A comparative study of Gaussian Graphical Model approaches for genomic data

The inference of networks of dependencies by Gaussian Graphical models on high-throughput data is an open issue in modern molecular biology. In this paper we provide a comparative study of three methods to obtain small sample and high dimension estimates of partial correlation coefficients: the Moore-Penrose pseudoinverse (PINV), residual correlation (RCM) and covariance-regularized method $(\ell_{2C})$. We first compare them on simulated datasets and we find that PINV is less stable in terms of AUC performance when the number of variables changes. The two regularized methods have comparable performances but $\ell_{2C}$ is much faster than RCM. Finally, we present the results of an application of $\ell_{2C}$ for the inference of a gene network for isoprenoid biosynthesis pathways in Arabidopsis thaliana.Comment: 7 pages, 1 figure, RevTex4, version to appear in the proceedings of 1st International Workshop on Pattern Recognition, Proteomics, Structural Biology and Bioinformatics: PR PS BB 2011, Ravenna, Italy, 13 September 201

Inhomogeneous charged pion condensation phenomenon in the NJL2_2 model with quark number and isospin chemical potentials

The properties of two-flavored massive Nambu--Jona-Lasinio model in (1+1)-dimensional spacetime are investigated in the presence of isospin and quark number chemical potentials. The consideration is performed in the large-$N_c$ limit, where $N_c$ is the number of colored quarks. It is shown in the framework of this model that charged pion condensation phenomenon of dense quark/hadron isotopically asymmetric matter is rather a spatially inhomogeneous than a homogeneous one.Comment: 11 pages, 8 figures; version accepted for publication in PRD. arXiv admin note: text overlap with arXiv:1106.2928, arXiv:1102.407

Cooling of a Compact Star with a LOFF Matter Core

Specific heat and neutrino emissivity due to direct URCA processes for quark matter in the color superconductive Larkin-Ovchinnikov-Fulde-Ferrell (LOFF) phase of Quantum-Chromodynamics have been evaluated. The cooling rate of simplified models of compact stars with a LOFF matter core is estimated.Comment: 3 pages, 1 figure, to appear in the proceedings of the Helmoltz International Summer School of Theoretical Physics on Dense Matter in Heavy Ion Collisions and Astrophysics, JINR, Dubna, Russia, 21 Aug - 1 Sep 200

Superfluid and Pseudo-Goldstone Modes in Three Flavor Crystalline Color Superconductivity

We study the bosonic excitations in the favorite cubic three flavor crystalline LOFF phases of QCD. We calculate in the Ginzburg-Landau approximation the masses of the eight pseudo Nambu-Goldstone Bosons (NGB) present in the low energy theory. We also compute the decay constants of the massless NGB Goldstones associated to superfluidity as well as those of the eight pseudo NGB. Differently from the corresponding situation in the Color-Flavor-Locking phase, we find that meson condensation phases are not expected in the present scenario.Comment: 10 pages, RevTeX4 class. Section IIIA enlarged, to appear on Phys. Rev.

A diagrammatic derivation of the meson effective masses in the neutral color-flavor-locked phase of Quantum Chromodynamics

We offer a diagrammatic derivation of the effective masses of the axial flavor excitations in the electrical and color neutral CFL phase of QCD. In particular we concentrate on the excitations with the quantum numbers of the kaons: we show how their effective chemical potentials, responsible of their Bose-Einstein condensation and found previously on the basis of pure symmetry arguments, arise at the microscopic level by loop effects. We perform also the numerical evaluation of the relevant loops in the whole CFL regime $M_s^2/2\mu\Delta\leqslant 1$, showing the existence of the enhancement of the kaon condensation with respect to the lowest order result. Finally we discuss the role of electrical and color neutrality in the microscopic calculation.Comment: 10 pages, 2 figures, RevTeX4 style. Version accepted for publication on JHEP. Some minor change in the tex

miRNA-mRNA integrated pathway analysis: an application to colorectal cancer

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Bulk viscosity in 2SC quark matter

The bulk viscosity of three-flavor color-superconducting quark matter originating from the nonleptonic process u+s u+d is computed. It is assumed that up and down quarks form Cooper pairs while the strange quark remains unpaired (2SC phase). A general derivation of the rate of strangeness production is presented, involving contributions from a multitude of different subprocesses, including subprocesses that involve different numbers of gapped quarks as well as creation and annihilation of particles in the condensate. The rate is then used to compute the bulk viscosity as a function of the temperature, for an external oscillation frequency typical of a compact star r-mode. We find that, for temperatures far below the critical temperature T_c for 2SC pairing, the bulk viscosity of color-superconducting quark matter is suppressed relative to that of unpaired quark matter, but for T >~ 10^(-3) T_c the color-superconducting quark matter has a higher bulk viscosity. This is potentially relevant for the suppression of r-mode instabilities early in the life of a compact star.Comment: 18 pages + appendices (28 pages total), 8 figures; v3: corrected numerical error in the plots; 2SC bulk viscosity is now larger than unpaired bulk viscosity in a wider temperature rang

Addressing the need for standardization of test methods for self-healing concrete: an inter-laboratory study on concrete with macrocapsules.

Development and commercialization of self-healing concrete is hampered due to a lack of standardized test methods. Six inter-laboratory testing programs are being executed by the EU COST action SARCOS, each focusing on test methods for a specific self-healing technique. This paper reports on the comparison of tests for mortar and concrete specimens with polyurethane encapsulated in glass macrocapsules. First, the pre-cracking method was analysed: mortar specimens were cracked in a three-point bending test followed by an active crack width control technique to restrain the crack width up to a predefined value, while the concrete specimens were cracked in a three-point bending setup with a displacement-controlled loading system. Microscopic measurements showed that with the application of the active control technique almost all crack widths were within a narrow predefined range. Conversely, for the concrete specimens the variation on the crack width was higher. After pre-cracking, the self-healing effect was characterized via durability tests: the mortar specimens were tested in a water permeability test and the spread of the healing agent on the crack surfaces was determined, while the concrete specimens were subjected to two capillary water absorption tests, executed with a different type of waterproofing applied on the zone around the crack. The quality of the waterproofing was found to be important, as different results were obtained in each absorption test. For the permeability test, 4 out of 6 labs obtained a comparable flow rate for the reference specimens, yet all 6 labs obtained comparable sealing efficiencies, highlighting the potential for further standardization

Reaction rates and transport in neutron stars

Understanding signals from neutron stars requires knowledge about the transport inside the star. We review the transport properties and the underlying reaction rates of dense hadronic and quark matter in the crust and the core of neutron stars and point out open problems and future directions.Comment: 74 pages; commissioned for the book "Physics and Astrophysics of Neutron Stars", NewCompStar COST Action MP1304; version 3: minor changes, references updated, overview graphic added in the introduction, improvements in Sec IV.A.

Strongly Correlated Quantum Fluids: Ultracold Quantum Gases, Quantum Chromodynamic Plasmas, and Holographic Duality

Strongly correlated quantum fluids are phases of matter that are intrinsically quantum mechanical, and that do not have a simple description in terms of weakly interacting quasi-particles. Two systems that have recently attracted a great deal of interest are the quark-gluon plasma, a plasma of strongly interacting quarks and gluons produced in relativistic heavy ion collisions, and ultracold atomic Fermi gases, very dilute clouds of atomic gases confined in optical or magnetic traps. These systems differ by more than 20 orders of magnitude in temperature, but they were shown to exhibit very similar hydrodynamic flow. In particular, both fluids exhibit a robustly low shear viscosity to entropy density ratio which is characteristic of quantum fluids described by holographic duality, a mapping from strongly correlated quantum field theories to weakly curved higher dimensional classical gravity. This review explores the connection between these fields, and it also serves as an introduction to the Focus Issue of New Journal of Physics on Strongly Correlated Quantum Fluids: from Ultracold Quantum Gases to QCD Plasmas. The presentation is made accessible to the general physics reader and includes discussions of the latest research developments in all three areas.Comment: 138 pages, 25 figures, review associated with New Journal of Physics special issue "Focus on Strongly Correlated Quantum Fluids: from Ultracold Quantum Gases to QCD Plasmas" (http://iopscience.iop.org/1367-2630/focus/Focus%20on%20Strongly%20Correlated%20Quantum%20Fluids%20-%20from%20Ultracold%20Quantum%20Gases%20to%20QCD%20Plasmas