bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron transport in nanoscale junctions with local anharmonic modes
Authors: Simine Lena , Segal Dvira
Published: July 2014

We study electron transport in nanojunctions in which an electron on a quantum dot or a molecule is interacting with an N-state local impurity, a harmonic (“Holstein”) mode, or a two-state system (“spin”). These two models, the Anderson-Holstein model and the spin-fermion model, can be conveniently transformed by a shift transformation into a form suitable for a perturbative expansion in the tunneling matrix element. We explore the current-voltage characteristics of the two models in the limit of high temperature and weak electron-metal coupling using a kinetic rate equation formalism, considering both the case of an equilibrated impurity, and the unequilibrated case. Specifically, we show that the analog of the Franck-Condon blockade physics is missing in the spin-fermion model. We complement this study by considering the low-temperature quantum adiabatic limit of the dissipative spin-fermion model, with fast tunneling electrons and a slow impurity. While a mean-field analysis of the Anderson-Holstein model suggests that nonlinear functionalities, bistability and hysteresis may develop, such effects are missing in the spin-fermion model at the mean-field level.
Temporal structure of aggregate power fluctuations in large-eddy simulations of extended wind-farms
Authors: Stevens Richard J. A. M. , Meneveau Charles
Published: July 2014

Fluctuations represent a major challenge for the incorporation of electric power from large wind-farms into power grids. Wind-farm power output fluctuates strongly in time, over various time scales. Understanding these fluctuations, especially their spatio-temporal characteristics, is particularly important for the design of backup power systems that must be readily available in conjunction with wind-farms. In this work we analyze the power fluctuations associated with the wind-input variability at scales between minutes to several hours, using large eddy simulations (LES) of extended wind-parks, interacting with the atmospheric boundary layer. LES studies enable careful control of parameters and availability of wind-velocities simultaneously across the entire wind-farm. The present study focuses on neutral atmospheric conditions and flat terrain, using actuator-disk representations of the individual wind-turbines. We consider power from various aggregates of wind-turbines such as the total average power signal, or signals from sub-averages within the wind-farm. Non-trivial correlations are observed due to the complex interactions between turbines placed downstream of each other, and they lead to noticeable spectral peaks at frequencies associated with the inter-turbine spacings when the wind-direction is completely fixed. In that case we observe that the frequency spectra of the total wind-farm output show a decay that follows approximately a −5/3 power-law scaling regime, qualitatively consistent with some observations made in field-scale operational wind-parks [J. Apt, “The power spectrum of power from wind-turbines,” J. Power Sources 169, 369 (2007)]. We find that these features are still observed when the wind-speed varies in magnitude. However, significant changes in the wind-direction over time tend to smooth out the observed spectral peak and reduce the extent of the observed −5/3 power-law.
Fabrication of optical multilayer for two-color phase plate in super-resolution microscope
Authors: Iketaki Yoshinori , Kitagawa Katsuichi , Hidaka Kohjiro , Kato Naoki , Hirabayashi Akira , Bokor Nandor
Published: July 2014

In super-resolution microscopy based on fluorescence depletion, the two-color phase plate (TPP) is an indispensable optical element, which can independently control the phase shifts for two beams of different color, i.e., the pump and erase beams. By controlling a phase shift of the erase beam through the TPP, the erase beam can be modulated into a doughnut shape, while the pump beam maintains the initial Gaussian shape. To obtain a reliable optical multiplayer (ML) for the TPP, we designed a ML with only two optical layers by performing numerical optimization. The measured phase shifts generated by the fabricated ML using interferometry correspond to the design values. The beam profiles in the focal plane are also consistent with theoretical results. Although the fabricated ML consists of only two optical layers, the ML can provide a suitable phase modulation function for the TPP in a practical super-resolution microscope.
A compact, diode laser based excitation system for microscopy of NV centers
Authors: Oeckinghaus Thomas , Stöhr Rainer , Kolesov Roman , Tisler Julia , Reinhard Friedemann , Wrachtrup Jörg
Published: July 2014

We demonstrate that a recently introduced family of direct-emitting green laser diodes is a simple yet efficient light source for excitation of NV centers in diamond. Thanks to their fast (sub-ns) response time, these sources are suitable for a broad variety of measurements, including pulsed optically detected magnetic resonance (ODMR) and fluorescence lifetime imaging. This feature, together with a drastically simplified design, is a significant advantage over the traditional excitation system comprising an Nd: YAG laser switched by an acousto-optic modulator. We introduce a simple design for such a compact laser system and experimentally verify that it enables simultaneous lifetime and ODMR measurements on NV centers. In particular, we find that the NV− charge state remains stable in spite of the short excitation wavelength of the new source.
Hydrogen activation, diffusion, and clustering on CeO2(111): A DFT+U study
Authors: Fernández-Torre Delia , Carrasco Javier , Ganduglia-Pirovano M. Verónica , Pérez Rubén
Published: July 2014

We present a comprehensive density functional theory+U study of the mechanisms underlying the dissociation of molecular hydrogen, and diffusion and clustering of the resulting atomic species on the CeO2(111) surface. Contrary to a widely held view based solely on a previous theoretical prediction, our results show conclusively that H2 dissociation is an activated process with a large energy barrier ∼1.0 eV that is not significantly affected by coverage or the presence of surface oxygen vacancies. The reaction proceeds through a local energy minimum – where the molecule is located close to one of the surface oxygen atoms and the H–H bond has been substantially weaken by the interaction with the substrate –, and a transition state where one H atom is attached to a surface O atom and the other H atom sits on-top of a Ce4+ ion. In addition, we have explored how several factors, including H coverage, the location of Ce3+ ions as well as the U value, may affect the chemisorption energy and the relative stability of isolated OH groups versus pair and trimer structures. The trimer stability at low H coverages and the larger upward relaxation of the surface O atoms within the OH groups are consistent with the assignment of the frequent experimental observation by non-contact atomic force and scanning tunneling microscopies of bright protrusions on three neighboring surface O atoms to a triple OH group. The diffusion path of isolated H atoms on the surface goes through the adsorption on-top of an oxygen in the third atomic layer with a large energy barrier of ∼1.8 eV. Overall, the large energy barriers for both, molecular dissociation and atomic diffusion, are consistent with the high activity and selectivity found recently in the partial hydrogenation of acetylene catalyzed by ceria at high H2/C2H2 ratios.
Wave characteristic analysis and wave energy resource evaluation in the China Sea
Authors: Zheng Chong Wei , Zhou Lin , Jia Ben Kai , Pan Jing , Li Xin
Published: July 2014

This study presents the characteristics of the China Sea wave energy resource and wave climate for the period August 1999 to July 2009, using a 10-yr hindcast wave data obtained from WAVEWATCH-III (WW3) numerical wave model forced with QuikSCAT/NCEP (QN) wind data. Results show that: (1) The China Sea wave field has significant seasonal differences, especially the South China Sea which is obviously affected by the monsoon. In JJA (June, July, August), the dominant wave direction is south to southwest. In DJF (December, January, February), the dominant wave direction is north to northeast. The Luzon Strait is the relative large center of significant wave height in DJF (2.4–2.8 m), SON (September, October, November) (2.0–2.4 m), and MAM (March, April, May) (1.0–1.4 m), while the southeast area of the Indo-China Peninsula is the large center in JJA (1.2–1.6 m). (2) The rough sea occurrence in the China Sea is relative low, of below 14% in each season. The relative high occurrence happened in DJF, followed by the SON, lowest in MAM. (3) The extreme wave height with return period of 20 yr in the Bohai Sea, Yellow Sea, low latitude of the South China Sea is below 8 m. The large areas mainly distribute in the middle latitude. The distribution of extreme wave height with return period of 30 yr is similar and about 2 m larger than that with return period of 20 yr. (4) We find the China Sea wave power increases gradually from MAM to DJF. The Luzon Strait is the relative large region of wave power in DJF (30–40 kW/m), SON (21–27 kW/m), and MAM (6–10 kW/m), while the southeast area of the Indo-China Peninsula is the large center in JJA (6–11 kW/m). (5) The stability of the China Sea wave power exhibits obvious regional and seasonal differences. The wave power is the most stable in DJF. The wave power in the north area of the South China and East Sea is apparently more stable than that in other sea areas, in the offshore is more stable than that in the near shore. (6) Judging from the value and stability of wave power, we find that the relative rich-energy region locates in the Luzon Strait and adjacent waters in DJF, SON, and MAM, while in the southeast area of the Indo-China Peninsula in JJA.
Vlasov multi-dimensional model dispersion relation
Authors: Lushnikov Pavel M. , Rose Harvey A. , Silantyev Denis A. , Vladimirova Natalia
Published: July 2014

A hybrid model of the Vlasov equation in multiple spatial dimension D > 1 [H. A. Rose and W. Daughton, Phys. Plasmas 18, 122109 (2011)], the Vlasov multi dimensional model (VMD), consists of standard Vlasov dynamics along a preferred direction, the z direction, and N flows. At each z, these flows are in the plane perpendicular to the z axis. They satisfy Eulerian-type hydrodynamics with coupling by self-consistent electric and magnetic fields. Every solution of the VMD is an exact solution of the original Vlasov equation. We show approximate convergence of the VMD Langmuir wave dispersion relation in thermal plasma to that of Vlasov-Landau as N increases. Departure from strict rotational invariance about the z axis for small perpendicular wavenumber Langmuir fluctuations in 3D goes to zero like θN, where θ is the polar angle and flows are arranged uniformly over the azimuthal angle.
Jeans self gravitational instability of strongly coupled quantum plasma
Authors: Sharma Prerana , Chhajlani R. K.
Published: July 2014

The Jeans self-gravitational instability is studied for quantum plasma composed of weakly coupled degenerate electron fluid and non-degenerate strongly coupled ion fluid. The formulation for such system is done on the basis of two fluid theory. The dynamics of weakly coupled degenerate electron fluid is governed by inertialess momentum equation. The quantum forces associated with the quantum diffraction effects and the quantum statistical effects act on the degenerate electron fluid. The strong correlation effects of ion are embedded in generalized viscoelastic momentum equation including the viscoelasticity and shear viscosities of ion fluid. The general dispersion relation is obtained using the normal mode analysis technique for the two regimes of propagation, i.e., hydrodynamic and kinetic regimes. The Jeans condition of self-gravitational instability is also obtained for both regimes, in the hydrodynamic regime it is observed to be affected by the ion plasma oscillations and quantum parameter while in the kinetic regime in addition to ion plasma oscillations and quantum parameter, it is also affected by the ion velocity which is modified by the viscosity generated compressional effects. The Jeans critical wave number and corresponding critical mass are also obtained for strongly coupled quantum plasma for both regimes.
Investigation of the propagation of a gigawatt pulsed electron beam in compositions of high-pressure gas
Authors: Sazonov R. V. , Kholodnaya G. E. , Ponomarev D. V. , Remnev G. E.
Published: July 2014

The paper presents the results of the experimental investigation of pulsed electron beam propagation with a varying current density (electron energy Ee = 350–400 keV; total current of a diode Ie up to 11 kA; (half-amplitude) pulse duration t = 60 ns, pulse energy We up to 120 J) in two- and three-component gas compositions used in the pulsed plasma chemical synthesis of nanosized oxides. The mean value of the specific absorbed energy within the zone of pulsed electron beam propagation with a current density of 0.05–0.06 kA/cm2 in gas compositions has been determined.
Polarization-induced surface charges in hydroxyapatite ceramics
Authors: Horiuchi N. , Nakaguki S. , Wada N. , Nozaki K. , Nakamura M. , Nagai A. , Katayama K. , Yamashita K.
Published: July 2014

Calcium hydroxyapatite (HAp; Ca10(PO4)6(OH)2) is a well-known biomaterial that is the main inorganic component of bones and teeth. Control over the surface charge on HAp would be a key advance in the development of the material for tissue engineering. We demonstrate here that surface charge can be induced by an electrical poling process using the Kelvin method. Positive and negative charges were induced on the HAp surface in response to the applied electric field in the poling process. The surface charging is attributed to dipole polarization that is homogeneously distributed in HAp. Additionally, the surface charging is considered to originate from the organization of OH− ions into a polar phase in the structure.
Linear growth rates of resistive tearing modes with sub-Alfvénic streaming flow
Authors: Wu L. N. , Ma Z. W.
Published: July 2014

The tearing instability with sub-Alfvénic streaming flow along the external magnetic field is investigated using resistive MHD simulation. It is found that the growth rate of the tearing mode instability is larger than that without the streaming flow. With the streaming flow, there exist two Alfvén resonance layers near the central current sheet. The larger perturbation of the magnetic field in two closer Alfvén resonance layers could lead to formation of the observed cone structure and can largely enhance the development of the tearing mode for a narrower streaming flow. For a broader streaming flow, a larger separation of Alfvén resonance layers reduces the magnetic reconnection. The linear growth rate decreases with increase of the streaming flow thickness. The growth rate of the tearing instability also depends on the plasma beta (β). When the streaming flow is embedded in the current sheet, the growth rate increases with β if β < βs, but decreases if β > βs. The existence of the specific value βs can be attributed to competition between the suppressing effect of β and the enhancing effect of the streaming flow on the magnetic reconnection. The critical value βs increases with increase of the streaming flow strength
All-optical switching in optically induced nonlinear waveguide couplers
Authors: Diebel Falko , Leykam Daniel , Boguslawski Martin , Rose Patrick , Denz Cornelia , Desyatnikov Anton S.
Published: July 2014

We experimentally demonstrate all-optical vortex switching in nonlinear coupled waveguide arrays optically induced in photorefractive media. Our technique is based on multiplexing of nondiffracting Bessel beams to induce various types of waveguide configurations. Using double- and quadruple-well potentials, we demonstrate precise control over the coupling strength between waveguides, the linear and nonlinear dynamics and symmetry-breaking bifurcations of guided light, and a power-controlled optical vortex switch.
Raman scattering in Si/SiGe nanostructures: Revealing chemical composition, strain, intermixing, and heat dissipation
Authors: Mala S. A. , Tsybeskov L. , Lockwood D. J. , Wu X. , Baribeau J.-M.
Published: July 2014

We present a quantitative analysis of Raman scattering in various Si/Si1-xGex multilayered nanostructures with well-defined Ge composition (x) and layer thicknesses. Using Raman and transmission electron microscopy data, we discuss and model Si/SiGe intermixing and strain. By analyzing Stokes and anti-Stokes Raman signals, we calculate temperature and discuss heat dissipation in the samples under intense laser illumination.
Robust random number generation using steady-state emission of gain-switched laser diodes
Authors: Yuan Z. L. , Lucamarini M. , Dynes J. F. , Fröhlich B. , Plews A. , Shields A. J.
Published: July 2014

We demonstrate robust, high-speed random number generation using interference of the steady-state emission of guaranteed random phases, obtained through gain-switching a semiconductor laser diode. Steady-state emission tolerates large temporal pulse misalignments and therefore significantly improves the interference quality. Using an 8-bit digitizer followed by a finite-impulse-response unbiasing algorithm, we achieve random number generation rates of 8 and 20 Gb/s, for laser repetition rates of 1 and 2.5 GHz, respectively, with a ±20% tolerance in the interferometer differential delay. We also report a generation rate of 80 Gb/s using partially phase-correlated short pulses. In relation to the field of quantum key distribution, our results confirm the gain-switched laser diode as a suitable light source, capable of providing phase-randomized coherent pulses at a clock rate of up to 2.5 GHz.
Dynamics of red blood cells in microporous membranes
Authors: Czerwinska Justyna , Rieger Michael , Uehlinger Dominik E.
Published: July 2014

We have performed microfluidic experiments with erythrocytes passing through a network of microchannels of 20–25 μm width and 5 μm of height. Red blood cells (RBCs) were flowing in countercurrent directions through microchannels connected by μm pores. Thereby, we have observed interesting flow dynamics. All pores were blocked by erythrocytes. Some erythrocytes have passed through pores, depending on the channel size and cell elasticity. Many RBCs split into two or more smaller parts. Two types of splits were observed. In one type, the lipid bilayer and spectrin network were cut at the same time. In the second type, the lipid bilayer reconnected, but the part of spectrin network stayed outside the cell forming a rope like structure, which could eventually break. The microporous membrane results in multiple breakups of the cells, which can have various clinical implications, e.g., glomerulus hematuria and anemia of patients undergoing dialysis. The cell breakup procedure is similar to the one observed in the droplet breakage of viscoelastic liquids in confinement.
Pressure induced spin transition revealed by iron M2,3-edge spectroscopy
Authors: Nyrow Alexander , Tse John S. , Hiraoka Nozomu , Desgreniers Serge , Büning Thomas , Mende Kolja , Tolan Metin , Wilke Max , Sternemann Christian
Published: July 2014

We present a method to characterize pressure induced magnetic high to low spin transition in iron sulphide using x-ray Raman scattering spectroscopy at the iron M2,3-edge. The advantage of this method is that the observed spectral changes between pressures of 1.7 GPa and 10.1 GPa can be used with the help of atomic multiplet calculations to determine the crystal field splitting parameters associated with the spin transition. We discuss the potential of this M2,3-edge spectroscopy to investigate the irons electronic spin state in-situ at the conditions of the inner Earth, i.e., at high temperature and high pressure, providing exciting opportunities for geophysical and materials science applications.
Bursts and Avalanches: The Dynamics of Polycentric Urban Evolution
Authors: Broitman Dani , Czamanski Daniel
Published: July 2014

Urban construction activities are subject to periods of fast expansion followed by periods of slow growth. Some of these expansions are limited in size, while others are huge. Therefore, it is not surprising that equilibrium-oriented classical models of urban spatial structure are hard pressed to explain the formation of modern cities with polycentric structure and births of subcenters in particular. To understand the development of cities' spatial patterns we present a model of urban spatial dynamics that is driven by two types of real-estate entrepreneurs that differ in their degree of risk aversion. The developers act in the shadow of the city planning board that formulates urban development policy and defines the boundaries of future residential expansions. The model's salient feature is the time lag between the time of purchase of property rights by land developers and the time of the realization of revenues. We assume that this lag varies in space, being much larger in locations that are not zoned for building. It can be reduced by the planning board in cases of high demand for dwellings. We use the model to demonstrate how the interaction between demand for dwellings, the choices taken by each type of developer, and planning policies leads to the creation of new urban subcenters. The model dynamics are characterized by long out-of-equilibrium periods followed by sudden bursts of construction activity that resembles self-organized criticality.
Are Residential Dwellers Marking and Claiming? Applying the Concepts to Humans Who Dwell Differently
Authors: Schelly Chelsea
Published: July 2014

Mitch Rose's paper in Environment and Planning D: Society and Space (volume 30, issue 5, pages 757–771) arguing that dwelling involves acts of marking and claiming offers bountiful conceptual tools for understanding the dwelling experience. Here, I apply Rose's ideas to the modern residential dweller and use this application to assess Rose's claims. Specifically, the typical and mainstream modern home dweller is contrasted with several different empirical case studies of people who dwell differently, using alternative technologies, practices, and forms of organization in residential dwelling. These case studies are explored using the language of ‘marking’ and ‘claiming’ as put forth by Rose (pace Martin Heidegger) to illustrate what these concepts offer for understanding the experience of dwelling in a home. The observations of residential dwellers who dwell differently suggest that Rose's concepts do help to elucidate the dwelling experience, but that intellectual assistance from other sources, including classical and contemporary pragmatist thought and the work of Marcel Mauss on the relationship between action and thought as well as Paul Harrison's claims regarding relationality and variation in dwelling, helps to further develop Rose's abstract formulaic and connect the dots between conceptualization and the empirical experiences of residential dwelling.
Population ecology of the eastern pygmy-possum (Cercartetus nanus) in a montane woodland in southern New South Wales
Authors: Harris Jamie M. , Goldingay Ross L. , Brooks Lyndon O.
Published: July 2014

The population dynamics of nectar-feeding non-flying mammals are poorly documented. We investigated aspects of the population ecology of the eastern pygmy-possum (Cercartetus nanus) in southern New South Wales. We captured 65 individuals over a 4-year period during 5045 trap-nights and 1179 nest-box checks. The body mass of adult males (mean ± s.e. = 24.6 ± 1.0 g) was marginally not significantly different (P = 0.08) from that of non-parous adult females (28.2 ± 1.9 g). Females gave birth to a single litter each year of 3–4 young during February–May. No juveniles were detected in spring of any year. Mark–recapture modelling suggested that survival probability was constant over time (0.78) while recapture probability (0.04–0.81) varied with season and trap effort. The local population (estimated at ~20–25 individuals) underwent a regular seasonal variation in abundance, with a decline in spring coinciding with the cessation of flowering by Banksia. A population trough in spring has been observed elsewhere. This appears to represent some local migration from the study area, suggesting a strategy of high mobility to track floral resources. Conservation of this species will depend on a more detailed understanding of how flowering drives population dynamics.
Does diet constrain the occupation of high elevations by macropods? A comparison between Macropus rufogriseus and Wallabia bicolor
Authors: Green K. , Davis N. E. , Robinson W. A.
Published: July 2014

The ability to utilise a diet of shrubs or trees is key to the survival of herbivores in deep snow. However, reduction in snow depth with climate change may allow herbivores into higher elevations where herbfields are dominant. Wallabia bicolor occurs above the winter snowline of the Snowy Mountains in the subalpine zone, whereas Macropus rufogriseus, does not although it is present in alpine Tasmania. The winter diet of W. bicolor in the Snowy Mountains consisted of shrubs, trees, and herbs. With >60% of food sources (shrubs and trees) available above the snow, the change from occupation of habitat below the winter snowline to above requires little change in its diet. Consumption of shrubs, forbs and monocots by M. rufogriseus was similar between the Snowy Mountains and alpine Tasmania. M. rufogriseus includes a high proportion of shrubs in its diet; however, it may be excluded from snow-covered habitat due to a lesser ability to utilise poor-quality browse. Globally, migratory herbivores respond to deep snow with seasonal movements. However, W. bicolor and M. rufogriseus are not migratory and can only occupy higher elevations of the Snowy Mountains as snow depth and duration diminish. Because they do not currently occupy the alpine zone and the vegetation has not evolved to accommodate their presence, their impact on alpine vegetation is likely to be greater than migratory alpine grazers/browsers.
First karyological report in Larnax and Deprea (Solanaceae)
Authors: Deanna Rocío , Barboza Gloria E. , Scaldaferro Marisel A.
Published: July 2014

Somatic chromosomes of 12 samples belonging to seven Larnax Miers species and three Deprea Raf. species are studied. Chromosome number and karyotype analysis of both genera are reported for the first time. All taxa have 2n = 24. The most frequent haploid karyotype formula (8 of 12 samples) is 9 metacentric (m) + 3 submetacentric (sm) chromosomes, whereas L. glabra (Standl.) N.W. Sawyer and Larnax sp. display 10 m + 2 sm. Karyotypes of L. nieva S. Leiva & N.W. Sawyer and D. cuyacensis (N.W. Sawyer & S. Leiva) S. Leiva & Lezama are remarkable for the highest number of sm chromosome pairs, with 7 m + 5 sm and 5 m + 7 sm, respectively, presenting the highest intrachromosomal asymmetry index (A1), whereas Larnax sp. and L. glabra show the lowest A1. Most samples (9 of 12) examined have only one pair of chromosomes with nucleolar organiser regions (NOR), whereas L. glabra, Larnax sp., and D. cuyacensis possess two pairs of NOR. Systematic considerations about the monophyly of Larnax and Deprea are provided. The different karyotype parameters obtained, together with morphological characters, are discussed to single out the species.
MnII-Doped ZnS Quantum Dots Modified with Tiopronin for Mercury(II) Detection
Authors: Liu Xin , Zhan Xun-Shou , Wu Fang-Ying , Ma Li-Hua
Published: July 2014

The simple, low-cost, and rapid detection of aqueous mercuric ions remains a challenge for environmental and biological monitoring and protection. We demonstrate herein a new analytical method to detect Hg2+ based on MnII-doped ZnS quantum dots modified with tiopronin. At pH 7.2, Hg2+ causes the fluorescence intensity of quantum dots modified with tiopronin to decrease linearly proportionally with the concentration of Hg2+. This method is non-responsive to general metal ions, surfactants, and some biomacromolecules even though their concentrations were greater than that of Hg2+. Therefore, a sensitive and selective fluorescence assay for Hg2+ with a low limit of detection (8.9 × 10–9 mol L–1) has been developed and its successful application in real samples such as tap water, lake water, and human serum are also discussed in detail.
Rheological Properties and Salt Resistance of a Hydrophobically Associating Polyacrylamide
Authors: Deng Quanhua , Li Haiping , Li Ying , Cao Xulong , Yang Yong , Song Xinwang
Published: July 2014

The rheological properties of electrolyte solution of a hydrophobically associating acrylamide-based copolymer (HA-PAM) containing hydrophobically modified monomer and sodium 2-acrylamido-2-methylpropanesulfonic sulfonate were investigated in this paper. The study mainly focussed on effects of electrolyte concentration, temperature, and shear rate on the solution rheological properties. HA-PAM exhibited much stronger salt tolerance and shearing resistance than the commonly used partially hydrolyzed polyacrylamide, and has great potential for application in tertiary oil recovery of oilfields with high salinity. The salt resistance mechanism of HA-PAM in solution was investigated by combining molecular simulation and experimental methods. The structure–performance relationship of the salt-resisting polymer may provide useful guidance for design and synthesis of novel water-soluble polymers with high salt resistance.
Do family factors protect against sexual risk behaviour and teenage pregnancy among multiply disadvantaged young people? Findings from an English longitudinal study
Authors: Bonell Chris , Wiggins Meg , Fletcher Adam , Allen Elizabeth
Published: July 2014

Background
Structure and parenting within family of origin have been found to be determinants of sexual risk and teenage pregnancy in the general youth population. Few studies have examined determinants of sexual risk among disadvantaged young people; those that do have not examined teenage pregnancy outcomes. Methods: Longitudinal data from a cohort of multiply disadvantaged at-risk young people aged 13–15 years living in deprived neighbourhoods in England (n = 1285) were analysed to examine how family structure, communication with parents and parental interest in education were associated with heterosexual debut, contraception use, expectation of teenage pregnancy and teenage pregnancy. Results: At follow-up, young women living with both biological parents were less likely than other young women to become pregnant (odds ratio (OR) = 0.21, 95% confidence interval (CI): 0.04–0.97). Young women who could talk to their mothers about private things were less likely to expect to become a teenage parent (OR = 0.61, 95% CI: 0.37–0.99). Those whose parents cared very much how they did at school were less likely to report contraception nonuse (OR = 0.44, 95% CI: 0.21–0.93). After adjustment, no associations between any family factors and sexual health outcomes were found for young men. Conclusions: We found limited evidence for family-related effects on sexual health risk or teenage pregnancy among disadvantaged young women in England and no evidence of risk factors within the home environment for young men’s outcomes. This suggests that targeted family-based interventions may not be appropriate for addressing these outcomes.
Direct phase-sensitive identification of a
d
-form factor density wave in underdoped cuprates
Authors: Fujita Kazuhiro , Hamidian Mohammad H. , Edkins Stephen D. , Kim Chung Koo , Kohsaka Yuhki , Azuma Masaki , Takano Mikio , Takagi Hidenori , Eisaki Hiroshi , Uchida Shin-ichi , Allais Andrea , Lawler Michael J. , Kim Eun-Ah , Sachdev Subir , Davis J. C. Séamus
Published: July 2014

Significance

High-temperature superconductivity emerges when holes are introduced into the antiferromagnetic, insulating CuO
2
plane of the cuprates. Intervening between the insulator and the superconductor is the mysterious pseudogap phase. Evidence has been accumulating that this phase supports an exotic density wave state that may be key to its existence. By introducing visualization techniques that discriminate the electronic structure at the two oxygen sites with each CuO
2
unit cell, we demonstrate that this density wave consists of periodic modulations maintaining a phase difference of
π
between every such pair of oxygen sites. Therefore, the cuprate pseudogap phase contains a previously unknown electronic state—a density wave with a
d-
symmetry form factor.
Reconsidering “Piłsudskiite nationalism”
Authors: Brykczynski Paul
Published: July 2014

This paper examines the intellectual underpinnings of the nationalism articulated by the followers of Marshal Józef Piłsudski (Piłsudskiites), who ruled Poland between 1926 and 1939. Scholarly consensus holds that modern Polish nationalism was solely the domain of the National Democratic movement. Conversely, the Piłsudskiites' conception of the nation is generally seen as anachronistic, poorly articulated, self-contradictory, and lacking a deeper intellectual foundation. Focusing on the formative years of the Second Polish Republic (1918-1922), this paper draws a link between Piłsudskiite political thought and the philosophy of the heterodox Marxist theorist Stanislaw Brzozowski. Re-examining the early writings of Piłsudski's followers in light of Brzozowski's philosophy, the paper presents the argument that “Piłsudskiite nationalism” was in fact deeply constructivist, surprisingly sophisticated, and no less “modern” than the nationalist discourse articulated by the National Democrats. In the process, the article interrogates and problematizes the classic “ethnic” vs. “civic” typology of nationalist movements.
The intraflagellar transport dynein complex of trypanosomes is made of a heterodimer of dynein heavy chains and of light and intermediate chains of distinct functions
Authors: Blisnick Thierry , Buisson Johanna , Absalon Sabrina , Marie Alexandra , Cayet Nadège , Bastin Philippe
Published: July 2014

Cilia and flagella are assembled by intraflagellar transport (IFT) of protein complexes that bring tubulin and other precursors to the incorporation site at their distal tip. Anterograde transport is driven by kinesin, whereas retrograde transport is ensured by a specific dynein. In the protist Trypanosoma brucei, two distinct genes encode fairly different dynein heavy chains (DHCs; ∼40% identity) termed DHC2.1 and DHC2.2, which form a heterodimer and are both essential for retrograde IFT. The stability of each heavy chain relies on the presence of a dynein light intermediate chain (DLI1; also known as XBX-1/D1bLIC). The presence of both heavy chains and of DLI1 at the base of the flagellum depends on the intermediate dynein chain DIC5 (FAP133/WDR34). In the IFT140RNAimutant, an IFT-A protein essential for retrograde transport, the IFT dynein components are found at high concentration at the flagellar base but fail to penetrate the flagellar compartment. We propose a model by which the IFT dynein particle is assembled in the cytoplasm, reaches the base of the flagellum, and associates with the IFT machinery in a manner dependent on the IFT-A complex.
Tie-Intertextuality, or, Intertextuality as Incorporation in the Tie-in Merchandise to Disney’sAlice in Wonderland(2010)
Authors: Elliott Kamilla
Published: July 2014

Tie-in merchandise for Walt Disney’s and Tim Burton’s film, Alice in Wonderland (2010), dislocates and modifies prior theories of intertextuality in adaptation studies with the intertextual practices of corporate entertainment franchises. Poststructuralist and postmodern theories of intertextuality construct it as a subversive and democratizing operation, dispersing meaning among texts, dismantling high/low art hierarchies, and redistributing interpretive authority among artists, professional critics, and ordinary audiences. Even when tie-in merchandise for the Disney-Burton film is subversive of mainstream Disney aesthetics and ideologies, Disney and its licensed tie-in merchandising affiliates engage in rhetoric and practices that reincorporate dispersed and contesting intertexts, producing a portmanteau of ‘tie-intertextuality’. Consumers as well as products are tied in or incorporated as corporate intertexts through a rhetoric and iconography of acting, interactivity, inspiration, incarnation, and fidelity. The effect is more one of capitalist dialogics than of the Marxist dialectics academics have traditionally championed in theories of intertextuality.
Farmland: Is It Currently Priced as an Attractive Investment?
Authors: Baker Timothy G. , Boehlje Michael D. , Langemeier Michael R.
Published: July 2014

Farmland prices have risen dramatically in recent years, which has attracted interest from the broader investment community. At the same time, concern is being expressed regarding another bubble in farmland prices. This paper studies and compares the farmland price to cash rent ratio (P/rent) with the price to earnings (P/E) ratio of stocks. We find that the farmland P/rent ratio has reached historical highs and is currently at the level of the P/E ratio of the S&P 500 during the tech bubble. Data from 1911 to 2012 are used to estimate the beta of farmland, a measure of the risk that farmland adds to a diversified portfolio. The beta is found to be very low over this period. Farmland returns are also regressed against expected and unexpected inflation, and we find that farmland moves relatively close to one‐to‐one with inflation. We also report 10‐ and 20‐year holding period returns for farmland and find that the relationship between return and the cyclically adjusted P/rent ratio is strongly negative. Moreover, the current cyclically adjusted P/rent ratio is extremely high, indicating a reason for caution when investors are considering farmland purchases.
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
Authors: Pasaniuc Bogdan , Zaitlen Noah , Shi Huwenbo , Bhatia Gaurav , Gusev Alexander , Pickrell Joseph , Hirschhorn Joel , Strachan David P. , Patterson Nick , Price Alkes L.
Published: July 2014

Motivation: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available.

Results: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1–5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case–control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of χ2 association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses.

Availability and implementation: Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/ .

Contact:  bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu

Supplementary information:  Supplementary materials are available at Bioinformatics online.
cc
SOL
omics
: a webserver for solubility prediction of endogenous and heterologous expression in
Escherichia coli
Authors: Agostini Federico , Cirillo Davide , Livi Carmen Maria , Delli Ponti Riccardo , Tartaglia Gian Gaetano
Published: July 2014

Summary: Here we introduce cc SOL omics , a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis.

Results: Using coil/disorder, hydrophobicity, hydrophilicity, β-sheet and α-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36 990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31 760 proteins sharing <30% sequence similarity.

Availability and implementation:  cc SOL omics can be freely accessed on the web at http://s.tartaglialab.com/page/ccsol_group . Documentation and tutorial are available at http://s.tartaglialab.com/static_files/shared/tutorial_ccsol_omics.html .

Contact:  gian.tartaglia@crg.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Intensity drift removal in LC/MS metabolomics by common variance compensation
Authors: Fernández-Albert Francesc , Llorach Rafael , Garcia-Aloy Mar , Ziyatdinov Andrey , Andres-Lacueva Cristina , Perera Alexandre
Published: July 2014

Liquid chromatography coupled to mass spectrometry (LC/MS) has become widely used in Metabolomics. Several artefacts have been identified during the acquisition step in large LC/MS metabolomics experiments, including ion suppression, carryover or changes in the sensitivity and intensity. Several sources have been pointed out as responsible for these effects. In this context, the drift effects of the peak intensity is one of the most frequent and may even constitute the main source of variance in the data, resulting in misleading statistical results when the samples are analysed. In this article, we propose the introduction of a methodology based on a common variance analysis before the data normalization to address this issue. This methodology was tested and compared with four other methods by calculating the Dunn and Silhouette indices of the quality control classes. The results showed that our proposed methodology performed better than any of the other four methods. As far as we know, this is the first time that this kind of approach has been applied in the metabolomics context.

Availability and implementation: The source code of the methods is available as the R package intCor at http://b2slab.upc.edu/software-and-downloads/intensity-drift-correction/ .

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cathelicidin rCRAMP stimulates rat mast cells to generate cysteinyl leukotrienes, synthesize TNF and migrate: involvement of PLC/A2, PI3K and MAPK signaling pathways
Authors: Bąbolewska Edyta , Pietrzak Anna , Brzezińska-Błaszczyk Ewa
Published: July 2014

Cathelicidins represent a family of cationic peptides involved in host defense systems. Apart from exerting direct anti-microbial effects, cathelicidins can regulate immune responses by affecting the activity of cells playing a role in antibacterial defense. Taking into account that mast cells are critical components of host defense, the aim of this study was to determine whether rat cathelicidin-related anti-microbial peptide (rCRAMP) can influence mast cell activity. We have demonstrated that activation of fully mature rat mast cells with rCRAMP resulted in generation and release of cysteinyl leukotrienes (cysLTs). However, rCRAMP failed to induce mast cell degranulation and histamine release. We also found that rCRAMP stimulated rat mast cells to synthesize TNF, but not CXCL8. What is more, this peptide induced GM-CSF, IL-1β, CCL2 and CCL3 but not IL-33 mRNA expression in mast cells. Finally, we showed that this cathelicidin serves as potent chemoattractant for rat mast cells. rCRAMP-mediated cysLT synthesis and mast cell migration were strongly inhibited by IL-10 pre-treatment. With the use of specific inhibitors, we established that activation of PLC/A2 and ERK1/2, but not p38, was required for rCRAMP-induced mast cell stimulation, while PI3K-dependent pathway is involved in both TNF synthesis and mast cell migration. Our results suggest that cathelicidins can amplify inflammatory responses by causing mast cells accumulation and by stimulating these cells to release potent pro-inflammatory mediators.
Exquisite allele discrimination by toehold hairpin primers
Authors: Byrom Michelle , Bhadra Sanchita , Jiang Yu Sherry , Ellington Andrew D.
Published: July 2014

The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer.
Calcitonin Gene–related Peptide Is Involved in Inflammatory Pain but Not in Postoperative Pain
Authors: Ishida Kumiko , Kawamata Tomoyuki , Tanaka Satoshi , Shindo Takayuki , Kawamata Mikito
Published: July 2014

Background:

The aim of this study was to clarify the roles of calcitonin gene–related peptide (CGRP) in postoperative pain and inflammatory pain.

Methods:

αCGRP knockout mice that the authors have developed and wild-type mice were used. Pain behaviors were assessed after incision and complete Freund’s adjuvant (CFA) injection. Changes in CGRP and c-Fos expression in the dorsal horn were also examined.

Results:

Guarding pain scores in αCGRP knockout mice were lower than those in wild-type mice at 24 h (3.8 ± 1.6 vs. 6.8 ± 1.5, P = 0.044) and 48 h (1.8 ± 1.7 vs. 6.0 ± 1.5, P = 0.001) after CFA injection (n = 8 to 9). Withdrawal latencies to heat stimulation in αCGRP knockout mice were higher than those in wild-type mice at 24 to 72 h after CFA injection (4.9 ± 1.0 vs. 3.4 ± 0.8 at 24 h, P = 0.04; 5.1 ± 0.3 vs. 3.2 ± 0.9 at 48 h, P = 0.047; and 5.4 ± 1.6 vs. 3.5 ± 0.5 s at 72 h, P = 0.045) (n = 11 to 13), but withdrawal thresholds to mechanical stimulation were comparable. CGRP expression was increased at 24 h after CFA injection in wild-type mice, and the c-Fos–positive profile was increased at 4 h after CFA injection (ipsilateral vs. contralateral: 12.3 ± 4.6 vs. 1.3 ± 1.9, P < 0.0001) and maintained at 24 h (10.0 ± 4.1 vs. 0.8 ± 1.3, P < 0.0001) (n = 4 to 6).

Conclusion:

These results suggest that contribution of the αCGRP system depends on the modality of pain and the stage of inflammation.