Self-avoiding fractional Brownian motion - The Edwards model

In this work we extend Varadhan's construction of the Edwards polymer model to the case of fractional Brownian motions in $\R^d$, for any dimension $d\geq 2$, with arbitrary Hurst parameters $H\leq 1/d$.Comment: 14 page

Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism

Background: The genes of plants can be up- or down-regulated during viral infection to influence the replication of viruses. Identification of these differentially expressed genes could shed light on the defense systems employed by plants and the mechanisms involved in the adaption of viruses to plant cells. Differential gene expression in Nicotiana benthamiana plants in response to infection with Bamboo mosaic virus (BaMV) was revealed using cDNA-amplified fragment length polymorphism (AFLP). Results: Following inoculation with BaMV, N. benthamiana displayed differential gene expression in response to the infection. Isolation, cloning, and sequencing analysis using cDNA-AFLP furnished 90 cDNA fragments with eight pairs of selective primers. Fifteen randomly selected genes were used for a combined virus-induced gene silencing (VIGS) knockdown experiment, using BaMV infection to investigate the roles played by these genes during viral infection, specifically addressing the means by which these genes influence the accumulation of BaMV protein. Nine of the 15 genes showed either a positive or a negative influence on the accumulation of BaMV protein. Six knockdown plants showed an increase in the accumulation of BaMV, suggesting that they played a role in the resistance to viral infection, while three plants showed a reduction in coat protein, indicating a positive influence on the accumulation of BaMV in plants. An interesting observation was that eight of the nine plants showing an increase in BaMV coat protein were associated with cell rescue, defense, death, aging, signal transduction, and energy production. Conclusions: This study reports an efficient and straightforward method for the identification of host genes involved in viral infection. We succeeded in establishing a cDNA-AFLP system to help track changes in gene expression patterns in N. benthamiana plants when infected with BaMV. The combination of both DNA-AFLP and VIGS methodologies made it possible to screen a large number of genes and identify those associated with infections of plant viruses. In this report, 9 of the 15 analyzed genes exhibited either a positive or a negative influence on the accumulation of BaMV in N. benthamiana plants

Motion of a driven tracer particle in a one-dimensional symmetric lattice gas

We study the dynamics of a tracer particle subject to a constant driving force $E$ in a one-dimensional lattice gas of hard-core particles whose transition rates are symmetric. We show that the mean displacement of the driven tracer grows in time, $t$, as $\sqrt{\alpha t}$, rather than the linear time dependence found for driven diffusion in the bath of non-interacting (ghost) particles. The prefactor $\alpha$ is determined implicitly, as the solution of a transcendental equation, for an arbitrary magnitude of the driving force and an arbitrary concentration of the lattice gas particles. In limiting cases the prefactor is obtained explicitly. Analytical predictions are seen to be in a good agreement with the results of numerical simulations.Comment: 21 pages, LaTeX, 4 Postscript fugures, to be published in Phys. Rev. E, (01Sep, 1996

Comparison of Genomes of Three Xanthomonas oryzae Bacteriophages

<p>Abstract</p> <p>Background</p> <p>Xp10 and OP1 are phages of <it>Xanthomonas oryzae </it>pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice plants, which were isolated in 1967 in Taiwan and in 1954 in Japan, respectively. We recently isolated the Xoo phage Xop411.</p> <p>Results</p> <p>The linear Xop411 genome (44,520 bp, 58 ORFs) sequenced here is 147 bp longer than that of Xp10 (60 ORFs) and 735 bp longer than that of OP1 (59 ORFs). The G+C contents of OP1 (51%) and Xop411 and Xp10 (52% each) are less than that of the host (65%). The 9-bp 3'-overhangs (5'-GGACAGTCT-3') in Xop411 and Xp10 are absent from OP1. More of the deduced Xop411 proteins share higher degrees of identity with Xp10 than with OP1 proteins, while the right end of the genomes of Xp10 and OP1, containing all predicted promoters, share stronger homology. Xop411, Xp10, and OP1 contain 8, 7, and 6 freestanding HNH endonuclease genes, respectively. These genes can be classified into five groups depending on their possession of the HNH domain (HNN or HNH type) and/or AP2 domain in intact or truncated forms. While the HNN-AP2 type endonuclease genes dispersed in the genome, the HNH type endonuclease genes, each with a unique copy, were located within the same genome context. Mass spectrometry and N-terminal sequencing showed nine Xop411 coat proteins, among which three were identified, six were assigned as coat proteins (4) and conserved phage proteins (2) in Xp10. The major coat protein, in which only the N-terminal methionine is removed, appears to exist in oligomeric forms containing 2 to 6 subunits. The three phages exhibit different patterns of domain duplication in the N-terminus of the tail fiber, which are involved in determination of the host range. Many short repeated sequences are present in and around the duplicated domains.</p> <p>Conclusion</p> <p>Geographical separation may have confined lateral gene transfer among the Xoo phages. The HNN-AP2 type endonucleases were more likely to transfer their genes randomly in the genome and may degenerate after successful transmission. Some repeated sequences may be involved in duplication/loss of the domains in the tail fiber genes.</p

Les analysis on cylinder cascade flow based on energy ratio coefficient

The flow field around the cylinder cascade is widely used to analyze the interaction of vortex shedding and the information on heat transfer. Large eddy simulation (LES) can be used to get the turbulent flow information in detail. The resolved largescale structures are determined by the size of the grid, and the turbulent vortex dissipation is modeled with a subgrid scale model. Whereas there is no accurate criterion to provide the subgrid scale with the physical meaning. Based on turbulent energy ratio coefficient and numerical simulation results with turbulent model, the subgrid was generated for the incompressible fluid flowing around a column of cylinder cascade with a gap-to-diameter ratio of 2. Smagorinsky-Lily (SM) model was applied to LES analysis. The turbulent flow information was compared with the experimental data by PIV. Two cases with different Reynolds numbers were studied. When the turbulent energy ratio coefficient reached to 30%- 40%, the turbulent dissipation could be captured by LES method with less grid number. The large scale vortex interaction behind the cylinder cascade was analyzed further. It is verified that LES method can be used for engineering based on the turbulent energy ratio coefficient with acceptable computational cost.papers presented to the 12th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Costa de Sol, Spain on 11-13 July 2016

Detection and modelling of contacts in explicit finite-element simulation of soft tissue biomechanics

Realistic modelling of soft-tissue biomechanics and mechanical interactions between tissues is an important part of surgical simulation, and may become a valuable asset in surgical image-guidance. Unfortunately, it is also computationally very demanding. Explicit matrix-free FEM solvers have been shown to be a good choice for fast tissue simulation, however little work has been done on contact algorithms for such FEM solvers. This work introduces such an algorithm that is capable of handling the scenarios typically encountered in image-guidance. The responses are computed with an evolution of the Lagrange-multiplier method first used by Taylor and Flanagan in PRONTO 3D with spatio-temporal smoothing heuristics for improved stability with coarser meshes and larger time steps. For contact search, a bounding-volume hierarchy (BVH) capable of identifying self collisions, and which is optimised for the small time steps by reducing the number of bounding-volume refittings between iterations through identification of geometry areas with mostly rigid motion and negligible deformation, is introduced. Further optimisation is achieved by integrating the self-collision criterion in the BVH creation and updating algorithms. The effectiveness of the algorithm is demonstrated on a number of artificial test cases and meshes derived from medical image data

Energy Relaxation in Nonlinear One-Dimensional Lattices

We study energy relaxation in thermalized one-dimensional nonlinear arrays of the Fermi-Pasta-Ulam type. The ends of the thermalized systems are placed in contact with a zero-temperature reservoir via damping forces. Harmonic arrays relax by sequential phonon decay into the cold reservoir, the lower frequency modes relaxing first. The relaxation pathway for purely anharmonic arrays involves the degradation of higher-energy nonlinear modes into lower energy ones. The lowest energy modes are absorbed by the cold reservoir, but a small amount of energy is persistently left behind in the array in the form of almost stationary low-frequency localized modes. Arrays with interactions that contain both a harmonic and an anharmonic contribution exhibit behavior that involves the interplay of phonon modes and breather modes. At long times relaxation is extremely slow due to the spontaneous appearance and persistence of energetic high-frequency stationary breathers. Breather behavior is further ascertained by explicitly injecting a localized excitation into the thermalized array and observing the relaxation behavior

Baculovirus Transduction of Mesenchymal Stem Cells: In Vitro Responses and In Vivo Immune Responses After Cell Transplantation

Baculovirus holds great promise for the genetic modification of mesenchymal stem cells (MSCs). However, whether baculovirus transduction provokes undesired MSCs responses that might compromise their in vivo applications has yet to be examined. Hereby, we unraveled that baculovirus transduction of human MSCs upregulated the transcription of interleukin (IL)-1 beta, interferon (IFN)-alpha and IL-6, but not tumor necrosis factor (TNF)-alpha and IFN-gamma. However, only IL-6 secretion was detectable by enzyme-linked immunosorbent assay (ELISA). Baculovirus transduction also stimulated transient, low level upregulation of human leukocyte antigen I (HLA-I) on the human MSCs surface, yet it did not either altered the HLA-II expression or impaired the MSCs ability to inhibit lymphocyte proliferation. After transplantation into allogeneic rats, the transduced rat MSCs elicited transient, mild macrophage responses, but the cells remained tolerant as judged by the persistence of transplanted cells and absence of CD8(+) T cells infiltration. Besides, transplantation of the transduced MSCs did not provoke systemic induction of monocytes and CD8(+) T cells. This study, for the first time, explores the responses of MSCs to virus transduction and confirms the safety of transplanting baculovirus-engineered MSCs into immunocompetent animals for cell-based gene therapy

Generalized Holographic Dark Energy Model

In this paper, the model of holographic Chaplygin gas has been extended to two general cases: first is the case of modified variable Chaplygin gas and secondly of the viscous generalized Chaplygin gas. The dynamics of the model are expressed by the use of scalar fields and the scalar potentials.Comment: 12 pages, to appear in Eur. Phys. J.