lowest enthalpy during storage.
Two Distinct EF-Tu Epitopes Induce Immune Responses in Rice and Arabidopsis
Authors: Furukawa Takehito , Inagaki Hiroaki , Takai Ryota , Hirai Hiroyuki , Che Fang-Sik
Published: November 2013

Plants sense potential pathogens by recognizing conserved pathogen-associated molecular patterns (PAMPs) that cause PAMP-triggered immunity (PTI). We previously reported that rice recognizes flagellin from the rice-incompatible N1141 strain of Acidovorax avenae and subsequently induces immune responses. Cell extracts isolated from flagellin-deficient N1141 (Δfla1141) still induced PTI responses, suggesting that Δfla1141 possesses an additional PAMP distinct from flagellin. Here, we show that elongation factor Tu (EF-Tu), one of the most abundant bacterial proteins, acts as a PAMP in rice and causes several PTI responses. In Brassicaceae species, EF-Tu and an N-acetylated peptide comprising the first 18 amino acids of the N-terminus, termed elf18, are fully active as inducers of PTI responses. By contrast, elf18 did not cause any immune responses in rice, whereas an EF-Tu middle region comprising Lys176 to Gly225, termed EFa50, is fully active as a PAMP in rice. In the leaves of rice plants, EF-Tu induced H2O2 generation and callose deposition, and also triggered resistance to coinfection with pathogenic bacteria. Taken together, these data demonstrate that rice recognizes EFa50, which is distinct from elf18, and that this epitope induces PTI responses.
Caulobacter

profunda sp. nov., isolated from deep freshwater sediment
Authors: Jin Long , La Hyun-Joon , Lee Hyung-Gwan , Lee Jay Jung , Lee Sanghyup , Ahn Chi-Yong , Oh Hee-Mock
Published: November 2013

The Gram-stain-negative, aerobic, non-spore-forming, motile, with a single polar flagellum, or non-motile (stalked) and rod-shaped bacteria, DS48-5-2T and DS48-6-3, were isolated from a sediment sample collected from a depth of 48 m taken from Daechung Reservoir, Republic of Korea. Comparative 16S rRNA gene sequence studies showed that the two isolates had clear affiliation with

Alphaproteobacteria

and the closest relatedness to

Caulobacter mirabilis

FWC 38T,

Caulobacter fusiformis

ATCC 15257T and

Caulobacter daechungensis

H-E3-2T showing 98.5 %, 97.3 % and 97.3 % 16S rRNA gene sequence similarity, respectively, and 96.1–96.7 % similarity to all other species of the genus

Caulobacter

. The two isolates shared 100 % 16S rRNA gene sequence similarity. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), C16 : 0, C18 : 0ω7c 11-methyl and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The G+C contents of the genomic DNA of strains DS48-5-2T and DS48-6-3 were 66.7 mol% and 66.2 mol%, respectively. DNA–DNA hybridization values of strains DS48-5-2T and DS48-6-3 with

C. mirabilis

FWC 38T,

C. fusiformis

ATCC 15257T and

C. daechungensis

H-E3-2T were 19.3 %–24.4 %. Thus, based on the evidence from polyphasic studies, it is proposed that strains DS48-5-2T and DS48-6-3 are representatives of a novel species in the genus

Caulobacter

, for which the name

Caulobacter

profunda sp. nov. is proposed. The type strain is DS48-5-2T ( = KCTC 32480T = JCM 19440T).
Antimicrobial efficacy and wound-healing property of a topical ointment containing nitric-oxide-loaded zeolites
Authors: Neidrauer Michael , Ercan Utku K. , Bhattacharyya Aparna , Samuels Joshua , Sedlak Jason , Trikha Ritika , Barbee Kenneth A. , Weingarten Michael S. , Joshi Suresh G.
Published: November 2013

Topical delivery of nitric oxide (NO) through a wound dressing has the potential to reduce wound infections and improve healing of acute and chronic wounds. This study characterized the antibacterial efficacy of an ointment containing NO-loaded, zinc-exchanged zeolite A that releases NO upon contact with water. The release rate of NO from the ointment was measured using a chemiluminescence detection system. Minimum bactericidal concentration assays were performed using five common wound pathogens, including Gram-negative bacteria (Escherichia coli and Acinetobacter baumannii), Gram-positive bacteria (Staphylococcus epidermidis and meticillin-resistant Staphylococcus aureus) and a fungus (Candida albicans). The time dependence of antimicrobial activity was characterized by performing log-reduction assays at four time points after 1–8 h ointment exposure. The cytotoxicity of the ointment after 24 h was assessed using cultured 3T3 fibroblast cells. Minimum microbicidal concentrations (MMCs) for bacterial organisms (5×107 c.f.u.) ranged from 50 to 100 mg ointment (ml media)−1; the MMC for C. albicans (5×104 c.f.u.) was 50 mg ointment (ml media)−1. Five to eight log reductions in bacterial viability and three log reductions in fungal viability were observed after 8 h exposure to NO–zeolite ointment compared with untreated organisms. Fibroblasts remained viable after 24 h exposure to the same concentration of NO–zeolite ointment as was used in antimicrobial tests. In parallel studies, full-thickness cutaneous wounds on Zucker obese rats healed faster than wounds treated with a control ointment. These data indicate that ointment containing NO-loaded zeolites could potentially be used as a broad-spectrum antimicrobial wound-healing dressing.