Establishment of a fully automatized microfluidic platform for the screening and characterization of novel Hepatitis B virus capsid assembly modulators

El procés de descobriment de fàrmacs s'enfronta a importants desafiaments a causa de la constant disminució dels guanys per medicament atesa la disminució en les noves aprovacions de la FDA combinada amb el constant augment dels costos i el temps de desenvolupament. Les plataformes integrades de detecció usant microfluídica van sorgir com a possibles solucions per accelerar el desenvolupament de molècules actives i reduir els requisits de temps i costos. El projecte VIRO-FLOW té com a objectiu identificar nous agents curatius per al virus de l'hepatitis B (VHB), integrant els avantatges de la química de flux continu amb tecnologies de bioassaigs in vitro en microfluídica. Durant aquesta tesi es va construir un sistema microfluídic aplicant dispositius modulars automatitzats. Es van redactar protocols d'avaluació per a les dades de fluorescència i reflexió, permetent el càlcul del factor Z, les desviacions estàndard, les corbes de dilució i els valors de concentracions efectives mitjanes màximes (EC50). La proteïna central del VHB (HBc) es va seleccionar com a objectiu principalEl proceso de descubrimiento de fármacos se enfrenta a importantes desafíos debido a la constante disminución de las ganancias por medicamento dada la disminución en las nuevas aprobaciones de la FDA combinada con el constante aumento de los costes y el tiempo de desarrollo. Las plataformas integradas de detección usando microfluídica surgieron como posibles soluciones para acelerar el desarrollo de moléculas activas y reducir los requisitos de tiempo y costes. El proyecto VIRO-FLOW tiene como objetivo la identificación de nuevos agentes curativos para el virus de la hepatitis B (VHB), integrando las ventajas de la química de flujo continuo con tecnologías de bioensayos in vitro en microfluídica. Durante la presente tesis se construyó un sistema microfluídico aplicando dispositivos modulares automatizados. Se redactaron protocolos de evaluación para los datos de fluorescencia y reflexión, permitiendo el cálculo del factor Z, desviaciones estándar, curvas de dilución y valores de concentraciones efectivas medias máximas (EC50). La proteína central del VHB (HBc) se seleccionó como objetivo principal.Drug Discovery as known today faces major challenges due to the constant decrease of earnings per drug given the decrease in new FDA approvements combined with the steadily rising development costs and time. Integrated microfluidic screening platforms emerged as possible solutions by accelerating the hit-to-lead development cycle and reducing time and cost requirements. The VIRO-FLOW project aims at the fast and efficient identification of novel curative agents for the Hepatitis B Virus (HBV), integrating the advantages of continuous flow chemistry with in vitro microfluidic bioassay technologies. During the present thesis a microfluidic system was built, applying automatized modular devices. Evaluation protocols were written for the fluorescence and reflection data, allowing the Z´-factor calculation, standard deviations, dilution curves, and half‐maximal effective concentrations (EC50) values. HBV core protein (HBc) was selected as primary target due to the ongoing demand for a functional cure to reduce the economic and social challenges imposed by the chronic diseas

Accelerating legacy applications with spatial computing devices

Heterogeneous computing is the major driving factor in designing new energy-efficient high-performance computing systems. Despite the broad adoption of GPUs and other specialized architectures, the interest in spatial architectures like field-programmable gate arrays (FPGAs) has grown. While combining high performance, low power consumption and high adaptability constitute an advantage, these devices still suffer from a weak software ecosystem, which forces application developers to use tools requiring deep knowledge of the underlying system, often leaving legacy code (e.g., Fortran applications) unsupported. By realizing this, we describe a methodology for porting Fortran (legacy) code on modern FPGA architectures, with the target of preserving performance/power ratios. Aimed as an experience report, we considered an industrial computational fluid dynamics application to demonstrate that our methodology produces synthesizable OpenCL codes targeting Intel Arria10 and Stratix10 devices. Although performance gain is not far beyond that of the original CPU code (we obtained a relative speedup of x 0.59 and x 0.63, respectively, for a single optimized main kernel, while only on the Stratix10 we achieved x 2.56 by replicating the main optimized kernel 4 times), our results are quite encouraging to drawn the path for further investigations. This paper also reports some major criticalities in porting Fortran code on FPGA architectures

Optimization of the methodology of configuration of mobile communication networks

The mobile communication network has been growing quickly, and the mobile network maintenance is becoming more complex, in performance, network coverage, energy, time consuming and expensive. The telecommunication service provider and mobile network telecommunication operator worries to what is the better methodology to optimizing a mobile network configuration and to improve the most efficient operation and functionality, to increase a superior performance in technical aspect (Create, and integrate new network planning in hardware and software level), economic aspect (cost reduction in maintenance) and environmental aspect (use of renewable energy through solar panels or wind power system). The work developed in this dissertation aims to propose an optimization of methodology of configuration of mobile communication network and build an automated configuration system in different technology (GSM, UMTS and LTE) to provide a good quality and improvement in its architecture to meet the requirement for a large number of services or application through distinct means transmission and using technology appropriate with a new generation of hardware to reach certain area in a Base Station Transmition (BTS) and a Radio Network Controller (RNC) that permit configure and integrated hardware and software issues in distinct networks technology (GSM, UMTS and LTE).A rede de comunicação móvel tem crescido rapidamente e ficando cada vez mais complexa, sendo cada vez mais complicado melhorar o desempenho, a cobertura, a eficiência energética e ao mesmo tempo aumentar o numero de utilizadores e serviços. O provedor de serviços de telecomunicações e a operadora de rede móvel têm de se preocupar em optimizar de forma a garantir a melhor configuração de rede móvel tendo em vista melhorar a operação e funcionalidade, a fim de esta ser mais eficiente, no seu desempenho. Relativamente aos aspectos técnicos (Criar novo planeamento e integrar a uma rede ao nível hardware e de software), aspecto econômico (redução de custo na manutenção) e aspecto ambiental (uso de energia renovável, quer através de painéis solares como de sistemas eólicos). O trabalho desenvolvido nesta dissertação visa propor uma otimização da metodologia de configuração das redes de comunicação móveis e construir um sistema de configuração automatizado em diferentes tecnologias (GSM, UMTS e LTE), para garantir os mais altos padrões de qualidade e atender a exigência de um grande número de serviços ou aplicações através de diferentes meios de transmissão e uso de tecnologia apropriada com uma nova geração de hardware para atingir determinada área em uma Estação de Transmissão de Base (BTS) e numa Rede de Controlador de Rádio (RNC) que permitem configurar e integrar diversos tipos de hardware e software em tecnologia de diferentes redes (GSM, UMTS e LTE)

Toward Fault-Tolerant Applications on Reconfigurable Systems-on-Chip

L'abstract è presente nell'allegato / the abstract is in the attachmen

xploring Genetic Interactions: from Tools Development with Massive Parallelization on GPGPU to Multi-Phenotype Studies on Dyslexia

Over a decade, genome-wide association studies (GWASs) have provided insightful information into the genetic architecture of complex traits. However, the variants found by GWASs explain just a small portion of heritability. Meanwhile, as large scale GWASs and meta-analyses of multiple phenotypes are becoming increasingly common, there is a need to develop computationally efficient models/tools for multi-locus studies and multi-phenotype studies. Thus, we were motivated to focus on the development of tools serving for epistatic studies and to seek for analysis strategy jointly analyzed multiple phenotypes. By exploiting the technical and methodological progress, we developed three R packages. SimPhe was built based on the Cockerham epistasis model to simulate (multiple correlated) phenotype(s) with epistatic effects. Another two packages, episcan and gpuEpiScan, simplified the calculation of EPIBALSTER and epiHSIC and were implemented with high performance, especially the package based on Graphics Processing Unit (GPU). The two packages can be employed by epistasis detection in both case-control studies and quantitative trait studies. Our packages might help drive down costs of computation and increase innovation in epistatic studies. Moreover, we explored the gene-gene interactions on developmental dyslexia, which is mainly characterized by reading problems in children. Multivariate meta-analysis was performed on genome-wide interaction study (GWIS) for reading-related phenotypes in the dyslexia dataset, which contains nine cohorts from different locations. We identified one genome-wide significant epistasis, rs1442415 and rs8013684, associated with word reading, as well as suggestive genetic interactions which might affect reading abilities. Except for rs1442415, which has been reported to influence educational attainment, the genetic variants involved in the suggestive interactions have shown associations with psychiatric disorders in previous GWASs, particularly with bipolar disorder. Our findings suggest making efforts to investigate not just the genetic interactions but also multiple correlated psychiatric disorders

Do-it-yourself instruments and data processing methods for developing marine citizen observatories

La consulta íntegra de la tesi, inclosos els articles no comunicats públicament per drets d'autor, es pot realitzar prèvia petició a l'Arxiu de la UPCWater is the most important resource for living on planet Earth, covering more than 70% of its surface. The oceans represent more than 97% of the planet total water and they are where more than the 99.5% of the living beings are concentrated. A great number of ecosystems depend on the health of these oceans; their study and protection are necessary. Large datasets over long periods of time and over wide geographical areas can be required to assess the health of aquatic ecosystems. The funding needed for data collection is considerable and limited, so it is important to look at new cost-effective ways of obtaining and processing marine environmental data. The feasible solution at present is to develop observational infrastructures that may increase significantly the conventional sampling capabilities. In this study we promote to achieve this solution with the implementation of Citizen Observatories, based on volunteer participation. Citizen observatories are platforms that integrate the latest information technologies to digitally connect citizens, improving observation skills for developing a new type of research known as Citizen Science. Citizen science has the potential to increase the knowledge of the environment, and aquatic ecosystems in particular, through the use of people with no specific scientific training to collect and analyze large data sets. We believe that citizen science based tools -open source software coupled with low-cost do-it-yourself hardware- can help to close the gap between science and citizens in the oceanographic field. As the public is actively engaged in the analysis of data, the research also provides a strong avenue for public education. This is the objective of this thesis, to demonstrate how open source software and low-cost do-it-yourself hardware are effectively applied to oceanographic research and how can it develop into citizen science. We analyze four different scenarios where this idea is demonstrated: an example of using open source software for video analysis where lobsters were monitored; a demonstration of using similar video processing techniques on in-situ low-cost do-it-yourself hardware for submarine fauna monitoring; a study using open source machine learning software as a method to improve biological observations; and last but not least, some preliminar results, as proof of concept, of how manual water sampling could be replaced by low-cost do-it-yourself hardware with optical sensors.L’aigua és el recurs més important per la vida al planeta Terra, cobrint més del 70% de la seva superfície. Els oceans representen més del 70% de tota l'aigua del planeta, i és on estan concentrats més del 99.5% dels éssers vius. Un gran nombre d'ecosistemes depenen de la salut d'aquests oceans; el seu estudi i protecció són necessaris. Grans conjunts de dades durant llargs períodes de temps i al llarg d’amples àrees geogràfiques poden ser necessaris per avaluar la salut dels ecosistemes aquàtics. El finançament necessari per aquesta recol·lecció de dades és considerable però limitat, i per tant és important trobar noves formes més rendibles d’obtenir i processar dades mediambientals marines. La solució factible actualment és la de desenvolupar infraestructures observacionals que puguin incrementar significativament les capacitats de mostreig convencionals. En aquest estudi promovem que es pot assolir aquesta solució amb la implementació d’Observatoris Ciutadans, basats en la participació de voluntaris. Els observatoris ciutadans són plataformes que integren les últimes tecnologies de la informació amb ciutadans digitalment connectats, millorant les capacitats d’observació, per desenvolupar un nou tipus de recerca coneguda com a Ciència Ciutadana. La ciència ciutadana té el potencial d’incrementar el coneixement del medi ambient, i dels ecosistemes aquàtics en particular, mitjançant l'ús de persones sense coneixement científic específic per recollir i analitzar grans conjunts de dades. Creiem que les eines basades en ciència ciutadana -programari lliure juntament amb maquinari de baix cost i del tipus "fes-ho tu mateix" (do-it-yourself en anglès)- poden ajudar a apropar la ciència del camp oceanogràfic als ciutadans. A mesura que el gran públic participa activament en l'anàlisi de dades, la recerca esdevé també una nova via d’educació pública. Aquest és l’objectiu d’aquesta tesis, demostrar com el programari lliure i el maquinari de baix cost "fes-ho tu mateix" s’apliquen de forma efectiva a la recerca oceanogràfica i com pot desenvolupar-se cap a ciència ciutadana. Analitzem quatre escenaris diferents on es demostra aquesta idea: un exemple d’ús de programari lliure per anàlisi de vídeos de monitoratge de llagostes; una demostració utilitzant tècniques similars de processat de vídeo en un dispositiu in-situ de baix cost "fes-ho tu mateix" per monitoratge de fauna submarina; un estudi utilitzant programari lliure d’aprenentatge automàtic (machine learning en anglès) com a mètode per millorar observacions biològiques; i finalment uns resultats preliminars, com a prova de la seva viabilitat, de com un mostreig manual de mostres d’aigua podria ser reemplaçat per maquinari de baix cost "fes-ho tu mateix" amb sensors òptics.Postprint (published version

Do-it-yourself instruments and data processing methods for developing marine citizen observatories

Water is the most important resource for living on planet Earth, covering more than 70% of its surface. The oceans represent more than 97% of the planet total water and they are where more than the 99.5% of the living beings are concentrated. A great number of ecosystems depend on the health of these oceans; their study and protection are necessary. Large datasets over long periods of time and over wide geographical areas can be required to assess the health of aquatic ecosystems. The funding needed for data collection is considerable and limited, so it is important to look at new cost-effective ways of obtaining and processing marine environmental data. The feasible solution at present is to develop observational infrastructures that may increase significantly the conventional sampling capabilities. In this study we promote to achieve this solution with the implementation of Citizen Observatories, based on volunteer participation. Citizen observatories are platforms that integrate the latest information technologies to digitally connect citizens, improving observation skills for developing a new type of research known as Citizen Science. Citizen science has the potential to increase the knowledge of the environment, and aquatic ecosystems in particular, through the use of people with no specific scientific training to collect and analyze large data sets. We believe that citizen science based tools -open source software coupled with low-cost do-it-yourself hardware- can help to close the gap between science and citizens in the oceanographic field. As the public is actively engaged in the analysis of data, the research also provides a strong avenue for public education. This is the objective of this thesis, to demonstrate how open source software and low-cost do-it-yourself hardware are effectively applied to oceanographic research and how can it develop into citizen science. We analyze four different scenarios where this idea is demonstrated: an example of using open source software for video analysis where lobsters were monitored; a demonstration of using similar video processing techniques on in-situ low-cost do-it-yourself hardware for submarine fauna monitoring; a study using open source machine learning software as a method to improve biological observations; and last but not least, some preliminar results, as proof of concept, of how manual water sampling could be replaced by low-cost do-it-yourself hardware with optical sensors.L’aigua és el recurs més important per la vida al planeta Terra, cobrint més del 70% de la seva superfície. Els oceans representen més del 70% de tota l'aigua del planeta, i és on estan concentrats més del 99.5% dels éssers vius. Un gran nombre d'ecosistemes depenen de la salut d'aquests oceans; el seu estudi i protecció són necessaris. Grans conjunts de dades durant llargs períodes de temps i al llarg d’amples àrees geogràfiques poden ser necessaris per avaluar la salut dels ecosistemes aquàtics. El finançament necessari per aquesta recol·lecció de dades és considerable però limitat, i per tant és important trobar noves formes més rendibles d’obtenir i processar dades mediambientals marines. La solució factible actualment és la de desenvolupar infraestructures observacionals que puguin incrementar significativament les capacitats de mostreig convencionals. En aquest estudi promovem que es pot assolir aquesta solució amb la implementació d’Observatoris Ciutadans, basats en la participació de voluntaris. Els observatoris ciutadans són plataformes que integren les últimes tecnologies de la informació amb ciutadans digitalment connectats, millorant les capacitats d’observació, per desenvolupar un nou tipus de recerca coneguda com a Ciència Ciutadana. La ciència ciutadana té el potencial d’incrementar el coneixement del medi ambient, i dels ecosistemes aquàtics en particular, mitjançant l'ús de persones sense coneixement científic específic per recollir i analitzar grans conjunts de dades. Creiem que les eines basades en ciència ciutadana -programari lliure juntament amb maquinari de baix cost i del tipus "fes-ho tu mateix" (do-it-yourself en anglès)- poden ajudar a apropar la ciència del camp oceanogràfic als ciutadans. A mesura que el gran públic participa activament en l'anàlisi de dades, la recerca esdevé també una nova via d’educació pública. Aquest és l’objectiu d’aquesta tesis, demostrar com el programari lliure i el maquinari de baix cost "fes-ho tu mateix" s’apliquen de forma efectiva a la recerca oceanogràfica i com pot desenvolupar-se cap a ciència ciutadana. Analitzem quatre escenaris diferents on es demostra aquesta idea: un exemple d’ús de programari lliure per anàlisi de vídeos de monitoratge de llagostes; una demostració utilitzant tècniques similars de processat de vídeo en un dispositiu in-situ de baix cost "fes-ho tu mateix" per monitoratge de fauna submarina; un estudi utilitzant programari lliure d’aprenentatge automàtic (machine learning en anglès) com a mètode per millorar observacions biològiques; i finalment uns resultats preliminars, com a prova de la seva viabilitat, de com un mostreig manual de mostres d’aigua podria ser reemplaçat per maquinari de baix cost "fes-ho tu mateix" amb sensors òptics

5G: Where is the Money?

One of the most relevant issues in the new Digital Transformation is how telcos could create new 5G ecosystems. The use of new 5G technologies enters the telecommunication market in a very disruptive way. Telcos could be prepared for another technological change since the telco industry lived many transformations in the past. With 5G and their disruptive technologies, the result will be, making telcos enter in a non-telco area. Because of that, they will need to interact with different verticals and new partners. There are many technical kinds of literature covering these new 5G technologies, but few of them, cover how telcos should manage and do business with them. Some studies affirm that The telco companies who do not understand that they must interact with others as part of the new ecosystem will eventually die. However, not all are bad news for telcos, the future is not written. There are new opportunities and considering the logical technological restrictions and the possible and realistic possibilities, there is an open space that will be defined by the decisions that will be taken by the industry. This paper aims to clarify these concepts behind the new business models which are its usages, and its roles in the information system domain. To do that, the paper identifies the terminologies used to describe new business models and reuses the previous literature to elaborate on the research. General usages, roles, and potential of the concept are also outlined. The intention of this dissertation is to be used by non-technical people. Basic concepts are explained in a very simple way to allow readers to have an overview of the technical issues needed to understand the conclusions. How to present technical information, in a non-technical way, represents an extra challenge for the author. Finally, concrete and pragmatic proposals will be offered to telco managers and CEOs, to start working in the direction towards monetization of 5G, helping them with company decisions.Master in NFV and SDN for 5G Networks. Curso 2018/201