bluuebunny/crossref_metadata_2025 huggingface dataset:
A new experimental device to evaluate eye ulcers using a multispectral electrical impedance technique
Authors: Bellotti Mariela I. , Bast Walter , Berra Alejandro , Bonetto Fabián J.
Published: August 2011

We present a novel experimental technique to determine eye ulcers in animals using a spectral electrical impedance technique. We expect that this technique will be useful in dry eye syndrome. We used a sensor that is basically a platinum (Pt) microelectrode electrically insulated by glass from a cylindrical stainless steel counter-electrode. This sensor was applied to the naked eye of New Zealand rabbits (2.0–3.5 kg in weight). Whereas half of the eyes were normal (control), we applied to the remainder a few drops of 20% (v/v) alcohol to produce an ulcer in the eye. Using a multispectral electrical impedance system we measured ulcerated and control eyes and observed significant difference between normal and pathological samples. We also investigated the effects of different applied pressures and natural degradation of initially normal eyes as a function of time. We believe that this technique could be sufficiently sensitive and repetitive to help diagnose ocular surface diseases such as dry eye syndrome.
Angular integrals in d dimensions
Authors: Somogyi Gábor
Published: August 2011

We discuss the evaluation of certain d-dimensional angular integrals which arise in perturbative field theory calculations. We find that the angular integral with n denominators can be computed in terms of a certain special function, the so-called H-function of several variables. We also present several illustrative examples of the general result and briefly consider some applications.
Perturbation solution for the viscoelastic 3D flow around a rigid sphere subject to simple shear
Authors: Housiadas Kostas D. , Tanner Roger I.
Published: August 2011

We study the steady, three-dimensional creeping, and viscoelastic flow around a freely rotating rigid sphere subject to simple shear flow imposed at infinity. The viscoelasticity of the ambient fluid is modeled using the second-order-fluid model, the Upper Convected Maxwell, the exponential affine Phan-Thien-Tanner, and the Giesekus constitutive equations. A spherical coordinate system with origin at the center of the sphere is used to describe the flow field. The solution of the governing equations is expanded as a series for small values of the Deborah number. The resulting sequence of differential equations is solved analytically up to second order and numerically up to fourth order in Deborah number by employing fully spectral representations for all the primary variables. In particular, Chebyshev polynomials are used in the radial coordinate and the double Fourier series in the longitudinal and latitudinal coordinates. The numerical results up to second-order agree within machine accuracy with the available analytical solutions clearly indicating the correctness and accuracy of the numerical method developed here. Analytical expressions for the angular velocity of the rigid sphere up to fourth order, which show the slowdown of the rotation of the sphere with respect to the Newtonian creeping case, are also derived. For small Deborah numbers, these expressions, along with those presented in a recent letter [Housiadas and Tanner, Phys. Fluids 23, 051702 (2011)] are in agreement with the few available experimental data and numerical results.
Gated electronic currents modulation and designs of logic gates with single molecular field effect transistors
Authors: Xu Yuqing , Fang Changfeng , Cui Bin , Ji Guomin , Zhai Yaxin , Liu Desheng
Published: August 2011

The electronic transport properties of a gated single 1,3-benzenedithiol molecular device are studied by using nonequilibrium Green's function in combination with density functional theory, which is hoped to complement the experiments. The results show that the external transverse gate electrodes can effectively tune the electronic transport properties of the molecular devices. Negative differential resistance behaviors are observed almost at the same source-drain bias when applied different gate voltages. Mechanisms are proposed for these phenomena. Designs of using one gated molecular device to realize five basic logic gates are also put forward.
A thin metal sheath lifts the EH to HE degeneracy in the cladding mode refractometric sensitivity of optical fiber sensors
Authors: Caucheteur C. , Chen C. , Voisin V. , Berini P. , Albert J.
Published: August 2011

The effective indices of the cladding modes of optical fibers depend on the refractive index of the medium surrounding the fiber. We show experimentally and theoretically that while cladding modes with similar effective indices normally have similar refractometric sensitivities, the addition of a 50 nm thick gold sheath enhances the sensitivity of some EH modes by more than one order of magnitude while nearly completely suppressing the sensitivity of neighbouring HE modes (by three orders of magnitude, down to insignificant levels). A differential sensitivity of ∼1000 nm/(refractive index unit) is experimentally reported between adjacent EH and HE grating resonances.
Molecular dynamics simulations of ion transport through carbon nanotubes. II. Structural effects of the nanotube radius, solute concentration, and applied electric fields
Authors: Beu Titus A.
Published: August 2011

The reported work extends previously published research on transport in aqueous ionic solutions through carbon nanotubes. Specifically, the effects of the nanotube radius, solute concentration, and applied external electric fields on the solution structuring are investigated in terms of spatial density distributions, pair distribution functions, and electrostatic potential profiles. Several simulated structural features are consistent with general theoretical results of nanofluidics and can be interpreted fairly well with respect to these (such as the Donnan-type voltages established at the channel apertures depending on the logarithm of the maximum ion concentration). The simulated properties are based on averages over the largest data collection times reported in the literature (0.8 μs), providing accurate estimates of the measured quantities.
Structure and optical properties of self-assembled multicomponent plasmonic nanogels
Authors: Cong T. , Wani S. N. , Paynter P. A. , Sureshkumar R.
Published: August 2011

Multicomponent plasmonic nanogels (PNGs) capable of broadband absorption of light in the 400−700 nm wavelength range were synthesized by the self-assembly of metal nanoparticles with wormlike surfactant micelles. Small angle x-ray scattering and rheological experiments suggest that the nanoparticles bridge micelle fragments to aid the formation a stable gel phase with exceptional color uniformity. Their optical absorbance could be robustly tuned by changing the nanoparticle type (Au/Ag), size, shape, and/or concentration. The PNGs have relatively low viscosity and are thermoreversible. Potential applications to the manufacturing of coatings and interfaces for solar energy harvesting and reconfigurable optical devices can be envisioned.
Doping of organic semiconductors induced by lithium fluoride/aluminum electrodes studied by electron spin resonance and infrared reflection-absorption spectroscopy
Authors: Głowacki E. D. , Marshall K. L. , Tang C. W. , Sariciftci N. S.
Published: August 2011

We report our investigations on the chemical doping mechanisms induced by LiF|Al electrodes evaporated onto fullerene thin films. Electron spin resonance (ESR) and infrared reflection-absorption spectroscopy (IRRAS) are utilized to characterize C60|Al and C60|LiF|Al interfaces. ESR spectra show that deposition of LiF followed by Al generates C60 radical anions and also the presence of an additional paramagnetic species of lower concentration that is present in all C60 films regardless of LiF. IRRAS clarifies the mechanism occurring at the C60|LiF|Al interface, showing that interaction between LiF and C60 followed by deposition of Al causes LiF clusters to chemically dissociate.
Soret motion in non-ionic binary molecular mixtures
Authors: Leroyer Yves , Würger Alois
Published: August 2011

We study the Soret coefficient of binary molecular mixtures with dispersion forces. Relying on standard transport theory for liquids, we derive explicit expressions for the thermophoretic mobility and the Soret coefficient. Their sign depends on composition, the size ratio of the two species, and the ratio of Hamaker constants. Our results account for several features observed in experiment, such as a linear variation with the composition; they confirm the general rule that small molecules migrate to the warm, and large ones to the cold.
Enhanced performance of dye-sensitized solar cells via plasmonic sandwiched structure
Authors: Lin Su-Jien , Lee Kuang-Che , Wu Jyun-Lin , Wu Jun-Yi
Published: August 2011

The plasmonic structure of sandwiched TiO2/NPs-Ag/TiO2 electrodes was fabricated by sputter technology and sol–gel and spin coating procedure to enhance the performance of dye-sensitized solar cells. The improvement of the incident photon to photocurrent efficiency spectrum corresponding to the strong absorption and damping reflection indicated light trapping of plasmonic structure to elongate the optical pathways of photons. More light trapped close to photocurrent collecting electrode provides better charge-collection and light harvesting efficiencies. As a result of improved dye absorption, about 23% enhancement in photocurrent density has been achieved.
DFT+U calculations of crystal lattice, electronic structure, and phase stability under pressure of TiO2 polymorphs
Authors: Arroyo-de Dompablo M. E. , Morales-García A. , Taravillo M.
Published: August 2011

This work investigates crystal lattice, electronic structure, relative stability, and high pressure behavior of TiO2 polymorphs (anatase, rutile, and columbite) using the density functional theory (DFT) improved by an on-site Coulomb self-interaction potential (DFT+U). For the latter the effect of the U parameter value (0 < U < 10 eV) is analyzed within the local density approximation (LDA+U) and the generalized gradient approximation (GGA+U). Results are compared to those of conventional DFT and Heyd-Scuseria-Ernzehorf screened hybrid functional (HSE06). For the investigation of the individual polymorphs (crystal and electronic structures), the GGA+U/LDA+U method and the HSE06 functional are in better agreement with experiments compared to the conventional GGA or LDA. Within the DFT+U the reproduction of the experimental band-gap of rutile/anatase is achieved with a U value of 10/8 eV, whereas a better description of the crystal and electronic structures is obtained for U < 5 eV. Conventional GGA/LDA and HSE06 fail to reproduce phase stability at ambient pressure, rendering the anatase form lower in energy than the rutile phase. The LDA+U excessively stabilizes the columbite form. The GGA+U method corrects these deficiencies; U values between 5 and 8 eV are required to get an energetic sequence consistent with experiments (Erutile < Eanatase < Ecolumbite). The computed phase stability under pressure within the GGA+U is also consistent with experimental results. The best agreement between experimental and computed transition pressures is reached for U ≈ 5 eV.
Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent
Authors: Kodama Ryota , Roth Roland , Harano Yuichi , Kinoshita Masahiro
Published: August 2011

The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1, …, m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.
Molecular dynamics study of nanoparticle stability at liquid interfaces: Effect of nanoparticle-solvent interaction and capillary waves
Authors: Cheung David L.
Published: August 2011

While the interaction of colloidal particles (sizes in excess of 100 nm) with liquid interfaces may be understood in terms of continuum models, which are grounded in macroscopic properties such as surface and line tensions, the behaviour of nanoparticles at liquid interfaces may be more complex. Recent simulations [D. L. Cheung and S. A. F. Bon, Phys. Rev. Lett. 102, 066103 (2009)]10.1103/PhysRevLett.102.066103 of nanoparticles at an idealised liquid-liquid interface showed that the nanoparticle-interface interaction range was larger than expected due, in part, to the action of thermal capillary waves. In this paper, molecular dynamics simulations of a Lennard-Jones nanoparticle in a binary Lennard-Jones mixture are used to confirm that these previous results hold for more realistic models. Furthermore by including attractive interactions between the nanoparticle and the solvent, it is found that the detachment energy decreases as the nanoparticle-solvent attraction increases. Comparison between the simulation results and recent theoretical predictions [H. Lehle and M. Oettel, J. Phys. Condens. Matter 20, 404224 (2008)]10.1088/0953-8984/20/40/404224 shows that for small particles the incorporation of capillary waves into the predicted effective nanoparticle-interface interaction improves agreement between simulation and theory.
High resolution, large field of view x-ray differential phase contrast imaging on a compact setup
Authors: Thuering T. , Modregger P. , Grund T. , Kenntner J. , David C. , Stampanoni M.
Published: August 2011

X-ray grating interferometry is a well established technique to perform differential phase contrast imaging on conventional x-ray tubes. So far, the application of this technique in commercial micro computed tomography scanners has remained a major challenge due to the compact setup geometry. In this letter, we report on the design of a compact imaging setup using a microfocus source. Due to the extreme wave front curvature, the gratings are fabricated on a flexible substrate, enabling precise cylindrical shaping. A laboratory setup and a modified SCANCO μCT100 scanner have been built, allowing high resolution and large field of view imaging.
Quantum optimal control for the full ensemble of randomly oriented molecules having different field-free Hamiltonians
Authors: Kurosaki Yuzuru , Ichihara Akira , Yokoyama Keiichi
Published: August 2011

We have presented the optimal control theory formulation to calculate optimal fields that can control the full ensemble of randomly oriented molecules having different field-free Hamiltonians. The theory is applied to the fifty-fifty mixture of randomly oriented 133CsI and 135CsI isotopomers and an optimal field is sought to achieve isotope-selective vibrational excitations with high efficiency. Rotational motion is frozen and two total times (T’s) of electric field duration, 460 000 and 920 000 a.u. (11.1 and 22.2 ps), are chosen in the present calculation. As a result, the final yields for T = 460 000 and 920 000 a.u. are calculated to be 0.706 and 0.815, respectively. The relatively high final yield obtained for T = 920 000 a.u. strongly suggests that a single laser pulse can control the full ensemble of randomly oriented non-identical molecules. The result is quite encouraging in terms of the application to isotope-separation processes.
Full-dimensional multi configuration time dependent Hartree calculations of the ground and vibrationally excited states of He2,3Br2 clusters
Authors: Valdés Álvaro , Prosmiti Rita , Villarreal Pablo , Delgado-Barrio Gerardo
Published: August 2011

Quantum dynamics calculations are reported for the tetra-, and penta-atomic van der Waals HeNBr2 complexes using the multiconfiguration time-dependent Hartree (MCTDH) method. The computations are carried out in satellite coordinates, and the kinetic energy operator in this set of coordinates is given. A scheme for the representation of the potential energy surface based on the sum of the three-body HeBr2 interactions at CSSD(T) level plus the He-He interaction is employed. The potential surfaces show multiple close lying minima, and a quantum description of such highly floppy multiminima systems is presented. Benchmark, full-dimensional converged results on ground vibrational/zero-point energies are reported and compared with recent experimental data available for all these complexes, as well as with previous variational quantum calculations for the smaller HeBr2 and He2Br2 complexes on the same surface. Some low-lying vibrationally excited eigenstates are also computed by block improved relaxation calculations. The binding energies and the corresponding vibrationally averaged structures are determined for different conformers of these complexes. Their relative stability is discussed, and contributes to evaluate the importance of the multiple-minima topology of the underlying potential surface.
Random lasing in low molecular weight organic thin films
Authors: Kéna-Cohen S. , Stavrinou P. N. , Bradley D. D. C. , Maier S. A.
Published: August 2011

We demonstrate that coherent random lasing can occur in solid-state dispersions of laser dyes 4-dicyanomethylene-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran and 4-dicyanomethylene-2-tert-butyl-6-(1,1,7,7-tetramethyljulolidin-4-yl-vinyl)-4H-pyran within a tris(8-hydroxy-quinolinato)aluminum matrix without the need for infiltrated scatterers. Random lasing thresholds as low as 90 μJ/cm2 are observed in 250 nm-thick films with 2-2.5% dye concentration. We find that the lasing threshold exhibits a power law decay with sample area, providing a simple test for the occurrence of random lasing. We discuss the implications of this result in the context of previous reports of lasing in these materials where feedback was provided by conventional optical resonators.
Identification of embedded charge defects in suspended silicon nanowires using a carbon-nanotube cantilever gate
Authors: Lan Yann-Wen , Nguyen Linh-Nam , Lai Shui-Jin , Lin Ming-Chou , Kuan Chieh-Hsiung , Chen Chii-Dong
Published: August 2011

A movable carbon nanotube (CNT) cantilever gate is developed for the detection of embedded charge defects in suspended nanowires. The CNT gate is composed of a gold probe welded to a thick CNT, which is in turn attached to a thinner CNT. The rigid welding of the thicker CNT to the gold probe allows for precise placement along the measured nanowire while the joint between the thinner and thicker CNT absorbs the push and pull forces of repeated relocation. For demonstration purpose, the CNT gate determines the site of the embedded charges and measures the amount of trapped electrons.
Energetic hydrogen atoms in wave driven discharges
Authors: Felizardo E. , Tatarova E. , Henriques J. , Dias F. M. , Ferreira C. M. , Gordiets B.
Published: August 2011

Doppler broadened Hγ emission was detected in high frequency (350 and 500 MHz) hydrogen surface wave sustained discharges, revealing the presence of fast excited H atoms with kinetic energies in the range 4–9 eV. Spatially resolved measurements of the Doppler-broadened emission indicate that these fast atoms are predominantly formed near the wall, which suggests that their generation may result from acceleration of H+ ions in the radial dc space charge field followed by recombination at the wall and the return of the neutral atom to the gas phase.
Entropic effects in the electric double layer of model colloids with size-asymmetric monovalent ions
Authors: Guerrero-García Guillermo Iván , González-Tovar Enrique , Olvera de la Cruz Mónica
Published: August 2011

The structure of the electric double layer of charged nanoparticles and colloids in monovalent salts is crucial to determine their thermodynamics, solubility, and polyion adsorption. In this work, we explore the double layer structure and the possibility of charge reversal in relation to the size of both counterions and coions. We examine systems with various size-ratios between counterions and coions (ion size asymmetries) as well as different total ion volume fractions. Using Monte Carlo simulations and integral equations of a primitive-model electric double layer, we determine the highest charge neutralization and electrostatic screening near the electrified surface. Specifically, for two binary monovalent electrolytes with the same counterion properties but differing only in the coion's size surrounding a charged nanoparticle, the one with largest coion size is found to have the largest charge neutralization and screening. That is, in size-asymmetric double layers with a given counterion's size the excluded volume of the coions dictates the adsorption of the ionic charge close to the colloidal surface for monovalent salts. Furthermore, we demonstrate that charge reversal can occur at low surface charge densities, given a large enough total ion concentration, for systems of monovalent salts in a wide range of ion size asymmetries. In addition, we find a non-monotonic behavior for the corresponding maximum charge reversal, as a function of the colloidal bare charge. We also find that the reversal effect disappears for binary salts with large-size counterions and small-size coions at high surface charge densities. Lastly, we observe a good agreement between results from both Monte Carlo simulations and the integral equation theory across different colloidal charge densities and 1:1-elec-trolytes with different ion sizes.
The limits of flexoelectricity in liquid crystals
Authors: Castles F. , Morris S. M. , Coles H. J.
Published: August 2011

The flexoelectric conversion of mechanical to electrical energy in nematic liquid crystals is investigated using continuum theory. Since the electrical energy produced cannot exceed the mechanical energy supplied, and vice-versa, upper bounds are imposed on the magnitudes of the flexoelectric coefficients in terms of the elastic and dielectric coefficients. For conventional values of the elastic and dielectric coefficients, it is shown that the flexoelectric coefficients may not be larger than a few tens of pC/m. This has important consequences for the future use of such flexoelectric materials in devices and the related energetics of distorted equilibrium structures.
Reasoning from paradigms and negative evidence
Authors: Macagno Fabrizio , Walton Douglas N.
Published: August 2011

Reasoning from negative evidence takes place where an expected outcome is tested for, and when it is not found, a conclusion is drawn based on the significance of the failure to find it. By using Gricean maxims and implicatures, we show how a set of alternatives, which we call a paradigm, provides the deep inferential structure on which reasoning from lack of evidence is based. We show that the strength of reasoning from negative evidence depends on how the arguer defines his conclusion and what he considers to be in the paradigm of negated alternatives. If we negate only two of the several possible alternatives, even if they are the most probable, the conclusion will be weak. However, if we deny all possible alternatives, the reasoning will be strong, and even in some cases deductively valid.
Measurements of bicoherence and long-range correlations during biasing in the HSX stellarator
Authors: Wilcox R.S. , van Milligen B.Ph. , Hidalgo C. , Anderson D.T. , Talmadge J.N. , Anderson F.S.B , Ramisch M.
Published: August 2011

The effect of biasing on edge fluctuations has been studied in the HSX stellarator using Langmuir probes. Biasing leads to an increase in the bicoherence of the poloidal electric field, as well as a simultaneous increase in long-range correlations of the floating potential, measured using toroidally separated Langmuir probes. These observations are consistent with zonal flow formation. A comparison has been made between experiments in an optimized quasi-symmetric magnetic configuration (quasi-helically symmetric—QHS) and a configuration with the symmetry intentionally degraded (mirror). The observed differences are insignificant and most likely unrelated to the change in configuration.
Nonlinear plasmonics at planar metal surfaces
Authors: Palomba Stefano , Harutyunyan Hayk , Renger Jan , Quidant Romain , van Hulst Niek F. , Novotny Lukas
Published: August 2011

We investigate the nonlinear optical response of a noble metal surface. We derive the components of the third-order nonlinear susceptibility and determine an absolute value of
χ
(3)
≈0.2 nm
2
 
V
−2
, a value that is more than two orders of magnitude larger than the values found for typical nonlinear laser crystals. Using nonlinear four-wave mixing (4WM) with incident laser pulses of frequencies
ω
1
and
ω
2
, we generate fields oscillating at the nonlinear frequency
ω
4WM
=2
ω
1
−
ω
2
. We identify and discuss three distinct regimes: (i) a regime where the 4WM field is propagating, (ii) a regime where it is evanescent, and (iii) a regime where the nonlinear response couples to surface plasmon polaritons.
How diversification rates and diversity limits combine to create large-scale species–area relationships
Authors: Kisel Yael , McInnes Lynsey , Toomey Nicola H. , Orme C. David L.
Published: August 2011

Species–area relationships (SARs) have mostly been treated from an ecological perspective, focusing on immigration, local extinction and resource-based limits to species coexistence. However, a full understanding across large regions is impossible without also considering speciation and global extinction. Rates of both speciation and extinction are known to be strongly affected by area and thus should contribute to spatial patterns of diversity. Here, we explore how variation in diversification rates and ecologically mediated diversity limits among regions of different sizes can result in the formation of SARs. We explain how this area-related variation in diversification can be caused by either the direct effects of area or the effects of factors that are highly correlated with area, such as habitat diversity and population size. We also review environmental, clade-specific and historical factors that affect diversification and diversity limits but are not highly correlated with region area, and thus are likely to cause scatter in observed SARs. We present new analyses using data on the distributions, ages and traits of mammalian species to illustrate these mechanisms; in doing so we provide an integrated perspective on the evolutionary processes shaping SARs.
Understanding global patterns of mammalian functional and phylogenetic diversity
Authors: Safi Kamran , Cianciaruso Marcus V. , Loyola Rafael D. , Brito Daniel , Armour-Marshall Katrina , Diniz-Filho José Alexandre F.
Published: August 2011

Documenting and exploring the patterns of diversity of life on Earth has always been a central theme in biology. Species richness despite being the most commonly used measure of diversity in macroecological studies suffers from not considering the evolutionary and ecological differences among species. Phylogenetic diversity (PD) and functional diversity (FD) have been proposed as alternative measures to overcome this limitation. Although species richness, PD and FD are closely related, their relationships have never been investigated on a global scale. Comparing PD and FD with species richness corroborated the general assumptions of surrogacy of the different diversity measures. However, the analysis of the residual variance suggested that the mismatches between the diversity measures are influenced by environmental conditions. PD increased relative to species richness with increasing mean annual temperature, whereas FD decreased with decreasing seasonality relative to PD. We also show that the tropical areas are characterized by a FD deficit, a phenomenon, that suggests that in tropical areas more species can be packed into the ecological space. We discuss potential mechanisms that could have resulted in the gradient of spatial mismatch observed in the different biodiversity measures and draw parallels to local scale studies. We conclude that the use of multiple diversity measures on a global scale can help to elucidate the relative importance of historical and ecological processes shaping the present gradients in mammalian diversity.
The shape of mammalian phylogeny: patterns, processes and scales
Authors: Purvis Andy , Fritz Susanne A. , Rodríguez Jesús , Harvey Paul H. , Grenyer Richard
Published: August 2011

Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.
Components of a Microinjection System
Authors: Komarova Yulia , Peloquin John , Borisy Gary
Published: August 2011

INTRODUCTION

Direct-pressure microinjection with a micropipette is an essential tool for introducing a variety of impermeant substances into the cytoplasm or nucleus of plant and animal cells. Microinjection remains the most direct method to gain insight into the function and dynamics of intracellular components, to produce transgenic animals, or to overcome male infertility. This article describes the basic components of a microinjection system.
Fixation of Drosophila Tissues for Immunofluorescence
Authors: Swedlow Jason
Published: August 2011

INTRODUCTION

The fruit fly Drosophila melanogaster has long been used to study the genetic factors involved in development, and the ability to localize molecules within the organism that allow genetic manipulation can be quite useful. This article discusses some of the issues relating to fixation of various Drosophila tissues for analysis by immunofluorescence microscopy. References to specific fixation protocols are included. The proper fixation protocol will depend on the structure to be visualized, the degree of preservation required, the preservation of antigenicity of the molecules of interest, and the level of resolution of the subsequent imaging. In addition, the fixation of thick tissues requires a protocol that effectively fixes the interior of the sample while not cross-linking the matrix so heavily that antibodies or other probes cannot penetrate efficiently and be washed out of the tissue. Particular attention is given to the handling of embryos, because these are used frequently and require special consideration.
Trichloroacetic Acid (TCA) Precipitation of Proteins
Authors: Link Andrew J. , LaBaer Joshua
Published: August 2011

INTRODUCTION

Cell or tissue extracts of proteins often contain interfering substances that must be removed. A number of methods are available for concentrating dilute protein solutions and simultaneously removing contaminating substances. Trichloroacetic acid (TCA)/acetone precipitation, as described here, is often used for this purpose.
In Situ Hybridization to Polytene Chromosomes in Drosophila Using Digoxigenin-Labeled Probes
Authors: Pardue Mary-Lou
Published: August 2011

INTRODUCTION

In situ hybridization to polytene chromosomes frequently is used to find the chromosomal site of a cloned DNA sequence, as well as to investigate the distribution of families of repeated sequences in the chromosome set and to measure the amount of a repeated sequence at different sites. These different experimental goals are best accomplished by variations of the technique. Simple mapping of genes and even gene fragments of a few hundred base pairs is easily done using nonradioactive probes. The simplest and most successful probes are made by random primer labeling of gel-purified fragments of cloned DNA. Digoxigenin (DIG) is commonly used for nonradioactive labeling, as are biotin-labeled probes, and biotin and DIG probes can be used in conjunction in double labeling experiments. DIG probes are detected with an antibody coupled to an enzyme or to a fluorescent dye. This protocol describes a procedure for labeling gel-purified DNA fragments with DIG and for performing in situ hybridization using an antibody coupled to alkaline phosphatase.
Generation and Staining of MARCM Clones in Drosophila: Figure 1.
Authors: Shrestha Brikha R. , Grueber Wesley B.
Published: August 2011

INTRODUCTION

Dendrite morphological diversity helps to define the properties of neural circuits by influencing circuit organization and information processing. Dendrite development has been shown to be driven by a combination of cell-intrinsic and -extrinsic factors. However, much remains to be discovered about the cellular and molecular mechanisms that give rise to unique yet highly stereotyped dendrite arbors of diverse neuronal types. Work in the last decade has established the Drosophila system as an excellent model for studies of dendrite morphogenesis. Mosaic analysis with a repressible cell marker (MARCM) permits resolution of dendrites at a single-cell level and genetic manipulation of individual neurons to assess gene function during neuronal morphogenesis. Mosaic systems for examining mutant phenotypes are advantageous for studies of larval stages because of the ability to discern cell-autonomous phenotypes at very high resolution. The protocol described here can be used to generate and label MARCM clones for the analysis of dendritic patterning and branching control in Drosophila.
OMX: A New Platform for Multimodal, Multichannel Wide-Field Imaging
Authors: Dobbie Ian M. , King Emma , Parton Richard M. , Carlton Peter M. , Sedat John W. , Swedlow Jason R. , Davis Ilan
Published: August 2011

INTRODUCTION

This article discusses the design principles and applications of the OMX microscope, a new platform that provides unprecedented mechanical and thermal stabilities coupled with a photon budget that is dramatically improved over traditional microscope platforms. These characteristics make the OMX microscope outstanding for fast live cell imaging and super-resolution imaging. Moreover, its open flexible architecture makes it particularly amenable to adding other modes of microscopy to the platform.
Methods for Exploring the Genetic Control of Sensory Neuron Dendrite Morphogenesis inDrosophila
Authors: Shrestha Brikha R. , Grueber Wesley B.
Published: August 2011

INTRODUCTION

Dendrite morphological diversity helps to define the properties of neural circuits by influencing circuit organization and information processing. Dendrite development has been shown to be driven by a combination of cell-intrinsic and -extrinsic factors. However, much remains to be discovered about the cellular and molecular mechanisms that give rise to unique yet highly stereotyped dendrite arbors of diverse neuronal types. Work in the last decade has established theDrosophilasystem as an excellent model for studies of dendrite morphogenesis. Work has been performed primarily in three systems: the dendritic arborization sensory neurons, the adult olfactory system, and the embryonic and larval motor system. Each of these systems offers a manageable number of neurons that are easily accessible, both optically and physically, and can be genetically manipulated to address a broad range of questions regarding dendrite development and patterning. This article provides a brief overview of the organization of these systems together with aspects of dendrite development that have been elucidated in recent years and methods for studying dendrite morphogenesis in embryonic and larval sensory neurons.
‘Doing it right?’– accessing the narratives of identity of newly qualified social workers through the lens of resilience: ‘I am, I have, I can’
Authors: Kearns Sarah , McArdle Karen
Published: August 2011

Using narrative enquiry, this paper accesses the construct of identity through exploring resilience in newly qualified social workers based in statutory children's services. In seeking to avoid deficit‐based models of this role, this paper aims to present inductively the ‘voice’ of three social workers in a semi‐rural authority, storying the positive ways in which resilience has developed during their first year. Using the Grotberg resilience framework (1995) –‘I am, I have, I can’– as an analytical tool at the interface of personal, professional and organizational identities, we conclude that ‘I am’ and ‘I have’ are more important than the skills dimension of ‘I can’. Positive role models, trust, ‘managed’ optimism, flexibility of support in and beyond induction, and, crucially, self‐efficacy and space for reflexivity, are more prominent as sources of resilience and strong identity. The reflexivity, inspired by the process of narrative enquiry, is an important contributor to self‐efficacy. We propose that a positive view of growth and identity is preferable to deficit models in the context of the transition between the two ‘communities of practice’ and of the challenges of the workplace. Organizational approaches based on this view will be more likely to promote a sustainable workforce.
Childhood overweight and asthma symptoms, the role of pro‐inflammatory proteins
Authors: Bekkers M. B. M. , Brunekreef B. , de Jongste J. C. , Kerkhof M. , Smit H. A. , Postma D. S. , Gehring U. , Wijga A. H.
Published: August 2011

Background Systemic inflammation is suggested as a mechanism by which overweight might induce asthma. However, few studies have linked childhood overweight, inflammation and asthma.

Objective To study the association between body mass index (BMI), asthma symptoms and pro‐inflammatory proteins.

Methods High‐sensitivity C‐reactive protein (hs‐CRP), complement factor 3 (C3) and 4 (C4) concentrations, and body weight and height were available for 359 4‐year‐old children participating in the Prevention and Incidence of Asthma and Mite Allergy birth cohort study. Data on asthma symptoms were obtained by yearly questionnaires. Logistic regression and generalized estimating equations were used to analyse the cross‐sectional and prospective associations between BMI, asthma symptoms and pro‐inflammatory proteins.

Results BMI was associated with asthma symptoms {odds ratio [OR] 1.43 [95% confidence interval (CI): 1.08–1.88] per BMI standard deviation scores [SDS]}. The inclusion of hs‐CRP, C3 and C4 in the statistical models did not change this association. C3 was cross‐sectionally associated with frequent asthma symptoms [OR per interquartile range of C3: 1.97 (95% CI: 1.20–3.24)] and prospectively with asthma symptoms [OR: 1.48 (95%CI: 1.04–2.09)], independent of BMI SDS.

Conclusions and Clinical Relevance We showed no evidence for a role of hs‐CRP, C3 and C4 in the association between BMI and asthma symptoms. C3 concentrations were associated with (frequent) asthma symptoms, independent of BMI.

Cite this as: M. B. M. Bekkers, B. Brunekreef, J. C. de Jongste, M. Kerkhof, H. A. Smit, D. S. Postma, U. Gehring and A. H. Wijga, Clinical & Experimental Allergy, 2012 (42) 95–103.
A Th1/Th2‐associated chemokine imbalance during infancy in children developing eczema, wheeze and sensitization
Authors: Abrahamsson T. R. , Sandberg Abelius M. , Forsberg A. , Björkstén B. , Jenmalm M. C.
Published: August 2011

Background Analyses of circulating chemokines offer novel tools to investigate the T helper (Th)1/Th2 imbalance in allergic disease in vivo.

Objective To relate circulating Th1‐ and Th2‐associated chemokines in infancy to allergic disease, sensitization and probiotic supplementation.

Methods Circulating levels of Th1‐associated CXC‐chemokine ligand (CXCL)9, CXCL10 and CXCL11 and Th2‐associated CC‐chemokine ligand (CCL)17 and CCL22 were assessed with Luminex and CCL18 with enzyme‐linked immunosorbent assay at birth (n=109), 6 (n=104), 12 (n=116) and 24 months (n=123) in 161 infants completing a double‐blind placebo‐controlled allergy prevention trial with Lactobacillus reuteri during the last month of gestation and through the first year of life. The infants were followed regarding the development of allergic disease and sensitization until 2 years of age.

Results The Th2‐associated chemokines CCL17 and CCL22 were the highest at birth and then decreased, whereas CCL18 and the Th1‐associated chemokines increased with age. High Th2‐associated chemokine levels were observed in children developing allergic disease. Sensitization was preceded by elevated levels of the Th2‐associated CCL22 and reduced levels of the Th1‐associated CXCL11 already at birth. The Th2‐associated CCL17 was also elevated at birth in infants developing recurrent wheeze. A high Th2/Th1 ratio (CCL22/CXCL10) at birth associated with both sensitization and eczema development. The presence of L. reuteri in stool in the first week of life was associated with low CCL17 and CCL22 and high CXCL11 levels at 6 months of age. High Th1‐associated chemokine levels were associated with day‐care.

Conclusion and Clinical Relevance Allergic disease and sensitization in infancy was associated with low circulating Th1‐ and high Th2‐associated chemokine levels already from birth. Circulating chemokines are useful for investigating the Th1/Th2 imbalance in allergic disease in vivo. Elucidation of the role of chemokines in allergic diseases may lead to future treatments (ClinicalTrials.gov NCT01285830).

Cite this as: T. R. Abrahamsson, M. Sandberg Abelius,, A. Forsberg, B. Björkstén and M. C. Jenmalm, Clinical & Experimental Allergy, 2011 (41) 1729–1739.
Effect of roasting on the allergenicity of major peanut allergens Ara h 1 and Ara h 2/6: the necessity of degranulation assays
Authors: Vissers Y. M. , Iwan M. , Adel‐Patient K. , Stahl Skov P. , Rigby N. M. , Johnson P. E. , Mandrup Müller P. , Przybylski‐Nicaise L. , Schaap M. , Ruinemans‐Koerts J. , Jansen A. P. H. , Mills E. N. C. , Savelkoul H. F. J. , Wichers H. J.
Published: August 2011

Background Peanuts are often consumed after roasting, a process that alters the three‐dimensional structure of allergens and leads to Maillard modification. Such changes are likely to affect their allergenicity.

Objective We aimed to establish the effect of thermal treatment mimicking the roasting process on the allergenicity of Ara h 1 and a mix of 2S albumins from peanut (Ara h 2/6).

Methods Ara h 1 and Ara h 2/6 were purified from raw peanuts and heated in a dry form for 20 min at 145 °C in the presence (R+g) or absence (R−g) of glucose, and soluble proteins were then extracted. Sera obtained from 12 well‐characterized peanut‐allergic patients were used to assess the IgE binding and degranulation capacities of the allergens.

Results Extensive heating at low moisture resulted in the hydrolysis of both Ara h 1 and Ara h 2/6. However, in contrast to Ara h 2/6, soluble R+g Ara h 1 formed large aggregates. Although the IgE‐binding capacity of R+g and R−g Ara h 1 was decreased 9000‐ and 3.6‐fold, respectively, compared with native Ara h 1, their capacity to elicit mediator release was increased. Conversely, both the IgE‐binding capacity and the degranulation capacity of R−g Ara h 2/6 were 600–700‐fold lower compared with the native form, although the presence of glucose during heating significantly moderated these losses.

Conclusions and Clinical Relevance Extensive heating reduced the degranulation capacity of Ara h 2/6 but significantly increased the degranulation capacity of Ara h 1. This observation can have important ramifications for component‐resolved approaches for diagnosis and demonstrates the importance of investigating the degranulation capacity in addition to IgE reactivity when assessing the effects of food processing on the allergenicity of proteins.

Cite this as: Y. M. Vissers, M. Iwan, K. Adel‐Patient, P. Stahl Skov, N. M. Rigby, P. E. Johnson, P. Mandrup Müller, L. Przybylski‐Nicaise, M. Schaap, J. Ruinemans‐Koerts, A. P. H. Jansen, E. N. C. Mills, H. F. J. Savelkoul and H. J. Wichers, Clinical & Experimental Allergy, 2011 (41) 1631–1642.
Interpretation of magnetic data over tilted basement blocks: an example from the northern North Sea
Authors: Salem Ahmed
Published: August 2011

This paper presents a procedure for interpreting magnetic data over tilted basement blocks. The objective of this procedure is to estimate source parameters of a tilted basement block from first‐ order derivatives of magnetic profile data. The method uses a model consisting of two superimposed infinite contacts with opposite dip. The procedure estimates the location of the crest (intersection of the two contacts) and the susceptibility contrast of the basement block from the total gradient anomaly data using a linear least‐squares method. Dip angles of the two contacts are estimated using iterative forward modelling of the tilt derivative anomaly data. The practical utility of the proposed approach is demonstrated using theoretical data and a field example from the northern North Sea.