Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays

BACKGROUND: Gene expression profiles of non-model mammals may provide valuable data for biomedical and evolutionary studies. However, due to lack of sequence information of other species, DNA microarrays are currently restricted to humans and a few model species. This limitation may be overcome by using arrays developed for a given species to analyse gene expression in a related one, an approach known as "cross-species analysis". In spite of its potential usefulness, the accuracy and reproducibility of the gene expression measures obtained in this way are still open to doubt. The present study examines whether or not hybridization values from cross-species analyses are as reproducible as those from same-species analyses when using Affymetrix oligonucleotide microarrays. RESULTS: The reproducibility of the probe data obtained hybridizing deer, Old-World primates, and human RNA samples to Affymetrix human GeneChip(® )U133 Plus 2.0 was compared. The results show that cross-species hybridization affected neither the distribution of the hybridization reproducibility among different categories, nor the reproducibility values of the individual probes. Our analyses also show that a 0.5% of the probes analysed in the U133 plus 2.0 GeneChip are significantly associated to un-reproducible hybridizations. Such probes-called in the text un-reproducible probe sequences- do not increase in number in cross-species analyses. CONCLUSION: Our study demonstrates that cross-species analyses do not significantly affect hybridization reproducibility of GeneChips, at least within the range of the mammal species analysed here. The differences in reproducibility between same-species and cross-species analyses observed in previous studies were probably caused by the analytical methods used to calculate the gene expression measures. Together with previous observations on the accuracy of GeneChips for cross-species analysis, our analyses demonstrate that cross-species hybridizations may provide useful gene expression data. However, the reproducibility and accuracy of these measures largely depends on the use of appropriated algorithms to derive the gene expression data from the probe data. Also, the identification of probes associated to un-reproducible hybridizations-useless for gene expression analyses- in the studied GeneChip, stress the need of a re-evaluation of the probes' performance

A Class of Computationally Fast First Order Finite Volume Solvers: PVM Methods

In this work, we present a class of fast first order finite volume solvers, named as PVM (Polynomial Viscosity Matrix), for balance laws or, more generally, for nonconservative hyperbolic systems. They are defined in terms of viscosity matrices computed by a suitable polynomial evaluation of a Roe matrix. These methods have the advantage that they only need some information about the eigenvalues of the system to be defined, and no spectral decomposition of Roe Matrix is needed. As consequence, they are faster than Roe method. These methods can be seen as a generalization of the schemes introduced by Degond et al. in [12] for balance laws and nonconservative systems. The first-order path conservative methods to be designed here are intended to be used as the basis for higher order methods for multi-dimensional problems. In this work, some well known solvers as Rusanov, Lax-Friedrichs, FORCE (see [30], [8]), GFORCE (see [31], [8]) or HLL (see [18]) are redefined under this form, and then some new solvers are proposed. Finally, some numerical tests are presented and the performance of the numerical schemes are compared among them and with Roe schem

IFCP solver for the the two-layer SWS.

The goal of this article is to design a new approximate Riemann solver for the two-layer shallow water system which is fast compared to Roe schemes and accurate compared to Lax-Friedrichs, FORCE, or GFORCE schemes (see[14]). This Riemann solver is based on a suitable decomposition of a Roe matrix (see [27]) by means of a parabolic viscosity matrix (see [16]) that captures some information concerning the intermediate characteristic fields. The corresponding first order numerical scheme, which is called IFCP (Intermediate Field Capturing Parabola) is linearly L∞-stable, well-balanced, and it doesn’t require an entropy-fix technique. Some numerical experiments are presented to compare the behavior of this new scheme with Roe and GFORCE method

Numerical treatment of the loss of hyperbolicity of the two-layer SWS.

In this work, a characterization of the hyperbolicity region for the two layer shallow-water system is proposed and checked. Next, some path-conservative finite volume schemes (see [11]) that can be used even if the system is not hyperbolic are presented, but they are not in general L2 linearly stable in that case. Then, we introduce a simple but efficient strategy to enforce the hyperbolicity of the two-layer shallow-water system consisting in adding to the system an extra amount of friction at every cell in which complex eigenvalues are detected at a given time step. The implementation is performed by a predictor/corrector strategy: first a numerical scheme is applied to the unmodified two-layer system, regardless of the hyperbolic character of the system. Next, we check if the predicted cell averages are in the hyperbolic region or not. If not, the mass-fluxes are corrected by adding a quadratic friction law between layers whose coefficient is computed so that the corrected cell average is as near as possible of the boundary of the hyperbolicity region. Finally, some numerical test have been performed to assess the efficiency of the proposed strateg

Esquemas 2D de alto orden basados en reconstrucciones de estado, para sistemas hiperbólicos no conservativos. Aplicación a problemas de transporte de sedimentos

En este trabajo se aborda la aproximación numérica del problema de arrastre de sedimentos causada por la evolución del agua. Para la componente hidrodinámica se consideran las ecuaciones de aguas poco profundas. La componente morfodinámica se define mediante una ecuación de continuidad, dada en función del caudal sólido. Ambas componentes constituyen un sistema acoplado que puede reescribirse como un sistema hiperbólico no conservativo (ver [4] A.M. Ferreiro Ferreiro. Desarrollo de técnicas de post-proceso de flujos hidrodinámicos, modelización de problemas de transporte de sedimentos y simulación numérica mediante técnicas de volúmenes finitos. Tesis Doctoral. Universidad de Sevilla. 2006). Se propone un esquema 2D generalizado de Roe con reconstrucciones de estado para sistemas hiperbólicos no conservativos (ver [4]), mediante esquemas de volúmenes finitos y el método de líneas (ver [5] J.A. García Rodríguez. Paralelización de esquemas de vol´umenes finitos: aplicación a la resolución de sistemas de tipo aguas someras. Tesis Doctoral. Universidad de Málaga. 2005), extendiendo los esquemas de alto orden para el caso 1D propuesto en [2] M.J. Castro, J.M. Gallardo and C. Parés. High order finite volume schemes based on reconstruction of states for solving hyperbolic systems with nonconservative products. Applications to shallow water systems. Math. Comp., 75: 1103-1134. 2006. La reconstrucción de estado empleada es de tipo MUSCL (ver [1] B. Van Leer. MUSCL. A new approach to numerical gas dynamics. Computing in plasma physics and astrophysics, Max-Planck-Institut fur plama physik.. Carchung, Germany, April 1976), que proporciona orden dos para mallas no estructuradas de volúmenes finitos de tipo arista. Finalmente se presenta un test num´erico en el que se estudia la evolución del ángulo de expansi´on de una monta˜na de arena (ver [4])

Sediment transport models in Shallow Water equations and numerical approach by high order finite volume methods.

This paper is concerned with the numerical approximation of bedload sediment transport due to water evolution. For the hydrodynamical component we consider Shallow Water equations. The morphodynamical component is defined by a continuity equation, which is defined in function of the solid transport discharge. We present several deterministic models, such as Meyer-Peter & Müller, Van Rijn or Grass model. We also present an unified definition for the solid transport discharge, and we compare with Grass model. Both components define a coupled system of equations that can be rewrite as a non-conservative hyperbolic system. To discretize it, we consider finite volume methods with or without flux limiters and high order state reconstructions. Finally we present several tests, where we observe numerically the order of the numerical schemes. Comparisons with analytical solutions and experimental data are also presented

Habilidades sociales en los adolescentes estudiantes de segundo año de Bachillerato General y opción Administrativo Contable sección “A” y “B” del turno matutino del Instituto Nacional de Usulután, durante el año 2016

La investigación tuvo como objetivo principal conocer las habilidades sociales de los adolescentes estudiantes de Segundo año de Bachillerato General y Administrativo Contable A y B del Instituto Nacional de Usulután y establecer la frecuencia de dichas habilidades así como también identificar si existen diferencias en las habilidades sociales según el tipo de familia y los factores que se dan en el desarrollo de las habilidades sociales. El diseño fue descriptivo, en esta investigación se aplico una ficha de evaluación para seleccionar a la población que sería encuestada, esto permitió conocer el tipo de familia de la cual provenía el adolescente para conformar la población por estratos de familias integradas y desintegras con ello se seleccionaron los participantes de manera intencionada y es a esta población a la cual se le aplico el inventario de Habilidades Sociales que permite conocer los niveles en cuatro áreas asertividad, autoestima, comunicación y toma de decisiones. Se utilizo el método cuantitativo que consistió en utilizar la recolección de datos y posteriormente aplicar la prueba Z, aceptando la hipótesis de investigación y rechazando la nula. El tipo de investigación es cuantitativo descriptivo porque se tiene una variable en estudio habilidades sociales la cual fue medida con una prueba y esta dio datos que se analizaron, dando resultados favorables ya que se poseen conductas socialmente hábiles. La población es de 232 adolescentes del sexo masculino y femenino, la muestra se obtuvo a través del programa de decisión de análisis STATS T M y se selecciono a 140 estudiantes 73 son de familias integradas y 67 de familias desintegras estos grupos fueron la población en la cual se investigo las habilidades sociales

A new Savage-Hutter type model for submarine avalanches and generated tsunami

In this paper we present a new two-layer model of Savage-Hutter type to study submarine avalanches. A layer composed of fluidized granular material is assumed to flow within an upper layer composed of an inviscid fluid (e. g. water). The model is derived in a system of local coordinates following a non-erodible bottom and takes into account its curvature. We prove that the model verifies an entropy inequality, preserves water at rest for a sediment layer and their solutions can be seen as particular solutions of incompressible Euler equations under hydrostatic assumptions. Buoyancy effects and the centripetal acceleration of the grain movement due to the curvature of the bottom are considered in the definition of the Coulomb term. We propose a two-step Roe type solver to discretize the presented model. It exactly preserves water at rest and no movement of the sediment layer, when its angle is smaller than the angle of repose, and up to second order all stationary solutions. Finally, some numerical tests are performed by simulating submarine and sub-aerial avalanches as well as the generated tsunami

Deducción y simulación numérica de un nuevo modelo de avalanchas submarinas

En este trabajo se estudia un nuevo modelo de tipo Savage-Hutter para avalanchas submarinas. El modelo obtenido es de tipo aguas someras bicapa en el que la capa superior representa al fluido y la capa inferior representa a un estrato de material granular. En la deducción del modelo se han tenido en cuenta diferentes leyes constitutivas en los tensores de esfuerzos, la porosidad del estrato de sedimento o roca y un término de fricción de tipo Coulomb. El modelo obtenido puede aplicarse en el estudio de problemas de avalanchas submarinas y algunos tipos de tsunamis. Finalmente se presentan la discretización del modelo obtenido mediante técnicas de vol´umenes finitos bien equilibrados y un ensayo numérico donde se modela una avalancha submarina

Well-balanced finite volume schemes for 2D non-homogeneous hyperbolic systems. Application to the dam-break of Aznalcóllar.

In this paper, we introduce a class of well-balanced finite volume schemes for 2D non-homogeneous hyperbolic systems. We extend the derivation of standard finite volume solvers for homogeneous systems to non-homogeneous ones using the method of lines. We study conservation and some well-balanced properties of the numerical scheme. We apply our solvers to shallow water equations: we prove that these exactly compute the water at rest solutions. We also perform some numerical tests, by comparing with 1D solutions, simulating the formation of a hydraulic drop and a hydraulic jump, and studying a real dam break: Aznalcóllar, an ecological disaster happened in the province of Seville, Spain in 1998