bluuebunny/crossref_metadata_2025 huggingface dataset:
Surfactant transport on highly viscous
surface films
Authors: MATAR O. K. , CRASTER R. V. , WARNER M. R. E.
Published: September 2002

We examine surfactant transport on a highly viscous film overlying a much less viscous
layer, aimed at situations within the smaller pulmonary airways, wherein the highly
viscous film corresponds to the mucus layer, that rides atop the Periciliary liquid
layer (PCL). To this end, we generate a variant of the lubrication approximation
by promoting terms which would have otherwise been neglected within standard
lubrication theory; this is reminiscent of theories involving free films, viscous jets
and threads. We also account for the presence of van der Waals forces, which could
rupture the thin bilayer fluid coating the small airways. This is a potential difficulty
for surfactant replacement therapy (SRT) since rupture will leave behind pools of
stranded surfactant thereby restricting the levels reaching the smallest airways and
potentially leading to clinical failure. In the present study, the presence of the mucus
for a wide range of system parameters using analytical techniques and numerical
simulations.
Dynamics of homogeneous bubbly flows
Part 1. Rise velocity and microstructure of
the bubbles
Authors: BUNNER BERNARD , TRYGGVASON GRÉTAR
Published: September 2002

Direct numerical simulations of the motion of up to 216 three-dimensional buoyant bubbles in periodic domains are presented. The full Navier–Stokes equations
are solved by a parallelized finite-difference/front-tracking method that allows a deformable interface between the bubbles and the suspending fluid and the inclusion
of surface tension. The governing parameters are selected such that the average rise
Reynolds number is about 12–30, depending on the void fraction; deformations
of the bubbles are small. Although the motion of the individual bubbles is unsteady,
the simulations are carried out for a sufficient time that the average behaviour of
the system is well defined. Simulations with different numbers of bubbles are used to
explore the dependence of the statistical quantities on the size of the system. Examination of the microstructure of the bubbles reveals that the bubbles are dispersed
approximately homogeneously through the flow field and that pairs of bubbles tend to
align horizontally. The dependence of the statistical properties of the flow on the void
fraction is analysed. The dispersion of the bubbles and the fluctuation characteristics,
or ‘pseudo-turbulence’, of the liquid phase are examined in Part 2.
Dynamics of homogeneous bubbly flows
Part 2. Velocity fluctuations
Authors: BUNNER BERNARD , TRYGGVASON GRÉTAR
Published: September 2002

Direct numerical simulations of the motion of up to 216 three-dimensional buoyant
bubbles in periodic domains are presented. The bubbles are nearly spherical and
have a rise Reynolds number of about 20. The void fraction ranges from 2% to
24%. Part 1 analysed the rise velocity and the microstructure of the bubbles. This
paper examines the fluctuation velocities and the dispersion of the bubbles and the
‘pseudo-turbulence’ of the liquid phase induced by the motion of the bubbles. It is
found that the turbulent kinetic energy increases with void fraction and scales with
the void fraction multiplied by the square of the average rise velocity of the bubbles.
The vertical Reynolds stress is greater than the horizontal Reynolds stress, but the
anisotropy decreases when the void fraction increases. The kinetic energy spectrum
follows a power law with a slope of approximately −3.6 at high wavenumbers.
Spinning instability of gaseous detonations
Authors: KASIMOV ASLAN R. , STEWART D. SCOTT
Published: September 2002

We investigate hydrodynamic instability of a steady planar detonation wave propagating in a circular tube to three-dimensional linear perturbations, using the normal
mode approach. Spinning instability is identified and its relevance to the well-known
spin detonation is discussed. The neutral stability curves in the plane of heat release
and activation energy exhibit bifurcations from low-frequency to high-frequency spinning modes as the heat release is increased at fixed activation energy. With a simple
Arrhenius model for the heat release rate, a remarkable qualitative agreement with
experiment is obtained with respect to the effects of dilution, initial pressure and
tube diameter on the behaviour of spin detonation. The analysis contributes to the
explanation of spin detonation which has essentially been absent since the discovery
of the phenomenon over seventy years ago.
Growth and collapse of cavitation bubbles near a
curved rigid boundary
Authors: TOMITA Y. , ROBINSON P. B. , TONG R. P. , BLAKE J. R.
Published: September 2002

Laser-induced cavitation bubbles near a curved rigid boundary are observed experimentally using high-speed photography. An image theory is applied to obtain
information on global bubble motion while a boundary integral method is employed
to gain a more detailed understanding of the behaviour of a liquid jet that threads
a collapsing bubble, creating a toroidal bubble. Comparisons between the theory
and experiment show that when a comparable sized bubble is located near a rigid
boundary the bubble motion is significantly influenced by the surface curvature of
the boundary, which is characterized by a parameter ζ, giving convex walls for ζ < 1,
concave walls for ζ > 1 and a flat wall when ζ = 1. If a boundary is slightly concave,
the most pronounced migration occurs at the first bubble collapse. The velocity of
a liquid jet impacting on the far side of the bubble surface tends to increase with
decreasing parameter ζ. In the case of a convex boundary, the jet velocity is larger
than that generated in the flat boundary case. Although the situation considered
here is restricted to axisymmetric motion without mean flow, this result suggests that
higher pressures can occur when cavitation bubbles collapse near a non-flat boundary.
Bubble separation, including the pinch-off phenomenon, is observed in the final stage
of the collapse of a bubble, with the oblate shape at its maximum volume attached to
the surface of a convex boundary, followed by bubble splitting which is responsible
for further bubble proliferation.
The linear stability of a core–annular flow in
an asymptotically corrugated tube
Authors: WEI HSIEN-HUNG , RUMSCHITZKI DAVID S.
Published: September 2002

This paper examines the core–annular flow of two immiscible fluids in a straight
circular tube with a small corrugation, in the limit where the ratio ε of the mean
undisturbed annulus thickness to the mean core radius and the corrugation (characterized by the parameter σ) are both asymptotically small and where the surface tension
is small. It is motivated by the problems of liquid–liquid displacement in irregular
rock pores such as occur in secondary oil recovery and in the evolution of the liquid
film lining the bronchii in the lungs whose diameters vary over different generations
of branching. We investigate the asymptotic base flow in this limit and consider the
linear stability of its leading order (in the corrugation parameter) solution. For the
chosen scalings of the non-dimensional parameters the core's base flow slaves that
of the annulus. The equation governing the leading-order interfacial position for a
given wall corrugation function shows a competition between shear and capillarity.
The former tends to align the interface shape with that of the wall and the latter
tends to introduce a phase shift, which can be of either sign depending on whether
the circumferential or the longitudinal component of capillarity dominates.
The asymptotic linear stability of this leading-order base flow reduces to a single
partial differential equation with non-constant coefficients deriving from the non-uniform
base flow for the time evolution of an interfacial disturbance. Examination
of a single mode k wall function allows the use of Floquet theory to analyse this
equation. Direct numerical solutions of the above partial differential equation agree
with the predictions of the Floquet analysis. The resulting spectrum is periodic in α-
space, α being the disturbance wavenumber space. The presence of a small corrugation
not only modifies (at order σ2) the primary eigenvalue of the system. In addition,
short-wave order-one disturbances that would be stabilized flowing to capillarity in the
absence of corrugation can, in the presence of corrugation and over time scales of
order ln(1/σ), excite higher wall harmonics (α±nk) leading to the growth of unstable
long waves. Similar results obtain for more complicated wall shape functions. The
main result is that a small corrugation makes a core–annular flow unstable to far
more disturbances than would destabilize the same uncorrugated flow system. A
companion paper examines that competition between this added destabilization due
to pore corrugation with the wave steepening and stabilization in the weakly nonlinear
regime.
The weakly nonlinear interfacial stability of a
core–annular flow in a corrugated tube
Authors: WEI HSIEN-HUNG , RUMSCHITZKI DAVID S.
Published: September 2002

A core–annular flow, the concurrent axial flow of two immiscible fluids in a circular
tube or pore with one fluid in the core and the other in the wetting annular region,
is frequently used to model technologically important flows, e.g. in liquid–liquid displacements in secondary oil recovery. Most of the existing literature assumes that the
pores in which such flows occur are uniform circular cylinders, and examine the interfacial stability of such systems as a function of fluid and interfacial properties. Since
real rock pores possess a more complex geometry, the companion paper examined the
linear stability of core–annular flows in axisymmetric, corrugated pores in the limit
of asymptotically weak corrugation. It found that short-wave disturbances that were
stable in straight tubes could couple to the wall's periodicity to excite unstable long
waves. In this paper, we follow the evolution of the axisymmetric, linearly unstable
waves for fluids of equal densities in a corrugated tube into the weakly nonlinear
regime. Here, we ask whether this continual generation of new disturbances by the
coupling to the wall's periodicity can overcome the nonlinear saturation mechanism
that relies on the nonlinear (kinematic-condition-derived) wave steepening of the
Kuramoto–Sivashinsky (KS) equation. If it cannot, and the unstable waves still saturate, then do these additional excited waves make the KS solutions more likely
to be chaotic, or does the dispersion introduced into the growth rate correction by
capillarity serve to regularize otherwise chaotic motions?

We find that in the usual strong surface tension limit, the saturation mechanism of
the KS mechanism remains able to saturate all disturbances. Moreover, an additional
capillary-derived nonlinear term seems to favour regular travelling waves over chaos,
and corrugation adds a temporal periodicity to the waves associated with their
periodical traversing of the wall's crests and troughs. For even larger surface tensions,
capillarity dominates over convection and a weakly nonlinear version of Hammond's
no-flow equation results; this equation, with or without corrugation, suggests further
growth. Finally, for a weaker surface tension, the leading-order base flow interface
follows the wall's shape. The corrugation-derived excited waves appear able to push
an otherwise regular travelling wave solution to KS to become chaotic, whereas
its dispersive properties in this limit seem insufficiently strong to regularize chaotic
motions.
On steep gravity waves meeting a vertical wall:
a triple instability
Authors: LONGUET-HIGGINS MICHAEL S. , DRAZEN DAVID A.
Published: September 2002

Theoretical arguments suggest that progressive gravity waves incident on a vertical
wall can produce periodic standing waves only if the incident wave steepness ak
is quite small, certainly less than 0.284. Laboratory experiments are carried out in
which an incident wave train of almost uniform amplitude meets a vertical barrier.
At wave steepnesses greater than 0.236 the resulting motion near the barrier is non-periodic. A growing instability is observed in which every third wave crest is steeper
than its neighbours. The steep waves develop sharp crests, or vertical jets. The two
neighbouring crests are rounded, at-topped, or of intermediate form. The instability
grows by a factor of about 2.2 for every three wave periods, almost independently of
the incident wave steepness.
Fluid pipes
Authors: HANCOCK MATTHEW J. , BUSH JOHN W. M.
Published: September 2002

We present the results of a combined theoretical and experimental investigation of
laminar vertical jets impinging on a deep fluid reservoir. We consider the parameter
regime where, in a pure water system, the jet is characterized by a stationary field
of capillary waves at its base. When the reservoir is contaminated by surfactant, the
base of the jet is void of capillary waves, cylindrical and quiescent: water enters the
reservoir as if through a rigid pipe. A theoretical description of the resulting fluid
pipe is deduced by matching extensional plug flow upstream of the pipe onto entry
pipe flow within it. Theoretical predictions for the pipe height are found to be in
excellent accord with our experimental results. An analogous theoretical description
of the planar fluid pipe expected to arise on a falling fluid sheet is presented.
Experiments on Lagrangian transport in steady
vortex-breakdown bubbles in a confined
swirling flow
Authors: SOTIROPOULOS FOTIS , WEBSTER DONALD R. , LACKEY TAHIRIH C.
Published: September 2002

In a recent study, Sotiropoulos et al. (2001) studied numerically the chaotic particle
paths in the interior of stationary vortex-breakdown bubbles that form in a closed
cylindrical container with a rotating lid. Here we report the first experimental verification of these numerical findings along with new insights into the dynamics of
vortex-breakdown bubbles. We visualize the Lagrangian transport within the bubbles
using planar laser-induced fluorescence (LIF) and show that even though the flow
fields are steady – from the Eulerian standpoint – the spatial distribution of the dye
tracer varies continuously, and in a seemingly random manner, over very long observation intervals. This finding is consistent with the arbitrarily long šil'nikov transients
of upstream-originating orbits documented numerically by Sotiropoulos et al. (2001).
Sequences of instantaneous LIF images also show that the steady bubbles exchange
fluid with the outer flow via random bursting events during which blobs of dye exit
the bubble through the spiral-in saddle. We construct experimental Poincaré maps
by time-averaging a sufficiently long sequence of instantaneous LIF images. Ergodic
theory concepts (Mezić & Sotiropoulos 2002) can be used to formally show that the
level sets of the resulting time-averaged light intensity field reveal the invariant sets
(unmixed islands) of the flow. The experimental Poincaré maps are in good agreement
with the numerical computations. We apply this method to visualize the dynamics
in the interior of the vortex-breakdown bubble that forms in the wake of the first
bubble for governing parameters in the steady, two-bubble regime. In striking contrast with the asymmetric image obtained for the first bubble, the time-averaged light
intensity field for the second bubble is remarkably axisymmetric. Numerical computations confirm this finding and further reveal that the apparent axisymmetry of this
bubble is due to the fact that orbits in its interior exhibit quasi-periodic dynamics.
We argue that this stark contrast in dynamics should be attributed to differences
in the swirl-to-axial velocity ratio in the vicinity of each bubble. By studying the
bifurcations of a simple dynamical system, with manifold topology resembling that
of a vortex-breakdown bubble, we show that sufficiently high swirl intensities can
stabilize the chaotic orbits, leading to quasi-periodic dynamics.
Numerical and experimental analysis of
two-dimensional separated flows
over a flexible sail
Authors: LORILLU O. , WEBER R. , HUREAU J.
Published: September 2002

This paper is a numerical analysis of the flow over a exible sail with the usual
two-dimensional model of ideal weightless incompressible fluid. The sail is assumed
to be impervious, inelastic and weightless, and may or may not be mounted on a
mast. Separated or attached flows are considered at any angle of attack. Our method
is validated by numerical and experimental results, i.e. the sail shape and velocity field
are determined by particle imaging velocimetry, and lift and drag by aerodynamic
balance. Despite the simplicity of the wake model we use (the Helmholtz model),
the computed free streamline geometry and especially the sail shape are in good
agreement with the experimental and numerical data.
Horizontal convection is non-turbulent
Authors: PAPARELLA F. , YOUNG W. R.
Published: September 2002

Consider the problem of horizontal convection: a Boussinesq fluid, forced by applying
a non-uniform temperature at its top surface, with all other boundaries insulating.
We prove that if the viscosity, ν, and thermal diffusivity, κ, are lowered to zero,
with σ
≡
ν/κ fixed, then the energy dissipation per unit mass, κ, also vanishes in
this limit. Numerical solutions of the two-dimensional case show that despite this
anti-turbulence theorem, horizontal convection exhibits a transition to eddying flow,
provided that the Rayleigh number is sufficiently high, or the Prandtl number σ
sufficiently small. We speculate that horizontal convection is an example of a flow
with a large number of active modes which is nonetheless not ‘truly turbulent’ because
ε→0 in the inviscid limit.
Steady planar straining flow past a rigid sphere
at moderate Reynolds number
Authors: BAGCHI P. , BALACHANDAR S.
Published: September 2002

This study focuses on the effect of spatial non-uniformity in the ambient flow on the
forces acting on a spherical particle at moderate particle Reynolds numbers. A scaling
analysis is performed to obtain conditions under which such effects are important. A
direct numerical simulation, based on spectral methods, is used to compute the three-dimensional time-dependent flow past a stationary sphere subject to a uniform flow
plus a planar straining flow. The particle Reynolds number, Re, in the range 10 to 300
covering different flow regimes, from unseparated flow to unsteady vortex shedding,
is considered. A variety of strain magnitudes and orientations are investigated. A
systematic comparison with the potential flow results and axisymmetric strain results
is given. Under elongational strain, both the planar and axisymmetric cases are found
to stabilize the sphere wake and delay the onset of unsteadiness, while compressional
strain leads to instability. In terms of separation angles, length of the recirculation
eddy and topology of the surface streamlines, planar and axisymmetric strains yield
nearly the same results. The drag force appears to have a linear relation with strain
magnitude in both cases, as predicted by the potential flow. However, contrary to the
potential flow results, the drag in planar strain is higher than that in axisymmetric
strain. The generation of higher drag is explained using the surface pressure and
vorticity distributions. Planar strain oriented at an angle with the oncoming uniform
flow is observed to break the symmetry of the wake and results in a lift or side
force. The variation of the drag and lift forces may be quite complex, and unlike
the potential flow results they may not be monotonic with strain magnitude. The
direction of the lift force may be opposite to that predicted by the inviscid and
low Reynolds number (Re [Lt ] 1) theories. This behaviour is dictated by the presence
or absence of a recirculation eddy. In the absence of a recirculation region at
low Reynolds numbers (Re < 20), or at a very high strain magnitude when the
recirculation region is suppressed, the results follow somewhat the pattern observed
in potential flow. However, with the presence of a recirculation region, results opposite
to those predicted by the potential theory are observed.
Capillary–gravity simultons in a liquid layer
Authors: HUANG GUOXIANG , VELARDE MANUEL G.
Published: September 2002

Simultaneous capillary–gravity solitary waves (simultons or quadratic solitons) are
shown to be possible in a rectangular liquid channel of arbitrary finite depth bounded
below by a solid plate and above with a free deformable surface with constant surface
tension. A second-harmonic resonance between two waveguide modes (fundamental
and second-harmonic waves) is studied with the inclusion of dispersion in the system.
The nonlinearly coupled amplitude equations for the two slowly varying envelopes
of the fundamental and the second-harmonic wave components are derived using
the method of multiple scales. Two types of capillary–gravity simulton solutions are
explicitly obtained and an experiment for observing such hydrodynamic simultons is
suggested.
The management of border disputes in African regional sub-systems: comparing West Africa and the Horn of Africa
Authors: Kornprobst Markus
Published: September 2002

In Africa, the management of border disputes varies from sub-region to sub-region. Most puzzling is the difference between West Africa and the Horn of Africa. In the latter, border disputes are much more likely to escalate into war than in the former. Seeking to solve this puzzle, this study focuses on the territorial integrity norm. It departs from existing accounts of this norm in two ways: first, it does not choose the region but the sub-region as the level of analysis. Second, it does not isolate the territorial integrity norm from its social context but analyses the interplay of the norm with the social structure in which it is embedded. It concludes that the territorial integrity norm in West Africa is part of a social structure different from that in the Horn of Africa. It is this difference that explains the different patterns of conflict management in the two sub-regions.
From Lash to Red Star: the pitfalls of counter-insurgency in Ethiopia, 1980–82
Authors: Tareke Gebru
Published: September 2002

By 1980, Ethiopia was gripped in escalating civil wars. After a series of punitive expeditions had failed to suppress them, the government organised large-scale operations in the early 1980s against the insurgencies in the eastern and northern territories. The operations seemed to have been informed by what is called ‘total strategy’. Although the emphasis was on the coercive component, the state also used psychological and economic incentives. The results were mixed. The eastern rebels were defeated more easily because they were factious. The northern campaign failed because of the rebels' staunchness and the terrain's unsuitability. In a cold test of wills, the Eritrean fighters not only held the offensive to a stalemate, but also went on to win total military victory. Same strategy, different outcomes: this suggests that no single counter-insurgency strategy can always have the same results as it is influenced by numerous factors that may vary from one place to another.
The politics of international election observation: the case of Zimbabwe in 2000
Authors: Laakso Liisa
Published: September 2002

The example of Zimbabwe in 2000 shows that in a context of violent election campaigning, the role of international election observation is an ambiguous one. Unlike earlier elections organised by the Zimbabwean government, international donors wanted to observe its 2000 parliamentary election amidst a deepening crisis. They noted that the elections would not be free and fair in their view. Neighbouring countries with a more positive view joined the observation exercise. The government's discriminatory invitation and accreditation policy, the observers' emphasis on the peacefulness of the polling rather than free and fair elections, and the selective publication of their reports in various media, were affected both by the political agendas of the domestic players and by the governments which sent the observers. The difference between the Western view of the government, which had changed drastically since the 1980s and early 1990s, and the view of neighbouring governments, was crucial and may become significant elsewhere in Africa.
Geographic variation in the abundance and morphology of the bryozoan Alcyonidium diaphanum (Ctenostomata: Alcyonidiidae) in UK coastal waters
Authors: Porter J.S. , Ellis J.R. , Hayward P.J. , Rogers S.I. , Callaway R.
Published: September 2002

The ctenostome bryozoan Alcyonidium diaphanum is widespread and abundant in the coastal waters of England and Wales. It was recorded in 77–90% of beam trawl catches in the eastern English Channel and southern North Sea, and in 53–73% of catches in the Bristol Channel and Irish Sea. The maximum catch rates in these two study areas were 1410 and 751 kg h−1 respectively. Alcyonidium diaphanum was most abundant in the greater Thames Estuary. Additional data from the North Sea indicated that A. diaphanum is widely distributed throughout the southern North Sea. Alcyonidium diaphanum was found intertidally in only seven of 99 locations sampled. Several different morphotypes were observed, ranging from cylindrical to lobate forms. The distribution patterns of various morphotypes are discussed.
Sulphur sources for chemoautotrophic nutrition of shallow water vestimentiferan tubeworms in Kagoshima Bay
Authors: Miura Tomoyuki , Nedachi Munetomo , Hashimoto Jun
Published: September 2002

To elucidate the sulphur sources for chemoautotrophy by the symbiotic bacteria of a vestimentiferan tubeworm, Lamellibrachia satsuma, living in Kagoshima Bay at depths of 80–100 m, we analysed the sulphur isotopic ratios of the animal tissues and compared them with environmental sulphur species collected in the field. Animals that had been maintained in an aquarium for over a year and supplied a known sulphur source were also investigated. The gas emitted from volcanic source in Kagoshima Bay contained rather heavy sulphide (+12·7 to +22·9‰ δ34S) compared with deep-sea hydrothermal vent systems (0 to +5‰). The tissue of the tubeworms contained very light sulphide (−21·5 to −25·9‰). It is inferred from the analysis of the aquarium-maintained specimens that the fractionation by the tubeworm or its symbiont was <1·5‰. The sulphur source assimilated by the tubeworms in the field is therefore inferred to have δ ratio −19·1 to −24·6‰. This means that only 9·7 to 25·0% of the sulphur in the worm tissues can be derived from the volcanic gas and the rest must come from other sources, such as microbial activity in the bottom sediment.
The life cycle of Clytia linearis and Clytia noliformis: metagenic campanulariids (Cnidaria: Hydrozoa) with contrasting polyp and medusa stages
Authors: Lindner Alberto , Migotto Alvaro E.
Published: September 2002

The life cycles of Clytia linearis and Clytia noliformis, two common campanulariids previously known solely from their polyp and young medusa stages, were investigated. Adult medusae of C. linearis have a bell diameter of 2·5–3·6 mm, and up to 29 tentacles. The bell is almost flat when relaxed and C-type microbasic mastigophore nematocysts form a cluster at the tip of the tentacles. Mature medusae of C. noliformis have a more hemispherical, saucer-shaped bell (3·5–4·5 mm in diameter), up to 16 tentacles, and no diagnostic nematocysts. Polyps of both species also differ in morphology, colour, and cnidome, and a possible resting structure is described for C. linearis. The relevance of characters from the perisarc and hydranths for taxonomy within the Campanulariidae is also evaluated, and whether the size of nematocysts is variable or not, and therefore appropriate for species identification.
An interesting new gastrotrich from littoral meiobenthos (Long Beach Island, USA), with a key to species of Tetranchyroderma (Gastrotricha: Macrodasyida)
Authors: Todaro M.A.
Published: September 2002

Marine representatives of the phylum Gastrotricha are reported for the first time from the State of New Jersey, USA. Littoral and shallow sublittoral sediment collected at Ship Bottom on Long Beach Island, near Atlantic City, yielded 11 species belonging to eight genera in six families in the orders Macrodasyida (four genera in three families) and Chaetonotida (four genera in three families). Littoral samples were richer than the one sublittoral sample (7 vs 4 spp.). Among the taxa was a large, undescribed species of Tetranchyroderma characterized by the following key traits: total body length up to 605 μm; cuticular covering complete, made up of pentancres; a pair of cephalic tentacles; dorsal adhesive tubes arranged in dorsal and dorsolateral columns; a pair of ventral adhesive tubes arising from a common base, near the perigenital area only on the right side; peculiar cuticular openings ‘stomata’ along the ventrolateral margins of the body; protogynous hermaphroditism. Tetranchyroderma weissi sp. nov. is, at least in the investigated location, restricted to the sediment layers below 20 cm of the intertidal zone, and is able to live in thiobiotic sediment. A key to the described species of the world based on easily discernible traits, visible in both living and formalin-fixed specimens is provided.
The ultrastructure of two types of muscle fibre cells in the cyprid of Balanus amphitrite (Crustacea: Cirripedia)
Authors: Lagersson Niklas C.
Published: September 2002

This study examined two types of muscle fibre, associated with entirely different tasks in the cyprid of Balanus amphitrite (Crustacea: Cirripedia), and detected a striking difference. The first fibre type is found in the antennulary system, which is used for selecting the most suitable substrate for continuance of the cirripede life cycle. The second fibre type is associated with the stereotyped swimming behaviour of the cyprid. The antennulary fibres have the characteristics of ‘slow’ fibres, whereas the thoracic fibres display the properties of ‘fast’ muscle fibres. The difference between the thoracic and antennulary muscles emphasizes the specialized morphology of the cirripede cyprid linked to their unique role in settlement.
Reproductive biology of the crab Munida subrugosa (Decapoda: Anomura: Galatheidae) in the Beagle Channel, Argentina
Authors: Tapella Federico , Lovrich Gustavo A. , Romero M. Carolina , Thatje Sven
Published: September 2002

Munida subrugosa was sampled monthly from November 1997 to November 1999 in the Beagle Channel by means of an epibenthic trawl. The reproductive cycle started in May, reflected by the occurrence of ovigerous females. Maximum size of oocytes, maximum value of gonadosomatic index in females (16·8 g mm carapace length [CL]−1) and males (1·6 g mm CL−1), and the proportion (∼70%) of ovigerous females with full egg-clutches occurred in June. Since the proportion of ovigerous females in October was ∼5% and the planktonic larvae reportedly hatch in September, the embryonic development lasted ∼90–120 days. Females and males attained physiological maturity at 9·9 and 8·0 mm CL respectively, and males reached morphometric maturity at 24·4 mm CL. Fecundity was correlated with female size (r=0·85) and was between 124 and 10,750 eggs per female. Average diameter of recently extruded eggs was 0·69 mm (SD±0·06 mm). At the beginning of the reproductive cycle, ovigerous females had partial broods of ∼300 eggs, which represented <5% of complete clutch.
Population biology and growth of the hermit crab Dardanus insignis at Armação do Itapocoroy, southern Brazil
Authors: Branco Joaquim Olinto , Turra Alexander , Souto Flávio Xavier
Published: September 2002

This study was conducted between January and December 1995 at Armação do Itapocoroy, Penha, Santa Catarina, southern Brazil. Monthly samples were carried out in the morning, afternoon, and evening using two over-trawls with 6 m at the opening, 3·0-cm mesh at the outer part and 2·0-cm mesh in the bag. Dardanus insignis was collected year round but with higher densities in September and October. The hermit crabs were more abundant during the evening than the afternoon but no differences were recorded between morning and both evening and afternoon. Females were slightly more abundant than males but the sex ratio did not differ from 1:1. Females were more abundant in the smallest size-classes (<1·8 cm) while males outnumbered females in the largest ones (>2·2 cm). The individuals of this population of D. insignis have a mean cephalothoracic length of 1·89±0·40 cm (range 1·00 to 3·90 cm) and a mean weight of 40·26±27·06 g. The size distribution showed an unimodal pattern, with males being larger than ovigerous females, which, in turn, were larger than non-ovigerous females. Dardanus insignis showed a seasonal reproductive pattern with a peak from September to November and complete absence of ovigerous females from April to August. The von Bertalanffy growth function (VBGF) with temporal oscillation fitted for this population of D. insignis had the following parameters: L∞=4·40 cm, K=0·60, C=0·95, WP=0·35. Recruitment was estimated to start in September and was extended to the following months. Estimates of longevity ranged from 20 to 62 months. A mortality rate of 2·21 was estimated based on the length converted catch curve. The cephalothoracic length of males and females showed, respectively, positive and negative allometry with both cephalothoracic width and crab weight.
Ingestion of mesozooplankton by three species of bivalve; Mytilus edulis, Cerastoderma edule and Aequipecten opercularis
Authors: Lehane Clare , Davenport John
Published: September 2002

Mytilus edulis, Cerastoderma edule and Aequipecten opercularis were found to ingest zooplankton when suspended in mesh cages in the water column in the Firth of Clyde. Zooplankters were also found in the stomachs of bivalves that had been taken directly from their natural habitat. The bivalves consumed a wide range of zooplankton species, but selectively consumed smaller categories of zooplankton present. Condition of zooplankton in the stomachs of the bivalves varied with zooplankton species. A degree of larviphagy was evident, particularly in Mytilus edulis.
A complex didemnid ascidian from Whangamata, New Zealand
Authors: Kott Patricia
Published: September 2002

An undescribed species of the genus Didemnum (Didemnidae) reported from installations in Whangamata Harbour (Coromandel Peninsula), has a unique and conspicuous three-dimensional growth form (possibly associated with vertical and undersurfaces it occupies). It is also distinguished by a combination of the few characters available to define these small, simplified, convergent organisms. Its stellate spicules are sparse except for a patchy layer in the surface test, primary common cloacal canals are the full depth of the zooids, nine vas deferens coils surround the testis, the gut is long forming a double loop, and larvae have six pairs of ectodermal ampullae. Eleven species said to belong to this genus have previously been reported from New Zealand, but only six are valid Didemnum spp., and they all are distinguished readily from the present species. Nevertheless, there is no evidence that the new species is introduced, and the simplest explanation of it occurrence is that it is part of the little known indigenous didemnid fauna of New Zealand.
Hedgehog gene in Qingdao amphioxus Branchiostoma belcheri tsingtauense: cloning and expression pattern in early development
Authors: Zhang Y. , Mao B. , Zhang S. , Zhang H.
Published: September 2002

A fragment of hedgehog was first isolated by polymerase chain reaction (PCR) from genomic DNA of Qingdao amphioxus using degenerate primers designed according to the conserved sequence in the second exon of hedgehog family. Then RT-PCR and rapid amplification of cDNA ends (3′ and 5′ RACE) were carried out using the mRNA of 18-h neurulae as template. The PCR products were sequenced and constituted a 3540 bp-long hedgehog gene, containing a complete open reading frame. The predicted protein is 415-amino-acids long, showing a high level of identity to other hedgehog proteins. The results show that Qingdao amphioxus contains one and probably only one hedgehog gene. Whole mount in situ hybridization revealed that hedgehog expressed in the prospective notochord, the notochord, floor plate of neural tube and mouth, similarly to its vertebrate homologue Sonic-hedgehog gene. This suggested that amphioxus hedgehog gene might function in the notochord induction to neural tube cells and in the development of the mouth.
Reproductive biology of the smoothback angel shark, Squatina oculata (Elasmobranchii: Squatinidae), from the coast of Senegal (eastern tropical Atlantic)
Authors: Capapé C. , Seck A.A. , Gueye-Ndiaye A. , Diatta Y. , Diop M.
Published: September 2002

Two species of genus Squatina were recorded off the coast of Senegal and Squatina oculata is the most commonly caught in the area. Adult males and females studied were over 820 and 890 mm total length (TL) respectively, with the largest male and the largest female recorded being 1450 mm and 1570 mm and weighed 37 kg and 39 kg respectively. The females were significantly heavier than the males. Size at birth was between 226 and 266 mm and weight at birth between 129 and 159 g. Weight of ripe oocytes ranged from 87·65 to 117·60 g (mean SD 101·73±&;8·65). Gestation lasts one year minimum. Squatina oculata is a lecithotrophic species. Counts of ripe oocytes, eggs, embryos and fully developed foetuses showed that ovarian fecundity is significantly higher than uterine fecundity. The former ranged from 8 to 20 (mean SD 12·04±5·80), the latter from 3 to 8 (mean SD 6·22±3·41). There is no relationship between size and the categories of fecundity. Adult males and females were more common than the other categories of specimens landed. Among adults, females were more numerous than males, mainly gravid specimens.
The community structure of larval fish populations in an area of the Celtic Sea in 1998
Authors: Acevedo S. , Dwane O. , Fives J.M.
Published: September 2002

Ichthyoplankton from an area in the Celtic Sea was studied to provide an insight into the fish larval community structure in March, May and June 1998. Three station groups were defined each month, Neritic, Transition and Oceanic. The Neritic assemblages included larval stages of coastal fish species and the Oceanic assemblages included mesopelagic and high-oceanic fish species which were not recorded from any of the Neritic stations. The Transition stations usually contained species characteristic of both the Neritic and Oceanic assemblages. It is suggested that these broad patterns of larval fish distributions are constant features of the Celtic Sea area, probably related to the spawning location of the adults. The area is, in general, species poor, with the Oceanic stations usually dominated by a single species, indicating the presence of a large spawning school of fish.
Sex differences in cleaning behaviour and diet of a Caribbean cleaning goby
Authors: Whiteman Elizabeth A. , Côté Isabelle M.
Published: September 2002

Male and female sharknose cleaning gobies Elacatinus evelynae (Gobiidae) occupying cleaning stations in monogamous pairs differed significantly in cleaning behaviour and diet. Females spent five times longer cleaning, took more bites from clients, engaged in more cleaning events on more client species, and cleaned at a higher rate than males. These behavioural differences tended to be reflected in the diet, with more females ingesting more client-gleaned items than males. These results are consistent with greater energetic requirements for reproduction for females. Male cleaning gobies were frequently absent from cleaning stations, presumably guarding eggs, and their presence at cleaning stations gave rise to foraging conflicts and interactions with females. The cleaning rate of females was significantly lowered by the presence of males, whether cleaning or not, whereas males cleaned for longer and took more bites when females were present. When cleaning the same client, males and females showed priority of first inspection, with females cleaning longer and taking more bites in cleaning events they initiated while males gained similar advantages in client- and male-initiated interactions. Furthermore, females initiated cleaning on larger clients, which may give them a foraging priority on a higher-quality resource since larger clients tend to have more ectoparasites. Finally, from a client's perspective, the cleaning service provided appears better in terms of length of inspection and bites taken when both males and females are at a cleaning station than when a single cleaner is present. However, the foraging differences and interactions between male and female cleaning gobies are of little consequence to clients since the cleaning service provided is simply reapportioned between males and females rather than changed by the interactions between gobies.
Feeding strategies of Polyacanthonotus rissoanus (Pisces: Notacanthidae) in the deep western Mediterranean
Authors: Carrassón M. , Matallanas J.
Published: September 2002

The feeding habits of Polyacanthonotus rissoanus, the sixth most abundant species below 1000 m on the deep slope of the Catalan Sea (western Mediterranean), were studied in the Mediterranean Sea. Samples were obtained at depths between 1000 and 2250 m. Diet was analysed for two seasons (summer and autumn) and three different bathymetric strata. The most important food items found were small epibenthic and suprabenthic crustaceans and polychaetes, and occasionally other groups such as Priapulida, Gastropoda and Foraminifera. At 1000–1425 m, the mysids were preferential prey, while in summer at all depths analysed, isopods were a dominant prey. Polychaetes have certain incidence in the diet only at 1000–1425 m, being a dominant prey in autumn. Individuals at the 1000–1425 m depth ingest larger numbers of prey of higher average sizes than those at 1425–2250 m. The scarcity of resources below 1200–1400 m resulted in diversification of diet and encouraged preying on deposited foraminiferans, molluscs or moving copepods.
Determination of the levels of indicator bacteria and Salmonella spp. in Chamelea gallina, L. and seawater on the coastline of Sile, Turkey
Authors: Altug G. , Bayrak Y.
Published: September 2002

Indicator bacteria and Salmonella spp. were investigated in both Chamelea gallina and seawater from six stations on the coastline of Sile, Turkey. Studies were carried out on 15 days from June to December in 1998–1999. Chamelea gallina samples which were collected at approximately 5–10 metres depth from the chosen stations were examined for faecal coliform, Escherichia coli and Salmonella spp. Bacteria numbers were highest in July and August. Bacteria distribution was found to be statistically significant between stations. No Salmonella spp. were detected in the samples.
A Desseria sp. from flathead mullet in South Africa
Authors: Smit N.J. , Eiras J.C. , Ranzani-Paiva M.J.T. , Davies A.J.
Published: September 2002

Five of 26 flathead mullet (Mugil cephalus) captured in the Seekoei River estuary in South Africa showed haemogregarine infections. Both trophozoites and gamonts were observed, and image analysis technology was used in parasite morphometric description. Gamonts were compared with those of Desseria mugili from Brazil and found to be different. The parasite mostly closely matched a haemogregarine previously illustrated, but not described from South Africa, and apparent lack of merogony suggested that it was a species of Desseria.
Otolith microstructure of the Russian sturgeon, Acipenser gueldenstadti
Authors: Arai Takaomi , Miyazaki Nobuyuki
Published: September 2002

Otolith microstructure of the Russian sturgeon, Acipenser gueldenstadti was examined in adult samples collected in the Caspian Sea. The microstructure of the otolith was the same among specimens. The anterior side of the sagitta grew in two directions elongating both the long and short arms, and the long arm sections exhibited 14–21 distinct translucent and opaque zones. Otolith increments in this species can be used for age determination.
Understanding protein folding with energy landscape theory Part I: Basic concepts
Authors: Plotkin Steven S. , Onuchic José N.
Published: September 2002

1. Introduction 111

2. Levinthal's paradox and energy landscapes 115

2.1 Including randomness in the energy function 121

2.2 Some effects of energetic correlations between structurally similar states 126

3. Resolution of problems by funnel theory 128

3.1 Physical origin of free-energy barriers 133

4. Generic mechanisms in folding 138

4.1 Collapse, generic and specific 139

4.2 Helix formation 139

4.3 Nematic ordering 141

4.4 Microphase separation 142

5. Signatures of a funneled energy landscape 145

6. Statistical Hamiltonians and self-averaging 152

7. Conclusions and future prospects 156

8. Acknowledgments 157

9. Appendix: Glossary of terms 157

10. References 158

The current explosion of research in molecular biology was made possible by the profound
discovery that hereditary information is stored and passed on in the simple, one-dimensional
(1D) sequence of DNA base pairs (Watson & Crick, 1953). The connection between heredity
and biological function is made through the transmission of this 1D information, through
RNA, to the protein sequence of amino acids. The information contained in this sequence is
now known to be sufficient to completely determine a protein's geometrical 3D structure, at
least for simpler proteins which are observed to reliably refold when denatured in vitro, i.e.
without the aid of any cellular machinery such as chaperones or steric (geometrical)
constraints due to the presence of a ribosomal surface (for example Anfinsen, 1973) (see
Fig. 1). Folding to a specific structure is typically a prerequisite for a protein to function,
and structural and functional probes are both often used in the laboratory to test for the
in vitro yield of folded proteins in an experiment.
A review of DNA sequencing techniques
Authors: França Lilian T. C. , Carrilho Emanuel , Kist Tarso B. L.
Published: September 2002

1. Summary 169

2. Introduction 170

3. Sanger's method and other enzymic methods 170

3.1 Random approach 171

3.2 Direct approach 171

3.3 Enzyme technology 175

3.4 Sample preparation 175

3.5 Labels and DNA labelling 176

3.5.1 Radioisotopes 176

3.5.2 Chemiluminescent detection 176

3.5.3 Fluorescent dyes 177

3.6 Fragment separation and analysis 180

3.6.1 Electrophoresis 180

3.6.2 Mass spectrometry – an alternative 182

4. Maxam & Gilbert and other chemical methods 183

5. Pyrosequencing – DNA sequencing in real time by the detection of released PPi 187

6. Single molecule sequencing with exonuclease 190

7. Conclusion 192

8. Acknowledgements 192

9. References 193

The four best known DNA sequencing techniques are reviewed. Important practical issues
covered are read-length, speed, accuracy, throughput, cost, as well as the automation of
sample handling and preparation. The methods reviewed are: (i) the Sanger method and its
most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other
chemical methods; (iii) the PyrosequencingTM method – DNA sequencing in real time by the
detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with
exonuclease (exonuclease digestion of a single molecule composed of a single strand of
fluorescently labelled deoxynucleotides). Each method is briefly described, the current
literature is covered, advantages, disadvantages, and the most suitable applications of each
method are discussed.
Is Christianity probable? Swinburne's apologetic programme
Authors: HASKER WILLIAM
Published: September 2002

Richard Swinburne's tetralogy on Christian doctrine, together with his earlier trilogy on the philosophy of theism, is one of the most important apologetic projects of recent times. This paper focuses on some difficulties with this project that stem from Swinburne's use of confirmation theory. Arguably, the problem of dwindling probabilities, pointed out by Plantinga, has not been solved. The paper is principally focused, however, on the ways in which Swinburne's confirmation theory contributes to his comparative neglect of the personal, existential dimension of Christianity. A solution for these difficulties is suggested but not elaborated.