bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrochemical synthesis and stabilization of cobalt nanoparticles
Authors: Ledo‐Suárez A. , Rodríguez‐Sánchez L. , Blanco M. C. , López‐Quintela M. A. 
Published: April 2006

AbstractCobalt nanoparticles (NPs) were synthesized via an electrochemical method in the presence of tetraalkylammonium salt. The nanometer dimensions of the NPs can be controlled in a simple way by adjustment of the current density. From these particles stable colloidal suspensions are prepared in the presence of a fatty acid (oleic acid) and triphenylphosphine. The colloidal system is stable against oxidation when they are kept in heptane (C7H16).Transmission electron microscopy (TEM) was employed to determine the core size and the shape of metal nanoparticles. The chemical interaction of the surfactant with the Co nanoparticles was studied by using Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). Thermogravimetric analysis (TGA) was used to study the thermal stability and the composition of the capped cobalt nanoparticles. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Assessment of body condition in Asian elephants (Elephas maximus)
Authors: Wemmer C. , Krishnamurthy V. , Shrestha S. , Hayek L.‐A. , Thant Myo , Nanjappa K.A. 
Published: April 2006

AbstractA method of assessing body condition of Asian elephants (Elephas maximus) is presented. The method uses visual assessment to assign numerical scores to six different regions of the body, which are totaled to give a numerical index ranging from 0–11. The relationship between the index and morphometric variables is compared for a sample of 119 juvenile and young adult elephants from southern India, Nepal, and Myanmar. Mean ages of males and females were similar. Mean index of body condition (with standard error [SE]) was 7.3±0.2 points. No significant correlation was found between index of body condition and age over both sexes (r=0.01, n=50). Results were equivalent when sexes were treated separately (females: r=0.03, n=24; males: r=0.01, n=26). Sexes did not differ in height of the shoulder or body condition in our sample, but there was significant sexual dimorphism in breadth of the zygomatic arch and three measures of subcutaneous fat: girth of neck, thickness of cervical fold, and thickness of anal flap. These three measures were also significantly correlated with each other. Our assessment method should prove a practical tool for ecologic studies, but the relationship of the index to percentage of body fat should be determined using heavy water dilution methodology. Zoo Biol 25:187–200, 2006. © 2006 Wiley‐Liss, Inc.
A Two-dimensional Boussinesq equation for water waves and some of its solutions
Authors: Johnson R. S. 
Published: April 2006

A two-dimensional Boussinesq equation,
\[u_{tt} - u_{xx} + 3(u^2)_{xx} - u_{xxxx} - u_{yy} = 0,\]
is introduced to describe the propagation of gravity waves on the surface of water, in particular the head-on collision of oblique waves. This equation combines the two-way propagation of the classical Boussinesq equation with the (weak) dependence on a second spatial variable, as occurs in the two-dimensional Korteweg-de Vries (2D KdV) (or KPII) equation. Exact and general solitary-wave, two-soliton and resonant solutions are obtained from the Hirota bilinear form of the equation. The existence of a distributed-soliton solution is investigated, but it is shown that this is not a possibility. However the connection with the classical 2D KdV equation (which does possess such a solution) is explored via a suitable parametric representation of the dispersion relation.A three-soliton solution is also constructed, but this exists only if an auxiliary constraint among the six parameters is satisfied; thus the two-dimensional Boussinesq equation is not one of the class of completely integrable equations, confirming the analysis of Hietarinta (1987). This constraint is automatically satisfied for the classical Boussinesq equation (which is completely integrable). Graphical reproductions of some of the solutions of the two-dimensional Boussinesq equations are also presented.
Secondary instability of flow in a curved duct of square cross-section
Authors: Mees Philip A. J. , Nandakumar K. , Masliyah J. H. 
Published: April 2006

Experiments and simulations of a travelling wave state of incompressible Newtonian flow in a curved duct of square cross-section are presented. The travelling wave mode develops from the well-documented steady four-cell flow state and is characterized by oscillations of the two Dean vortices near the centre of the outer wall.The oscillations were induced by a carefully positioned pin at 5° from the inlet of the curved section along the symmetry line of the cross-section. It was shown that the travelling wave state is characteristic for curved duct flow and that the pin made it possible to observe the oscillations within the 270° long curved duct. Travelling waves were observed at flow rates above Dn = 170 (Dn = Re/(R/a)1/2, where Re is the Reynolds number, R is the radius of curvature of the duct and a is the duct dimension. The curvature ratio, R/a, is 15.1).If no other disturbances are imposed, the oscillations are the result of the selective amplification of random disturbances in the flow, leading to a broad frequency spectrum. The travelling wave was found to lock in to an imposed periodic disturbance at a selected frequency. The flow structure of the locked state was investigated in detail, using flow visualization and a one-component laser Doppler anemometer to measure streamwise or spanwise velocities. Direct numerical simulations using the package CFDS-FLOW3D are in very good agreement with the experiments and confirm the existence of a fully developed, streamwise-periodic travelling wave state.The inflow region between the two Dean vortices, which transports low-speed fluid away from the outer wall, creates strongly inflectional spanwise profiles of the streamwise velocity. Similarities with twisting vortices in a curved channel and sinuous oscillations of Görtler vortices show that the travelling waves observed here result from a secondary shear instability of these spanwise inflectional profiles.
Miscible displacements in capillary tubes. Part 2. Numerical simulations
Authors: Chen Ching-Yao , Meiburg Eckart 
Published: April 2006

Numerical simulations are presented which, in conjunction with the accompanying experimental investigation by Petitjeans & Maxworthy (1996), are intended to elucidate the miscible flow that is generated if a fluid of given viscosity and density displaces a second fluid of different such properties in a capillary tube or plane channel. The global features of the flow, such as the fraction of the displaced fluid left behind on the tube walls, are largely controlled by dimensionless quantities in the form of a Péclet number Pe, an Atwood number At, and a gravity parameter. However, further dimensionless parameters that arise from the dependence on the concentration of various physical properties, such as viscosity and the diffusion coefficient, result in significant effects as well.The simulations identify two distinct Pe regimes, separated by a transitional region. For large values of Pe, typically above O(10), a quasi-steady finger forms, which persists for a time of O(Pe) before it starts to decay, and Poiseuille flow and Taylor dispersion are approached asymptotically. Depending on the strength of the gravitational forces, we observe a variety of topologically different streamline patterns, among them some that leak fluid from the finger tip and others with toroidal recirculation regions inside the finger. Simulations that account for the experimentally observed dependence of the diffusion coefficient on the concentration show the evolution of fingers that combine steep external concentration layers with smooth concentration fields on the inside. In the small-Pe regime, the flow decays from the start and asymptotically reaches Taylor dispersion after a time of O(Pe).An attempt was made to evaluate the importance of the Korteweg stresses and the consequences of assuming a divergence-free velocity field. Scaling arguments indicate that these effects should be strongest when steep concentration fronts exist, i.e. at large values of Pe and At. However, when compared to the viscous stresses, Korteweg stresses may be relatively more important at lower values of these parameters, and we cannot exclude the possibility that minor discrepancies observed between simulations and experiments in these parameter regimes are partially due to these extra stresses.
Breakage of a drop of inviscid fluid due to a pressure fluctuation at its surface
Authors: Shreekumar  , Kumar R. , Gandhi K. S. 
Published: April 2006

In this work, an attempt is made to gain a better understanding of the breakage of low-viscosity drops in turbulent flows by determining the dynamics of deformation of an inviscid drop in response to a pressure variation acting on the drop surface. Known scaling relationships between wavenumbers and frequencies, and between pressure fluctuations and velocity fluctuations in the inertial subrange are used in characterizing the pressure fluctuation. The existence of a maximum stable drop diameterdmaxfollows once scaling laws of turbulent flow are used to correlate the magnitude of the disruptive forces with the duration for which they act.Two undetermined dimensionless quantities, both of order unity, appear in the equations of continuity, motion, and the boundary conditions in terms of pressure fluctuations applied on the surface. One is a constant of proportionality relating root-mean-square values of pressure and velocity differences between two points separated by a distancel. The other is a Weber number based on turbulent stresses acting on the drop and the resisting stresses in the drop due to interfacial tension. The former is set equal to 1, and the latter is determined by studying the interaction of a drop of diameter equal todmaxwith a pressure fluctuation of length scale equal to the drop diameter. The model is then used to study the breakage of drops of diameter greater thandmaxand those with densities different from that of the suspending fluid.It is found that, at least during breakage of a drop of diameter greater thandmaxby interaction with a fluctuation of equal length scale, a satellite drop is always formed between two larger drops. When very large drops are broken by smaller-length-scale fluctuations, highly deformed shapes are produced suggesting the possibility of further fragmentation due to instabilities. The model predicts that as the dispersed-phase density increases,dmaxdecreases.
Temperature-dependences of the kinetics of reactions of papain and actinidin with a series of reactivity probes differing in key molecular recognition features
Authors: Gul Sheraz , Mellor Geoffrey W. , Thomas Emrys W. , Brocklehurst Keith 
Published: April 2006

The temperature-dependences of the second-order rate constants (k) of the reactions of the catalytic site thiol groups of two cysteine peptidases papain (EC 3.4.22.2) and actinidin (EC 3.4.22.14) with a series of seven 2-pyridyl disulphide reactivity probes (R-S-S-2-Py, in which R provides variation in recognition features) were determined at pH 6.7 at temperatures in the range 4–30 °C by stopped-flow methodology and were used to calculate values of ΔS‡, ΔH‡ and ΔG‡. The marked changes in ΔS‡ from negative to positive in the papain reactions consequent on provision of increase in the opportunities for key non-covalent recognition interactions may implicate microsite desolvation in binding site–catalytic site signalling to provide a catalytically relevant transition state. The substantially different behaviour of actinidin including apparent masking of changes in ΔH‡ by an endothermic conformational change suggests a difference in mechanism involving kinetically significant conformational change.
TEF-1 and C/EBPβ are major p38α MAPK-regulated transcription factors in proliferating cardiomyocytes
Authors: Ambrosino Concetta , Iwata Tomoko , Scafoglio Claudio , Mallardo Massimo , Klein Rüdiger , Nebreda Angel R. 
Published: April 2006

p38 MAPKs (mitogen-activated protein kinases) play important roles in the regulation of cellular responses to environmental stress. Recently, this signalling pathway has also been implicated in the regulation of processes unrelated to stress, for example, in T lymphocytes and cardiomyocytes. In order to identify molecular targets responsible for the housekeeping functions of p38 MAPKs, we have analysed the differences in the transcriptomes of normally proliferating wild-type and p38α knockout immortalized embryonic cardiomyocytes. Interestingly, many potential components of the myocardium extracellular matrix were found to be upregulated in the absence of p38α. Further analysis of the microarray data identified TEF-1 (transcriptional enhancer factor-1), a known regulator of heart-specific gene expression, and C/EBPβ (CCAAT/enhancer-binding protein β), as the two transcription factors the binding sites of which were most enriched in the promoters of p38α-regulated genes. We have focused on the study of the extracellular matrix component COL1A1 (α1 chain of type I collagen) and found evidence for the involvement of both TEF-1 and C/EBPβ in the p38α-dependent inhibition of COL1A1 transcription. Our data therefore show that p38 MAPKs regulate TEF-1 and C/EBPβ transcriptional activity in the absence of environmental stress and suggests a role for p38α in the expression of extracellular matrix components that maintain organ architecture.
Identification of Ebp1 as a component of cytoplasmicbcl-2mRNP (messenger ribonucleoprotein particle) complexes
Authors: Bose Sudeep K. , Sengupta Tapas K. , Bandyopadhyay Sumita , Spicer Eleanor K. 
Published: April 2006

The 3′-UTR (untranslated region) of bcl-2 mRNA contains an ARE (AU-rich element) that potentially regulates the stability of bcl-2 mRNA in a cell specific fashion. Previous studies have demonstrated that multiple proteins interact with bcl-2 mRNA in HL-60 (human leukaemia-60) cells, potentially contributing to the overexpression of Bcl-2 protein. Treatment of HL-60 cells with taxol or okadaic acid has been shown to induce destabilization of bcl-2 mRNA, which was associated with decreased binding of trans-acting factors to bcl-2 mRNA. Nucleolin has been identified as one of the bcl-2 mRNA-binding proteins [Sengupta, Bandyopadhyay, Fernandes and Spicer (2004) J. Biol. Chem. 279, 10855–10863]. In an effort to identify additional bcl-2 mRNA-binding proteins, two polypeptides of approx. 45 kDa and 60 kDa were isolated from HL-60 cells by AREbcl-2 (transcripts that contain bcl-2 AREs) RNA affinity chromatography. These proteins were identified as the human proliferation associated protein, Ebp1, and human DRBP76 (double stranded RNA-binding protein 76) respectively, by MALDI (matrix-assisted laser-desorption ionization)-MS. RNA electrophoretic mobility shift assays indicated that recombinant Ebp1 binds to AREbcl-2 RNA but not to the group 1 ARE present in GM-CSF (granulocyte macrophage-colony stimulating factor) mRNA in vitro. Antibody supershift assays demonstrated that Ebp1 is present in protein–AREbcl-2 RNA complexes formed with cytosolic HL-60 extracts. The interaction of Ebp1 with bcl-2 mRNA in HL-60 cells was also demonstrated by RNA co-immunoprecipitation assays. This interaction was not detected in extracts of taxol-treated HL-60 cells. Immunoprecipitation assays further revealed that Ebp1 co-precipitates with nucleolin from HL-60 cytoplasmic extracts. The observation that co-precipitation was decreased when extracts were treated with RNase suggests that Ebp1 and nucleolin are present in the same bcl-2 mRNP (messenger ribonucleoprotein particle) complexes. RNA-decay assays further demonstrated that Ebp1 decreased the rate of decay of β-globin–AREbcl-2 transcripts in HL-60 cell extracts. Collectively, these results indicate a novel function for Ebp1 in contributing to the regulation of bcl-2 expression in HL-60 cells.
Src-family kinases mediate an outside-in signal necessary for β2 integrins to achieve full activation and sustain firm adhesion of polymorphonuclear leucocytes tethered on E-selectin
Authors: Totani Licia , Piccoli Antonio , Manarini Stefano , Federico Lorenzo , Pecce Romina , Martelli Nicola , Cerletti Chiara , Piccardoni Paola , Lowell Clifford A. , Smyth Susan S. , Berton Giorgio , Evangelista Virgilio 
Published: April 2006

In cell suspensions subjected to high-shear rotatory motion, human PMN (polymorphonuclear cells) adhered to E-selectin-expressing CHO (Chinese-hamster ovary) cells (CHO-E), and formed homotypic aggregates when challenged by E-selectin–IgG fusion protein, by a mechanism that involved β2 integrins. Both heterotypic and homotypic PMN adhesion was accompanied by tyrosine phosphorylation of a 110 kDa protein (P110). This event was prevented by blocking anti-(β2 integrin) antibodies and by inhibitors of Src-family kinases, suggesting that it was part of an ‘outside-in’ signalling that was initiated by integrin engagement. Interestingly, Src-family kinase inhibitors prevented β2-integrin-mediated (i) homotypic PMN adhesion triggered by E-selectin–IgG, (ii) heterotypic CHO-E/PMN adhesion in mixed-cell suspensions, and (iii) firm adhesion of PMN to CHO-E monolayers under physiological flow. Similarly to PMN treated with Src-family kinase inhibitors, PMN from hck−/−fgr−/− and hck−/−fgr−/−lyn−/− mice showed significant impairment of β2-integrin-mediated adhesion to CHO-E. Moreover, the expression of β2 integrin activation epitopes at the sites of cell–cell contact in CHO-E/PMN conjugates was abolished by Src-family kinase inhibitors. One component of P110 was identified as the FAK (focal adhesion kinase) Pyk2 (proline-rich tyrosine kinase 2), which was phosphorylated in a β2 integrin- and Src-family-kinase-dependent manner. Thus, Src-family kinases, and perhaps Pyk2, mediate a signal necessary for β2 integrin function in PMN tethered by E-selectin.
Analysis of restriction sites and Southern blotting of two molecular markers linked to grape seedless gene
Authors: Ke-Qiang Yang , Yue-Jin Wang , Jin-Jin Zhang , Xi-Ping Wang , Yi-Zhen Wan , Jian-Xia Zhang 
Published: April 2006

AbstractThe cloning and sequencing of two specific molecular markers linked to grape (Vitis vinifera) seedless gene indicated that the full lengths of the markers, 39970524-5-564 (GenBank accession number: AY327513) and 39970524-6-1538 (GenBank accession number: AY327514), were 564 bp and 1538 bp, respectively. The restriction sites of sequences 39970524-5-564 and 39970524-6-1538 were analysed with Wingene231 software. The results indicated that there were 29 and 130 restriction sites in 39970524-5-564 and 39970524-6-1538, respectively, digested by restriction enzymes with recognition sites of six or more than six bases. There was no cleavage site in 39970524-5-564 and there was one site at 135 bp of 39970524-6-1538 when these two markers were digested by EcoRI. Both markers can not be digested by HindIII. Therefore, the full length of 39970524-5-564 and of the two bands of 39970524-6-1538 (1400 bp and 135 bp) could be cut out from the pGEMR-T Easy Vector by EcoRI. The labelled DNA of 39970524-5-564, used as a probe for Southern blotting with genomic DNA from Red Globe, Flame Seedless, Thompson Seedless, four seedless hybrids and three seeded hybrids, showed a unique hybrid band present in all seedless individuals, but absent in all seeded individuals. It was further indicated that the specific marker 39970524-5-564 was derived from the genome of seedless grapes.
Microfertilization of oocytes and culture of embryos in goat
Authors: Xiao-E Zhao , Yan-Fei Yang , Feng-Jun Liu , Yong-Sheng Wang , Hao Wu , Yu-Qiang Li , Yong Zhang 
Published: April 2006

AbstractIn vitro development of goat embryos obtained by fertilizing oocytes using intracytoplasmic sperm injection (ICSI) was investigated. The results showed that the blastocyst rate was significantly higher (P<0.05) when the embryos were co-cultured with granular cells (GCs) in media CR1aa supplemented with 10% bovine follicular fluid (BFF) (22.2%) than with 5% (13.1%) and 15% BFF (2.7%). When embryos were co-cultured with GCs in SOFaa media, the highest blastocyst rate was obtained from supplementation with 10% BFF (25.1%), which was significantly different from 5% (12.9%) and 15% BFF (3.0%) groups. When 10% BFF and fetus bovine serum (FBS) were added into CR1aa or SOFaa media, the goat ICSI blastocyst rates were 22.6 and 26.9% or 5.8 and 6.1% respectively. These results suggest that both CR1aa and SOFaa could be used as culture media for goat ICSI embryos, 10% BFF could significantly increase the blastocyst rate and BFF was more efficient than FBS for the early in vitro development of goat ICSI embryos.
How accurately can we control the FDR in analyzing microarray data?
Authors: Jung Sin-Ho , Jang Woncheol 
Published: April 2006

AbstractSummary: We want to evaluate the performance of two FDR-based multiple testing procedures by Benjamini and Hochberg (1995, J. R. Stat. Soc. Ser. B, 57, 289–300) and Storey (2002, J. R. Stat. Soc. Ser. B, 64, 479–498) in analyzing real microarray data. These procedures commonly require independence or weak dependence of the test statistics. However, expression levels of different genes from each array are usually correlated due to coexpressing genes and various sources of errors from experiment-specific and subject-specific conditions that are not adjusted for in data analysis. Because of high dimensionality of microarray data, it is usually impossible to check whether the weak dependence condition is met for a given dataset or not. We propose to generate a large number of test statistics from a simulation model which has asymptotically (in terms of the number of arrays) the same correlation structure as the test statistics that will be calculated from the given data and to investigate how accurately the FDR-based testing procedures control the FDR on the simulated data. Our approach is to directly check the performance of these procedures for a given dataset, rather than to check the weak dependency requirement. We illustrate the proposed method with real microarray datasets, one where the clinical endpoint is disease group and another where it is survival.Contact: jung0005@mc.duke.edu
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
Authors: Sundaresh Suman , Doolan Denise L. , Hirst Siddiqua , Mu Yunxiang , Unal Berkay , Davies D. Huw , Felgner Philip L. , Baldi Pierre 
Published: April 2006

Abstract
Motivation: We present a study of antigen expression signals from a newly developed high-throughput protein microarray technique. These signals are a measure of antibody–antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development.
Results: We investigate the characteristics of these expression profiles and show that noise models, normalization, variance estimation and differential expression analysis techniques developed in the context of DNA microarray analysis can be adapted and applied to these protein arrays. Using a high-dimensional dataset containing measurements of expression profiles of antibody reactivity against each protein (295 antigens and 9 controls) in 42 malaria (Plasmodium falciparum) protein arrays derived from 22 donors with various clinical presentations of malaria, we present a methodology for the analysis and identification of significantly expressed antigens targeted by immune responses for individual sera, groups of sera and across stages of infection. We also conduct a short study highlighting the top immunoreactive antigens where we identify three novel high priority antigens for future evaluation.
Availability: All software programs (in R) used for the analysis described in this paper are freely available for academic purposes at
Contact: pfbaldi@uci.edu