A generalized mechanistic codon model.

Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models.

Ultramarathon is an outstanding model for the study of adaptive responses to extreme load and stress.

ABSTRACT: Ultramarathons comprise any sporting event involving running longer than the traditional marathon length of 42.195 km (26.2 miles). Studies on ultramarathon participants can investigate the acute consequences of ultra-endurance exercise on inflammation and cardiovascular or renal consequences, as well as endocrine/energetic aspects, and examine the tissue recovery process over several days of extreme physical load. In a study published in BMC Medicine, Schütz et al. followed 44 ultramarathon runners over 4,487 km from South Italy to North Cape, Norway (the Trans Europe Foot Race 2009) and recorded daily sets of data from magnetic resonance imaging, psychometric, body composition and biological measurements. The findings will allow us to better understand the timecourse of degeneration/regeneration of some lower leg tissues such as knee joint cartilage, to differentiate running-induced from age-induced pathologies (for example, retropatelar arthritis) and finally to assess the interindividual susceptibility to injuries. Moreover, it will also provide new information about the complex interplay between cerebral adaptations/alterations and hormonal influences resulting from endurance exercise and provide data on the dose-response relationship between exercise and brain structure/function. Overall, this study represents a unique attempt to investigate the limits of the adaptive response of human bodies.Please see related article: http://www.biomedcentral.com/1741-7015/10/78.

CO2 emissions embodied in international trade: A multiregional Inputoutput model for Spain

As a result of globalization and free trade agreements, international trade is enormously growing and inevitably putting more pressure on the environment over the last few decades. This has drawn the attention of both environmentalist and economist in response to the ever growing concerns of climate change and urgent need of international action for its mitigation. In this work we aim at analyzing the implication of international trade in terms of CO2 between Spain and its important partners using a multi-regional input-output (MRIO) model. A fully integrated 13 regions MRIO model is constructed to examine the pollution responsibility of Spain both from production and consumption perspectives. The empirical results show that Spain is a net importer of CO2 emissions which is equivalent to 29% of its emission due to production. Even though the leading partner with regard to import values are countries such as Germany, France, Italy and Great Britain, the CO2 embodied due to trade with China takes the largest share. This is mainly due to the importation of energy intensive products from China coupled with Chinese poor energy mix which is dominated by coal-power plant. The largest portion (67%) of the global imported CO2 emissions is due to intermediate demand requirements by production sectors. Products such as Motor vehicles, chemicals, a variety of machineries and equipments, textile and leather products, construction materials are the key imports that drive the emissions due to their production in the respective exporting countries. Being at its peak in 2005, the Construction sector is the most responsible activity behind both domestic and imported emissions.

Determining the best population-level alcohol consumption model and its impact on estimates of alcohol-attributable harms.

BACKGROUND: The goals of our study are to determine the most appropriate model for alcohol consumption as an exposure for burden of disease, to analyze the effect of the chosen alcohol consumption distribution on the estimation of the alcohol Population- Attributable Fractions (PAFs), and to characterize the chosen alcohol consumption distribution by exploring if there is a global relationship within the distribution. METHODS: To identify the best model, the Log-Normal, Gamma, and Weibull prevalence distributions were examined using data from 41 surveys from Gender, Alcohol and Culture: An International Study (GENACIS) and from the European Comparative Alcohol Study. To assess the effect of these distributions on the estimated alcohol PAFs, we calculated the alcohol PAF for diabetes, breast cancer, and pancreatitis using the three above-named distributions and using the more traditional approach based on categories. The relationship between the mean and the standard deviation from the Gamma distribution was estimated using data from 851 datasets for 66 countries from GENACIS and from the STEPwise approach to Surveillance from the World Health Organization. RESULTS: The Log-Normal distribution provided a poor fit for the survey data, with Gamma and Weibull distributions providing better fits. Additionally, our analyses showed that there were no marked differences for the alcohol PAF estimates based on the Gamma or Weibull distributions compared to PAFs based on categorical alcohol consumption estimates. The standard deviation of the alcohol distribution was highly dependent on the mean, with a unit increase in alcohol consumption associated with a unit increase in the mean of 1.258 (95% CI: 1.223 to 1.293) (R2 = 0.9207) for women and 1.171 (95% CI: 1.144 to 1.197) (R2 = 0. 9474) for men. CONCLUSIONS: Although the Gamma distribution and the Weibull distribution provided similar results, the Gamma distribution is recommended to model alcohol consumption from population surveys due to its fit, flexibility, and the ease with which it can be modified. The results showed that a large degree of variance of the standard deviation of the alcohol consumption Gamma distribution was explained by the mean alcohol consumption, allowing for alcohol consumption to be modeled through a Gamma distribution using only average consumption.

Multi-scale label interaction to improve object detection and segmentation

The project aims at advancing the state of the art in the use of context information for classification of image and video data. The use of context in the classification of images has been showed of great importance to improve the performance of actual object recognition systems. In our project we proposed the concept of Multi-scale Feature Labels as a general and compact method to exploit the local and global context. The feature extraction from the discriminative probability or classification confidence label field is of great novelty. Moreover the use of a multi-scale representation of the feature labels lead to a compact and efficient description of the context. The goal of the project has been also to provide a general-purpose method and prove its suitability in different image/video analysis problem. The two-year project generated 5 journal publications (plus 2 under submission), 10 conference publications (plus 2 under submission) and one patent (plus 1 pending). Of these publications, a relevant number make use of the main result of this project to improve the results in detection and/or segmentation of objects.

Does T Helper Differentiation Correlate with Resistance or Susceptibility to Infection with L. major? Some Insights From the Murine Model.

The murine model of Leishmania major infection has been an invaluable tool in understanding T helper differentiation in vivo. The initial evidence for a role of distinct CD4(+) T helper subsets in the outcome of infection was first obtained with this experimental model. The development of CD4(+) Th1 cells was associated with resolution of the lesion, control of parasite replication, and resistance to re-infection in most of the mouse strains investigated (i.e., C57BL/6). In contrast, differentiation of CD4(+) Th2 cells correlated with the development of unhealing lesions, and failure to control parasite load in a few strains (i.e., BALB/c). Since these first reports, an incredible amount of effort has been devoted to understanding the various parameters involved in the differentiation of these, and more recently discovered T helper subsets such as Th17 and T regulatory cells. The discovery of cross-talk between T helper subsets, as well as their plasticity force us to reevaluate the events driving a protective/deleterious T helper immune response following infection with L. major in mice. In this review, we describe the individual contributions of each of these CD4(+) T helper subsets following L. major inoculation, emphasizing recent advances in the field, such as the impact of different substrains of L. major on the pathogenesis of disease.

SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

CodeML (part of the PAML package) im- plements a maximum likelihood-based approach to de- tect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses.

Union activism in an inclusive model of industrial relations : evidence from an Spanish case

In this article we analyze the reasons, within the context of Spanish industrial relations, for trade union members’ active participation in their regional union. The case of Spain is particularly interesting as the unions’ main activity, collective bargaining, is a public good. The text, based on research involving a representative survey of members of a regional branch of the “Workers” Commissions” (Comisiones Obreras) trade union, provides empirical evidence that the union presence in the workplace has a significant influence on members’ propensity for activism. By contrast, the alternative hypothesis based on instrumental reasons appears of little relevance in the Spanish industrial relations context.

Kyrie eleison [VIII] : 13 °Centenaire de St. Grégoire Magno : chant grégorien d'aprés la 2e édition de Solesmes / [Dom Antonio] Rella, chef de choeur

[Chant grégorien. Messe]

Excuse me, but your accent is very unusual. The complexity of establishing third languages in Inglourious Basterds. Applying a model of translation analysis to dubbing

The growing multilingual trend in movie production comes with a challenge for dubbing translators since they are increasingly confronted with more than one source language. The main purpose of this master’s thesis is to provide a case study on how these third languages (see CORRIUS and ZABALBEASCOA 2011) are rendered. Another aim is to put a particular focus on their textual and narrative functions and detect possible shifts that might occur in translations. By applying a theoretical model for translation analysis (CORRIUS and ZABALBEASCOA 2011), this study describes how third languages are rendered in the German, Spanish, and Italian dubbed versions of the 2009 Tarantino movie Inglourious Basterds. A broad range of solution-types are thereby revealed and prevalent restrictions of the translation process identified. The target texts are brought in context with some sociohistorical aspects of dubbing in order to detect prevalent norms of the respective cultures andto discuss the acceptability of translations (TOURY 1995). The translatability potential of even highly complex multilingual audiovisual texts is demonstrated in this study. Moreover, proposals for further studies in multilingual audiovisual translation are outlined and the potential for future investigations in this field thereby emphasised.

El documental multimèdia interactiu: una proposta de model d'anàlisi

El propòsit d‘aquest treball de recerca és l‘estudi del procés actual de convergència entre el gènere documental tradicional i el gènere documental interactiu en línia. Pretenem examinar com les noves tecnologies digitals transformen les lògiques de creació i de producció del documental audiovisual convencional. Volem presentar un primer estat de la qüestió sobre les línies de confluència entre els dos àmbits, argumentar una proposta de definició i de caracterització del nou gènere interactiu i avançar unes propostes de model d‘anàlisi del documental multimèdia interactiu, que serà objecte de fonamentació i d‘aplicació en la futura tesi doctoral

Classificació de sons percussius amb un model generatiu

El treball que presentem a continuació desenvolupa un marc teòric i pràctic per a l'avaluació i estudi d'un model generatiu aplicat a tasques discriminatives de senyals sonores sense component harmònica. El model generatiu està basat en la construcció de l'anomenada deep belief network, un tipus de xarxa neuronal generativa que permet realitzar tasques de classificació i regressió com també de reconstrucció dels seus estats interns.A partir de l'anàlisi realitzada hem pogut obtenir resultats en classificació aparellats amb els resultats de l'estat de l'art de classificadors de sons inharmònics. Tot i no establir una clara superioritat envers altres mètodes, el present treball ha permés desenvolupar una anàlisi per almodel avaluat amb moltes possibilitats de millora en un futur per altres treballs. Al llarg del treball es demostra la seva eficàcia en tasques discriminatives, com també la capacitat de reduir la dimensionalitat de les dades d'entrada al model i les possibilitats de reconstruir els seus estats interns per a obtenir unes sortides de dades de la xarxa similars a les entrades de descriptors.El desenvolupament centrat en la deep belief network ens ha permés construir un entorn unificat d'avaluació de diferents mètodes d'aprenentatge, construcció i adequació de diferents descriptors sonors i una posterior visualització d'estats interns del mateix, que han possibilitat una avaluaciócomparativa i unificada respecte altres mètodes classificadors de l'estat de l'art. També ens ha permés desenvolupar una implementació en un llenguatge d'alt nivell, que ha reportat més significància per a l'enteniment i anàlisi del model avaluat, amb una argumentació més sòlida.Els resultats i l'anàlisi que reportem són significatius i positius per al model avaluat, i degut a la poca literatura existent en el camp de classificació de sons inharmònics com els sons percussius,creiem que és una aportació interessant i significativa per al camp en el que s'engloba el treball.

Derivats financers al mercat espanyol: el Model de Black-Scholes i corbes de volatilitat per opcions sobre l'índex niniIBEX-35

El nostre treball es centrarà en conèixer i aprendre les nocions bàsiques del mercat financer espanyol, primer; i aplicar uns coneixements per veure si es verifica unahipòtesi plantejada, després. La incògnita que volem resoldre és la següent: comprovarsi tots els supòsits i resultats que faciliten els models teòrics emprats en l’estudi dels mercats financers a l’hora de la veritat es compleixen.D’entre els múltiples conceptes que ens proporcionen els estudis de mercatsfinancers ens centrarem sobretot en el model de Black-Scholes i els somriures devolatilitat per desenvolupar el nostre treball. Després de cercar les dades necessàries a través de la web del M.E.F.F., entrevistar-nos amb professionals del sector i fer un seguiment d’aproximadament dos mesos dels moviments de les opcions sobre l’Índex Mini-Íbex 35, amb l’ajuda d’un programa informàtic en llenguatge C, hem calculat les corbes de volatilitat de les opcions sobre l’Índex Mini-Íbex 35.Les conclusions més importants que hem extret són que el Model de Black-Scholes, malgrat va revolucionar el món dels mercats financers, està basat en 2 supòsits que no es compleixen a la realitat: la distribució lognormal del preu de les accions i unavolatilitat constant. Tal i com hem pogut comprovar, la corba de volatilitat de lesopcions sobre l’Índex Mini-Íbex 35 és decreixent amb el preu d’exercici i laMoneyness, tal i com sostenen les teories dels somriures de volatilitat; per tant, no és constant. A més, hem comprovat que a mesura que s’apropa el venciment d’una opció,el preu acordat de l’actiu subjacent a l’opció s’apropa al preu de mercat.