Parallelization of whole genome alignment

With the advent of High performance computing, it is now possible to achieve orders of magnitude performance and computation e ciency gains over conventional computer architectures. This thesis explores the potential of using high performance computing to accelerate whole genome alignment. A parallel technique is applied to an algorithm for whole genome alignment, this technique is explained and some experiments were carried out to test it. This technique is based in a fair usage of the available resource to execute genome alignment and how this can be used in HPC clusters. This work is a rst approximation to whole genome alignment and it shows the advantages of parallelism and some of the drawbacks that our technique has. This work describes the resource limitations of current WGA applications when dealing with large quantities of sequences. It proposes a parallel heuristic to distribute the load and to assure that alignment quality is mantained.

Wage structures and family economies in the Catalan textile industry in an age of nascent capitalism

This paper deals with changes in managerial practices in Catalonia in anage of nascent capitalism (1830-1925) and adaptive family strategies inorder to face the absence of state welfare. During the 19 t h Century andin the absence of recorded labor contracts, human resources of the firmwere organized by means of implicit contracts and informal labor markets.With the advent of scientific organization of labor, wage per hour workedbegan to be recorded. This is why in the 1920s the perfect competitionmodel applies to our case. On the other hand, in the same period, and inthe absence of state welfare, ideas stemming from cooperative game theoryapply to the pattern of household income formation. Kin related networkswere used to improve the living standards of the household. In thisparticular direction we also show that there was a demonstration effectby means of which migrant s living standards were higher than those ofnatives.

Collaborative explicit plasticity framework: a conceptual scheme for the generation of plastic and group-aware user interfaces

The advent of new advances in mobile computing has changed the manner we do our daily work, even enabling us to perform collaborative activities. However, current groupware approaches do not offer an integrating and efficient solution that jointly tackles the flexibility and heterogeneity inherent to mobility as well as the awareness aspects intrinsic to collaborative environments. Issues related to the diversity of contexts of use are collected under the term plasticity. A great amount of tools have emerged offering a solution to some of these issues, although always focused on individual scenarios. We are working on reusing and specializing some already existing plasticity tools to the groupware design. The aim is to offer the benefits from plasticity and awareness jointly, trying to reach a real collaboration and a deeper understanding of multi-environment groupware scenarios. In particular, this paper presents a conceptual framework aimed at being a reference for the generation of plastic User Interfaces for collaborative environments in a systematic and comprehensive way. Starting from a previous conceptual framework for individual environments, inspired on the model-based approach, we introduce specific components and considerations related to groupware.

Trace me if you can: the use of intrinsic biogeochemical markers in marine top predators

Human activities have serious impacts on marine apex predators. Inadequate knowledge of the spatial and trophic ecology of these marine animals ultimately compromises the viability of their populations and impedes our ability to use them as environmental biomonitors. Intrinsic biogeochemical markers, such as stable isotopes, fatty acids, trace elements, and chemical pollutants, are increasingly being used to trace the spatial and trophic ecology of marine top predators. Notable advances include the emergence of the first oceanographic"isoscapes" (isotopic geographic gradients), the advent of compound-specific isotopic analyses, improvements in diet reconstruction through Bayesian statistics, and tissue analysis of tracked animals to ground-truth biogeochemical profiles. However, most researchers still focus on only a few tracers. Moreover, insufficient knowledge of the biogeochemical integration in tissues, fractionation and routing processes, and geographic and temporal variability in baseline levels continue to hamper the resolution and potential of these markers in studying the spatial and feeding ecology of top predators.

Environmental determinants of foraging strategies in Cory"s shearwaters Calonectris diomedea

Despite the advent of devices to track seabird movements, the extent to which productive areas and oceanic winds influence foraging strategies is still not fully understood. We investigated the main environmental determinants of foraging strategies in Cory"s shearwaters Calonectris diomedea by combining satellite-tracking information from 14 birds breeding on the Canary Islands with concurrent data on chlorophyll a (chl a) concentrations and oceanic winds. Additionally, we took blood samples at the end of each foraging trip and analysed carbon (C) and nitrogen (N) stable isotopes to examine the use of trophic resources. All birds showed commuting trips, concentrating foraging activity exclusively on the African continental shelf. Foraging locations showed a strong association with chl a concentrations, suggesting birds select foraging areas according to prey availability. In contrast with other breeding colonies where Cory"s shearwaters use a dual-foraging method, birds showed a unimodal strategy and did not show differences in C and N isotope signatures in plasma, confirming that close proximity to highly productive areas strongly influences foraging strategies. In addition, birds tracked during 2 consecutive trips foraged in the same area, suggesting that high resource availability promotes fidelity to feeding grounds also at coarse scales. Persistent northeast trade winds blew during the study period, and commuting trips followed a consistent clockwise movement with a southwest heading while the birds foraged along the continental shelf, suggesting that birds used tail winds to reduce their flying costs. Our results corroborate that oceanographic conditions in the vicinity of the breeding colony have a strong effect on foraging strategies of pelagic seabirds.

Progress Towards to Equity Market Integration in Eastern Europe

The advent of the European Union has decreased the diversification benefits available from country based equity market indices in the region. This paper measures the increase in stock integration between the three largest new EU members (Hungary, the Czech Republic and Poland who joined in May 2004) and the Euro-zone. A potentially gradual transition in correlations is accommodated in a single VAR model by embedding smooth transition conditional correlation models with fat tails, spillovers, volatility clustering, and asymmetric volatility effects. At the country market index level all three Eastern European markets show a considerable increase in correlations in 2006. At the industry level the dates and transition periods for the correlations differ, and the correlations are lower although also increasing. The results show that sectoral indices in Eastern European markets may provide larger diversification opportunities than the aggregate market. JEL classifications: C32; C51; F36; G15 Keywords: Multivariate GARCH; Smooth Transition Conditional Correlation; Stock Return Comovement; Sectoral correlations; New EU Members

Towards an emotion-driven interactive music system: ridging the gaps between affect, physiology and sound generation

Report for the scientific sojourn at the Stanford University from January until June 2007. Music is well known for affecting human emotional states, yet the relationship between specific musical parameters and emotional responses is still not clear. With the advent of new human-computer interaction (HCI) technologies, it is now possible to derive emotion-related information from physiological data and use it as an input to interactive music systems. Providing such implicit musical HCI will be highly relevant for a number of applications including music therapy, diagnosis, nteractive gaming, and physiologically-based musical instruments. A key question in such physiology-based compositions is how sound synthesis parameters can be mapped to emotional states of valence and arousal. We used both verbal and heart rate responses to evaluate the affective power of five musical parameters. Our results show that a significant correlation exists between heart rate and the subjective evaluation of well-defined musical parameters. Brightness and loudness showed to be arousing parameters on subjective scale while harmonicity and even partial attenuation factor resulted in heart rate changes typically associated to valence. This demonstrates that a rational approach to designing emotion-driven music systems for our public installations and music therapy applications is possible.

Configuración de la entrada/salida paralela para el cómputo de altas prestaciones

La E/S Paralela es un área de investigación que tiene una creciente importancia en el cómputo de Altas Prestaciones. Si bien durante años ha sido el cuello de botella de los computadores paralelos en la actualidad, debido al gran aumento del poder de cómputo, el problema de la E/S se ha incrementado y la comunidad del Cómputo de Altas Prestaciones considera que se debe trabajar en mejorar el sistema de E/S de los computadores paralelos, para lograr cubrir las exigencias de las aplicaciones científicas que usan HPC. La Configuración de la Entrada/Salida (E/S) Paralela tiene una gran influencia en las prestaciones y disponibilidad, por ello es importante “Analizar configuraciones de E/S paralela para identificar los factores claves que influyen en las prestaciones y disponibilidad de la E/S de Aplicaciones Científicas que se ejecutan en un clúster”. Para realizar el análisis de las configuraciones de E/S se propone una metodología que permite identificar los factores de E/S y evaluar su influencia para diferentes configuraciones de E/S formada por tres fases: Caracterización, Configuración y Evaluación. La metodología permite analizar el computador paralelo a nivel de Aplicación Científica, librerías de E/S y de arquitectura de E/S, pero desde el punto de vista de la E/S. Los experimentos realizados para diferentes configuraciones de E/S y los resultados obtenidos indican la complejidad del análisis de los factores de E/S y los diferentes grados de influencia en las prestaciones del sistema de E/S. Finalmente se explican los trabajos futuros, el diseño de un modelo que de soporte al proceso de Configuración del sistema de E/S paralela para aplicaciones científicas. Por otro lado, para identificar y evaluar los factores de E/S asociados con la disponibilidad a nivel de datos, se pretende utilizar la Arquitectura Tolerante a Fallos RADIC.

An Ontology for Open Rubric Exchange on the Web

While the Internet has given educators access to a steady supply of Open Educational Resources, the educational rubrics commonly shared on the Web are generally in the form of static, non-semantic presentational documents or in the proprietary data structures of commercial content and learning management systems.With the advent of Semantic Web Standards, producers of online resources have a new framework to support the open exchange of software-readable datasets. Despite these advances, the state of the art of digital representation of rubrics as sharable documents has not progressed.This paper proposes an ontological model for digital rubrics. This model is built upon the Semantic Web Standards of the World Wide Web Consortium (W3C), principally the Resource Description Framework (RDF) and Web Ontology Language (OWL).

Hierachy-based methodology for producing educational contents with maximal reutilization

Computer based training or distance education are facing dramatic changes withthe advent of standardization efforts, some of them concentrating in maximal reuse.This is of paramount importance for a sustainable -cost affordable- production ofeducational materials. Reuse in itself should not be a goal, though, since manymethodological aspects might be lost. In this paper we propose two contentproduction approaches for the InterMediActor platform under a competence-basedmethodology: either a bottom-up approach where content is designed from scratchor a top-down methodology where existing material can be gradually adapted tofulfil requisites to be used with maximal flexibility into InterMediActor.

Contribución al diseño de GNSS-SDR, un receptor GNSS de código abierto

[ANGLÈS] This project introduces GNSS-SDR, an open source Global Navigation Satellite System software-defined receiver. The lack of reconfigurability of current commercial-of-the-shelf receivers and the advent of new radionavigation signals and systems make software receivers an appealing approach to design new architectures and signal processing algorithms. With the aim of exploring the full potential of this forthcoming scenario with a plurality of new signal structures and frequency bands available for positioning, this paper describes the software architecture design and provides details about its implementation, targeting a multiband, multisystem GNSS receiver. The result is a testbed for GNSS signal processing that allows any kind of customization, including interchangeability of signal sources, signal processing algorithms, interoperability with other systems, output formats, and the offering of interfaces to all the intermediate signals, parameters and variables. The source code release under the GNU General Public License (GPL) secures practical usability, inspection, and continuous improvement by the research community, allowing the discussion based on tangible code and the analysis of results obtained with real signals. The source code is complemented by a development ecosystem, consisting of a website (http://gnss-sdr.org), as well as a revision control system, instructions for users and developers, and communication tools. The project shows in detail the design of the initial blocks of the Signal Processing Plane of the receiver: signal conditioner, the acquisition block and the receiver channel, the project also extends the functionality of the acquisition and tracking modules of the GNSS-SDR receiver to track the new Galileo E1 signals available. Each section provides a theoretical analysis, implementation details of each block and subsequent testing to confirm the calculations with both synthetically generated signals and with real signals from satellites in space.

Enteral nutrition as primary therapy in Crohn's disease

The developments in enteral feeding for Crohn's disease in the past decade are critically reviewed. The advent of amino acid based chemically defined elemental diets signalled the end of 'total bowel rest' in the management of these patients. Subsequently, controlled clinical trials showed that elemental diets were as effective as corticosteroids in inducing clinical remission in patients with acute exacerbations of Crohn's disease. The later use of peptide based elemental diets, in Crohn's disease produced somewhat conflicting results. The initial uncontrolled studies suggest that polymeric whole protein diets might also be effective in the management of acute exacerbations of the disease, casting in turn doubts concerning the role of dietary antigens in the pathogenesis of Crohn's disease. Results of controlled studies comparing the use of elemental and polymeric diets as primary therapy in Crohn's disease have, however, also produced conflicting results. The results of one recent controlled trial in which

Presència de Rousseau a Catalunya: entre el mite i la realitat

En aquest article s’ofereix un perfil del pensament de Rousseau a partir de la seva relació amb la filosofia estoica i la seva dependència respecte de les idees de Montaigne, alhora que es remarca —atenint-se a la Professió de fe del vicari savoià— la dimensió religiosa i espiritual de la seva cosmovisió. Sobre la base d’aquests supòsits es revisa l’impacte de les idees de Rousseau en el Romanticisme del segle xix, sense perdre de vista les crítiques que la seva pedagogia va merèixer dels ideòlegs del Noucentisme (Eugeni d’Ors, Joaquim Xirau). Finalment, es conclou que la presència de la pedagogia de Rousseau en el Moviment de Renovació Pedagògica, viscut durant les primeres dècades del segle xx a Catalunya, constitueix més un horitzó que no pas una realitat bastida sistemàticament i sòlidament.

A Middleware architecture for Unmanned Aircraft Avionics

An Unmanned Aerial Vehicle is a non-piloted airplane designed to operate in dangerous and repetitive situations. With the advent of UAV's civil applications, UAVs are emerging as a valid option in commercial scenarios. If it must be economically viable, the same platform should implement avariety of missions with little reconguration time and overhead.This paper presents a middleware-based architecture specially suited to operate as a exible payload and mission controller in a UAV. The system is composed of low-costcomputing devices connected by network. The functionality is divided into reusable services distributed over a number ofnodes with a middleware managing their lifecycle and communication.Some research has been done in this area; yetit is mainly focused on the control domain and in its realtime operation. Our proposal differs in that we address the implementation of adaptable and reconfigurable unmannedmissions in low-cost and low-resources hardware.

Smart antennas in software radio base stations

The application of adaptive antenna techniques to fixed-architecture base stations has been shown to offer wide-ranging benefits, including interference rejection capabilities or increased coverage and spectral efficiency.Unfortunately, the actual implementation ofthese techniques to mobile communication scenarios has traditionally been set back by two fundamental reasons. On one hand, the lack of flexibility of current transceiver architectures does not allow for the introduction of advanced add-on functionalities. On the other hand, theoften oversimplified models for the spatiotemporal characteristics of the radio communications channel generally give rise toperformance predictions that are, in practice, too optimistic. The advent of software radio architectures represents a big step toward theintroduction of advanced receive/transmitcapabilities. Thanks to their inherent flexibilityand robustness, software radio architecturesare the appropriate enabling technology for theimplementation of array processing techniques.Moreover, given the exponential progression ofcommunication standards in coexistence andtheir constant evolution, software reconfigurabilitywill probably soon become the only costefficientalternative for the transceiverupgrade. This article analyzes the requirementsfor the introduction of software radio techniquesand array processing architectures inmultistandard scenarios. It basically summarizesthe conclusions and results obtained withinthe ACTS project SUNBEAM,1 proposingalgorithms and analyzing the feasibility ofimplementation of innovative and softwarereconfigurablearray processing architectures inmultistandard settings.