MaxSSmap: A GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes. We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the highest scoring fragment for exact alignment. We evaluate MaxSSmap's accuracy and runtime when mapping simulated Illumina E.coli and human chromosome one reads of different lengths and 10\% to 30\% mismatches with gaps to the E.coli genome and human chromosome one. We also demonstrate applications on real data by mapping ancient horse DNA reads to modern genomes and unmapped paired reads from NA12878 in 1000 genomes. We show that MaxSSmap attains comparable high accuracy and low error to fast Smith-Waterman programs yet has much lower runtimes. We show that MaxSSmap can map reads rejected by BWA and NextGenMap with high accuracy and low error much faster than if Smith-Waterman were used. On short read lengths of 36 and 51 both MaxSSmap and Smith-Waterman have lower accuracy compared to at higher lengths. On real data MaxSSmap produces many alignments with high score and mapping quality that are not given by NextGenMap and BWA. The MaxSSmap source code is freely available from http://www.cs.njit.edu/usman/MaxSSmap

Two series of polyhedral fundamental domains for Lorentz bi-quotients

The main aim of this paper is to give two infinite series of examples of Lorentz space forms that can be obtained from Lorentz polyhedra by identification of faces. These Lorentz space forms are bi-quotients of the form $\Gamma_1\backslash G/\Gamma_2$, where $G=\widetilde{\operatorname{SU}(1,1)}\cong\widetilde{\operatorname{SL}(2,{\mathbb R})}$ is a simply connected Lie group with the Lorentz metric given by the Killing form, $\Gamma_1$ and $\Gamma_2$ are discrete subgroups of $G$ and $\Gamma_2$ is cyclic. A construction of polyhedral fundamental domains for the action of $\Gamma_1\times\Gamma_2$ on $G$ via $(g,h)\cdot x=gxh^{-1}$ was given in the earlier work of the second author. In this paper we give an explicit description of the fundamental domains obtained by this construction for two infinite series of groups. These results are connected to singularity theory as the bi-quotients $\Gamma_1\backslash G/\Gamma_2$ appear as links of certain quasi-homogeneous $\mathbb Q$-Gorenstein surface singularities, i.e.\ the intersections of the singular variety with sufficiently small spheres around the isolated singular point.Comment: 16 pages, 6 figures, 2 tables of figure

American Options Based on Malliavin Calculus and Nonparametric Variance Reduction Methods

This paper is devoted to pricing American options using Monte Carlo and the Malliavin calculus. Unlike the majority of articles related to this topic, in this work we will not use localization fonctions to reduce the variance. Our method is based on expressing the conditional expectation E[f(St)/Ss] using the Malliavin calculus without localization. Then the variance of the estimator of E[f(St)/Ss] is reduced using closed formulas, techniques based on a conditioning and a judicious choice of the number of simulated paths. Finally, we perform the stopping times version of the dynamic programming algorithm to decrease the bias. On the one hand, we will develop the Malliavin calculus tools for exponential multi-dimensional diffusions that have deterministic and no constant coefficients. On the other hand, we will detail various nonparametric technics to reduce the variance. Moreover, we will test the numerical efficiency of our method on a heterogeneous CPU/GPU multi-core machine

A Lagrangian for Hamiltonian vector fields on singular Poisson manifolds

On a manifold equipped with a bivector field, we introduce for every Hamiltonian a Lagrangian on paths valued in the cotangent space whose stationary points projects onto Hamiltonian vector fields. We show that the remaining components of those stationary points tell whether the bivector field is Poisson or at least defines an integrable distribution - a class of bivector fields generalizing twisted Poisson structures that we study in detail.Comment: 27 page

Investigation of the effect of consolidation on cement flow behaviour

International audienceOne of the main problems affecting the flow of cement bulk powder is the formation of cohesive arching at the outlet of the hopper, causing blockage of the silo opening and bridge formation. A simple concept is established which outlines these complications. In this context, the interactions of particles lead to a high degree of consolidation of the cement powder and an increase of adhesion force due to the small size and the large surface area of the cement particles. The results from the consolidation test and the flow properties (cohesion) show that the cement powder flow is mainly controlled by internal forces (Van der Waals and adhesion forces) and external forces. These forces have a direct influence on the powder structure, leading to a variable packing behaviour. Since the problem is attributable mainly to interparticle forces, before storage of the cement powder in the silo, the powder should be fluidised with air at a high velocity to disintegrate the cohesive structure and to overcome this undesirable property of cement flow

Quand les acteurs débattent sur les oasis du Nefzaoua

International audienceA l'heure actuelle, la filière phoenicicole en Tunisie reste certainement rentable. Pour preuve, les extensions des exploitations dattières continuent à se pratiquer et les acteurs clefs de la filière avouent que « tout se vend et rien ne se perd ». Cependant, ces mêmes acteurs témoignent de leur inquiétude quant à l'avenir de la filière. Les problèmes auxquels ils font face deviennent de plus en plus aigus. Des solutions individuelles sont pratiquement impossibles à mettre en œuvre. Les pouvoirs publics et la profession n'ont pas prévu de réponses fondées sur une vision prospective et ne disposent pas de la réactivité exigée par des problématiques complexes. Une réflexion systémique aboutissant à des démarches pragmatiques durables et impliquant toutes les parties prenantes autour d'une vision commune s'impose d'une façon urgente. Car, en dépit des bonnes volontés des opérateurs et des efforts consentis par les institutions gouvernementales en faveur de la filière, des contraintes structurelles restent encore posées et méritent d'être traitées dans l'immédiat en vue de pérenniser la filière

Creating a media relations plan for the Institute of Public Administration in Saudi Arabia

A media relations’ plan plays an important role in communication between a governmental agency and the media. A well-developed, principle-based plan helps agencies convey messages to the public and the media, and to ultimately, achieve their goals. Scholars have noted that government agencies in countries such as Saudi Arabia have lagged behind other areas in developing effective media relations’ plans. To address this problem, this project created a media relations plan for the Institute of Public Administration in Saudi Arabia (IPA) that could also be used by similar agencies. The plan takes into account the cultural, economical and governmental circumstances that keep agencies in Saudi Arabia from using the media effectively. The method included analysis of standards for media relations plans developed by trade organizations such as the Public Relations Society of America and the International Public Relations Association, ascertainment of current media relations activities of the Institute of Pubic Administration through an examination of documents and website content, and analysis of the media relations plan of the U.S. Office of Personnel Management through the examination of documents and website content.Department of JournalismThesis (M.A.

Riccati equations as a scale-relativistic gateway to quantum mechanics

Applying the resolution-scale relativity principle to develop a mechanics of non-differentiable dynamical paths, we find that, in one dimension, stationary motion corresponds to an Ito process driven by the solutions of a Riccati equation. We verify that the corresponding Fokker-Planck equation is solved for a probability density corresponding to the squared modulus of the solution of the Schrodinger equation for the same problem. Inspired by the treatment of the one-dimensional case, we identify a generalization to time dependent problems in any number of dimensions. The Ito process is then driven by a function which is identified as establishing the link between non-differentiable dynamics and standard quantum mechanics. This is the basis for the scale relativistic interpretation of standard quantum mechanics and, in the case of applications to chaotic systems, it leads us to identify quantum-like states as characterizing the entire system rather than the motion of its individual constituents.Comment: 16 pages, no figur

Les pratiques du contrôle de gestion face au changement

Face à une économie mondiale caractérisée par l'ouverture des marchés, la libéralisation des échanges et l'avènement des technologies de l'information ; les entreprises sont contraintes de remettre en cause leurs pratiques de contrôle de gestion, ainsi que leur modèle d'organisation afin d'améliorer leur performance et d'être compétitives, condition nécessaire à leur pérennité. L'objet de cette communication consiste à étudier l'évolution des pratiques du contrôle de gestion face aux nouveaux besoins des entreprises qui sont confrontées à une turbulence de leur environnement. L'illustration sera faite à partir d'une validation empirique dans le contexte tunisien.contrôle de gestion; changement organisationnel; performance