bluuebunny/crossref_metadata_2025 huggingface dataset:
The dynamics of intrusions into a density-stratified crossflow
Authors: Baines Peter G.
Published: July 2013

Buoyant fluid from a steady source (such as a volcanic eruption) in a stratified environment (such as the atmosphere) rises to an equilibrium level where it spreads as a homogenous intrusion. Here the dynamics of such an intrusion in the presence of a mean ambient flow are examined with semi-analytical models. The intrusive flow is irrotational, and is governed by mass conservation and a form of the Bernoulli equation that relates the intrusion velocity and its thickness. Two types of source are considered—one in which the initial flow from the source is radially symmetric, which is appropriate for weak crosswinds, and another in which it is unidirectional, which also applies to strong crosswinds. In the absence of wind, the outward flow from the radial source is radially uniform and supercritical in the hydraulic sense, with decreasing thickness and increasing speed with distance from the source. In the presence of a crosswind, however, unless the crosswind is very strong a stagnation point exists on the upstream side of the radial source, where the intrusion thickness reaches a maximum. There are two types of flow solution: those where the flow is wholly subcritical, and others where the flow is “transcritical,” being subcritical on the upstream side of the source, and supercritical on the downstream side. It is these transcritical solutions with a supercritical spreading tail that are relevant to flows from isolated sources. For these flows, the upstream stagnation point is quite close to the source, and its position is remarkably insensitive to the strength of the crossflow, relative to that of the source. As a consequence, the position of this stagnation point gives a direct measure of the strength of the source. The external flow is mostly directed horizontally around the intrusion, much as if the latter were a rigid obstacle. The behaviour of the flow in the far-field tail of the intrusion is analysed for both the inviscid case, and for the more realistic one in which the intrusive flow is affected by the drag of its motion relative to that of the environment. The second type of flow, from the unidirectional source, has the same asymptotic behaviour, but the near-field flow changes with increasing distance, from one with maximum thickness on the centerline to one with minimum thickness there. Apart from the fluid dynamical aspects, the results have potential significance for interpretation of geological sediments.
All-out band structure and band offset ab initio predictions for AlN/GaN and AlP/GaP interfaces
Authors: Filho O. P. Silva , Ribeiro M. , Pelá R. R. , Teles L. K. , Ferreira L. G. , Marques M.
Published: July 2013

We studied the electronic properties of the AlP/GaP and AlN/GaN interfaces and their cubic constituents. The work is developed using approximate quasiparticle approach LDA-1/2 method. First, we provide a detailed calculation of bulk AlN, AlP, GaN, and GaP. In addition to accurate results for fundamental band gap, we also obtained accurate electronic transition levels along valence and conduction bands profiles, compared to experiments and theoretical results using GW and hybrid functionals methods. For the conduction (valence) band offset we obtained 0.27 eV (0.43 eV) for AlP/GaP and 1.47 eV (0.36 eV) for AlN/GaN interfaces, in good agreement with experimental results.
Rheometry of granular materials in cylindrical Couette cells: Anomalous stress caused by gravity and shear
Authors: Gutam Kamala Jyotsna , Mehandia Vishwajeet , Nott Prabhu R.
Published: July 2013

The cylindrical Couettedevice is commonly employed to study the rheology of fluids, but seldom used for dense granular materials.Plasticity theories used for granular flows predict a stress field that is independent of the shear rate, but otherwise similar to that in fluids. In this paper we report detailed measurements of the stress as a function of depth, and show that the stress profile differs fundamentally from that of fluids, from the predictions of plasticity theories, and from intuitive expectation. In the static state, a part of the weight of the material is transferred to the walls by a downward vertical shear stress, bringing about the well-known Janssen saturation of the stress in vertical columns. When the material is sheared, the vertical shear stress changes sign, and the magnitudes of all components of the stress rise rapidly with depth. These qualitative features are preserved over a range of the Couette gap and shear rate, for smooth and rough walls and two model granular materials. To explain the anomalous rheological response, we consider some hypotheses that seem plausible a priori, but show that none survive after careful analysis of the experimental observations. We argue that the anomalous stress is due to an anisotropic fabric caused by the combined actions of gravity, shear,and frictional walls, for which we present indirect evidence from our experiments. A general theoretical framework for anisotropicplasticity is then presented. The detailed mechanics of how an anisotropic fabric is brought about by the above-mentioned factors is not clear,and promises to be a challenging problem for future investigations.
Quantitative test of the time dependent Gintzburg-Landau equation for sheared granular flow in two dimensions
Authors: Saitoh Kuniyasu , Hayakawa Hisao
Published: July 2013

We examine the validity of the time-dependent Ginzburg-Landau equation of granular fluids for a plane shear flow under the Lees-Edwards boundary condition derived from a weakly nonlinear analysis through the comparison with the result of discrete element method. We verify quantitative agreements in the time evolution of the area fraction and the velocity fields, and also find qualitative agreement in the granular temperature.
A dip coating process for large area silicon-doped high performance hematite photoanodes
Authors: Hu Yelin , Bora Debajeet K. , Boudoire Florent , Häussler Florian , Graetzel Michael , Constable Edwin C. , Braun Artur
Published: July 2013

A facile and low-cost dip-coating process for the deposition of silicon doped hematite films (Si:α-Fe2O3) for hydrogen production by solar water splitting in photo-electrochemical cells (PEC) is presented. The precursors include iron nitrate, oleic acid, tetraethyl orthosilicate (TEOS) and tetrahydrofuran as dispersion agent. Sequential dip coating on transparent conducting oxides glass substrates with heat treatment steps at 500 °C and 760 °C yields mesoporous Si:α-Fe2O3 with a roughness factor of 17 and photocurrent densities >1 mA/cm2 at 1.23 V vs. reversible hydrogen electrode with SiOx underlayer and surface modification. A PEC demonstrator with 80 cm2 active area in 1 M potassium hydroxide yields a photocurrent of 35 mA at 1.5 AM irradiation with the corresponding hydrogen evolution at a Pt wire counter electrode.
Exchange narrowing and exciton delocalization in disordered J aggregates: Simulated peak shapes in the two dimensional spectra
Authors: Han Jiao , Zhang Houyu , Abramavicius Darius
Published: July 2013

Delocalized excitons in elementary linear J aggregates of two-level molecules absorb a photon into the low-energy edge of an exciton band. Absorption of a second photon is blue-shifted as the lowest energy state is occupied. This setup of states leads to a double-peak feature in a set of two dimensional photon echo spectra for excitonic bands. The delocalization properties of excitons, thus, strongly affect the peak lineshapes and their relative amplitudes. Simulations of various two dimensional spectra of a linear J aggregate are presented and possible schemes to quantitatively characterize the peak profiles are suggested. This allows to relate observable peak lineshapes to the exciton delocalization.
Investigation of oxygen dissociation and vibrational relaxation at temperatures 4000–10 800 K
Authors: Ibraguimova L. B. , Sergievskaya A. L. , Levashov V. Yu. , Shatalov O. P. , Tunik Yu. V. , Zabelinskii I. E.
Published: July 2013

The oxygen absorbance was studied at wavelengths 200–270 nm in Schumann-Runge system behind the front of a strong shock wave. Using these data, the vibrational temperature Tv behind the front of shock waves was measured at temperatures 4000–10 800 K in undiluted oxygen. Determination of Tv was based on the measurements of time histories of absorbance for two wavelengths behind the shock front and on the results of detail calculations of oxygen absorption spectrum. Solving the system of standard quasi-one-dimensional gas dynamics equations and using the measured vibrational temperature, the time evolution of oxygen concentration and other gas parameters in each experiment were calculated. Based on these data, the oxygen dissociation rate constants were obtained for thermal equilibrium and thermal non-equilibrium conditions. Furthermore, the oxygen vibrational relaxation time was also determined at high temperatures. Using the experimental data, various theoretical and empirical models of high-temperature dissociation were tested, including the empirical model proposed in the present work.
Grand-canonical quantized liquid density-functional theory in a Car-Parrinello implementation
Authors: Walther Christian F. J. , Patchkovskii Serguei , Heine Thomas
Published: July 2013

Quantized Liquid Density-Functional Theory (QLDFT) [S. Patchkovskii and T. Heine, Phys. Rev. E 80, 031603 (2009)]10.1103/PhysRevE.80.031603, a method developed to assess the adsorption of gas molecules in porous nanomaterials, is reformulated within the grand canonical ensemble. With the grand potential it is possible to compare directly external and internal thermodynamic quantities. In our new implementation, the grand potential is minimized utilizing the Car-Parrinello approach and gives, in particular for low temperature simulations, a significant computational advantage over the original canonical approaches. The method is validated against original QLDFT, and applied to model potentials and graphite slit pores.
Second-order many-body perturbation expansions of vibrational Dyson self-energies
Authors: Hermes Matthew R. , Hirata So
Published: July 2013

Second-order many-body perturbation theories for anharmonic vibrational frequencies and zero-point energies of molecules are formulated, implemented, and tested. They solve the vibrational Dyson equation self-consistently by taking into account the frequency dependence of the Dyson self-energy in the diagonal approximation, which is expanded in a diagrammatic perturbation series up to second order. Three reference wave functions, all of which are diagrammatically size consistent, are considered: the harmonic approximation and diagrammatic vibrational self-consistent field (XVSCF) methods with and without the first-order Dyson geometry correction, i.e., XVSCF[n] and XVSCF(n), where n refers to the truncation rank of the Taylor-series potential energy surface. The corresponding second-order perturbation theories, XVH2(n), XVMP2[n], and XVMP2(n), are shown to be rigorously diagrammatically size consistent for both total energies and transition frequencies, yield accurate results (typically within a few cm−1 at n = 4 for water and formaldehyde) for both quantities even in the presence of Fermi resonance, and have access to fundamentals, overtones, and combinations as well as their relative intensities as residues of the vibrational Green's functions. They are implemented into simple algorithms that require only force constants and frequencies of the reference methods (with no basis sets, quadrature, or matrix diagonalization at any stage of the calculation). The rules for enumerating and algebraically interpreting energy and self-energy diagrams are elucidated in detail.
Weighted mechanical models for residual stress determination using x-ray diffraction
Authors: Murray Conal E. , Bedell Stephen W. , Ryan E. Todd
Published: July 2013

Determining the mechanical response of thin films by diffraction-based methods requires appropriate elastic models. Weighting factors associated with the linear combination of Reuss and Voigt x-ray elastic constants are compared to the experimental values determined through linear, least-squares regression of diffraction data collected from multiple reflections of several materials. It is found that the optimal weighting factors, x*, determined by the experimental data of Cu, Ni, and Ti thin films vary significantly from those calculated under the Kröner and Neerfeld limits. The discrepancies may be due to plastic effects on the mechanical models that assume linear elastic behavior. The corresponding residual stress values under these limits exhibit a closer correspondence, where the relative variation among the mechanical models scales with the elastic anisotropy of the material.
Ultrafast intramolecular relaxation dynamics of Mg- and Zn-bacteriochlorophyll a
Authors: Kosumi Daisuke , Nakagawa Katsunori , Sakai Shunsuke , Nagaoka Yuya , Maruta Satoshi , Sugisaki Mitsuru , Dewa Takehisa , Nango Mamoru , Hashimoto Hideki
Published: July 2013

Ultrafast excited-state dynamics of the photosynthetic pigment (Mg-)bacteriochlorophyll a and its Zn-substituted form were investigated by steady-state absorption/fluorescence and femtosecond pump-probe spectroscopic measurements. The obtained steady-state absorption and fluorescence spectra of bacteriochlorophyll a in solution showed that the central metal compound significantly affects the energy of the Qx state, but has almost no effect on the Qy state. Photo-induced absorption spectra were recorded upon excitation of Mg- and Zn-bacteriochlorophyll a into either their Qx or Qy state. By comparing the kinetic traces of transient absorption, ground-state beaching, and stimulated emission after excitation to the Qx or Qy state, we showed that the Qx state was substantially incorporated in the ultrafast excited-state dynamics of bacteriochlorophyll a. Based on these observations, the lifetime of the Qx state was determined to be 50 and 70 fs for Mg- and Zn-bacteriochlorophyll a, respectively, indicating that the lifetime was influenced by the central metal atom due to the change of the energy gap between the Qx and Qy states.
Non-hexagonal symmetry-induced functional T graphene for the detection of carbon monoxide
Authors: Liu Chun-Sheng , Jia Ran , Ye Xiao-Juan , Zeng Zhi
Published: July 2013

Unlike on hexagonal graphene where Li atoms tend to cluster, using density functional theory, we demonstrate that Li atoms remain isolated on tetrasymmetrical T graphene due to a nonuniform charge distribution in T graphene. Furthermore, we examine the adsorption of several common gas molecules and find that Li-decorated T graphene exhibits a high sensitivity to CO. The CO adsorption strength can be manipulated by an external electric field, resulting in a short recovery time. Our results provide an insight to build promising nanosensors based on two-dimensional carbonic materials beyond hexagonal symmetry.
The spin and orbital moment of Fen (n = 2–20) clusters
Authors: Yuan H. K. , Chen H. , Kuang A. L. , Tian C. L. , Wang J. Z.
Published: July 2013

Complementary to the recent experimental finding that the orbital magnetic moment is strongly quenched in small Fe clusters [M. Niemeyer, K. Hirsch, V. Zamudio-Bayer, A. Langenberg, M. Vogel, M. Kossick, C. Ebrecht, K. Egashira, A. Terasaki, T. Möller, B. v. Issendorff, and J. T. Lau, Phys. Rev. Lett. 108, 057201 (2012)]10.1103/PhysRevLett.108.057201, we provide the theoretical understanding of the spin and orbital moments as well as the electronic properties of neutral and cation Fen clusters (n = 2–20) by taking into account the effects of strong electronic correlation, spin-orbit coupling, and noncollinearity of inter-atomic magnetization. The generalized gradient approximation (GGA)+U method is used and its effluence on the magnetic moment is emphasized. We find that without inclusion of the Coulomb interaction U, the spin (orbital) moments have an average value between 2.69 and 3.50 μB/atom (0.04 and 0.08 μB/atom). With inclusion of U, the magnetic value is between 2.75 and 3.80 μB/atom (0.10 and 0.30 μB/atom), which provide an excellent agreement with the experimental measurements. Our results confirm that the spin moments are less quenched, while the orbital moments are strongly quenched in small Fe clusters. Both GGA and GGA+U functionals always yield collinear magnetic ground-state solutions for the fully relaxed Fe structures. Geometrical evolution, as a function of cluster size, illustrates that the icosahedral morphology competes with the hexagonal-antiprism morphology for large Fe clusters. In addition, the calculated trends of ionization potentials, electron affinities, fragment energies, and polarizabilities generally agree with respective experimental observations.
Target duality in ${\cal N}{=}\,8$N=8 superconformal mechanics and the coupling of dual pairs
Authors: Gonzales Marcelo , Khodaee Sadi , Lechtenfeld Olaf , Toppan Francesco
Published: July 2013

We couple dual pairs of \documentclass[12pt]{minimal}\begin{document}${\cal N}{=}\,8$\end{document}N=8 superconformal mechanics with conical targets of dimension d and 8−d. The superconformal coupling generates an oscillator-type potential on each of the two target factors, with a frequency depending on the respective dual coordinates. In the case of the inhomogeneous (3,8,5) model, which entails a monopole background, it is necessary to add an extra supermultiplet of constants for half of the supersymmetry. The \documentclass[12pt]{minimal}\begin{document}${\cal N}{=}\,4$\end{document}N=4 analog, joining an inhomogeneous (1,4,3) with a (3,4,1) multiplet, is also analyzed in detail.
Angular distribution of energy spectrum in two-dimensional β-plane turbulence in the long-wave limit
Authors: Saito Izumi , Ishioka Keiichi
Published: July 2013

The time-evolution of two-dimensional decaying turbulence governed by the long-wave limit, in which LD/L → 0, of the quasi-geostrophic equation is investigated numerically. Here, LD is the Rossby radius of deformation, and L is the characteristic length scale of the flow. In this system, the ratio of the linear term that originates from the β-term to the nonlinear terms is estimated by a dimensionless number, \documentclass[12pt]{minimal}\begin{document}$\gamma =\beta L_{\rm D}^2/U$\end{document}γ=βLD2/U, where β is the latitudinal gradient of the Coriolis parameter, and U is the characteristic velocity scale. As the value of γ increases, the inverse energy cascade becomes more anisotropic. When γ ⩾ 1, the anisotropy becomes significant and energy accumulates in a wedge-shaped region where \documentclass[12pt]{minimal}\begin{document}$|l|>\sqrt{3}|k|$\end{document}|l|>3|k| in the two-dimensional wavenumber space. Here, k and l are the longitudinal and latitudinal wavenumbers, respectively. When γ is increased further, the energy concentration on the lines of \documentclass[12pt]{minimal}\begin{document}$l=\pm \sqrt{3}k$\end{document}l=±3k is clearly observed. These results are interpreted based on the conservation of zonostrophy, which is an extra invariant other than energy and enstrophy and was determined in a previous study. Considerations concerning the appropriate form of zonostrophy for the long-wave limit and a discussion of the possible relevance to Rossby waves in the ocean are also presented.
A dark-field microscope for background-free detection of resonance fluorescence from single semiconductor quantum dots operating in a set-and-forget mode
Authors: Kuhlmann Andreas V. , Houel Julien , Brunner Daniel , Ludwig Arne , Reuter Dirk , Wieck Andreas D. , Warburton Richard J.
Published: July 2013

Optically active quantum dots, for instance self-assembled InGaAs quantum dots, are potentially excellent single photon sources. The fidelity of the single photons is much improved using resonant rather than non-resonant excitation. With resonant excitation, the challenge is to distinguish between resonance fluorescence and scattered laser light. We have met this challenge by creating a polarization-based dark-field microscope to measure the resonance fluorescence from a single quantum dot at low temperature. We achieve a suppression of the scattered laser exceeding a factor of 107 and background-free detection of resonance fluorescence. The same optical setup operates over the entire quantum dot emission range (920–980 nm) and also in high magnetic fields. The major development is the outstanding long-term stability: once the dark-field point has been established, the microscope operates for days without alignment. The mechanical and optical designs of the microscope are presented, as well as exemplary resonance fluorescence spectroscopy results on individual quantum dots to underline the microscope's excellent performance.
Note: Geiger tube coincidence counter for lower atmosphere radiosonde measurements
Authors: Harrison R. G. , Nicoll K. A. , Lomas A. G.
Published: July 2013

Atmospheric profiles of cosmic rays and radioactivity can be obtained using adapted meteorological radiosondes, for which Geiger tubes remain widely used detectors. Simultaneous triggering of two tubes provides an indication of energetic events. As, however, only small volume detectors can be carried, the event rate is small, which, due to the rapid balloon ascent, cannot be circumvented using long averaging periods. To derive count rates at low altitudes, a microcontroller is used to determine the inter-event time. This yields estimates of the coincidence rate below 5 km, where the coincidence rate is too small to determine solely by event counting.
Competing atomic and molecular mechanisms of thermal oxidation—SiC versus Si
Authors: Shen Xiao , Tuttle Blair R. , Pantelides Sokrates T.
Published: July 2013

Oxidation is widely used to fabricate complex materials and structures, controlling the properties of both the oxide and its interfaces. It is commonly assumed that the majority diffusing species in the oxide is the dominant oxidant, as is for Si oxidation. It is not possible, however, to account for the experimental data of SiC oxidation using such an assumption. We report first-principles calculations of the pertinent atomic-scale processes, account for the observations, and demonstrate that, for Si-face SiC, interface bonding dictates that atomic oxygen, the minority diffusing species, is the dominant oxidant.
Clogging in micromachined Joule-Thomson coolers: Mechanism and preventive measures
Authors: Cao H. S. , Vanapalli S. , Holland H. J. , Vermeer C. H. , ter Brake H. J. M.
Published: July 2013

Micromachined Joule-Thomson coolers can be used for cooling small electronic devices. However, a critical issue for long-term operation of these microcoolers is the clogging caused by the deposition of water that is present as impurity in the working fluid. We present a model that describes the deposition process considering diffusion and kinetics of water molecules. In addition, the deposition and sublimation process was imaged, and the experimental observation fits well to the modeling predictions. By changing the temperature profile along the microcooler, the operating time of the microcooler under test at 105 K extends from 11 to 52 h.
Determination of effective work function of Pr0.7Ca0.3MnO3 and Pt films on ZrOx using terraced-oxide method
Authors: Bi Lei , Pandey Sumeet C. , Ramaswamy Nirmal
Published: July 2013

We have determined the effective work function (Φm,eff) of thin-film sputter-deposited Pr0.7Ca0.3MnO3 (PCMO) on atomic-layer-deposited ZrOx. Pt/PCMO/ZrOx/SiO2/Si and Pt/ZrOx/SiO2/Si metal-oxide-semiconductor (MOS) capacitors were fabricated. The Φm,eff were extracted from capacitance-voltage curves of the MOS capacitors by using flat-band voltage versus effective-oxide-thickness plots. PCMO was crystallized using a high-temperature anneal step and crystallinity was confirmed by x-ray diffraction and transmission electron microscopy. Φm,eff of polycrystalline PCMO and Pt on ZrOx was determined to be 5.43 eV and 5.40 eV, respectively. The significantly higher Φm,eff of PCMO is attributed to the presence of oxygen-rich PCMO(002)/ZrOx interfaces as indicated by our density-functional-theory calculations.
Bandgap determination based on electrical quantum efficiency
Authors: Helmers Henning , Karcher Christian , Bett Andreas W.
Published: July 2013

A procedure to determine the bandgap of a semiconductor material from spectral electrical quantum efficiency measurements is presented. The procedure is based on the disorder-related exponential band tailing at energies below the bandgap, i.e., exponential onset of the absorption coefficient (often referred to as Urbach's rule). The procedure is applied to three materials, namely, Ga0.50In0.50P, Ga0.99In0.01As, and Ge, and the temperature-dependent bandgaps are derived for a temperature range of 278 to 443 K. The results are compared and validated with data from the literature and electroluminescence measurements.
Orientation dependence of electrocaloric effects in Pb(Zn1/3Nb2/3)-PbTiO3 single crystals
Authors: Chukka Rami , Vandrangi Suresh , Chen Zuhuang , You Lu , Wang Junling , Yang Ping , Chen Lang
Published: July 2013

Electrocaloric effects of (001), (011) and (111) oriented single crystals have been thoroughly investigated to study the ferroelectric-ferroelectric (FE-FE) phase transition induced isothermal entropy changes in 0.94Pb(Zn1/3Nb2/3)O3–0.06PbTiO3 (PZN-PT) material. The results showed that the PZN-PT crystals oriented in (111) direction exhibit ∼ 38% higher electrocaloric cooling values near lower critical phase transitions from rhombohedral (R) to tetragonal (T) phases in PZN-PT crystals, compared to those oriented in (011) direction. Though (111) samples display higher cooling values, (011) samples showed broader cooling curves due to their easily switchable characteristics between R and T phases.
Transforming Small, Medium, and Microscale Enterprises? Information-Communication Technologies (Icts) and Industrial Change in Tanzania
Authors: Murphy James T
Published: July 2013

The changing structure of international trade offers new opportunities for Africa, and some believe that new information communication technologies (ICTs)—especially mobile phones, the Internet, and computers—can accelerate and deepen the region's integration into the world economy. This paper evaluates such claims through an in-depth empirical analysis of ICT use and its contribution to small, medium, and microscale enterprises (SMMEs) and industrial development in Tanzania's wood products and furniture sector. Drawing on concepts from time geography and sociotechnical transition theory, the analysis determines whether, how, and why (not) ICTs are enabling SMMEs to overcome constraints on their activities and whether the industrial regime governing and guiding the activities of firms is being transformed through ICT-driven changes in communication and information management practices. The findings detail the ways in which ICTs are (not) becoming integrated into the everyday industrial practices, highlight the implications of this integration for the industry's development, and demonstrate how research into ICT for development can benefit from a deeper and more critical understanding of the contexts in which technological diffusion occurs—conceptualized here as activity constraints and sociotechnical regimes.
Turning Financial Markets inside Out: Polanyi, Performativity and Disembeddedness
Authors: Muellerleile Chris
Published: July 2013

In light of the spread of markets across the globe and deeper into daily life, this paper argues for a more robust analysis and application of Karl Polanyi's conception of (dis)embedded markets coupled with the performativity thesis authored mainly by Michel Callon. It suggests that while disembeddedness as a concept is necessary for an analysis of contemporary financial markets that are increasingly self-referential, it is not sufficient. Despite the suggestion of a gulf between Polanyian and Callonian economics, there are important similarities in the two frameworks. The similarities are considered along with the considerable difference, all in an attempt to develop a more robust methodological framework for analyzing financial markets. Performativity, it is argued, can help fill the gaps in Polanyi's embeddedness framework, albeit only when that concept's tendency to produce aspatial and apolitical arguments are taken seriously. The paper uses an abbreviated case study of the development of US financial derivative markets in the 1970s and 1980s to argue that markets must be considered in light of both their institutional and geographic entanglements as well as their (dis)embeddedness in systems of calculativeness and mathematical modeling. Specifically the paper analyzes the tension between the derivative origin story authored by Donald MacKenzie, which focuses on neoclassical pricing models like the Black—Scholes—Merton option pricing formula, and my own empirical research, which suggests the urban-economic geography of Chicago played a key role in the development of these instruments.
N-Aryl Atropisomerism Induces Facial Selectivity in Benzonitrile Oxide Cycloadditions with Exocyclic Methylene Benzosultams
Authors: Ryan Sarah J. , Francis Craig L. , Savage G. Paul
Published: July 2013

N-aryl methylene benzo-fused sultams (2,3-dihydrobenzo[d]isothiazole 1,1-dioxides) underwent [3+2] cycloaddition with benzonitrile oxide to give 5-spiro isoxazoline adducts with complete regioselectivity. Steric hindrance by atropisomerism around the N-aryl bond induced facial selectivity in these cycloadditions.
Health professional consultation and use of conservative management strategies in patients with knee or hip osteoarthritis awaiting orthopaedic consultation
Authors: Haskins Robin , Henderson Judith M. , Bogduk Nikolai
Published: July 2013

The aim of this study was to determine the extent to which patients with hip and knee osteoarthritis (OA) referred for orthopaedic consultation at a large Australian public hospital reported using conservative management strategies as recommended by current practice guidelines. A therapist-assisted questionnaire was employed within the context of a standard physiotherapy assessment in a consecutive cohort of patients with hip or knee OA. Two hundred and two patients with hip or knee OA comprised the included sample. Thirty-nine percent (n = 79) reported having only previously consulted their general practitioner. Only 20% (n = 41) felt that they had been sufficiently educated about the diagnosis, their treatment options and prognosis. Thirty-three percent (n = 66) had not previously engaged in any non-pharmacological management strategy considered a core clinical practice guideline recommendation. The findings of this study suggest that several inconsistencies may exist between current Australian clinical practice and OA clinical guideline recommendations. Identification of the barriers to the use of conservative management requires timely investigation coupled with a national implementation framework to support the translation of guideline recommendations into practice.
Comparison of Two Life History Strategies after Impoundment of a Historically Anadromous Stock of Columbia River Redband Trout
Authors: Holecek Dean E. , Scarnecchia Dennis L.
Published: July 2013

In this study we collected information on abundance, age structure, migration, and exploitation to characterize the population demographics and reproductive characteristics of a historically anadromous Columbia River Redband Trout Oncorhynchus mykiss gairdneri population now isolated in a southwestern Idaho reservoir and limited to resident and adfluvial life histories. We estimated there were 3,905 adfluvial individuals in Mann Creek Reservoir in October 2008 based on a mark–recapture population estimate. The adfluvial population sex ratio of 2.78 females per male captured at a weir, peak spawn timing near the peak of the hydrograph (late April), age at spawning (4–6 years), and growth patterns (slow growth in the stream followed by rapid growth in the reservoir) were all characteristic of an anadromous population. Resident fish abundance was not estimated, but the fish were characterized by relatively slow growth, earlier sexual maturity, and a reverse sex ratio (0.23 females per male) compared with the adfluvial fish. The two life histories (resident and adfluvial) and their differential use by the sexes are consistent with life history theory, which suggests female salmonids maximize fitness by increasing body size and fecundity while males attempt to maximize survival at the expense of growth. The migratory fish in this drainage that could have historically exercised an anadromous life history appear to be exercising the next‐best option, an adfluvial life history, which has relatively similar costs and benefits to the anadromous form as distinct from the stream‐resident form. Future studies should evaluate other similar native populations isolated in reservoir systems because these populations could play a role in recovery of endangered steelhead (anadromous Rainbow Trout) populations in the western USA.
The Female Gaze in The Blind Owl by Sadeq Hedayat and Lost Highway by David Lynch
Authors: Abdolmaleki Kara
Published: July 2013

In feminist theory, the “female gaze” is a reaction to the imbalance of power created by the “male gaze”. Yet, since the concept lacks sound grounding in theory, it solely poses “a simple (antagonistic) response” to male voyeurism. This article traces the manifestations of the female gaze in Lost Highway and The Blind Owl, a film noir and a novella. It is concluded that instead of offsetting the imbalance of power, the female gaze only reverses it, turning the concept into yet another catchphrase of patriarchal hegemony to further commodify and subjugate women.
Rethinking Women's Empowerment
Authors: Porter Elisabeth
Published: July 2013

This article examines how orthodox ideas of empowerment have changed for women living in contexts of insecurity. Drawing on fieldwork interviews on women, peace and security in Fiji, Sri Lanka and Timor-Leste, the article reveals a range of culturally different ideas on empowerment that emphasise the community. The interview material raises new questions about the centrality of security to many women's concepts of empowerment. The article suggests holistic ways to rethink context-driven empowerment within broad-based notions of peace and security.
The Effects of Front-Associated Wind Events and Resultant Sediment Resuspension on Dietary Habits and Caloric Intake of Bay Anchovy and Age-0 Atlantic Croaker in Mobile Bay, Alabama
Authors: Jackson Jered B. , Cowan James H.
Published: July 2013

We examined the effects of wind-driven sediment resuspension on the stomach fullness, prey composition, and caloric intake of Bay Anchovy Anchoa mitchilli, a particulate planktivore, and age-0 Atlantic Croaker Micropogonias undulatus, a benthic omnivore, in Mobile Bay, Alabama. Mobile Bay is a shallow estuary in the northern Gulf of Mexico with substrates ranging from silt to small sand. High-wind events were associated with cold fronts and were characterized by wind velocities ≥4.0 m/s. Bay Anchovy stomachs were less full during such events and gut contents contained greater contributions by low-calorie items. Atlantic Croaker stomach fullness did not differ significantly with wind speed. However, prey composition during high-wind events shifted toward high-calorie items. These scenarios imply that high-wind events in Mobile Bay could have an adverse effect on energy uptake by resident Bay Anchovy but may benefit energy uptake by Atlantic Croaker.

Received December 14, 2012; accepted March 23, 2013
Myosin-1c regulates the dynamic stability of E-cadherin–based cell–cell contacts in polarized Madin–Darby canine kidney cells
Authors: Tokuo Hiroshi , Coluccio Lynne M.
Published: July 2013

Cooperation between cadherins and the actin cytoskeleton controls the formation and maintenance of cell–cell adhesions in epithelia. We find that the molecular motor protein myosin-1c (Myo1c) regulates the dynamic stability of E-cadherin–based cell–cell contacts. In Myo1c-depleted Madin–Darby canine kidney cells, E-cadherin localization was dis­organized and lateral membranes appeared less vertical with convoluted edges versus control cells. In polarized monolayers, Myo1c-knockdown (KD) cells were more sensitive to reduced calcium concentration. Myo1c separated in the same plasma membrane fractions as E-cadherin, and Myo1c KD caused a significant reduction in the amount of E-cadherin recovered in one peak fraction. Expression of green fluorescent protein (GFP)–Myo1c mutants revealed that the phosphatidylinositol-4,5-bisphosphate–binding site is necessary for its localization to cell–cell adhesions, and fluorescence recovery after photobleaching assays with GFP-Myo1c mutants revealed that motor function was important for Myo1c dynamics at these sites. At 18°C, which inhibits vesicle recycling, Myo1c-KD cells accumulated more E-cadherin–positive vesicles in their cytoplasm, suggesting that Myo1c affects E-cadherin endocytosis. Studies with photoactivatable GFP–E-cadherin showed that Myo1c KD reduced the stability of E-cadherin at cell–cell adhesions. We conclude that Myo1c stabilizes E-cadherin at adherens junctions in polarized epithelial cells and that the motor function and ability of Myo1c to bind membrane are critical.
Plasma membrane domains enriched in cortical endoplasmic reticulum function as membrane protein trafficking hubs
Authors: Fox Philip D. , Haberkorn Christopher J. , Weigel Aubrey V. , Higgins Jenny L. , Akin Elizabeth J. , Kennedy Matthew J. , Krapf Diego , Tamkun Michael M.
Published: July 2013

In mammalian cells, the cortical endoplasmic reticulum (cER) is a network of tubules and cisterns that lie in close apposition to the plasma membrane (PM). We provide evidence that PM domains enriched in underlying cER function as trafficking hubs for insertion and removal of PM proteins in HEK 293 cells. By simultaneously visualizing cER and various transmembrane protein cargoes with total internal reflectance fluorescence microscopy, we demonstrate that the majority of exocytotic delivery events for a recycled membrane protein or for a membrane protein being delivered to the PM for the first time occur at regions enriched in cER. Likewise, we observed recurring clathrin clusters and functional endocytosis of PM proteins preferentially at the cER-enriched regions. Thus the cER network serves to organize the molecular machinery for both insertion and removal of cell surface proteins, highlighting a novel role for these unique cellular microdomains in membrane trafficking.
A complex of Cox4 and mitochondrial Hsp70 plays an important role in the assembly of the cytochrome c oxidase
Authors: Böttinger Lena , Guiard Bernard , Oeljeklaus Silke , Kulawiak Bogusz , Zufall Nicole , Wiedemann Nils , Warscheid Bettina , van der Laan Martin , Becker Thomas
Published: July 2013

The formation of the mature cytochrome c oxidase (complex IV) involves the association of nuclear- and mitochondria-encoded subunits. The assembly of nuclear-encoded subunits like cytochrome c oxidase subunit 4 (Cox4) into the mature complex is poorly understood. Cox4 is crucial for the stability of complex IV. To find specific biogenesis factors, we analyze interaction partners of Cox4 by affinity purification and mass spectroscopy. Surprisingly, we identify a complex of Cox4, the mitochondrial Hsp70 (mtHsp70), and its nucleotide-exchange factor mitochondrial GrpE (Mge1). We generate a yeast mutant of mtHsp70 specifically impaired in the formation of this novel mtHsp70-Mge1-Cox4 complex. Strikingly, the assembly of Cox4 is strongly decreased in these mutant mitochondria. Because Cox4 is a key factor for the biogenesis of complex IV, we conclude that the mtHsp70-Mge1-Cox4 complex plays an important role in the formation of cytochrome c oxidase. Cox4 arrests at this chaperone complex in the absence of mature complex IV. Thus the mtHsp70-Cox4 complex likely serves as a novel delivery system to channel Cox4 into the assembly line when needed.
Modulation of inositol polyphosphate levels regulates neuronal differentiation
Authors: Loss Omar , Wu Chun Ting , Riccio Antonella , Saiardi Adolfo
Published: July 2013

The binding of neurotrophins to tropomyosin receptor kinase receptors initiates several signaling pathways, including the activation of phospholipase C-γ, which promotes the release of diacylglycerol and inositol 1,4,5-trisphosphate (IP3). In addition to recycling back to inositol, IP3serves as a precursor for the synthesis of higher phosphorylated inositols, such as inositol 1,3,4,5,6-pentakisphosphate (IP5) and inositol hexakisphosphate (IP6). Previous studies on the effect of neurotrophins on inositol signaling were limited to the analysis of IP3and its dephosphorylation products. Here we demonstrate that nerve growth factor (NGF) regulates the levels of IP5and IP6during PC12 differentiation. Furthermore, both NGF and brain-derived neurotrophic factor alter IP5and IP6intracellular ratio in differentiated PC12 cells and primary neurons. Neurotrophins specifically regulate the expression of IP5-2 kinase (IP5-2K), which phosphorylates IP5into IP6. IP5-2K is rapidly induced after NGF treatment, but its transcriptional levels sharply decrease in fully differentiated PC12 cells. Reduction of IP5-2K protein levels by small interfering RNA has an effect on the early stages of PC12 cell differentiation, whereas fully differentiated cells are not affected. Conversely, perturbation of IP5-2K levels by overexpression suggests that both differentiated PC12 cells and sympathetic neurons require low levels of the enzyme for survival. Therefore maintaining appropriate intracellular levels of inositol polyphosphates is necessary for neuronal survival and differentiation.
The Arf GAP SMAP2 is necessary for organized vesicle budding from the trans-Golgi network and subsequent acrosome formation in spermiogenesis
Authors: Funaki Tomo , Kon Shunsuke , Tanabe Kenji , Natsume Waka , Sato Sayaka , Shimizu Tadafumi , Yoshida Naomi , Wong Won Fen , Ogura Atsuo , Ogawa Takehiko , Inoue Kimiko , Ogonuki Narumi , Miki Hiromi , Mochida Keiji , Endoh Keisuke , Yomogida Kentarou , Fukumoto Manabu , Horai Reiko , Iwakura Yoichiro , Ito Chizuru , Toshimori Kiyotaka , Watanabe Toshio , Satake Masanobu
Published: July 2013

The trans-Golgi network (TGN) functions as a hub organelle in the exocytosis of clathrin-coated membrane vesicles, and SMAP2 is an Arf GTPase-activating protein that binds to both clathrin and the clathrin assembly protein (CALM). In the present study, SMAP2 is detected on the TGN in the pachytene spermatocyte to the round spermatid stages of spermatogenesis. Gene targeting reveals that SMAP2-deficient male mice are healthy and survive to adulthood but are infertile and exhibit globozoospermia. In SMAP2-deficient spermatids, the diameter of proacrosomal vesicles budding from TGN increases, TGN structures are distorted, acrosome formation is severely impaired, and reorganization of the nucleus does not proceed properly. CALM functions to regulate vesicle sizes, and this study shows that CALM is not recruited to the TGN in the absence of SMAP2. Furthermore, syntaxin2, a component of the soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) complex, is not properly concentrated at the site of acrosome formation. Thus this study reveals a link between SMAP2 and CALM/syntaxin2 in clathrin-coated vesicle formation from the TGN and subsequent acrosome formation. SMAP2-deficient mice provide a model for globozoospermia in humans.
SW#–GPU-enabled exact alignments on genome scale
Authors: Korpar Matija , Šikić Mile
Published: July 2013

Summary: We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith–Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

Availability: Source code and installation instructions freely available for download at http://complex.zesoi.fer.hr/SW.html.

Contact:  mile.sikic@fer.hr

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA
Authors: Jost Daniel
Published: July 2013

Summary: Local opening of the DNA double helix is required in many fundamental biological processes and is, in part, controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties with other available datasets.

Availability and implementation: Source codes freely available for download at http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistdna, implemented in Fortran90 and supported on any Unix-based operating system (Linux, Mac OS X).

Contact:  daniel.jost@ens-lyon.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Harder Than It Looks: Coding Political Knowledge on the ANES
Authors: DeBell Matthew
Published: July 2013

Political knowledge research faces a problem, perhaps even a crisis. For two decades, the American National Election Studies asked open-ended questions about political knowledge and coded answers using procedures that are neither reliable nor replicable and that were never shown to be optimally valid. Consequently, conclusions based on these widely used measures of the public's competence are in doubt. This article presents several new and overdue methodological improvements: coding knowledge data using formal and specific coding rules based on a substantive rationale for the validity of the codes, recognizing partially correct answers, using multiple coders working independently, using machine coding, and testing reliability and validity. The new methods are an improvement because they are transparent and replicable and they produce valid and extremely reliable knowledge data. Further, machine coding produces codes nearly identical to those from a team of human coders, at much lower cost.
Volatile Anesthetics Improve Survival after Cecal Ligation and Puncture
Authors: Herrmann Inge K. , Castellon Maricela , Schwartz David E. , Hasler Melanie , Urner Martin , Hu Guochang , Minshall Richard D. , Beck-Schimmer Beatrice
Published: July 2013

Background:

Sepsis remains a leading cause of death in intensive care units. There is growing evidence that volatile anesthetics have beneficial immunomodulatory effects on complex inflammation-mediated conditions. The authors investigated the effect of volatile anesthetics on the overall survival of mice in a sepsis model of cecal ligation and puncture (CLP).

Methods:

Mice (N = 12 per treatment group) were exposed to anesthetic concentrations of desflurane, isoflurane, and sevoflurane either during induction of sepsis or when the mice showed pronounced symptoms of inflammation. Overall survival, as well as organ function and inflammation was compared with the CLP group without intervention.

Results:

With desflurane and sevoflurane conditioning (1.2 minimal alveolar concentration for 2 h immediately after induction of CLP) overall survival was improved to 58% and 83%, respectively, compared with 17% in the untreated CLP group. Isoflurane did not significantly affect outcome. Application of sevoflurane 24 h after sepsis induction significantly improved overall survival to 66%.

Conclusions:

Administration of the volatile anesthetics desflurane and sevoflurane reduced CLP-induced mortality. Anesthesia may be a critical confounder when comparing study data where different anesthesia protocols were used.