bluuebunny/crossref_metadata_2025_split huggingface dataset:
On spatially growing baroclinic waves in the ocean
Authors: Hogg Nelson G. 
Published: April 2006

It is shown that spatially growing waves with complex wavenumber and real frequency can exist in a baroclinic flow and that these waves are substantially different from the more commonly studied temporally growing ones. They are bounded by a low wavenumber cut-off which separates them from the temporally growing waves. Their amplitude and phase change most rapidly near their steering level and are almost depth independent away from it. Most of the energy conversion from mean flow to the waves occurs at this level. It is suggested that these motions may be forced by steady disturbances such as bottom relief.The theory is compared with recent observations of strong small-scale motions in a region of rough topography of MODE and in the vicinity of the Gulf Stream. The vertical structure can be well matched with the theory but the complex wavenumber appears to be a factor of 2–3 greater than that predicted.
A stationary oblique breaking wave for laboratory testing of surfboards
Authors: Hornung H. G. , Killen P. 
Published: April 2006

A surface gravity wave obliquely incident on a sloping beach is broken near the beach and has a smooth surface further out. Viewed in the frame of reference of the transition from the smooth to the broken part, the flow is steady, and the wave is oblique to the free stream. By placing a suitably shaped obstacle in a flume operated at high Froude number, such a wave can be generated. Experiments in which a wave of 18 cm height was generated are described and the wave shape and some of its characteristics presented. In particular, the dividing stream surface separating that part of the flow which curls over into the break from the part that flows smoothly over the obstacle is discussed.Model surfboards can ride this wave unsupported, provided the correctly scaled weight loads them at the right centre-of-mass position. This makes it possible to determine the forces on the board without a balance. A comparison of the measured forces with estimates, particularly of the drag, indicate that viscous and surface-tension phenomena introduce only small scale effects in the Froude number modelling. While the results are not sufficiently accurate to draw definite conclusions about the effects of surf board shape, they indicate clearly that surf board flows may be modelled with quantitative success in the laboratory.
On the dynamics of finite-amplitude baroclinic waves as a function of supercriticality
Authors: Pedlosky Joseph 
Published: April 2006

A finite-amplitude model of baroclinic instability is studied in the case where the cross-stream scale is large compared with the Rossby deformation radius and the dissipative and advective time scales are of the same order. A theory is developed that describes the nature of the wave field as the shear supercriticality increases beyond the stability threshold of the most unstable cross-stream mode and penetrates regions of higher supercriticality. The set of possible steady nonlinear modes is found analytically. It is shown that the steady cross-stream structure of each finite-amplitude mode is a function of the supercriticality.Integrations of initial-value problems show, in each case, that the final state realized is the state characterized by the finite-amplitude mode with the largest equilibrium amplitude. The approach to this steady state is oscillatory (nonmonotonic). Further, each steady-state mode is a well-defined mixture of linear cross-stream modes.
Features of a separating turbulent boundary layer in the vicinity of separation
Authors: Simpson Roger L. , Strickland J. H. , Barr P. W. 
Published: April 2006

Measurements of a separating two-dimensional incompressible boundary layer with an airfoil-type pressure distribution are reported. Unique mean and fluctuation velocity measurements and the distribution of the fraction of the time γp during which the flow moves downstream were obtained in the separated region using a directionally sensitive laser anemometer. Linearized hot-film anemometer measurements of mean velocities, turbulent shearing stress and intensities, eddy speeds, spectra and dissipation were made for γp > 0·8. The wall shearing stress, bursting frequencies, wall speed and spanwise structure were obtained using flush-surface hot-film sensors. The turbulent/non-turbulent interfacial intermittency γ and the frequency of passage of turbulent bulges were determined using smoke as a turbulence marker and the laser anemometer system for illumination and signal detection.Upstream of separation the velocity profile correlations of Perry & Schofield (1973) are supported within the uncertainty of the data. Normal-stress effects are very important, influencing $-\overline{uv}/\overline{q^2} $ and the dissipation length correlations, and directly providing sizable terms in the momentum and turbulence energy equations. The criteria of Sandborn for turbulent separation and fully developed separation are found to hold. Downstream of separation there is apparent similarity of $\overline{u^2}$, U and γp throughout the shear flow. The passive low velocity backflow near the wall apparently just serves to satisfy continuity requirements after the energetic outer-region flow has deflected away from the wall upon separation.The wall bursting frequency nA scales on outer velocity and length scales, with U∞/δnA ≈ 10, or about twice the value observed for zero-pressure-gradient flows. The non-dimensional spanwise spacing of wall eddies is given approximately by the relation λzUM/v ≈ 100 upstream of separation, where $U_M = (- \overline{uv}_{\max})^{\frac{1}{2}}$. The speed of wall eddies is found to be about 14Uτ.
Experiments on the fine structure of turbulence
Authors: Narayanan M. A. Badri , Rajagopalan S. , Narasimha R. 
Published: April 2006

Investigations have been carried out of some aspects of the fine-scale structure of turbulence in grid flows, in boundary layers in a zero pressure gradient and in a boundary layer in a strong favourable pressure gradient leading to relaminarization. Using a narrow-band filter with suitable mid-band frequencies, the properties of the fine-scale structure (appearing as high frequency pulses in the filtered signal) were analysed using the variable discriminator level technique employed earlier by Rao, Narasimha & Badri Narayanan (1971). It was found that, irrespective of the type of flow, the characteristic pulse frequency (say Np) defined by Rao et al. was about 0·6 times the frequency of the zero crossings.It was also found that, over the small range of Reynolds numbers tested, the ratio of the width of the fine-scale regions to the Kolmogorov scale increased linearly with Reynolds number in grid turbulence as well as in flat-plate boundarylayer flow. Nearly lognormal distributions were exhibited by this ratio as well as by the interval between successive zero crossings.The values of Np and of the zero-crossing rate were found to be nearly constant across the boundary layer, except towards its outer edge and very near the wall. In the zero-pressure-gradient boundary-layer flow, very near the wall the high frequency pulses were found to occur mostly when the longitudinal velocity fluctuation u was positive (i.e. above the mean), whereas in the outer part of the boundary layer the pulses more often occurred when u was negative. During acceleration this correlation between the fine-scale motion and the sign of u was less marked.
Theory of the almost-highest wave: the inner solution
Authors: Longuet-Higgins M. S. , Fox M. J. H. 
Published: April 2006

This paper investigates the flow near the summit of steep, progressive gravity wave when the crest is still rounded but the flow is approaching Stokes's corner flow. The natural length scale in the neighbourhood of the summit is seen to be l =q2/2g, where g denotes gravity and q is the particle speed at the crest in a reference frame moving with the wave speed. We show that a class of self-similar smooth local flows exists which satisfy the free-surface condition and which tend to Stokes's corner flow when the radial distance r becomes large compared withl. The behaviour of the solution at large values of r/l is shown to depend on the roots of the transcendental equation
\[
K \tan h K = \pi/2\surd{3}.
\]
The two real roots correspond to a damped oscillation of the free surface decaying like (l/r)½. The positive imaginary roots correspond to perturbations vanishing like higher negative powers of r.The complete flow is calculated by transforming the domain onto the interior of a circle in the complex plane and expanding the potential at the surface in a Fourier series. The computation is checked by an independent method, based on approximating the flow by a sequence of dipoles. The profile of the surface is found to intersect its asymptote at large values of r/l. This implies that the maximum slope slightly exceeds 30°. The computed value 30·37° is in close agreement with that obtained by extrapolating the maximum slopes of steep gravity waves, as calculated by previous authors. The vertical acceleration of a particle at the crest is 0·388g. In the far field, however, the acceleration tends to the value ½g corresponding to the Stokes corner flow.
Characterization of the amino acid response element within the human sodium-coupled neutral amino acid transporter 2 (SNAT2) System A transporter gene
Authors: Palii Stela S. , Thiaville Michelle M. , Pan Yuan-Xiang , Zhong Can , Kilberg Michael S. 
Published: April 2006

The neutral amino acid transport activity, System A, is enhanced by amino acid limitation of mammalian cells. Of the three gene products that encode System A activity, the one that exhibits this regulation is SNAT2 (sodium-coupled neutral amino acid transporter 2). Fibroblasts that are deficient in the amino acid response pathway exhibited little or no induction of SNAT2 mRNA. Synthesis of SNAT2 mRNA increased within 1–2 h after amino acid removal from HepG2 human hepatoma cells. The amino acid responsive SNAT2 genomic element that mediates the regulation has been localized to the first intron. Increased binding of selected members of the ATF (activating transcription factor) and C/EBP (CCAAT/enhancer-binding protein) families to the intronic enhancer was established both in vitro and in vivo. In contrast, there was no significant association of these factors with the SNAT2 promoter. Expression of exogenous individual ATF and C/EBP proteins documented that specific family members are associated with either activation or repression of SNAT2 transcription. Chromatin immunoprecipitation analysis established in vivo that amino acid deprivation led to increased RNA polymerase II recruitment to the SNAT2 promoter.
Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose
Authors: Alberto François , Jordi Emmanuelle , Henrissat Bernard , Czjzek Mirjam 
Published: April 2006

Thermotoga maritima invertase (β-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases β-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves β-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed β-propeller catalytic domain linked to a β-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule α-D-galactopyranosyl-(1,6)-α-D-glucopyranosyl-β-D-fructofuranoside (raffinose) at 1.87 Å (1 Å=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.
AuberGene—a sensitive genome alignment tool
Authors: Szklarczyk Radek , Heringa Jaap 
Published: April 2006

Abstract
Motivation: The accumulation of genome sequences will only accelerate in the coming years. We aim to use this abundance of data to improve the quality of genomic alignments and devise a method which is capable of detecting regions evolving under weak or no evolutionary constraints.
Results: We describe a genome alignment program AuberGene, which explores the idea of transitivity of local alignments. Assessment of the program was done based on a 2 Mbp genomic region containing the CFTR gene of 13 species. In this region, we can identify 53% of human sequence sharing common ancestry with mouse, as compared with 44% found using the usual pairwise alignment. Between human and tetraodon 93 orthologous exons are found, as compared with 77 detected by the pairwise human-tetraodon comparison.
AuberGene allows the user to (1) identify distant, previously undetected, conserved orthogonal regions such as ORFs or regulatory regions; (2) identify neutrally evolving regions in related species which are often overlooked by other alignment programs; (3) recognize false orthologous genomic regions. The increased sensitivity of the method is not obtained at the cost of reduced specificity. Our results suggest that, over the CFTR region, human shares 10% more sequence with mouse than previously thought (∼50%, instead of 40% found with the pairwise alignment).
Availability: The source code and tracks for UCSC Genome Browser generated with the program are available from .
Contact: heringa@cs.vu.nl
Analysis assistant for single-molecule force spectroscopy data on membrane proteins—MPTV
Authors: Mueller Frank , Muller Daniel J. , Labudde Dirk 
Published: April 2006

Abstract
Summary: Force-distance (F-D) curves of single membrane proteins reveal information on inter- and intramolecular interactions occurring within a protein and between proteins. However, the analysis of single-molecule force spectroscopy data is a time consuming and complex process requiring objective criteria. In most cases the user requires additional information to interpret F-D curves. Therefore we developed a software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. This representation establishes a basis for detailed interpretation of the protein structure and its underlying molecular interactions. Various integrated bioinformatic features further assist in the interpretation of measured and assigned molecular interactions that determine membrane protein folding, structure, stability and function. Web queries and programs about the topology are directly linked. Motifs, helix types, representation of Venn diagrams and the complete functionality of the program Jmol belong to it.
Availability: The program MPTV is freely available from the website at
Contact: dirk.labudde@biotec.tu.dresden.de
Corrosive induced carcinoma of esophagus: Report of three patients and review of literature
Authors: Kochhar Rakesh , Sethy Pradeepta Kumar , Kochhar Suman , Nagi Birinder , Gupta Narinder Mohan 
Published: April 2006

AbstractPatients with corrosive induced esophageal strictures have more than a 1000‐fold risk of developing carcinoma of the esophagus. We report three cases of corrosion carcinoma seen by us (a team of gastroenterologists, radiologists and a surgeon) in the last 15 years. Two cases were among 156 patients with corrosive induced strictures on our follow‐up, and constituted the only corrosion carcinoma out of 650 esophageal carcinomas operated on by us. Nearly all reported patients with corrosion carcinoma in the published literature had consumed an alkali, but two of our three patients had consumed an acid.
Ocular lesions in Watanabe heritable hyperlipidemic rabbits
Authors: Kouchi Mami , Ueda Yoshinaka , Horie Hiroshi , Tanaka Kohji 
Published: April 2006

AbstractHyperlipidemic ocular lesions are described for Watanabe heritable hyperlipidemic (WHHL) rabbits. Male WHHL rabbits 8 months old exhibited serum hyperlipidemia and ophthalmoscopically yellowish‐white lesions along the corneoscleral junction and in the iris. Histopathologically, foamy macrophages aggregated in the stroma of the cornea, iris, and ciliary body were observed. These findings have been interpreted as lipid keratopathy. In addition, multiple clusters of a large number of foamy macrophages occurred throughout the choroid and sclera in association with the blood vessels. The lesions in the choroid and sclera could not be detected ophthalmoscopy, yet were much more prominent than those in the cornea, iris, and ciliary body, suggesting greater involvement and earlier onset of lipidosis at these sites associated with hyperlipidemia in WHHL rabbits.
Ophthalmomyiasis interna anterior in a cat: surgical resolution
Authors: Stiles Jean , Rankin Amy 
Published: April 2006

AbstractA 4‐year‐old Domestic short‐haired cat was presented for severe anterior uveitis in the right eye associated with a Cuterebra spp. larva in the anterior chamber. This report describes successful surgical removal of the parasite with preservation of vision.
Drusen and lipid‐filled retinal pigment epithelium cells in a rhesus macula
Authors: Anderson Mark , Dawson William W. , Gonzalez‐Martinez Janis , Curcio Christine A. 
Published: April 2006

AbstractA middle‐aged rhesus monkey with detailed clinical history exhibited progression of a macular abnormality with a variety of clinical drusen and pigment changes typical of the Cayo Santiago phenotype. Numerous frozen sections of one sample of the macular retina/retinal pigment epithelium (RPE)/choroid showed a single classical druse but extensive single and clustered lipid‐filled RPE cells. The monkey exhibited functional outer retinal decline and an insignificant number of ‘window defects’ as found among signs of relatively benign human macular aging. The clinical and histologically defined results agree if lipid‐filled RPE cells are included among the clinically apparent signs of drusen.
Leptospirosis and panuveitis in a dog
Authors: Townsend Wendy M. , Stiles Jean , Krohne Sheryl G. 
Published: April 2006

AbstractA case of panuveitis as a result of leptospiral infection in an 8‐year‐old Jack Russell Terrier is reported. Mild hyphema, aqueous flare, and partial serous retinal detachments were noted in both eyes on initial ophthalmic examination. The serum microscopic agglutination testing forLeptospiraserovarieties revealed titers of 1 : 12 800 forLeptospira canicola and1 : 200 forLeptospira icterohemorrhagiae.With medical therapy, the panuveitis resolved and functional vision was regained. Four weeks after the initial presentation, convalescent titers were 1 : 200 forL. canicolaand 1 : 100 forL. icterohemorrhagiae. The incidence of leptospirosis, along with difficulties diagnosing, and current medical therapies for this disease are also discussed.
Evaluation of canine serum for the presence of antiretinal autoantibodies in sudden acquired retinal degeneration syndrome
Authors: Keller Rachel L. , Kania Stephen A. , Hendrix Diane V. H. , Ward Daniel A. , Abrams Kenneth 
Published: April 2006

AbstractObjective To determine the presence of serum antiretinal antibodies in sudden acquired retinal degeneration syndrome (SARDS) affected dogs and the size of the antigen to which these antibodies bind via the use of enzyme‐linked immunosorbent assay (ELISA) and Western blot immunoassays.Animals studied Serum was collected from 13 dogs affected by SARDS and five dogs with normal ocular examinations.Procedures All serum samples were subjected to ELISA with saline‐soluble canine retinal tissue and Western blot analyses with SDS solubilized normal canine retinal tissue as the antigen. Antirecoverin (23 kDa) and antiheat shock cognate (65 kDa) antibodies were used as positive controls for both procedures. Affinity‐purified goat antidog IgG and IgM labeled with horseradish peroxidase were used for all clinical samples and goat antirabbit IgG was used as the secondary antibody for the positive controls.Results ELISA demonstrated antibody reaction with all samples. Western blot immunoassays identified multiple bands in all canine serum samples, as well as in negative controls. Approximate sizes of the bands were 25 and 50 kDa, corresponding to IgG light and heavy chains, respectively.Conclusion No antiretinal autoantibodies were identified in the serum of dogs affected by SARDS as compared to normal canine patients.
Canine limbal melanoma: 30 cases (1992–2004). Part 2. Treatment with lamellar resection and adjunctive strontium‐90β plesiotherapy – efficacy and morbidity
Authors: Donaldson David , Sansom Jane , Adams Vicky 
Published: April 2006

AbstractObjectives To evaluate the efficacy of lamellar resection and adjunctive90Sr‐β plesiotherapy in the management of canine limbal melanoma and the frequency and morbidity of early and late‐onset side effects following treatment.Design Retrospective study.Animals studied Thirty dogs treated for limbal melanoma at the Animal Health Trust (AHT), between 1992 and 2004.Methods Medical records were reviewed and information collected on the radiation dose administered, duration of follow‐up, and the frequency of early‐ and late‐onset ocular side effects. Follow‐up information was obtained by re‐examination of patients or completion of a telephone interview with the referring veterinary surgeons or the owners.Results Recurrence of limbal melanoma occurred in 1 of 30 cases (3%; 95% CI: 0.2–14%). One or more side effects occurred in 16 of 30 cases (53%; 95% CI: 28.1–74.9). The occurrence of side effects was not associated with the number of sites treated or the total surface dose of radiation. Short‐term side effects were reported in 16/30 cases (53%) and included corneal scarring (12/30), corneal neovascularization (6/30), conjunctivitis with or without granulation tissue formation (5/30), lipid keratopathy (1/30), and localized bullous keratopathy (2/30). Long‐term side effects were reported in 6 of 30 cases (20%) cases and included deep scleral thinning (5/30), focal scleromalacia (3/30), globe perforation (2/30), lipid keratopathy (3/30), localized bullous keratopathy (1/30), and sectoral cortical cataract (1/30).Conclusions Lamellar resection and adjunctive90Sr‐β plesiotherapy is relatively easy to perform, is minimally invasive, and extremely well tolerated by patients. The treatment is highly efficacious in the management of canine limbal melanoma. Modification of the radiation dosimetry, in particular reducing the total dose of radiation and the dose per radiation fraction, is necessary to reduce the incidence of late onset side effects.
An intelligent semantic e‐learning framework using context‐aware Semantic Web technologies
Authors: Huang Weihong , Webster David , Wood Dawn , Ishaya Tanko 
Published: April 2006

AbstractRecent developments of e‐learning specifications such as Learning Object Metadata (LOM), Sharable Content Object Reference Model (SCORM), Learning Design and other pedagogy research in semantic e‐learning have shown a trend of applying innovative computational techniques, especially Semantic Web technologies, to promote existing content‐focused learning services to semantic‐aware and personalised learning services. To facilitate this transforming process, this paper presents a novel context‐aware semantic e‐learning approach to integrate content provision, learning process and learner personality in an integrated semantic e‐learning framework. As the basis of the computational framework, a scalable and extensible generic context model is proposed to structure the semantics of contextual relations and concepts in various contexts, such as learning content description, learning model, knowledge object representation and learner personality. Corresponding technical and pedagogical developments of this framework also consider compatibility issues with existing technologies (eg, XML/Resource Description Framework) and specifications (eg, IEEE LOM) in order to achieve the best interoperability.