Gene expression patterns during adaptation of a helminth parasite to different environmental niches

Using a genomic microarray, gene expression at three different developmental stages of the schistosome parasite were analyzed, resulting in the identification of 1154 developmentally enriched transcripts

Reconstructed Rough Growing Interfaces; Ridgeline Trapping of Domain Walls

We investigate whether surface reconstruction order exists in stationary growing states, at all length scales or only below a crossover length, $l_{\rm rec}$. The later would be similar to surface roughness in growing crystal surfaces; below the equilibrium roughening temperature they evolve in a layer-by-layer mode within a crossover length scale $l_{\rm R}$, but are always rough at large length scales. We investigate this issue in the context of KPZ type dynamics and a checker board type reconstruction, using the restricted solid-on-solid model with negative mono-atomic step energies. This is a topology where surface reconstruction order is compatible with surface roughness and where a so-called reconstructed rough phase exists in equilibrium. We find that during growth, reconstruction order is absent in the thermodynamic limit, but exists below a crossover length $l_{\rm rec}>l_{\rm R}$, and that this local order fluctuates critically. Domain walls become trapped at the ridge lines of the rough surface, and thus the reconstruction order fluctuations are slaved to the KPZ dynamics

Canonical phase space approach to the noisy Burgers equation

Presenting a general phase approach to stochastic processes we analyze in particular the Fokker-Planck equation for the noisy Burgers equation and discuss the time dependent and stationary probability distributions. In one dimension we derive the long-time skew distribution approaching the symmetric stationary Gaussian distribution. In the short time regime we discuss heuristically the nonlinear soliton contributions and derive an expression for the distribution in accordance with the directed polymer-replica model and asymmetric exclusion model results.Comment: 4 pages, Revtex file, submitted to Phys. Rev. Lett. a reference has been added and a few typos correcte

Simulation of Flow of Mixtures Through Anisotropic Porous Media using a Lattice Boltzmann Model

We propose a description for transient penetration simulations of miscible and immiscible fluid mixtures into anisotropic porous media, using the lattice Boltzmann (LB) method. Our model incorporates hydrodynamic flow, diffusion, surface tension, and the possibility for global and local viscosity variations to consider various types of hardening fluids. The miscible mixture consists of two fluids, one governed by the hydrodynamic equations and one by diffusion equations. We validate our model on standard problems like Poiseuille flow, the collision of a drop with an impermeable, hydrophobic interface and the deformation of the fluid due to surface tension forces. To demonstrate the applicability to complex geometries, we simulate the invasion process of mixtures into wood spruce samples.Comment: Submitted to EPJ

Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids

We use a modified Shan-Chen, noiseless lattice-BGK model for binary immiscible, incompressible, athermal fluids in three dimensions to simulate the coarsening of domains following a deep quench below the spinodal point from a symmetric and homogeneous mixture into a two-phase configuration. We find the average domain size growing with time as $t^\gamma$, where $\gamma$ increases in the range $0.545 < \gamma < 0.717$, consistent with a crossover between diffusive $t^{1/3}$ and hydrodynamic viscous, $t^{1.0}$, behaviour. We find good collapse onto a single scaling function, yet the domain growth exponents differ from others' works' for similar values of the unique characteristic length and time that can be constructed out of the fluid's parameters. This rebuts claims of universality for the dynamical scaling hypothesis. At early times, we also find a crossover from $q^2$ to $q^4$ in the scaled structure function, which disappears when the dynamical scaling reasonably improves at later times. This excludes noise as the cause for a $q^2$ behaviour, as proposed by others. We also observe exponential temporal growth of the structure function during the initial stages of the dynamics and for wavenumbers less than a threshold value.Comment: 45 pages, 18 figures. Accepted for publication in Physical Review

Simulations of amphiphilic fluids using mesoscale lattice-Boltzmann and lattice-gas methods

We compare two recently developed mesoscale models of binary immiscible and ternary amphiphilic fluids. We describe and compare the algorithms in detail and discuss their stability properties. The simulation results for the cases of self-assembly of ternary droplet phases and binary water-amphiphile sponge phases are compared and discussed. Both models require parallel implementation and deployment on large scale parallel computing resources in order to achieve reasonable simulation times for three-dimensional models. The parallelisation strategies and performance on two distinct parallel architectures are compared and discussed. Large scale three dimensional simulations of multiphase fluids requires the extensive use of high performance visualisation techniques in order to enable the large quantities of complex data to be interpreted. We report on our experiences with two commercial visualisation products: AVS and VTK. We also discuss the application and use of novel computational steering techniques for the more efficient utilisation of high performance computing resources. We close the paper with some suggestions for the future development of both models.Comment: 30 pages, 9 figure

Simulation of the many-body dynamical quantum Hall effect in an optical lattice

We propose an experimental scheme to simulate the many-body dynamical quantum Hall effect with ultra-cold bosonic atoms in a one-dimensional optical lattice. We first show that the required model Hamiltonian of a spin-1/2 Heisenberg chain with an effective magnetic field and tunable parameters can be realized in this system. For dynamical response to ramping the external fields, the quantized plateaus emerge in the Berry curvature of the interacting atomic spin chain as a function of the effective spin-exchange interaction. The quantization of this response in the parameter space with the interaction-induced topological transition characterizes the many-body dynamical quantum Hall effect. Furthermore, we demonstrate that this phenomenon can be observed in practical cold-atom experiments with numerical simulations.Comment: 8 pages, 3 figures; accepted in Quantum Information Processin

American Academy of Periodontology best evidence consensus statement on modifying periodontal phenotype in preparation for orthodontic and restorative treatment

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154649/1/jper10498.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154649/2/jper10498_am.pd

Metformin Reduces Desmoplasia in Pancreatic Cancer by Reprogramming Stellate Cells and Tumor-Associated Macrophages

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly desmoplastic tumor with a dismal prognosis for most patients. Fibrosis and inflammation are hallmarks of tumor desmoplasia. We have previously demonstrated that preventing the activation of pancreatic stellate cells (PSCs) and alleviating desmoplasia are beneficial strategies in treating PDAC. Metformin is a widely used glucose-lowering drug. It is also frequently prescribed to diabetic pancreatic cancer patients and has been shown to associate with a better outcome. However, the underlying mechanisms of this benefit remain unclear. Metformin has been found to modulate the activity of stellate cells in other disease settings. In this study, we examine the effect of metformin on PSC activity, fibrosis and inflammation in PDACs. Methods/Results In overweight, diabetic PDAC patients and pre-clinical mouse models, treatment with metformin reduced levels of tumor extracellular matrix (ECM) components, in particular hyaluronan (HA). In vitro, we found that metformin reduced TGF-ß signaling and the production of HA and collagen-I in cultured PSCs. Furthermore, we found that metformin alleviates tumor inflammation by reducing the expression of inflammatory cytokines including IL-1β as well as infiltration and M2 polarization of tumor-associated macrophages (TAMs) in vitro and in vivo. These effects on macrophages in vitro appear to be associated with a modulation of the AMPK/STAT3 pathway by metformin. Finally, we found in our preclinical models that the alleviation of desmoplasia by metformin was associated with a reduction in ECM remodeling, epithelial-to-mesenchymal transition (EMT) and ultimately systemic metastasis. Conclusion: Metformin alleviates the fibro-inflammatory microenvironment in obese/diabetic individuals with pancreatic cancer by reprogramming PSCs and TAMs, which correlates with reduced disease progression. Metformin should be tested/explored as part of the treatment strategy in overweight diabetic PDAC patients