Validation and Evaluation

In this technical report, we present prototypical implementations of innovative tools and methods for personalized and contextualized (multimedia) search, collaborative ontology evolution, ontology evaluation and cost models, and dynamic access and trends in distributed (semantic) knowledge, developed according to the working plan outlined in Technical Report TR-B-12-04. The prototypes complete the next milestone on the path to an integral Corporate Semantic Web architecture based on the three pillars Corporate Ontology Engineering, Corporate Semantic Collaboration, and Corporate Semantic Search, as envisioned in TR-B-08-09

Transmissão e apresentação de conteúdos de sensores médicos

Mestrado em Sistemas de InformaçãoThis document covers the design, implementation and evaluation of a system that receives, processes and presents live streams of vital signs from sensors attached to a person’s body or in his surrounding environment. This is used either to prevent, analyse and/or act upon a critical scenario of emergency. Due to this critical scenarios where the system can be used, a distributed approach is implemented. Its aim is to reduce the risk of failure and give the possibility of transparent resource scaling according to the needs. Moreover, it is fully modularized for feature extensability and multiple sensor type support. Its Web interface is meant to provide a multi-platform access to the system, as long as the platform has a browser installed. It has a responsive design, according to the screen size of the client device, be it a smartphone, a tablet or a desktop computer. Given the maturity of Web applications and services available, it is easy to add the support for different visualization frameworks or services.Este documento apresenta o design, implementação e avaliação de um sistema que recebe, processa e apresenta emissões instantâneas de dados vitais de sensores ligados a uma pessoa ou ao meio em que esta se insere. Este é usado para prevenção, análise e/ou acção perante uma situação de emergência. Dados os cenários críticos one o sistema pode ser usado, este é composto por uma arquitectura distribuída, com o intuito de reduzir o risco de o sistema parar por alguma falha, e dar a possibilidade de expandir ou reduzir a capacidade de processamento de acordo com a necessidade de utilização. Além disso, é também um sistema completamante modular e suporta o desevolvimento de módulos com novas funcionalidades ou suporte para diferentes tipos de sensores. A sua interface Web permite o acesso ao sistema, independentemente da plataforma utilizada, desde que esta tenha um browser. Está preparada para ter um design responsivo, de acordo com o tamanho do ecrã do dispositivo, seja um telemóvel, um tablet ou um computador de mesa. Dada a maturidade das aplicações e serviços Web disponíveis, é fácil extender também a interface para suportar novoso tipos de visualizações de informação.Diese Arbeit behandelt Design, Implementierung und Evaluation eines Systems, das live übertragene Vitalparameter von Sensoren empfängt, verarbeitet und darstellt, die an einem menschlichen Körper angebracht sind oder in seiner Umgebung. Es wird genutzt um kritischen Unfallszenarien vorzubeugen, sie zu analysieren und/oder auf sie zu reagieren. Aufgrund dieser kritischen Szenarien, in denen das System genutzt werden kann, wird ein verteilter Ansatz implementiert. Das Ziel ist es die Fehlerrate zu reduzieren und, bedarfsabhängig, die Möglichkeit zur tranparenten Skalierung der Ressourcen zu geben. Desweiteren ist das System voll modularisiert, um Erweiterbarkeit und die Unterstützung vieler Sensortypen zu gewährleisten. Das Webinterface bietet Zugang von verschiedensten Plattformen, solange ein Browser installiert ist. Es hat ein responsives Webdesign, dass sich and die Bildschirmgröße jedes Nutzergerätes anpasst, sei es ein Smartphone, Tablet oder Desktop Computer. Der gegebene Reifegrad von Webapplikationen und -diensten ermöglicht die Unterstützung verschiedener Visualisierungsframeworks oder -dienste

Characterization, Avoidance and Repair of Packet Collisions in Inter-Vehicle Communication Networks

This work proposes a combined and accurate simulation of wireless channel, physical layer and networking aspects in order to bridge the gaps between the corresponding research communities. The resulting high fidelity simulations enable performance optimizations across multiple layers, and are used in the second part of this thesis to evaluate the impact of fast-fading channel characteristics on Carrier-Sense Multiple Access, and to quantify the benefit of successive interference cancellation

Characterization, Avoidance and Repair of Packet Collisions in Inter-Vehicle Communication Networks

This work proposes a combined and accurate simulation of wireless channel, physical layer and networking aspects in order to bridge the gaps between the corresponding research communities. The resulting high fidelity simulations enable performance optimizations across multiple layers, and are used in the second part of this thesis to evaluate the impact of fast-fading channel characteristics on Carrier-Sense Multiple Access, and to quantify the benefit of successive interference cancellation

Force-spectroscopy of small ligands binding to nucleic acids

[cat] Les tècniques de molècula individual permeten seguir les reaccions biomoleculars amb una resolució sense precedents, proveint als científics d’una sèrie d’instruments per a mesurar magnituds físiques i investigar sistemes experimentals difícilment accessibles amb les tradi­cionals mesures en volum (és a dir a on les mesures es realitzen amb mols de reactiu). Particularment, les pinces òptiques permeten manipular i aplicar forces a molècules individuals i determinar-ne així les seves propietats elàstiques i termodinàmiques. L’atrapament òptic es basa en l’ús d’un feix làser focalitzat per exercir una força òptica a les microesferes (diàmetre ~ 3 µm), que queden confinades a prop del punt focal a causa de la conservació del moment lineal. Els experiments de micromanipulació es realitzen unint els extrems de la molècula que es vol estudiar a la superfícies de dues microesferes diferents, podent així aplicar forces a la molècula quan desplacem una microesfera respecte de l’altra. Per ancorar les molècules a la superfície de les microesferes s’utilitzen unions moleculars que tenen una alta a.nitat (p.ex. enllaç biotina-estreptavidina). Típicament els experiments amb pinces òptiques consisteixen en la micromanipulació d’àcids nucleics (ADN, ARN) o proteïnes de forma individual. Per exemple, una molècula d’ADN pot ésser estirada per a estudiar-ne les propietats elàstiques, o oberta mecànicament (separant les dues cadenes que formen la doble hèlix) per a mesurar les energies lliures d’aparellament entre bases. Un gran nombre d’agents anticancerígens tenen com a diana els àcids nucleics, a on s’hi uneixen afi i efecte de dur a terme la seva acció citotòxica (p. ex. interferint amb processos cel·lulars essencials com són la replicació, la transcripció o els mecanismes de reparació). Per entendre el seu mecanisme d’acció és important conéixer en quines posicions, amb quina a.nitat, i amb quina cinètica s’uneixen a diferents seqüències d’ADN. Els experiments de molècula individual amb pinces òptiques permeten determinar la termodinàmica i cinètica d’unió de molts d’aquests lligands, especialment aquells difícils de caracteritzar mitjançant mesures en volum. És per això que un dels objectius principals d’aquesta tesi ha estat aprofitar les potencialitats de les mesures de molècula individual per a caracteritzar pèptids anti­cancerígens poc solubles i difícils d’estudiar amb tècniques alternatives: des de la cinètica i termodinàmica d’unió, a l’especi.citat en seqüència i la cinètica d’autoacoblament.[eng] Single-molecule techniques allow to following biomolecular reactions with unprecedented resolution. Particularly, optical tweezers can be used to manipulate and apply forces to individual molecules tethered between plastic beads that are optically-trapped. Optical trapping is achieved by using highly focused laser beams that exert a gradient force onto the micrometer-sized dielectric particles that become confined close to the focal position of the laser. By specifically attaching the ends of the molecule under study to two optically-trapped beads, it is possible to manipulate and apply forces to an individual molecule. Typical experiments with optical tweezers consist in manipulating nucleic acids (DNA, RNA) or proteins one at a time. For instance DNA molecules can be stretched to measure its elastic properties, or unzipped to measure their base-pairing energies. Many small anticancer drugs target nucleic acids to exert their cytotoxic activity against cancer cells. To understand their mechanism of action it is important to know in which positions, how strong, and how fast do they bind to different specific sites in DNA. Single-molecule optical tweezers experiments can be used to unravel the binding thermodynamics and kinetics of many of these ligands, especially those difficult to characterize with bulk techniques. Thiocoraline is one of such drugs, and binds DNA through bis-intercalation. Experiments with optical tweezers show that the kinetics of intercalation are very slow (hours) and strongly force-dependent: force facilitates binding but slows down unbinding. Experiments performed in different conditions also reveal that the binding pathway proceeds through a mono-intercalated intermediate that causes the observed slow kinetics. In this sense, we present a three-state model that offers a theoretical framework from which the kinetic rates of the reaction can be extracted, and that could be useful to characterize other bis-intercalators. We also show that DNA unzipping experiments can be used to determine the preferred binding sequences of Thiocoraline, finding that it preferentially clamps CpG steps. This methodology is potentially very useful as it provides direct access to the preferred binding sites of small ligands due to its thermodynamic stability with one base pair resolution and without the requirement of restriction enzymes or radioactive labeling. This single-molecule footprinting technique is also adapted to a magnetic tweezers instrument in order to perform parallelized measurements. The fact that bis-intercalation does not modify the persistence length of dsDNA is also found in the pulling experiments. From the elasticity measurements, we also extract equilibrium quantitates of the interaction by using classic statistical models. This combination of DNA stretching and unzipping assays can also be used to follow how the anticancer agent Kahalalide F self-assembles and compacts DNA. Kahalalide F forms nanometric particles that are positively charged able to bind and condense DNA. The binding reaction shows to phases: an initial compaction of electrostatic origin, and its subsequent stiffening due to the hydrophobic collapse of the complex. The combination of quantitative force-spectroscopy measurements with AFM images of the complexes and other bulk tech- niques (DLS, EM) provides a consistent picture of the compaction and aggregation process. Modeling of the experiments provides the thermodynamic parameters of the interaction that are complemented with kinetic measurements. A simple technique to study ssDNA with optical tweezers is also presented and used to study how the stiffness of the polyanion affects the compaction process. We exploit this methodology to understand how the stiffness of the polyanion affects the compaction kinetics, and later on, we also show its utility to study the elasticity of ssDNA under varying ionic conditions. Finally, the utility of this methodology to study self-assembly and aggregation is explored with amyloidogenic peptides involved in neurodegenerative disorders

New Techniques to Improve Network Security

With current technologies it is practically impossible to claim that a distributed application is safe from potential malicious attacks. Vulnerabilities may lay at several levels (criptographic weaknesses, protocol design flaws, coding bugs both in the application and in the host operating system itself, to name a few) and can be extremely hard to find. Moreover, sometimes an attacker does not even need to find a software vulnerability, as authentication credentials might simply “leak” ouside from the network for several reasons. Luckily, literature proposes several approaches that can contain these problems and enforce security, but the applicability of these techniques is often greatly limited due to the high level of expertise required, or simply because of the cost of the required specialized hardware. Aim of this thesis is to focus on two security enforcment techniques, namely formal methods and data analysis, and to present some improvements to the state of the art enabling to reduce both the required expertise and the necessity of specialized hardware

Evolvable Smartphone-Based Point-of-Care Systems For In-Vitro Diagnostics

Recent developments in the life-science -omics disciplines, together with advances in micro and nanoscale technologies offer unprecedented opportunities to tackle some of the major healthcare challenges of our time. Lab-on-Chip technologies coupled with smart-devices in particular, constitute key enablers for the decentralization of many in-vitro medical diagnostics applications to the point-of-care, supporting the advent of a preventive and personalized medicine. Although the technical feasibility and the potential of Lab-on-Chip/smart-device systems is repeatedly demonstrated, direct-to-consumer applications remain scarce. This thesis addresses this limitation. System evolvability is a key enabler to the adoption and long-lasting success of next generation point-of-care systems by favoring the integration of new technologies, streamlining the reengineering efforts for system upgrades and limiting the risk of premature system obsolescence. Among possible implementation strategies, platform-based design stands as a particularly suitable entry point. One necessary condition, is for change-absorbing and change-enabling mechanisms to be incorporated in the platform architecture at initial design-time. Important considerations arise as to where in Lab-on-Chip/smart-device platforms can these mechanisms be integrated, and how to implement them. Our investigation revolves around the silicon-nanowire biological field effect transistor, a promising biosensing technology for the detection of biological analytes at ultra low concentrations. We discuss extensively the sensitivity and instrumentation requirements set by the technology before we present the design and implementation of an evolvable smartphone-based platform capable of interfacing lab-on-chips embedding such sensors. We elaborate on the implementation of various architectural patterns throughout the platform and present how these facilitated the evolution of the system towards one accommodating for electrochemical sensing. Model-based development was undertaken throughout the engineering process. A formal SysML system model fed our evolvability assessment process. We introduce, in particular, a model-based methodology enabling the evaluation of modular scalability: the ability of a system to scale the current value of one of its specification by successively reengineering targeted system modules. The research work presented in this thesis provides a roadmap for the development of evolvable point-of-care systems, including those targeting direct-to-consumer applications. It extends from the early identification of anticipated change, to the assessment of the ability of a system to accommodate for these changes. Our research should thus interest industrials eager not only to disrupt, but also to last in a shifting socio-technical paradigm

A Functional, Comprehensive and Extensible Multi-Platform Querying and Transformation Approach

This thesis is about a new model querying and transformation approach called FunnyQT which is realized as a set of APIs and embedded domain-specific languages (DSLs) in the JVM-based functional Lisp-dialect Clojure. Founded on a powerful model management API, FunnyQT provides querying services such as comprehensions, quantified expressions, regular path expressions, logic-based, relational model querying, and pattern matching. On the transformation side, it supports the definition of unidirectional model-to-model transformations, of in-place transformations, it supports defining bidirectional transformations, and it supports a new kind of co-evolution transformations that allow for evolving a model together with its metamodel simultaneously. Several properties make FunnyQT unique. Foremost, it is just a Clojure library, thus, FunnyQT queries and transformations are Clojure programs. However, most higher-level services are provided as task-oriented embedded DSLs which use Clojure's powerful macro-system to support the user with tailor-made language constructs important for the task at hand. Since queries and transformations are just Clojure programs, they may use any Clojure or Java library for their own purpose, e.g., they may use some templating library for defining model-to-text transformations. Conversely, like every Clojure program, FunnyQT queries and transformations compile to normal JVM byte-code and can easily be called from other JVM languages. Furthermore, FunnyQT is platform-independent and designed with extensibility in mind. By default, it supports the Eclipse Modeling Framework and JGraLab, and support for other modeling frameworks can be added with minimal effort and without having to modify the respective framework's classes or FunnyQT itself. Lastly, because FunnyQT is embedded in a functional language, it has a functional emphasis itself. Every query and every transformation compiles to a function which can be passed around, given to higher-order functions, or be parametrized with other functions