A new optimization algorithm for network component analysis based on convex programming

Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing, 2009, p. 509-512Paper no. 2203Network component analysis (NCA) has been established as a promising tool for reconstructing gene regulatory networks from microarray data. NCA is a method that can resolve the problem of blind source separation when the mixing matrix instead has a known sparse structure despite the correlation among the source signals. The original NCA algorithm relies on alternating least squares (ALS) and suffers from local convergence as well as slow convergence. In this paper, we develop new and more robust NCA algorithms by incorporating additional signal constraints. In particular, we introduce the biologically sound constraints that all nonzero entries in the connectivity network are positive. Our new approach formulates a convex optimization problem which can be solved efficiently and effectively by fast convex programming algorithms. We verify the effectiveness and robustness of our new approach using simulations and gene regulatory network reconstruction from experimental yeast cell cycle microarray data. ©2009 IEEE.published_or_final_versio

Domain freezing in potassium dihydrogen phosphate, triglycine sulfate, and CuAlZnNi

The temperature dependence of the dielectric constant and dissipation in potassium dihydrogen phosphate (KDP), its deuterated compound (DKDP), triglycine sulfate (TGS), and TGS doped with α-alanine (LATGS) has been studied at various frequencies. It is found that the relaxation time of domain freezing in KDP and DKDP in the kHz range can be described by the Vogel-Fulcher relation. Evidence of domain freezing in TGS is presented through an analysis of relaxation time related to domain walls and a comparison between TGS and LATGS. Studies of internal friction and compliance show preliminary evidence of domain freezing in CuAlZnNi alloy. A domain-freezing model is proposed based upon the collective pinning of randomly distributed pinning centers to domain walls. Some key experiments related to domain freezing, such as (1) the Vogel-Fulcher relation for relaxation time; (2) the size effect of domain freezing; (3) two kinds of relaxation in low- and high-frequency ranges, respectively; and (4) the dependence of TF on defect density and applied field, etc., are explained.published_or_final_versio

Polymorphism of the pig-implantation protein 3 (preis3) gene and its association with litter size traits

The pre-implantation protein 3 (prei3), which might play a role in pre-implantation embryogenesis, is one of the promising candidate genes for litter size traits in pigs. In this study, a single nucleotide polymorphism (SNP: T802G) in intron 6 of the pig prei3 gene was detected and a genotyping assay for this SNP was developed. An association study for this SNP with litter size was performed in two independent populations. One population consisted of crossbred sows derived from Landrace, Large White, Chinese Tongcheng and/or Chinese Meishan (Line DIV). The other population constituted of crossbred animals derived from Chinese Qingping and Duroc (QD). Statistical analysis demonstrated that, in first parity, 2.65 more piglets were born and 3.82 more piglets were born alive in sows in Line DIV with genotype TT than with genotype GG. For second and subsequent litters, in both the DIV and QD lines there were significant differences in the number of piglets born alive between TG and GG sows, with the TG sows producing more piglets born alive than the GG sows. These results suggest that the prei3 SNP is significantly associated with litter size in the two populations studied, and could be useful in selection for increasing litter size in pigs. Further investigations on more pig populations with large sample sizes are needed to confirm this. South African Journal of Animal Science Vol. 36(3) 2006: 209-21

Group analysis and exact solutions of a class of variable coefficient nonlinear telegraph equations

A complete group classification of a class of variable coefficient (1+1)-dimensional telegraph equations $f(x)u_{tt}=(H(u)u_x)_x+K(u)u_x$, is given, by using a compatibility method and additional equivalence transformations. A number of new interesting nonlinear invariant models which have non-trivial invariance algebras are obtained. Furthermore, the possible additional equivalence transformations between equations from the class under consideration are investigated. Exact solutions of special forms of these equations are also constructed via classical Lie method and generalized conditional transformations. Local conservation laws with characteristics of order 0 of the class under consideration are classified with respect to the group of equivalence transformations.Comment: 23 page

Polymeric additives to enhance the functional properties of calcium phosphate cements

The vast majority of materials used in bone tissue engineering and regenerative medicine are based on calcium phosphates due to their similarity with the mineral phase of natural bone. Among them, calcium phosphate cements, which are composed of a powder and a liquid that are mixed to obtain a moldable paste, are widely used. These calcium phosphate cement pastes can be injected using minimally invasive surgery and adapt to the shape of the defect, resulting in an entangled network of calcium phosphate crystals. Adding an organic phase to the calcium phosphate cement formulation is a very powerful strategy to enhance some of the properties of these materials. Adding some water-soluble biocompatible polymers in the calcium phosphate cement liquid or powder phase improves physicochemical and mechanical properties, such as injectability, cohesion, and toughness. Moreover, adding specific polymers can enhance the biological response and the resorption rate of the material. The goal of this study is to overview the most relevant advances in this field, focusing on the different types of polymers that have been used to enhance specific calcium phosphate cement properties

Activation kinetics of single P2X receptors

After the primary structure of P2X receptors had been identified, their function had to be characterized on the molecular level. Since these ligand-gated ion channels become activated very quickly after binding of ATP, methods with adequate time resolution have to be applied to investigate the early events induced by the agonist. Single-channel recordings were performed to describe conformational changes on P2X2, P2X4, and P2X7 receptors induced by ATP and also by allosteric receptor modifiers. The main results of these studies and the models of P2X receptor kinetics derived from these observations are reviewed here. The investigation of purinoceptors by means of the patch clamp technique following site-directed mutagenesis will probably reveal more details of P2X receptor function at the molecular level

Low-grade pelvic masses with spindle cell and fibroblastic proliferation: a case report

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Similarity solutions for unsteady shear-stress-driven flow of Newtonian and power-law fluids : slender rivulets and dry patches

Unsteady flow of a thin film of a Newtonian fluid or a non-Newtonian power-law fluid with power-law index N driven by a constant shear stress applied at the free surface, on a plane inclined at an angle α to the horizontal, is considered. Unsteady similarity solutions representing flow of slender rivulets and flow around slender dry patches are obtained. Specifically, solutions are obtained for converging sessile rivulets (0 < α < π/2) and converging dry patches in a pendent film (π/2 < α < π), as well as for diverging pendent rivulets and diverging dry patches in a sessile film. These solutions predict that at any time t, the rivulet and dry patch widen or narrow according to |x|3/2, and the film thickens or thins according to |x|, where x denotes distance down the plane, and that at any station x, the rivulet and dry patch widen or narrow like |t|−1, and the film thickens or thins like |t|−1, independent of N

Disentangling Cooper-pair formation above Tc from the pseudogap state in the cuprates

The discovery of the pseudogap in the cuprates created significant excitement amongst physicists as it was believed to be a signature of pairing, in some cases well above the room temperature. In this "pre-formed pairs" scenario, the formation of pairs without quantum phase rigidity occurs below T*. These pairs condense and develop phase coherence only below Tc. In contrast, several recent experiments reported that the pseudogap and superconducting states are characterized by two different energy scales, pointing to a scenario, where the two compete. However a number of transport, magnetic, thermodynamic and tunneling spectroscopy experiments consistently detect a signature of phase-fluctuating superconductivity above leaving open the question of whether the pseudogap is caused by pair formation or not. Here we report the discovery of a spectroscopic signature of pair formation and demonstrate that in a region of the phase diagram commonly referred to as the "pseudogap", two distinct states coexist: one that persists to an intermediate temperature Tpair and a second that extends up to T*. The first state is characterized by a doping independent scaling behavior and is due to pairing above Tc, but significantly below T*. The second state is the "proper" pseudogap - characterized by a "checker board" pattern in STM images, the absence of pair formation, and is likely linked to Mott physics of pristine CuO2 planes. Tpair has a universal value around 130-150K even for materials with very different Tc, likely setting limit on highest, attainable Tc in cuprates. The observed universal scaling behavior with respect to Tpair indicates a breakdown of the classical picture of phase fluctuations in the cuprates.Comment: 9 pages, 4 figure