Sea flavor content of octet baryons and intrinsic five-quark Fock states

Sea quark contents of the octet baryons are investigated by employing an extended chiral constituent quark approach, which embodies higher Fock five-quark components in the baryons wave-functions. The well-known flavor asymmetry of the nucleon sea $\bar{d}-\bar{u}$, is used as input to predict the probabilities of $\bar{u}$, $\bar{d}$ and $\bar{s}$ in the nucleon, $\Lambda$, $\Sigma$ and $\Xi$ baryons, due to the intrinsic five-quark components in the baryons wave functions.Comment: 22 page

Anomalies in non-stoichiometric uranium dioxide induced by pseudo-phase transition of point defects

A uniform distribution of point defects in an otherwise perfect crystallographic structure usually describes a unique pseudo phase of that state of a non-stoichiometric material. With off-stoichiometric uranium dioxide as a prototype, we show that analogous to a conventional phase transition, these pseudo phases also will transform from one state into another via changing the predominant defect species when external conditions of pressure, temperature, or chemical composition are varied. This exotic transition is numerically observed along shock Hugoniots and isothermal compression curves in UO2 with first-principles calculations. At low temperatures, it leads to anomalies (or quasi-discontinuities) in thermodynamic properties and electronic structures. In particular, the anomaly is pronounced in both shock temperature and the specific heat at constant pressure. With increasing of the temperature, however, it transforms gradually to a smooth cross-over, and becomes less discernible. The underlying physical mechanism and characteristics of this type of transition are encoded in the Gibbs free energy, and are elucidated clearly by analyzing the correlation with the variation of defect populations as a function of pressure and temperature. The opportunities and challenges for a possible experimental observation of this phase change are also discussed.Comment: 11 pages, 5 figure

Wetting and bonding characteristics of selected liquid-metals with a high power diode laser treated alumina bioceramic

Changes in the wettability characteristics of an alumina bioceramic occasioned by high power diode laser (HPDL) surface treatment were apparent from the observed reduction in the contact angle. Such changes were due to the HPDL bringing about reductions the surface roughness, increases in the surface O2 content and increases in the polar component of the surface energy. Additionally, HPDL treatment of the alumina bioceramic surface was found to effect an improvement in the bonding characteristics by increasing the work of adhesion. An electronic approach was used to elucidate the bonding characteristics of the alumina bioceramic before and after HPDL treatment. It is postulated that HPDL induced changes to the alumina bioceramic produced a surface with a reduced bandgap energy which consequently increased the work of adhesion by increasing the electron transfer at the metal/oxide interface and thus the metal-oxide interactions. Furthermore, it is suggested that the increase in the work of adhesion of the alumina bioceramic after HPDL treatment was due to a correlation existing between the wettability and ionicity of the alumina bioceramic; for it is believed that the HPDL treated surface is less ionic in nature than the untreated surface and therefore exhibits better wettability characteristics

Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets

© 2015 Liu et al. Motivation: Deciphering gene interaction networks (GINs) from time-course gene expression (TCGx) data is highly valuable to understand gene behaviors (e.g., activation, inhibition, time-lagged causality) at the system level. Existing methods usually use a global or local proximity measure to infer GINs from a single dataset. As the noise contained in a single data set is hardly self-resolved, the results are sometimes not reliable. Also, these proximity measurements cannot handle the co-existence of the various in vivo positive, negative and time-lagged gene interactions. Methods and results: We propose to infer reliable GINs from multiple TCGx datasets using a novel conserved subsequential pattern of gene expression. A subsequential pattern is a maximal subset of genes sharing positive, negative or time-lagged correlations of one expression template on their own subsets of time points. Based on these patterns, a GIN can be built from each of the datasets. It is assumed that reliable gene interactions would be detected repeatedly. We thus use conserved gene pairs from the individual GINs of the multiple TCGx datasets to construct a reliable GIN for a species. We apply our method on six TCGx datasets related to yeast cell cycle, and validate the reliable GINs using protein interaction networks, biopathways and transcription factor-gene regulations. We also compare the reliable GINs with those GINs reconstructed by a global proximity measure Pearson correlation coefficient method from single datasets. It has been demonstrated that our reliable GINs achieve much better prediction performance especially with much higher precision. The functional enrichment analysis also suggests that gene sets in a reliable GIN are more functionally significant. Our method is especially useful to decipher GINs from multiple TCGx datasets related to less studied organisms where little knowledge is available except gene expression data

Close binary evolution I. The tidally induced shear mixing in rotating binaries

We study how tides in a binary system induce some specific internal shear mixing, able to substantially modify the evolution of close binaries prior to mass transfer. We construct numerical models accounting for tidal interactions, meridional circulation, transport of angular momentum, shears and horizontal turbulence and consider a variety of orbital periods and initial rotation velocities. Depending on orbital periods and rotation velocities, tidal effects may spin down (spin down Case) or spin up (spin up Case) the axial rotation. In both cases, tides may induce a large internal differential rotation. The resulting tidally induced shear mixing (TISM) is so efficient that the internal distributions of angular velocity and chemical elements are greatly influenced. The evolutionary tracks are modified, and in both cases of spin down and spin up, large amounts of nitrogen can be transported to the stellar surfaces before any binary mass transfer. Meridional circulation, when properly treated as an advection, always tends to counteract the tidal interaction, tending to spin up the surface when it is braked down and vice versa. As a consequence, the times needed for the axial angular velocity to become equal to the orbital angular velocity may be larger than given by typical synchronization timescales. Also, due to meridional circulation some differential rotation remains in tidally locked binary systems.Comment: 10 pages, 18 figures, Accepted for publication in Astronomy and Astrophysic

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems biology. The first contribution in this paper is of theoretical nature. We establish a tight link between two seemingly different algorithms and prove that Elastic Net regression can be reduced to SVM with squared hinge loss classification. Our second contribution is to derive a practical algorithm based on this reduction. The reduction enables us to utilize prior efforts in speeding up and parallelizing SVMs to obtain a highly optimized and parallel solver for the Elastic Net and Lasso. With a simple wrapper, consisting of only 11 lines of MATLAB code, we obtain an Elastic Net implementation that naturally utilizes GPU and multi-core CPUs. We demonstrate on twelve real world data sets, that our algorithm yields identical results as the popular (and highly optimized) glmnet implementation but is one or several orders of magnitude faster.Comment: 10 page

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

© 2015 Song et al.; licensee BioMed Central Ltd. Background: Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression relationship is not the only regulatory relationship between miRNAs and their targets, and some miRNAs can positively regulate a mRNA by binding at the 5' UTR of the mRNA.Results: This work focuses on the detection of both inverse and positive regulatory relationships from a paired miRNA and mRNA expression data set of HCV patients through a 'change-to-change' method which can derive connected discriminatory rules. Our study uncovered many novel miRNA-mRNA regulatory modules. In particular, it was revealed that GFRA2 is positively regulated by miR-557, miR-765 and miR-17-3p that probably bind at different locations of the 5' UTR of this mRNA. The expression relationship between GFRA2 and any of these three miRNAs has not been studied before, although separate research for this gene and these miRNAs have all drawn conclusions linked to hepatocellular carcinoma. This suggests that the binding of mRNA GFRA2 with miR-557, miR-765, or miR-17-3p, or their combinations, is worthy of further investigation by experimentation. We also report another mRNA QKI which has a strong inverse expression relationship with miR-129 and miR-493-3p which may bind at the 3' UTR of QKI with a perfect sequence match. Furthermore, the interaction between hsa-miR-129-5p (previous ID: hsa-miR-129) and QKI is supported with CLIP-Seq data from starBase. Our method can be easily extended for the expression data analysis of other diseases.Conclusion: Our rule discovery method is useful for integrating binding information and expression profile for identifying HCV miRNA-mRNA regulatory modules and can be applied to the study of the expression profiles of other complex human diseases

A Weak Gravity Conjecture for Scalar Field Theories

We show that the recently proposed weak gravity conjecture\cite{AMNV0601} can be extended to a class of scalar field theories. Taking gravity into account, we find an upper bound on the gravity interaction strength, expressed in terms of scalar coupling parameters. This conjecture is supported by some two-dimensional models and noncommutative field theories.Comment: version published in JHE

Anisotropic but nodeless superconducting gap in the presence of spin density wave in iron-pnictide superconductor NaFe1-xCoxAs

The coexisting regime of spin density wave (SDW) and superconductivity in the iron pnictides represents a novel ground state. We have performed high resolution angle-resolved photoemission measurements on NaFe1-xCoxAs (x = 0.0175) in this regime and revealed its distinctive electronic structure, which provides some microscopic understandings of its behavior. The SDW signature and the superconducting gap are observed on the same bands, illustrating the intrinsic nature of the coexistence. However, because the SDW and superconductivity are manifested in different parts of the band structure, their competition is non-exclusive. Particularly, we found that the gap distribution is anisotropic and nodeless, in contrast to the isotropic superconducting gap observed in an SDW-free NaFe1-xCoxAs (x=0.045), which puts strong constraints on theory.Comment: 5 pages, 4 figures + supplementary informatio