Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Modeling sequencing errors by combining Hidden Markov models.

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Cracking the BAFF code.

The tumour necrosis factor (TNF) family members B cell activating factor (BAFF) and APRIL (a proliferation-inducing ligand) are crucial survival factors for peripheral B cells. An excess of BAFF leads to the development of autoimmune disorders in animal models, and high levels of BAFF have been detected in the serum of patients with various autoimmune conditions. In this Review, we consider the possibility that in mice autoimmunity induced by BAFF is linked to T cell-independent B cell activation rather than to a severe breakdown of B cell tolerance. We also outline the mechanisms of BAFF signalling, the impact of ligand oligomerization on receptor activation and the progress of BAFF-depleting agents in the clinical setting.

Trans-Atlantic Pedagogy for Teaching Pre-Service Teachers ICT: Bringing forward cultural issues

Projecte de recerca elaborat a partir d’una estada a la Universitat de Toronto, Canadà, des d’octubre del 2006 a febrer del 2007. El projecte Barchito és un projecte Interrnacional que va involucrar tres universitats: La Universitat Autònoma de Barcelona, la Universitat de Toronto (Canadà) i la Universitat de Roosevelt (USA). El seu objectiu principal era posar en contacte estudiants de les tres universitats (de tres cursos diferents) per discutir al voltant de temes com ara l'ensenyament/aprenentatge i elements culturals de cada país. Aquest projecte presenta la natura de l'experiència des de la visió dels participants: alumnat i professorat. Superant diferències inicials de llengua, els participants van aprendre d'altra cultura, van aprendre sobre altres maneres d'ensenyar i van aprendre, en definitiva, sobre ells mateixos. L'eina d'aprenentatge col.laboratiu els va ajudar a sobrepassar el context immediat, emprant per això, l'eina tecnològica anomenada: Knowledge Forum.

Cooperative strategies for imperfect CSI scenarios based on distributed Alamouti

Les comunicacions cooperatives estan guanyant un gran interès en les comunicacions modernes degut a que permeten millorar la transmissió dʼinformació entre un emissor i un receptor utilitzant una sèrie de terminals situats entre ells. Aquest projecte és un estudi complet del sistemes cooperatius, analitzant el seu rendiment i comparant lʼús dʼun sol dʼaquests terminals amb lʼús del codi Alamouti, que utilitza dos terminals. Primer hi ha una introducció als sistemes cooperatius i a la teoria de la informació. Després hem estudiat un sistema cooperatiu amb la teoria de la informació com a base, en termes de probabilitat de fallada del sistema, i posteriorment lʼhem adaptat a un sistema cooperatiu real utilitzant una modulació QPSK, estudiant la seva probabilitat dʼerror de paquet. Finalment es proposen diversos protocols que permeten millorar el rendiment del sistema cooperatiu estudiat.

Stochastic Search Variable Selection in Vector Error Correction Models with an Application to a Model of the UK Macroeconomy

This paper develops methods for Stochastic Search Variable Selection (currently popular with regression and Vector Autoregressive models) for Vector Error Correction models where there are many possible restrictions on the cointegration space. We show how this allows the researcher to begin with a single unrestricted model and either do model selection or model averaging in an automatic and computationally efficient manner. We apply our methods to a large UK macroeconomic model.

Le code-switching comme ressource stratégique pour la gestion de l'interaction multilingue : coordination et leadership dans un groupe de travail

In this article, we analyze a multilingual interaction in a students' working group and hypothesize a correlation between management of languages in interaction and leadership. We consider Codeswitching as one of the most relevant observables in multilingual interaction and attempt to analyze how it is used by speakers. After a brief presentation of three theoretical and analytical conceptions of Code-switching in interaction (Auer, Mondada & Myers Scotton), we define Code-switching as an interactional, strategical, multilingual resource exploited by speakers to achieve various interactionaland non interactional goals. We then show in two CA-like analysis how multilingual strategical resources occur in the interactional practices of the analyzed working group, and how they are exploited by speakers in order to organize interaction, work, tasks, and to construct one's leadership.We also consider the metadiscourses of the students about their own practices and multilingualism in general, in order to confront them to their actual multilingual practices. We draw the hypothesis that discrepancies observed between metadiscourses and practices can be explained through the development of (meta)discourses showing a unilingual conception in describing multilingual practices.

Forward Looking and Myopic Regional Computable General Equilibrium Models. How Significant is the Distinction?

We present a stylized intertemporal forward-looking model able that accommodates key regional economic features, an area where the literature is not well developed. The main difference, from the standard applications, is the role of saving and its implication for the balance of payments. Though maintaining dynamic forward-looking behaviour for agents, the rate of private saving is exogenously determined and so no neoclassical financial adjustment is needed. Also, we focus on the similarities and the differences between myopic and forward-looking models, highlighting the divergences among the main adjustment equations and the resulting simulation outcomes.

The Forward Premium Puzzle and The Euro

This paper evaluates the forward premium puzzle using the Euro exchange rate. Unlike previous studies, our analysis utilizes time-varying parameter methods and is based on two approaches for evaluation of the puzzle; the traditional approach analyzing the sensitivity of interest rate differentials to the forward premium, and the other looking into deviations from the covered interest rate parity (CIRP) condition. Then we provide evidence that the forward premium puzzle indeed became more prominent around the time of the recent crisis periods such as the Lehman Shock and the Euro crisis. This is also shown to be consistent with a deterioration in the CIRP.

Ampliació i millora d'un vehicle teledirigit

En el projecte Ampliació i millora d’un vehicle teledirigit s’ha dut a terme l’ampliació d’un prototip de vehicle ràdio controlat fent servir dues plaques Arduino Duemilanove. Una es situa en el comandament i l’altra en el vehicle i controlen el comportament dels dos dispositius. Es transmet la informació necessària entre elles a través de dos mòduls XBee que posteriorment se’ls hi incorpora. Les plaques fetes servir en el prototip inicial eren unes SARD-13192 de Freescale i el primer que es fa en aquest sentit és una revisió del codi font utilitzat i l’adaptació a les plaques Arduino. Un acceleròmetre ADXL335 que s’incorpora a una de les plaques permet que el prototip es pugui controlar segons la posició del comandament. A més, un cop finalitzat el nou prototip és capaç de desplaçar-se endavant i endarrere, girar aturat i en moviment, i a diferents velocitats que es representen en tot moment en uns LEDs. També guarda l’últim circuit efectuat que es pot reproduir a voluntat de l’usuari, i emmagatzema les dades del recorregut de tota una sessió per exportar a l’ordinador. Per últim s’han dut a terme les proves necessàries per constatar que totes les millores s’han implementat amb èxit.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Phylogenetic Code in the Cloud - Can it Meet the Expectations?

Cloud computing has recently become very popular, and several bioinformatics applications exist already in that domain. The aim of this article is to analyse a current cloud system with respect to usability, benchmark its performance and compare its user friendliness with a conventional cluster job submission system. Given the current hype on the theme, user expectations are rather high, but current results show that neither the price/performance ratio nor the usage model is very satisfactory for large-scale embarrassingly parallel applications. However, for small to medium scale applications that require CPU time at certain peak times the cloud is a suitable alternative.

IPH Response to Dept of Justice and Equality Review of the Code of Practice on the Sale and Display of Alcohol in Mixed Trading Premises

IPH responded to the Department of Justice, Equality and Defence review of the voluntary Code of Practice for the display and sale of alcohol in supermarkets, convenience stores and similar mixed trading outlets. The voluntary Code was introduced in 2008 as an alternative to the statutory rules for structural separation of alcohol products in mixed trading outlets which are set out in section 9 of the Intoxicating Liquor Act 2008. Interested bodies and individuals were invited to submit comments on the Compliance Report for 2011 and on the effectiveness of the voluntary approach to structural separation by 20th December 2011. The Minister said he intended to also seek the views of the Minister for Health and the Joint Oireachtas Committee on Justice, Defence and Equality before reaching any decision on whether to bring the statutory rules in the 2008 Act into operation.