Expression activation analysis: Exploring the statistics to robustly call activation outliers

Cancer Driver Genes are genes whose mutations can increase cell growth. Oncogenes and Tumor Suppressor Genes are among them. The former are genes that when activated, may cause normal cells to become cancer cells and grow in the body, while the latter are genes that help control cell growth and if mutated, may lead to cancer. Therefore, it is of interest for researchers to detect and call those genes. OUTRIDER, a denoising-autoencoder based method for detecting gene expression outliers in RNA-seq data, was previously developed in the lab. However, OUTRIDER can currently only fit genes that are generally expressed across samples. In cancer, genes that are usually not expressed but become activated in cancer cells can be potential Oncogenes. The aim of this bachelor's thesis has been to try to identify those Oncogenes, as well as the Tumor Suppressor Genes and Cancer Driver Genes in total, from RNA-Seq. Counts from The Cancer Genome Atlas and Mixed-Lineage Leukemia have been used in order to propose two different models. First, a cutoff model, which finds a set of genes that get activated or deactivated in just a small percentage of the samples. Secondly, a z-score model, consisting of getting a set of z-score outliers computed gene-wise

Discurso de contestación al de ingreso en la Academia de D. Antonio Pérez Ramos

Abstract not availabl

Fitato: estudis sobre la seva activitat biològica i els efectes sobre la prevenció de les calcificacions patològiques

En aquesta Tesi Doctoral es pretén seguir aprofundint en l’estudi de l’activitat biològica del fitat, molècula que està demostrant unes inusitades, i fins fa poc desconegudes, propietats com inhibidor del desenvolupament de calcificaciones patològiques. En primer lloc, es presenten tres metodologies analítiques per a la determinació simple y sensible del myo-inositol i del fitat a nivells fisiològics. Posteriorment, es dedica un capítol a l’estudi de l’absorció oral i tòpica del fitat, avaluant després els seus efectes sobre la prevenció de calcificaciones distròfiques subepitelials. Finalment, es demostra que el fitat administrat oralment en una dosi elevada i a llarg termini no provoca problemes de biodisponibilitat i per altra banda, s’estudien els efectes de diferents sals de fitat sobre la disminució de la calciúria, demostrant-se que aquests efectes depenen bàsicament del tipus de sal emprada, essent el fitat potàssic el que provoca una disminució més important del calci urinari.En esta Tesis Doctoral se pretende seguir profundizando en el estudio de la actividad biológica del fitato, molécula que está demostrando unas inusitadas, y hasta hace poco desconocidas, propiedades como inhibidor del desarrollo de calcificaciones patológicas. En primer lugar, se presentan tres metodologías analíticas para la determinación simple y sensible del myo-inositol y del fitato a niveles fisiológicos. Posteriormente, se dedica un capítulo al estudio de la absorción oral y tópica del fitato, evaluando después sus efectos sobre la prevención de calcificaciones distróficas subepiteliales. Finalmente, se demuestra que el fitato administrado oralmente en una dosis elevada y a largo plazo no causa problemas de biodisponibilidad y por otra parte, se estudian los efectos de diferentes sales de fitato sobre la dismunución de la calciuria, demostrándose que éstos dependen básicamente del tipo de sal utilizada, siendo el fitato potásico el que provoca una disminución más importante del calcio urinario.The purpose of this Doctoral Thesis is to complete the knowledge of the biological activity of phytate, which is a molecule that has recently demonstrated unknown properties as an inhibitor of pathological calcifications. First of all, three analytical methodologies are presented for the simple and sensitive determination of myo-inositol and phytate at physiological levels. Next, oral and topic absorption of phytate are studied, evaluating its effects on the prevention of subepithelial dystrophic calcifications. Finally, it is demonstrated in a long-term study that oral phytate at high doses does not provoke bioavailability problems and, on the other hand, the effects of different phytate salts on urinary calcium reduction are studied, being potassium phytate the most effective salt

Projecte bàsic d'aerogenerador flotant de formigó al Golf de Lleó

Projecte bàsic d'aerogenerador offshore sobre estructura flotant de formigó tipus SPAR al Golf de Lleó

Modeling and simulation of an HVDC network for offshore wind farms

En aquest projecte una eina de simulació per a xarxes HVDC que inclouen parcs eòlics marins ha estat programada en funció del seu model analític, descrit anteriorment. El rendiment d’aquest programa es optimitzat posteriorment a través de l’aplicació de diferents mètodes numèrics, modificació de l’estructura algorítmica, o l’ús d’eines d’optimització específiques disponibles amb el programa MATLAB. Els resultats prenen la forma de comparacions entre les opcions disponibles per dur a terme la simulació i conclusions sobre la naturalesa del model matemàtic que es pot extreure d’elles

Evaluation of probabilistic constellation shaping performance in Flex Grid over multicore fiber dynamic optical backbone networks [Invited]

In this paper, we present a worst-case methodology for estimating the attainable spectral efficiency over end-to-end paths across a Flex Grid over multicore fiber (MCF) optical network. This methodology accounts for physical link noise, as well as for the signal-to-noise ratio in the Add module (SNR TX ) of spatial-division-multiplexing-enabled reconfigurable optical add and drop multiplexers (SDM-ROADMs), introducing a dominant noise contribution over that of their Bypass and Drop modules. The proposed methodology is subsequently used to quantify the benefits that probabilistic constellation shaping (PCS) can bring to Flex-Grid/MCF dynamic optical backbone networks, compared to using traditional polarization-multiplexed modulation formats. In a first step, insight is provided into the spectral efficiency attainable along the precomputed end-to-end paths in two reference backbone networks, either using PCS or traditional modulation formats. Moreover, in each one of these networks, two SNR TX values are identified: the SNR TX yielding the maximum average paths’ spectral efficiency, as well as an SNR TX that, although slightly degrading the average paths’ spectral efficiency (by 10%), would yet enable a cost-effective SDM-ROADM Add module implementation. Extensive simulations are conducted to analyze PCS offered load gains under 1% bandwidth blocking probability. Furthermore, the study lastly focuses on finding out whether lower fragmentation levels in Flex-Grid/MCF dynamic optical backbone networks can push PCS benefits even further.Funding: Agencia Estatal de Investigación (PID2020-118011GB-C21, PID2020-118011GB-C22, RED2018-102585-T).Peer ReviewedPostprint (author's final draft