bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional large-eddy motions and fine-scale activity in a plane turbulent wake
Authors: Ferré J. A. , Mumford J. C. , Savill A. M. , Giralt Francesc
Published: April 2006

A pattern recognition technique has been applied to simultaneously sampled multipoint hot-wire anemometry data obtained in the far wake of a circular cylinder. Data from both the streamwise fluctuating velocity field and the temperature field have been analysed employing a computer code that uses a correlation approach to automatically detect and ensemble average flow patterns and patterns for mean-square fluctuations. Statistical tests then allow the significance and contribution to the turbulence intensity of the detected structures to be evaluated. This procedure has been used to infer the three-dimensional topology of the double-roller eddies previously identified in the far-wake region and to relate these to the motions responsible for entrainment. It appears that the two types of motion are not independent, but are linked together, forming parts of horseshoe vortex structures which account for at least 40% of the total turbulence energy. These structures originate near the centre of the flow, may extend across the centreline and typically occur in groups of about three. The resulting picture of the flow dynamics is related to the conclusions drawn from similar data by other workers and a possible regeneration mechanism is presented. The addition to the code of a fine-scale activity indicator, the choice of which is discussed in some detail, has allowed the relationship between these energetic large-scale motions and smaller eddies to be investigated. It seems that the most intense fine-scale activity is associated with the vortical cores of the double-roller eddies. It is shown that this observation is consistent with the concepts of ‘isotropy’ and ‘spotiness’ of the dissipative scales. It also suggests that the horseshoe vortices loose energy both to their own secondary instabilities and to smaller scales resulting from the breakup of other highly strained large eddies.
On unsymmetrically impinging jets
Authors: Keller Joseph B.
Published: April 2006

Two impinging two-dimensional incompressible inviscid fluid jets of known widths and velocities produce two outgoing jets. The speeds of the outgoing jets are readily determined from the Bernoulli equation. Their two widths and two directions (four quantities) are related by conservation of mass and conservation of two components of momentum (three relations). Because these three conservation relations do not suffice to determine the four unknowns, Milne-Thomson (1968) states on p. 302 that ‘a unique solution is, in general, not possible’. He incorrectly attributes this indeterminateness to disregard of ‘the initial conditions from which this steady motion is supposed to arise’.
Turbulent dispersion of particles in self-generated homogeneous turbulence
Authors: Parthasarathy R. N. , Faeth G. M.
Published: April 2006

Turbulent dispersion of particles in their self-generated homogeneous turbulent field was studied both experimentally and theoretically. Measurements involved nearly monodisperse spherical glass particles (nominal diameters of 0.5, 1.0 and 2.0 mm) falling with uniform particle number fluxes in a nearly stagnant water bath. Particle Reynolds numbers based on terminal velocities were 38, 156, and 545 for the three particle sizes. The flows were dilute with particle volume fractions less than 0.01%. Measurements included particle motion calibrations, using motion-picture shadowgraphs; and streamwise and cross-stream mean and fluctuating particle velocities, using a phase-discriminating laser velocimeter. Liquid-phase properties were known from earlier work. Particle properties were predicted based on random-walk calculations using statistical time-series methods to simulate liquid velocities along the particle path.

Calibrations showed that particle drag properties were within 14% of estimates based on the standard drag correlation for spheres, however, the particles (particularly the 1.0 and 2.0 mm diameter particles) exhibited self-induced lateral motion even in motionless liquid due to eddy-shedding and irregularities of shape. Particle velocity fluctuations were primarily a function of the rate of dissipation of kinetic energy in the liquid since this variable controls liquid velocity fluctuations. Streamwise particle velocity fluctuations were much larger than cross-stream particle velocity fluctuations (2–5:1) largely due to varying terminal velocities caused by particle size variations. Cross-stream particle and liquid velocity fluctuations were comparable owing to the combined effects of turbulent dispersion and self-induced motion. Predicted mean and fluctuating particle velocities were in reasonably good agreement with the measurements after accounting for effects of particle size variations and self-induced motion. However, the theory must be extended to treat self-induced motion and to account for observations that this motion was affected by the turbulent environment.
Local baroclinic instability of flow over variable topography
Authors: Samelson R. M. , Pedlosky J.
Published: April 2006

Local baroclinic instability is studied in a two-layer quasi-geostrophic model. Variable meridional bottom slope controls the local supercriticality of a uniform zonal flow. Solutions are found by matching pressure, velocity, and upper-layer vorticity across longitudes where the bottom slope changes abruptly so as to destabilize the flow in a central interval of limited zonal extent. In contrast to previous results from heuristic models, an infinite number of modes exist for arbitrarily short intervals. For long intervals, modal growth rates and frequencies approach the numerical and WKB results for the most unstable mode. For intervals of length comparable to and smaller than the wavelengths of unstable waves in the homogeneous problem, the WKB results lose accuracy. The modes retain large growth rates (about half maximum) for intervals as short as the internal deformation radius. Evidently, the deformation radius and not the homogeneous instability determines the fundamental scale for local instability. Maximum amplitudes occur near the downstream edge of the unstable interval. Lower-layer amplitudes decay downstream more rapidly than upper-layer amplitudes. For short intervals, the instability couples motions with widely disparate horizontal scales in the upper and lower layers. Heat flux is more strictly confined than amplitude. Growth rates increase linearly with weak supercriticality.
Axisymmetric vortex breakdown Part 2. Physical mechanisms
Authors: Brown G. L. , Lopez J. M.
Published: April 2006

The physical mechanisms for vortex breakdown which, it is proposed here, rely on the production of a negative azimuthal component of vorticity, are elucidated with the aid of a simple, steady, inviscid, axisymmetric equation of motion. Most studies of vortex breakdown use as a starting point an equation for the azimuthal vorticity (Squire 1960), but a departure in the present study is that it is explored directly and not through perturbations of an initial stream function. The inviscid equation of motion that is derived leads to a criterion for vortex breakdown based on the generation of negative azimuthal vorticity on some stream surfaces. Inviscid predictions are tested against results from numerical calculations of the Navier-Stokes equations for which breakdown occurs.
The sound field due to an oscillating bubble near an indented free surface
Authors: Longuet-Higgins Michael S.
Published: April 2006

The problem is solved of the flow due to a rapidly oscillating source situated near a plane surface with a hemispherical indentation. The strength of the far-field flow is evaluated, and also the natural frequency of oscillation of a small bubble centred at the same position as the source.
Turbulent Couette flow profiles that maximize the efficiency function
Authors: Smith L. M.
Published: April 2006

A previous study revealed that only maximization of the efficiency function, from among a large class of mean field moments, results in both a logarithmic law and a velocity defect law in turbulent Poiseuille channel flow. The efficiency function, [Escr ], is the product of a drag coefficient and the ratio of the fluctuation and mean dissipation rate integrals. Here, maximum [Escr ] is explored in Couette flow to test its generality as a statistical stability criterion for turbulent shear flows. The optimal flow exhibits a logarithmic law but does not have a velocity defect law. A decreasing velocity defect is predicted for Reynolds numbers up to 30 000. This prediction is shown to be supported by the existing data, which are limited to Reynolds numbers less than 20 000.
Instability and transition of disturbed flow over a rotating disk
Authors: Faller Alan J.
Published: April 2006

Disturbed flow over a rotating disk can lead to transition of the von Kármán boundary layer at a much lower Reynolds number, Re, (i.e. smaller radius) than that due to the well-known Type 1 stationary mode of instability. This early transition is due to the excitation of the Type 2 instability, similar to that found in the Ekman layer. Detailed numerical values of the growth rates, phase speeds, group velocities, neutral curves, and other characteristics of these two instabilities have been calculated over a wide range of parameters. Neutral curves for the Ekman and Bödewadt boundary layers also are presented. The minimum critical Reynolds numbers for the von Kármán, Ekman and Bödewadt layers are Rec(2) = 69.4, 54.3, and 15.1 with wavelengths L = 22.5, 20.1, and 16.6 and at angles ε = −19.0°, −23.1°, and −33.2°, respectively. These minimum critical values frequently do not well describe laboratory observations, however, because at larger Re other modes grow more rapidly and dominate the flow.

The computed results are in excellent agreement with laboratory observations wherever comparison is possible. The growth of representative Type 1 instabilities with radius is shown to lead to N-factors greater than 9 at Re = 520 as appears to be necessary for transition to turbulence by the interaction of Type 1 with the basic flow. The growth of Type 2 instabilities with radius can lead to three additional mechanisms of transition. The necessary levels of excitation of Type 2 for these different mechanisms are estimated.

A sequence of photographs from a ciné film illustrate one of the transition mechanisms discussed: the interaction of Type 2 instabilities and a secondary instability that is nearly perpendicular to the Type 2 vortices.
The stability of a two-dimensional vorticity filament under uniform strain
Authors: Dritschel D. G. , Haynes P. H. , Juckes M. N. , Shepherd T. G.
Published: April 2006

The quantitative effects of uniform strain and background rotation on the stability of a strip of constant vorticity (a simple shear layer) are examined. The thickness of the strip decreases in time under the strain, so it is necessary to formulate the linear stability analysis for a time-dependent basic flow. The results show that even a strain rate γ (scaled with the vorticity of the strip) as small as 0.25 suppresses the conventional Rayleigh shear instability mechanism, in the sense that the r.m.s. wave steepness cannot amplify by more than a certain factor, and must eventually decay. For γ < 0.25 the amplification factor increases as γ decreases; however, it is only 3 when γ ė 0.065. Numerical simulations confirm the predictions of linear theory at small steepness and predict a threshold value necessary for the formation of coherent vortices. The results help to explain the impression from numerous simulations of two-dimensional turbulence reported in the literature that filaments of vorticity infrequently roll up into vortices. The stabilization effect may be expected to extend to two- and three-dimensional quasi-geostrophic flows.
A ray method for near-shore plumes in a shallow-water flow
Authors: Smith Ronald
Published: April 2006

Far from a shoreline, the spreading of a contaminant plume in a shallow-water flow can be predicted easily and accurately by a ray-tracing method. Unfortunately, the concentration predictions become singular at a beach, where the ray paths have a caustic. In this paper a uniform approximation is derived which remains valid at a beach. It is shown how the singular ray solutions corresponding to rays incident to and transmitted from the beach can be combined to construct the uniform approximation.
Modulated, frequency-locked, and chaotic cross-waves
Authors: Underhill William B. , Lichter Seth , Bernoff Andrew J.
Published: April 2006

Measurements were made of the wave height of periodic, quasi-periodic, and chaotic parametrically forced cross-waves in a long rectangular channel. In general, three frequencies (and their harmonics) may be observed: the subharmonic frequency and two slow temporal modulations — a one-mode instability associated with streamwise variation and a sloshing motion associated with spanwise variation. Their interaction, as forcing frequency, f, and forcing amplitude, a, were varied, produced a pattern of Arnold tongues in which two or three frequencies were locked. The overall picture of frequency-locked and -unlocked regions is explained in terms of the Arnold tongues predicted by the circle-map theory describing weakly coupled oscillators. Some of the observed tongues are apparently folded by a subcritical bifurcation, with the tips of the tongues lying on the unstable manifold folded under the observed stable manifold. Near the intersection of the neutral stability curves for two adjacent modes, a standing wave localized on one side of the tank was observed in agreement with the coupled-mode analysis of Ayanle, Bernoff & Lichter (1990). At large cross-wave amplitudes, the spanwise wave structure apparently breaks up, because of modulational instability, into coherent soliton-like structures that propagate in the spanwise direction and are reflected by the sidewalls.
Burgers equation with a fractional derivative; hereditary effects on nonlinear acoustic waves
Authors: Sugimoto N.
Published: April 2006

This paper deals with initial-value problems for the Burgers equation with the inclusion of a hereditary integral known as the fractional derivative of order ½. Emphasis is placed on the difference between the local and global dissipation due to the second-order and the half-order derivatives, respectively. Exploiting the smallness of the coefficient of the second-order derivative, an asymptotic analysis is first developed. When a discontinuity appears, the matched-asymptotic expansion method is employed to derive a uniformly valid solution. If the coefficient of the half-order derivative is also small, as is usually the case, the evolution comprises three stages, namely a lossless near field, an intermediate Burgers region, and a hereditary far field. In view of these results, the equation is then solved numerically, under various initial conditions, by finite-difference and spectral methods. It is revealed that the effect of the fractional derivative accumulates slowly to give rise to a significant dissipation and distortion of the waveform globally, which is to be contrasted with the effect of the second-order derivative, significant only locally, in a thin 'shock layer’.
Diffraction of waves by obstacles and inhomogeneities in fluids: a report on Euromech Colloquium 271
Authors: Evans D. V.
Published: April 2006

This first Euromech Colloquium to be held in Kiev attracted 74 participants including 19 from outside the USSR: from Austria, Bulgaria, France, Germany, Italy, Japan, Norway, Poland, Portugal and the United Kingdom. Despite unexpected absences or delays for some participants due to travel difficulties, a full programme of talks, each followed by a lively discussion, was maintained throughout the entire three and a half days of the Colloquium. In addition considerable space was set aside for posters, which ensured that the discussions were not confined to the lecture theatre. The colloquium was dominated by two major areas of interest: scattering of acoustic waves by elastic shells or bodies, and problems of surface gravity-wave diffraction. Also presented was a selection of widely varying topics within the general area of wave diffraction. A summary of the presented talks is given below.
Throughflow effects on convective instability in superposed fluid and porous layers
Authors: Chen Falin
Published: April 2006

We implement a linear stability analysis of the convective instability in superposed horizontal fluid and porous layers with throughflow in the vertical direction. It is found that in such a physical configuration both stabilizing and destabilizing factors due to vertical throughflow can be enhanced so that a more precise control of the buoyantly driven instability in either a fluid or a porous layer is possible. For ζ = 0.1 (ζ, the depth ratio, defined as the ratio of the fluid-layer depth to the porous-layer depth), the onset of convection occurs in both fluid and porous layers, the relation between the critical Rayleigh number Rcm and the throughflow strength γm is linear and the Prandtl-number (Prm) effect is insignificant. For ζ ≥ 0.2, the onset of convection is largely confined to the fluid layer, and the relation becomes Rcm ∼ γ2m for most of the cases considered except for Prm = 0.1 with large positive γm where the relation Rcm ∼ γ3m holds. The destabilizing mechanisms proposed by Nield (1987 a, b) due to throughflow are confirmed by the numerical results if considered from the viewpoint of the whole system. Nevertheless, from the viewpoint of each single layer, a different explanation can be obtained.
Management of the transgender voice
Authors: McNeill E J M
Published: April 2006

Transsexualism is a condition involving a paradoxical feeling of belonging to the opposite sex. Acquiring a sex-appropriate voice is a crucial part of the patient gaining acceptance in their new gender. Speech and language therapists and otolaryngologists play an important role in influencing communication behaviour in transgender patients by altering the fundamental frequency of speech to one acceptable for the patient's sex.

Review of the literature suggests that speech and language therapy is successful at creating an acceptable fundamental frequency in transgender patients, as well as influencing other communication behaviours. Laryngeal surgery, such as cricothyroid approximation, has an important role in raising the fundamental frequency in those who do not achieve acceptable voice via non-surgical means. There is little information on patient satisfaction and quality of life measures. Research is currently underway to explore this aspect further.
Inequality and the Knowledge Economy: Running to Stand Still?
Authors: Hudson John
Published: April 2006

Central to the Blair government's economic and social policies has been the promotion of a more ‘knowledge-based economy’. However, some commentators have suggested that the knowledge economy stretches income distributions and polarises skilled and unskilled workers. Drawing on empirical data about the UK case to explore such claims, this paper concludes that there is a significant positive correlation between the extent to which a region's economy has become ‘knowledge based’ and its level of income inequality. It argues this finding has important policy relevant implications.
Partnership and Privacy – Tension or Settlement? The Case of Adult Mental Health Services
Authors: 6 Perri , Bellamy Christine , Raab Charles , Warren Adam
Published: April 2006

Mental health is a good example of a field where imperatives for partnership or collaborative working can be in tension with those for client confidentiality. Both imperatives have been reinforced by additional regulation in recent years, in response to major inquiries. Professionals face the dilemma that either sharing clients' or patients' information or not sharing it could lead to outcomes for which they might be blamed; any rule adopted risks one or other type of error. This article examines two cases from a larger interview-based study of how local organisations are trying practically to reconcile these competing pressures.
Communities in Partnership: Developing a Strategic Voice
Authors: Taylor Marilyn
Published: April 2006

The increasing emphasis on community participation across the globe is well-documented. In the UK, it has been a central theme in neighbourhood renewal policy, where communities are expected to engage not only at neighbourhood level but also to take their place alongside public and private sector players in local strategic partnerships at city- or district-wide levels. Engaging communities beyond the neighbourhood poses particular challenges for the voluntary and community sector infrastructure. This article draws on an evaluation of the UK government's Community Participation Programmes to identify the challenges of scaling up to these levels and how these can be addressed.
The pupal specifier
broad
directs progressive morphogenesis in a direct-developing insect
Authors: Erezyilmaz Deniz F. , Riddiford Lynn M. , Truman James W.
Published: April 2006

A key regulatory gene in metamorphosing (holometabolous) insect life histories is the transcription factor
broad
(
br
), which specifies pupal development. To determine the role of
br
in a direct-developing (hemimetabolous) insect that lacks a pupal stage, we cloned
br
from the milkweed bug,
Oncopeltus fasciatus
(
Of’br
). We find that, unlike metamorphosing insects, in which
br
expression is restricted to the larval–pupal transition,
Of’br
mRNA is expressed during embryonic development and is maintained at each nymphal molt but then disappears at the molt to the adult. Induction of a supernumerary nymphal stage with a juvenile hormone (JH) mimic prevented the disappearance of
br
mRNA. In contrast, induction of a precocious adult molt by application of precocene II to third-stage nymphs caused a loss of
br
mRNA at the precocious adult molt. Thus, JH is necessary to maintain
br
expression during the nymphal stages. Injection of
Of’br
dsRNA into either early third- or fourth-stage nymphs caused a repetition of stage-specific pigmentation patterns and prevented the normal anisometric growth of the wing pads without affecting isometric growth or molting. Therefore,
br
is necessary for the mutable (heteromorphic) changes that occur during hemimetabolous development. Our results suggest that metamorphosis in insects arose as expression of
br
, which conveys competence for change, became restricted to one postembryonic instar. After this shift in
br
expression, the progressive changes that occur within the nymphal series in basal insects became compressed to the one short period of morphogenesis seen in the larva-to-pupa transition of holometabolous insects.
A plant-based oral vaccine to protect against systemic intoxication by Shiga toxin type 2
Authors: Wen Sharon X. , Teel Louise D. , Judge Nicole A. , O’Brien Alison D.
Published: April 2006

Hemolytic uremic syndrome, the leading cause of kidney failure in children, often follows infection with enterohemorrhagic
Escherichia coli
and is mediated by the Shiga type toxins, particularly type 2 (Stx2), produced by such strains. The challenge in protecting against this life-threatening syndrome is to stimulate an immune response at the site of infection while also protecting against Shiga intoxication at distal sites such as the kidney. As one approach to meeting this challenge, we sought to develop and characterize a prototypic orally delivered, plant-based vaccine against Stx2, an AB
5
toxin. First, we genetically inactivated the Stx2 active A subunit gene and then optimized both subunit genes for expression in plants. The toxoid genes were then transformed into the
Nicotiana tabacum
(tobacco) cell line NT-1 by
Agrobacterium tumefaciens
-mediated transformation. Toxoid expression was detected in NT-1 cell extracts, and the assembly of the holotoxoid was confirmed. Finally, mice were immunized by feeding with the toxoid-expressing NT-1 cells or by parenteral immunization followed by oral vaccination (prime–boost strategy). The immunized mice produced Stx2-specific mucosal IgA and Stx2-neutralizing serum IgG. The protective efficacy of these responses was assessed by challenging the immunized mice with
E. coli
O91:H21 strain B2F1, an isolate that produces an activatable variant of Stx2 (Stx2d) and is lethal to mice. The oral immunization fully protected mice from the challenge. Results of this study demonstrated that a plant-based oral vaccine can confer protection against lethal systemic intoxication.
Fractional Calcium Absorption Is Increased in Girls with Rett Syndrome
Authors: Motil Kathleen J. , Schultz Rebecca J. , Abrams Steven , Ellis Kenneth J. , Glaze Daniel G.
Published: April 2006

Background:

Rett syndrome (RTT), an X‐linked neurodevelopmental disorder primarilyaffecting girls, is characterized in part by osteopenia and increased risk of skeletal fractures. We hypothesized that decreased intestinal calcium (Ca) absorption relative to dietary Ca intake and increased renal Ca excretion might cause these problems in RTT.

Objective:

We measured fractional Ca absorption, urinary Ca loss, dietary Ca intake, and the hormonal factors regulating Ca metabolism to determine whether abnormalities in Ca balance might relate to poor bone mineralization in RTT girls and to evaluate the contribution of these factors to the overall dietary Ca needs of RTT girls.

Study Design:

Ten RTT girls and 10 controls, matched for age, sex, and pubertal status, were given a 3 day constant Ca diet that mimicked their habitual intakes. At the end of each dietary period, girls received single doses of 42Ca (intravenous) and 46Ca (oral). Fractional urinary excretion of 42Ca, 46Ca, 24 hour urinary Ca, and urinary cortisol excretion were determined. Serum Ca, phosphorous, alkaline phosphatase, vitamin D metabolites, parathyroid hormone (PTH), and osteocalcin were measured in the postabsorptive state. Bone mineral content (BMC) was measured by dual‐energy x‐ray absorptiometry.

Results:

Fractional Ca absorption was significantly higher in RTT than in control girls (mean ± SDp, 52 vs. 33 ± 13%). Dietary Ca intake (mean ± SDp, 1,100 vs. 1,446 ± 440 g/d) and net Ca absorption (mean ± SDp, 513 vs. 362 ± 306 mg/d) did not differ significantly between RTT and controls, respectively. Although urinary Ca excretion did not differ between groups, the increased urinary Ca:creatinine ratio (mean ± SDp, 0.39 vs. 0.23 ± 0.38) was consistent with clinical hypercalcuria and paralleled the significantly increased urinary cortisol excretion (mean ± SDp, 3.1 vs. 1.7 ± 1.1 mg/kg lean body mass per day) in the RTT girls. BMC was significantly lower in RTT than in controls (mean ± SDp, 527 vs. 860 ± 275 g). Serum Ca, P, alkaline phosphatase, vitamin D metabolites, PTH, and osteocalcin concentrations did not differ between the groups.

Conclusion:

Fractional Ca absorption showed a compensatory increase in the presence of adequate dietary Ca intakes, mild hypercalcuria, and pronounced bone mineral deficits in RTT girls. Whether supplemental dietary Ca could enhance fractional Ca absorption and improve bone mineralization in RTT girls is unknown.
Natural History and Symptomatology of Helicobacter pylori in Childhood and Factors Determining the Epidemiology of Infection
Authors: Özen Ahmet , Ertem Deniz , Pehlivanoglu Ender
Published: April 2006

Background:

High seroprevalence rates for Helicobacter pylori have been reported in developing countries, yet few studies exist determining the pattern of change in the epidemiology of H. pylori infection in children. The knowledge of acquisition and loss rates of H. pylori and the relevance to the sociodemographic properties and the symptomatology of infection may provide clues for lifestyle changes that might protect children from infection, and also, it may provide rationale for eradication, screening, and protection policies. Our aim was to conduct a prospective study to elucidate the outcome, rate of acquisition, and loss of H. pylori infection in a population of healthy children.

Methods:

This study is based on follow‐up of 327 healthy Turkish children aged 3 to 12 years. The follow‐up was conducted 6 years after the baseline examination. Helicobacter pylori status was determined by 13C‐urea breath test. Children were investigated for sociodemographic variables and several symptoms.

Results:

Data from 136 (41%) of 327 children were available. The prevalence of infection increased from 52.9% to 56.6%, mainly increasing in children younger than 10 years. The incidence of H. pylori infection among previously uninfected children was 14%, and the loss rate of infection among previously infected children was 5.5% during the follow‐up. Socioeconomic status, household density, and antibiotic use during last 6 months were inversely related to H. pylori prevalence. Children infected with H. pylori were complaining more often of headache but not of abdominal pain or dyspepsia.

Conclusions:

In this study, the acquisition rate of H. pylori infection was 2.5‐fold higher than the loss of infection, and the acquisition mostly occurred before 10 years of age. Data regarding acquisition and loss of H. pylori infection are critical for understanding the epidemiology of infection and development of preventive and treatment strategies.
Speciation in Pararge (Satyrinae: Nymphalidae) butterflies – North Africa is the source of ancestral populations of all Pararge species
Authors: WEINGARTNER ELISABET , WAHLBERG NIKLAS , NYLIN SÖREN
Published: April 2006

Abstract The genus Pararge comprises three species: P. aegeria, distributed in Europe and North Africa; P. xiphia, endemic to Madeira; and P. xiphioides, endemic to the Canary Islands. Two subspecies are recognized in P. aegeria, P. a. tircis and P. a. aegeria, distributed in northern and southern Europe, respectively. In the 1970s, P. aegeria appeared on Madeira. However, despite the status of P. aegeria as a model species in ecological studies, the evolutionary history of Pararge remains unknown. We studied the phylogenetic relationships of the three Pararge species, using the mitochondrial gene cytochrome oxidase subunit I and the nuclear gene wingless to infer modes and times of speciation. On the basis of our analyses, Pararge forms a strongly supported monophyletic group, with the DNA haplotypes of the three species also forming well‐supported monophyletic groups. We found that P. xiphia diverged first from the common ancestor a maximum of five million years ago, with P. xiphioides and P. aegeria being sister species that diverged a maximum of three million years ago. The two subspecies, P. a. tircis and P. a. aegeria, were not distinguishable on the basis of DNA haplotypes; instead, our data clearly distinguished between European specimens and those from North Africa. Madeiran P. aegeria has North African haplotypes and thus originated from there rather than from Europe. We hypothesize that the Mediterranean Sea forms a strong barrier to dispersal for Pararge butterflies, and has done so for approximately the past one million years.
Re‐evaluating the recycling hypothesis in the germinal centre
Authors: Moreira Joana S , Faro José
Published: April 2006

Mathematical models have been used to study different aspects of the germinal centre reaction, in particular, affinity maturation of antibodies and the hypothesis of recycling. So far, interpretation of several theoretical and experimental results has pointed to the existence of recycling. However, theoretical models have seldom been compared with experimental data from specific immune responses and the potential relevance of recycling in the germinal centre is still an open problem. In this article, we propose a model without recycling that takes into account selection mechanisms that were previously uncovered experimentally. We apply the model to several experimental systems that use different Ag and compare the results with experimental data of affinity maturation whenever available. The results obtained for a primary immune response to the hapten (4‐hydroxy‐3‐nitrophenyl)‐acetyl show that recycling is not a necessary mechanism to achieve the level of affinity maturation observed in germinal centre reactions. Similar levels of affinity maturation are obtained for other responses, although for antibodies involving several affinity‐enhancing mutations the affinity maturation obtained with the model is much lower. Interpretation of these results and consequences towards the concept of recycling are discussed.
Multistage Evaluation of Measurement Error in a Reliability Study
Authors: Liu Aiyi , Schisterman Enrique F. , Wu Chengqing
Published: April 2006

SummaryWe introduce sequential testing procedures for the planning and analysis of reliability studies to assess an exposure's measurement error. The designs allow repeated evaluation of reliability of the measurements and stop testing if early evidence shows the measurement error is within the level of tolerance. Methods are developed and critical values tabulated for a number of two‐stage designs. The methods are exemplified using an example evaluating the reliability of biomarkers associated with oxidative stress.
The genetic basis of circadian behavior
Authors: Oster H.
Published: April 2006

In most species, an endogenous timing system synchronizes physiology and behavior to the rhythmic succession of day and night. The mammalian circadian pacemaker residing in the suprachiasmatic nuclei (SCN) of the hypothalamus controls peripheral clocks throughout the brain and the body via humoral and neuronal transmission. On the cellular level, these clockworks consist of a set of interwoven transcriptional/translational feedback loops. Recent work emphasizes the tissue specificity of some components of these molecular clockworks and the differential regulation of their rhythmicity by the SCN.
Antibiofilm Activity of GlmU Enzyme Inhibitors against Catheter-Associated Uropathogens
Authors: Burton Euan , Gawande Purushottam V. , Yakandawala Nandadeva , LoVetri Karen , Zhanel George G. , Romeo Tony , Friesen Albert D. , Madhyastha Srinivasa
Published: April 2006

The colonization of uropathogenic bacteria on urinary catheters resulting in biofilm formation frequently leads to the infection of surrounding tissue and often requires removal of the catheter. Infections associated with biofilms are difficult to treat since they may be more than 1,000 times more resistant to antibiotics than their planktonic counterparts. We have developed an antibiofilm composition comprising an
N
-acetyl-
d
-glucosamine-1-phosphate acetyltransferase (GlmU) inhibitor and protamine sulfate, a cationic polypeptide. The antibiofilm activity of GlmU inhibitors, such as iodoacetamide (IDA),
N
-ethyl maleimide (NEM), and NEM analogs, including
N
-phenyl maleimide,
N
,
N
′-(1,2-phenylene)dimaleimide (oPDM), and
N
-(1-pyrenyl)maleimide (PyrM), was tested against that of catheter-associated uropathogens. Both IDA and NEM inhibited biofilm formation in
Escherichia coli
. All NEM analogs showed antibiofilm activity against clinical isolates of
E. coli
,
Pseudomonas aeruginosa
,
Klebsiella pneumoniae
,
Staphylococcus epidermidis
, and
Enterococcus faecalis
. The combination of oPDM with protamine sulfate (PS) enhanced its antibiofilm activity and reduced its effective concentration to as low as 12.5 μM. In addition, we found that the in vitro inhibitory activity of oPDM-plus-PS-coated silicone catheters against
P. aeruginosa
and
S. epidermidis
colonization was superior to that of catheters coated with silver hydrogel. Confocal scanning laser microscopy further confirmed that the oPDM-plus-PS-coated silicone catheters were almost free from bacterial colonization. Thus, a broad-spectrum antibiofilm composition comprising a GlmU inhibitor and protamine sulfate shows promise for use in anti-infective coatings for medical devices, including urinary catheters.
Streptococcus pneumoniae
Isolates Resistant to Telithromycin
Authors: Rantala M. , Haanperä-Heikkinen M. , Lindgren M. , Seppälä H. , Huovinen P. , Jalava J. ,   the Finnish Study Group for Antimicrobial Resistance
Published: April 2006

The telithromycin susceptibility of 210 erythromycin-resistant pneumococci was tested with the agar diffusion method. Twenty-six
erm
(B)-positive isolates showed heterogeneous resistance to telithromycin, which was manifested by the presence of colonies inside the inhibition zone. When these cells were cultured and tested, they showed stable, homogeneous, and high-level resistance to telithromycin.
Macrolide-Resistant
Streptococcus pyogenes
in Norway: Population Structure and Resistance Determinants
Authors: Littauer P. , Caugant D. A. , Sangvik M. , Høiby E. A. , Sundsfjord A. , Simonsen G. S. ,   the Norwegian Macrolide Study Group
Published: April 2006

A 2.7% prevalence of macrolide resistance in 1,657 Norwegian clinical
Streptococcus pyogenes
isolates was primarily due to
erm
(TR) (59%) and
mef
(A) (20%). Four clonal complexes comprised 75% of the strains. Macrolide resistance in
S. pyogenes
in Norway is imported as resistant strains or locally selected in internationally disseminated susceptible clones.
Different Domains of CD81 Mediate Distinct Stages of Hepatitis C Virus Pseudoparticle Entry
Authors: Bertaux Claire , Dragic Tatjana
Published: April 2006

The CD81 tetraspanin was first identified as a hepatitis C virus (HCV) receptor by its ability to bind the soluble ectodomain of envelope glycoprotein E2 (sE2). More recently, it has been suggested that CD81 is necessary but not sufficient for HCV entry into target cells. Here we present further evidence that putative human hepatocyte-specific factors act in concert with CD81 to mediate sE2 binding and HCV pseudoparticle (HCVpp) entry. Moreover, we show that CD81-mediated HCVpp entry entails E2 binding to residues in the large extracellular loop as well as molecular events mediated by the transmembrane and intracellular domains of CD81. The concept that CD81 receptor function progresses in stages is further supported by our finding that anti-CD81 monoclonal antibodies inhibit HCVpp entry by different mechanisms. The half-life of CD81-HCVpp binding was determined to be approximately 17 min, and we propose that binding is followed by CD81 oligomerization, partitioning into cholesterol-rich membrane domains, or other, lateral protein-protein interactions. This results in the formation of a receptor-virus complex that undergoes endocytosis and pH-dependent membrane fusion.
Cellular Splicing and Transcription Regulatory Protein p32 Represses Adenovirus Major Late Transcription and Causes Hyperphosphorylation of RNA Polymerase II
Authors: Öhrmalm Christina , Akusjärvi Göran
Published: April 2006

The cellular protein p32 is a multifunctional protein, which has been shown to interact with a large number of cellular and viral proteins and to regulate several important activities like transcription and RNA splicing. We have previously shown that p32 regulates RNA splicing by binding and inhibiting the essential SR protein ASF/SF2. To determine whether p32 also functions as a regulator of splicing in virus-infected cells, we constructed a recombinant adenovirus expressing p32 under the transcriptional control of an inducible promoter. Much to our surprise the results showed that p32 overexpression effectively blocked mRNA and protein expression from the adenovirus major late transcription unit (MLTU). Interestingly, the p32-mediated inhibition of MLTU transcription was accompanied by an approximately 4.5-fold increase in Ser 5 phosphorylation and an approximately 2-fold increase in Ser 2 phosphorylation of the carboxy-terminal domain (CTD). Further, in p32-overexpressing cells the efficiency of RNA polymerase elongation was reduced approximately twofold, resulting in a decrease in the number of polymerase molecules that reached the end of the major late L1 transcription unit. We further show that p32 stimulates CTD phosphorylation in vitro. The inhibitory effect of p32 on MLTU transcription appears to require the CAAT box element in the major late promoter, suggesting that p32 may become tethered to the MLTU via an interaction with the CAAT box binding transcription factor.
On Improving 4-km Mesoscale Model Simulations
Authors: Deng Aijun , Stauffer David R.
Published: April 2006

A previous study showed that use of analysis-nudging four-dimensional data assimilation (FDDA) and improved physics in the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5) produced the best overall performance on a 12-km-domain simulation, based on the 18–19 September 1983 Cross-Appalachian Tracer Experiment (CAPTEX) case. However, reducing the simulated grid length to 4 km had detrimental effects. The primary cause was likely the explicit representation of convection accompanying a cold-frontal system. Because no convective parameterization scheme (CPS) was used, the convective updrafts were forced on coarser-than-realistic scales, and the rainfall and the atmospheric response to the convection were too strong. The evaporative cooling and downdrafts were too vigorous, causing widespread disruption of the low-level winds and spurious advection of the simulated tracer. In this study, a series of experiments was designed to address this general problem involving 4-km model precipitation and gridpoint storms and associated model sensitivities to the use of FDDA, planetary boundary layer (PBL) turbulence physics, grid-explicit microphysics, a CPS, and enhanced horizontal diffusion. Some of the conclusions include the following: 1) Enhanced parameterized vertical mixing in the turbulent kinetic energy (TKE) turbulence scheme has shown marked improvements in the simulated fields. 2) Use of a CPS on the 4-km grid improved the precipitation and low-level wind results. 3) Use of the Hong and Pan Medium-Range Forecast PBL scheme showed larger model errors within the PBL and a clear tendency to predict much deeper PBL heights than the TKE scheme. 4) Combining observation-nudging FDDA with a CPS produced the best overall simulations. 5) Finer horizontal resolution does not always produce better simulations, especially in convectively unstable environments, and a new CPS suitable for 4-km resolution is needed. 6) Although use of current CPSs may violate their underlying assumptions related to the size of the convective element relative to the grid size, the gridpoint storm problem was greatly reduced by applying a CPS to the 4-km grid.
Rain Retrieval from TMI Brightness Temperature Measurements Using a TRMM PR–Based Database
Authors: Viltard Nicolas , Burlaud Corinne , Kummerow Christian D.
Published: April 2006

This study focuses on improving the retrieval of rain from measured microwave brightness temperatures and the capability of the retrieved field to represent the mesoscale structure of a small intense hurricane. For this study, a database is constructed from collocated Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) and the TRMM Microwave Imager (TMI) data resulting in about 50 000 brightness temperature vectors associated with their corresponding rain-rate profiles. The database is then divided in two: a retrieval database of about 35 000 rain profiles and a test database of about 25 000 rain profiles. Although in principle this approach is used to build a database over both land and ocean, the results presented here are only given for ocean surfaces, for which the conditions for the retrieval are optimal. An algorithm is built using the retrieval database. This algorithm is then used on the test database, and results show that the error can be constrained to reasonable levels for most of the observed rain ranges. The relative error is nonetheless sensitive to the rain rate, with maximum errors at the low and high ends of the rain intensities (+60% and −30%, respectively) and a minimum error between 1 and 7 mm h−1. The retrieval method is optimized to exhibit a low total bias for climatological purposes and thus shows a high standard deviation on point-to-point comparisons. The algorithm is applied to the case of Hurricane Bret (1999). The retrieved rain field is analyzed in terms of structure and intensity and is then compared with the TRMM PR original rain field. The results show that the mesoscale structures are indeed well reproduced even if the retrieved rain misses the highest peaks of precipitation. Nevertheless, the mesoscale asymmetries are well reproduced and the maximum rain is found in the correct quadrant. Once again, the total bias is low, which allows for future calculation of the heat sources/sinks associated with precipitation production and evaporation.
Correcting Active Scatterometer Data for the Effects of Rain Using Passive Radiometer Data
Authors: Hilburn K. A. , Wentz F. J. , Smith D. K. , Ashcroft P. D.
Published: April 2006

A model for the effects of rain on scatterometer data is proposed. Data from the Advanced Microwave Scanning Radiometer (AMSR) and the SeaWinds scatterometer, both on the Midori-II satellite, are used. The model includes three basic rain effects: attenuation, rain roughening of the sea surface, and volumetric backscatter. Attenuation is calculated directly from the radiometer data and beam filling is explicitly addressed. The model simultaneously solves for both the rain roughening and volumetric backscatter. Fitting the coefficients of the model requires an estimate of the radar cross section because of wind roughening, and NCEP Global Data Assimilation System (GDAS) wind vectors are used for this purpose. Both the derived rain roughening and volumetric backscatter are similar to results in published work, but the values are slightly smaller, especially for vertical polarization. Drop size distribution variability is accounted for by formulating the radar equation in terms of the parameters of the radiative transfer equation and using additional radiometric information. Explicit inclusion of vertical profile variability results in an underdetermined problem, but it is implicitly included in fitting the model to the data. The correction makes large improvements in wind speeds and modest improvements in wind directions. Wind statistics and specific examples are shown to illustrate the nature of the improvements. The correction is limited, however, by measurement mismatch issues and the nonlinear nature of the wind retrieval.
Measurement of Surface Area of 3‐D Body Scans to Assess the Effectiveness of Hats for Sun Protection
Authors: Lee Young‐A , Ashdown Susan P. , Slocum Ann C.
Published: April 2006

Three‐dimensional (3‐D) body scans of golfers in active positions were used to generate a simulation of UV exposure by projecting a cone from the brims of a selection of five hat styles with different brim designs onto the body from two sun angles. From these scans, researchers measured the total body area that would be protected from UV exposure by calculating the surface area shadowed by the hat brims. Objective measurement data can provide valuable measures of protection to help the designer create attractive and functional hats and clothing for sun protection. The 3‐D scanner is an important new tool for designers that allow visualization and manipulation of 3‐D images and sophisticated image measurement and analyses.