Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

Proprioceptive force estimation and control for teleoperation in radioactive environments

A medida que se incrementa la energía de los aceleradores de partículas o iones pesados como el CERN o GSI, de los reactores de fusión como JET o ITER, u otros experimentos científicos, se va haciendo cada vez más imprescindible el uso de técnicas de manipulación remota para la interacción con el entorno sujeto a la radiación. Hasta ahora la tasa de dosis radioactiva en el CERN podía tomar valores cercanos a algunos mSv para tiempos de enfriamiento de horas, que permitían la intervención humana para tareas de mantenimiento. Durante los primeros ensayos con plasma en JET, se alcanzaban valores cercanos a los 200 μSv después de un tiempo de enfriamiento de 4 meses y ya se hacía extensivo el uso de técnicas de manipulación remota. Hay una clara tendencia al incremento de los niveles de radioactividad en el futuro en este tipo de instalaciones. Un claro ejemplo es ITER, donde se esperan valores de 450 Sv/h en el centro del toroide a los 11 días de enfriamiento o los nuevos niveles energéticos del CERN que harán necesario una apuesta por niveles de mantenimiento remotos. En estas circunstancias se enmarca esta tesis, que estudia un sistema de control bilateral basado en fuerza-posición, tratando de evitar el uso de sensores de fuerza/par, cuyo contenido electrónico los hace especialmente sensitivos en estos ambientes. El contenido de este trabajo se centra en la teleoperación de robots industriales, que debido a su reconocida solvencia y facilidad para ser adaptados a estos entornos, unido al bajo coste y alta disponibilidad, les convierte en una alternativa interesante para tareas de manipulación remota frente a costosas soluciones a medida. En primer lugar se considera el problema cinemático de teleoperación maestro-esclavo de cinemática disimilar y se desarrolla un método general para la solución del problema en el que se incluye el uso de fuerzas asistivas para guiar al operador. A continuación se explican con detalle los experimentos realizados con un robot ABB y que muestran las dificultades encontradas y recomendaciones para solventarlas. Se concluye el estudio cinemático con un método para el encaje de espacios de trabajo entre maestro y esclavo disimilares. Posteriormente se mira hacia la dinámica, estudiándose el modelado de robots con vistas a obtener un método que permita estimar las fuerzas externas que actúan sobre los mismos. Durante la caracterización del modelo dinámico, se realizan varios ensayos para tratar de encontrar un compromiso entre complejidad de cálculo y error de estimación. También se dan las claves para modelar y caracterizar robots con estructura en forma de paralelogramo y se presenta la arquitectura de control deseada. Una vez obtenido el modelo completo del esclavo, se investigan diferentes alternativas que permitan una estimación de fuerzas externas en tiempo real, minimizando las derivadas de la posición para minimizar el ruido. Se comienza utilizando observadores clásicos del estado para ir evolucionando hasta llegar al desarrollo de un observador de tipo Luenberger-Sliding cuya implementación es relativamente sencilla y sus resultados contundentes. También se analiza el uso del observador propuesto durante un control bilateral simulado en el que se compara la realimentación de fuerzas obtenida con las técnicas clásicas basadas en error de posición frente a un control basado en fuerza-posición donde la fuerza es estimada y no medida. Se comprueba como la solución propuesta da resultados comparables con las arquitecturas clásicas y sin embargo introduce una alternativa para la teleoperación de robots industriales cuya teleoperación en entornos radioactivos sería imposible de otra manera. Finalmente se analizan los problemas derivados de la aplicación práctica de la teleoperación en los escenarios mencionados anteriormente. Debido a las condiciones prohibitivas para todo equipo electrónico, los sistemas de control se deben colocar a gran distancia de los manipuladores, dando lugar a longitudes de cable de centenares de metros. En estas condiciones se crean sobretensiones en controladores basados en PWM que pueden ser destructivas para el sistema formado por control, cableado y actuador, y por tanto, han de ser eliminadas. En este trabajo se propone una solución basada en un filtro LC comercial y se prueba de forma extensiva que su inclusión no produce efectos negativos sobre el control del actuador. ABSTRACT As the energy on the particle accelerators or heavy ion accelerators such as CERN or GSI, fusion reactors such as JET or ITER, or other scientific experiments is increased, it is becoming increasingly necessary to use remote handling techniques to interact with the remote and radioactive environment. So far, the dose rate at CERN could present values near several mSv for cooling times on the range of hours, which allowed human intervention for maintenance tasks. At JET, they measured values close to 200 μSv after a cooling time of 4 months and since then, the remote handling techniques became usual. There is a clear tendency to increase the radiation levels in the future. A clear example is ITER, where values of 450 Sv/h are expected in the centre of the torus after 11 days of cooling. Also, the new energetic levels of CERN are expected to lead to a more advanced remote handling means. In these circumstances this thesis is framed, studying a bilateral control system based on force-position, trying to avoid the use of force/torque sensors, whose electronic content makes them very sensitive in these environments. The contents of this work are focused on teleoperating industrial robots, which due its well-known reliability, easiness to be adapted to these environments, cost-effectiveness and high availability, are considered as an interesting alternative to expensive custom-made solutions for remote handling tasks. Firstly, the kinematic problem of teloperating master and slave with dissimilar kinematics is analysed and a new general approach for solving this issue is presented. The solution includes using assistive forces in order to guide the human operator. Coming up next, I explain with detail the experiments accomplished with an ABB robot that show the difficulties encountered and the proposed solutions. This section is concluded with a method to match the master’s and slave’s workspaces when they present dissimilar kinematics. Later on, the research studies the dynamics, with special focus on robot modelling with the purpose of obtaining a method that allows to estimate external forces acting on them. During the characterisation of the model’s parameters, a set of tests are performed in order to get to a compromise between computational complexity and estimation error. Key points for modelling and characterising robots with a parallelogram structure are also given, and the desired control architecture is presented. Once a complete model of the slave is obtained, different alternatives for external force estimation are review to be able to predict forces in real time, minimizing the position differentiation to minimize the estimation noise. The research starts by implementing classic state observers and then it evolves towards the use of Luenberger- Sliding observers whose implementation is relatively easy and the results are convincing. I also analyse the use of proposed observer during a simulated bilateral control on which the force feedback obtained with the classic techniques based on the position error is compared versus a control architecture based on force-position, where the force is estimated instead of measured. I t is checked how the proposed solution gives results comparable with the classical techniques and however introduces an alternative method for teleoperating industrial robots whose teleoperation in radioactive environments would have been impossible in a different way. Finally, the problems originated by the practical application of teleoperation in the before mentioned scenarios are analysed. Due the prohibitive conditions for every electronic equipment, the control systems should be placed far from the manipulators. This provokes that the power cables that fed the slaves devices can present lengths of hundreds of meters. In these circumstances, overvoltage waves are developed when implementing drives based on PWM technique. The occurrence of overvoltage is very dangerous for the system composed by drive, wiring and actuator, and has to be eliminated. During this work, a solution based on commercial LC filters is proposed and it is extensively proved that its inclusion does not introduce adverse effects into the actuator’s control.

Proposal of a trust and reputation model to provide recommendation in open quality oriented environments

El auge y penetración de las nuevas tecnologías junto con la llamada Web Social están cambiando la forma en la que accedemos a la medicina. Cada vez más pacientes y profesionales de la medicina están creando y consumiendo recursos digitales de contenido clínico a través de Internet, surgiendo el problema de cómo asegurar la fiabilidad de estos recursos. Además, un nuevo concepto está apareciendo, el de pervasive healthcare o sanidad ubicua, motivado por pacientes que demandan un acceso a los servicios sanitarios en todo momento y en todo lugar. Este nuevo escenario lleva aparejado un problema de confianza en los proveedores de servicios sanitarios. Las plataformas de eLearning se están erigiendo como paradigma de esta nueva Medicina 2.0 ya que proveen un servicio abierto a la vez que controlado/supervisado a recursos digitales, y facilitan las interacciones y consultas entre usuarios, suponiendo una buena aproximación para esta sanidad ubicua. En estos entornos los problemas de fiabilidad y confianza pueden ser solventados mediante la implementación de mecanismos de recomendación de recursos y personas de manera confiable. Tradicionalmente las plataformas de eLearning ya cuentan con mecanismos de recomendación, si bien están más enfocados a la recomendación de recursos. Para la recomendación de usuarios es necesario acudir a mecanismos más elaborados como son los sistemas de confianza y reputación (trust and reputation) En ambos casos, tanto la recomendación de recursos como el cálculo de la reputación de los usuarios se realiza teniendo en cuenta criterios principalmente subjetivos como son las opiniones de los usuarios. En esta tesis doctoral proponemos un nuevo modelo de confianza y reputación que combina evaluaciones automáticas de los recursos digitales en una plataforma de eLearning, con las opiniones vertidas por los usuarios como resultado de las interacciones con otros usuarios o después de consumir un recurso. El enfoque seguido presenta la novedad de la combinación de una parte objetiva con otra subjetiva, persiguiendo mitigar el efecto de posibles castigos subjetivos por parte de usuarios malintencionados, a la vez que enriquecer las evaluaciones objetivas con información adicional acerca de la capacidad pedagógica del recurso o de la persona. El resultado son recomendaciones siempre adaptadas a los requisitos de los usuarios, y de la máxima calidad tanto técnica como educativa. Esta nueva aproximación requiere una nueva herramienta para su validación in-silico, al no existir ninguna aplicación que permita la simulación de plataformas de eLearning con mecanismos de recomendación de recursos y personas, donde además los recursos sean evaluados objetivamente. Este trabajo de investigación propone pues una nueva herramienta, basada en el paradigma de programación orientada a agentes inteligentes para el modelado de comportamientos complejos de usuarios en plataformas de eLearning. Además, la herramienta permite también la simulación del funcionamiento de este tipo de entornos dedicados al intercambio de conocimiento. La evaluación del trabajo propuesto en este documento de tesis se ha realizado de manera iterativa a lo largo de diferentes escenarios en los que se ha situado al sistema frente a una amplia gama de comportamientos de usuarios. Se ha comparado el rendimiento del modelo de confianza y reputación propuesto frente a dos modos de recomendación tradicionales: a) utilizando sólo las opiniones subjetivas de los usuarios para el cálculo de la reputación y por extensión la recomendación; y b) teniendo en cuenta sólo la calidad objetiva del recurso sin hacer ningún cálculo de reputación. Los resultados obtenidos nos permiten afirmar que el modelo desarrollado mejora la recomendación ofrecida por las aproximaciones tradicionales, mostrando una mayor flexibilidad y capacidad de adaptación a diferentes situaciones. Además, el modelo propuesto es capaz de asegurar la recomendación de nuevos usuarios entrando al sistema frente a la nula recomendación para estos usuarios presentada por el modo de recomendación predominante en otras plataformas que basan la recomendación sólo en las opiniones de otros usuarios. Por último, el paradigma de agentes inteligentes ha probado su valía a la hora de modelar plataformas virtuales complejas orientadas al intercambio de conocimiento, especialmente a la hora de modelar y simular el comportamiento de los usuarios de estos entornos. La herramienta de simulación desarrollada ha permitido la evaluación del modelo de confianza y reputación propuesto en esta tesis en una amplia gama de situaciones diferentes. ABSTRACT Internet is changing everything, and this revolution is especially present in traditionally offline spaces such as medicine. In recent years health consumers and health service providers are actively creating and consuming Web contents stimulated by the emergence of the Social Web. Reliability stands out as the main concern when accessing the overwhelming amount of information available online. Along with this new way of accessing the medicine, new concepts like ubiquitous or pervasive healthcare are appearing. Trustworthiness assessment is gaining relevance: open health provisioning systems require mechanisms that help evaluating individuals’ reputation in pursuit of introducing safety to these open and dynamic environments. Technical Enhanced Learning (TEL) -commonly known as eLearning- platforms arise as a paradigm of this Medicine 2.0. They provide an open while controlled/supervised access to resources generated and shared by users, enhancing what it is being called informal learning. TEL systems also facilitate direct interactions amongst users for consultation, resulting in a good approach to ubiquitous healthcare. The aforementioned reliability and trustworthiness problems can be faced by the implementation of mechanisms for the trusted recommendation of both resources and healthcare services providers. Traditionally, eLearning platforms already integrate recommendation mechanisms, although this recommendations are basically focused on providing an ordered classifications of resources. For users’ recommendation, the implementation of trust and reputation systems appears as the best solution. Nevertheless, both approaches base the recommendation on the information from the subjective opinions of other users of the platform regarding the resources or the users. In this PhD work a novel approach is presented for the recommendation of both resources and users within open environments focused on knowledge exchange, as it is the case of TEL systems for ubiquitous healthcare. The proposed solution adds the objective evaluation of the resources to the traditional subjective personal opinions to estimate the reputation of the resources and of the users of the system. This combined measure, along with the reliability of that calculation, is used to provide trusted recommendations. The integration of opinions and evaluations, subjective and objective, allows the model to defend itself against misbehaviours. Furthermore, it also allows ‘colouring’ cold evaluation values by providing additional quality information such as the educational capacities of a digital resource in an eLearning system. As a result, the recommendations are always adapted to user requirements, and of the maximum technical and educational quality. To our knowledge, the combination of objective assessments and subjective opinions to provide recommendation has not been considered before in the literature. Therefore, for the evaluation of the trust and reputation model defined in this PhD thesis, a new simulation tool will be developed following the agent-oriented programming paradigm. The multi-agent approach allows an easy modelling of independent and proactive behaviours for the simulation of users of the system, conforming a faithful resemblance of real users of TEL platforms. For the evaluation of the proposed work, an iterative approach have been followed, testing the performance of the trust and reputation model while providing recommendation in a varied range of scenarios. A comparison with two traditional recommendation mechanisms was performed: a) using only users’ past opinions about a resource and/or other users; and b) not using any reputation assessment and providing the recommendation considering directly the objective quality of the resources. The results show that the developed model improves traditional approaches at providing recommendations in Technology Enhanced Learning (TEL) platforms, presenting a higher adaptability to different situations, whereas traditional approaches only have good results under favourable conditions. Furthermore the promotion period mechanism implemented successfully helps new users in the system to be recommended for direct interactions as well as the resources created by them. On the contrary OnlyOpinions fails completely and new users are never recommended, while traditional approaches only work partially. Finally, the agent-oriented programming (AOP) paradigm has proven its validity at modelling users’ behaviours in TEL platforms. Intelligent software agents’ characteristics matched the main requirements of the simulation tool. The proactivity, sociability and adaptability of the developed agents allowed reproducing real users’ actions and attitudes through the diverse situations defined in the evaluation framework. The result were independent users, accessing to different resources and communicating amongst them to fulfil their needs, basing these interactions on the recommendations provided by the reputation engine.

Multi-textured 3D humanoid reconstruction through passive and active automatic techniques = Reconstrucción de humanoides 3D multi-texturados mediante técnicas pasivas y activas automáticas

The proliferation of video games and other applications of computer graphics in everyday life demands a much easier way to create animatable virtual human characters. Traditionally, this has been the job of highly skilled artists and animators that painstakingly model, rig and animate their avatars, and usually have to tune them for each application and transmission/rendering platform. The emergence of virtual/mixed reality environments also calls for practical and costeffective ways to produce custom models of actual people. The purpose of the present dissertation is bringing 3D human scanning closer to the average user. For this, two different techniques are presented, one passive and one active. The first one is a fully automatic system for generating statically multi-textured avatars of real people captured with several standard cameras. Our system uses a state-of-the-art shape from silhouette technique to retrieve the shape of subject. However, to deal with the lack of detail that is common in the facial region for these kind of techniques, which do not handle concavities correctly, our system proposes an approach to improve the quality of this region. This face enhancement technique uses a generic facial model which is transformed according to the specific facial features of the subject. Moreover, this system features a novel technique for generating view-independent texture atlases computed from the original images. This static multi-texturing system yields a seamless texture atlas calculated by combining the color information from several photos. We suppress the color seams due to image misalignments and irregular lighting conditions that multi-texturing approaches typically suffer from, while minimizing the blurring effect introduced by color blending techniques. The second technique features a system to retrieve a fully animatable 3D model of a human using a commercial depth sensor. Differently to other approaches in the current state of the art, our system does not require the user to be completely still through the scanning process, and neither the depth sensor is moved around the subject to cover all its surface. Instead, the depth sensor remains static and the skeleton tracking information is used to compensate the user’s movements during the scanning stage. RESUMEN La popularización de videojuegos y otras aplicaciones de los gráficos por ordenador en el día a día requiere una manera más sencilla de crear modelos virtuales humanos animables. Tradicionalmente, estos modelos han sido creados por artistas profesionales que cuidadosamente los modelan y animan, y que tienen que adaptar específicamente para cada aplicación y plataforma de transmisión o visualización. La aparición de los entornos de realidad virtual/mixta aumenta incluso más la demanda de técnicas prácticas y baratas para producir modelos 3D representando personas reales. El objetivo de esta tesis es acercar el escaneo de humanos en 3D al usuario medio. Para ello, se presentan dos técnicas diferentes, una pasiva y una activa. La primera es un sistema automático para generar avatares multi-texturizados de personas reales mediante una serie de cámaras comunes. Nuestro sistema usa técnicas del estado del arte basadas en shape from silhouette para extraer la forma del sujeto a escanear. Sin embargo, este tipo de técnicas no gestiona las concavidades correctamente, por lo que nuestro sistema propone una manera de incrementar la calidad en una región del modelo que se ve especialmente afectada: la cara. Esta técnica de mejora facial usa un modelo 3D genérico de una cara y lo modifica según los rasgos faciales específicos del sujeto. Además, el sistema incluye una novedosa técnica para generar un atlas de textura a partir de las imágenes capturadas. Este sistema de multi-texturización consigue un atlas de textura sin transiciones abruptas de color gracias a su manera de mezclar la información de color de varias imágenes sobre cada triángulo. Todas las costuras y discontinuidades de color debidas a las condiciones de iluminación irregulares son eliminadas, minimizando el efecto de desenfoque de la interpolación que normalmente introducen este tipo de métodos. La segunda técnica presenta un sistema para conseguir un modelo humano 3D completamente animable utilizando un sensor de profundidad. A diferencia de otros métodos del estado de arte, nuestro sistema no requiere que el usuario esté completamente quieto durante el proceso de escaneado, ni mover el sensor alrededor del sujeto para cubrir toda su superficie. Por el contrario, el sensor se mantiene estático y el esqueleto virtual de la persona, que se va siguiendo durante el proceso, se utiliza para compensar sus movimientos durante el escaneado.

Harvested populations are more variable only in more variable environments

Acknowledgments This work was funded by NERC grant NE/C510467/1 (T. G. Benton and S. B. Piertney) and a University of Leeds Faculty Postdoctoral Fellowship (T. C. Cameron). Data Accessibility The original time series and body size data from these experiments are available to download from DRYAD entry number http://dx.doi.org/10.5061/dryad.bq135.

Successful external fertilization in turbulent environments.

Mathematical and experimental simulations predict that external fertilization is unsuccessful in habitats characterized by high water motion. A key assumption of such predictions is that gametes are released in hydrodynamic regimes that quickly dilute gametes. We used fucoid seaweeds to examine whether marine organisms in intertidal and subtidal habitats might achieve high levels of fertilization by restricting their release of gametes to calm intervals. Fucus vesiculosus L. (Baltic Sea) released high numbers of gametes only when maximal water velocities were below ca. 0.2 m/s immediately prior to natural periods of release, which occur in early evening in association with lunar cues. Natural fertilization success measured at two sites was always close to 100%. Laboratory experiments confirmed that (i) high water motion inhibits gamete release by F. vesiculosus and by the intertidal fucoids Fucus distichus L. (Maine) and Pelvetia fastigiata (J. Ag.) DeToni (California), and (ii) showed that photosynthesis is required for high gamete release. These data suggest that chemical changes in the boundary layer surrounding adults during photosynthesis and/or mechanosensitive channels may modulate gamete release in response to changing hydrodynamic conditions. Therefore, sensitivity to environmental factors can lead to successful external fertilization, even for species living in turbulent habitats.

Alternativas de análise para experimentos G × E multiatributo

Geralmente, nos experimentos genótipo por ambiente (G × E) é comum observar o comportamento dos genótipos em relação a distintos atributos nos ambientes considerados. A análise deste tipo de experimentos tem sido abordada amplamente para o caso de um único atributo. Nesta tese são apresentadas algumas alternativas de análise considerando genótipos, ambientes e atributos simultaneamente. A primeira, é baseada no método de mistura de máxima verossimilhança de agrupamento - Mixclus e a análise de componentes principais de 3 modos - 3MPCA, que permitem a análise de tabelas de tripla entrada, estes dois métodos têm sido muito usados na área da psicologia e da química, mas pouco na agricultura. A segunda, é uma metodologia que combina, o modelo de efeitos aditivos com interação multiplicativa - AMMI, modelo eficiente para a análise de experimentos (G × E) com um atributo e a análise de procrustes generalizada, que permite comparar configurações de pontos e proporcionar uma medida numérica de quanto elas diferem. Finalmente, é apresentada uma alternativa para realizar imputação de dados nos experimentos (G × E), pois, uma situação muito frequente nestes experimentos, é a presença de dados faltantes. Conclui-se que as metodologias propostas constituem ferramentas úteis para a análise de experimentos (G × E) multiatributo.

Robotic control systems based on bioinspired multi-agent systems: application of the principles of neuroscience to robotics

Robotics is a field that presents a large number of problems because it depends on a large number of disciplines, devices, technologies and tasks. Its expansion from perfectly controlled industrial environments toward open and dynamic environment presents a many new challenges, such as robots household robots or professional robots. To facilitate the rapid development of robotic systems, low cost, reusability of code, its medium and long term maintainability and robustness are required novel approaches to provide generic models and software systems who develop paradigms capable of solving these problems. For this purpose, in this paper we propose a model based on multi-agent systems inspired by the human nervous system able to transfer the control characteristics of the biological system and able to take advantage of the best properties of distributed software systems.

Multi-agent system for control of robots inspired on the distributed activity and hormonal regulation of humans

Robotics is an emerging field with great activity. Robotics is a field that presents several problems because it depends on a large number of disciplines, technologies, devices and tasks. Its expansion from perfectly controlled industrial environments toward open and dynamic environment presents a many new challenges. New uses are, for example, household robots or professional robots. To facilitate the low cost, rapid development of robotic systems, reusability of code, its medium and long term maintainability and robustness are required novel approaches to provide generic models and software systems who develop paradigms capable of solving these problems. For this purpose, in this paper we propose a model based on multi-agent systems inspired by the human nervous system able to transfer the control characteristics of the biological system and able to take advantage of the best properties of distributed software systems. Specifically, we model the decentralized activity and hormonal variation.

Feature selection by multi-objective optimisation: Application to network anomaly detection by hierarchical self-organising maps

Feature selection is an important and active issue in clustering and classification problems. By choosing an adequate feature subset, a dataset dimensionality reduction is allowed, thus contributing to decreasing the classification computational complexity, and to improving the classifier performance by avoiding redundant or irrelevant features. Although feature selection can be formally defined as an optimisation problem with only one objective, that is, the classification accuracy obtained by using the selected feature subset, in recent years, some multi-objective approaches to this problem have been proposed. These either select features that not only improve the classification accuracy, but also the generalisation capability in case of supervised classifiers, or counterbalance the bias toward lower or higher numbers of features that present some methods used to validate the clustering/classification in case of unsupervised classifiers. The main contribution of this paper is a multi-objective approach for feature selection and its application to an unsupervised clustering procedure based on Growing Hierarchical Self-Organising Maps (GHSOMs) that includes a new method for unit labelling and efficient determination of the winning unit. In the network anomaly detection problem here considered, this multi-objective approach makes it possible not only to differentiate between normal and anomalous traffic but also among different anomalies. The efficiency of our proposals has been evaluated by using the well-known DARPA/NSL-KDD datasets that contain extracted features and labelled attacks from around 2 million connections. The selected feature sets computed in our experiments provide detection rates up to 99.8% with normal traffic and up to 99.6% with anomalous traffic, as well as accuracy values up to 99.12%.

Three-dimensional planar model estimation using multi-constraint knowledge based on k-means and RANSAC

Plane model extraction from three-dimensional point clouds is a necessary step in many different applications such as planar object reconstruction, indoor mapping and indoor localization. Different RANdom SAmple Consensus (RANSAC)-based methods have been proposed for this purpose in recent years. In this study, we propose a novel method-based on RANSAC called Multiplane Model Estimation, which can estimate multiple plane models simultaneously from a noisy point cloud using the knowledge extracted from a scene (or an object) in order to reconstruct it accurately. This method comprises two steps: first, it clusters the data into planar faces that preserve some constraints defined by knowledge related to the object (e.g., the angles between faces); and second, the models of the planes are estimated based on these data using a novel multi-constraint RANSAC. We performed experiments in the clustering and RANSAC stages, which showed that the proposed method performed better than state-of-the-art methods.

3D Visual Data-Driven Spatiotemporal Deformations for Non-Rigid Object Grasping Using Robot Hands

Sensing techniques are important for solving problems of uncertainty inherent to intelligent grasping tasks. The main goal here is to present a visual sensing system based on range imaging technology for robot manipulation of non-rigid objects. Our proposal provides a suitable visual perception system of complex grasping tasks to support a robot controller when other sensor systems, such as tactile and force, are not able to obtain useful data relevant to the grasping manipulation task. In particular, a new visual approach based on RGBD data was implemented to help a robot controller carry out intelligent manipulation tasks with flexible objects. The proposed method supervises the interaction between the grasped object and the robot hand in order to avoid poor contact between the fingertips and an object when there is neither force nor pressure data. This new approach is also used to measure changes to the shape of an object’s surfaces and so allows us to find deformations caused by inappropriate pressure being applied by the hand’s fingers. Test was carried out for grasping tasks involving several flexible household objects with a multi-fingered robot hand working in real time. Our approach generates pulses from the deformation detection method and sends an event message to the robot controller when surface deformation is detected. In comparison with other methods, the obtained results reveal that our visual pipeline does not use deformations models of objects and materials, as well as the approach works well both planar and 3D household objects in real time. In addition, our method does not depend on the pose of the robot hand because the location of the reference system is computed from a recognition process of a pattern located place at the robot forearm. The presented experiments demonstrate that the proposed method accomplishes a good monitoring of grasping task with several objects and different grasping configurations in indoor environments.

Hydraulic conductivity and experiments of sediment beds

In marine environments, sediments from different sources are stirred and dispersed, generating beds that are composed of mixed and layered sediments of differing grain sizes. Traditional engineering formulations used to predict erosion thresholds are however, generally for unimodal sediment distributions, and so may be inadequate for commonly occurring coastal sediments. We tested the transport behavior of deposited and mixed sediment beds consisting of a simplified two-grain fraction (silt (D50 = 55 µm) and sand (D50 = 300 µm)) in a laboratory-based annular flume with the objective of investigating the parameters controlling the stability of a sediment bed. To mimic recent deposition of particles following large storm events and the longer-term result of the incorporation of fines in coarse sediment, we designed two suites of experiments: (1) "the layering experiment": in which a sandy bed was covered by a thin layer of silt of varying thickness (0.2 - 3 mm; 0.5 - 3.7 wt %, dry weight in a layer 10 cm deep); and (2) "the mixing experiment" where the bed was composed of sand homogeneously mixed with small amounts of silt (0.07 - 0.7 wt %, dry weight). To initiate erosion and to detect a possible stabilizing effect in both settings, we increased the flow speeds in increments up to 0.30 m/s. Results showed that the sediment bed (or the underlying sand bed in the case of the layering experiment) stabilized with increasing silt composition. The increasing sediment stability was defined by a shift of the initial threshold conditions towards higher flow speeds, combined with, in the case of the mixed bed, decreasing erosion rates. Our results show that even extremely low concentrations of silt play a stabilizing role (1.4% silt (wt %) on a layered sediment bed of 10 cm thickness). In the case of a mixed sediment bed, 0.18% silt (wt %, in a sample of 10 cm depth) stabilized the bed. Both cases show that the depositional history of the sediment fractions can change the erosion characteristics of the seabed. These observations are summarized in a conceptual model that suggests that, in addition to the effect on surface roughness, silt stabilizes the sand bed by pore-space plugging and reducing the inflow in the bed, and hence increases the bed stability. Measurements of hydraulic conductivity on similar bed assemblages qualitatively supported this conclusion by showing that silt could decrease the permeability by up to 22% in the case of a layered bed and by up to 70% in the case of a mixed bed.

Development and use of a computer simulation model for the evaluation of design and control alternatives for intersections of minor roads with multi-lane rural highways: field studies and model validation. Interim report.

Federal Highway Administration, Washington, D.C.

Development and use of a computer simulation model for the evaluation of design and control alternatives for intersections of minor roads with multi-lane rural highways: model application. Interim report.

Federal Highway Administration, Washington, D.C.