The ovarian cancer oncobiome.

Humans and other mammals are colonized by microbial agents across the kingdom which can represent a unique microbiome pattern. Dysbiosis of the microbiome has been associated with pathology including cancer. We have identified a microbiome signature unique to ovarian cancers, one of the most lethal malignancies of the female reproductive system, primarily because of its asymptomatic nature during the early stages in development. We screened ovarian cancer samples along with matched, and non-matched control samples using our pan-pathogen array (PathoChip), combined with capture-next generation sequencing. The results show a distinct group of viral, bacterial, fungal and parasitic signatures of high significance in ovarian cases. Further analysis shows specific viral integration sites within the host genome of tumor samples, which may contribute to the carcinogenic process. The ovarian cancer microbiome signature provides insights for the development of targeted therapeutics against ovarian cancers

Linear rr-Matrix Algebra for Systems Separable\\ in Parabolic Coordinates

We consider a hierarchy of many particle systems on the line with polynomial potentials separable in parabolic coordinates. Using the Lax representation, written in terms of $2\times 2$ matrices for the whole hierarchy, we construct the associated linear $r$-matrix algebra with the $r$-matrix dependent on the dynamical variables. A dynamical Yang-Baxter equation is discussed.Comment: 10 pages, LaTeX. Submitted to Phys.Lett.

Entropic force and its cosmological implications

We investigate a possibility of realizing the entropic force into the cosmology. A main issue is how the holographic screen is implemented in the Newtonian cosmology. Contrary to the relativistic realization of Friedmann equations, we do not clarify the connection between Newtonian cosmology and entropic force because there is no way of implementing the holographic screen in the Newtonian cosmology.Comment: 16 pages, no figures, version "Accepted for publication in Astrophysics & Space Science

The dual parametrization for gluon GPDs

We consider the application of the dual parametrization for the case of gluon GPDs in the nucleon. This provides opportunities for the more flexible modeling unpolarized gluon GPDs in a nucleon which in particular contain the invaluable information on the fraction of nucleon spin carried by gluons. We perform the generalization of Abel transform tomography approach for the case of gluons. We also discuss the skewness effect in the framework of the dual parametrization. We strongly suggest to employ the fitting strategies based on the dual parametrization to extract the information on GPDs from the experimental data.Comment: 37 pages, 2 figure

Modulational Instability in Equations of KdV Type

It is a matter of experience that nonlinear waves in dispersive media, propagating primarily in one direction, may appear periodic in small space and time scales, but their characteristics --- amplitude, phase, wave number, etc. --- slowly vary in large space and time scales. In the 1970's, Whitham developed an asymptotic (WKB) method to study the effects of small "modulations" on nonlinear periodic wave trains. Since then, there has been a great deal of work aiming at rigorously justifying the predictions from Whitham's formal theory. We discuss recent advances in the mathematical understanding of the dynamics, in particular, the instability of slowly modulated wave trains for nonlinear dispersive equations of KdV type.Comment: 40 pages. To appear in upcoming title in Lecture Notes in Physic

Conditional quantitative trait locus mapping of wheat seed protein-fraction in relation to starch content

Protein and starch are important in wheat quality and yield. To understand the genetic relationship between protein and starch at the quantitative trait locus (QTL)/gene level, 168 doubled haploid (DH) lines were used at three locations over 2 years. The QTLs for proteinfraction contents and starch content were analyzed by unconditional and conditional QTL mapping. We detected 17 unconditional additive QTLs (four albumin QTLs, three globulin QTLs, six gliadin QTLs, four glutenin QTLs) controlling protein-fraction contents. We detected 19 conditional QTLs (five albumin QTLs, three globulin QTLs, five gliadin QTLs, six glutenin QTLs) based on starch content. Of these QTLs, QAlu1B, QGlo6A, QGli1B, QGli7A, QGlu1B and QGlu1D increased the protein-fraction contents independent of the starch content. These QTLs could regulate the usual inverse relationship between protein and starch in wheat seeds. The results could possibly be used in the simultaneous improvement of grain protein and starch content in wheat breeding

Genome-wide association study for flour color-related traits and polyphenol oxidase activity in common wheat

This study aimed to clarify the genetic mechanisms behind wheat flour color. Flour colorrelated traits (L*, a*, and b*) and polyphenol oxidase (PPO) activity are important parameters that influence the end-use quality of wheat. Dissecting the genetic bases and exploring important chromosomal loci of these traits are extremely important for improving wheat quality. The diverse panel of 205 elite wheat varieties (lines) was genotyped using a highdensity Illumina iSelect 90K single-nucleotide polymorphisms (SNPs) assay to disclose the genetic mechanism of flour color-related traits and PPO activity. In 2 different environments and their mean values (MV), 28, 30, 24, and 12 marker-trait associations (MTAs) were identified for L*, a*, b* traits, and PPO activity, respectively. A single locus could explain from 5.52% to 20.01% of the phenotypic variation for all analyzed traits. Among them, 5 highly significant SNPs (P ≤ 0.0001), 11 stable SNPs (detected in all environments) and 25 multitrait MTAs were identified. Especially, BS00000020_51 showed pleiotropic effects on L*, a*, and b*, and was detected in all environments with the highest phenotypic contribution rates. Furthermore, this SNP was also found to be co-associated with wheat grain hardness, ash content, and pasting temperature of starch in previous studies. The identification of these significantly associated SNPs is helpful in revealing the genetic mechanisms of wheat colorrelated traits, and also provides a reference for follow-up molecular marker-assisted selection in wheat breeding

Birkhoff type decompositions and the Baker-Campbell-Hausdorff recursion

We describe a unification of several apparently unrelated factorizations arisen from quantum field theory, vertex operator algebras, combinatorics and numerical methods in differential equations. The unification is given by a Birkhoff type decomposition that was obtained from the Baker-Campbell-Hausdorff formula in our study of the Hopf algebra approach of Connes and Kreimer to renormalization in perturbative quantum field theory. There we showed that the Birkhoff decomposition of Connes and Kreimer can be obtained from a certain Baker-Campbell-Hausdorff recursion formula in the presence of a Rota-Baxter operator. We will explain how the same decomposition generalizes the factorization of formal exponentials and uniformization for Lie algebras that arose in vertex operator algebra and conformal field theory, and the even-odd decomposition of combinatorial Hopf algebra characters as well as to the Lie algebra polar decomposition as used in the context of the approximation of matrix exponentials in ordinary differential equations.Comment: accepted for publication in Comm. in Math. Phy

Rate-equation calculations of the current flow through two-site molecular device and DNA-based junction

Here we present the calculations of incoherent current flowing through the two-site molecular device as well as the DNA-based junction within the rate-equation approach. Few interesting phenomena are discussed in detail. Structural asymmetry of two-site molecule results in rectification effect, which can be neutralized by asymmetric voltage drop at the molecule-metal contacts due to coupling asymmetry. The results received for poly(dG)-poly(dC) DNA molecule reveal the coupling- and temperature-independent saturation effect of the current at high voltages, where for short chains we establish the inverse square distance dependence. Besides, we document the shift of the conductance peak in the direction to higher voltages due to the temperature decrease.Comment: 12 pages, 6 figure

Aharonov-Bohm spectral features and coherence lengths in carbon nanotubes

The electronic properties of carbon nanotubes are investigated in the presence of disorder and a magnetic field parallel or perpendicular to the nanotube axis. In the parallel field geometry, the $\phi_{0}(=hc/e)$-periodic metal-insulator transition (MIT) induced in metallic or semiconducting nanotubes is shown to be related to a chirality-dependent shifting of the energy of the van Hove singularities (VHSs). The effect of disorder on this magnetic field-related mechanism is considered with a discussion of mean free paths, localization lengths and magnetic dephasing rate in the context of recent experiments.Comment: 22 pages, 6 Postscript figures. submitted to Phys. Rev.