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Analyses of pig genomes provide insight into porcine demography and evolution
Groenen, Martien A. M.,Archibald, Alan L.,Uenishi, Hirohide,Tuggle, Christopher K.,Takeuchi, Yasuhiro,Rothschild, Max F.,Rogel-Gaillard, Claire,Park, Chankyu,Milan, Denis,Megens, Hendrik-Jan,Li, Sheng Nature Publishing Group, a division of Macmillan P 2012 Nature Vol.491 No.7424
For 10,000??years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ?? million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
Toward the computational rheometry of filled polymeric fluids
황욱렬,Martien A. Hulsen 한국유변학회 2006 Korea-Australia rheology journal Vol.18 No.4
We present a short review for authors' previous work on direct numerical simulations for inertialess hard particle suspensions formulated either with a Newtonian fluid or with viscoelastic polymeric fluids to understand the microstructural evolution and the bulk material behavior. We employ two well-defined bi-periodic domain concepts such that a single cell problem with a small number of particles may represent a large number of repeated structures: one is the sliding bi-periodic frame for simple shear flow and the other is the extensional bi-periodic frame for planar elongational flow. For implicit treatment of hydrodynamic interaction between particle and fluid, we use the finite-element/fictitious-domain method similar to the distributed Lagrangian multiplier (DLM) method together with the rigid ring description. The bi-periodic boundary conditions can be effectively incorportated as constraint equations and implemented by Lagrangian multipliers. The bulk stress can be evaluated by simple boundary integrals of stresslets on the particle boundary in such formulations. Some 2-D example results are presented to show effects of the solid fraction and the particle configuration on the shear and elongational viscosity along with the micro-structural evolution for both particles and fluid. Effects of the fluid elasticity has been also presented.
Direct numerical simulations of hard particle suspensions in planar elongational flow
Hwang, Wook Ryol,Hulsen, Martien A. Elsevier 2006 Journal of non-Newtonian fluid mechanics Vol.136 No.2
<P><B>Abstract</B></P><P>We present a new direct simulation technique of inertialess particle suspensions in planar elongational flow of a Newtonian fluid. The extensional bi-periodic domain concept is introduced such that a single cell problem with a small number of particles may represent a large number of repeated structures of such a cell in planar elongational flow. For implicit treatment of the hydrodynamic interaction between particles and fluid, we employ a finite-element/fictitious-domain method similar to the distributed Lagrangian multipliers (DLM) method together with a rigid-ring description of the particle. The extensional bi-periodic frame is incorporated by constraint equations with Lagrangian multipliers and is implemented by the mortar element method. In our formulation, the bulk stress is evaluated by simple boundary integrals. Concentrating on 2D circular disk particles, we present numerical examples of single-particle, two-particle and 100-particle problems in the extensional bi-periodic frame. We discuss effects of solid fraction and particle configuration on the elongational viscosity of the suspension, in comparison with simple shear flow. We found that, at zero strain, the relative elongational viscosity is almost the same as the relative shear viscosity in simple shear for moderately concentrated suspensions. There is a small increase in elongational viscosity for large strains, which is related to an anisotropic distribution of the particles.</P>
Toward the computational rheometry of filled polymeric fluids
Hwang, Wook-Ryol,Hulsen Martien A. The Korean Society of Rheology 2006 Korea-Australia rheology journal Vol.18 No.4
We present a short review for authors' previous work on direct numerical simulations for inertialess hard particle suspensions formulated either with a Newtonian fluid or with viscoelastic polymeric fluids to understand the microstructural evolution and the bulk material behavior. We employ two well-defined bi-periodic domain concepts such that a single cell problem with a small number of particles may represent a large number of repeated structures: one is the sliding bi-periodic frame for simple shear flow and the other is the extensional bi-periodic frame for planar elongational flow. For implicit treatment of hydrodynamic interaction between particle and fluid, we use the finite-element/fictitious-domain method similar to the distributed Lagrangian multiplier (DLM) method together with the rigid ring description. The bi-periodic boundary conditions can be effectively incorportated as constraint equations and implemented by Lagrangian multipliers. The bulk stress can be evaluated by simple boundary integrals of stresslets on the particle boundary in such formulations. Some 2-D example results are presented to show effects of the solid fraction and the particle configuration on the shear and elongational viscosity along with the micro-structural evolution for both particles and fluid. Effects of the fluid elasticity has been also presented.
Simulation of extrudate swell using an extended finite element method
Choi, Young-Joon,Hulsen, Martien A. 한국유변학회 2011 Korea-Australia rheology journal Vol.23 No.3
An extended finite element method (XFEM) is presented for the simulation of extrudate swell. A temporary arbitrary Lagrangian-Eulerian (ALE) scheme is incorporated to cope with the movement of the free surface. The main advantage of the proposed method is that the movement of the free surface can be simulated on a fixed Eulerian mesh without any need of re-meshing. The swell ratio of an upper-convected Maxwell fluid is compared with those of the moving boundary-fitted mesh problems of the conventional ALE technique, and those of Crochet & Keunings (1980). The proposed XFEM combined with the temporary ALE scheme can provide similar accuracy to the boundary-fitted mesh problems for low Deborah numbers. For high Deborah numbers, the method seems to be more stable for the extrusion problem.
Simulation of extrudate swell using an extended finite element method
Young Joon Choi,Martien A. Hulsen 한국유변학회 2011 Korea-Australia rheology journal Vol.23 No.3
An extended finite element method (XFEM) is presented for the simulation of extrudate swell. A temporary arbitrary Lagrangian-Eulerian (ALE) scheme is incorporated to cope with the movement of the free surface. The main advantage of the proposed method is that the movement of the free surface can be simulated on a fixed Eulerian mesh without any need of re-meshing. The swell ratio of an upper-convected Maxwell fluid is compared with those of the moving boundary-fitted mesh problems of the conventional ALE technique, and those of Crochet & Keunings (1980). The proposed XFEM combined with the temporary ALE scheme can provide similar accuracy to the boundary-fitted mesh problems for low Deborah numbers. For high Deborah numbers, the method seems to be more stable for the extrusion problem.
Wicaksono, Psycha Anindya,Sismindari, Sismindari,Martien, Ronny,Ismail, Hilda Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.4
Ribosome-inactivating protein (RIP) from Mirabilis jalapa L. leaves has cytotoxic effects on breast cancer cell lines but is less toxic towards normal cells. However, it can easily be degraded after administration so it needs to be formulated into nanoparticles to increase its resistance to enzymatic degradation. The objectives of this study were to develop a protein extract of M. jalapa L. leaves (RIP-MJ) incorporated into nanoparticles conjugated with Anti-EpCAM antibodies, and to determine its cytotoxicity and selectivity in the T47D breast cancer cell line. RIP-MJ was extracted from red-flowered M. jalapa L. leaves. Nanoparticles were formulated based on polyelectrolyte complexation using low viscosity chitosan and alginate, then chemically conjugated with anti-EpCAM antibody using EDAC based on carbodiimide reaction. RIP-MJ nanoparticles were characterised for the particle size, polydispersity index, zeta potential, particle morphology, and entrapment efficiency. The cytotoxicity of RIP-MJ nanoparticles against T47D and Vero cells was then determined with MTT assay. The optimal formula of RIP-MJ nanoparticles was obtained at the concentration of RIP-MJ, low viscosity chitosan and alginate respectively 0.05%, 1%, and 0.4% (m/v). RIP-MJ nanoparticles are hexagonal with high entrapment efficiency of 98.6%, average size of 130.7 nm, polydispersity index of 0.380 and zeta potential +26.33 mV. The $IC_{50}$ values of both anti-EpCAM-conjugated and non-conjugated RIP-MJ nanoparticles for T47D cells (13.3 and $14.9{\mu}g/mL$) were lower than for Vero cells (27.8 and $33.6{\mu}g/mL$). The $IC_{50}$ values of conjugated and non-conjugated RIP-MJ for both cells were much lower than $IC_{50}$ values of non-formulated RIP-MJ (>$500{\mu}g/mL$).