bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual observations of the flow around a half-submerged oscillating sphere
Authors: Taneda Sadatoshi
Published: April 2006

Visual observations are made on the flow around a sphere which is half-submerged in still water and forced to oscillate up and down. It is found that three kinds of steady flows are generated in the water: the surface flow, the undersurface flow, and the vertical jet flow. The surface flow is produced in the very thin layer on the water surface. The undersurface flow is induced in the thick layer under the water surface. The vertical jet flow is ejected vertically from the bottom of the sphere. The surface flow and the undersurface flow are produced only when petal-shaped waves are generated on the water surface. The velocity of the undersurface flow is much smaller than that of the surface flow.
The analysis and modelling of dilatational terms in compressible turbulence
Authors: Sarkar S. , Erlebacher G. , Hussaini M. Y. , Kreiss H. O.
Published: April 2006

It is shown that the dilatational terms that need to be modelled in compressible turbulence include not only the pressure-dilatation term but also another term - the compressible dissipation. The nature of the compressible velocity field, which generates these dilatational terms, is explored by asymptotic analysis of the compressible Navier-Stokes equations in the case of homogeneous turbulence. The lowest-order equations for the compressible field are solved and explicit expressions for some of the associated one-point moments are obtained. For low Mach numbers, the compressible mode has a fast timescale relative to the incompressible mode. Therefore, it is proposed that, in moderate Mach number homogeneous turbulence, the compressible component of the turbulence is in quasi-equilibrium with respect to the incompressible turbulence. A non-dimensional parameter which characterizes this equilibrium structure of the compressible mode is identified. Direct numerical simulations (DNS) of isotropic, compressible turbulence are performed, and their results are found to be in agreement with the theoretical analysis. A model for the compressible dissipation is proposed; the model is based on the asymptotic analysis and the direct numerical simulations. This model is calibrated with reference to the DNS results regarding the influence of compressibility on the decay rate of isotropic turbulence. An application of the proposed model to the compressible mixing layer has shown that the model is able to predict the dramatically reduced growth rate of the compressible mixing layer.
Lubricated pipelining: stability of core–annular flow. Part 4. Ginzburg–Landau equations
Authors: Chen Kangping , Joseph Daniel D.
Published: April 2006

Nonlinear stability of core-annular flow near points of the neutral curves at which perfect core-annular flow loses stability is studied using Ginzburg-Landau equations. Most of the core-annular flows are always unstable. Therefore the set of core-annular flows having critical Reynolds numbers is small, so that the set of flows for which our analysis applies is small. An efficient and accurate algorithm for computing all the coefficients of the Ginzburg-Landau equation is implemented. The nonlinear flows seen in the experiments do not appear to be modulations of monochromatic waves, and we see no evidence for soliton-like structures. We explore the bifurcation structure of finite-amplitude monochromatic waves at criticality. The bifurcation theory is consistent with observations in some of the flow cases to which it applies and is not inconsistent in the other cases.
Numerical simulations of three-dimensional thermal convection in a fluid with strongly temperature-dependent viscosity
Authors: Ogawa Masaki , Schubert Gerald , Zebib Abdelfattah
Published: April 2006

Numerical calculations are presented for the steady three-dimensional structure of thermal convection of a fluid with strongly temperature-dependent viscosity in a bottom-heated rectangular box. Viscosity is assumed to depend on temperature T as exp (− ET), where E is a constant; viscosity variations across the box r (= exp (E)) as large as 105 are considered. A stagnant layer or lid of highly viscous fluid develops in the uppermost coldest part of the top cold thermal boundary layer when r > rc1, where r = rc1 ≡ 1.18 × 103Rt0.309 and Rt is the Rayleigh number based on the viscosity at the top boundary. Three-dimensional convection occurs in a rectangular pattern beneath this stagnant lid. The planform consists of hot upwelling plumes at or near the centre of a rectangle, sheets of cold sinking fluid on the four sides, and cold sinking plume concentrations immersed in the sheets. A stagnant lid does not develop, i.e. convection involves all of the fluid in the box when r < rc1. The whole-layer mode of convection occurs in a three-dimensional bimodal pattern when r > rc2 = 3.84 × 106Rt−1.35. The planform of the convection is rectangular with the coldest parts of the sinking fluid and the hottest part of the upwelling fluid occurring as plumes at the four corners and at the centre of the rectangle, respectively. Both hot uprising plumes and cold sinking plumes have sheet-like extensions, which become more well-developed as r increases. The whole-layer mode of convection occurs as two-dimensional rolls when r < min (rc1, rc2). The Nusselt number Nu depends on the viscosity at the top surface more strongly in the regime of whole-layer convection than in the regime of stagnant-lid convection. In the whole-layer convective regime, Nu depends more strongly on the viscosity at the top surface than on the viscosity at the bottom boundary.
A line sink in a rotating stratified fluid
Authors: Mcdonald N. Robb , Imberger Jörg
Published: April 2006

The two-dimensional flow of an unbounded rotating stratified fluid towards a link sink is studied. The initial-value problem of suddenly initiating the sink flow is solved in Laplace space for a non-diffusive, inviscid fluid using the linearized Boussinesq equations. The solution shows that the sink flow is established by inertio–gravity waves radiated from the sink and that the initial development of the flow depends critically on the ratio of the inertial frequency, f, to the buoyancy frequency, N. For f < N the flow collapses to a horizontal withdrawal layer structure. The final steady state resembles potential flow in which the vertical axis is shrunk by a factor of f/N with a superimposed azimuthal velocity. Viscous, diffusive and nonlinear effects are studied using scaling analysis. A classification scheme based on two parameters delineating various force balance regimes and giving the corresponding withdrawal layer thicknesses is presented. The results show that under certain conditions rotation may cause a thicker withdrawal layer than would be observed if there were no rotation.
The free compressible viscous vortex
Authors: Colonius Tim , Lele Sanjiva K. , Moin Parviz
Published: April 2006

The effects of compressibility on free (unsteady) viscous heat-conducting vortices are investigated. Analytical solutions are found in the limit of large, but finite, Reynolds number, and small, but finite, Mach number. The analysis shows that the spreading of the vortex causes a radial flow. This flow is given by the solution of an ordinary differential equation (valid for any Mach number), which gives the dependence of the radial velocity on the tangential velocity, density, and temperature profiles of the vortex; estimates of the radial velocity found by solving this equation are found to be in good agreement with numerical solutions of the full equations. The experiments of Mandella (1987) also report a radial flow in the vortex, but their estimates are much larger than the analytical predictions, and it is found that the flow inferred from the iexperiments violates the Second Law of Thermodynamics for two-dimensional axisymmetric flow. It is speculated that three-dimensionality is the cause of this discrepancy. To obtain detailed analytical solutions, the equations for the viscous evolution are expanded in powers of Mach number, M. Solutions valid to O(M2), are discussed for vortices with finite circulation. Two specific initial conditions – vortices with initially uniform entropy and with initially uniform density – are analysed in detail. It is shown that swirling axisymmetric compressible flows generate negative radial velocities far from the vortex core owing to viscous effects, regardless of the initial distributions of vorticity, density and entropy.
Numerical simulations of the quasi-stationary stage of ripple excitation by steep gravity–capillary waves
Authors: Ruvinsky K. D. , Feldstein F. I. , Freidman G. I.
Published: April 2006

The dependence of the parameters of capillary–gravity ripples on the characteristics of the steep surface waves (in the range 4–20 cm) that excite them is found. For steep 4–6 cm waves calculations are performed on the basis of the improved first Stokes method. Qualitative coincidence of the theoretical results with the experimental data is shown. For 7–20 cm waves the results are obtained by the multiple-scale method where the large-scale motion and the driving force for the ripple are found by the improved first Stokes method. Qualitative agreement between theory and experiment in this wavelength range is achieved.
The release of air bubbles from an underwater nozzle
Authors: Longuet-Higgins Michael S. , Kerman Bryan R. , Lunde Knud
Published: April 2006

Air bubbles released from an underwater nozzle emit an acoustical pulse which is of interest both for the study of bubble detachment and for elucidating the mechanism of sound generation by a newly formed bubble. In this paper we calculate theoretically the sequence of bubble shapes from a given nozzle and show that there is for each nozzle a bubble of maximum volume vmax Assuming that the bubble becomes detached at its ‘neck’, and that the volume of the detached bubble equals the volume V* of the undetached bubble above its ’neck’, we determine for each nozzle diameter D an acoustic frequency f* corresponding to 'slow’ bubble release.

Experiments show that the acoustic frequency, hence the bubble size, depends on the rate of air.flow to the bubble, but for slow rates of flow the frequency f is very close to the theoretical frequency f*.

High-speed photographs suggest that when the bubble pinches off. the limiting form of the surface is almost a cone. This is accounted for by assuming a line sink along the axis of symmetry. Immediately following pinch-off there is evidence of the formation of an axial jet going upwards into the bubble. This may play a part in stimulating the emission of sound.
Weir flows and waterfalls
Authors: Dias Frédéric , Tuck E. O.
Published: April 2006

Two-dimensional free-surface flows, which are uniform far upstream in a channel of finite depth that ends suddenly, are computed numerically. The ending is in the form of a vertical wall, which may force the flow upward before it falls down forever as a jet under the effect of gravity. Both subcritical and supercritical solutions are presented. The subcritical solutions are a one-parameter family of solutions, the single parameter being the ratio between the height of the wall and the height of the uniform flow far upstream. On the other hand, the supercritical solutions are a two-parameter family of solutions, the second parameter being the Froude number. Moreover, for some combinations of the parameters, it is shown that the solution is not unique.
The multifractal nature of turbulent energy dissipation
Authors: Meneveau Charles , Sreenivasan K. R.
Published: April 2006

The intermittency of the rate of turbulent energy dissipation ε is investigated experimentally, with special emphasis on its scale-similar facets. This is done using a general formulation in terms of multifractals, and by interpreting measurements in that light. The concept of multiplicative processes in turbulence is (heuristically) shown to lead to multifractal distributions, whose formalism is described in some detail. To prepare proper ground for the interpretation of experimental results, a variety of cascade models is reviewed and their physical contents are analysed qualitatively. Point-probe measurements of ε are made in several laboratory flows and in the atmospheric surface layer, using Taylor's frozen-flow hypothesis. The multifractal spectrum f(α) of ε is measured using different averaging techniques, and the results are shown to be in essential agreement among themselves and with our earlier ones. Also, long data sets obtained in two laboratory flows are used to obtain the latent part of the f(α) curve, confirming Mandelbrot's idea that it can in principle be obtained from linear cuts through a three-dimensional distribution. The tails of distributions of box-averaged dissipation are found to be of the square-root exponential type, and the implications of this finding for the f(α) distribution are discussed. A comparison of the results to a variety of cascade models shows that binomial models give the simplest possible mechanism that reproduces most of the observations. Generalizations to multinomial models are discussed.
Trapped modes in open channels
Authors: Evans D. V. , Linton C. M.
Published: April 2006

Trapped or edge-wave modes are well-known in linear water-wave theory. They occur at discrete frequencies below a certain cutoff frequency and consist of local oscillations trapped near a long horizontal submerged body in finite or infinite depth or over a sloping beach. Less well known is the existence of trapped modes in certain problems in acoustics where the governing equation is the Helmholtz equation. Jones (1953) has proved the existence of such modes which correspond to point-eigenvalues of the spectrum of the differential operator satisfying certain boundary conditions in a semi-infinite region. In this paper we describe a constructive method for determining point-eigenvalues or trapped-mode frequencies in two specific problems in which the two-imensional Helmholtz equation is satisfied.

The problems arise from a consideration of the fluid motion in a long narrow wave tank with a free water surface which contains a vertical cylinder of uniform horizontal cross-section extending throughout the water depth. Separation of the depth dependence results in Helmholtz's equation with Neumann boundary conditions. By seeking solutions which are antisymmetric with respect to the centreline of the channel, trapped modes are constructed for the case of a cylinder of rectangular cross-section placed symmetrically in the centre of the channel and also for the case of a symmetric rectangular indentation in the tank walls. These problems do not appear to be covered directly by Jones’ theory and whilst the method described provides convincing numerical evidence, it falls short of a rigorous existence proof. Extensions to other purely acoustic problems having no water-wave interpretation, including problems which are covered by the general theory of Jones, are also discussed.
Two-layer geostrophic vortex dynamics. Part 2. Alignment and two-layer V-states
Authors: Polvani L. M.
Published: April 2006

The process of alignment, a new fundamental interaction between vortices in a stratified and rapidly rotating fluid, is defined and studied in detail in the context of the two-layer quasi-geostrophic model. Alignment occurs when two vortices in different density layers coalesce by reducing their horizontal separation. It is found that only vortices whose radii are comparable with or larger than the Rossby deformation radius can align. In the same way as the merger process (in a single two-dimensional layer) is related to the reverse energy cascade of two-dimensional turbulence, geostrophic potential vorticity alignment is related the barotropic-to-baroclinic energy cascade of geostrophic turbulence in two layers. It is also shown how alignment is intimately connected with the existence of two-layer doubly connected geostrophic potential vorticity equilibria (V-states), for which the analysis of the geometry of the stream function in the corotating frame is found to be a crucial diagnostic. The finite-area analogues of the hetons of Hogg & Stommel (1985) are also determined: they consist of a propagating pair of opposite-signed potential vorticity patches located in different layers.
An investigation of transition to turbulence in bounded oscillatory Stokes flows Part 1. Experiments
Authors: Akhavan R. , Kamm R. D. , Shapiro A. H.
Published: April 2006

Experimental results on flow-field statistics are presented for turbulent oscillatory flow in a circular pipe for the range of Reynolds numbers Reδ = U0δ/ν (U0 = amplitude of cross-sectional mean velocity, δ = (2ν/ω)½) = Stokes layer thickness) from 550 to 2000 and Stokes parameters Λ = R/δ (R = radius of the pipe) from 5 to 10. Axial and radial velocity components were measured simultaneously using a two-colour laser-Doppler anemometer, providing information on ensemble-averaged velocity profiles as well as various turbulence statistics for different phases during the cycle. In all flows studied, turbulence appeared explosively towards the end of the acceleration phase of the cycle and was sustained throughout the deceleration phase. During the turbulent portion of the cycle, production of turbulence was restricted to the wall region of the pipe and was the result of turbulent bursts. The statistics of the resulting turbulent flow showed a great deal of similarity to results for steady turbulent pipe flows; in particular the three-layer description of the flow consisting of a viscous sublayer, a logarithmic layer (with von Kármán constant = 0.4) and an outer wake could be identified at each phase if the corresponding ensemble-averaged wall-friction velocities were used for normalization. Consideration of similarity laws for these flows reveals that the existence of a logarithmic layer is a dimensional necessity whenever at least two of the scales R, u*/ω and ν/u* are widely separated; with the exact structure of the flow being dependent upon the parameters u*/Rω and u2*/ων. During the initial part of the acceleration phase, production of turbulence as well as turbulent Reynolds stresses were reduced to very low levels and the velocity profiles were in agreement with laminar theory. Nevertheless, the fluctuations retained a small but finite energy. In Part 2 of this paper, the major features observed in these experiments are used as a guideline, in conjunction with direct numerical simulations of the ‘perturbed’ Navier–Stokes equations for oscillatory flow in a channel, to identify the nature of the instability that is most likely to be responsible for transition in this class of flows.
Inviscid spatial stability of a three-dimensional compressible mixing layer
Authors: Grosch C. E. , Jackson T. L.
Published: April 2006

We present the results of a study of the inviscid spatial stability of a parallel three-dimensional compressible mixing layer. The parameters of this study are the Mach number of the fast stream, the ratio of the speed of the slow stream to that of the fast stream, the ratio of the temperature of the slow stream to that of the fast stream, the direction of the crossflow in the fast stream, the frequency, and the direction of propagation of the disturbance wave. Stability characteristics of the flow as a function of these parameters are given. Certain theoretical results are presented which show the interrelations between these parameters and their effects on the stability characteristics. In particular, the three-dimensional stability problem for a three-dimensional mixing layer at Mach zero can be transformed to a two-dimensional stability problem for an equivalent two-dimensional mean flow. There exists a one-parameter family of curves such that for any given direction of mean flow and of wave propagation one can apply this transformation and obtain the growth rate from the universal curves. For supersonic couvective Mach numbers, certain combinations of crossflow angle and propagation angle of the disturbance can increase the growth rates by a factor of about two. and thus enhance mixing.
Using Solution-Focused Questioning to Facilitate the Process of Change in Cognitive Behavioural Therapy for Food Neophobia in Adults
Authors: Postma Kirstine , Kumar Rao Nasa Sanjay
Published: April 2006

Food neophobia is a specific phobia of trying new foods. Its treatment in adults has been rarely described. The only paper that related a therapeutic intervention for food neophobia in adults reported a time-consuming effort for both clients and several staff involved. This paper provides a case example of using solution focused brief therapy questioning techniques to facilitate the process of change in a young adult with this diagnosis. It aims to explain how solution focused techniques can be used and in what way those techniques differ from more traditional cognitive-behavioural therapy approaches.
Diagnosing and Remedying the Failings of Official Participation Schemes: The CLEAR Framework
Authors: Lowndes Vivien , Pratchett Lawrence , Stoker Gerry
Published: April 2006

Drawing on extensive research, the article proposes a diagnostic tool for assessing official schemes to encourage participation and discusses remedial measures that might be taken to tackle problems. According to the CLEAR framework, people participate when they can: when they have the resources necessary to make their argument. People participate when they feel part of something: they like to participate because it is central to their sense of identity. They participate when they are enabled to do so by an infrastructure of civic networks and organisations. People participate when they are directly asked for their opinion. Finally, people participate when they experience the system they are seeking to influence as responsive.
Macrovascular Contribution in Activation Patterns of Working Memory
Authors: Tomasi Dardo G , Caparelli Elisabeth C
Published: April 2006

Brain activation maps of blood oxygenation level dependent (BOLD) signals during functional magnetic resonance imaging (fMRI) are sensitive to unwanted contributions from large vessels. Most BOLD-fMRI studies are based on a stimulus-correlated modulation of the MRI signal amplitude that is sensitive to desired microvascular effects and unwanted macrovascular effects. Aiming to suppress macrovascular effects in activation patterns, this BOLD-fMRI study evaluates brain activation during a verbal working memory task (2-back) in healthy volunteers ( n =18) using the amplitude and phase components of the MRI signal. The use of the first time point as a phase reference allowed us to eliminate phase wrapping artifacts and increase the statistical power of ‘phase’ activation, and this information was used to filter out voxels with significant macrovascular (i.e., draining and pial veins) contribution in ‘amplitude’ activation patterns. Across subjects, the task produced large modulations of the relative phase in the occipital, dorsolateral prefrontal, and parietal cortices, suggesting a common distribution of draining veins in these regions across subjects, and in the rostral frontal cortex, probably associated to stimulus-correlated motion of the head. The phase filtering method partially suppressed BOLD responses in the superior and lateral prefrontal, parietal, and occipital cortices; therefore the commonly reported brain activation in these cortices during working memory tasks may include significant macrovascular contributions. This study suggests that the phase information embedded in the MRI signal can be used to suppress unwanted macrovascular contributions in fMRI studies.
Development of three-dimensional photonic-crystal waveguides at optical-communication wavelengths
Authors: Imada Masahiro , Lee Lye Hoe , Okano Makoto , Kawashima Shoichi , Noda Susumu
Published: April 2006

Photonic crystals have a photonic band gap (PBG) in which light propagation and emission is prohibited. In particular, three-dimensional (3D) photonic crystals have a complete PBG in all directions, which might allow the complete control of light emission and propagation in devices. Here, we report the first demonstration of light propagation in a 3D photonic-crystal waveguide at optical communication wavelengths. A line defect is introduced into a 3D photonic crystal composed of nine stacked layers, having a complete PBG in the 1.55μm wavelength region. Light incident on the waveguide edge successfully propagates along the line-defect waveguide. The propagation characteristics agree with the calculated photonic band diagram of the structure. The calculated results indicate that lossless propagation becomes possible by increasing the number of layers in the device. These results are an important step toward the realization of multifunctional 3D photonic chips integrated within a small region.
Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems
Authors: Wacker Michael , Feldman Mario F. , Callewaert Nico , Kowarik Michael , Clarke Bradley R. , Pohl Nicola L. , Hernandez Marcela , Vines Enrique D. , Valvano Miguel A. , Whitfield Chris , Aebi Markus
Published: April 2006

The PglB oligosaccharyltransferase (OTase) of
Campylobacter jejuni
can be functionally expressed in
Escherichia coli
, and its relaxed oligosaccharide substrate specificity allows the transfer of different glycans from the lipid carrier undecaprenyl pyrophosphate to an acceptor protein. To investigate the substrate specificity of PglB, we tested the transfer of a set of lipid-linked polysaccharides in
E. coli
and
Salmonella enterica
serovar Typhimurium. A hexose linked to the C-6 of the monosaccharide at the reducing end did not inhibit the transfer of the O antigen to the acceptor protein. However, PglB required an acetamido group at the C-2. A model for the mechanism of PglB involving this functional group was proposed. Previous experiments have shown that eukaryotic OTases have the same requirement, suggesting that eukaryotic and prokaryotic OTases catalyze the transfer of oligosaccharides by a conserved mechanism. Moreover, we demonstrated the functional transfer of the
C. jejuni
glycosylation system into
S. enterica
. The elucidation of the mechanism of action and the substrate specificity of PglB represents the foundation for engineering glycoproteins that will have an impact on biotechnology.
Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia
Authors: Åberg Karolina , Saetre Peter , Jareborg Niclas , Jazin Elena
Published: April 2006

The quaking viable mouse mutation (qk
v
) is a deletion including the 5′ regulatory region of the quaking gene (
Qki
), which causes body tremor and severe dysmyelination in mouse. The function of the human quaking gene, called quaking homolog KH domain RNA-binding (mouse) (
QKI
), is not well known. We have previously shown that
QKI
is a new candidate gene for schizophrenia. Here we show that human
QKI
mRNA levels can account for a high proportion (47%) of normal interindividual mRNA expression variation (and covariation) of six oligodendrocyte-related genes (
PLP1
,
MAG
,
MBP
,
TF
,
SOX10
, and
CDKN1B
) in 55 human brain autopsy samples from individuals without psychiatric diagnoses. In addition, the tightly coexpressed myelin-related genes (
PLP1
,
MAG
, and
TF
) have decreased mRNA levels in 55 schizophrenic patients, as compared with 55 control individuals, and most of this difference (68–96%) can be explained by variation in the relative mRNA levels of
QKI-7kb
, the same
QKI
splice variant previously shown to be down-regulated in patients with schizophrenia. Taken together, our results suggest that QKI levels may regulate oligodendrocyte differentiation and maturation in human brain, in a similar way as in mouse. Moreover, we hypothesize that previously observed decreased activity of myelin-related genes in schizophrenia might be caused by disturbed
QKI
splicing.
Soy Protein Infant Formulae and Follow‐On Formulae
Authors:   ESPGHAN Committee on Nutrition:, Agostoni Carlo , Axelsson Irene , Goulet Olivier , Koletzko Berthold , Michaelsen Kim Fleischerm , Puntis John , Rieu Daniel , Rigo Jacques , Shamir Raanan , Szajewska Hania , Turck Dominique
Published: April 2006

This comment by the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) Committee on Nutrition summarizes available information on the composition and use of soy protein formulae as substitutes for breastfeeding and cows' milk protein formulae as well as on their suitability and safety for supporting adequate growth and development in infants. Soy is a source of protein that is inferior to cows' milk, with a lower digestibility and bioavailability as well as a lower methionine content. For soy protein infant formulae, only protein isolates can be used, and minimum protein content required in the current European Union legislation is higher than that of cows' milk protein infant formulae (2.25 g/100 kcal vs. 1.8 g/100kcal). Soy protein formulae can be used for feeding term infants, but they have no nutritional advantage over cows' milk protein formulae and contain high concentrations of phytate, aluminum, and phytoestrogens (isoflavones), which might have untoward effects. There are no data to support the use of soy protein formulae in preterm infants. Indications for soy protein formulae include severe persistent lactose intolerance, galactosemia, and ethical considerations (e.g., vegan concepts). Soy protein formulae have no role in the prevention of allergic diseases and should not be used in infants with food allergy during the first 6 months of life. If soy protein formulae are considered for therapeutic use in food allergy after the age of 6 months because of their lower cost and better acceptance, tolerance to soy protein should first be established byclinical challenge. There is no evidence supporting the use of soy protein formulae for the prevention or management of infantile colic, regurgitation, or prolonged crying.
Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy
Authors: Xu Jing , Plaxco Kevin W. , Allen S. James
Published: April 2006

Biological polymers are expected to exhibit functionally relevant, global, and subglobal collective modes in the terahertz (THz) frequency range (i.e., picosecond timescale). In an effort to monitor these collective motions, we have experimentally determined the absorption spectrum of solvated bovine serum albumin (BSA) from 0.3 to 3.72 THz (10–124 cm−1). We successfully extract the terahertz molar absorption of the solvated BSA from the much stronger attenuation of water and observe in the solvated protein a dense, overlapping spectrum of vibrational modes that increases monotonically with increasing frequency. We see no evidence of distinct, strong, spectral features, suggesting that no specific collective vibrations dominate the protein's spectrum of motions, consistent with the predictions of molecular dynamics simulations and normal mode analyses of a range of small proteins. The shape of the observed spectrum resembles the ideal quadratic spectral density expected for a disordered ionic solid, indicating that the terahertz normal mode density of the solvated BSA may be modeled, to first order, as that of a three‐dimensional elastic nanoparticle with an aperiodic charge distribution. Nevertheless, there are important detailed departures from that of a disordered inorganic solid or the normal mode densities predicted for several smaller proteins. These departures are presumably the spectral features arising from the unique molecular details of the solvated BSA. The techniques used here and measurements have the potential to experimentally confront theoretical calculations on a frequency scale that is important for macromolecular motions in a biologically relevant water environment.
Ligand binding by TPR domains
Authors: Cortajarena Aitziber L. , Regan Lynne
Published: April 2006

Tetratricopeptide repeat (TPR) domains bind specific peptide ligands and are thought to mediate protein–protein interactions in a variety of biological systems. Here we compare peptide ligand‐binding by several different TPR domains. We present specific examples that demonstrate that TPR domains typically undergo little or no structural rearrangement upon ligand binding. Our data suggest that, contrary to a recent proposal, coupled folding and binding is not the common mechanism of ligand recognition by TPR domains.
Betting the Future Online
Authors: Williams Leighton Vaughan
Published: April 2006

The Internet has brought, among other things, the online betting exchange. From desks in the City or from laptops on sunny beaches, those in the know or out of it can place bets with each other on anything under the sun, whether likely—Australia beating England at cricket—or the reverse. If you have a hunch that a genetically engineered Tyrannosaur will wander down Oxford Street next year, and if you want to put money on it, Internet betting exchanges will find someone to accommodate you. Leighton Vaughan Williams explains how a simple change in tax regime has brought something other than just a more efficient gambling system. It has created a strangely accurate way of foretelling the future.
The Lost Gamblers
Authors: Griffiths Mark
Published: April 2006

For some, gambling is a harmless pleasure. For others it is a wrecker of lives. Charities such as Gamblers Anonymous (gamblersanonymous.org.uk) and Gamcare (Gamcare.org.uk) exist to help such people; but why do they find themselves addicted to gambling and unable to resist its allure? Gambling behaviour is complex, yet most psychological research has confined itself to narrow areas of specialisation. Dr Mark Griffiths tells us that a more integrated approach is needed to understand the power of the gamble.
Who Wins the Football?
Authors: Goddard John
Published: April 2006

Portsmouth have dumped their manager—will it change their results? Chelsea are on a winning streak—does it mean anything? Media pundits and sports fans—and punters—devote time and energy to speculation about who will win Saturday's beautiful game. The discussions—in pubs, newspapers and dressing rooms—are usually based on subjective opinion, or evidence that is at best partial or impressionistic. Can statisticians do better? John Goddard offers a large-scale analysis of patterns in English league results from the past 35 football seasons—new managers, winning and losing streaks, home advantages and all.
Stakes and Chips
Authors: Johnson Oliver
Published: April 2006

Gambling has provided centuries of inspiration to probabilists and statisticians. The process continues. There also exist fundamental links between betting and a newer subject, Information Theory, which began with Claude Shannon and his ground-breaking 1948 paper A Mathematical Theory of Communication.

It is a result which arises very naturally. A successful gambler and a successful data compression algorithm must both accurately estimate probability distributions. There are practical results as well as theoretical: Shannon and colleagues, including the legendary gambler and mathematician Edward Thorp, actually attempted to apply results from information theory in Las Vegas casinos and stock market transactions. Oliver Johnson examines the connections.
Career Story: The Importance of being ERNIE
Authors: Shirley Stephanie
Published: April 2006

ERNIE is the Electronic Random Number Indicator Equipment that caused huge interest in 1957 when it began selecting prize-winners for the new Premium Bonds, the first government-sponsored gamble in Britain in modern times. Stephanie Shirley was a young statistician working on ERNIE. Today, as Steve Shirley or Dame Stephanie, she is one of the wealthiest women in Britain—not through winning on Premium Bonds herself, but through the pioneering software company she formed which, for the first time, gave female-friendly employment to women programmers (and statisticians) who had children and dependants at home to care for. She is now a major philanthropist and a driving force for research into the social effects of the Internet and into autism. She has given more than £50 million to charities in those fields. Julian Champkin interviews her.
Teach Statistics? You Bet!
Authors: Croucher John S.
Published: April 2006

The study of statistics has a reputation among students for being difficult, irrelevant, boring and an unwanted compulsory intrusion into their studies—and that reputation is sometimes deserved. But it does not have to be that way. John Croucher used sport and gambling to transform his lecture theatre, and turned the teaching of statistics into an astonishing Australian success story.
Comparative In Vitro Efficacies of Various Catheter Lock Solutions
Authors: Sherertz Robert J. , Boger Michael S. , Collins Casey A. , Mason Lori , Raad Issam I.
Published: April 2006

MEDTA (minocycline-edetate calcium disodium), taurolidine (2%)-polyvinylpyrolidine (5%) (T/PVP), and ethanol as potential catheter lock solutions have a unique mechanism of action, broad-spectrum activity, and anticoagulant properties. Traditional lock solutions minocycline (M), rifampin (R), ciprofloxacin (C), and vancomycin, except pharmacologic concentrations of C and R and of M and R, were less effective than MEDTA and T/PVP.
Expansion and Diversification of Virus-Specific T Cells following Immunization of Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Individuals with a Recombinant Modified Vaccinia Virus Ankara/HIV-1 Gag Vaccine
Authors: Dorrell Lucy , Yang Hongbing , Ondondo Beatrice , Dong Tao , di Gleria Kati , Suttill Annie , Conlon Christopher , Brown Denise , Williams Patricia , Bowness Paul , Goonetilleke Nilu , Rostron Tim , Rowland-Jones Sarah , Hanke Tomáš , McMichael Andrew
Published: April 2006

Affordable therapeutic strategies that induce sustained control of human immunodeficiency virus type 1 (HIV-1) replication and are tailored to the developing world are urgently needed. Since CD8+and CD4+T cells are crucial to HIV-1 control, stimulation of potent cellular responses by therapeutic vaccination might be exploited to reduce antiretroviral drug exposure. However, therapeutic vaccines tested to date have shown modest immunogenicity. In this study, we performed a comprehensive analysis of the changes in virus-specific CD8+and CD4+T-cell responses occurring after vaccination of 16 HIV-1-infected individuals with a recombinant modified vaccinia virus Ankara-vectored vaccine expressing the consensus HIV-1 clade A Gag p24/p17 sequences and multiple CD8+T-cell epitopes during highly active antiretroviral therapy. We observed significant amplification and broadening of CD8+and CD4+gamma interferon responses to vaccine-derived epitopes in the vaccinees, without rebound viremia, but not in two unvaccinated controls followed simultaneously. Vaccine-driven CD8+T-cell expansions were also detected by tetramer reactivity, predominantly in the CD45RA−CCR7+or CD45RA−CCR7−compartments, and persisted for at least 1 year. Expansion was associated with a marked but transient up-regulation of CD38 and perforin within days of vaccination. Gag-specific CD8+and CD4+T-cell proliferation also increased postvaccination. These data suggest that immunization with MVA.HIVA is a feasible strategy to enhance potentially protective T-cell responses in individuals with chronic HIV-1 infection.
Comparison of Simian Immunodeficiency Virus SIVagmVer Replication and CD4
+
T-Cell Dynamics in Vervet and Sabaeus African Green Monkeys
Authors: Goldstein Simoy , Brown Charles R. , Ourmanov Ilnour , Pandrea Ivona , Buckler-White Alicia , Erb Christopher , Nandi Jayashree S. , Foster Gabriel J. , Autissier Patrick , Schmitz Jörn E. , Hirsch Vanessa M.
Published: April 2006

The simian immunodeficiency viruses (SIV) naturally infect a wide range of African primates, including African green monkeys (AGM). Despite moderate to high levels of plasma viremia in naturally infected AGM, infection is not associated with immunodeficiency. We recently reported that SIVagmVer90 isolated from a naturally infected vervet AGM induced AIDS following experimental inoculation of pigtailed macaques. The goal of the present study was to evaluate the replication of this isolate in two species of AGM, sabaeus monkeys (
Chlorocebus sabaeus
) and vervets (
C. pygerythrus
). Inoculation of sabaeus AGM with SIVagmVer90 resulted in low and variable primary and set-point viremia (<10
2
to 10
4
copies/ml). In contrast, inoculation of vervet AGM with either SIVagmVer90 or blood from a naturally infected vervet (Ver1) resulted in high primary viremia and moderate plateau levels, similar to the range seen in naturally infected vervets from this cohort. CD4
+
T cells remained stable throughout infection, even in AGM with persistent high viremia. Despite the lack of measurable lymphadenopathy, infection was associated with an increased number of Ki-67
+
T cells in lymph node biopsies, consistent with an early antiviral immune response. The preferential replication of SIVagmVer in vervet versus sabaeus AGM shows that it is critical to match AGM species and SIV strains for experimental models of natural SIV infection.
Receptor-Independent Infection of Murine Coronavirus: Analysis by Spinoculation
Authors: Watanabe Rie , Matsuyama Shutoku , Taguchi Fumihiro
Published: April 2006

A highly neurovirulent murine coronavirus JHMV (wild-type [wt] JHMV) is known to spread from cells infected via the murine coronavirus mouse hepatitis virus receptor (MHVR) to cells without MHVR (MHVR-independent infection), whereas a mutant virus isolated from wt JHMV, srr7, spread only in an MHVR-dependent fashion. These observations were obtained by the overlay of JHMV-infected cells onto receptor-negative cells that are otherwise resistant to wt JHMV infection. MHVR-independent infection is hypothetically thought to be attributed to a naturally occurring fusion activation of the wt JHMV S protein, which did not occur in the case of srr7. Attachment of S protein on cells without MHVR during the S-protein activation process seems to be a key condition. Thus, in the present study, we tried to see whether wt JHMV virions that are attached on MHVR-negative cells are able to infect those cells. In order to make virions attach to the cell surface without MHVR, we have used spinoculation, namely, the centrifugation of cells together with inoculated virus at 3,000 rpm for 2 h. This procedure forces viruses to attach to the cell surface, as revealed by quantitative estimation of attached virions by real-time PCR and also facilitated wt JHMV infection to MHVR-negative cells, but failed to do so for srr7. Virions of both wt and srr7 attached on MHVR-negative cells by spinoculation were facilitated for infection in the presence of a soluble form of MHVR that induces conformational changes of both wt and srr7. It was further revealed that wt JHMV S1, but not srr7, was released from the cell surface when S protein was expressed on cells. These observations support the hypothesis that attachment of the virion to MHVR-negative cells is a critical step and that a unique feature of wt JHMV S1 to be released from S2 in a naturally occurring event is involved in an MHVR-independent infection.
Molecular and Biological Characterization of Deformed Wing Virus of Honeybees (
Apis mellifera
L.)
Authors: Lanzi Gaetana , de Miranda Joachim R. , Boniotti Maria Beatrice , Cameron Craig E. , Lavazza Antonio , Capucci Lorenzo , Camazine Scott M. , Rossi Cesare
Published: April 2006

Deformed wing virus (DWV) of honeybees (
Apis mellifera
) is closely associated with characteristic wing deformities, abdominal bloating, paralysis, and rapid mortality of emerging adult bees. The virus was purified from diseased insects, and its genome was cloned and sequenced. The genomic RNA of DWV is 10,140 nucleotides in length and contains a single large open reading frame encoding a 328-kDa polyprotein. The coding sequence is flanked by a 1,144-nucleotide 5′ nontranslated leader sequence and a 317-nucleotide 3′ nontranslated region, followed by a poly(A) tail. The three major structural proteins, VP1 (44 kDa), VP2 (32 kDa), and VP3 (28 kDa), were identified, and their genes were mapped to the N-terminal section of the polyprotein. The C-terminal part of the polyprotein contains sequence motifs typical of well-characterized picornavirus nonstructural proteins: an RNA helicase, a chymotrypsin-like 3C protease, and an RNA-dependent RNA polymerase. The genome organization, capsid morphology, and sequence comparison data indicate that DWV is a member of the recently established genus
Iflavirus
.
Double-Stranded RNA Is Produced by Positive-Strand RNA Viruses and DNA Viruses but Not in Detectable Amounts by Negative-Strand RNA Viruses
Authors: Weber Friedemann , Wagner Valentina , Rasmussen Simon B. , Hartmann Rune , Paludan Søren R.
Published: April 2006

Double-stranded RNA (dsRNA) longer than 30 bp is a key activator of the innate immune response against viral infections. It is widely assumed that the generation of dsRNA during genome replication is a trait shared by all viruses. However, to our knowledge, no study exists in which the production of dsRNA by different viruses is systematically investigated. Here, we investigated the presence and localization of dsRNA in cells infected with a range of viruses, employing a dsRNA-specific antibody for immunofluorescence analysis. Our data revealed that, as predicted, significant amounts of dsRNA can be detected for viruses with a genome consisting of positive-strand RNA, dsRNA, or DNA. Surprisingly, however, no dsRNA signals were detected for negative-strand RNA viruses. Thus, dsRNA is indeed a general feature of most virus groups, but negative-strand RNA viruses appear to be an exception to that rule.
MAGNETIC SUSCEPTIBILITY OF COLLAPSED STARS IN HADRON AND QUARK PHASES
Authors: JIANG W. Z. , VAN GIAI N.
Published: April 2006

In this paper the formulae of magnetic susceptibility (MS) of charged particles are deduced in nonrelativistic and relativistic mean-field approximations in bulk matter. The analytic relativistic expression at high densities and strong fields, deduced for the de Hass–van Alphen (HVA) oscillation, shows that the oscillation frequency is proportional to the square of chemical potential and the reciprocal of the field, and is independent of the temperature. Numerical calculations are performed at finite temperatures and in a field range where the equation of state is not sensitive to the field. The nonoscillatory MS of the protoneutron star, which is dominated by the contributions of electrons (and light quarks, if deconfined) and is almost independent of the field, decreases as the protoneutron matter becomes denser. The numerical results for the HVA oscillation are also given. The oscillation amplitude becomes larger as the star becomes colder. We find that superposition of the HVA oscillations changes the oscillation properties drastically if the color deconfinement occurs at high densities.
BOUND ENERGY MASSES OF MESONS CONTAINING THE FOURTH GENERATION AND ISO-SINGLET QUARKS
Authors: IKHDAIR SAMEER M. , SEVER RAMAZAN
Published: April 2006

The fourth Standard Model (SM) family quarks and weak iso-singlet quarks predicted by E6GUT are considered. The spin-average of the pseudoscalar η4(n1S0) and vector ψ4(n3S1) quarkonium binding masses of the new mesons formed by the fourth Standard Model (SM) family and iso-singlet E6with their mixings to ordinary quarks are investigated. Further, the fine and hyperfine mass splittings of the these states are also calculated. We solved the Schrödinger equation with logarithmic and Martin potentials using the shifted large-N expansion technique. Our results are compared with other models to gauge the reliability of the predictions and point out differences.