bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Candidate Transcription Factor Binding Sites in the Cattle Genome
Authors: Bickhart Derek M. , Liu George E. 
Published: February 2013

Abstract
A resource that provides candidate transcription factor binding sites (TFBSs) does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach—using sequence conservation across cattle, human and dog—and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection (MGC) annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCK1, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the Illumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http://bfgl.anri.barc.usda.gov/BovineTFBS/ or http://199.133.54.77/BovineTFBS.
On the best design for undulatory swimming
Authors: Eloy Christophe 
Published: February 2013

AbstractMost aquatic vertebrates swim by passing a bending wave down their bodies, a swimming mode known as undulatory propulsion. Except for very elongated swimmers like eels and lampreys, these animals have generally evolved to a similar shape: an anterior streamlined region of large volume separated from a caudal fin by a caudal peduncle of reduced cross-section. However, the link between this particular shape and the hydrodynamical constraints remains to be explored. Here, this question is addressed by seeking the optimal design for undulatory swimmers with an evolutionary algorithm. Animals of varying elliptic cross-section are considered whose motions are prescribed by arbitrary periodic curvature laws. In the elongated-body limit, reactive and resistive forces can be formulated at any cross-section, allowing the recoil motion and the mean swimming speed of a given animal to be calculated. A bi-objective optimization problem then consists of finding body shapes and corresponding motions associated with the lowest energetic costs, the highest stride lengths (which is a dimensionless measure of swimming speed) or any trade-offs between the two. For biologically relevant parameters, this optimization calculation yields two distinct ‘species’: one specialized in economical swimming and the other in large stride lengths. By comparing the attributes and performance of these numerically obtained swimmers with data on undulatory-swimming animals, it is argued that evolution is consistent with the selection of species with low energetic costs.
Interaction between feedback aeroacoustic and acoustic resonance mechanisms in a cavity flow: a global stability analysis
Authors: Yamouni Sami , Sipp Denis , Jacquin Laurent 
Published: February 2013

AbstractWe perform a global stability analysis of a flow over an open cavity, characterized by a Reynolds number, based on the upstream velocity and the cavity length, of $7500$. We compute base flows and unstable global modes of the flow for different Mach numbers ranging from $0$ to $0. 9$. In the incompressible regime ($M= 0$), we show that the flow is subject to global instabilities due to Kelvin–Helmholtz instabilities in the shear layer, which become strengthened by a hydrodynamic pressure feedback. The influence of the boundary-layer thickness and of the length-to-depth ratio of the cavity on these shear-layer modes has been investigated. In the compressible regime ($M\gt 0$), we have shown that all unstable global modes are continuously connected to the incompressible shear-layer modes as $M\rightarrow 0$. These shear-layer modes correspond to the beginning of branches of global modes, whose frequencies evolve (as a function of the Mach number), in accordance with the feedback aeroacoustic mechanism (Rossiter, Tech. Rep. Aero. Res. Counc. R. & M., 1964). We have also identified branches of global modes behaving in agreement with acoustic resonance mechanisms (East, J. Sound Vib., vol. 3, 1966, pp. 277–287; Tam, J. Sound Vib., vol. 49, 1976, pp. 353–364; Koch, AIAA J., vol. 43, 2005, pp. 2342–2349). At the intersections between both types of branches, the growth rate of the global modes is seen to display a local maximum. Along the aeroacoustic feedback branches, the number of vortical structures in the shear layer is kept constant, while the pressure pattern inside the cavity is conserved along the acoustic resonance branches. We show that both the feedback aeroacoustic and acoustic resonance mechanisms are at play over the entire subsonic regime, from $M= 0$ to $M= 0. 9$. At low Mach numbers, we suggest that it is still the feedback aeroacoustic mechanism that selects the frequency, even though the fundamental acoustic resonance mode is also important due to enhancing the response. At higher Mach numbers, we observe that the pressure pattern of the acoustic resonance modes (fundamental acoustic modes, first longitudinal acoustic modes, first longitudinal-depth acoustic modes) inside the cavity determines the directivity of the radiated noise. Links with experimental results are finally discussed.
Reynolds number and aspect ratio effects on the leading-edge vortex for rotating insect wing planforms
Authors: Harbig R. R. , Sheridan J. , Thompson M. C. 
Published: February 2013

AbstractPrevious studies investigating the effect of aspect ratio ($\mathit{AR}$) for insect-like regimes have reported seemingly different trends in aerodynamic forces, however no detailed flow observations have been made. In this study, the effect of$\mathit{AR}$and Reynolds number on the flow structures over insect-like wings is explored using a numerical model of an altered fruit fly wing revolving at a constant angular velocity. Increasing the Reynolds number for an$\mathit{AR}$of 2.91 resulted in the development of a dual leading-edge vortex (LEV) structure, however increasing$\mathit{AR}$at a fixed Reynolds number generated the same flow structures. This result shows that the effects of Reynolds number and$\mathit{AR}$are linked. We present an alternative scaling using wing span as the characteristic length to decouple the effects of Reynolds number from those of$\mathit{AR}$. This results in a span-based Reynolds number, which can be used to independently describe the development of the LEV. Indeed, universal behaviour was found for various parameters using this scaling. The effect of$\mathit{AR}$on the vortex structures and aerodynamic forces was then assessed at different span-based Reynolds numbers. Scaling the flow using the wing span was found to apply when a strong spanwise velocity is present on the leeward side of the wing and therefore may prove to be useful for similar studies involving flapping or rotating wings at high angles of attack.
Three-vortex quasi-geostrophic dynamics in a two-layer fluid. Part 1. Analysis of relative and absolute motions
Authors: Sokolovskiy M. A. , Koshel K. V. , Verron J. 
Published: February 2013

AbstractThe results presented here examine the quasi-geostrophic dynamics of a point vortex structure with one upper-layer vortex and two identical bottom-layer vortices in a two-layer fluid. The problem of three vortices in a barotropic fluid is known to be integrable. This fundamental result is also valid in a stratified fluid, in particular a two-layer one. In this case, unlike the barotropic situation, vortices belonging to the same layer or to different layers interact according to different formulae. Previously, this occurrence has been poorly investigated. In the present work, the existence conditions for stable stationary (translational and rotational) collinear two-layer configurations of three vortices are obtained. Small disturbances of stationary configurations lead to periodic oscillations of the vortices about their undisturbed shapes. These oscillations occur along elliptical orbits up to the second order of the Hamiltonian expansion. Analytical expressions for the parameters of the corresponding ellipses and for oscillation frequencies are obtained. In the case of finite disturbances, vortex motion becomes more complicated. In this case we have made a classification of all possible movements, by analysing phase portraits in trilinear coordinates and by computing numerically the characteristic trajectories of the absolute and relative vortex motions.
Three-vortex quasi-geostrophic dynamics in a two-layer fluid. Part 2. Regular and chaotic advection around the perturbed steady states
Authors: Koshel K. V. , Sokolovskiy M. A. , Verron J. 
Published: February 2013

AbstractWe study fluid-particle motion in the velocity field induced by a quasi-stationary point vortex structure consisting of one upper-layer vortex and two identical vortices in the bottom layer of a rotating two-layer fluid. The regular regimes are investigated, and the possibility of chaotic regimes (chaotic advection) under the effect of quite small non-stationary disturbances of stationary configurations has been shown. Examples of different scenarios are given for the origin and development of chaos. We analyse the role played by the stochastic layer in the processes of mixing and in the capture of fluid particles within a vortex area. We also study the influence of stratification on these effects. It is shown that regular and chaotic advection situations exhibit significant differences in the two layers.
Longitudinal and transverse flow over a cavity containing a second immiscible fluid
Authors: Schönecker Clarissa , Hardt Steffen 
Published: February 2013

AbstractAn analytical solution for the low-Reynolds-number flow field of a shear flow over a rectangular cavity containing a second immiscible fluid is derived. While flow of a single-phase fluid over a cavity is a standard case investigated in fluid dynamics, flow over a cavity that is filled with a second immiscible fluid has received little attention. The flow field inside the cavity is considered to define a boundary condition for the outer flow, which takes the form of a Navier slip condition with locally varying slip length. The slip-length function is determined heuristically from the related problem of lid-driven cavity flow. Based on the Stokes equations and complex analysis, it is then possible to derive a closed analytical expression for the flow field over the cavity for both the transverse and the longitudinal case. The result is a comparatively simple function, which displays the dependence of the flow field on the cavity geometry and the medium filling the cavity. The analytically computed expression agrees well with results obtained from a numerical solution of the Navier–Stokes equations.
Scaling behaviour in Rayleigh–Bénard convection with and without rotation
Authors: King E. M. , Stellmach S. , Buffett B. 
Published: February 2013

AbstractRotating Rayleigh–Bénard convection provides a simplified dynamical analogue for many planetary and stellar fluid systems. Here, we use numerical simulations of rotating Rayleigh–Bénard convection to investigate the scaling behaviour of five quantities over a range of Rayleigh ($1{0}^{3} \lesssim \mathit{Ra}\lesssim 1{0}^{9} $), Prandtl ($1\leq \mathit{Pr}\leq 100$) and Ekman ($1{0}^{- 6} \leq E\leq \infty $) numbers. The five quantities of interest are the viscous and thermal boundary layer thicknesses, ${\delta }_{v} $ and ${\delta }_{T} $, mean temperature gradients, $\beta $, characteristic horizontal length scales, $\ell $, and flow speeds, $\mathit{Pe}$. Three parameter regimes in which different scalings apply are quantified: non-rotating, weakly rotating and rotationally constrained. In the rotationally constrained regime, all five quantities are affected by rotation. In the weakly rotating regime, ${\delta }_{T} $, $\beta $ and $\mathit{Pe}$, roughly conform to their non-rotating behaviour, but ${\delta }_{v} $ and $\ell $ are still strongly affected by the Coriolis force. A summary of scaling results is given in table 2.
Naturally bounded plumes
Authors: Mehaddi Rabah , Candelier Fabien , Vauquelin Olivier 
Published: February 2013

AbstractThis paper investigates theoretically the vertical evolution of a turbulent plume into a linearly stratified ambient fluid, by regarding it as composed of two distinct regions. In the first region, called the positive buoyant region, the plume buoyancy and the plume momentum act in the same upward direction, whereas in the second region, called the negative buoyant region, they act in opposite directions. In a first step, analytical expressions for the plume variables at the transition height (i.e. between the two regions) are obtained from one-dimensional conservation equations, using the plume entrainment model and under the Boussinesq approximation. In a second step, these variables are used in order to determine analytically the buoyancy and volume fluxes as well as the density deficit of the plume at its top. In this investigation, the transition height (denoted ${z}_{t} $) and the total plume height (denoted ${z}_{p} $) are obtained in the form of two integrals. These integrals are evaluated asymptotically in three different cases associated with particular flow regimes. Finally, the limit of the Boussinesq assumption for such flows is discussed.
On the scaling of air layer drag reduction
Authors: Elbing Brian R. , Mäkiharju Simo , Wiggins Andrew , Perlin Marc , Dowling David R. , Ceccio Steven L. 
Published: February 2013

AbstractAir-induced drag reduction was investigated on a 12.9 m long flat plate test model at a free stream speed of$6. 3~\mathrm{m} ~{\mathrm{s} }^{- 1} $. Measurements of the local skin friction, phase velocity profiles (liquid and gas) and void fraction profiles were acquired at downstream distances to 11.5 m, which yielded downstream-distance-based Reynolds numbers above 80 million. Air was injected within the boundary layer behind a 13 mm backward facing step (BFS) while the incoming boundary layer was perturbed with vortex generators in various configurations immediately upstream of the BFS. Measurements confirmed that air layer drag reduction (ALDR) is sensitive to upstream disturbances, but a clean boundary layer separation line (i.e. the BFS) reduces such sensitivity. Empirical scaling of the experimental data was investigated for: (a) the critical air flux required to establish ALDR; (b) void fraction profiles; and (c) the interfacial velocity profiles. A scaling of the critical air flux for ALDR was developed from balancing shear-induced lift forces and buoyancy forces on a single bubble within a shear flow. The resulting scaling successfully collapses ALDR results from the current and past studies over a range of flow conditions and test model configurations. The interfacial velocity and void fraction profiles were acquired and scaled within the bubble drag reduction (BDR), ALDR and transitional ALDR regimes. The BDR interfacial velocity profile revealed that there was slip between phases. The ALDR results showed that the air layer thickness was nominally three-quarters of the total volumetric flux (per unit span) of air injected divided by the free stream speed. Furthermore, the air layer had an average void fraction of 0.75 and a velocity of approximately 0.2 times the free stream speed. Beyond the air layer was a bubbly mixture that scaled in a similar fashion to the BDR results. Transitional ALDR results indicate that this regime was comprised of intermittent generation and subsequent fragmentation of an air layer, with the resulting drag reduction determined by the fraction of time that an air layer was present.
No steady water waves of small amplitude are supported by a shear flow with a still free surface
Authors: Kozlov Vladimir , Kuznetsov Nikolay 
Published: February 2013

AbstractThe two-dimensional free-boundary problem describing steady gravity waves with vorticity on water of finite depth is considered. It is proved that no small-amplitude waves are supported by a horizontal shear flow whose free surface is still, that is, it is stagnant in a coordinate frame such that the flow is time-independent in it. The class of vorticity distributions for which such flows exist includes all positive constant distributions, as well as linear and quadratic ones with arbitrary positive coefficients.
Nonlinear resonant interactions of interfacial waves in horizontal stratified channel flows
Authors: Campbell Bryce K. , Liu Yuming 
Published: February 2013

AbstractWe consider the problem of nonlinear resonant interactions of interfacial waves with the presence of a linear interfacial instability in an inviscid two-fluid stratified flow through a horizontal channel. The resonant triad consists of a (linearly) unstable wave and two stable waves, one of which has a wavelength that can be much longer than that of the unstable component. Of special interest is the development of the long wave by energy transfer from the base flow due to the coupled effect of nonlinear resonance and interfacial instability. By use of the method of multiple scales, we derive the interaction equations which govern the time evolution of the amplitudes of the interacting waves including the effect of interfacial instability. The solution of the evolution equations shows that depending on the flow conditions, the (stable) long wave can achieve a bi-exponential growth rate through the resonant interaction with the unstable wave. Moreover, the unstable wave can grow unboundedly even when the nonlinear self-interaction effect is included, as do the stable waves in the associated resonant triad. For the verification of the theoretical analysis and the practical application involving a broadbanded spectrum of waves, we develop an effective direct simulation method, based on a high-order pseudo-spectral approach, which accounts for nonlinear interactions of interfacial waves up to an arbitrary high order. The direct numerical simulations compare well with the theoretical analysis for all of the characteristic flows considered, and agree qualitatively with the experimental observation of slug development near the entrance of two-phase flow into a pipe.
Density difference-driven segregation in a dense granular flow
Authors: Tripathi Anurag , Khakhar D. V. 
Published: February 2013

AbstractWe consider the segregation of spheres of equal size and different density flowing over an inclined plane, theoretically and computationally by means of distinct element method (DEM) simulations. In the first part of the work, we study the settling of a single higher-density particle in the flow of otherwise identical particles. We show that the motion of the high-density tracer particle can be understood in terms of the buoyancy and drag forces acting on it. The buoyancy force is given by Archimedes principle, with an effective volume associated with the particle, which depends upon the local packing fraction, $\phi $. The buoyancy arises primarily from normal forces acting on the particle, and tangential forces have a negligible contribution. The drag force on a sphere of diameter $d$ sinking with a velocity $v$ in a granular medium of apparent viscosity $\eta $ is given by a modified Stokes law, ${F}_{d} = c\pi \eta dv$. The coefficient ($c$) is found to decrease with packing fraction. In the second part of the work, we consider the case of binary granular mixtures of particles of the same size but differing in density. A continuum model for segregation is presented, based on the single-particle results. The number fraction profile for the heavy particles at equilibrium is obtained in terms of the effective temperature, defined by a fluctuation–dissipation relation. The model predicts the equilibrium number fraction profiles at different inclination angles and for different mass ratios of the particles, which match the DEM results very well. Finally, a complete model for the theoretical prediction of the flow and number fraction profiles for a mixture of particles of different density is presented, which combines the segregation model with a model for the rheology of mixtures. The model predictions agree quite well with the simulation results.
Harvey, by Hercules! The Hero of the Blood’s Circulation
Authors: O’ROURKE BOYLE MARJORIE 
Published: February 2013

AbstractThis article continues the analyses inMedical History52 (2008), 73–90, 365–86 of William Harvey’s self-understanding as the philosopher and discoverer of the blood’s circulation. Harvey brilliantly and subversively assumed the persona of the mythological Hercules to embody his own anatomical labour inDe motu cordis et sanguinis(1628). He reprised the role in self-defence against accusations in the College of Physicians, London, of his breach of faith with medical tradition. Harvey sought to usurp the medical epithet ‘a second Hercules’ by reforming humanist dependence on ancient texts as authoritative medicine. A knowledge of the theory and practice of Renaissance humanism discloses his identification with the Herculean labour of cleansing the Augean stable. He employed anatomical demonstration against Galen’s porous cardiac septum, which admitted blood across the ventricles. Harvey’s oathmeherculeswore against Galen’sDiato assert the necessity of opening an alternate route for the blood flow. His Herculean labour was to dam the cardiac septum and divert the blood flow into a continuous channel through the arteries and veins. His circulation of the blood also imitated Hercules’ successful dependence on the force of the water flow to flush the Augean stable. Harvey’scopiadid not denote a quantitative amount but a powerful supply. Harvey aspired to be, like Hercules, immortal, a term which the College belatedly acknowledged. This cultural analysis exposes Harvey’s professional issues and personal ambitions, so to promote a fuller understanding of his historic role in medical discovery.
‘Searching for the People in Charge’: Appraising the 1983 Griffiths NHS Management Inquiry
Authors: GORSKY MARTIN 
Published: February 2013

AbstractThis is the first of two related articles in the present volume which examine the recent history of health services management using the case of the British National Health Service (NHS). In the historiography of the NHS the 1980s is widely seen as a watershed, when public policy first sought to introduce market disciplines into its operation. Administrative and managerial reforms were central to this process, and their origins and impact have been the subject of continuing debate. This article examines and evaluates one of the key events in this history, the Griffiths NHS Inquiry of 1983, which put in place the principles of ‘general management’ in the NHS. Drawing on both documentary records and oral evidence it offers fresh perspectives on the reasons why the Conservative government embarked on this reform, on the workings of the inquiry team under the leadership of the businessman Roy Griffiths, and on the uneven course of the implementation of his recommendations. While its initial impact arguably did not meet the expectations of its supporters, it is suggested that several of Griffiths’ key concerns have grown, not diminished, in importance as aspects of subsequent health politics. These include: the need for clinician involvement in NHS management and financing; the conundrum of how to depoliticise the central direction of the service while retaining political accountability; the desirability of measuring and improving performance; and the question of how best to incorporate the wishes of patients and public in the decision-making arena.