p-BioSPRE-an information and communication technology framework for transnational biomaterial sharing and access

Biobanks represent key resources for clinico-genomic research and are needed to pave the way to personalised medicine. To achieve this goal, it is crucial that scientists can securely access and share high-quality biomaterial and related data. Therefore, there is a growing interest in integrating biobanks into larger biomedical information and communication technology (ICT) infrastructures. The European project p-medicine is currently building an innovative ICT infrastructure to meet this need. This platform provides tools and services for conducting research and clinical trials in personalised medicine. In this paper, we describe one of its main components, the biobank access framework p-BioSPRE (p-medicine Biospecimen Search and Project Request Engine). This generic framework enables and simplifies access to existing biobanks, but also to offer own biomaterial collections to research communities, and to manage biobank specimens and related clinical data over the ObTiMA Trial Biomaterial Manager. p-BioSPRE takes into consideration all relevant ethical and legal standards, e.g., safeguarding donors’ personal rights and enabling biobanks to keep control over the donated material and related data. The framework thus enables secure sharing of biomaterial within open and closed research communities, while flexibly integrating related clinical and omics data. Although the development of the framework is mainly driven by user scenarios from the cancer domain, in this case, acute lymphoblastic leukaemia and Wilms tumour, it can be extended to further disease entities.

Visual programming in a heterogeneous multi-core environment

É do conhecimento geral de que, hoje em dia, a tecnologia evolui rapidamente. São criadas novas arquitecturas para resolver determinadas limitações ou problemas. Por vezes, essa evolução é pacífica e não requer necessidade de adaptação e, por outras, essa evolução pode Implicar mudanças. As linguagens de programação são, desde sempre, o principal elo de comunicação entre o programador e o computador. Novas linguagens continuam a aparecer e outras estão sempre em desenvolvimento para se adaptarem a novos conceitos e paradigmas. Isto requer um esforço extra para o programador, que tem de estar sempre atento a estas mudanças. A Programação Visual pode ser uma solução para este problema. Exprimir funções como módulos que recebem determinado Input e retomam determinado output poderá ajudar os programadores espalhados pelo mundo, através da possibilidade de lhes dar uma margem para se abstraírem de pormenores de baixo nível relacionados com uma arquitectura específica. Esta tese não só mostra como combinar as capacidades do CeII/B.E. (que tem uma arquitectura multi­processador heterogénea) com o OpenDX (que tem um ambiente de programação visual), como também demonstra que tal pode ser feito sem grande perda de performance. ABSTRACT; lt is known that nowadays technology develops really fast. New architectures are created ln order to provide new solutions for different technology limitations and problems. Sometimes, this evolution is pacific and there is no need to adapt to new technologies, but things also may require a change every once ln a while. Programming languages have always been the communication bridge between the programmer and the computer. New ones keep coming and other ones keep improving ln order to adapt to new concepts and paradigms. This requires an extra-effort for the programmer, who always needs to be aware of these changes. Visual Programming may be a solution to this problem. Expressing functions as module boxes which receive determined Input and return determined output may help programmers across the world by giving them the possibility to abstract from specific low-level hardware issues. This thesis not only shows how the CeII/B.E. (which has a heterogeneous multi-core architecture) capabilities can be combined with OpenDX (which has a visual programming environment), but also demonstrates that lt can be done without losing much performance.

User Interface Abstraction for enabling TV set based Inclusive Access to the Information Society

199 p.

Comunicación audio visual y creatividad como recurso para producir nuevas formas de periodismo cultural local: estudio de caso, la tradición artesanal en el cantón Cuenca

No existe en Cuenca un proyecto de investigación periodística y de producción audiovisual que indague, recopile y presente información sobre aquellas profesiones tradicionales heredadas a través del tiempo y que poco a poco se van perdiendo con miras a extinguirse completamente. Este proyecto, de cierta manera, puede ser innovador, ya que involucra dos áreas: comunicación audiovisual y redacción dentro del periodismo. Se involucran por el hecho de presentar información relevante, a través de un producto final, visual y escrito, que enseñe de quéforma estas profesiones son desarrolladas por diferentes actores humanos, sus contextos y sus procesos, con la intención de servir de apoyo investigativo cultural en el ámbito local y nacional.

O museu virtual Google Art Project : um estudo de caso em contexto de ensino-aprendizagem da educação visual

A educação na arte e pela arte confere a todos os seus intervenientes a estimulação da sua criatividade e da sua consciência cultural, proporcionando meios para se exprimirem e participarem ativamente no mundo que nos rodeia. A integração das tecnologias de informação e comunicação no processo de ensino-aprendizagem veio alargar o papel que a arte pode desempenhar neste processo, promovendo novas formas de aprender, de ensinar e de pensar. Assim, a utilização de ambientes virtuais em contexto educativo tem revelado um enorme potencial, sobretudo ao nível da comunicação e da interação entre alunos e obras de arte. Neste sentido, considerou-se importante desenvolver um estudo de caso em contexto de sala de aula da Educação Visual, promovendo uma aprendizagem baseada na articulação entre a observação, interpretação e análise da obra de arte e o museu virtual. Assim o principal objetivo deste estudo foi avaliar as potencialidades do Google Art Project, enquanto objeto de aprendizagem, na promoção da aprendizagem na área da literacia em artes. Para além disso, procurámos ainda avaliar se a utilização de ferramentas multimédia como o referido Google Art Project e o Quadro Interativo, constituem fatores de motivação na aprendizagem da disciplina de Educação Visual. Do ponto de vista metodológico desenvolvemos uma estratégia baseada na investigação-ação. Procurámos, por um lado, descobrir e compreender o significado de uma realidade vivida por um grupo de alunos e, por outro lado, refletir sobre a prática educativa com o intuito de a melhorar e transformar. Este estudo envolveu cinco turmas do sexto ano do ensino público. Para a recolha de dados utilizámos técnicas baseadas na conversação e na observação, no questionário e nas notas de campo. Os resultados deste estudo revelam que as ferramentas tecnológicas utilizadas podem efetivamente contribuir para a promoção da aprendizagem dos alunos na área da Educação Visual, mais concretamente ao nível do domínio da literacia artística, da representação e da interpretação visual.

A novel methodology for simulating contact-line behavior in capillary-driven flows

Despite the wide swath of applications where multiphase fluid contact lines exist, there is still no consensus on an accurate and general simulation methodology. Most prior numerical work has imposed one of the many dynamic contact-angle theories at solid walls. Such approaches are inherently limited by the theory accuracy. In fact, when inertial effects are important, the contact angle may be history dependent and, thus, any single mathematical function is inappropriate. Given these limitations, the present work has two primary goals: 1) create a numerical framework that allows the contact angle to evolve naturally with appropriate contact-line physics and 2) develop equations and numerical methods such that contact-line simulations may be performed on coarse computational meshes.

Fluid flows affected by contact lines are dominated by capillary stresses and require accurate curvature calculations. The level set method was chosen to track the fluid interfaces because it is easy to calculate interface curvature accurately. Unfortunately, the level set reinitialization suffers from an ill-posed mathematical problem at contact lines: a ``blind spot'' exists. Standard techniques to handle this deficiency are shown to introduce parasitic velocity currents that artificially deform freely floating (non-prescribed) contact angles. As an alternative, a new relaxation equation reinitialization is proposed to remove these spurious velocity currents and its concept is further explored with level-set extension velocities.

To capture contact-line physics, two classical boundary conditions, the Navier-slip velocity boundary condition and a fixed contact angle, are implemented in direct numerical simulations (DNS). DNS are found to converge only if the slip length is well resolved by the computational mesh. Unfortunately, since the slip length is often very small compared to fluid structures, these simulations are not computationally feasible for large systems. To address the second goal, a new methodology is proposed which relies on the volumetric-filtered Navier-Stokes equations. Two unclosed terms, an average curvature and a viscous shear VS, are proposed to represent the missing microscale physics on a coarse mesh.

All of these components are then combined into a single framework and tested for a water droplet impacting a partially-wetting substrate. Very good agreement is found for the evolution of the contact diameter in time between the experimental measurements and the numerical simulation. Such comparison would not be possible with prior methods, since the Reynolds number Re and capillary number Ca are large. Furthermore, the experimentally approximated slip length ratio is well outside of the range currently achievable by DNS. This framework is a promising first step towards simulating complex physics in capillary-dominated flows at a reasonable computational expense.

Design de comunicação e a cultura visual portuguesa

Dissertação de Mestrado para obtenção do grau de Mestre em Design de Comunicação, apresentada na Universidade de Lisboa - Faculdade de Arquitectura.

Personalidade da marca

Dissertação para obtenção do grau de Mestre em Design de Comunicação, apresentada na Universidade de Lisboa - Faculdade de Arquitetura.

Interface de app para dispositivos móveis de universidade virtual, caso da UAb

O avanço das tecnologias de informação continua a mudar os paradigmas de ensino e aprendizagem. Os meios disponíveis são cada vez mais diversificados e, com a necessidade de procurar novos estudantes e diversificar o público-alvo, as instituições de ensino superior estão a repensar os seus modelos de negócio e estratégias pedagógicas. A proliferação de dispositivos móveis catalisa uma aposta crescente no ensino a distância (EaD) no sentido de proporcionar aprendizagens em mobilidade (m-learning). No entanto, as soluções existentes para m-learning são ainda pouco adaptadas às recentes metodologias de EaD, na maioria das vezes funcionando como extensão de um ambiente virtual de aprendizagem ou com muito foco nos conteúdos. Sendo a Universidade Aberta (UAb) a única instituição de ensino superior público em Portugal de ensino a distância, com um modelo pedagógico próprio, constitui um natural caso de aplicação de tecnologia móvel em novos contextos de aprendizagem, importando por isso estudar e desenhar os mecanismos de interação mais adequados com professores e estudantes em mobilidade. Adotou-se neste trabalho a metodologia Design Science Research, tendo sido identificadas as características e comportamentos de potenciais utilizadores, e definidas as funcionalidades que devem ser disponibilizadas na primeira versão de uma aplicação para dispositivos móveis (app) no contexto do ensino a distância. É proposto o design da interface dessa app, usando o modelo da UAb como caso de aplicação, e disponibilizada uma lista de orientações para o desenvolvimento do protótipo funcional. Da investigação realizada, concluiu-se que a interface proposta constitui um modelo válido para o desenho de uma app para aprendizagens em mobilidade, no regime de ensino de uma universidade virtual. A partir deste modelo, as instituições de ensino superior podem desenvolver apps adaptando-se ao avanço das Tecnologias de Informação e Comunicação e ficarem alinhadas com as necessidades dos seus alunos e docentes, particularmente se dispuserem de oferta formativa a distância.

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments.

Learning data-driven models of non-verbal behaviors for building rapport using an intelligent virtual agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness.^ Evidence-based patient-centered Brief Motivational Interviewing (BMI) interventions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary.^ Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems.^ To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14].^

Cognitive and Visual Speech Contributions to Speech Perception in Challenging Listening Conditions

Speech perception routinely takes place in noisy or degraded listening environments, leading to ambiguity in the identity of the speech token. Here, I present one review paper and two experimental papers that highlight cognitive and visual speech contributions to the listening process, particularly in challenging listening environments. First, I survey the literature linking audiometric age-related hearing loss and cognitive decline and review the four proposed causal mechanisms underlying this link. I argue that future research in this area requires greater consideration of the functional overlap between hearing and cognition. I also present an alternative framework for understanding causal relationships between age-related declines in hearing and cognition, with emphasis on the interconnected nature of hearing and cognition and likely contributions from multiple causal mechanisms. I also provide a number of testable hypotheses to examine how impairments in one domain may affect the other. In my first experimental study, I examine the direct contribution of working memory (through a cognitive training manipulation) on speech in noise comprehension in older adults. My results challenge the efficacy of cognitive training more generally, and also provide support for the contribution of sentence context in reducing working memory load. My findings also challenge the ubiquitous use of the Reading Span test as a pure test of working memory. In a second experimental (fMRI) study, I examine the role of attention in audiovisual speech integration, particularly when the acoustic signal is degraded. I demonstrate that attentional processes support audiovisual speech integration in the middle and superior temporal gyri, as well as the fusiform gyrus. My results also suggest that the superior temporal sulcus is sensitive to intelligibility enhancement, regardless of how this benefit is obtained (i.e., whether it is obtained through visual speech information or speech clarity). In addition, I also demonstrate that both the cingulo-opercular network and motor speech areas are recruited in difficult listening conditions. Taken together, these findings augment our understanding of cognitive contributions to the listening process and demonstrate that memory, working memory, and executive control networks may flexibly be recruited in order to meet listening demands in challenging environments.

Opérationnalisation des actes de langage en interface Homme-Machine tangible et avancée pour un assistant culinaire destiné à des personnes ayant un traumatisme crânien cérébral

Les activités de la vie quotidienne sont indispensables pour le bien-être physique et moral. Pour que celle-ci soit réussie par les personnes ayant un traumatisme crânien cérébral (TCC), une aide technologique s’avère souvent nécessaire. Les troubles cognitifs empêchent les personnes ayant un TCC de rester chez elles. L’assistant culinaire est un outil composé de trois sous-systèmes: assistance, supervision et communication. L’assistant permet aux personnes ayant un TCC de cuisiner un repas chaud en proposant à celles-ci des stratégies d’assistance cognitive. Ce mémoire présente le sous-système de communication, qui établit la communication entre la personne ayant un TCC et l’assistant culinaire. Nous avons utilisé la méthode LUCID pour concevoir le sous-système de communication. Tout d’abord, nous avons commencé par l’étape prospective et d’exploration pour définir les membres de l’équipe et leurs rôles, afin de comprendre le comportement des personnes ayant un TCC. Pour la compréhension des comportements, nous avons utilisé les persona et des scénarios. Nous avons conçu trois persona principaux (TCC sévère, modéré et léger) et deux secondaires (proche aidant et ergothérapeute). Après la validation des persona, nous avons construit deux scénarios, un sans assistance qui permet de comprendre la gradation d’assistance donnée par l’ergothérapeute durant l’évaluation, un avec assistance pour concevoir les fonctionnalités de l’assistant culinaire et d’établir la communication entre les trois sous-systèmes et l’utilisateur. Ensuite, nous avons conçu les interfaces de l’assistant culinaire selon chaque profil des AVQ. Finalement nous avons développé le sous-système de communication en utilisant des actes de langage pour définir la communication entre les trois sous-systèmes de communication et la gradation de l’assistance, des web service REST comme une technologie qui rend chaque sous-système indépendant. L’assistant culinaire est en cours de développement. Enfin, ultérieurement les différentes fonctionnalités de l’assistant seront testées dans l’appartement de laboratoire DOMUS, et ensuite il sera implémenté auprès de personnes ayant un TCC pour une utilisation régulière chez elles.

Por baixo da pele outra pele: conjunto de obras artísticas. Corpo, ecrã e interface para uma visualidade háptica interativa

A tese teórico-prática de doutoramento apresentada contempla a investigação, a criação, a produção e a conceptualização da instalação artística interativa intitulada Por baixo da pele outra pele. A Obra é constituída por três objetos tridimensionais concebidos à escala humana. Recorre a materiais flexíveis, como têxteis, convidando o público (interator), à envolvência física, numa relação corporal sensorial e sensual com a obra. Os objetos contêm dispositivos técnicos interativos e sensores tácteis, que, ao serem utilizados, desencadeiam estímulos multissensoriais no espectador. A instalação interativa focaliza a experiência háptica e íntima do interator considerando os seus mecanismos sensoriais e cognitivos como um potencial aparato na construção de experiências fenomenológicas, singulares e individuais. A autora considera a interatividade enquanto elemento potenciador da experiência estética visual háptica. Na argumentação conceitual da obra, reflete-se sobre o tema da visualidade háptica interativa a partirdos conceitos de ecrã, corpo e interface, assim como de endossensorialidade. Instrumentam-se metodologias de investigação em ação, experimentais e observacionais. Apresentam-se os processos investigativos, criativos e técnicos necessários ao desenvolvimento e à materialização da instalação artística. A investigação revela-se de grande interesse para o avanço da pesquisa de novas linguagens experimentais apresentando estratégias de criação artística que, ao privilegiarem o corpo físico e fenomenológico do interator, transpõe a experiência háptica interativa para um grau interno de imersão motoro-sensorial; Underneath the skin another skin: art installation. Body, screen and interface towards an interactive haptic visuality. Abstract: The theoretical-practical doctorate dissertation presents the research and conceptual framework behind, and the processes leading to, the creation and production of the interactive installation art piece Underneath the skin, another skin. The piece is presented in the shape of three human-scale tridimentional objects. It is made from flexible materials, such as textiles, inviting the (interacting) audience, to physically engage in a bodily sensorial, and sensuous, relationship with the artwork. The objects enclose interactive devices and tactile sensors that, when used, trigger in the interactor multiple sensorial stimuli. The interactive installation focuses on the interactor's intimate haptic experience taking in consideration his or hers sensorial and cognitive mechanisms as a potential apparatus in the construction of unique individual phenomenological experiences. The author understands interactivity as a triggering element into an haptic visual aesthetical experience. The supporting conceptual reasoning deals with thought and criticism on interactive haptic visuality applied to the concepts of screen, body and interface, as well as with that of endo-sensoriality. The dissertation describes the use of experimental and observation research methodologies. It also elaborates on the research, creative and technical processes at play in the installation's development and realization. The research at hand has shown great potential for the further development of new experimental languages, as it presents art-creation strategies privileging the interactor's physical and phenomenological body, and thus able to take the interactive haptic experience onto an greater inner level of motor-sensorial immersion.

Plasticity and neuromodulation of the extended recurrent visual network

The extended visual network, which includes occipital, temporal and parietal posterior cortices, is a system characterized by an intrinsic connectivity consisting of bidirectional projections. This network is composed of feedforward and feedback projections, some hierarchically arranged and others bypassing intermediate areas, allowing direct communication across early and late stages of processing. Notably, the early visual cortex (EVC) receives considerably more feedback and lateral inputs than feedforward thalamic afferents, placing it at the receiving end of a complex cortical processing cascade, rather than just being the entrance stage of cortical processing of retinal input. The critical role of back-projections to visual cortices has been related to perceptual awareness, amplification of neural activity in lower order areas and improvement of stimulus processing. Recently, significant results have shown behavioural evidence suggesting the importance of reentrant projections in the human visual system, and demonstrated the feasibility of inducing their reversible modulation through a transcranial magnetic stimulation (TMS) paradigm named cortico-cortical paired associative stimulation (ccPAS). Here, a novel research line for the study of recurrent connectivity and its plasticity in the perceptual domain was put forward. In the present thesis, we used ccPAS with the aim of empowering the synaptic efficacy, and thus the connectivity, between the nodes of the visuocognitive system to evaluate the impact on behaviour. We focused on driving plasticity in specific networks entailing the elaboration of relevant social features of human faces (Chapters I & II), alongside the investigation of targeted pathways of sensory decisions (Chapter III). This allowed us to characterize perceptual outcomes which endorse the prominent role of the EVC in visual awareness, fulfilled by the activity of back-projections originating from distributed functional nodes.