Functional and effective connectivity in MEG. Application to the study of epilepsy

Nuestro cerebro contiene cerca de 1014 sinapsis neuronales. Esta enorme cantidad de conexiones proporciona un entorno ideal donde distintos grupos de neuronas se sincronizan transitoriamente para provocar la aparición de funciones cognitivas, como la percepción, el aprendizaje o el pensamiento. Comprender la organización de esta compleja red cerebral en base a datos neurofisiológicos, representa uno de los desafíos más importantes y emocionantes en el campo de la neurociencia. Se han propuesto recientemente varias medidas para evaluar cómo se comunican las diferentes partes del cerebro a diversas escalas (células individuales, columnas corticales, o áreas cerebrales). Podemos clasificarlos, según su simetría, en dos grupos: por una parte, la medidas simétricas, como la correlación, la coherencia o la sincronización de fase, que evalúan la conectividad funcional (FC); mientras que las medidas asimétricas, como la causalidad de Granger o transferencia de entropía, son capaces de detectar la dirección de la interacción, lo que denominamos conectividad efectiva (EC). En la neurociencia moderna ha aumentado el interés por el estudio de las redes funcionales cerebrales, en gran medida debido a la aparición de estos nuevos algoritmos que permiten analizar la interdependencia entre señales temporales, además de la emergente teoría de redes complejas y la introducción de técnicas novedosas, como la magnetoencefalografía (MEG), para registrar datos neurofisiológicos con gran resolución. Sin embargo, nos hallamos ante un campo novedoso que presenta aun varias cuestiones metodológicas sin resolver, algunas de las cuales trataran de abordarse en esta tesis. En primer lugar, el creciente número de aproximaciones para determinar la existencia de FC/EC entre dos o más señales temporales, junto con la complejidad matemática de las herramientas de análisis, hacen deseable organizarlas todas en un paquete software intuitivo y fácil de usar. Aquí presento HERMES (http://hermes.ctb.upm.es), una toolbox en MatlabR, diseñada precisamente con este fin. Creo que esta herramienta será de gran ayuda para todos aquellos investigadores que trabajen en el campo emergente del análisis de conectividad cerebral y supondrá un gran valor para la comunidad científica. La segunda cuestión practica que se aborda es el estudio de la sensibilidad a las fuentes cerebrales profundas a través de dos tipos de sensores MEG: gradiómetros planares y magnetómetros, esta aproximación además se combina con un enfoque metodológico, utilizando dos índices de sincronización de fase: phase locking value (PLV) y phase lag index (PLI), este ultimo menos sensible a efecto la conducción volumen. Por lo tanto, se compara su comportamiento al estudiar las redes cerebrales, obteniendo que magnetómetros y PLV presentan, respectivamente, redes más densamente conectadas que gradiómetros planares y PLI, por los valores artificiales que crea el problema de la conducción de volumen. Sin embargo, cuando se trata de caracterizar redes epilépticas, el PLV ofrece mejores resultados, debido a la gran dispersión de las redes obtenidas con PLI. El análisis de redes complejas ha proporcionado nuevos conceptos que mejoran caracterización de la interacción de sistemas dinámicos. Se considera que una red está compuesta por nodos, que simbolizan sistemas, cuyas interacciones se representan por enlaces, y su comportamiento y topología puede caracterizarse por un elevado número de medidas. Existe evidencia teórica y empírica de que muchas de ellas están fuertemente correlacionadas entre sí. Por lo tanto, se ha conseguido seleccionar un pequeño grupo que caracteriza eficazmente estas redes, y condensa la información redundante. Para el análisis de redes funcionales, la selección de un umbral adecuado para decidir si un determinado valor de conectividad de la matriz de FC es significativo y debe ser incluido para un análisis posterior, se convierte en un paso crucial. En esta tesis, se han obtenido resultados más precisos al utilizar un test de subrogadas, basado en los datos, para evaluar individualmente cada uno de los enlaces, que al establecer a priori un umbral fijo para la densidad de conexiones. Finalmente, todas estas cuestiones se han aplicado al estudio de la epilepsia, caso práctico en el que se analizan las redes funcionales MEG, en estado de reposo, de dos grupos de pacientes epilépticos (generalizada idiopática y focal frontal) en comparación con sujetos control sanos. La epilepsia es uno de los trastornos neurológicos más comunes, con más de 55 millones de afectados en el mundo. Esta enfermedad se caracteriza por la predisposición a generar ataques epilépticos de actividad neuronal anormal y excesiva o bien síncrona, y por tanto, es el escenario perfecto para este tipo de análisis al tiempo que presenta un gran interés tanto desde el punto de vista clínico como de investigación. Los resultados manifiestan alteraciones especificas en la conectividad y un cambio en la topología de las redes en cerebros epilépticos, desplazando la importancia del ‘foco’ a la ‘red’, enfoque que va adquiriendo relevancia en las investigaciones recientes sobre epilepsia. ABSTRACT There are about 1014 neuronal synapses in the human brain. This huge number of connections provides the substrate for neuronal ensembles to become transiently synchronized, producing the emergence of cognitive functions such as perception, learning or thinking. Understanding the complex brain network organization on the basis of neuroimaging data represents one of the most important and exciting challenges for systems neuroscience. Several measures have been recently proposed to evaluate at various scales (single cells, cortical columns, or brain areas) how the different parts of the brain communicate. We can classify them, according to their symmetry, into two groups: symmetric measures, such as correlation, coherence or phase synchronization indexes, evaluate functional connectivity (FC); and on the other hand, the asymmetric ones, such as Granger causality or transfer entropy, are able to detect effective connectivity (EC) revealing the direction of the interaction. In modern neurosciences, the interest in functional brain networks has increased strongly with the onset of new algorithms to study interdependence between time series, the advent of modern complex network theory and the introduction of powerful techniques to record neurophysiological data, such as magnetoencephalography (MEG). However, when analyzing neurophysiological data with this approach several questions arise. In this thesis, I intend to tackle some of the practical open problems in the field. First of all, the increase in the number of time series analysis algorithms to study brain FC/EC, along with their mathematical complexity, creates the necessity of arranging them into a single, unified toolbox that allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of them. I developed such a toolbox for this aim, it is named HERMES (http://hermes.ctb.upm.es), and encompasses several of the most common indexes for the assessment of FC and EC running for MatlabR environment. I believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis and will entail a great value for the scientific community. The second important practical issue tackled in this thesis is the evaluation of the sensitivity to deep brain sources of two different MEG sensors: planar gradiometers and magnetometers, in combination with the related methodological approach, using two phase synchronization indexes: phase locking value (PLV) y phase lag index (PLI), the latter one being less sensitive to volume conduction effect. Thus, I compared their performance when studying brain networks, obtaining that magnetometer sensors and PLV presented higher artificial values as compared with planar gradiometers and PLI respectively. However, when it came to characterize epileptic networks it was the PLV which gives better results, as PLI FC networks where very sparse. Complex network analysis has provided new concepts which improved characterization of interacting dynamical systems. With this background, networks could be considered composed of nodes, symbolizing systems, whose interactions with each other are represented by edges. A growing number of network measures is been applied in network analysis. However, there is theoretical and empirical evidence that many of these indexes are strongly correlated with each other. Therefore, in this thesis I reduced them to a small set, which could more efficiently characterize networks. Within this framework, selecting an appropriate threshold to decide whether a certain connectivity value of the FC matrix is significant and should be included in the network analysis becomes a crucial step, in this thesis, I used the surrogate data tests to make an individual data-driven evaluation of each of the edges significance and confirmed more accurate results than when just setting to a fixed value the density of connections. All these methodologies were applied to the study of epilepsy, analysing resting state MEG functional networks, in two groups of epileptic patients (generalized and focal epilepsy) that were compared to matching control subjects. Epilepsy is one of the most common neurological disorders, with more than 55 million people affected worldwide, characterized by its predisposition to generate epileptic seizures of abnormal excessive or synchronous neuronal activity, and thus, this scenario and analysis, present a great interest from both the clinical and the research perspective. Results revealed specific disruptions in connectivity and network topology and evidenced that networks’ topology is changed in epileptic brains, supporting the shift from ‘focus’ to ‘networks’ which is gaining importance in modern epilepsy research.

Theoretical study of band alignment in nano-porous ZnO interacting with substituted Phthalocyanines

The aim of this work is the theoretical study of the band alignment between the two components of a hybrid organic-inorganic solar-cell. The working organic molecules are metal tetra-sulphonated phthalocyanines (M-Pc) and the inorganic material is nano-porous ZnO growth in the 001 direction. The theoretical calculations are being made using the density functional theory (DFT) using a GGA functional with the SIESTA code, which projects electron wave functions and density onto a real space grid and uses as basis set a linear combination of numerical, finite-range localized atomic orbitals. We also used the DFT+U method included in the code that allows a semi-empirical inclusion of electronic correlations in the description of electronic spectra for systems such as zinc oxide.

Two-layer particle filter for multiple target detection and tracking

This paper deals with the detection and tracking of an unknown number of targets using a Bayesian hierarchical model with target labels. To approximate the posterior probability density function, we develop a two-layer particle filter. One deals with track initiation, and the other with track maintenance. In addition, the parallel partition method is proposed to sample the states of the surviving targets.

Refined second law of thermodynamics for fast random processes

We establish a refined version of the Second Law of Thermodynamics for Langevin stochastic processes describing mesoscopic systems driven by conservative or non-conservative forces and interacting with thermal noise. The refinement is based on the Monge-Kantorovich optimal mass transport and becomes relevant for processes far from quasi-stationary regime. General discussion is illustrated by numerical analysis of the optimal memory erasure protocol for a model for micron-size particle manipulated by optical tweezers.

Current in coherent quantum systems connected to mesoscopic Fermi reservoirs

We study particle current in a recently proposed model for coherent quantum transport. In this model, a system connected to mesoscopic Fermi reservoirs (meso-reservoir) is driven out of equilibrium by the action of super-reservoirs thermalized to prescribed temperatures and chemical potentials by a simple dissipative mechanism described by the Lindblad equation. We compare exact (numerical) results with theoretical expectations based on the Landauer formula.

Resilience in Cloud Computing for Critical Systems. Resilience, Dependability, Reliability in the use of Cloud Computing in Critical Systems in Public Organizations.

La informática se está convirtiendo en la quinta utilidad (gas, agua, luz, teléfono) en parte debido al impacto de Cloud Computing en las mayorías de las organizaciones. Este uso de informática es usada por cada vez más tipos de sistemas, incluidos Sistemas Críticos. Esto tiene un impacto en la complejidad internad y la fiabilidad de los sistemas de la organización y los que se ofrecen a los clientes. Este trabajo investiga el uso de Cloud Computing por sistemas críticos, centrándose en las dependencias y especialmente en la fiabilidad de estos sistemas. Se han presentado algunos ejemplos de su uso, y aunque su utilización en sistemas críticos no está extendido, se presenta cual puede llegar a ser su impacto. El objetivo de este trabajo es primero definir un modelo que pueda representar de una forma cuantitativa las interdependencias en fiabilidad y interdependencia para las organizaciones que utilicen estos sistemas, y aplicar este modelo en un sistema crítico del campo de sanidad y mostrar sus resultados. Los conceptos de “macro-dependability” y “micro-dependability” son introducidos en el modelo para la definición de interdependencia y para analizar la fiabilidad de sistemas que dependen de otros sistemas. ABSTRACT With the increasing utilization of Internet services and cloud computing by most organizations (both private and public), it is clear that computing is becoming the 5th utility (along with water, electricity, telephony and gas). These technologies are used for almost all types of systems, and the number is increasing, including Critical Infrastructure systems. Even if Critical Infrastructure systems appear not to rely directly on cloud services, there may be hidden inter-dependencies. This is true even for private cloud computing, which seems more secure and reliable. The critical systems can began in some cases with a clear and simple design, but evolved as described by Egan to "rafted" networks. Because they are usually controlled by one or few organizations, even when they are complex systems, their dependencies can be understood. The organization oversees and manages changes. These CI systems have been affected by the introduction of new ICT models like global communications, PCs and the Internet. Even virtualization took more time to be adopted by Critical systems, due to their strategic nature, but once that these technologies have been proven in other areas, at the end they are adopted as well, for different reasons such as costs. A new technology model is happening now based on some previous technologies (virtualization, distributing and utility computing, web and software services) that are offered in new ways and is called cloud computing. The organizations are migrating more services to the cloud; this will have impact in their internal complexity and in the reliability of the systems they are offering to the organization itself and their clients. Not always this added complexity and associated risks to their reliability are seen. As well, when two or more CI systems are interacting, the risks of one can affect the rest, sharing the risks. This work investigates the use of cloud computing by critical systems, and is focused in the dependencies and reliability of these systems. Some examples are presented together with the associated risks. A framework is introduced for analysing the dependability and resilience of a system that relies on cloud services and how to improve them. As part of the framework, the concepts of micro and macro dependability are introduced to explain the internal and external dependability on services supplied by an external cloud. A pharmacovigilance model system has been used for framework validation.

Hardware-Based Particle Filter with Evolutionary Resampling Stage

Autonomous systems require, in most of the cases, reasoning and decision-making capabilities. Moreover, the decision process has to occur in real time. Real-time computing means that every situation or event has to have an answer before a temporal deadline. In complex applications, these deadlines are usually in the order of milliseconds or even microseconds if the application is very demanding. In order to comply with these timing requirements, computing tasks have to be performed as fast as possible. The problem arises when computations are no longer simple, but very time-consuming operations. A good example can be found in autonomous navigation systems with visual-tracking submodules where Kalman filtering is the most extended solution. However, in recent years, some interesting new approaches have been developed. Particle filtering, given its more general problem-solving features, has reached an important position in the field. The aim of this thesis is to design, implement and validate a hardware platform that constitutes itself an embedded intelligent system. The proposed system would combine particle filtering and evolutionary computation algorithms to generate intelligent behavior. Traditional approaches to particle filtering or evolutionary computation have been developed in software platforms, including parallel capabilities to some extent. In this work, an additional goal is fully exploiting hardware implementation advantages. By using the computational resources available in a FPGA device, better performance results in terms of computation time are expected. These hardware resources will be in charge of extensive repetitive computations. With this hardware-based implementation, real-time features are also expected.

Modelling and Control of Stepper Motors for High Accuracy Positioning Systems Used in Radioactive Environments

Hybrid Stepper Motors are widely used in open-loop position applications. They are the choice of actuation for the collimators in the Large Hadron Collider, the largest particle accelerator at CERN. In this case the positioning requirements and the highly radioactive operating environment are unique. The latter forces both the use of long cables to connect the motors to the drives which act as transmission lines and also prevents the use of standard position sensors. However, reliable and precise operation of the collimators is critical for the machine, requiring the prevention of step loss in the motors and maintenance to be foreseen in case of mechanical degradation. In order to make the above possible, an approach is proposed for the application of an Extended Kalman Filter to a sensorless stepper motor drive, when the motor is separated from its drive by long cables. When the long cables and high frequency pulse width modulated control voltage signals are used together, the electrical signals difer greatly between the motor and drive-side of the cable. Since in the considered case only drive-side data is available, it is therefore necessary to estimate the motor-side signals. Modelling the entire cable and motor system in an Extended Kalman Filter is too computationally intensive for standard embedded real-time platforms. It is, in consequence, proposed to divide the problem into an Extended Kalman Filter, based only on the motor model, and separated motor-side signal estimators, the combination of which is less demanding computationally. The efectiveness of this approach is shown in simulation. Then its validity is experimentally demonstrated via implementation in a DSP based drive. A testbench to test its performance when driving an axis of a Large Hadron Collider collimator is presented along with the results achieved. It is shown that the proposed method is capable of achieving position and load torque estimates which allow step loss to be detected and mechanical degradation to be evaluated without the need for physical sensors. These estimation algorithms often require a precise model of the motor, but the standard electrical model used for hybrid stepper motors is limited when currents, which are high enough to produce saturation of the magnetic circuit, are present. New model extensions are proposed in order to have a more precise model of the motor independently of the current level, whilst maintaining a low computational cost. It is shown that a significant improvement in the model It is achieved with these extensions, and their computational performance is compared to study the cost of model improvement versus computation cost. The applicability of the proposed model extensions is demonstrated via their use in an Extended Kalman Filter running in real-time for closed-loop current control and mechanical state estimation. An additional problem arises from the use of stepper motors. The mechanics of the collimators can wear due to the abrupt motion and torque profiles that are applied by them when used in the standard way, i.e. stepping in open-loop. Closed-loop position control, more specifically Field Oriented Control, would allow smoother profiles, more respectful to the mechanics, to be applied but requires position feedback. As mentioned already, the use of sensors in radioactive environments is very limited for reliability reasons. Sensorless control is a known option but when the speed is very low or zero, as is the case most of the time for the motors used in the LHC collimator, the loss of observability prevents its use. In order to allow the use of position sensors without reducing the long term reliability of the whole system, the possibility to switch from closed to open loop is proposed and validated, allowing the use of closed-loop control when the position sensors function correctly and open-loop when there is a sensor failure. A different approach to deal with the switched drive working with long cables is also presented. Switched mode stepper motor drives tend to have poor performance or even fail completely when the motor is fed through a long cable due to the high oscillations in the drive-side current. The design of a stepper motor output fillter which solves this problem is thus proposed. A two stage filter, one devoted to dealing with the diferential mode and the other with the common mode, is designed and validated experimentally. With this ?lter the drive performance is greatly improved, achieving a positioning repeatability even better than with the drive working without a long cable, the radiated emissions are reduced and the overvoltages at the motor terminals are eliminated.

A packing computational method relating fractal particle size distribution and void fraction in granular media

The study of granular systems is of great interest to many fields of science and technology. The packing of particles affects to the physical properties of the granular system. In particular, the crucial influence of particle size distribution (PSD) on the random packing structure increase the interest in relating both, either theoretically or by computational methods. A packing computational method is developed in order to estimate the void fraction corresponding to a fractal-like particle size distribution.

Thermodynamic aproach to particle size distribution in granular media

The study of particulate systems is of great interest in many fields of science and technology. Soil, sediments, powders, granular materials, colloidal and particulate suspensions are examples of systems involving many size particles. For those systems, the statistical description of the particle size distribution (PSD), that is, the mathematical distribution that defines the relative amounts of particles present, sorted according to size, is a crutial issue. The PSD can be important in understanding soil hydraulic properties, the geological origin or sediments or the physical and chemical properties of granular materials and ceramics, among others.

A Packing Computational Method Relating Fractal Particle Size Distribution and Void Fraction in Granular Media

The study of granular systems is of great interest to many fields of science and technology. The packing of particles affects to the physical properties of the granular system. In particular, the crucial influence of particle size distribution (PSD) on the random packing structure increase the interest in relating both, either theoretically or by computational methods. A packing computational method is developed in order to estimate the void fraction corresponding to a fractal-like particle size distribution.

Interaction between interconnected and isolated grounding systems: a case study of transferred potentials

The effect caused by ground fault current in a complex system of interacting electrodes is theoretically studied. The calculation applies to a specific case in which a set of interconnected electrodes, which are part of a grounding facility network, are activated by a ground fault current. Transferred potentials to adjacent passive electrodes are calculated and the most relevant parameters of the electrode system are evaluated. Finally, the convenience of connecting the grounding electrodes is discussed.

Time-multiscale methods for the simulation of slow transport problems in atomistic systems

En esta tesis presentamos una teoría adaptada a la simulación de fenómenos lentos de transporte en sistemas atomísticos. En primer lugar, desarrollamos el marco teórico para modelizar colectividades estadísticas de equilibrio. A continuación, lo adaptamos para construir modelos de colectividades estadísticas fuera de equilibrio. Esta teoría reposa sobre los principios de la mecánica estadística, en particular el principio de máxima entropía de Jaynes, utilizado tanto para sistemas en equilibrio como fuera de equilibrio, y la teoría de las aproximaciones del campo medio. Expresamos matemáticamente el problema como un principio variacional en el que maximizamos una entropía libre, en lugar de una energía libre. La formulación propuesta permite definir equivalentes atomísticos de variables macroscópicas como la temperatura y la fracción molar. De esta forma podemos considerar campos macroscópicos no uniformes. Completamos el marco teórico con reglas de cuadratura de Monte Carlo, gracias a las cuales obtenemos modelos computables. A continuación, desarrollamos el conjunto completo de ecuaciones que gobiernan procesos de transporte. Deducimos la desigualdad de disipación entrópica a partir de fuerzas y flujos termodinámicos discretos. Esta desigualdad nos permite identificar la estructura que deben cumplir los potenciales cinéticos discretos. Dichos potenciales acoplan las tasas de variación en el tiempo de las variables microscópicas con las fuerzas correspondientes. Estos potenciales cinéticos deben ser completados con una relación fenomenológica, del tipo definido por la teoría de Onsanger. Por último, aportamos validaciones numéricas. Con ellas ilustramos la capacidad de la teoría presentada para simular propiedades de equilibrio y segregación superficial en aleaciones metálicas. Primero, simulamos propiedades termodinámicas de equilibrio en el sistema atomístico. A continuación evaluamos la habilidad del modelo para reproducir procesos de transporte en sistemas complejos que duran tiempos largos con respecto a los tiempos característicos a escala atómica. ABSTRACT In this work, we formulate a theory to address simulations of slow time transport effects in atomic systems. We first develop this theoretical framework in the context of equilibrium of atomic ensembles, based on statistical mechanics. We then adapt it to model ensembles away from equilibrium. The theory stands on Jaynes' maximum entropy principle, valid for the treatment of both, systems in equilibrium and away from equilibrium and on meanfield approximation theory. It is expressed in the entropy formulation as a variational principle. We interpret atomistic equivalents of macroscopic variables such as the temperature and the molar fractions, wich are not required to be uniform, but can vary from particle to particle. We complement this theory with Monte Carlo summation rules for further approximation. In addition, we provide a framework for studying transport processes with the full set of equations driving the evolution of the system. We first derive a dissipation inequality for the entropic production involving discrete thermodynamic forces and fluxes. This discrete dissipation inequality identifies the adequate structure for discrete kinetic potentials which couple the microscopic field rates to the corresponding driving forces. Those kinetic potentials must finally be expressed as a phenomenological rule of the Onsanger Type. We present several validation cases, illustrating equilibrium properties and surface segregation of metallic alloys. We first assess the ability of a simple meanfield model to reproduce thermodynamic equilibrium properties in systems with atomic resolution. Then, we evaluate the ability of the model to reproduce a long-term transport process in complex systems.

Engineering Computational Emotion - A Reference Model for Emotion in Artificial Systems

Emotion is generally argued to be an influence on the behavior of life systems, largely concerning flexibility and adaptivity. The way in which life systems acts in response to a particular situations of the environment, has revealed the decisive and crucial importance of this feature in the success of behaviors. And this source of inspiration has influenced the way of thinking artificial systems. During the last decades, artificial systems have undergone such an evolution that each day more are integrated in our daily life. They have become greater in complexity, and the subsequent effects are related to an increased demand of systems that ensure resilience, robustness, availability, security or safety among others. All of them questions that raise quite a fundamental challenges in control design. This thesis has been developed under the framework of the Autonomous System project, a.k.a the ASys-Project. Short-term objectives of immediate application are focused on to design improved systems, and the approaching of intelligence in control strategies. Besides this, long-term objectives underlying ASys-Project concentrate on high order capabilities such as cognition, awareness and autonomy. This thesis is placed within the general fields of Engineery and Emotion science, and provides a theoretical foundation for engineering and designing computational emotion for artificial systems. The starting question that has grounded this thesis aims the problem of emotion--based autonomy. And how to feedback systems with valuable meaning has conformed the general objective. Both the starting question and the general objective, have underlaid the study of emotion, the influence on systems behavior, the key foundations that justify this feature in life systems, how emotion is integrated within the normal operation, and how this entire problem of emotion can be explained in artificial systems. By assuming essential differences concerning structure, purpose and operation between life and artificial systems, the essential motivation has been the exploration of what emotion solves in nature to afterwards analyze analogies for man--made systems. This work provides a reference model in which a collection of entities, relationships, models, functions and informational artifacts, are all interacting to provide the system with non-explicit knowledge under the form of emotion-like relevances. This solution aims to provide a reference model under which to design solutions for emotional operation, but related to the real needs of artificial systems. The proposal consists of a multi-purpose architecture that implement two broad modules in order to attend: (a) the range of processes related to the environment affectation, and (b) the range or processes related to the emotion perception-like and the higher levels of reasoning. This has required an intense and critical analysis beyond the state of the art around the most relevant theories of emotion and technical systems, in order to obtain the required support for those foundations that sustain each model. The problem has been interpreted and is described on the basis of AGSys, an agent assumed with the minimum rationality as to provide the capability to perform emotional assessment. AGSys is a conceptualization of a Model-based Cognitive agent that embodies an inner agent ESys, the responsible of performing the emotional operation inside of AGSys. The solution consists of multiple computational modules working federated, and aimed at conforming a mutual feedback loop between AGSys and ESys. Throughout this solution, the environment and the effects that might influence over the system are described as different problems. While AGSys operates as a common system within the external environment, ESys is designed to operate within a conceptualized inner environment. And this inner environment is built on the basis of those relevances that might occur inside of AGSys in the interaction with the external environment. This allows for a high-quality separate reasoning concerning mission goals defined in AGSys, and emotional goals defined in ESys. This way, it is provided a possible path for high-level reasoning under the influence of goals congruence. High-level reasoning model uses knowledge about emotional goals stability, letting this way new directions in which mission goals might be assessed under the situational state of this stability. This high-level reasoning is grounded by the work of MEP, a model of emotion perception that is thought as an analogy of a well-known theory in emotion science. The work of this model is described under the operation of a recursive-like process labeled as R-Loop, together with a system of emotional goals that are assumed as individual agents. This way, AGSys integrates knowledge that concerns the relation between a perceived object, and the effect which this perception induces on the situational state of the emotional goals. This knowledge enables a high-order system of information that provides the sustain for a high-level reasoning. The extent to which this reasoning might be approached is just delineated and assumed as future work. This thesis has been studied beyond a long range of fields of knowledge. This knowledge can be structured into two main objectives: (a) the fields of psychology, cognitive science, neurology and biological sciences in order to obtain understanding concerning the problem of the emotional phenomena, and (b) a large amount of computer science branches such as Autonomic Computing (AC), Self-adaptive software, Self-X systems, Model Integrated Computing (MIC) or the paradigm of models@runtime among others, in order to obtain knowledge about tools for designing each part of the solution. The final approach has been mainly performed on the basis of the entire acquired knowledge, and described under the fields of Artificial Intelligence, Model-Based Systems (MBS), and additional mathematical formalizations to provide punctual understanding in those cases that it has been required. This approach describes a reference model to feedback systems with valuable meaning, allowing for reasoning with regard to (a) the relationship between the environment and the relevance of the effects on the system, and (b) dynamical evaluations concerning the inner situational state of the system as a result of those effects. And this reasoning provides a framework of distinguishable states of AGSys derived from its own circumstances, that can be assumed as artificial emotion.

New systems of management to improve the health and welfare of rabbits in farm conditions = Nuevos sistemas de cría y manejo para mejorar la salud y bienestar de conejos de granja

El objetivo general de esta Tesis Doctoral fue evaluar nuevos sistemas de alojamiento y cría de conejos de granja, estudiando tanto parámetros comportamentales (experimento 1) como productivos y reproductivos (experimento 3). Además, se evaluaron diferentes técnicas de muestreo con el fin de optimizar el tiempo empleado para el estudio del comportamiento animal (experimento 2). En el experimento 1, se estudió el comportamiento de conejas alojadas en dos tipos de jaulas (TJ), convencionales vs. alternativas con una plataforma elevada, en distintos estados fisiológicos (EF), lactantes y gestantes. Se observó el comportamiento de 12 conejas reproductoras con grabaciones de una duración de 24 h continuas. Independientemente del EF y TJ, las conejas pasaron gran parte de su tiempo sobre el reposapatas (57,7 %, de media). Sin embargo, debido al uso de la plataforma (23,0% del tiempo, de media), las conejas lactantes permanecieron un 36,6 % menos de tiempo (P<0,001) sobre el reposapatas y las gestantes un 27,0% menos (P<0,001) sobre el enrejillado en jaulas alternativas que en convencionales. En las jaulas alternativas, las conejas podían adoptar la postura “levantada”, sin embargo ésta fue observada solamente en conejas gestantes una media de 4,6 veces al día. Las conejas bebieron con mas frecuencia en jaulas convencionales que en alternativas (24,6 vs 19,1 veces al día; P<0,05). Se observó una mayor duración y frecuencia del comportamiento “interactuando con compañeras” en conejas gestantes alojadas en jaulas convencionales (276 s/d y 4,6 veces/d; P<0,05). La frecuencia de “interactuando con gazapos” fue menor en jaulas alternativas que en convencionales (2,4 vs 8,6 veces al día; P<0,01). La hora del día afectó al comportamiento de las conejas, teniendo un comportamiento menos activo durante las horas centrales del día. Durante las horas de oscuridad, las conejas estuvieron más inquietas realizando comportamientos como ‘encabritarse’ o amamantar, coincidiendo éstos en el tiempo en el cual las conejas pasaron más tiempo en la plataforma. Las conejas utilizaron frecuentemente la plataforma, independientemente del estado fisiológico. En la fase de lactación, las conejas utilizaron la plataforma para huir de los intentos de mamar por parte de los gazapos cuando éstas no estaban receptivas. El uso de la plataforma puede dar lugar a problemas higiénicos debidos tanto por la acumulación de heces sobre ella como por la caída de heces y orina sobre los animales que están en la parte inferior. La ausencia de estereotipias por parte de las conejas tanto en jaulas alternativas como en convencionales no sugiere una falta de bienestar debida al sistema de alojamiento. En el experimento 2, se compararon distintos métodos de observación simplificada con respecto un método de referencia usando grabaciones continuas de 24 h para la evaluación del comportamiento de conejas en distintos estados fisiológicos (gestantes y lactantes) alojadas en dos tipos de jaulas (convencionales y alternativas). Se analizaron un total de 576 h de grabaciones continuas de 24 h en 12 conejas reproductoras al final del periodo de lactación y en las mismas conejas después del destete. Los comportamientos observados se clasificaron en tres categorías independientes (localización en la jaula, postura y comportamientos funcionales). Se utilizaron grabaciones continuas de 24 h como método de referencia para validar otros cuatro métodos de observación simplificados, utilizando grabaciones de distinta duración y frecuencia a lo largo del día. Métodos regulares: corto y largo con 2.4 y 8 h de observación respectivamente, y métodos irregulares: corto y largo con 6 y 8 h de observación, respectivamente. Como resultado, se observó que independientemente del sistema de alojamiento, el mejor método para reducir el tiempo de observación necesario para evaluar el comportamiento de conejas reproductoras depende del tipo de variable a estudiar y del estado fisiológico de las conejas. En gestantes, los métodos irregulares no fueron adecuados para estimar comportamientos de larga duración tales como tumbada, sentada, descansando y acicalándose. Sin embargo, en ambos estados fisiológicos, los métodos regulares fueron precisos para los comportamientos de los grupos localización y postura y para comportamientos funcionales de larga duración. Por otro lado, los coeficientes de variación de los comportamientos poco frecuentes realizados principalmente durante el periodo de oscuridad fueron muy altos, y el método irregular largo obtuvo los menores errores de estimación para éstos comportamientos. En el experimento 3, se estudió el efecto de un uso combinado de lactaciones largas (hasta 46 días) con jaulas alternativas sobre los parámetros productivos y reproductivos de 104 conejas y sus camadas durante cinco ciclos reproductivos. La mitad de las conejas fueron alojadas en jaulas polivalentes convencionales (39 cm x 100 cm x 30 cm) y la otra mitad en jaulas polivalentes alternativas (39 cm x 100 cm x 60 cm), con una plataforma elevada. Dentro de cada grupo de alojamiento, la mitad de las conejas se destetaron a 32 días y la otra mitad a 46 días tras el parto. Las lactaciones más largas afectaron negativamente al peso (P<0,001), contenido en grasa y energía (P<0,05) de las conejas al final del periodo de lactación, pero éste efecto disminuyó con el número de partos. La fertilidad, prolificidad y la mortalidad de las conejas no fue afectada por la duración de la lactación. El destete tardío dio lugar a un mayor tamaño y peso de la camada al final del periodo de crecimiento (8,9 y 11,3 %, respectivamente) y a un menor índice de conversión por jaula durante el todo el periodo experimental (13,5 %) con respecto al destete convencional (P<0,001). Éstos resultados fueron paralelos a la menor mortalidad global (12,6 vs 17,6 %; P<0,05) observada en gazapos con destete tardío. Las diferencias en los parámetros productivos con las distintas edades al destete sólo fueron observadas en los ciclos con peor estado sanitario (tercer y quinto ciclo), en los cuales el destete tardío redujo la mortalidad. El tipo de jaula no afectó al peso de la coneja, condición corporal, mortalidad, fertilidad ni tamaño de camada durante los cinco primeros ciclos reproductivos. Sin embargo, el peso de la camada y el índice de conversión a los 21 días de edad fueron 4,2% mayor (P<0,001) y 5,0% menor (P<0,005) en animales alojados en jaulas alternativas que en jaulas convencionales. A día 59 las jaulas alternativas dieron lugar a camadas más pesadas (P<0,01); sin embargo, éste efecto fue influenciado por la densidad alcanzada en cada ciclo, ya que cuando la densidad de los animales fue menor que 40kg/m2 (tercer y quinto ciclo), el efecto del tipo de jaula sobre el peso de la camada no fue significativo. De los resultados obtenidos se puede concluir que el uso combinado de lactaciones más largas y jaulas con mayor superficie disponible con una plataforma elevada podría ser una alternativa para mejorar el bienestar animal en determinadas situaciones productivas. ABSTRACT The general aim of this PhD Thesis was to evaluate new housing and husbandry systems of farmed rabbits, studying behavioral (experiment 1), productive and reproductive (experiment 3) parameters. Moreover, different sampling techniques were evaluated in order to optimize the assessment of rabbit behaviour (experiment 2). In experiment 1, the behaviour of rabbit does housed in two different types of cage (TC), conventional vs. alternative with an elevated platform, at different physiological stages (PS), lactation and gestation was to study. Behavioural observations were carried out on 12 commercial rabbit does using continuous 24 hour video recording. Independently of PS and TC, rabbit does spent most of their time on foot mats (57.7 %, as average). However, due to the use of platforms (23.0% of time, as average), lactating does spent 36.6% less time (P<0.001) on foot mats and gestating does spent 27.0% less (P<0.001) time on wire mesh in alternative cages than in conventional cages. Alternative cages allowed for standing posture but this behaviour was only observed in gestating does (4.6 times a day, as average). Frequency of drinking was higher in conventional than in alternative cages (24.6 vs. 19.1 times a day; P<0.05). Gestating does housed in conventional cages reached the highest duration and frequency of interacting with neighbours (276 s/d and 4.6 times/d; P<0.05). The frequency of interacting with kits was lower in alternative than in conventional cages (2.4 vs. 8.6 times a day; P<0.01). Does’ behaviour was influenced by hour of day, being less active at the midday hours. During dark hours rabbit does more frequently performed restless behaviour such as hyperactivity or nursing, matching the time at which rabbit does spent more time on the platform. The platform was frequently used by rabbit does, independent of their physiological state, and during late lactation phase, when mothers were not receptive to nursing, does housed in alternative cages used the platform as a mean to flee from kids trying to suckle. The use of the platform might lead to hygienic problems due to retained faeces on the platform and faeces and urine falling onto animals located in the lower part of the cage. Stereotypies were not observed in any housing system, therefore conventional cages do not suggest lack of animal welfare. In experiment 2, it was compared the results of different simplified sampling methods of behavioural data with respect to reference records of 24-h in order to assess rabbit does behaviours at different physiological stages (gestation and lactation) in animals housed in two types of cages (conventional and alternative). A total of 576 h of continuous video of 12 rabbit does at the end of lactation and on the same females after weaning were analysed. The behavioural observations were studied using three independent categories of classification (location in the cage, posture and functional behaviours). Continuous behavioural recordings of 24 h were considered as the reference method to validate another 4 sampling methods of data collection by aggregated video recordings of different frequency and duration (regular short and long methods with 2.4 and 8 h of observation respectively, and irregular short and long methods with 6 and 8 h of observation, respectively). The current results showed that, independently of housing system, the best method to reduce the total observation time required to assess rabbit does behaviour depends on the trait studied and physiological stage of does. In gestating does, irregular methods were not suitable to estimate behaviours of long duration such as lying, sitting, resting and grooming. However, in both physiological stages, regular methods were accurate for location behaviours, postures and functional behaviours of long duration. Instead, for the study of infrequent behaviours performed mainly during dark period, where coefficients of variation were high, the irregular long method led to the lowest mean estimation errors. In experiment 3, the effects of the combined use of long lactation periods (46 days) with alternative cages on the reproductive and growth performance of 104 rabbit does and their litters during five consecutive reproductive cycles were studied. Half of does were housed in conventional polyvalent cages (39 cm x 100 cm x 30 cm) and the other half in alternative polyvalent cages (39 cm x 100 cm x 60 cm), with a raised platform. Half of the rabbit does in each type of cages were weaned at 32 and the other half at 46 days after parturition. Longer lactations affected negatively to body weight (P<0.001), fat and energy content (P<0.05) of rabbit does at the end of the lactation period, but this effect decreased with the number of parturitions. Fertility, prolificacy and doe mortality were not affected by lactation length. Late weaning led to higher litter size (by 8.9 %) and litter weight (by 11.3 %) at the end of growing period and lower feed conversion ratio per cage during the overall experimental period (13.5 %) than standard weaning (P<0.001). These results were parallels to a lower mortality (12.6 vs 17.6 %; P<0.05) of young rabbit weaned later during the overall experimental period. Differences in performances at different weaning ages were only observed during cycles with worst health status (third and fifth cycles) in which late weaning decreased mortality. Type of cage did not affect doe body weight and body condition, mortality, fertility, prolificacy and litter size during the five firsts reproductive cycles. Nevertheless, at day 21 litter weight and feed conversion ratio were 4.2 % higher (P<0.001) and 5.0 % lower (P<0.005) in animals housed in alternative than in conventional cages. Alternative cages also led to heavier litters at 59 days (P<0.01); however, this effect was influenced by density reached in each cycle, as when the density of animals was lower than 40 kg/m2 (cycles three and five), the difference of litter weight between alternative and conventional cages was not significant. From the results obtained it can be concluded that the combined use of longer lactations and cages with higher available surface with a raised platform could be an alternative to improve animal welfare in some productive situations.