Data size sufficiency analyses of haplotype inference algortihms

We present experimental and theoretical analyses of data requirements for haplotype inference algorithms. Our experiments include a broad range of problem sizes under two standard models of tree distribution and were designed to yield statistically robust results despite the size of the sample space. Our results validate Gusfield's conjecture that a population size of n log n is required to give (with high probability) sufficient information to deduce the n haplotypes and their complete evolutionary history. The experimental results inspired our experimental finding with theoretical bounds on the population size. We also analyze the population size required to deduce some fixed fraction of the evolutionary history of a set of n haplotypes and establish linear bounds on the required sample size. These linear bounds are also shown theoretically.

Generalized multiresolution analyses with given multiplicity functions

Generalized multiresolution analyses are increasing sequences of subspaces of a Hilbert space H that fail to be multiresolution analyses in the sense of wavelet theory because the core subspace does not have an orthonormal basis generated by a fixed scaling function. Previous authors have studied a multiplicity function m which, loosely speaking, measures the failure of the GMRA to be an MRA. When the Hilbert space H is L2(Rn), the possible multiplicity functions have been characterized by Baggett and Merrill. Here we start with a function m satisfying a consistency condition which is known to be necessary, and build a GMRA in an abstract Hilbert space with multiplicity function m.

Rehabilitación multimodal en cirugía electiva colorrectal: análisis de resultados, impacto en los costes hospitalarios y curva de aprendizaje

Els objectius són avaluar la seguretat, resultats i l’impacte en els costs d’un programa de rehabilitació multimodal en cirurgia colorrectal, així com estudiar la influència de la experiència de l’equip en el seu compliment i resultats. Estudi prospectiu de cohorts consecutives. La rehabilitació multimodal no augmenta la morbilitat ni la mortalitat. A més a més disminueix l’estada a l’hospital en 3 dies sense incrementar els reingressos. També s’associa a una disminució dels costs totals de 912 euros per pacient. El compliment del protocol millora amb l’experiència de l’equip multidisciplinari, accelerant la recuperació dels pacients i conseqüentment l’alta precoç.

Natural abundance of stable isotopes (15N and 13C) and isotopic fractionation of sea bream muscle as markers of food and culture conditions and its relationship with metabolic and proteomic analyses

Els isòtops estables com a traçadors de la cadena alimentària, s'han utilitzat per caracteritzar la relació entre els consumidors i els seus aliments, ja que el fraccionament isotòpic implica una discriminació en contra de certs isòtops. Però les anàlisis d'isòtops estables (SIA), també es poden dur a terme en peixos cultivats amb dietes artificials, com la orada (Sparus aurata), la especie más cultivada en el Mediterráneo. Canvis en l'abundància natural d'isòtops estables (13C i 15N) en els teixits i les seves reserves poden reflectir els canvis en l'ús i reciclatge dels nutrients ja que els enzims catabòlics implicats en els processos de descarboxilació i desaminació mostren una preferència pels isòtops més lleugers. Per tant, aquestes anàlisis ens poden proporcionar informació útil sobre l'estat nutricional i metabòlic dels peixos. L'objectiu d'aquest projecte va ser determinar la capacitat dels isòtops estables per ser utilitzats com a marcadors potencials de la capacitat de creixement i condicions de cria de l'orada. En aquest sentit, les anàlisis d'isòtops estables s'han combinat amb altres metabòlics (activitats citocrom-c-oxidasa, COX, i citrat sintasa, CS) i els paràmetres de creixement (ARN/ADN). El conjunt de resultats obtinguts en els diferents estudis realitzats en aquest projecte demostra que el SIA, en combinació amb altres paràmetres metabòlics, pot servir com una eina eficaç per discriminar els peixos amb millor potencial de creixement, així com a marcador sensible de l'estat nutricional i d'engreix. D'altra banda, la combinació de l'anàlisi d'isòtops estables amb les eines emergents, com ara tècniques de proteòmica (2D-PAGE), ens proporciona nous coneixements sobre els canvis metabòlics que ocorren en els músculs dels peixos durant l‟increment del creixement muscular induït per l'exercici.

Grain size analyses in tin-lead glazes based on 2d-sections

A problem in the archaeometric classification of Catalan Renaissance pottery is the fact, thatthe clay supply of the pottery workshops was centrally organized by guilds, and thereforeusually all potters of a single production centre produced chemically similar ceramics.However, analysing the glazes of the ware usually a large number of inclusions in the glaze isfound, which reveal technological differences between single workshops. These inclusionshave been used by the potters in order to opacify the transparent glaze and to achieve a whitebackground for further decoration.In order to distinguish different technological preparation procedures of the single workshops,at a Scanning Electron Microscope the chemical composition of those inclusions as well astheir size in the two-dimensional cut is recorded. Based on the latter, a frequency distributionof the apparent diameters is estimated for each sample and type of inclusion.Following an approach by S.D. Wicksell (1925), it is principally possible to transform thedistributions of the apparent 2D-diameters back to those of the true three-dimensional bodies.The applicability of this approach and its practical problems are examined using differentways of kernel density estimation and Monte-Carlo tests of the methodology. Finally, it istested in how far the obtained frequency distributions can be used to classify the pottery

Agrupador de imágenes multimodal no supervisado

Trabajo Fin de Máster donde se implementa un método multimodal para la clasificación de imágenes sin etiquetar y sin intervención humana.

The Multiscenario Multienvironment BioSecure Multimodal Database (BMDB)

A new multimodal biometric database designed and acquired within the framework of the European BioSecure Network of Excellence is presented. It is comprised of more than 600 individuals acquired simultaneously in three scenarios: 1) over the Internet, 2) in an office environment with desktop PC, and 3) in indoor/outdoor environments with mobile portable hardware. The three scenarios include a common part of audio/video data. Also, signature and fingerprint data have been acquired both with desktop PC and mobile portable hardware. Additionally, hand and iris data were acquired in the second scenario using desktop PC. Acquisition has been conducted by 11 European institutions. Additional features of the BioSecure Multimodal Database (BMDB) are: two acquisitionsessions, several sensors in certain modalities, balanced gender and age distributions, multimodal realistic scenarios with simple and quick tasks per modality, cross-European diversity, availability of demographic data, and compatibility with other multimodal databases. The novel acquisition conditions of the BMDB allow us to perform new challenging research and evaluation of eithermonomodal or multimodal biometric systems, as in the recent BioSecure Multimodal Evaluation campaign. A description of this campaign including baseline results of individual modalities from the new database is also given. The database is expected to beavailable for research purposes through the BioSecure Association during 2008.

Daisy: un libro digital abierto, multimodal y accesible

Se presenta el formato de libro multimedia Daisy que permite integrar texto, sonido, imágenes y vídeo de forma sincronizada y con una navegación avanzada por el texto y el audio que lo hace altamente usable para lecturas en digital. También se presenta su componente principal DTBook xml, disposición estructurada del texto que permite generar formatos alternativos. El artículo detalla las diferencias de Daisy respecto a otros audiolibros, los dispositivos de lectura existentes y su adopción en el mercado y en la enseñanza. Si se abaratan los costes de los aparatos lectores y se soluciona la gestión de derechos digitales, tiene muchas posibilidades de convertirse en estrella para editar libros digitales.

Precursor uptake assays and metabolic analyses in isolated tomato fruit chromoplasts

Background Carotenoids are the most widespread group of pigments found in nature. In addition to their role in the physiology of the plant, carotenoids also have nutritional relevance as their incorporation in the human diet provides health benefits. In non-photosynthetic tissues, carotenoids are synthesized and stored in specialized plastids called chromoplasts. At present very little is known about the origin of the metabolic precursors and cofactors required to sustain the high rate of carotenoid biosynthesis in these plastids. Recent proteomic data have revealed a number of biochemical and metabolic processes potentially operating in fruit chromoplasts. However, considering that chloroplast to chromoplast differentiation is a very rapid process during fruit ripening, there is the possibility that some of the proteins identified in the proteomic analysis could represent remnants no longer having a functional role in chromoplasts. Therefore, experimental validation is necessary to prove whether these predicted processes are actually operative in chromoplasts. Results A method has been established for high-yield purification of tomato fruit chromoplasts suitable for metabolic studies. Radiolabeled precursors were efficiently incorporated and further metabolized in isolated chromoplast. Analysis of labeled lipophilic compounds has revealed that lipid biosynthesis is a very efficient process in chromoplasts, while the relatively low incorporation levels found in carotenoids suggest that lipid production may represent a competing pathway for carotenoid biosynthesis. Malate and pyruvate are efficiently converted into acetyl-CoA, in agreement with the active operation of the malic enzyme and the pyruvate dehydrogenase complex in the chromoplast. Our results have also shown that isolated chromoplasts can actively sustain anabolic processes without the exogenous supply of ATP, thus suggesting that these organelles may generate this energetic cofactor in an autonomous way. Conclusions We have set up a method for high yield purification of intact tomato fruit chromoplasts suitable for precursor uptake assays and metabolic analyses. Using targeted radiolabeled precursors we have been able to unravel novel biochemical and metabolic aspects related with carotenoid and lipid biosynthesis in tomato fruit chromoplasts. The reported chromoplast system could represent a valuable platform to address the validation and characterization of functional processes predicted from recent transcriptomic and proteomic data.

DnaSP, DNA polymorphism analyses by the coalescent and other methods

DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (~5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp

Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Auto- and allopolyploidy in Centaurea sect. Acrocentron s.l. (Asteraceae, Cardueae): karyotype and chromosome banding pattern analyses

Dysploidy and polyploidy are well documented in the large genus Centaurea, especially in sect. Acrocentron and in a small group of species from the Iberian Peninsula described as sect. Chamaecyanus, closely related to Acrocentron. We have explored two interesting cases of polyploid series in both sections: the polyploid series of Centaurea toletana in sect. Chamaecyanus and the series of C. ornata group in sect. Acrocentron. We have carried out a karyological study using both classic karyotype analyses and chromosome banding with fluorochromes.

Multimodal Strategies in Development.Predictive Value of early simultaneosgesture-speech comination

The present study investigates the predictive value of the early appearance of simultaneous pointing-speech combinations. An experimental task was used to obtain a communicative productive sample from nineteen children at 1;0 and 1;3. Infant’s communicative productions, in combination with gaze joint engagement patterns, were analyzed in relation to different social conditions. The results show a significant effect of age and social condition on infants’ communicative productions. Gesture-speech combinations seem to work as a strong communicative resource to attract the adult’s attention in social demanding communicative contexts. Gaze joint engagement was used in combination with simultaneous pointing-speech combinations to attract adults’ attention during social demanding conditions. Finally, the use of simultaneous pointing-speech combinations at 1;0 in demanding conditions predicted greater expressive vocabulary acquisition at 1;3 and 1;6. These results indicate that the use of gesture-speech combinations may be considered a significant step towards the early integration of language components.