Study of the development and verification of an integrated code for UAV design

L'objectiu d'aquest estudi és desenvolupar una eina de disseny d'aeronaus utilitzant algoritmes d'optimització per a facilitar el procés. Es pretén incorporar el codi d'estudi i simulació de les actuacions d'un UAV desenvolupat per l'equip Trencalòs Team en un software de disseny aerodinàmic ja existent, ja sigui XFLR5 o AVL. Les funcions objectiu incorporades seran les que l'equip considera per a la participació en el concurs internacional Air Cargo Challenge, amb la intenció de desenvolupar una eina de treball per a Trencalòs que permeti fer un disseny òptim dins del marc de la competició. El treball es dividirà en tres etapes: 1. Incorporació del codi desenvolupat per Trencalòs al software de disseny aerodinàmic2. Fer ús dels algoritmes d'optimització de funcions objectiu per a facilitar el procés de disseny3. Verificació els resultats obtinguts.

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample. Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace. Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed

Estructura del genoma

El genoma és una estructura altament dinàmica amb una certa tendència a la inestabilitat, i està, per tant, subjecte a l'escrutini de la selecció natural. En el camí d'entendre el genoma hem pogut observar el paper clau que tenen les repeticions (de tota mena) per comprendre l'evolució estructural del genoma humà i com es relaciona l'estructura i la funció. Així, recentment, hem pogut apreciar que, a part de les variacions clàssiques i els SNP (polimorfismes d'un sol nucleòtid), els mamífers (com a mínim els ratolins i els humans) tenim una estructura dels nostres genomes altament variable. L'estudi de les regions variants en nombre de còpia (structural variants o copy number polymorphism) ens ha permès observar que els canvis en l'estructura tenen repercussió en l'expressió dels gens, que es tradueixen tant en variabilitat fenotípica entre individus com, en casos més extrems, en malalties. En aquest capítol donarem una visió sobre l'estructura i el dinamisme del genoma, centrantnos en aspectes evolutius del polimorfisme humà i la malaltia.Every mammalian genome is an unstable and highly dynamic structure and therefore subjected to the strict evaluation of natural selection. In the last decades, we have changed our vocabulary and we have been using genomics instead of genetics, mainly because of the revolution on our research techniques. In the way of the understanding of the genomes, we realized how important repeats are and their role in the evolution of the structure of the human genome and how this structure and different functions are related. We have seen for instance that besides of the variation caused for SNPs (Single Nucleotide Polymorphism), the mammals (and specifically humans) are highly structural variant. The study of SVs (Structural Variant regions) and CNPs (Copy Number Polymorphisms) has allowed us to see that changes in structure have important consequences, from genomic diseases to simply affecting genes and its expression and hence, being responsible of the huge phenotypical variability observed among individuals. In this chapter, we will give our view on the structure and dynamism of the genome, from an evolutionary point of view, covering human polymorphism and diseases

MLPAstats: An R GUI package for the integrated analysis of copy number alterations using MLPA data

<p>Abstract</p> <p>Background</p> <p>Multiplex-Dependent Probe Amplification (MLPA) is a cost-effective experimental method for candidate gene studies, aimed at the identification of copy number alterations. The analysis of such genetic variants, from electropherogram peak intensities, involves two main stages. First, peak normalization for each probe is required to remove the contribution of probe size to peak intensity. Second, the statistical significance of peak alteration between case and control samples is estimated. A number of methods have been proposed in each step with varying levels of complexity and precision. However, there is no single framework from which the results of each method and possible combinations at each step can be assessed.</p> <p>Results</p> <p>We present <monospace>MLPAstats</monospace>, an <monospace>R</monospace> package designed to integrate the methods for exploring different analysis scenarios in a reliable way. A GUI has been developed to allow researchers to find their optimal analysis strategy.</p> <p>Conclusions</p> <p><monospace>MLPAstats</monospace> is an analysis tool that promotes the use of cost-effective MLPA suitable for candidate gene studies. Its <monospace>R</monospace> implementation allows future methods to be easily incorporated, while its GUI will facilitate its use by non-expert analysts. A vignette describing a set-by-step tutorial is also available with the package.</p