bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Boundary Turbulence on Canyon Flows Forced by Periodic Along-Shelf Currents
Authors: Boyer Don L. , Sommeria Joel , Mitrovic Andjelka Srdic , Pakala V. K. Chaitanya , Smirnov Sergey A. , Etling Dieter 
Published: June 2006

Abstract
Previous laboratory experiments and associated numerical models of laminar flows forced by oscillatory, along-shelf background currents are extended to include some of the effects of boundary-generated turbulence. The experiments are conducted in the 13-m-diameter rotating-flow facility in Grenoble, France. Two pairs of case studies, one at a large forcing velocity (designated as FAST) for which the boundary layers are fully turbulent during part of the flow cycle and one at relatively smaller forcing (SLOW) for which transitional boundary layers are operative at the higher speeds of the background flow, are conducted. Smooth and artificially roughened boundaries are considered, respectively, for each of these pairs. Phase-averaged and time-mean velocity, vertical vorticity, and horizontal divergence fields are found to be qualitatively similar to those of previous laminar experiments. The similarities in the time-mean fields are that (i) within the canyon they are dominated by cyclonic vorticity with maxima centered near the shelf break; (ii) within and in the vicinity of the canyon the general circulation pattern includes a net transport into the canyon through its mouth, a net upwelling in the canyon interior, a transport away from the canyon over the shelf break along both sides of the canyon, and, by inference, a return flow to the deep ocean; and (iii) the interior time-mean flow is characterized by a well-defined coastal current whose axis follows the shelf in the vicinity of the shelf break, with the coast on the right. It is found that the measurements of the characteristic speed of the residual or time-mean flow within the canyon for the transitional and fully turbulent experiments do not follow the scaling law derived earlier for laminar experiments. An alternative scaling analysis for large-Reynolds-number flows is thus derived. Although sufficient numbers of experiments are not available to test the hypothesis fully, the measurements available for the fully turbulent flows are consistent with the theory advanced.
Upstream Internal Hydraulic Jumps
Authors: Cummins Patrick F. , Armi Laurence , Vagle Svein 
Published: June 2006

Abstract
In stratified tidal flow over a sill, the character of the upstream response is determined by a Froude number Fs based on the stratification near the surface. This is distinguished from the Froude number governing the response in the neighborhood of the sill crest, which is based on the weak density step associated with a flow bifurcation. For moderate values of Fs, the upstream response consists of nonlinear waves or a weak undular bore. For larger values of Fs, a strong, quasi-stationary, internal hydraulic jump dominates the upstream response. At sufficiently large values of Fs, the upstream bore is swept downstream and lost. Acoustic backscatter and velocity data are presented for the case of a strong internal bore or gravity current in a tidally modulated sill flow. Numerical simulations with varying near-surface stratification are presented to illustrate the upstream responses at different values of Fs. The theory of two-layer hydraulic flows is invoked to account for the development of the upstream jump.
What Fraction of a Kelvin Wave Incident on a Narrow Strait Is Transmitted?
Authors: Johnson Helen L. , Garrett Chris 
Published: June 2006

Abstract
Parameters governing the fraction of a Kelvin wave transmitted through a narrow gap or channel include time dependence, nonlinearity, friction, and strait geometry, yet only limited regions of this parameter space have been explored. Linear inviscid models (which neglect advective and frictional terms in the momentum equations) predict that 100% of the volume flux of a low-frequency Kelvin wave or steady boundary current incident on a narrow strait is transmitted, even when the strait width becomes infinitesimally small. Here the nonlinear, inviscid, flat bottom problem is considered, and it is shown that, provided the geometry varies slowly, the quasi-steady solution can be found in the rotating-hydraulics literature. In the narrow channel limit the fraction transmitted can be approximated by a simple prediction based on nonrotating hydraulics. Unless an incoming Kelvin wave has a large amplitude in comparison with the background layer depth, the strait width must be considerably smaller than the deformation radius before it limits the volume flux passing through. Results also show that a Kelvin wave of given volume flux will squeeze through a narrower gap if it is pushed rather than pulled.
Toward a Unified Scaling Relation for Interfacial Fluxes
Authors: Lorke Andreas , Peeters Frank 
Published: June 2006

AbstractInterfacial fluxes, that is, gas exchange at the water–atmosphere interface and benthic fluxes at the sediment–water interface, are often parameterized in terms of wind speed or turbulent friction velocity, with numerous empirical relationships obtained from individual experiments. The present study attempts to combine the general outcome of such experiments at both interfaces into a universal scaling relation for the thicknesses of the viscous and diffusive sublayers in terms of the Kolmogorov and Batchelor length scales, respectively. Transfer velocities can then be described in terms of the Schmidt number of the respective tracer and in terms of the turbulence dissipation rate. Applying law-of-the-wall scaling to convert dissipation rates into an appropriate friction velocity estimate results in a mechanistic description of the transfer velocity, which is comparable to common empirical parameterizations. It is hypothesized, however, that the dissipation rate and hence the directly estimated level of turbulence provide a more appropriate variable for the parameterization of interfacial fluxes than wind speed or turbulent friction velocity inferred from law-of-the-wall scaling.
Survey ofPseudomonas aeruginosagenotypes in colonised cystic fibrosis patients
Authors: Van daele S. , Vaneechoutte M. , De Boeck K. , Knoop C. , Malfroot A. , Lebecque P. , Leclercq-Foucart J. , Van Schil L. , Desager K. , De Baets F. 
Published: June 2006

The current authors aimed to examine whether cystic fibrosis (CF) patients in Belgium sharedPseudomonas aeruginosagenotypes and to compare the genotypes of isolates from the same patients during two consecutive years. A Belgian databank of theP. aeruginosagenotypes of all colonised CF patients was created.Sputum samples from a total of 276P. aeruginosacolonised patients during 2003, and from a subgroup of 95 patients in 2004, were analysed. Patients were asked about any social contact between each other by questionnaire. AllP. aeruginosaisolates exhibiting different colonial morphology on McConkey agar were first genotyped using arbitrarily primed PCR, whereafter single representatives of each randomly amplified polymorphic DNA-type were further genotyped by fluorescent amplified fragment length polymorphism analysis.In the 213 patients from whomP. aeruginosacould be cultured (resulting in 910 isolates), a total of 163 genotypes were found. The majority (75%) of patients harboured only one genotype. In most of the limited number of clusters, previous contacts between patients could be suspected. In 80% of the patients studied during both years,P. aeruginosagenotype remained unchanged.In conclusion, most colonised cystic fibrosis patients harbour only onePseudomonas aeruginosagenotype, despite showing different colonial morphotypes. The number of clusters is limited, and most patients seem to retain the same genotypic strain during both years.
Improving the accuracy of protein secondary structure prediction using structural alignment
Authors: Montgomerie Scott , Sundararaj Shan , Gallin Warren J , Wishart David S 
Published: June 2006

AbstractBackgroundThe accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high.ResultsWe have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25%) onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based) secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics) indicate that this new method can achieve a Q3 score approaching 88%.ConclusionBy using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible athttp://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs, databases (and server) can be downloaded and run locally.
In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India
Authors: Thangaraj Kumarasamy , Chaubey Gyaneshwer , Singh Vijay Kumar , Vanniarajan Ayyasamy , Thanseem Ismail , Reddy Alla G , Singh Lalji 
Published: June 2006

Abstract

Background
Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups.

Results
Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31.

Conclusion
Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.
Community-based surveillance of malaria vector larval habitats: a baseline study in urban Dar es Salaam, Tanzania
Authors: Vanek Michael J , Shoo Bryson , Mtasiwa Deo , Kiama Michael , Lindsay Steven W , Fillinger Ulrike , Kannady Khadija , Tanner Marcel , Killeen Gerry F 
Published: June 2006

Abstract

Background
As the population of Africa rapidly urbanizes it may be possible to protect large populations from malaria by controlling aquatic stages of mosquitoes. Here we present a baseline evaluation of the ability of community members to detect mosquito larval habitats with minimal training and supervision in the first weeks of an operational urban malaria control program.

Methods
The Urban Malaria Control Programme of Dar es Salaam recruited and provided preliminary training to teams of Community-Owned Resource Persons (CORPs) who performed weekly surveys of mosquito breeding sites. Two trained mosquito biologists accompanied each of these teams for one week and evaluated the sensitivity of this system for detecting potential Anopheles habitats.

Results
Overall, 42.4% of 986 habitats surveyed by an inspection team had previously been identified by CORPs. Agricultural habitats were detected less often than other habitats (30.8% detected, Odds Ratio [95%CI] = 0.46 [0.29–0.73], P = 0.001). Non-agricultural artificial habitats were less suitable than other habitats (29.3% occupancy, OR = 0.69 [0.46–1.03], P = 0.066) but still constituted 45% (169/289) of occupied habitats because of their abundance (51 % of all habitats).

Conclusion
The levels of coverage achieved by modestly trained and supported CORPs at the start of the Dar es Salaam UMCP were insufficient to enable effective suppression of malaria transmission through larval control. Further operational research is required to develop surveillance systems that are practical, affordable, effective and acceptable so that community-based integrated vector management can be implemented in cities across Africa.
Quantum dots – a versatile tool in plant science?
Authors: Müller Frank , Houben Andreas , Barker Peter E , Xiao Yan , Käs Josef A , Melzer Michael 
Published: June 2006

Abstract
An optically stable, novel class of fluorophores (quantum dots) for in situ hybridisation analysis was tested to investigate their signal stability and intensity in plant chromosome analyses. Detection of hybridisation sites in situ was based on fluorescence from streptavidin-linked inorganic crystals of cadmium selenide. Comparison of quantum dots (QDs) with conventional detection systems (Alexa 488) in immunolabeling experiments demonstrated greater sensitivity than the conventional system. In contrast, detection of QDs in in situ hybridisation of several plant chromosomes, using several high-copy sequences, was less sensitve than Alexa 488. Thus, semiconductor nanocrystal fluorophores are more suitable for immunostaining but not for in situ hybridisation of plant chromosomes.
Modulation of granulocyte-endothelium interactions by antileukoproteinase: inhibition of anti-type II collagen antibody-induced leukocyte attachment to the synovial endothelium
Authors: Sehnert Bettina , Gierer Philip , Ibrahim Saleh , Kühl Anja , Voll Reinhard , Nandakumar Kutty Selva , Holmdahl Rikard , Hallmann Rupert , Vollmar Brigitte , Burkhardt Harald 
Published: June 2006

AbstractAntileukoproteinase (ALP) is a physiological inhibitor of granulocytic serine proteases that has been shown to have anti-inflammatory properties in addition to its antiproteolytic activity. On the basis of its potential to block anti-collagen type II (CII) antibody-induced arthritis (CAIA) and to suppress the conformational activation of β2-integrins in leukocytes, the present study was undertaken to investigate its interference with leukocyte adherence to cytokine-activated endothelium. The potential of recombinant ALP to block the interactions of leukocytes with the endothelial lining was concomitantly investigated in vitro and in vivo. Thus, intravital fluorescence microscopic imaging of leukocyte rolling and firm adhesion to postcapillary venules were performed in the knee joints of DBA1/J mice after intravenous injection of anti-CII mAbs. An IL-1β-activated endothelial layer formed by a murine glomerular cell line (glEND.2) was used to assay the interaction with human leukocytes in vitro. Electromobility shift and luciferase reporter gene assays permitted the analysis of cytokine-induced activation of the NF-κB pathway. Fluorescence-activated cell sorting was applied to determine endothelial E-selectin expression. Leukocyte rolling and firm adhesion to the synovial endothelium in an early response to the anti-CII antibody transfer were significantly decreased in ALP-pretreated mice. Concomitantly, ALP suppressed the IL-1β-induced NF-κB activation and the upregulation of E-selectin expression in glEND.2 cells in vitro. These findings support the notion that the newly uncovered properties of ALP to interfere with cytokine signalling and upregulation of adhesion molecules in endothelial cells are likely to contribute to the therapeutic potential of ALP in immune-complex-induced tissue injury.
The MHC2TA-168A>G gene polymorphism is not associated with rheumatoid arthritis in Austrian patients
Authors: Yazdani-Biuki Babak , Brickmann Kerstin , Wohlfahrt Klaus , Mueller Thomas , März Winfried , Renner Wilfried , Gutjahr Manuela , Langsenlehner Uwe , Krippl Peter , Wascher Thomas C , Paulweber Bernhard , Graninger Winfried , Brezinschek Hans-Peter 
Published: June 2006

AbstractAn association between susceptibility to rheumatoid arthritis (RA) and a common -168A>G polymorphism in the MHC2TA gene with differential major histocompatibility complex (MHC) II molecule expression was recently reported in a Swedish population. The objective of the present study was to replicate this finding by examining the -168A>G polymorphism in an Austrian case–control study. Three hundred and sixty-two unrelated RA cases and 351 sex-matched and age-matched controls as well as 1,709 Austrian healthy individuals were genotyped. All participants were from the same ethnic background. Genotyping was performed using 5' allelic discrimination assays. The association between susceptibility to RA and the -168A>G single nucleotide polymorphism was examined by chi-square test. Comparison was made assuming a dominant effect (AG + GG genotypes versus AA genotype). In contrast to the primary report, the frequency of MHC2TA -168G allele carriers was not significantly different between patients and controls in the Austrian cohort. The homozygous MHC2TA -168 GG genotype was more frequent in matched controls than in Austrian RA patients. There was no association between the presence of RA-specific autoantibodies and the MHC2TA -168 GG genotype. In this cohort of Austrian patients, no association between the MHC2TA polymorphism and RA was found.
ESR Studies on Poly(methyl acrylate) Radicals in the Frozen State
Authors: Sugiyama Yoshio 
Published: June 2006

Abstract
Poly(methyl acrylate) radical and poly(methyl acrylate-α-d) radical, generated from the polymerization of methyl acrylate (MA) and methyl acrylate-α-d (MA-d) in the frozen (solid) state, have been investigated by Electron Spin Resonance (ESR). The α-position selective deuteration of poly(MA) radical made the shoulders of poly(MA) radical emerge as more clearly isolated peaks. Both ESR spectra of poly(MA) radicals and those of poly(MA-d) radicals were simulated for the conformational ratio 2.2 between a stable conformation and eclipsed conformations. The energy difference between the stable conformation and two eclipsed conformations was estimated to be 0.27 kcal mol−1 for poly(MA) radical in the thermal equilibrium solid state.
Preparation and Some Properties of One Structural Isomer of Tetra-Substituted Phthalocyanine; 1,8,15,22-Tetrakis(pentan-3′-yloxy)phthalocyanine and Its Metal(II) Complexes
Authors: Kasuga Kuninobu , Asano Kenichiro , Lin Liang , Sugimori Tamotsu , Handa Makoto , Abe Koji , Kikkawa Takahiro , Fujiwara Takaji 
Published: June 2006

Abstract
The title phthalocyanine (1) was prepared from 3-(pentan-3′-yloxy)phthalonitrile, of which a bulky substituent on the 3-position caused an exclusive formation of 1 out of the possible structural isomers.
Complexes of magnesium(II), cobalt(II), nickel(II), copper(II), and zinc(II) were prepared by refluxing a DMF solution of 1 and corresponding metal(II) chlorides, and were characterized by the absorption and 1H NMR spectra as well as elemental analyses.
Magnesium(II) and zinc(II) complexes showed a new band at the longer wavelength side of the Q band in chloroform, probably due to the formation of a face-to-face slipped dimer.
Compound 1 and its magnesium(II), nickel(II), or copper(II) complex showed three ring-oxidative and reductive processes, and the zinc(II) complex showed four in dichloromethane in their cyclic voltammograms. The cobalt(II) complex showed five processes, two of which arose from a central cobalt(II) ion. The oxidation of the cobalt(II) ion occurred at a more negative potential in DMF.
The crystal structure of the nickel(II) complex was determined by an X-ray analysis; substitution on the 1,8,15, and 22 positions of the ring by pentan-3-yloxy groups was confirmed. The molecules are stacked with a distance of 3.32 Å between the phthalocyanine rings.
Convenient Preparation of Pheophytin b from Plant Extract through the C7-Reduced Intermediate
Authors: Oba Toru , Masada Yukiko , Tamiaki Hitoshi 
Published: June 2006

Abstract
A new method for the large scale preparation of Pheophytin (=Pheo) b is presented. The difficulty in chromatographic isolation of Pheo a and b, tetrapyrrole pigments, from the large amount of plant extract was overcome by an increase in polarity of the pigment given by a selective modification of Pheo b. Treatment of plant extract containing both Pheo a and b, carotenoids, lipids, etc. with a mild reductant t-BuNH2BH3 induced selective reduction of the C7-formyl group of Pheo b, but left unaffected other carbonyl moieties of the molecules. The resulting compound 7-hydroxymethyl-Pheo b was readily separated from intact Pheo a by silica gel column chromatography. Pure Pheo b was obtained by oxidation of the 7-hydroxymethyl-Pheo b with pyridinium chlorochromate. One of the reasons why the present method is superior to the previous ones is that Pheo a was obtained simultaneously as an intact form. Another is the utility of the intermediate compound, 7-hydroxymethyl-Pheo b: as the starting material for syntheses of various compounds as well as a model of ingredients in the photosynthetic systems, such as a light-harvesting apparatus of green photosynthetic bacteria.
Radical Cyclization of Allyl 2-Iodophenyl Ether, N,N-Diallyl-2-iodoaniline, and 2-Iodoethanal Acetal by Means of Trialkylmanganate(II)
Authors: Inoue Rie , Nakao Junko , Shinokubo Hiroshi , Oshima Koichiro 
Published: June 2006

Abstract
Treatment of allyl 2-halophenyl ethers with tributylmanganate (n-Bu3MnLi or n-Bu3MnMgBr) provided dihydrobenzofuran derivatives in good yield. Indoline derivatives are also produced effectively starting from 2-iodoaniline compounds. The reaction could proceed by the following sequences: (1) formation of a radical by treatment of iodophenol or iodoaniline derivatives with tributylmanganate(II), (2) radical cyclization, and (3) recombination of radical and manganese species giving alkylmanganese(II) compound. The reaction proved to proceed in the presence of a catalytic amount of manganese(II) chloride under atmospheric oxygen. The manganese catalyzed radical cyclization could also be applied to 2-iodoethanal acetal, in which case the presence of oxygen was not necessary.
Anomalous Electronic Absorption in Lapacholi–Alcohol Solutions
Authors: Portugal Samira da Guia Mello , Herrera Juan Omar Machuca , Brinn Ira Mark 
Published: June 2006

Abstract
An anomalous band at the red end of the absorption spectrum of lapachol (an anti-cancer compound) appears when the solvent used is a lighter molecular-weight alcohol, but not in purely aqueous solution. This band does not follow Beer’s law, and is attributed to a weak transition of the structurally modified monomeric ortho naphthoquinone tautomer in these solvents. The “normal” para tautomer is considered to exist predominantly in the dimeric form at all concentrations above approximately 10−4 M. This interpretation is supported by spectroscopic data on structurally related compounds, as well as molecular-orbital calculations.