mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

BACKGROUND: Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. RESULTS: Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. CONCLUSIONS: mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly

Universality for orthogonal and symplectic Laguerre-type ensembles

We give a proof of the Universality Conjecture for orthogonal (beta=1) and symplectic (beta=4) random matrix ensembles of Laguerre-type in the bulk of the spectrum as well as at the hard and soft spectral edges. Our results are stated precisely in the Introduction (Theorems 1.1, 1.4, 1.6 and Corollaries 1.2, 1.5, 1.7). They concern the appropriately rescaled kernels K_{n,beta}, correlation and cluster functions, gap probabilities and the distributions of the largest and smallest eigenvalues. Corresponding results for unitary (beta=2) Laguerre-type ensembles have been proved by the fourth author in [23]. The varying weight case at the hard spectral edge was analyzed in [13] for beta=2: In this paper we do not consider varying weights. Our proof follows closely the work of the first two authors who showed in [7], [8] analogous results for Hermite-type ensembles. As in [7], [8] we use the version of the orthogonal polynomial method presented in [25], [22] to analyze the local eigenvalue statistics. The necessary asymptotic information on the Laguerre-type orthogonal polynomials is taken from [23].Comment: 75 page

Quantum conductance problems and the Jacobi ensemble

In one dimensional transport problems the scattering matrix $S$ is decomposed into a block structure corresponding to reflection and transmission matrices at the two ends. For $S$ a random unitary matrix, the singular value probability distribution function of these blocks is calculated. The same is done when $S$ is constrained to be symmetric, or to be self dual quaternion real, or when $S$ has real elements, or has real quaternion elements. Three methods are used: metric forms; a variant of the Ingham-Seigel matrix integral; and a theorem specifying the Jacobi random matrix ensemble in terms of Wishart distributed matrices.Comment: 10 page

On the partial connection between random matrices and interacting particle systems

In the last decade there has been increasing interest in the fields of random matrices, interacting particle systems, stochastic growth models, and the connections between these areas. For instance, several objects appearing in the limit of large matrices arise also in the long time limit for interacting particles and growth models. Examples of these are the famous Tracy-Widom distribution functions and the Airy_2 process. The link is however sometimes fragile. For example, the connection between the eigenvalues in the Gaussian Orthogonal Ensembles (GOE) and growth on a flat substrate is restricted to one-point distribution, and the connection breaks down if we consider the joint distributions. In this paper we first discuss known relations between random matrices and the asymmetric exclusion process (and a 2+1 dimensional extension). Then, we show that the correlation functions of the eigenvalues of the matrix minors for beta=2 Dyson's Brownian motion have, when restricted to increasing times and decreasing matrix dimensions, the same correlation kernel as in the 2+1 dimensional interacting particle system under diffusion scaling limit. Finally, we analyze the analogous question for a diffusion on (complex) sample covariance matrices.Comment: 31 pages, LaTeX; Added a section concerning the Markov property on space-like path

Deppining of a Superfluid Vortex Inside a Circular Defect

In this work we study the process of depinning of a quantum of circulation trapped inside a disk by an applied two dimensional superflow. We use the Gross-Pitaevskii model to describe the neutral superfluid. The collective coordinate dynamics is derived directly from the condensate equation of motion, the nonlinear Schroedinger equation, and it is used to obtain an expression for the critical velocity as a function of the defect radius. This expression is compared with a numerical result obtained from the time independent nonlinear Schroedinger equation. Below the critical velocity, we obtain the dependence of the semiclassical nucleation rate with the flow velocity at infinity. Above the critical velocity, the classical vortex depinning is illustrated with a numerical simulation of the time dependent nonlinear Schroedinger equation.Comment: 8 pages, 5 figures, uses revtex and epsf.st

On Eigenvalues of the sum of two random projections

We study the behavior of eigenvalues of matrix P_N + Q_N where P_N and Q_N are two N -by-N random orthogonal projections. We relate the joint eigenvalue distribution of this matrix to the Jacobi matrix ensemble and establish the universal behavior of eigenvalues for large N. The limiting local behavior of eigenvalues is governed by the sine kernel in the bulk and by either the Bessel or the Airy kernel at the edge depending on parameters. We also study an exceptional case when the local behavior of eigenvalues of P_N + Q_N is not universal in the usual sense.Comment: 14 page

A rocky planet transiting a nearby low-mass star

M-dwarf stars -- hydrogen-burning stars that are smaller than 60 per cent of the size of the Sun -- are the most common class of star in our Galaxy and outnumber Sun-like stars by a ratio of 12:1. Recent results have shown that M dwarfs host Earth-sized planets in great numbers: the average number of M-dwarf planets that are between 0.5 to 1.5 times the size of Earth is at least 1.4 per star. The nearest such planets known to transit their star are 39 parsecs away, too distant for detailed follow-up observations to measure the planetary masses or to study their atmospheres. Here we report observations of GJ 1132b, a planet with a size of 1.2 Earth radii that is transiting a small star 12 parsecs away. Our Doppler mass measurement of GJ 1132b yields a density consistent with an Earth-like bulk composition, similar to the compositions of the six known exoplanets with masses less than six times that of the Earth and precisely measured densities. Receiving 19 times more stellar radiation than the Earth, the planet is too hot to be habitable but is cool enough to support a substantial atmosphere, one that has probably been considerably depleted of hydrogen. Because the host star is nearby and only 21 per cent the radius of the Sun, existing and upcoming telescopes will be able to observe the composition and dynamics of the planetary atmosphere.Comment: Published in Nature on 12 November 2015, available at http://dx.doi.org/10.1038/nature15762. This is the authors' version of the manuscrip

Asymptotics of Selberg-like integrals: The unitary case and Newton's interpolation formula

We investigate the asymptotic behavior of the Selberg-like integral $$\frac1{N!}\int_{[0,1]^N}x_1^p\prod_{i<j}(x_i-x_j)^2\prod_ix_i^{a-1}(1-x_i)^{b-1}dx_i$$, as $N\to\infty$ for different scalings of the parameters $a$ and $b$ with $N$. Integrals of this type arise in the random matrix theory of electronic scattering in chaotic cavities supporting $N$ channels in the two attached leads. Making use of Newton's interpolation formula, we show that an asymptotic limit exists and we compute it explicitly

Anti-cancer effects and mechanism of actions of aspirin analogues in the treatment of glioma cancer

INTRODUCTION: In the past 25 years only modest advancements in glioma treatment have been made, with patient prognosis and median survival time following diagnosis only increasing from 3 to 7 months. A substantial body of clinical and preclinical evidence has suggested a role for aspirin in the treatment of cancer with multiple mechanisms of action proposed including COX 2 inhibition, down regulation of EGFR expression, and NF-κB signaling affecting Bcl-2 expression. However, with serious side effects such as stroke and gastrointestinal bleeding, aspirin analogues with improved potency and side effect profiles are being developed. METHOD: Effects on cell viability following 24 hr incubation of four aspirin derivatives (PN508, 517, 526 and 529) were compared to cisplatin, aspirin and di-aspirin in four glioma cell lines (U87 MG, SVG P12, GOS – 3, and 1321N1), using the PrestoBlue assay, establishing IC50 and examining the time course of drug effects. RESULTS: All compounds were found to decrease cell viability in a concentration and time dependant manner. Significantly, the analogue PN517 (IC50 2mM) showed approximately a twofold increase in potency when compared to aspirin (3.7mM) and cisplatin (4.3mM) in U87 cells, with similar increased potency in SVG P12 cells. Other analogues demonstrated similar potency to aspirin and cisplatin. CONCLUSION: These results support the further development and characterization of novel NSAID derivatives for the treatment of glioma