bluuebunny/crossref_metadata_2025 huggingface dataset:
Basement membrane integrity and keratinization in healthy and ulcerated bovine hoof tissue
Authors: Hendry Kay AK , Knight Christopher H , Galbraith Hugh , Wilde Colin J
Published: February 2003

Damage to, or deterioration of, the keratinized horn tissue of the bovine hoof claw culminates ultimately in the development of solear ulceration. We have observed abnormal keratin distribution at the site of solear ulceration in the bovine claw that may be due to alteration of the positional cues of the keratinocytes. In this study we have characterized key cell biological changes associated with ulceration in the claw that may precipitate abnormal keratinization. Loss of basement membrane at sites of ulceration was found by immunofluorescent detection of laminin and integrins. In other tissues, basement membrane breakdown results from degradation by matrix metalloproteinases (MMPs). Similarly, elevated levels of MMPs 2 and 9 were observed in ulcerated bovine claw tissue both by zymography and, quantitatively, by assay of enzyme activity. In the sole of claws that contained an ulcer, tissue distal to the ulcer site also had elevated MMP 2 when compared with healthy sole tissue from the same animals, as did sole tissue of claws recovering from ulceration. Tissue inhibitor of metalloproteinase 2 (TIMP 2) was detected by ELISA in healthy tissue. TIMP 2 tended to be lower in diseased tissue distal to ulcer sites, and was significantly lower in ulcerated tissue. MMP 2 was located by immunofluorescence in the dermal and basal epidermal region of sole tissue, in the region of the basement membrane. Increased punctate staining of material in the dermis was associated with ulcerated material. ELISA of TIMP 2 in tissue extracts enriched for dermis or epidermis confirmed that the inhibitor was located predominantly in the dermis. To investigate a possible causal relationship between basement membrane anchorage and epidermal keratinization, the effect of function-blocking antibodies to laminins and integrins was tested in tissue explant cultures prepared from healthy sole tissue. Anti-integrin antibody treatment had no effect on either protein or DNA synthesis. In contrast, in the presence of anti-laminin antibody, protein synthesis was decreased in a concentration-dependent manner, a significant effect being observed at the highest concentration after treatment for 24 h. At this concentration, DNA synthesis was also decreased after 48 h of culture, an effect that may be relevant to a hibernal reduction in claw cell turnover, and the associated seasonal vulnerability of cows to claw damage. The results provide evidence for basement membrane disruption at ulcer sites, and an increased potential for disruption in the diseased claw, and a causal link between this and abnormal epidermal keratinization. Basement membrane disruption is in turn associated with reciprocal changes in MMPs and their inhibitors, favouring extracellular proteolysis. Whether MMP activation is the primary cause of dermal–epidermal deterioration and, if so, how MMP activation is triggered, remains to be determined.
Kinetics of hydroxymethylfurfural, lactulose and furosine formation in milk with different fat content
Authors: Claeys Wendie L , Van Loey Ann M , Hendrickx Marc E
Published: February 2003

In the context of the general applicability of hydroxymethylfurfural (HMF), lactulose and furosine as time-temperature integrators (TTIs) for thermal processing of milk, the influence of milk fat content was studied. Formation kinetics were analysed for milk with fat content of 4·0±<0·1%. In previous experiments, it was observed that, under isothermal and non-isothermal heating conditions, formation of the three chemical compounds could be described by pseudo-zero order kinetics. Since the kinetic model was known, the experimental design could be simplified. Data were analysed by a non-linear regression procedure and results were evaluated by construction of joint confidence regions and temperature time tolerance (TTT-) diagrams. Formation kinetics of HMF and lactulose was not affected by milk fat content. Regarding furosine, significant differences were observed between kinetic parameters in whole, semi-skimmed and skimmed milk. The observed differences however were negligible in the context of process impact evaluation.
Association of denatured whey proteins with casein micelles in heated reconstituted skim milk and its effect on casein micelle size
Authors: Anema Skelte G , Li Yuming
Published: February 2003

When skim milk at pH 6·55 was heated (75 to 100 °C for up to 60 min), the casein micelle size, as monitored by photon correlation spectroscopy, was found to increase during the initial stages of heating and tended to plateau on prolonged heating. At any particular temperature, the casein micelle size increased with longer holding times, and, at any particular holding time, the casein micelle size increased with increasing temperature. The maximum increase in casein micelle size was about 30–35 nm. The changes in casein micelle size were poorly correlated with the level of whey protein denaturation. However, the changes in casein micelle size were highly correlated with the levels of denatured whey proteins that were associated with the casein micelles. The rate of association of the denatured whey proteins with the casein micelles was considerably slower than the rate of denaturation of the whey proteins. Removal of the whey proteins from the skim milk resulted in only small changes in casein micelle size during heating. Re-addition of β-lactoglobulin to the whey-protein-depleted milk caused the casein micelle size to increase markedly on heat treatment. The changes in casein micelle size induced by the heat treatment of skim milk may be a consequence of the whey proteins associating with the casein micelles. However, these associated whey proteins would need to occlude a large amount of serum to account for the particle size changes. Separate experiments showed that the viscosity changes of heated milk and the estimated volume fraction changes were consistent with the particle size changes observed. Further studies are needed to determine whether the changes in size are due to the specific association of whey proteins with the micelles or whether a low level of aggregation of the casein micelles accompanies this association behaviour. Preliminary studies indicated lower levels of denatured whey proteins associated with the casein micelles and smaller changes in casein micelle size occurred as the pH of the milk was increased from pH 6·5 to pH 6·7.
Evidence of a relationship between autolysis of starter bacteria and lipolysis in Cheddar cheese during ripening
Authors: Collins Yvonne F , McSweeney Paul LH , Wilkinson Martin G
Published: February 2003

Cell viability, autolysis and lipolysis were studied in Cheddar cheese made using Lactococcus lactis subsp. cremoris AM2 or Lactococcus lactis subsp. cremoris HP. Cheddar cheese was made in triplicate over a 3 month period and ripened for 238 days at 8 °C. Cell viability in cheese was lower for AM2 (a non-bitter strain) than for strain HP (a bitter strain). Autolysis, monitored by the level of the intracellular marker enzyme, lactate dehydrogenase (EC 1.1.1.27) in cheese ‘juice’ extracted by hydraulic pressure, was much greater in the cheese made using AM2 than that made with HP. Lipolysis was determined by the increase during ripening of individual free fatty acids (FFA) from butyric (C4[ratio ]0) to linolenic acid (C18[ratio ]3) measured using a high performance liquid chromatographic technique. Levels of individual FFA from butyric (C4[ratio ]0) to linolenic (C18[ratio ]3) acids increased significantly (P<0·05) during ripening in cheeses made with either starter culture. Palmitic (C16[ratio ]0) and oleic (C18[ratio ]1) acids were the most abundant FFA throughout ripening in all cheeses. Levels of caprylic (C8[ratio ]0), myristic (C14[ratio ]0), palmitic (C16[ratio ]0) and stearic (C18[ratio ]0) acids were significantly higher (P<0·05) in cheeses manufactured with Lc. lactis subsp. cremoris AM2 than in cheeses manufactured with Lc. lactis subsp. cremoris HP. Differences in levels of lipolysis between strains was not due to differences in the specific lipolytic or esterolytic activities in cell free extracts of the strains as measured by activity on triolein (lipase) and p-nitrophenylbutyrate (esterase) substrates. Therefore, evidence is provided for a relationship between the extent of starter cell autolysis and the level of lipolysis during Cheddar cheese ripening.
Isolation, purification and characterization of chymosin from riverine buffalo (Bubalos bubalis)
Authors: Mohanty Ashok K , Mukhopadhyay Utpal K , Kaushik Jai K , Grover Sunita , Batish Virender K
Published: February 2003

Chymosin, an aspartyl proteinase, is used for curdling of milk and manufacture of cheese. We report the purification and the physicochemical properties of chymosin isolated from the abomasal tissue of buffalo calves. The enzyme preparation extracted from buffalo abomasal tissues could be purified 29–fold using anion exchange and gel filtration chromatography. The molecular weight of the purified enzyme was 35·6 kDa on SDS-PAGE. Partial N-terminal amino acid sequence of the first eight amino acid sequences of buffalo chymosin was identical to the first eight amino acid sequences of cattle chymosin. Buffalo chymosin exhibited a skewed bell-shaped stability profile as a function of temperature with maximum activity near 55 °C. Milk clotting activity decreased gradually as pH increased. The enzyme became completely inactive, however, above pH 7·0. The ratio of milk clotting to proteolytic activity was 3·03. When compared with cattle chymosin, there were subtle differences in the stability and relative proteolytic activity of buffalo chymosin.
Repeatability estimates for milk coagulation traits and non-coagulation of milk in Finnish Ayrshire cows
Authors: Tyrisevä Anna-Maria , Ikonen Tiina , Ojala Matti
Published: February 2003

Effects of systematic environmental factors and milk production and quality traits on milk coagulation properties (MCP), and on repeatability of those traits were estimated from 979 milk samples collected once a month over a period of 2 years from 83 Finnish Ayrshire cows. Estimation was based on a multitrait animal model and REML methodology. In addition, persistence of non-coagulation of milk in individual cows, and factors associated with it were established from a sub sample of 24 cows producing non-coagulating (NC) milk at least once. MCP were at their best during the first lactation, at the beginning and at the end of lactation, and during grazing seasons. Variation in MCP with systematic environmental factors was partly due to variation in composition and quality of milk, especially in pH and ln (somatic cell count, SCC). Coefficients of repeatability for milk coagulation time and curd firmness were 0·65 and 0·68. These estimates were of the same magnitude as those for protein content, but were higher than those for daily milk yield, fat content, pH, and SCC. Based on the repeatability estimates for the milk coagulation traits and effects of the environmental factors, cows should be sampled at least three times during a lactation to estimate reliably breeding values for the milk coagulation traits. A total of 10% of the milk samples did not coagulate in 30 min after addition of rennet. Cows that produced NC milk at least once (30% of the cows) could be classified into those that produced NC milk only a few times during a lactation and those that produced NC milk at almost every sampling. Based on logistic regression analyses, peak and mid-lactation, high milk yield, low protein and fat content and high pH increased the risk of non-coagulation of milk.
Chronic oxytocin treatment causes reduced milk ejection in dairy cows
Authors: Bruckmaier Rupert M
Published: February 2003

The major milk fraction stored in the bovine udder, the alveolar milk, is not available for milk removal before being actively shifted to the cisternal cavities by the milk ejection reflex (Knight et al. 1994; Pfeilsticker et al. 1996). Tactile teat stimulation, provided by the liner throughout milking, causes continuous release of oxytocin from the neuro-pituitary into the blood circulation, which induces myoepithelial contraction and shifting of alveolar milk into the cistern until the end of milking (Bruckmaier et al. 1994; Crowley & Armstrong, 1992; Gorewit et al. 1983; Lefcourt & Akers, 1983). However, milk ejection during machine milking is not complete. A residual milk fraction of 10–30% remains in the udder and is only removed after administration of supraphysiological amounts of oxytocin, usually at least 10 i.u. of oxytocin injected i.v. (Bruckmaier & Blum, 1998). In dairy practice, exogenous oxytocin is often used at high dosages to treat disturbed or incomplete milk ejection. It is reported by farmers and veterinarians that after long-term use of exogenous oxytocin animals become addicted to the treatment and withdrawal of oxytocin causes reduced milk ejection.
Proteolysis in rennet-coagulated Spanish hard cheeses made from milk preserved by refrigeration and addition of carbon dioxide
Authors: Ruas-Madiedo Patricia , Bada-Gancedo Juan Carlos , Delgado Teresa , Gueimonde Miguel , de los Reyes-Gavilán Clara G
Published: February 2003

On-farm refrigeration of milk reduces the growth rate of mesophilic bacteria so allowing longer storage time of raw milk before processing. However, refrigeration creates a selective pressure favouring the multiplication of psychrotrophic bacteria present as normal contaminants in raw milk. Psychrotrophs are killed by most of the currently employed pasteurization and sterilization treatments of milk but they can produce extracellular heat-stable proteinases and lipases, which are capable of degrading various milk components, affecting the storage-life of heat-processed milk and the quality of dairy products (Champagne et al. 1994; Shah, 1994).
Estimation of inbreeding in cattle using RAPD markers
Authors: Bhattacharya Tarun K , Kumar Pushpendra , Joshi Jamuna D , Kumar Satish
Published: February 2003

Inbreeding indicates the degree of homozygosity at a locus within a population. Normally inbreeding is estimated in terms of a coefficient calculated from the pedigree of an individual. If no history is available, however, there is no way to estimate the inbreeding coefficient. Sometimes, data on individuals are missing, and that too can prevent the estimation of the inbreeding coefficient, which is essential for formulation of a breeding programme at the farm level and for breed development.
Heterogeneity of proteolytic enzyme activities in milk samples of different somatic cell count
Authors: Somers Joanne M , O'Brien Bernadette , Meaney William J , Kelly Alan L
Published: February 2003

Milk contains the alkaline proteinase plasmin and lysosomal proteinases; the significance of the latter is ill-defined. The objective of this study was to investigate composition and activities of several different proteolytic enzymes in milk samples of varying somatic cell count (SCC). Increasing milk SCC was correlated with increased plasmin, cathepsin D and cysteine protease activities, with concomitant increases in proteolysis in milk. Addition of plasmin inhibitors confirmed the heterogeneity of proteinase activities in milk, as urea-PAGE analysis of milk samples showed casein hydrolysis in milk after 7 d storage even in samples with inhibitors added; extent and heterogeneity of proteolysis was correlated with milk SCC. Rennet coagulation properties were not significantly correlated with SCC, or activities of measured enzymes. Milk of increasing SCC also exhibited decreased physical stability during incubation of milk at 37 °C. Pasteurized milk was more stable than raw milk, suggesting that the enzyme(s) or mechanisms leading to such instability are impaired by pasteurization. Overall, milk has a very heterogeneous proteolytic enzyme population, with a higher significance of non-plasmin enzymes, such as cathepsin D and cysteine proteinases, than perhaps previously recognised.
On the instability of a falling film due to
localized heating
Authors: SKOTHEIM JAN M. , THIELE UWE , SCHEID BENOIT
Published: February 2003

We analyse the stability of a thin film falling under the influence of gravity down a
locally heated plate. Marangoni flow, due to local temperature changes influencing
the surface tension, opposes the gravitationally driven Poiseuille flow and forms a
horizontal band at the upper edge of the heater. The thickness of the band increases
with the surface tension gradient, until an instability forms a rivulet structure periodic
in the transverse direction. We study the dependence of the critical Marangoni number,
a non-dimensional measure of the surface tension gradient at the onset of instability,
on the associated Bond and Biot numbers, non-dimensional measures of the curvature
pressure and heat-conductive properties of the film respectively. We develop a model
based on long-wave theory to calculate base-state solutions and their linear stability.
We obtain dispersion relations, which give us the wavelength and growth rate of the
fastest growing mode. The calculated film profile and wavelength of the most unstable
mode at the instability threshold are in quantitative agreement with the experimental
results. We show via an energy analysis of the most unstable linear eigenmode that the
instability is driven by gravity and an interaction between base-state curvature and
the perturbation thickness. In the case of non-zero Biot number transverse variations
of the temperature profile also contribute to destabilization.
The mixing layer over a deep cavity at
high-subsonic speed
Authors: FORESTIER NICOLAS , JACQUIN LAURENT , GEFFROY PHILIPPE
Published: February 2003

The flow over a cavity at a Mach number 0.8 is considered. The cavity is deep with
an aspect ratio (length over depth) L/D = 0.42. This deep cavity flow exhibits several
features that makes it different from shallower cavities. It is subjected to very regular
self-sustained oscillations with a highly two-dimensional and periodic organization
of the mixing layer over the cavity. This is revealed by means of a high-speed
schlieren technique. Analysis of pressure signals shows that the first tone mode is the
strongest, the others being close to harmonics. This departs from shallower cavity
flows where the tones are usually predicted well by the standard Rossiter’s model.
A two-component laser-Doppler velocimetry system is also used to characterize the
phase-averaged properties of the flow. It is shown that the formation of coherent
vortices in the region close to the boundary layer separation has some resemblance to
the ‘collective interaction mechanism’ introduced by Ho & Huang (1982) to describe
mixing layers subjected to strong sub-harmonic forcing. Otherwise, the conditional
statistics show close similarities with those found in classical forced mixing layers
except for the production of random perturbations, which reaches a maximum in
the structure centres, not in the hyperbolic regions with which turbulence production
is usually associated. An attempt is made to relate this difference to the elliptic
instability that may be observed here thanks to the particularly well-organized nature
of the flow.
Tsunami run-up and draw-down
on a plane beach
Authors: CARRIER GEORGE F. , WU TAI TEI , YEH HARRY
Published: February 2003

Tsunami run-up and draw-down motions on a uniformly sloping beach are evaluated
based on fully nonlinear shallow-water wave theory. The nonlinear equations of
mass conservation and linear momentum are first transformed to a single linear
hyperbolic equation. To solve the problem with arbitrary initial conditions, we apply
the Fourier–Bessel transform, and inversion of the transform leads to the Green
function representation. The solutions in the physical time and space domains are then
obtained by numerical integration. With this semi-analytic solution technique, several
examples of tsunami run-up and draw-down motions are presented. In particular,
detailed shoreline motion, velocity field, and inundation depth on the shore are
closely examined. It was found that the maximum flow velocity occurs at the moving
shoreline and the maximum momentum flux occurs in the vicinity of the extreme draw-down
location. The direction of both the maximum flow velocity and the maximum
momentum flux depend on the initial waveform: it is in the inshore direction when
the initial waveform is predominantly depression and in the offshore direction when
the initial waves have a dominant elevation characteristic.
Amplitude growth rate of a Richtmyer–Meshkov
unstable two-dimensional interface to
intermediate times
Authors: ZABUSKY NORMAN J. , KOTELNIKOV ALEXEI D. , GULAK YURIY , PENG GAOZHU
Published: February 2003

The Richtmyer–Meshkov instability in an incompressible and compressible stratified
two-dimensional ideal flow is studied analytically and numerically. For the incompressible
problem, we initialize a single small-amplitude sinusoidal perturbation of
wavelength λ, we compute a series expansion for the amplitude a in powers of t up
to t(11) with the MuPAD computer algebra environment. This involves harmonics up
to eleven. The simulations are performed with two codes: incompressible, a vortex-in-
cell numerical technique which tracks a single discontinuous density interface; and
compressible, PPM for a shock-accelerated case with a finite interfacial transition
layer (ITL). We identify properties of the interface at time t = tM at which it first
becomes ‘multivalued’. Here, we find the normalized width of the ‘spike’ is related
to the Atwood number by (wm/λ)−0.5 = −0.33A. A high-order Pad approximation
is applied to the analytical series during early time and gives excellent results for
the interface growth rate a˙. However, at intermediate times, t > tM, the agreement
between numerical results and different-order Padé approximants depends on the
Atwood number. During this phase, our numerical solutions give a˙∝O(t−1) for small
A and a˙∝O(t−0.4) for A = 0.9. Experimental data of Prasad et al. (2000) for SF6
(post shock Atwood number = 0.74) shows an exponent between −0.68 and −0.72
and we obtain −0.683 for the compressible simulation. For this case, we illustrate
the important growth of vortex-accelerated (secondary) circulation deposition of both
signs of vorticity and the complex nature of the roll-up region.
Mixed velocity–passive scalar statistics in
high-Reynolds-number turbulence
Authors: MYDLARSKI L.
Published: February 2003

Statistics of the mixed velocity–passive scalar field and its Reynolds number
dependence are studied in quasi-isotropic decaying grid turbulence with an imposed mean
temperature gradient. The turbulent Reynolds number (using the Taylor microscale as
the length scale), Rλ, is varied over the range 85 [les ] Rλ [les ] 582. The passive scalar under
consideration is temperature in air. The turbulence is generated by means of an active
grid and the temperature fluctuations result from the action of the turbulence on the
mean temperature gradient. The latter is created by differentially heating elements at
the entrance to the wind tunnel plenum chamber. The mixed velocity–passive scalar
field evolves slowly with Reynolds number. Inertial-range scaling exponents of the
co-spectra of transverse velocity and temperature,
Evθ(k1), and its real-space analogue,
the ‘heat flux structure function,’
〈Δv(r)Δθ(r)〉, show a slow evolution
towards their
theoretical predictions of −7/3 and 4/3, respectively. The sixth-order longitudinal
mixed structure functions, 〈(Δu(r))2(Δθ(r))4〉, exhibit inertial-range structure function
exponents of 1.36–1.52. However, discrepancies still exist with respect to the various
methods used to estimate the scaling exponents, the value of the scalar intermittency
exponent, μθ, and the effects of large-scale phenomena (namely shear, decay and
turbulent production of 〈θ2〉) on 〈(Δu(r))2(Δθ(r))4〉. All the measured fine-scale statistics
required to be zero in a locally isotropic flow are, or tend towards, zero in the limit
of large Reynolds numbers. The probability density functions (PDFs) of Δv(r)Δθ(r)
exhibit roughly exponential tails for large separations and super-exponential tails
for small separations, thus displaying the effects of internal intermittency. As the
Reynolds number increases, the PDFs become symmetric at the smallest scales – in
accordance with local isotropy. The expectation of the transverse velocity fluctuation
conditioned on the scalar fluctuation is linear for all Reynolds numbers, with slope
equal to the correlation coefficient between v and θ. The expectation of (a surrogate
of) the Laplacian of the scalar reveals a Reynolds number dependence when conditioned on the transverse velocity fluctuation (but displays no such dependence when
conditioned on the scalar fluctuation). This former Reynolds number dependence is
consistent with Taylor’s diffusivity independence hypothesis. Lastly, for the statistics
measured, no violations of local isotropy were observed.
Magnetohydrodynamic convection in a vertical
slot with horizontal magnetic field
Authors: BURR ULRICH , BARLEON LEOPOLD , JOCHMANN PAUL , TSINOBER ARKADY
Published: February 2003

This article presents an experimental study of magnetohydrodynamic convection in a
tall vertical slot under the influence of a horizontal magnetic field. The test fluid is an
eutectic sodium potassium Na22K78 alloy with a small Prandtl number of Pr ≈ 0:02.
The experimental setup covers Rayleigh numbers in the range 103 [lsim ] Ra [lsim ] 8×104
and Hartmann numbers 0 < M < 1600. The effect of the magnetic field on the
convective heat transport is determined not only by damping as expected from
Joule dissipation but also, for magnetic fields not too strong, the convective heat
transfer may be considerably enhanced compared to ordinary hydrodynamic (OHD)
flow. Estimates of the isotropy properties of the flow by a four-element temperature
probe demonstrate that the increase in convective heat transport accompanies the
formation of strong local anisotropy of the turbulent eddies in the sense of an
alignment of the main direction of vorticity with the magnetic field. The reduced
three-dimensional nonlinearities in non-isotropic flow favour the formation of largescale
vortex structures compared to OHD flow, which are more effective for convective
heat transport. Along with the formation of quasi-two-dimensional vortex structures,
temperature fluctuations may be considerably enhanced in a magnetic field that is
not too strong. However, above Hartmann numbers M [gsim ] 400 the formerly strongly
time-dependent flow suddenly becomes stationary with an extended region of high
convective heat transport at stationary flow. Finally, for very high Hartmann numbers
the convective motion is strongly suppressed and the heat transport is reduced to a
state close to pure heat conduction.
Instability of quasi-geostrophic vortices in a
two-layer ocean with a thin upper layer
Authors: BENILOV E. S.
Published: February 2003

We examine the stability of a quasi-geostrophic vortex in a two-layer ocean with a
thin upper layer on the f-plane. It is assumed that the vortex has a sign-definite swirl
velocity and is localized in the upper layer, whereas the disturbance is present in both
layers. The stability boundary-value problem admits three types of normal modes:
fast (upper-layer-dominated) modes, responsible for equivalent-barotropic instability,
and two slow baroclinic types (mixed- and lower-layer-dominated modes). Fast modes
exist only for unrealistically small vortices (with a radius smaller than half of the
deformation radius), and this paper is mainly focused on the slow modes. They
are examined by expanding the stability boundary-value problem in powers of the
ratio of the upper-layer depth to the lower-layer depth. It is demonstrated that the
instability of slow modes, if any, is associated with critical levels, which are located at
the periphery of the vortex. The complete (sufficient and necessary) stability criterion
with respect to slow modes is derived: the vortex is stable if and only if the potential-vorticity
gradient at the critical level and swirl velocity are of the same sign. Several
vortex profiles are examined, and it is shown that vortices with a slowly decaying
periphery are more unstable baroclinically and less barotropically than those with a
fast-decaying periphery, with the Gaussian profile being the most stable overall. The
asymptotic results are verified by numerical integration of the exact boundary-value
problem, and interpreted using oceanic observations.
The physical mechanism for vortex merging
Authors: CERRETELLI C. , WILLIAMSON C. H. K.
Published: February 2003

In this paper, we study the interaction of two co-rotating trailing vortices. It is
well-known that vortices of like-sign ultimately merge to form a single vortex, and
there has been much work on measuring and predicting the initial conditions for the
onset of merger, especially concerning the critical vortex core radius. However, the
physical mechanism causing this merger has received little attention. In this work,
we directly measure the structure of the antisymmetric vorticity field that causes the
co-rotating vortices to be pushed towards each other during merger. We discover
that the form of the antisymmetric vorticity comprises two counter-rotating vortex
pairs, whose induced velocity field readily pushes the two centroids together. The
merging velocity computed from the antisymmetric vorticity field agrees closely with
the merging velocity measured directly from the total (original) flow field.

The co-rotating vortex pair evolves through four distinct phases. The initial stage
comprises a diffusive growth, which can be either viscous or turbulent. In either case,
the number of turns that they rotate around one another until the vortices start
to merge increases with Reynolds number (Re). If one observes the streamlines in
a rotating reference frame (moving with the vortices), then one finds an inner and
outer recirculating region of the flow bounded by a separatrix streamline. When the
vortices grow large enough in the first stage, diffusion across the separatrix places
vorticity into the outer recirculating region of the flow, and this leads to the generation
of the antisymmetric vorticity, causing convective merger. This second (convective)
stage corresponds to the motion of the vortex centroids towards each other, and is a
process which is almost independent of viscosity. During the late part of this stage,
the antisymmetric vorticity is diminished by a symmetrization process, and the final
merging into one vorticity structure is achieved by a second diffusive stage. The fourth
and ultimate phase is one where the merged vortex core grows by diffusion.
Hydraulic control of homogeneous
shear flows
Authors: GARRETT CHRIS , GERDES FRANK
Published: February 2003

If a shear flow of a homogeneous fluid preserves the shape of its velocity profile, a standard
formula for the condition for hydraulic control suggests that this is achieved when
the depth-averaged flow speed is less than (gh)1/2. On the other hand, shallow-water
waves have a speed relative to the mean flow of more than (gh)1/2, suggesting that
information could propagate upstream. This apparent paradox is resolved by showing
that the internal stress required to maintain a constant velocity profile depends on
flow derivatives along the channel, thus altering the wave speed without introducing
damping. By contrast, an inviscid shear flow does not maintain the same profile
shape, but it can be shown that long waves are stationary at a position of hydraulic
control.
Dynamics of target patterns in
low-Prandtl-number convection
Authors: SIGGERS JENNIFER H.
Published: February 2003

Axisymmetric Rayleigh–Bénard convection in a cylinder with vertical axis is studied.
The nonlinear behaviour is investigated near the onset of convection using an
eigenfunction expansion. It is found that initially a steady target pattern develops;
the number of rolls depends only on the aspect ratio of the box. At about 5%
beyond onset, an oscillatory pattern develops, in which the number of rolls oscillates
between two adjacent values. The transitions between the initial steady state and this
oscillatory pattern are also investigated, and fall into two main categories. As the
Rayleigh number is reduced to the transition point, either the period of the travelling
wave tends to infinity, whilst its amplitude stays finite, or there is a sudden transition
to a vascillating pattern, the amplitude of which becomes smaller and finally vanishes,
whilst the period remains finite. The results are compared with experimental work.
Modelling the motion of particles around
choanoflagellates
Authors: ORME B. A. A. , BLAKE J. R. , OTTO S. R.
Published: February 2003

The three-dimensional particle paths due to a helical beat pattern of the flagellum of
a sessile choanoflagellate, Salpingoeca Amphoridium (SA), are modelled and compared
to the experimental observations of Pettitt (2001). The organism’s main components
are a flagellum and a cell body which are situated above a substrate such that the
interaction between these entities is crucial in determining the fluid flow around the
choanoflagellate. This flow of fluid can be characterized as Stokes flow and a flow
field analogous to one created by the flagellum is generated by a distribution of
stokeslets and dipoles along a helical curve.

The model describing the flow considers interactions between a slender flagellum,
an infinite flat plane (modelling the substrate) and a sphere (modelling the cell
body). The use of image systems appropriate to Green’s functions for a sphere
and plane boundary are described following the method of Higdon (1979a). The
computations predict particle paths representing passive tracers from experiments
and their motion illustrates overall flow patterns. Figures are presented comparing
recorded experimental data with numerically generated results for a number of
particle paths. The principal results show good qualitative agreement with the main
characteristics of flows observed in the experimental study of Pettitt (2001).
Marangoni instability of a thin liquid film heated
from below by a local heat source
Authors: KALLIADASIS SERAFIM , KIYASHKO ALLA , DEMEKHIN E. A.
Published: February 2003

We consider the motion of a liquid film falling down a heated planar substrate. Using
the integral-boundary-layer approximation of the Navier–Stokes/energy equations
and free-surface boundary conditions, it is shown that the problem is governed by
two coupled nonlinear partial differential equations for the evolution of the local
film height and temperature distribution in time and space. Two-dimensional steady-state
solutions of these equations are reported for different values of the governing
dimensionless groups. Our computations demonstrate that the free surface develops
a bump in the region where the wall temperature gradient is positive. We analyse the
linear stability of this bump with respect to disturbances in the spanwise direction.
We show that the operator of the linearized system has both a discrete and an
essential spectrum. The discrete spectrum bifurcates from resonance poles at certain
values of the wavenumber for the disturbances in the transverse direction. The
essential spectrum is always stable while part of the discrete spectrum becomes
unstable for values of the Marangoni number larger than a critical value. Above
this critical Marangoni number the growth rate curve as a function of wavenumber
has a finite band of unstable modes which increases as the Marangoni number
increases.
What vibrations tell about proteins
Authors: Barth Andreas , Zscherp Christian
Published: February 2003

1. Introduction 370

2. Infrared (IR) spectroscopy – general principles 372

2.1 Vibrations 372

2.2 Information that can be derived from the vibrational spectrum 372

2.3 Absorption of IR light 375

3. Protein IR absorption 376

3.1 Amino-acid side-chain absorption 376

3.2 Normal modes of the amide group 381

4. Interactions that shape the amide I band 382

4.1 Overview 382

4.2 Through-bond coupling 383

4.3 Hydrogen bonding 383

4.4 Transition dipole coupling (TDC) 383

5. The polarization and IR activity of amide I modes 387

5.1 The coupled oscillator system 387

5.2 Optically allowed transitions 388

5.3 The infinite parallel β-sheet 388

5.4 The infinite antiparallel β-sheet 389

5.5 The infinite α-helix 390

6. Calculation of the amide I band 391

6.1 Overview 391

6.2 Perturbation treatment by Miyazawa 393

6.3 The parallel β-sheet 394

6.4 The antiparallel β-sheet 395

6.5 The α-helix 396

6.6 Other secondary structures 398

7. Experimental analysis of protein secondary structure 398

7.1 Band fitting 398

7.2 Methods using calibration sets 401

7.3 Prediction quality 403

8. Protein stability 404

8.1 Thermal stability 404

8.2 1H/2H exchange 406

9. Molecular reaction mechanisms of proteins 408

9.1 Reaction-induced IR difference spectroscopy 408

9.2 The origin of difference bands 409

9.3 The difference spectrum seen as a fingerprint of conformational change 410

9.4 Molecular interpretation: strategies of band assignment 416

10. Outlook 419

11. Acknowledgements 420

12. References 420

This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.
Protein dynamics studied by neutron scattering
Authors: Gabel Frank , Bicout Dominique , Lehnert Ursula , Tehei Moeava , Weik Martin , Zaccai Giuseppe
Published: February 2003

1. Introduction 328

2. Basic concepts of neutron scattering 329

2.1 Introduction 329

2.2 Neutron-scattering functions 331

2.3 Coherent and incoherent neutron scattering. The particular role of hydrogen in incoherent scattering 332

2.4 Total elastic scattering, EISF and mean square displacement (MSD) 333

2.5 Quasielastic scattering and relaxation function 334

2.6 Inelastic scattering and density of states 335

3. Experimental aspects and instruments 335

3.1 Energy and space resolution 335

3.2 General sample aspects 335

3.3 Potential effects of D2O on dynamics 336

3.4 Experimental 2H (deuterium) labelling 336

4. Physics of protein dynamics 336

4.1 Models 336

4.2 The dynamical transition 338

4.3 Effective force constants 339

5. Dynamics of hydrated protein powders 339

5.1 First experiments on myoglobin 340

5.2 Dynamical transitions in other proteins 340

5.3 The role of hydration water 341

5.4 Influence of the solvent 344

5.5 Diffusional motions within proteins by QENS 346

5.6 Inelastic neutron scattering and vibrational spectra 347

5.7 Conclusions 351

6. Membranes 352

6.1 Lipid bilayers 353

6.2 BR and the purple membrane (PM) 353

6.2.1 The dynamical transition in the PM 353

6.2.2 QENS from oriented PM 354

6.2.3 Hydration dependence of PM motions 355

6.2.4 Local dynamics in PM studied by isotope labelling 356

6.2.5 Dynamics of different BR conformations 357

7. Protein solutions 358

7.1 From powders to solutions 358

7.2 Water dynamics and solvent dependence of the dynamical transition in proteins 359

8. Comparing neutron scattering with other techniques 359

9. Biological relevance 360

9.1 Dynamics–activity relations 360

9.2 Dynamics–stability relations (adaptation to extreme environments) 360

9.3 Protein folding 361

10. Acknowledgements 364

11. References 364

This review of protein dynamics studied by neutron scattering focuses on data collected in the last 10 years. After an introduction to thermal neutron scattering and instrumental aspects, theoretical models that have been used to interpret the data are presented and discussed. Experiments are described according to sample type, protein powders, solutions and membranes. Neutron-scattering results are compared to those obtained from other techniques. The biological relevance of the experimental results is discussed. The major conclusion of the last decade concerns the strong dependence of internal dynamics on the macromolecular environment.
Words and Bodies: A Discourse on Male Sexuality in Late Eighteenth-Century English Representational Practices
Authors: Kobialka Michal
Published: February 2003

In 1772, William Kenrick published Love in the Suds, a direct attack on David Garrick. In 1776, Humphrey Nettle [William Jackson] published Sodom and Onan, a satire against Samuel Foote. Both of these texts make explicit charges of homosexuality against the two men. Why were these two actors singled out at this particular moment: serendipity or a new mechanism of power? An examination, thus, is required, of the representational practices operating within and without theatre, through which accepted sexual practices and new forms of personhood were normalized and put into discourse in late eighteenth-century London. The fact that this was to be achieved by placing actor's image and actor's body, occupying an ambiguous social position, under close scrutiny, points to a new economy in performing cultural and societal norms.
Psychodrama: Hypertheatricality and Sexual Excess on the Gothic Stage
Authors: Haggerty George E.
Published: February 2003

Gothic drama deals obsessively with the spectacle of pale, broken and effectively castrated masculinity. The scopic epistemology of gothic drama insists that the emaciated male form be fetishized as the lost paternal origin of the dramatic action and the source of psychological dread. These plays embrace ‘unnatural absurdity’ as a way of breaking through the complacency of bourgeois ideology and challenging sexual normativity with the spectacle of sexual excess. The resulting ‘sensationalism’ begins to suggest a revolution in the coding and decoding of sexual identities, just at the moment when such identities are being produced for the purposes of wholesale cultural labelling, as well as to articulate theatricalized resistance to the normative dictates that those identities presuppose.
coMEDIA electrONica: Performing Intermediality in Contemporary Theatre
Authors: Boenisch Peter M.
Published: February 2003

Although the concept of ‘intermediality’ recently has gained prominence within the discourse of Theatre Studies, still various contradictory definitions of that term circulate, none of which applies insight from the field of Media Theory to theatre. Rather than clinging to the banal formula ‘theatre + media = intermedial theatre’ and thus perpetuating the idea of medial specificity, an approach to intermediality informed by Media Theory stresses underlying strategies of processing all kinds of information, including the aesthetic, within a certain period. Consequently, theatre's genuine ‘mediality’ already implies its ‘intermediality’, which in fact can be traced back all the way to classical Greek drama. Within the present transformation from McLuhan's ‘Gutenberg Galaxy’ into an ‘electrONic culture’, theatre now trains its spectators in cognitive strategies of that emerging cultural paradigm. The performance Circulation Module by the Japanese group NEST reflects these significant repercussions of electrONic culture on theatrical performance at the turn of the twenty-first century.
Shakespeare as Virtual Event
Authors: Li Lan Yong
Published: February 2003

The implications of a technology of virtualization invite the question: ‘How does the constitution of Shakespeare as a performance event stand to be changed by its performance in the virtual?’ Performance as a virtual event on the internet alters a number of balances that are still in place for those who only see it by going to the theatre. It modifies the production of the audience's participation in performances, by weighting their response towards the performability (rather than the performance) of the play in question, and by incorporating that participation into the play's public profile and publicity. It also changes the territory of the production space and activity by an exposure of the company's cultural and commercial space, a space that presents itself in terms of solicitation of the internet audience's engagement. But virtual performance can also constitute itself as adjacency, as theatrical critique in a mediation between Shakespeare theatre and other forms of performance. Finally, there is no simple opposition between the live and its mediated reproduction, since it is the mediatization that enables – animates – the ‘liveness’ of the actor in performance.
Staging the Televised (Nation)
Authors: Callens Johan
Published: February 2003

The performative uses which Mark Ravenhill's Faust (Faust Is Dead) (1997) and Anna Deavere Smith's Twilight: Los Angeles, 1992 (1993), no matter how different, have made of the televised 1992 Los Angeles riots, underwrite Hal Foster's thesis that the 1990s have been confronted with a ‘return of the real’ in art and theory, through the insistence upon a renewed grounding in actual bodies and social sites, after the 1970s paradigm of art-as-text (Foucault) and the 1980s' art-as-simulacrum (Baudrillard). As such, Ravenhill's play and Smith's docudrama permit a commentary on the terrorist attacks in New York on 11 September 2001, when two planes crashed into the World Trade Center thereby further exploding the nation's semblance of reality and the false immunity it fosters.
Consuming the Asian Other in Singapore: Interculturalism in TheatreWorks' Desdemona
Authors: Peterson William
Published: February 2003

The Singaporean company TheatreWorks, under the artistic direction of Ong Keng Sen, has been responsible for the creation of a number of large-scale Asian intercultural works that have toured to international festivals from Adelaide to Hamburg. Among the best known of these are Lear and Desdemona, both of which use Shakespeare as a point of departure for new performance pieces that bring together practitioners representing a wide range of traditional and contemporary art forms. Unlike other intercultural experiments, in Lear and Desdemona practitioners stay largely within the frame of their own performance and linguistic traditions, creating a work which, especially in the case of Desdemona, is far from seamless. Using the 2000 production of Desdemona as an object of inquiry, this model of Asian intercultural production is examined against the backdrop of the politics of one's location, the troubled audience response to the work in Singapore and Adelaide, and the current state of intercultural theory.
Editorial
Authors: Singleton Brian
Published: February 2003

This collection addresses issues of performativity and the practices of representation, both historically at the interfaces of theatre practitioners and sexual practices, and intermedially at the intersection of performance and the constructed liveness of mediatized events. The formula of the performative as a ‘doing’ by a thing done, as phrased by Elin Diamond, neatly conveys the ‘mediation’ of the events which are extra-performative and locates performance in a particular tense, thus heightening the tension between the simulation of an act and its enaction.