GPU acceleration of Levenshtein distance computation between long strings

Altres ajuts: acords transformatius de la UABComputing edit distance for very long strings has been hampered by quadratic time complexity with respect to string length. The WFA algorithm reduces the time complexity to a quadratic factor with respect to the edit distance between the strings. This work presents a GPU implementation of the WFA algorithm and a new optimization that can halve the elements to be computed, providing additional performance gains. The implementation allows to address the computation of the edit distance between strings having hundreds of millions of characters. The performance of the algorithm depends on the similarity between the strings. For strings longer than million characters, the performance is the best ever reported, which is above TCUPS for strings with similarities greater than 70% and above one hundred TCUPS for 99.9% similarity

GPU acceleration of Levenshtein distance computation between long strings

Computing edit distance for very long strings has been hampered by quadratic time complexity with respect to string length. The WFA algorithm reduces the time complexity to a quadratic factor with respect to the edit distance between the strings. This work presents a GPU implementation of the WFA algorithm and a new optimization that can halve the elements to be computed, providing additional performance gains. The implementation allows to address the computation of the edit distance between strings having hundreds of millions of characters. The performance of the algorithm depends on the similarity between the strings. For strings longer than million characters, the performance is the best ever reported, which is above TCUPS for strings with similarities greater than 70% and above one hundred TCUPS for 99.9% similarity.This research was supported by the European Union Regional Development Fund (ERDF) within the framework of the ERDF Operational Program of Catalonia 2014–2020 with a grant of 50% of the total cost eligible under the Designing RISC-V based Accelerators for next generation computers project (DRAC) [001-P-001723], in part by the Catalan Government under grant 2017-SGR-1624, and in part by the Spanish Ministry of Science, Innovation and Universities under grant RTI2018-095209-B-C22.Peer ReviewedPostprint (published version

Simple real-time QRS detector with the MaMeMi filter

AbstractDetection of QRS complexes in ECG signals is required to determine heart rate, and it is an important step in the study of cardiac disorders. ECG signals are usually affected by noise of low and high frequency. To improve the accuracy of QRS detectors several methods have been proposed to filter out the noise and detect the characteristic pattern of QRS complex. Most of the existing methods are at a disadvantage from relatively high computational complexity or high resource needs making them less optimized for its implementation on portable embedded systems, wearable devices or ultra-low power chips. We present a new method to detect the QRS signal in a simple way with minimal computational cost and resource needs using a novel non-linear filter

Deorphanization of receptors: Applying screening techniques to two orphan GPCRs

Trabalho Final de Mestrado Integrado, Ciências Farmacêuticas, Universidade de Lisboa, Faculdade de Farmácia, 2019Os recetores acoplados à proteína G representam uma das maiores famílias de recetores de superfície e uma das maiores fontes de alvos terapêuticos atualmente. No entanto, uma grande percentagem destes recetores não estão adequadamente caraterizados ou são classificados enquanto recetores órfãos. Ensaios farmacológicos como o ensaio de recrutamento da β-arrestina constituem uma das abordagens possíveis para desorfanizar recetores. Neste trabalho, apliquei o sistema de ensaio farmacológico que mencionei anteriormente a dois recetores: GPR37 e MRGPRX3. O GPR37 tem sido principalmente associado a uma apresentação de início precoce de Parkinson. Esta associação deve-se aos seus padrões de expressão no organismo e ao seu papel enquanto substrato da ubiquitina E3, parkin. Não foi ainda possível determinar um ligando para este recetor que seja universalmente aceite. Dois compostos foram propostos, porém foram recebidos com controvérsia na comunidade científica, tendo surgido estudos tanto a apoiar, como a descredibilizar esta reivindicação. A sua associação com Parkinsonismo Juvenil torna este recetor um alvo farmacológico muito atrativo, pelo que a sua desorfanização se tem tornado um objetivo importante na área. A literatura disponível relativamente ao MRGPRX3 é consideravelmente mais diminuta. Embora a família em que se insere, recetores acoplados à proteína G relacionados com o gene Mas, seja amplamente estudada, este recetor, com expressão exclusiva em mamíferos, continua a apresentar-se como um mistério. As únicas pistas relativamente a um possível papel fisiológico ou fisiopatológico são a sua expressão no organismo. É especulado que, de forma semelhante a outros recetores da sua família, o MRGPRX3 esteja envolvido em processos de sinalização da via da dor e/ou prurido. Debruçar-me-ei sobre a triagem de compostos nestes recetores. A abordagem relativamente aos compostos a testar foi delineada com base numa revisão da literatura e com base na informação que tínhamos disponível. O objetivo deste trabalho seria a identificação de um composto que produzisse ativação do recetor e que nos permitisse retirar algumas pistas, em termos de estrutura, de qual poderá ser o ligando endógeno destes recetores.G-Protein Coupled Receptors represent one of the largest families of cellular receptors discovered and one of the main sources of attractive drug targets. In contrast, it also has a large number of understudied or orphan receptors. Pharmacological assays such as β-Arrestin recruitment assays, are one of the possible approaches for deorphanization of receptors. In this work, I applied the assay system previously mentioned to screen compounds in two orphan receptors, GRP37 and MRGPRX3. GPR37 has been primarily associated with a form of early onset Parkinsonism due to its’ expression patterns, and physiological role as substrate to ubiquitin E3, parkin. Although extensive literature regarding this receptor is available, the identification of a universally recognized ligand has not yet been possible. Two compounds were proposed as ligands, but both were met with controversy. These receptor association with Autosomal Recessive Juvenile Parkinson positions it as a very attractive drug target, and as such its’ deorphanization is a prime objective for investigators in this area. Regarding MRGPRX3 information is much scarcer. Although it is part of a well-studied family, Mas Related G-Protein Receptors, this gene, found only in mammalian genome, remains elusive. Its’ expression patterns are the only indicators of a possible physiological or pathophysiological role. Similarly to other receptors of the same family, MRGPRX3 is though to be involved in the pain and/or itch pathway, but no factual evidence of said involvement has been presented yet. Here I will focus on compounds’ screening on these receptors. The approach we used was directed for each of them and based on literature revision and on the information we had available at the time. We hoped to find a compound that produces activation of the receptors in order to allow us to withdraw some structure related clues for what the endogenous ligand of these receptors might be.Rheinische Friedrich-Wilhelms-Universität Bonn; Farmácia Pimpão; Hospital Cuf Descoberta

Characterization of the degradation behaviour of Passive Fire Protector materials

Passive Fire Protection (PFP) is used to protect industrial equipment against accidental fires, delaying the temperature rise and the loss of mechanical properties of the structural materials. If properly applied, this may prevent failures, losses of containment and accident escalation phenomena. In this way the adoption of FPF represents an important safety measure to prevent "serious danger to human health and/or the environment" as required by the Seveso Directives for major hazard installations. Some PFP materials (e.g. epoxy intumescent coatings) may undergo significant degradation during fire exposure, accompained by devolatilization and variation of their physical properties. Modelling the performance of PFP materials would require a through investigation of the degradation behaviour. In the present work, the degradation of commercial PFP materials exposed to high temperatures will be analyzed using Thermo-Gravimetric (TG) techniques. The significant decomposition steps will be identified and apparent kinetic models will be developed for the description of the weight loss behaviour.Outgoin

Diseño y cálculo de sistemas de climatización para salas estériles de cosmética

Este proyecto consiste en el diseño y cálculo de un sistema de climatización para salas limpias de productos farmacéuticos en una fábrica ubicada en Puçol, Valencia. Las salas limpias, también denominadas salas blancas, son locales en los que prima un nivel de contaminación bajo. La fábrica de Sesderma en Puçol está destinada a la elaboración de productos cosméticos y complementos alimenticios. Se estudiarán las salas en la planta primera que estarán compuestas por varias salas de fabricación, laboratorios y zonas de almacenamiento. El objetivo final es el dimensionamiento de todos los elementos involucrados en la climatización de dichas salas para mantener ciertas condiciones en el ambiente. Para realizar este proyecto se deben tener en cuenta las condiciones interiores y exteriores, es decir, los factores que puedan afectar a las salas. Encontramos un total de 55 salas, en 7 zonas distintas, que requerirán sistemas independientes de climatización, es decir, 7 climatizadores cada uno con dos circuitos separados, uno de impulsión y otro de retorno. Los cálculos para un correcto dimensionamiento están divididos en varios pasos. Primero, se deben estimar las cargas térmicas para después poder calcular los caudales. Más tarde se hará el dimensionamiento de los conductos y otros elementos que aportarán una pérdida de carga para poder finalmente dimensionar los climatizadores. Por último, se incluirá un pliego de condiciones, un presupuesto y un cronograma de obra.Ingeniería Mecánic