bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterotic vacua from general (non‐) Abelian bundles
Authors: Weigand T. 
Published: April 2006

AbstractWe report on the construction of four‐dimensional string vacua by considering general abelian and non‐abelian bundles on an internal Calabi‐Yau for both heterotic theories. The structure of the resulting gauge sector is extremely rich and gives rise to many new model building possibilities. We analyse the chiral spectrum including the contribution from heterotic five‐branes and provide the general consistency conditions. The one‐loop corrected supersymmetry condition on the bundles is found to be that of π‐stability. As an application we present a supersymmetric Standard‐Model like example for the SO(32) string with U(n) bundles on an elliptically fibered Calabi‐Yau.
Stringy effects for spinning strings and the Bethe ansatz
Authors: Schäfer‐Nameki S. , Zamaklar M. 
Published: April 2006

AbstractThe one‐loop worldsheet corrections to spinning strings in the sl(2) subsector of AdS5 × S5 are compared to the quantum string Bethe ansatz. The evaluation of the energy shift is performed in two regimes: a) in the large 𝒥 limit, using zeta‐function regularization and b) in the limit of large winding number. The first computation agrees with the Bethe ansatz in the first three orders while the second computation leads to a disagreement with the string Bethe ansatz prediction at leading order. Careful analysis of the zeta‐function regularization shows, that in this approach perturbative as well as non‐perturbative terms in the string sums are missed. Hence, this together with the result b), implies that the proposed quantum string Bethe equations do not reproduce all terms in the exact string result.
Global multiple‐sequence alignment with repeats
Authors: Sammeth Michael , Heringa Jaap 
Published: April 2006

AbstractRepeating fragments in biological sequences are often essential for structure and function. Over the years, many methods have been developed to recognize repeats or to multiply align protein sequences. However, the integration of these two methodologies has been largely unexplored to date. Here, we present a new method capable of globally aligning multiple input sequences under the constraints of a given repeat analysis. The method supports different stringency modes to adapt to various levels of detail and reliability of the repeat information available. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Fish assemblages and stream hydraulics: consistent relations across spatial scales and regions
Authors: Lamouroux N. , Cattanéo F. 
Published: April 2006

AbstractGeneral relationships between organisms and their habitat, consistent across spatial scales and regions, suggest the existence of repeatable ecological processes and are useful for the management of stream networks. From published data, we defined four guilds of European fish species with contrasting preferences for microhabitat hydraulics within stream reaches. At the scale of stream reaches and across 139 French sites (590 460 fishes sampled), we analysed how fish guild proportions were related to reach hydraulics (proportion of pools vs. riffles %POOL; median discharge by unit width Q50/W). The strongest correlations were observed between two fish guilds and %POOL (p < 0.001, r2 ≥ 0.41) and between one fish guild proportion and Q50/W (p < 0.001, r2 = 0.10). These reach–scale relationships were consistent across six large French basins, and consistent with the analyses made at the microhabitat scale. Therefore, microhabitat preferences for hydraulics are strong enough to generate consistent reach‐scale community responses to hydraulics across regions, despite the influence of other filters such as temperature, nutrient levels or history. The distribution of basic geomorphic features (pools, riffles) in streams and their modification (by dams, weirs and dikes) can modify the proportion of fish guilds by up to 80%, probably contributing to the long‐term decline of riffle‐dwelling species in Europe. Copyright © 2006 John Wiley & Sons, Ltd.
Analysis of the swimming of elastic slender bodies excited by an external force
Authors: Lavie A. M. 
Published: April 2006

The essential difference, from the theoretical point of view, between an externally excitedlciody and a fish is that the latter can apply lateral vibratory movements at any part of its surface, whereas in the ‘artificial fish’ lateral vibrations are applied only at the point where the external force acts on the body. A good example which illustrates how the artificial fish swims is the ‘Pod’. The Pod is a medical device consisting of a small magnet attached to a plastic ‘tail’. If the Pod is placed in a patient's blood vessel, and an alternating magnetic field is applied, the magnet oscillates angularly and the plastic tail causes it to swim. The purpose of the device is to deliver medicaments at any desired location in the circulatory system.In this paper the theory of swimming of elastic slender bodies excited by an external force is presented. Special reference is made to the hydrodynamic forces acting on a swimming cylinder in viscous fluctuating flow. The results obtained are used in the analysis of the propulsion mechanism of the Pod.
Thermoconvective instabilities in a porous medium bounded by two concentric horizontal cylinders
Authors: Caltagirone Jean-Paul 
Published: April 2006

The study of natural convection in a saturated porous medium bounded by two concentric, horizontal, isothermal cylinders reveals different types of evolution according to the experimental conditions and the geometrical configuration of the model. At small Rayleigh numbers the state of the system corresponds to a regime of pseudo-conduction. The isotherms are coaxial with the cylinders. At larger Rayleigh numbers a regime of steady two-dimensional convection sets in between the two cylinders. Finally, for Rayleigh numbers above the critical Rayleigh number Ra*c the phenomena become three-dimensional and fluctuating. The appearance of these different regimes depends, moreover, on the geometry considered and, in particular, on two numbers: R, the ratio of the radii of the cylinders, and A, the ratio of the length of the cylinders to the radius of the inner one. In order to approach these experimental observations and to obtain realistic theoretical models, several methods of solving the equations have been used.The perturbation method yields information about the thermal field and the heat transfer between the cylinders under conditions close to the equilibrium state.A numerical two-dimensional model enables us to extend the range of investigation and to represent properly the phenomena when steady convection appreciably modifies the temperature distribution and the velocities within the porous layer.Neither of these models allows account to be taken of the instabilities observed experimentally above a critical Rayleigh number Ra*c. For this reason, a study of stability has been carried out using a Galerkin method based on equations corresponding to an initial state of steady convection. The results obtained show the importance of three-dimensional effects for the onset of fluctuating convection. The critical transition Rayleigh number Ra*c is thus determined in terms of the ratio of the radii R by solving an eigenvalue problem.A numerical three-dimensional model based on the method of finite elements has thus been developed in order to point out the different types of evolution with time. Steady two-dimensional convection and fluctuating three-dimensional convection have been actually found by calculation. The solution of the system of equations by the method of finite elements is briefly described.The experimental and theoretical results are then compared and a general physical interpretation is given.
Turbulent flow in a rectangular duct
Authors: Melling A. , Whitelaw J. H. 
Published: April 2006

A detailed experimental study of developing turbulent flow in a rectangular duct was made using a laser-Doppler anemometer. The purposes of the work were to obtain data of value to fluid mechanicists, particularly those interested in the development and testing of mathematical turbulence models, and to evaluate the performance of the anemometer. For the first purpose, contours of axial mean velocity and turbulence intensity were measured in the developing flow, and all three mean velocity components and five of the six Reynolds stresses were obtained in the nearly fully developed flow.The symmetry of the present flow appears to be better than that of previous measurements and the range of measurements is more extensive. In addition, the laser-Doppler anemometer has the potential advantage, particularly in the measurement of secondary velocities, of avoiding probe interference.
Hydromechanics of lunate-tail swimming propulsion. Part 2
Authors: Chopra M. G. , Kambe T. 
Published: April 2006

This paper investigates the propulsive performance of the lunate tails of aquatic animals achieving high propulsive efficiency (the hydromechanical efficiency being defined as the ratio of the work done by the mean forward thrust to the mean rate at which work is done by the tail movements on the surrounding fluid). Small amplitude heaving and pitching motions of a finite flat-plate wing of general planform with a rounded leading edge and a sharp trailing edge are considered. This is a generalization of Chopra's (1974) work on model rectangular tails. This motion characterizes vertical oscillations of the horizontal tail flukes of some cetacean mammals. The same oscillations, turned through a right angle to become horizontal motions of side-slip and yaw, characterize the caudal fins of certain fast-swimming fishes; viz. wahoo, tunny, wavyback skipjack, etc., from the Percomorphi and whale shark, porbeagle, etc., from the Selachii. Davies’ (1963, 1976) method of finding the loading distribution on the wing and generalized force coefficients, through approximate solution of an integral equation relating the loading and the upwash (lifting-surface theory), is used to find the total thrust and the rate of working of the tail, which in turn specify the hydromechanical swimming performance of the animals. The physical parameters concerned are the tail aspect ratio ((span)2/planform area), the reduced frequency (angular frequency x typical length/forward speed), the feathering parameter (the ratio of the tail slope to the slope of the path of the pitching axis), the position of the pitching axis, and the curved shapes of the leading and trailing edges. The variation of the thrust and the propulsive efficiency with these parameters has been discussed to indicate the optimum shape of the tail. It is found that, compared with a rectangular tail, a curved leading edge as in lunate tails gives a reduced thrust contribution from the leading-edge suction for the same total thrust; however, a sweep angle of the leading edge exceeding about 30° leads to a marked reduction of efficiency. Another implication of the present analysis is that no negative work is involved in the actual oscillation of the tail.The present results are used to obtain an estimate of the drag coefficient for the motion of the animals, based on observed data and the computed thrust. The results show some evidence of differences between the CD's for cetacean mammals and scombroid fish respectively. Some discussion of this difference is also given.
Obliquely interacting solitary waves
Authors: Miles John W. 
Published: April 2006

Nonlinear oblique interactions between two slightly dispersive gravity waves (in particular, solitary waves) of dimensionless amplitudes α1 and α2 (relative to depth) and relative inclination 2ϕ (between wave normals) are classified as weak if sin2ϕ α1,2 or strong if ϕ2 = O(α1,2). Weak interactions permit superposition of the individual solutions of the Korteweg-de Vries equation in first approximation; the interaction term, which is O(α1α2), then is determined from these basic solutions.Strong interactions are intrinsically nonlinear. It is shown that these interactions are phase-conserving (the sum of the phases of the incoming waves is equal to the sum of the phases of the outgoing waves) if |α2-α1 > (2ϕ)2 but not if |α2-α1| (2ϕ)2 (e.g. the reflexion problem, for which the interacting waves are images and α2 = α1). It also is shown that the interactions are singular, in the sense that regular incoming waves with sech2 profiles yield singular outgoing waves with - csch2 profiles, if
\[
\psi_{-}< |\psi| < \psi_{+},\quad{\rm where}\quad\psi_{\pm}={\textstyle\frac{1}{2}}\left|(3\alpha_2)^{\frac{1}{2}}\pm(3\alpha_1)^{\frac{1}{2}}\right|.
\]Regular interactions appear to be impossible within this singular regime, and its end points, |ϕ| = ϕ±, are associated with resonant interactions.
On a theory of amplitude vacillation in baroclinic waves
Authors: Smith R. K. 
Published: April 2006

This study contributes to the theory of amplitude vacillation for finite amplitude baroclinic waves in a two-layer, quasi-geostrophic, zonal flow as worked out by Pedlosky. In a recent paper the author has shown that Pedlosky omitted a certain side-wall boundary condition on the mean zonal flow. The neglect of this boundary condition results in an unspecified energy source at the side-wall boundaries and the physical problem is incorrectly posed.In this paper, Pedlosky's analysis is repeated but with the side-wall boundary condition included. It is shown that the side-wall energy source is negligible only when the zonal wavenumber of the disturbance is large compared with the meridional wavenumber, and not otherwise. Moreover, the energy conversions to and from mean zonal kinetic energy corresponding to Pedlosky's calculations and those given here have essential differences, although for fixed meridional wavenumber, these differences become less pronounced as the zonal wavenumber increases.It is also shown that, when the side-wall condition is included, the mean flow distortion associated with the wave is different in structure to that which occurs when the condition is omitted. However, as the total disturbance wavenumber a increases, the influence of the side wall on the mean flow structure is confined to a boundary layer of width comparable with the internal deformation radius 2½a−1.Even when the deformation radius is comparable with the channel width, the conclusions of Pedlosky (1972) concerning the existence of stable periodic solutions are correct, providing viscous effects are vanishingly small, and the criteria for stability of the steady solutions obtained herein are not significantly different from those given by Pedlosky. In this viscous regime, we have also studied the evolution to limit-cycle solutions.Evolution in the case where viscous effects are small on the time scale for the initial growth of an incipient wave, but not vanishingly small, will be discussed in a subsequent paper.
Thermal convection in a Hele-Shaw cell
Authors: Hartline Beverly K. , Lister C. R. B. 
Published: April 2006

We derive the Rayleigh number RHS for thermal convection in a Hele-Shaw cell with gap width d and full width (gap plus walls) Y. For the state of marginal stability, the system of equations is found to be formally identical to that describing flow through a uniform porous medium, if d3/12Y is identified as the Hele-Shaw permeability. Thus Lapwood's (1948) thermal-instability analysis should apply, and the critical Rayleigh number should be 4π2 when the cell has impermeable isothermal boundaries.Baker's (1966) pH-indicator method for visualizing fluid flow has been adapted for use in a Hele-Shaw cell. In addition to revealing the convection pattern clearly, this technique proves to be an especially sensitive detector of incipient flow, and a highly accurate means of verifying the onset of convection. Our experiments confirm that the critical Hele-Shaw Rayleigh number is 40 ± 2, thereby validating our theoretically derived expression for the Rayleigh number. We also measure the vertical flow velocity wm and find that wm∝ (R2HS−402)½ closely fits our data for 40 < RHS < 140.
Prediction of the contributions to the Reynolds stress from bursting events in open-channel flows
Authors: Nakagawa Hiroji , Nezu Iehisa 
Published: April 2006

In this paper we intend to predict the magnitude of the contribution to the Reynolds stress of bursting events: ‘ejections’, ‘sweeps’, ‘inward interactions’ and ‘outward interactions’. We shall do this by making use of the conditional probability distribution of the Reynolds stress −uv, which can be derived by applying the cumulant-discard method to the Gram-Charlier probability distribution of the two variablesuandv. The Reynolds-stress fluctuations in openchannel flows over smooth and rough beds are measured by dual-sensor hot-film anemometers, whose signals are conditionally sampled and sorted into the four quadrants of theu, vplane by using a high-speed digital data processing system.We shall verify that even the third-order conditional probability distribution of the Reynolds stress shows fairly good agreement with the experimental results and that the sequence of events in the bursting process, i.e. ejections, sweeps and interactions, is directly related to the turbulent energy budget in the form of turbulent diffusion. Also, we shall show that the roughness effect is marked in the area from the wall to the middle of the equilibrium region, and that sweeps appear to be more important than ejections as the roughness increases and as the distance from the wall decreases.
The conformational state of polyphenol oxidase from field bean (Dolichos lablab) upon SDS and acid-pH activation
Authors: Kanade Santosh R. , Paul Beena , Rao A. G. Appu , Gowda Lalitha R. 
Published: April 2006

Field bean (Dolichos lablab) contains a single isoform of PPO (polyphenol oxidase) – a type III copper protein that catalyses the o-hydroxylation of monophenols and oxidation of o-diphenols using molecular oxygen – and is a homotetramer with a molecular mass of 120 kDa. The enzyme is activated manyfold either in the presence of the anionic detergent SDS below its critical micellar concentration or on exposure to acid-pH. The enhancement of kcat upon activation is accompanied by a marked shift in the pH optimum for the oxidation of t-butyl catechol from 4.5 to 6.0, an increased sensitivity to tropolone, altered susceptibility to proteolytic degradation and decreased thermostability. The Stokes radius of the native enzyme is found to increase from 49.1±2 to 75.9±0.6 Å (1 Å=0.1 nm). The activation by SDS and acid-pH results in a localized conformational change that is anchored around the catalytic site of PPO that alters the microenvironment of an essential glutamic residue. Chemical modification of field bean and sweet potato PPO with 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide followed by kinetic analysis leads to the conclusion that both the enzymes possess a core carboxylate essential to activity. This enhanced catalytic efficiency of PPO, considered as an inducible defence oxidative enzyme, is vital to the physiological defence strategy adapted by plants to insect herbivory and pathogen attack.
Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Authors: Ramsland Paul A. , Terzyan Simon S. , Cloud Gwendolyn , Bourne Christina R. , Farrugia William , Tribbick Gordon , Geysen H. Mario , Moomaw Carolyn R. , Slaughter Clive A. , Edmundson Allen B. 
Published: April 2006

The 2.6 Å (1 Å=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel point and monitor the formation of an ordered hydroscopic gel of Yvo IgM upon cooling. If a cryoglobulin forms gels in peripheral tissues and organs, the associated swelling and damage to microvasculature can result in considerable morbidity and mortality. The three-dimensional structure of the branched N-linked oligosaccharide associated with the CH1 domain (first constant domain of heavy chain) is reported. The carbohydrate may act to shield part of the lateral surface of the CH1 domain and crowd the junction between the CH1 and CH2 domains, thereby limiting the segmental flexibility of the Fab arms in intact Yvo IgM, especially at low temperatures. Recently, Yvo IgM was shown to have the properties of a naturally occurring proteolytic antibody [Paul, Karle, Planque, Taguchi, Salas, Nishiyama, Handy, Hunter, Edmundson and Hanson (2004) J. Biol. Chem. 279, 39611–39619; Planque, Bangale, Song, Karle, Taguchi, Poindexter, Bick, Edmundson, Nishiyama and Paul (2004) J. Biol Chem. 279, 14024–14032]. The Yvo protein displayed the ability to cleave, by a nucleophilic mechanism, the amide bonds of a variety of serine protease substrates and the gp120 coat protein of HIV. An atypical serine, arginine and glutamate motif is located in the middle of the Yvo antigen-binding site and displays an overall geometry that mimics the classical serine, histidine and aspartate catalytic triad of serine proteases. Our present findings indicate that pre-existing or natural antibodies can utilize at least one novel strategy for the cleavage of peptide bonds.
Collagen binding by the mannose receptor mediated through the fibronectin type II domain
Authors: Napper Catherine E. , Drickamer Kurt , Taylor Maureen E. 
Published: April 2006

The macrophage mannose receptor is the prototype for a family of receptors each having an extracellular region consisting of an N-terminal cysteine-rich domain related to the R-type carbohydrate-recognition domain of ricin, a fibronectin type II domain and eight to ten domains related to C-type carbohydrate-recognition domains. The mannose receptor acts as a molecular scavenger, clearing harmful glycoconjugates or micro-organisms through recognition of their defining carbohydrate structures. Cell-adhesion assays, as well as collagen-binding assays, have now been used to show that the mannose receptor can also bind collagen and that the fibronectin type II domain mediates this activity. Neither of the two types of sugar-binding domain in the receptor is involved in collagen binding. Fibroblasts expressing the mannose receptor adhere to type I, type III and type IV collagens, but not to type V collagen, and the adherence is inhibited by isolated mannose receptor fibronectin type II domain. The fibronectin type II domain shows the same specificity for collagen as the whole receptor, binding to type I, type III and type IV collagens. This is the first activity assigned to the fibronectin type II domain of the mannose receptor. The results suggest additional roles for this multifunctional receptor in mediating collagen clearance or cell–matrix adhesion.