Expression profiles have been successfully determined by using hybridization- and tagbased technologies, even though such approaches suffer from limits and drawbacks and lack information about rare RNA species, emerging as contributors to pathological phenotypes in humans (1-8). The introduction of next generation sequencing (NGS) technologies, revealing mammalian transcriptomes' complexity, has shown that a small fraction of transcribed sequences (<2%) is represented by mRNA (9). However, the unprecedented level of sensitivity in the data produced by NGS platforms brings with it the power to make several biological observations, at the cost of a considerable effort in the development of new bioinformatics tools and computational strategies to deal with these massive data files. Indeed, for these large-scale analyses, data transferring, processing and handling may represent a computational bottleneck. Another issue is the availability of software required to perform one or more downstream analysis (1). To this purpose, in this paper we describe the computational strategies used to analyze different aspects of a wholetranscriptome. In particular, we illustrate the results of the analysis performed on a dataset obtained from a strand-specific RNA sequenicng of ribosomal-depleted samples, isolated from a cell type impaired in the Down syndrome

Bioventing is a subsoil bio-remediation technique which improves the activity of bacteria to transform contaminants into less hazardous compounds by inflating air through wells. The mathematical model describes the bacteria population dynamics and the dynamics of a multiphase, multicomponent fluid in porous media and in this paper a simple version of it will be described. A critical point of the design problem is to choose well positions and air flow rates to optimise the biodegradation process. The numerical simulation and some initial optimisation design results for the simple model proposed will be reported. The decontamination time required for different flow rates and for different well spatial configurations will be compared.

The theory of relativity describes the laws of physics in a given space-time. However, a physical theory must provide observational predictions expressed in terms of measurements, which are the outcome of practical experiments and observations. Ideal for readers with a mathematical background and a basic knowledge of relativity, this book will help readers understand the physics behind the mathematical formalism of the theory of relativity. It explores the informative power of the theory of relativity, and highlights its uses in space physics, astrophysics and cosmology. Readers are given the tools to pick out from the mathematical formalism those quantities that have physical meaning and which can therefore be the result of a measurement. The book considers the complications that arise through the interpretation of a measurement, which is dependent on the observer who performs it. Specific examples of this are given to highlight the awkwardness of the problem.

Coalescence growth of droplets is a fundamental process for liquid cloud evolution. The initiation of collisions and coalescence occurs when a few droplets become large enough to fall. Gravitational collisions represent the most efficient mechanism for multi-disperse solutions, when droplets span a large variety of sizes. However, turbulence provides another mechanism for droplets coalescence, taking place also in the case of uniform condensational growth leading to narrow droplet-size spectra. We consider the problem of estimating the rate of collisions of small droplets dispersed in a highly turbulent medium. The problem is investigated by means of high-resolution direct numerical simulations of a three-dimensional turbulent flow, seeded with inertial particles, up to resolutions of 2048^3 grid points. Rate of collision is estimated in terms of the probability to find particles at close positions, and of the statistics of particles velocity. In particular, we show that the statistics of velocity differences between inertial particles suspended in an incompressible turbulent flow is extremely intermittent. When particles are separated by distances of the order of their diameter, the competition between quiet regular regions and multivalued caustics leads to a quasi bi-fractal behavior of the particle velocity statistics, with high-order moments bringing the signature of caustics. This results in large probabilities that close particles have important velocity differences. Together with preferential concentration of particles in low-vorticity regions, caustics contribute to speed-up collisions between inertial particles. Implications for the early stage of rain droplets formation are discussed.

We study the inverse problem of determining the relative orientations of the moving C- and N-terminal domains in a flexible protein from measurements of its mean magnetic susceptibility tensor ? ̄ . The latter is an integral average of rotations of the corresponding magnetic susceptibility tensor ?. The largest fraction of time that the two terminals can stay in a given orientation, still producing the ? ̄ measurements, is the maximal probability of that orientation. We extend this definition to any measurable subset of the rotation group. This extension permits a quantitative assessment of the results when the generating distribution is either continuous or discrete. We establish some properties of the maximal probability and present some numerical experiments.

We study the facial structure and Carathéodory number of the convex hull of an orbit of the group of rotations in R3 acting on the space of pairs of anisotropic symmetric 3 × 3 tensors. This is motivated by the problem of determining the structure of some proteins in an aqueous solution.

Phase separation of a two-dimensional van der Waals fluid subject to a gravitational force is studied by numerical simulations based on lattice Boltzmann methods implemented with a finite difference scheme. A growth exponent alpha = 1 is measured in the direction of the external force.