PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Stability of Switched Feedback Time-Varying Dynamic Systems Based on the Properties of the Gap Metric for Operators

The stabilization of dynamic switched control systems is focused on and based on an operator-based formulation. It is assumed that the controlled object and the controller are described by sequences of closed operator pairs (L, C) on a Hilbert space H of the input and output spaces and it is related to the existence of the inverse of the resulting input-output operator being admissible and bounded. The technical mechanism addressed to get the results is the appropriate use of the fact that closed operators being sufficiently close to bounded operators, in terms of the gap metric, are also bounded. That philosophy is followed for the operators describing the input-output relations in switched feedback control systems so as to guarantee the closed-loop stabilization.

On Best Proximity Point Theorems and Fixed Point Theorems for p-Cyclic Hybrid Self-Mappings in Banach Spaces

This paper relies on the study of fixed points and best proximity points of a class of so-called generalized point-dependent (K-Lambda)hybrid p-cyclic self-mappings relative to a Bregman distance Df, associated with a Gâteaux differentiable proper strictly convex function f in a smooth Banach space, where the real functions Lambda and K quantify the point-to-point hybrid and nonexpansive (or contractive) characteristics of the Bregman distance for points associated with the iterations through the cyclic self-mapping.Weak convergence results to weak cluster points are obtained for certain average sequences constructed with the iterates of the cyclic hybrid self-mappings.

Some Results on Fixed and Best Proximity Points of Multivalued

This paper is devoted to investigate the fixed points and best proximity points of multivalued cyclic self-mappings on a set of subsets of complete metric spaces endowed with a partial order under a generalized contractive condition involving a Hausdorff distance. The existence and uniqueness of fixed points of both the cyclic self-mapping and its associate composite self-mappings on each of the subsets are investigated, if the subsets in the cyclic disposal are nonempty, bounded and of nonempty convex intersection. The obtained results are extended to the existence of unique best proximity points in uniformly convex Banach spaces.

Cosmology in an accelerated universe: observations and phenomenology

En las últimas décadas la cosmología ha experimentado notables avances como consecuencia del desarrollo de nuevos experimentos que nos han abastecido con precisos datos observacionales. La calidad de estos datos ha permitido construir una imagen global del universo actual; un universo acelerado compuesto principalmente por materia oscura (23%) distinta a la materia ordinaria (5%), y energía oscura (70%), la componente del universo que contrarresta el efecto gravitatorio y explica la expansión acelerada de éste. Con la existencia de estas dos principales componentes se puede explicar la situación actual del universo y los fenómenos que tienen lugar en él. Sin embargo, su naturaleza es todavía un misterio, por lo que nos encontramos ante un largo y apasionante camino que recorrer.Es en este contexto donde se enmarca el trabajo presentado en esta tesis, cuyo principal objetivo es ir más allá y obtener algunas pistas nuevas sobre la naturaleza de la energía oscura. Las investigaciones llevadas a cabo durante esta tesis tratan de hacer frente a este sector ¿oscuro" desde varias perspectivas, combinando la teoría y el análisis de datos astronómicos.Como primer acercamiento, en el capítulo 2 se propone un nuevo modelo para unificar el sector ¿oscuro¿: materia y energía oscura. En los capítulos 3 y 4 se aborda el problema de la energía oscura desde una nueva perspectiva y se presentan unas nuevas parametrizaciones de la ecuación de estado de la energía oscura. Por último, en el capítulo 5, a través de los datos del fondo cósmico de microondas, se da un paso más allá en física de las épocas tempranas del universo, y se obtienen restricciones sobre el exceso de densidad de radiación observado. Por otra parte, se da una explicación a este fenómeno: se atribuye este exceso al fondo cósmico de ondas gravitacionales primordiales producido por las cuerdas cósmicas, bajo condiciones adiabáticas.

On Bounded Strictly Positive Operators of Closed Range and Some Applications to Asymptotic Hyperstability of Dynamic Systems

The problem discussed is the stability of two input-output feedforward and feedback relations, under an integral-type constraint defining an admissible class of feedback controllers. Sufficiency-type conditions are given for the positive, bounded and of closed range feed-forward operator to be strictly positive and then boundedly invertible, with its existing inverse being also a strictly positive operator. The general formalism is first established and the linked to properties of some typical contractive and pseudocontractive mappings while some real-world applications and links of the above formalism to asymptotic hyperstability of dynamic systems are discussed later on.

On a Class of Self-Adjoint Compact Operators in Hilbert Spaces and Their Relations with Their Finite-Range Truncations

This paper investigates a class of self-adjoint compact operators in Hilbert spaces related to their truncated versions with finite-dimensional ranges. The comparisons are established in terms of worst-case norm errors of the composite operators generated from iterated computations. Some boundedness properties of the worst-case norms of the errors in their respective fixed points in which they exist are also given. The iterated sequences are expanded in separable Hilbert spaces through the use of numerable orthonormal bases.

Best Proximity Points of Generalized Semicyclic Impulsive Self-Mappings: Applications to Impulsive Differential and Difference Equations

This paper is devoted to the study of convergence properties of distances between points and the existence and uniqueness of best proximity and fixed points of the so-called semicyclic impulsive self-mappings on the union of a number of nonempty subsets in metric spaces. The convergences of distances between consecutive iterated points are studied in metric spaces, while those associated with convergence to best proximity points are set in uniformly convex Banach spaces which are simultaneously complete metric spaces. The concept of semicyclic self-mappings generalizes the well-known one of cyclic ones in the sense that the iterated sequences built through such mappings are allowed to have images located in the same subset as their pre-image. The self-mappings under study might be in the most general case impulsive in the sense that they are composite mappings consisting of two self-mappings, and one of them is eventually discontinuous. Thus, the developed formalism can be applied to the study of stability of a class of impulsive differential equations and that of their discrete counterparts. Some application examples to impulsive differential equations are also given.

Asymptotic Hyperstability of a Class of Linear Systems under Impulsive Controls Subject to an Integral Popovian Constraint

This paper is focused on the study of the important property of the asymptotic hyperstability of a class of continuous-time dynamic systems. The presence of a parallel connection of a strictly stable subsystem to an asymptotically hyperstable one in the feed-forward loop is allowed while it has also admitted the generation of a finite or infinite number of impulsive control actions which can be combined with a general form of nonimpulsive controls. The asymptotic hyperstability property is guaranteed under a set of sufficiency-type conditions for the impulsive controls.

Advances in Nonlinear Complexity Analysis for Partial Differential Equations

1 p. -- [Editorial Material]

Herramienta software para el análisis de rendimiento de redes 4G

[ES]El objetivo de este proyecto ha sido desarrollar una herramienta software que permita medir el rendimiento de redes con tecnología móvil 4G, también conocida como LTE. Para ello se ha creado un sistema software que está compuesto por una aplicación móvil y un servidor de aplicaciones. El sistema en conjunto realiza la función de recoger indicadores de calidad de la red móvil de diversa índole, que posteriormente son procesados utilizando herramientas software matemáticas, para así obtener gráficas y mapas que permiten analizar la situación y el rendimiento de una red 4G concreta. El desarrollo del software ha llegado a nivel de prototipo y se han realizado pruebas reales con él obteniendo resultados positivos de funcionamiento.

Study of crystal structure and phase transition studies in perovskite-type oxides using powder-diffraction techniques and symmetry-mode analysis.

251 p.

Implementación de sistema ETCS en entorno cliente-servidor.

[ES]La interoperabilidad entre distintas redes ferroviarias europeas es muy escasa. Para dar solución a este problema, la Unión Europea creó el sistema europeo de gestión del tráfico ferroviario (ERTMS), encargado de crear un estándar único para toda la red europea. El objetivo de este proyecto es la implementación del sistema ETCS ( European Train Control System ) en un entorno cliente-servidor. La implementación incluye el sistema del tren y el del centro de control (RBC). Se ha implementado de forma que se pueda operar sobre dos protocolos de red transporte, de forma que será compatible tanto para redes orientadas a la conexión (TCP) como no orientadas a conexión (UDP).

Contributions to Ensemble Classifiers with Image Analysis Applications

134 p.

A Novel Scheduling Index Rule Proposal for QoE Maximization in Wireless Networks

This paper deals with the resource allocation problem aimed at maximizing users' perception of quality in wireless channels with time-varying capacity. First of all, we model the subjective quality-aware scheduling problem in the framework of Markovian decision processes. Then, given that the obtaining of the optimal solution of this model is unachievable, we propose a simple scheduling index rule with closed-form expression by using a methodology based on Whittle approach. Finally, we analyze the performance of the achieved scheduling proposal in several relevant scenarios, concluding that it outperforms the most popular existing resource allocation strategies.