Analysis of regulatory network involved in mechanical induction of embryonic stem cell differentiation

Embryonic stem cells are conventionally differentiated by modulating specific growth factors in the cell culture media. Recently the effect of cellular mechanical microenvironment in inducing phenotype specific differentiation has attracted considerable attention. We have shown the possibility of inducing endoderm differentiation by culturing the stem cells on fibrin substrates of specific stiffness [1]. Here, we analyze the regulatory network involved in such mechanically induced endoderm differentiation under two different experimental configurations of 2-dimensional and 3-dimensional culture, respectively. Mouse embryonic stem cells are differentiated on an array of substrates of varying mechanical properties and analyzed for relevant endoderm markers. The experimental data set is further analyzed for identification of co-regulated transcription factors across different substrate conditions using the technique of bi-clustering. Overlapped bi-clusters are identified following an optimization formulation, which is solved using an evolutionary algorithm. While typically such analysis is performed at the mean value of expression data across experimental repeats, the variability of stem cell systems reduces the confidence on such analysis of mean data. Bootstrapping technique is thus integrated with the bi-clustering algorithm to determine sets of robust bi-clusters, which is found to differ significantly from corresponding bi-clusters at the mean data value. Analysis of robust bi-clusters reveals an overall similar network interaction as has been reported for chemically induced endoderm or endodermal organs but with differences in patterning between 2-dimensional and 3-dimensional culture. Such analysis sheds light on the pathway of stem cell differentiation indicating the prospect of the two culture configurations for further maturation. © 2012 Zhang et al

Dark viscous fluid described by a unified equation of state in cosmology

We generalize the $\Lambda$CDM model by introducing a unified EOS to describe the Universe contents modeled as dark viscous fluid, motivated by the fact that a single constant equation of state (EOS) $p=-p_0$ ($p_0>0$) reproduces the $\Lambda$CDM model exactly. This EOS describes the perfect fluid term, the dissipative effect, and the cosmological constant in a unique framework and the Friedmann equations can be analytically solved. Especially, we find a relation between the EOS parameter and the renormalizable condition of a scalar field. We develop a completely numerical method to perform a $\chi^2$ minimization to constrain the parameters in a cosmological model directly from the Friedmann equations, and employ the SNe data with the parameter $\mathcal{A}$ measured from the SDSS data to constrain our model. The result indicates that the dissipative effect is rather small in the late-time Universe.Comment: 4 pages, 2 figures. v2: new materials added. v3: matches the version to appear in IJMP

Evolution of deformations in medium-mass nuclei

Evolution of quadrupole deformations in $sd$ and $pf$ shell nuclei with mass A= 18$\sim$56 is studied by using deformed Skyrme Hartree-Fock (HF) model with pairing correlations. We point out that the quadrupole deformations of the nuclei with the isospin T=0 and T=1 show strong mass number dependence as a clear manifestation of dynamical evolution of deformation in nuclear many-body systems. The competition between the deformation driving particle-vibration coupling and the closed shell structure is shown in a systematic study of the ratios between the proton and neutron deformations in nuclei with T=$|$T$_z|$=1. Calculated quadrupole and hexadecapole deformations are compared with shell model results and available experimental data. A relation between the skin thickness and the intrinsic Q$_2$ moments is also discussed.Comment: 26 pages, 8figure

Joint multicast routing and channel assignment in multiradio multichannel wireless mesh networks using simulated annealing

This is the post-print version of the article - Copyright @ 2008 Springer-VerlagThis paper proposes a simulated annealing (SA) algorithm based optimization approach to search a minimum-interference multicast tree which satisfies the end-to-end delay constraint and optimizes the usage of the scarce radio network resource in wireless mesh networks. In the proposed SA multicast algorithm, the path-oriented encoding method is adopted and each candidate solution is represented by a tree data structure (i.e., a set of paths). Since we anticipate the multicast trees on which the minimum-interference channel assignment can be produced, a fitness function that returns the total channel conflict is devised. The techniques for controlling the annealing process are well developed. A simple yet effective channel assignment algorithm is proposed to reduce the channel conflict. Simulation results show that the proposed SA based multicast algorithm can produce the multicast trees which have better performance in terms of both the total channel conflict and the tree cost than that of a well known multicast algorithm in wireless mesh networks.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1

Stripe, checkerboard, and liquid-crystal ordering from anisotropic p-orbital Fermi surfaces in optical lattices

We study instabilities of single-species fermionic atoms in the p-orbital bands in two-dimensional optical lattices at noninteger filling against interactions. Charge density wave and orbital density wave orders with stripe or checkerboard patterns are found for attractive and repulsive interactions, respectively. The superfluid phase, usually expected of attractively interacting fermions, is strongly suppressed. We also use field theory to analyze the possible phase-transitions from orbital stripe order to liquid-crystal phases and obtain the phase diagram. The condition of nearly-perfect Fermisurface nesting, which is key to the above results, is shown robustly independent of fermion fillings in such p-orbital systems, and the $(2k_F,\pm2k_F)$ momentum of density wave oscillation is highly tunable. Such remarkable features show the promise of making those exotic orbital phases, which are of broad interest in condensed-matter physics, experimentally realizable with optical lattice gases.Comment: final version, 8 pages, 5 figure

Localization of fermionic fields on braneworlds with bulk tachyon matter

Recently, Pal and Skar in [arXiv:hep-th/0701266] proposed a mechanism to arise the warped braneworld models from bulk tachyon matter, which are endowed with a thin brane and a thick brane. In this framework, we investigate localization of fermionic fields on these branes. As in the 1/2 spin case, the field can be localized on both the thin and thick branes with inclusion of scalar background. In the 3/2 spin extension, the general supergravity action coupled to chiral supermultiplets is considered to produce the localization on both the branes as a result.Comment: 9 pages, no figure