bluuebunny/crossref_metadata_2025_split huggingface dataset:
Separation of cationic polymer particles and characterization of avidin‐immobilized particles by capillary electrophoresis
Authors: Okamoto Yukihiro , Kitagawa Fumihiko , Otsuka Koji 
Published: February 2006

AbstractCationic polymer microparticles have received much attention especially in the field of biotechnology, such that their analysis and separation have become important. So far, the separation of cationic polymer particles with different size using CE has not been achieved and the cationic particles migrated as if they are negatively charged, probably due to electrostatic interaction between capillary wall and cationic polymer particles. In this paper, the separation of cationic polymer microparticles by CE was investigated in detail. The separation of cationic particles with different size was achieved in CE by taking into account the interaction between sample particles and the inner surface of capillaries. By employing a poly(vinyl alcohol)‐coated capillary, a better size separation of amine‐modified latex particles was obtained compared to a Polybrene‐coated capillary. It was elucidated that the composition, concentration, and pH of the background solution were also important factors in the separation of colloidal particles to avoid the surface adsorption and the characteristic aggregation of polymer particles. Furthermore, the CE analysis was applied to the characterization of cationic protein‐immobilized particles.
Proteome analysis of human plasma and amniotic fluid by Off‐Gel™ isoelectric focusing followed by nano‐LC‐MS/MS
Authors: Michel Philippe E. , Crettaz David , Morier Patrick , Heller Manfred , Gallot Denis , Tissot Jean‐Daniel , Reymond Frédéric , Rossier Joel S. 
Published: February 2006

AbstractThis paper presents a comparative proteomic analysis of human maternal plasma and amniotic fluid (AF) samples from the same patient at term of pregnancy in order to find specific AF proteins as markers of premature rupture of membranes, a complication frequently observed during pregnancy. Maternal plasma and the corresponding AF were immunodepleted in order to remove the six most abundant proteins before the systematic analysis of their protein composition. The protein samples were then fractionated by IEF Off‐Gel™ electrophoresis (OGE), digested and analyzed with nano‐LC‐MS/MS separation, revealing a total of 73 and 69 proteins identified in maternal plasma and AF samples, respectively. The proteins identified in AF have been compared to those identified in the mother plasma as well as to the reference human plasma protein list reported by Anderson et al. (Mol. Cell. Proteomics 2004, 3, 311–326). This comparison showed that 26 proteins were exclusively present in AF and not in plasma among which 10 have already been described to be placenta or pregnancy specific. As a further validation of the method, plasma proteins fractionated by OGE and analysed by nano‐LC‐MS/MS have been compared to the Swiss 2‐D PAGE reference map by reconstructing a map that matches 2‐D gel and OGE experimental data. This representation shows that 36 of 49 reference proteins could be identified in both data sets, and that isoform shifts in pI are well conserved in the OGE data sets.
Coordinated and reversible reduction of enzymes involved in terminal oxidative metabolism in skeletal muscle mitochondria from a riboflavin‐responsive, multiple acyl‐CoA dehydrogenase deficiency patient
Authors: Gianazza Elisabetta , Vergani Lodovica , Wait Robin , Brizio Carmen , Brambilla Daniela , Begum Shajna , Giancaspero Teresa A. , Conserva Francesca , Eberini Ivano , Bufano Daniela , Angelini Corrado , Pegoraro Elena , Tramontano Anna , Barile Maria 
Published: February 2006

AbstractIn this case report we studied alterations in mitochondrial proteins in a patient suffering from recurrent profound muscle weakness, associated with ethylmalonic‐adipic aciduria, who had benefited from high dose of riboflavin treatment. Morphological and biochemical alterations included muscle lipid accumulation, low muscle carnitine content, reduction in fatty acid β‐oxidation and reduced activity of complexes I and II of the respiratory chain. Riboflavin therapy partially or totally reversed these symptoms and increased the level of muscle flavin adenine dinucleotide, suggesting that aberrant flavin cofactor metabolism accounted for the disease. Proteomic investigation of muscle mitochondria revealed decrease or absence of several flavoenzymes, enzymes related to flavin cofactor‐dependent mitochondrial pathways and mitochondrial or mitochondria‐associated calcium‐binding proteins. All these deficiencies were completely rescued after riboflavin treatment. This study indicates for the first time a profound involvement of riboflavin/flavin cofactors in modulating the level of a number of functionally coordinated polypeptides involved in fatty acyl‐CoA and amino acid metabolism, extending the number of enzymatic pathways altered in riboflavin‐responsive multiple acyl‐CoA dehydrogenase deficiency.
A new type of migrating zone boundary in electrophoresis: 3. The hybrid boundary and stacking criteria
Authors: Gebauer Petr , Malá Zdena , Boček Petr 
Published: February 2006

AbstractThis article investigates the principles of stacking of analytes by a zone of a bulk sample component that possesses one hybrid boundary. The model system investigated comprises a transient stacking zone in a BGE where the rear boundary of this zone is a hybrid one. A theoretical description of such a system is given, and general rules and mathematical criteria for quantitative stacking are presented. These criteria are based on comparison of migration velocities of analytes to be stacked and velocities of the boundaries of the stacking zone. It is shown that the presence of a hybrid boundary brings about additional constraints for stacking of analytes due to the presence of the sharp part of the hybrid boundary that migrates faster than regular sharp boundary of this zone. An experimental example related to the described theory is also shown.
Capillary electrophoresis using copolymers of different composition as physical coatings: A comparative study
Authors: Erny Guillaume L. , Elvira Carlos , San Román Julio , Cifuentes Alejandro 
Published: February 2006

AbstractIn this work, a comparative study on the use of different polymers as physically adsorbed coatings for CE is presented. It is demonstrated that the use of ad hoc synthesized polymers as coatings allows tailoring the EOF in CE increasing the flexibility of this analytical technique. Namely, different polymers were synthesized at our laboratory using different percentages of ethylpyrrolidine methacrylate (EpyM) and N,N‐dimethylacrylamide (DMA). Thus, by modifying the percentage of EpyM and DMA monomers it is possible to manipulate the positive charge of the copolymer, varying the global electrical charge on the capillary wall and with that the EOF. These coated capillaries are obtained by simply flushing a given EpyM–DMA aqueous solution into bare silica capillaries. It is shown that by using these coated capillaries at adequate pHs, faster or more resolved CE separations can be achieved depending on the requirements of each analysis. Moreover, it is demonstrated that these coated capillaries reduce the electrostatic adsorption of basic proteins onto the capillary wall. Furthermore, EpyM–DMA coatings allow the reproducible chiral separation of enantiomers through the partial filling technique (PFT). The EpyM–DMA coated capillaries are demonstrated to provide reproducible EOF values independently of the pH and polymer composition with%RSD values lower than 2% for the same day. It is also demonstrated that the coating procedure is reproducible between capillaries. The compatibility of this coating protocol with CE in microchips is discussed.
A filtering technique for system of reaction–diffusion equations
Authors: Dupros F. , Garbey M. , Fitzgibbon W. E. 
Published: February 2006

AbstractIn this paper, we present a fast parallel solver designed for a system of reaction–convection–diffusion equations. A typical application is the large‐scale computing of air quality models for which the main solver corresponds to reaction–diffusion–convection equations. Another potential application is the numerical simulation of population models where several colonies compete. Reaction–diffusion systems can be integrated in time by pointwise Newton iteration when all space‐dependent terms are explicit in the time integration. A Newton–Jacobi iteration makes this scheme implicit. Such methods are easy to code and have scalable parallelism. However, they are numerically inefficient. An alternative method is to use operator splitting, decoupling the time integration of the reaction from the time integration of convection–diffusion. However, such methods may not be time accurate thanks to the stiffness of the reaction term and are complex to parallelize with good scalability. A second alternative is to use matrix‐free Newton–Krylov methods. These techniques are particularly efficient provided that a good parallel preconditioner is customized to the application. The method is then not trivial to implement. We propose here a new family of fast, easy to code and numerically efficient reaction–diffusion solvers based on a filtering technique that stabilizes the explicit treatment of the diffusion terms. The scheme is completely explicit with respect to space, and the postprocessing to stabilize time stepping uses a simple FFT. We demonstrate the potential of this numerical scheme with two examples in air quality models that usually require the implicit treatment of diffusion terms and have compared our solution to classical schemes for two nonlinear reaction–diffusion problems. For general reaction–diffusion problems on tensorial product grids with regular space step, the filtering process can be applied as a black box postprocessing procedure. Further, we demonstrate on critical components of the algorithm the high potential of parallelism of our method on medium‐scale parallel computers. Copyright © 2006 John Wiley & Sons, Ltd.
Stability of high‐speed two‐layer film casting of Newtonian fluids
Authors: Zhang Jing , Khayat Roger E. , Wang Wei 
Published: February 2006

AbstractThe steady‐state flow and its linear stability are investigated for the isothermal two‐layer film casting process. Newtonian fluids are considered in this study. The continuity of traction is ensured at the interface, and the axial velocity is assumed to be uniform across each film layer separately. The effects of inertia, gravity, fluid parameters and processing conditions on the steady‐state flow and its stability are studied. The results indicate that the fluid properties and the processing conditions have significant influence on the flow. The flow stability is strongly dependent on the layer layout with respect to the take‐up rolling process. The frequency of the (unstable) disturbance is insensitive to flow and processing parameters. Copyright © 2006 John Wiley & Sons, Ltd.
Continuous, discontinuous and coupled discontinuous–continuous Galerkin finite element methods for the shallow water equations
Authors: Dawson Clint , Westerink Joannes J. , Feyen Jesse C. , Pothina Dharhas 
Published: February 2006

AbstractWe consider the approximation of the depth‐averaged two‐dimensional shallow water equations by both a traditional continuous Galerkin (CG) finite element method as well as two discontinuous Galerkin (DG) approaches. The DG method is locally conservative, flux‐continuous on each element edge, and is suitable for both smooth and highly advective flows. A novel technique of coupling a DG method for continuity with a CG method for momentum is developed. This formulation is described in detail and validation via numerical testing is presented. Comparisons between a widely used CG approach, a conventional DG method, and the novel coupled discontinuous–continuous Galerkin method illustrates advantages and disadvantages in accuracy and efficiency. Copyright © 2006 John Wiley & Sons, Ltd.
Simulation of an impinging jet in a crossflow using a Reynolds stress transport model
Authors: Worth Nicholas A. , Yang Zhiyin 
Published: February 2006

AbstractAn impinging jet in a crossflow is a flow case representative of a jet‐lift aircraft operating in ground effect. Accurate modelling of this flow field is essential in predicting the practical flow problems associated with these aircraft; in particular the ingestion of hot gas into the engine intakes, and the importance of the ground vortex contribution towards this. This paper describes a numerical study of this flow using the Reynolds averaged Navier–Stokes (RANS) approach with a Reynolds stress transport model (RSM), validating the current results against experimental data and comparing with other numerical results. A grid‐independent solution was determined and the importance of correct inlet geometry modelling demonstrated. Although slight improvements over the eddy‐viscosity approach are produced, the RSM model fails to predict the correct ground vortex centre location, and vortex attachment to the impinging jet, demonstrating that the RANS approach used to solve a highly unsteady, time‐dependent phenomenon is likely to result in the poor predictions seen. Therefore although the current approach does offer advantages over the k–ε model, it still may only be suitable for gross flow‐field approximations, as part of preliminary studies. For more accurate investigation of configuration‐dependent effects, further investigation into the LES approach is recommended. Copyright © 2006 John Wiley & Sons, Ltd.
Solving a fully nonlinear highly dispersive Boussinesq model with mesh‐less least square‐based finite difference method
Authors: Wang Benlong , Liu Hua 
Published: February 2006

AbstractCombining mesh‐less finite difference method and least square approximation, a new numerical model is developed for water wave propagation model in two horizontal dimensions. In the numerical formulation of the method, the approximation of the unknown functions and their derivatives are constructed on a set of nodes in a local circular‐shaped region. The Boussinesq equations studied in this paper is a fully nonlinear and highly dispersive model, which is composed of the exact boundary conditions and the truncated series expansion solution of the Laplace equation. The resultant system involves a sparse, unsymmetrical matrix to be solved at each time step of the simulation. Matrix solutions are studied to reduce the computing resource requirements and improve the efficiency and accuracy. The convergence properties of the present numerical method are investigated. Preliminary verifications are given for nonlinear wave shoaling problems; the numerical results agree well with experimental data available in the literature. Copyright © 2006 John Wiley & Sons, Ltd.
On the efficiency and quality of numerical solutions in CFD problems using the interface strip preconditioner for domain decomposition methods
Authors: Paz Rodrigo R. , Nigro Norberto M. , Storti Mario A. 
Published: February 2006

AbstractIn this paper, some pathologies found for simple tests solved by means of preconditioned full iterative schemes are presented. According to these results (Sections 4 and 5), the accuracy deterioration observed should be considered as a warning for the final application given to these solutions. Even though it is well known that full iterative solvers are not the best selection for comparison, they were chosen because they are widely used by the computational fluid dynamic (CFD) community for a diversity of complex fluid dynamics applications.FEM simulated solutions are compared with analytical solutions or measured data for problems that have been considered as ‘benchmarks’ in the CFD literature. For this purpose, the study of the solution obtained via parallelized iterative methods that have been extensively used (e.g. conjugate gradients (CG), GMRes global iteration and its variants, ‘overlapping’ and ‘non‐overlapping’ additive Schwarz domain decomposition schemes) in CFD computations and those obtained with the new interface strip preconditioner (J. Comput. Meth. Sci. Engng 2003; Int. J. Numer. Meth. Engng 2005; 62(13):1873–1894) for the Schur complement method is carried out. The idea is to present the new solver as an alternative to obtain more accurate and faster solutions in the context of monolithic and non‐monolithic schemes applied to a internal/external viscous compressible/incompressible flows around bodies of complex shapes.Therefore, the target of this work is to show how the reliability of CFD codes is affected by the solver selection and why domain decomposition methods should be viewed not only as a more efficient strategy, but also to guarantee the solution quality. Copyright © 2006 John Wiley & Sons, Ltd.
Study of a plane‐free jet exhausting from a channel by vortex‐in‐cell method
Authors: Knani Mohamed Ali , Boisson Henri‐Claude , Giovannini André , Lili Taieb 
Published: February 2006

AbstractA two‐dimensional simulation of a plane jet exhausting from a channel has been performed using the vortex in cell algorithm in the Reynolds number range of 100–900. The vorticity is generated on the wall of the entrance channel whose length has been fixed in order to obtain a fully developed velocity profile at the entry of the jet. The transient behaviour of the velocity field starting from rest has been observed until reaching a quasi steady regime. The mean value of the velocity field is compared with the results of a finite volume computation on the same mesh. The velocity fluctuations obtained using this method are analysed. Their effect on the mean flow is estimated to be smaller than the viscous effect. Copyright © 2006 John Wiley & Sons, Ltd.
A 3D second‐order accurate projection‐based Finite Volume code on non‐staggered, non‐uniform structured grids with continuity preserving properties: application to buoyancy‐driven flows
Authors: Denaro F. M. 
Published: February 2006

AbstractIt is well known that exact projection methods (EPM) on non‐staggered grids suffer for the presence of non‐solenoidal spurious modes. Hence, a formulation for simulating time‐dependent incompressible flows while allowing the discrete continuity equation to be satisfied up to machine‐accuracy, by using a Finite Volume‐based second‐order accurate projection method on non‐staggered and non‐uniform 3D grids, is illustrated. The procedure exploits the Helmholtz–Hodge decomposition theorem for deriving an additional velocity field that enforces the discrete continuity without altering the vorticity field. This is accomplished by first solving an elliptic equation on a compact stencil that is by performing a standard approximate projection method (APM). In such a way, three sets of divergence‐free normal‐to‐face velocities can be computed. Then, a second elliptic equation for a scalar field is derived by prescribing that its additional discrete gradient ensures the continuity constraint based on the adopted linear interpolation of the velocity. Characteristics of the double projection method (DPM) are illustrated in details and stability and accuracy of the method are addressed. The resulting numerical scheme is then applied to laminar buoyancy‐driven flows and is proved to be stable and efficient. Copyright © 2006 John Wiley & Sons, Ltd.
Riemann solvers with evolved initial conditions
Authors: Toro E. F. 
Published: February 2006

AbstractThe scope of this paper is three fold. We first formulate upwind and symmetric schemes for hyperbolic equations with non‐conservative terms. Then we propose upwind numerical schemes for conservative and non‐conservative systems, based on a Riemann solver, the initial conditions of which are evolved non‐linearly in time, prior to a simple linearization that leads to closed‐form solutions. The Riemann solver is easily applied to complicated hyperbolic systems. Finally, as an example, we formulate conservative schemes for the three‐dimensional Euler equations for general compressible materials and give numerical results for a variety of test problems for ideal gases in one and two space dimensions. Copyright © 2006 John Wiley & Sons, Ltd.
Petrov–Galerkin finite element stabilization for two‐phase flows
Authors: Giordano Michele , Magi Vinicio 
Published: February 2006

AbstractA finite element model for incompressible laminar two‐phase flows is presented. A two‐fluid model, describing the laminar non‐equilibrium flow of two incompressible phases, is discretized by means of a properly designed streamline upwind Petrov–Galerkin (SUPG) finite element procedure. Such a procedure is consistent with a continuous pressure equation. The design and the implementation of the algorithm are presented together with its validation throughout a comparison with simulations available in the literature. Copyright © 2006 John Wiley & Sons, Ltd.
Assessment of alaryngeal speech using a sound‐producing voice prosthesis in relation to sex and pharyngoesophageal segment tonicity
Authors: van der Torn M. , van Gogh C. D. L. , Verdonck‐de Leeuw I. M. , Festen J. M. , Verkerke G. J. , Mahieu H. F. 
Published: February 2006

AbstractBackground.A pneumatic artificial sound source incorporated in a regular tracheoesophageal shunt valve may improve alaryngeal voice quality.Methods.In 20 laryngectomees categorized for sex and pharyngoesophageal segment tonicity, a prototype sound‐producing voice prosthesis (SPVP) is evaluated for a brief period and compared with their regular tracheoesophageal shunt speech.Results.Perceptual voice evaluation by an expert listener and acoustical analysis demonstrate a uniform rise of vocal pitch when using the SPVP. Female laryngectomees with an atonic pharyngoesophageal segment gain vocal strength with the SPVP. Exerted tracheal pressure and airflow rate are equivalent to those required for regular tracheoesophageal shunt valves. However, communicative suitability and speech intelligibility deteriorate by the SPVP for most patients. Tracheal phlegm clogging the SPVP is a hindrance for most patients.Conclusions.The SPVP raises vocal pitch. Female laryngectomees with an atonic or severely hypotonic pharyngoesophageal segment can benefit from a stronger voice with the SPVP. © 2005 Wiley Periodicals, Inc. Head Neck 28: 400–412, 2006
Matrix metalloproteases in head and neck cancer
Authors: Rosenthal Eben L. , Matrisian Lynn M. 
Published: February 2006

AbstractMatrix metalloproteases (MMPs) are a collection of enzymes capable of cleaving extracellular matrix components, growth factors, and cell‐surface receptors. MMPs modulate most aspects of tumorigenesis and are highly expressed in cancer compared with normal tissues. Preclinical studies have demonstrated that head and neck squamous cell carcinomas (HNSCCs) express high levels of MMPs in vivo and that inhibition of these enzymes in vitro and in mouse models decreases invasion and metastasis. However, the clinical trials for MMP inhibitors have failed to demonstrate a significant survival advantage in most cancers. The disparity between preclinical and clinical studies has led to the reevaluation of how MMP functions in cancer and the design of clinical trials for molecularly targeted agents. Mouse model data and analysis of HNSCC tumor specimens suggests that membrane type‐1 MMP (MT1‐MMP) may be a critical enzyme in tumor cell invasion and survival in vivo. This accumulated data provide evidence for development of selective MT1‐MMP inhibitors as therapy in HNSCC. © 2005 Wiley Periodicals, Inc. Head Neck, 2006