Supporting policy-based contextual reconfiguration and adaptation in ubiquitous computing

In order for pervasive computing systems to be able to perform tasks which support us in everyday life without requiring attention from the users of the environment, they need to adapt themselves in response to context. This makes context-awareness in general, and context-aware adaptation in particular, an essential requirement for pervasive computing systems. Two of the features of context-awareness are: contextual reconfiguration and contextual adaptation in which applications adapt their behaviour in response to context. We combine both these features of context-awareness to provide a broad scope of adaptation and put forward a system, called Policy-Based Contextual Reconfiguration and Adaptation (PCRA) that provides runtime support for both. The combination of both context-aware reconfiguration and context-aware adaptation provides a broad scope of adaptation and hence allows the development of diverse adaptive context-aware applications. However, another important issue is the choice of an effective means for developing, modifying and extending such applications. The main argument forming the basis of this thesis is that we advocate the use of a policy-based programming model and argue that it provides more effective means for developing, modifying and extending such applications. This thesis addresses other important surrounding issues which are associated with adaptive context-aware applications. These include the management of invalid bindings and the provision of seamless caching support for remote services involved in bindings for improved performance. The bindings may become invalid due to failure conditions that can arise due to network problems or migration of software components, causing bindings between the application component and remote service to become invalid. We have integrated reconfiguration support to manage bindings, and seamless caching support for remote services in PCRA. This thesis also describes the design and implementation of PCRA, which enables development of adaptive context-aware applications using policy specifications. Within PCRA, adaptive context-aware applications are modelled by specifying binding policies and adaptation policies. The use of policies within PCRA simplifies the development task because policies are expressed at a high-level of abstraction, and are expressed independently of each other. PCRA also allows the dynamic modification of applications since policies are independent units of execution and can be dynamically loaded and removed from the system. This is a powerful and useful capability as applications may evolve over time, i.e. the user needs and preferences may change, but re-starting is undesirable. We evaluate PCRA by comparing its features to other systems in the literature, and by performance measures

INTERACTIONS BETWEEN THE MEDIAL PREOPTIC NUCLEUS AND MESOLIMBIC REWARD PATHWAY IN THE REGULATION OF SOCIOSEXUAL BEHAVIORS

A major challenge facing members of most vertebrate animal species is to evaluate the intricate social, physiological, and environmental information they encounter and integrate this information to display the appropriate social behaviors in an adaptive manner. In the case of sociosexual encounters, different brain mechanisms interact to orchestrate information about the salience of the external stimuli along with the physiological and environmental conditions and incorporate them to be able to display fitting sexual behaviors. For all vertebrate species, the medial preoptic nucleus (POM) is a key integrative site in the regulation of male sexual behavior. It is responsive to the hormonal milieu and thus to key aspects of the physiological and environmental conditions. On the other hand, the mesolimbic dopamine system plays an important role in the attribution of incentive salience to sexually relevant cues. There is strong theoretical reasoning as well as experimental evidence suggesting a potential interplay between medial preoptic nucleus and mesolimbic system, however there has been a paucity of studies investigating this interactions and its regulation of male sexual behaviors. This dissertation sets out to elucidate how these two systems communicate with each other to modulate male sexual behaviors based on studies in Japanese quail (Coturnix japonica). Quail have emerged as an excellent species in which to investigate the neuroendocrine regulation of male-typical sexual motivation and performance. To this goal, (1) first we demonstrate that both POM and parts of the mesolimbic system are implicated in appetitive and consummatory sexual behaviors via immediate early gene studies. (2) Subsequently we establish an anatomical location for nucleus accumbens in avian species by employing a variety of immunohistochemical and hodological markers to examine homologies with mammalian species. This investigation enabled us to explore further the functions of nucleus accumbens in the control sexual behaviors and again we demonstrated the involvement of this nucleus in regulation of sexual behavior in both males and females based on immediate early gene expression measures. (3) Subsequently, studies employing the lesion of dopaminergic inputs to the POM and Ac demonstrated that dopamine function in POM and Ac is necessary for the initiation of appetitive and consummatory sexual behaviors. (4) This study was followed by an experiment utilizing an asymmetrical inactivation strategy that focused on the POM and VTA. Our findings provide novel evidence for interplay between POM and VTA in modulation of appetitive but not consummatory sexual behaviors. (5) To investigate how this interaction is implemented we combined tract-tracing methods with immediate early genes and demonstrated that efferent projections from POM to VTA are implicated in sexual behaviors. Overall, this series of experiments demonstrates that appetitive aspects of male sexual behavior are regulated via interplay of POM and VTA. These findings provide novel insight as to how organisms evaluate complex social, physiological, and environmental inputs when processing stimuli with high value in a sexual context

A Multi-Criteria Framework to Assist on the Design of Internet-of-Things Systems

The Internet-of-Things (IoT), considered as Internet first real evolution, has become immensely important to society due to revolutionary business models with the potential to radically improve Human life. Manufacturers are engaged in developing embedded systems (IoT Systems) for different purposes to address this new variety of application domains and services. With the capability to agilely respond to a very dynamic market offer of IoT Systems, the design phase of IoT ecosystems can be enhanced. However, select the more suitable IoT System for a certain task is currently based on stakeholder’s knowledge, normally from lived experience or intuition, although it does not mean that a proper decision is being made. Furthermore, the lack of methods to formally describe IoT Systems characteristics, capable of being automatically used by methods is also an issue, reinforced by the growth of available information directly connected to Internet spread. Contributing to improve IoT Ecosystems design phase, this PhD work proposes a framework capable of fully characterise an IoT System and assist stakeholder’s on the decision of which is the proper IoT System for a specific task. This enables decision-makers to perform a better reasoning and more aware analysis of diverse and very often contradicting criteria. It is also intended to provide methods to integrate energy consumptionsimulation tools and address interoperability with standards, methods or systems within the IoT scope. This is addressed using a model-driven based framework supporting a high openness level to use different software languages and decision methods, but also for interoperability with other systems, tools and methods

Digital Biomarker Models for Prediction of Infectious Disease Susceptibility

Acute respiratory viral infection (ARVI) represents one of the most prevalent infectious diseases affecting mankind. With the threat of COVID-19 still looming over us, we have witnessed the substantial threat ARVI poses to world health and economy, extinguishing millions of lives and costing trillions of dollars. This sets the context for the research of this thesis: using digital biomarkers to distinguish between individuals who are susceptible to becoming severely infected and/or infectious before an infection is clinically detectable. The development of such biomarkers can have both clinical and epidemiological impact in terms of identifying individuals who are either vulnerable to severe infection or those who may become highly infectious. The digital biomarkers and associated analysis methods are developed and validated on longitudinal data collected by our clinical collaborators from two different ARVI challenge studies. The first study provides data on healthy human volunteers who were inoculated with the common cold and the second study provides data on volunteers inoculated with the flu. Digital biomarkers include molecular, physiological and cognitive data continuously collected from blood, wearable devices and cognitive testing of the study participants. The findings of our research on digitally measurable susceptibility factors are wide-ranging. We find that circadian rhythm at the molecular scale (biochronicity) plays an important role in mediating both the susceptibility and the response to severe infection, revealing groups of gene expression markers that differentiate the responses of low infected and high infected individuals. Using a high dimensional representation of physiological signals from a wearable device, we find that an infection response and its onset time can be reliably predicted at least 24 hours before peak infection time. We find that a certain measure of variability in pre-exposure cognitive function is highly associated with the post-exposure severity of infection.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169966/1/yayazhai_1.pd

Pervasive computing reference architecture from a software engineering perspective (PervCompRA-SE)

Pervasive computing (PervComp) is one of the most challenging research topics nowadays. Its complexity exceeds the outdated main frame and client-server computation models. Its systems are highly volatile, mobile, and resource-limited ones that stream a lot of data from different sensors. In spite of these challenges, it entails, by default, a lengthy list of desired quality features like context sensitivity, adaptable behavior, concurrency, service omnipresence, and invisibility. Fortunately, the device manufacturers improved the enabling technology, such as sensors, network bandwidth, and batteries to pave the road for pervasive systems with high capabilities. On the other hand, this domain area has gained an enormous amount of attention from researchers ever since it was first introduced in the early 90s of the last century. Yet, they are still classified as visionary systems that are expected to be woven into people’s daily lives. At present, PervComp systems still have no unified architecture, have limited scope of context-sensitivity and adaptability, and many essential quality features are insufficiently addressed in PervComp architectures. The reference architecture (RA) that we called (PervCompRA-SE) in this research, provides solutions for these problems by providing a comprehensive and innovative pair of business and technical architectural reference models. Both models were based on deep analytical activities and were evaluated using different qualitative and quantitative methods. In this thesis we surveyed a wide range of research projects in PervComp in various subdomain areas to specify our methodological approach and identify the quality features in the PervComp domain that are most commonly found in these areas. It presented a novice approach that utilizes theories from sociology, psychology, and process engineering. The thesis analyzed the business and architectural problems in two separate chapters covering the business reference architecture (BRA) and the technical reference architecture (TRA). The solutions for these problems were introduced also in the BRA and TRA chapters. We devised an associated comprehensive ontology with semantic meanings and measurement scales. Both the BRA and TRA were validated throughout the course of research work and evaluated as whole using traceability, benchmark, survey, and simulation methods. The thesis introduces a new reference architecture in the PervComp domain which was developed using a novel requirements engineering method. It also introduces a novel statistical method for tradeoff analysis and conflict resolution between the requirements. The adaptation of the activity theory, human perception theory and process re-engineering methods to develop the BRA and the TRA proved to be very successful. Our approach to reuse the ontological dictionary to monitor the system performance was also innovative. Finally, the thesis evaluation methods represent a role model for researchers on how to use both qualitative and quantitative methods to evaluate a reference architecture. Our results show that the requirements engineering process along with the trade-off analysis were very important to deliver the PervCompRA-SE. We discovered that the invisibility feature, which was one of the envisioned quality features for the PervComp, is demolished and that the qualitative evaluation methods were just as important as the quantitative evaluation methods in order to recognize the overall quality of the RA by machines as well as by human beings

Going beyond GWAS: New methods to interpret association signals

The aim of genetics is to understand the genetic basis of traits by linking genetic variability to phenotypic variability. In recent years, progress in the field of complex human trait genetics led to the discovery of thousands of common genetic variants robustly associated with complex human traits through genome-wide association studies (GWAS). However, it is currently unclear how to best to tackle the challenge of interpreting variants in the context of the biology involved. My work explored various avenues to help in this challenge. One strategy for interpretation is pathway analysis, where prior biological knowledge is formalized into sets of genes with annotated functions and results from genetics studies are searched for enrichments. Using this approach, one can connect the biological processes to the investigated trait. For this purpose, I developed a methodology to calculate pathway enrichments from GWAS results in an efficient way and in agreement with statistical principles. As a first step, the methodology combines results for SNPs in a gene region into a single gene wise p-value, with methods that are both fast and have a high level of numerical precision. The speed allows controlling the pathway enrichment step for potential correlation between genes leading to statistically correct p-values. This methodology was implemented in a software tool called Pascal. Its performance was tested on a large set of GWAS results and compared favorably to other methods. Efforts were made to ensure that the software would be easy to use by a wider community. Another challenge in the interpretation of GWAS results is to understand the reasons a genetic variant leads to changes in phenotype. Most uncovered variants seem to impact gene regulation. Therefore, understanding chromatin architecture will be crucial to understand the regulatory consequences of genetic variants. One feature of eukaryotic chromatin is that it can take the form of a compacted state making it inaccessible to most regulatory factors. To help elucidate which factors play a role in moving between compacted an open state, I developed an new method of integrative data analysis for transcription factor motif, DNase1 hypersensitivity and gene expression data. Transcription factor motif and DNase1 hypersensitivity were combined to calculate chromatin accessibility scores. These in turn were associated to gene expression using a linear mixed modeling approach. Applying this method on large public datasets predicted a set of candidate chromatin accessibility regulators. This set was heavily enriched in ’pioneer factors’: factors that can bind and open compacted chromatin, suggesting that the approach did indeed uncover regulators of chromatin accessibility. A major hindrance to the interpretation of human variants uncovered by GWAS is that it is not possible to perform genetic manipulations to validate and build on the findings. Therefore, investigations using model organisms remain relevant. To further the understanding of the genetics of fly growth control, I helped in the statistical analysis of a GWAS data set in an . The study is noteworthy for its extensive environmental control and follow-up experiments on candidate genes. -- La génétique cherche à comprendre la base génétique de caractères observables, dits phénotypes, en liant la variabilité génétique à la variabilité phénotypique. Ces dernières années, les progrès apportés à la génétique des phénotypes complexes ont amené à la découverte de milliers de variations génétiques associées significativement à des phénotypes humains complexes, au moyen de l’étude d’association pangénomique, communément appelée GWAS (de l’anglais Genome-Wide Association Study). Cependant, interpréter ces associations dans leur contexte biologique reste un défi. Mon travail a consisté à explorer différentes possibilités pour y répondre. Une des stratégies pour relier un phénotype étudié aux processus biologiques est l’analyse par voies moléculaires, où l’on recherche un enrichissement des associations GWAS parmi l’ensemble de groupes de gènes de fonctions cohérentes. Cette analyse permet ainsi de relier des processus biologiques au phénotype étudié. Dans ce but, j’ai développé une méthode calculant avec efficacité l’enrichissement des voies moléculaires des associations GWAS. La méthode combine les résultats des polymorphismes dans la région d’un gène en une probabilité pour un gène, au moyen de méthodes rapides et précises. La vitesse permet de contrôler l’étape d’enrichissement des voies pour une corrélation potentielle entre les gènes, menant à des probabilités statistiquement correctes. J’ai implémenté cette méthode dans le logiciel Pascal. Sa performance a été testé sur un large jeu de résultats GWAS et il surpasse les autres méthodes. Des efforts ont été fait afin d’assurer que le logiciel soit facile d’utilisation pour la communauté scientifique. Un autre défi lié à l’interprétation des résultats GWAS est de comprendre les raisons pour lesquelles une variation génétique résulte en un changement phénotypique. La plupart des variations découvertes semblent affecter la régulation des gènes. Ainsi, comprendre l’architecture de la chromatine est crucial pour appréhender les conséquences régulatrices de ces variations. Une des caractéristiques de la chromatine des eucaryotes est qu’elle peut être compactée, la rendant inaccessible à la plupart des facteurs de régulations. Pour trouver quels sont les facteurs jouant un rôle dans le passage entre états compacté et ouverts, j’ai développé une nouvelle méthode intégrant l’analyse des motifs de facteurs de transcription, l’hypersensibilité de la Dnase1 et les données d’expression des gènes. Les deux premiers critères ont été combiné pour calculer des scores d’accessibilité de la chromatine. Ils ont ensuite été associés à l’expression des gènes en utilisant un modèle linéaire mixte. L’application de cette méthode sur des larges données publiques a prédit des régulateurs candidats d’accessibilité de la chromatine. Ce jeu était enrichi en “facteurs pionniers”, qui s’accrochent et ouvrent la chromatine compactée, suggérant que cette approche a en effet permis de découvrir des régulateurs d’accessibilité à la chromatine. Un obstacle majeur dans l’interprétation des variations humaines découvertes par GWAS est qu’il n’est pas possible de réaliser des manipulations génétiques permettant de valider ces découvertes, d’où l’utilisation d’organismes modèles. Afin de comprendre davantage la génétique du contrôle de croissance des mouches, j’ai aidé à l’analyse statistique de données de GWAS d’une population L’étude est remarquable pour son contrôle environnemental étendu et ses expériences de suivi sur les gènes candidats

Semantic middleware development for the Internet of Things

After the extraordinary spread of the World Wide Web during the last fifteen years, engineers and developers are pushing now the Internet to its next border. A new conception in computer science and networks communication has been burgeoning during roughly the last decade: a world where most of the computers of the future will be extremely downsized, to the point that they will look like dust at its most advanced prototypes. In this vision, every single element of our “real” world has an intelligent tag that carries all their relevant data, effectively mapping the “real” world into a “virtual” one, where all the electronically augmented objects are present, can interact among them and influence with their behaviour that of the other objects, or even the behaviour of a final human user. This is the vision of the Internet of the Future, which also draws ideas of several novel tendencies in computer science and networking, as pervasive computing and the Internet of Things. As it has happened before, materializing a new paradigm that changes the way entities interrelate in this new environment has proved to be a goal full of challenges in the way. Right now the situation is exciting, with a plethora of new developments, proposals and models sprouting every time, often in an uncoordinated, decentralised manner away from any standardization, resembling somehow the status quo of the first developments of advanced computer networking, back in the 60s and the 70s. Usually, a system designed after the Internet of the Future will consist of one or several final user devices attached to these final users, a network –often a Wireless Sensor Network- charged with the task of collecting data for the final user devices, and sometimes a base station sending the data for its further processing to less hardware-constrained computers. When implementing a system designed with the Internet of the Future as a pattern, issues, and more specifically, limitations, that must be faced are numerous: lack of standards for platforms and protocols, processing bottlenecks, low battery lifetime, etc. One of the main objectives of this project is presenting a functional model of how a system based on the paradigms linked to the Internet of the Future works, overcoming some of the difficulties that can be expected and showing a model for a middleware architecture specifically designed for a pervasive, ubiquitous system. This Final Degree Dissertation is divided into several parts. Beginning with an Introduction to the main topics and concepts of this new model, a State of the Art is offered so as to provide a technological background. After that, an example of a semantic and service-oriented middleware is shown; later, a system built by means of this semantic and service-oriented middleware, and other components, is developed, justifying its placement in a particular scenario, describing it and analysing the data obtained from it. Finally, the conclusions inferred from this system and future works that would be good to be tackled are mentioned as well. RESUMEN Tras el extraordinario desarrollo de la Web durante los últimos quince años, ingenieros y desarrolladores empujan Internet hacia su siguiente frontera. Una nueva concepción en la computación y la comunicación a través de las redes ha estado floreciendo durante la última década; un mundo donde la mayoría de los ordenadores del futuro serán extremadamente reducidas de tamaño, hasta el punto que parecerán polvo en sus más avanzado prototipos. En esta visión, cada uno de los elementos de nuestro mundo “real” tiene una etiqueta inteligente que porta sus datos relevantes, mapeando de manera efectiva el mundo “real” en uno “virtual”, donde todos los objetos electrónicamente aumentados están presentes, pueden interactuar entre ellos e influenciar con su comportamiento el de los otros, o incluso el comportamiento del usuario final humano. Ésta es la visión del Internet del Futuro, que también toma ideas de varias tendencias nuevas en las ciencias de la computación y las redes de ordenadores, como la computación omnipresente y el Internet de las Cosas. Como ha sucedido antes, materializar un nuevo paradigma que cambia la manera en que las entidades se interrelacionan en este nuevo entorno ha demostrado ser una meta llena de retos en el camino. Ahora mismo la situación es emocionante, con una plétora de nuevos desarrollos, propuestas y modelos brotando todo el rato, a menudo de una manera descoordinada y descentralizada lejos de cualquier estandarización, recordando de alguna manera el estado de cosas de los primeros desarrollos de redes de ordenadores avanzadas, allá por los años 60 y 70. Normalmente, un sistema diseñado con el Internet del futuro como modelo consistirá en uno o varios dispositivos para usuario final sujetos a estos usuarios finales, una red –a menudo, una red de sensores inalámbricos- encargada de recolectar datos para los dispositivos de usuario final, y a veces una estación base enviando los datos para su consiguiente procesado en ordenadores menos limitados en hardware. Al implementar un sistema diseñado con el Internet del futuro como patrón, los problemas, y más específicamente, las limitaciones que deben enfrentarse son numerosas: falta de estándares para plataformas y protocolos, cuellos de botella en el procesado, bajo tiempo de vida de las baterías, etc. Uno de los principales objetivos de este Proyecto Fin de Carrera es presentar un modelo funcional de cómo trabaja un sistema basado en los paradigmas relacionados al Internet del futuro, superando algunas de las dificultades que pueden esperarse y mostrando un modelo de una arquitectura middleware específicamente diseñado para un sistema omnipresente y ubicuo. Este Proyecto Fin de Carrera está dividido en varias partes. Empezando por una introducción a los principales temas y conceptos de este modelo, un estado del arte es ofrecido para proveer un trasfondo tecnológico. Después de eso, se muestra un ejemplo de middleware semántico orientado a servicios; después, se desarrolla un sistema construido por medio de este middleware semántico orientado a servicios, justificando su localización en un escenario particular, describiéndolo y analizando los datos obtenidos de él. Finalmente, las conclusiones extraídas de este sistema y las futuras tareas que sería bueno tratar también son mencionadas