Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, function of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells has only very recently been proposed (Jerusalem et al., 2013). In this paper, we present the implementation details of Neurite: the finite difference parallel program used in this reference. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite-explicit and implicit-were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between lectrophysiology and mechanics (Jerusalem et al., 2013). This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted.

Finite element code-based modeling of a multi-feature isolation system and passive alleviation of possible inner pounding

The existing seismic isolation systems are based on well-known and accepted physical principles, but they are still having some functional drawbacks. As an attempt of improvement, the Roll-N-Cage (RNC) isolator has been recently proposed. It is designed to achieve a balance in controlling isolator displacement demands and structural accelerations. It provides in a single unit all the necessary functions of vertical rigid support, horizontal flexibility with enhanced stability, resistance to low service loads and minor vibration, and hysteretic energy dissipation characteristics. It is characterized by two unique features that are a self-braking (buffer) and a self-recentering mechanism. This paper presents an advanced representation of the main and unique features of the RNC isolator using an available finite element code called SAP2000. The validity of the obtained SAP2000 model is then checked using experimental, numerical and analytical results. Then, the paper investigates the merits and demerits of activating the built-in buffer mechanism on both structural pounding mitigation and isolation efficiency. The paper addresses the problem of passive alleviation of possible inner pounding within the RNC isolator, which may arise due to the activation of its self-braking mechanism under sever excitations such as near-fault earthquakes. The results show that the obtained finite element code-based model can closely match and accurately predict the overall behavior of the RNC isolator with effectively small errors. Moreover, the inherent buffer mechanism of the RNC isolator could mitigate or even eliminate direct structure-tostructure pounding under severe excitation considering limited septation gaps between adjacent structures. In addition, the increase of inherent hysteretic damping of the RNC isolator can efficiently limit its peak displacement together with the severity of the possibly developed inner pounding and, therefore, alleviate or even eliminate the possibly arising negative effects of the buffer mechanism on the overall RNC-isolated structural responses.

Modelos de elementos finitos explícitos para explosiones en estructuras reticuladas de hormigón armado : aplicaciones al estudio del colapso de edificios

La frecuencia con la que se producen explosiones sobre edificios, ya sean accidentales o intencionadas, es reducida, pero sus efectos pueden ser catastróficos. Es deseable poder predecir de forma suficientemente precisa las consecuencias de estas acciones dinámicas sobre edificaciones civiles, entre las cuales las estructuras reticuladas de hormigón armado son una tipología habitual. En esta tesis doctoral se exploran distintas opciones prácticas para el modelado y cálculo numérico por ordenador de estructuras de hormigón armado sometidas a explosiones. Se emplean modelos numéricos de elementos finitos con integración explícita en el tiempo, que demuestran su capacidad efectiva para simular los fenómenos físicos y estructurales de dinámica rápida y altamente no lineales que suceden, pudiendo predecir los daños ocasionados tanto por la propia explosión como por el posible colapso progresivo de la estructura. El trabajo se ha llevado a cabo empleando el código comercial de elementos finitos LS-DYNA (Hallquist, 2006), desarrollando en el mismo distintos tipos de modelos de cálculo que se pueden clasificar en dos tipos principales: 1) modelos basados en elementos finitos de continuo, en los que se discretiza directamente el medio continuo mediante grados de libertad nodales de desplazamientos; 2) modelos basados en elementos finitos estructurales, mediante vigas y láminas, que incluyen hipótesis cinemáticas para elementos lineales o superficiales. Estos modelos se desarrollan y discuten a varios niveles distintos: 1) a nivel del comportamiento de los materiales, 2) a nivel de la respuesta de elementos estructurales tales como columnas, vigas o losas, y 3) a nivel de la respuesta de edificios completos o de partes significativas de los mismos. Se desarrollan modelos de elementos finitos de continuo 3D muy detallados que modelizan el hormigón en masa y el acero de armado de forma segregada. El hormigón se representa con un modelo constitutivo del hormigón CSCM (Murray et al., 2007), que tiene un comportamiento inelástico, con diferente respuesta a tracción y compresión, endurecimiento, daño por fisuración y compresión, y rotura. El acero se representa con un modelo constitutivo elastoplástico bilineal con rotura. Se modeliza la geometría precisa del hormigón mediante elementos finitos de continuo 3D y cada una de las barras de armado mediante elementos finitos tipo viga, con su posición exacta dentro de la masa de hormigón. La malla del modelo se construye mediante la superposición de los elementos de continuo de hormigón y los elementos tipo viga de las armaduras segregadas, que son obligadas a seguir la deformación del sólido en cada punto mediante un algoritmo de penalización, simulando así el comportamiento del hormigón armado. En este trabajo se denominarán a estos modelos simplificadamente como modelos de EF de continuo. Con estos modelos de EF de continuo se analiza la respuesta estructural de elementos constructivos (columnas, losas y pórticos) frente a acciones explosivas. Asimismo se han comparado con resultados experimentales, de ensayos sobre vigas y losas con distintas cargas de explosivo, verificándose una coincidencia aceptable y permitiendo una calibración de los parámetros de cálculo. Sin embargo estos modelos tan detallados no son recomendables para analizar edificios completos, ya que el elevado número de elementos finitos que serían necesarios eleva su coste computacional hasta hacerlos inviables para los recursos de cálculo actuales. Adicionalmente, se desarrollan modelos de elementos finitos estructurales (vigas y láminas) que, con un coste computacional reducido, son capaces de reproducir el comportamiento global de la estructura con una precisión similar. Se modelizan igualmente el hormigón en masa y el acero de armado de forma segregada. El hormigón se representa con el modelo constitutivo del hormigón EC2 (Hallquist et al., 2013), que también presenta un comportamiento inelástico, con diferente respuesta a tracción y compresión, endurecimiento, daño por fisuración y compresión, y rotura, y se usa en elementos finitos tipo lámina. El acero se representa de nuevo con un modelo constitutivo elastoplástico bilineal con rotura, usando elementos finitos tipo viga. Se modeliza una geometría equivalente del hormigón y del armado, y se tiene en cuenta la posición relativa del acero dentro de la masa de hormigón. Las mallas de ambos se unen mediante nodos comunes, produciendo una respuesta conjunta. En este trabajo se denominarán a estos modelos simplificadamente como modelos de EF estructurales. Con estos modelos de EF estructurales se simulan los mismos elementos constructivos que con los modelos de EF de continuo, y comparando sus respuestas estructurales frente a explosión se realiza la calibración de los primeros, de forma que se obtiene un comportamiento estructural similar con un coste computacional reducido. Se comprueba que estos mismos modelos, tanto los modelos de EF de continuo como los modelos de EF estructurales, son precisos también para el análisis del fenómeno de colapso progresivo en una estructura, y que se pueden utilizar para el estudio simultáneo de los daños de una explosión y el posterior colapso. Para ello se incluyen formulaciones que permiten considerar las fuerzas debidas al peso propio, sobrecargas y los contactos de unas partes de la estructura sobre otras. Se validan ambos modelos con un ensayo a escala real en el que un módulo con seis columnas y dos plantas colapsa al eliminar una de sus columnas. El coste computacional del modelo de EF de continuo para la simulación de este ensayo es mucho mayor que el del modelo de EF estructurales, lo cual hace inviable su aplicación en edificios completos, mientras que el modelo de EF estructurales presenta una respuesta global suficientemente precisa con un coste asumible. Por último se utilizan los modelos de EF estructurales para analizar explosiones sobre edificios de varias plantas, y se simulan dos escenarios con cargas explosivas para un edificio completo, con un coste computacional moderado. The frequency of explosions on buildings whether they are intended or accidental is small, but they can have catastrophic effects. Being able to predict in a accurate enough manner the consequences of these dynamic actions on civil buildings, among which frame-type reinforced concrete buildings are a frequent typology is desirable. In this doctoral thesis different practical options for the modeling and computer assisted numerical calculation of reinforced concrete structures submitted to explosions are explored. Numerical finite elements models with explicit time-based integration are employed, demonstrating their effective capacity in the simulation of the occurring fast dynamic and highly nonlinear physical and structural phenomena, allowing to predict the damage caused by the explosion itself as well as by the possible progressive collapse of the structure. The work has been carried out with the commercial finite elements code LS-DYNA (Hallquist, 2006), developing several types of calculation model classified in two main types: 1) Models based in continuum finite elements in which the continuous medium is discretized directly by means of nodal displacement degrees of freedom; 2) Models based on structural finite elements, with beams and shells, including kinematic hypothesis for linear and superficial elements. These models are developed and discussed at different levels: 1) material behaviour, 2) response of structural elements such as columns, beams and slabs, and 3) response of complete buildings or significative parts of them. Very detailed 3D continuum finite element models are developed, modeling mass concrete and reinforcement steel in a segregated manner. Concrete is represented with a constitutive concrete model CSCM (Murray et al., 2007), that has an inelastic behaviour, with different tension and compression response, hardening, cracking and compression damage and failure. The steel is represented with an elastic-plastic bilinear model with failure. The actual geometry of the concrete is modeled with 3D continuum finite elements and every and each of the reinforcing bars with beam-type finite elements, with their exact position in the concrete mass. The mesh of the model is generated by the superposition of the concrete continuum elements and the beam-type elements of the segregated reinforcement, which are made to follow the deformation of the solid in each point by means of a penalty algorithm, reproducing the behaviour of reinforced concrete. In this work these models will be called continuum FE models as a simplification. With these continuum FE models the response of construction elements (columns, slabs and frames) under explosive actions are analysed. They have also been compared with experimental results of tests on beams and slabs with various explosive charges, verifying an acceptable coincidence and allowing a calibration of the calculation parameters. These detailed models are however not advised for the analysis of complete buildings, as the high number of finite elements necessary raises its computational cost, making them unreliable for the current calculation resources. In addition to that, structural finite elements (beams and shells) models are developed, which, while having a reduced computational cost, are able to reproduce the global behaviour of the structure with a similar accuracy. Mass concrete and reinforcing steel are also modeled segregated. Concrete is represented with the concrete constitutive model EC2 (Hallquist et al., 2013), which also presents an inelastic behaviour, with a different tension and compression response, hardening, compression and cracking damage and failure, and is used in shell-type finite elements. Steel is represented once again with an elastic-plastic bilineal with failure constitutive model, using beam-type finite elements. An equivalent geometry of the concrete and the steel is modeled, considering the relative position of the steel inside the concrete mass. The meshes of both sets of elements are bound with common nodes, therefore producing a joint response. These models will be called structural FE models as a simplification. With these structural FE models the same construction elements as with the continuum FE models are simulated, and by comparing their response under explosive actions a calibration of the former is carried out, resulting in a similar response with a reduced computational cost. It is verified that both the continuum FE models and the structural FE models are also accurate for the analysis of the phenomenon of progressive collapse of a structure, and that they can be employed for the simultaneous study of an explosion damage and the resulting collapse. Both models are validated with an experimental full-scale test in which a six column, two floors module collapses after the removal of one of its columns. The computational cost of the continuum FE model for the simulation of this test is a lot higher than that of the structural FE model, making it non-viable for its application to full buildings, while the structural FE model presents a global response accurate enough with an admissible cost. Finally, structural FE models are used to analyze explosions on several story buildings, and two scenarios are simulated with explosive charges for a full building, with a moderate computational cost.

Estimation of Perceived Quality in Convergent Services

Triple-Play (3P) and Quadruple-Play (4P) services are being widely offered by telecommunication services providers. Such services must be able to offer equal or higher quality levels than those obtained with traditional systems, especially for the most demanding services such as broadcast IPTV. This paper presents a matrix-based model, defined in terms of service components, user perceptions, agent capabilities, performance indicators and evaluation functions, which allows to estimate the overall quality of a set of convergent services, as perceived by the users, from a set of performance and/or Quality of Service (QoS) parameters of the convergent IP transport network

Linear global instability of non-orthogonal incompressible swept attachment-line boundary layer flow

Instability of the orthogonal swept attachment line boundary layer has received attention by local1, 2 and global3–5 analysis methods over several decades, owing to the significance of this model to transition to turbulence on the surface of swept wings. However, substantially less attention has been paid to the problem of laminar flow instability in the non-orthogonal swept attachment-line boundary layer; only a local analysis framework has been employed to-date.6 The present contribution addresses this issue from a linear global (BiGlobal) instability analysis point of view in the incompressible regime. Direct numerical simulations have also been performed in order to verify the analysis results and unravel the limits of validity of the Dorrepaal basic flow7 model analyzed. Cross-validated results document the effect of the angle _ on the critical conditions identified by Hall et al.1 and show linear destabilization of the flow with decreasing AoA, up to a limit at which the assumptions of the Dorrepaal model become questionable. Finally, a simple extension of the extended G¨ortler-H¨ammerlin ODE-based polynomial model proposed by Theofilis et al.4 is presented for the non-orthogonal flow. In this model, the symmetries of the three-dimensional disturbances are broken by the non-orthogonal flow conditions. Temporal and spatial one-dimensional linear eigenvalue codes were developed, obtaining consistent results with BiGlobal stability analysis and DNS. Beyond the computational advantages presented by the ODE-based model, it allows us to understand the functional dependence of the three-dimensional disturbances in the non-orthogonal case as well as their connections with the disturbances of the orthogonal stability problem.

Accelerating CFD via local POD plus Galerkin projections

Se desarrollan varias técnicas basadas en descomposición ortogonal propia (DOP) local y proyección de tipo Galerkin para acelerar la integración numérica de problemas de evolución, de tipo parabólico, no lineales. Las ideas y métodos que se presentan conllevan un nuevo enfoque para la modelización de tipo DOP, que combina intervalos temporales cortos en que se usa un esquema numérico estándard con otros intervalos temporales en que se utilizan los sistemas de tipo Galerkin que resultan de proyectar las ecuaciones de evolución sobre la variedad lineal generada por los modos DOP, obtenidos a partir de instantáneas calculadas en los intervalos donde actúa el código numérico. La variedad DOP se construye completamente en el primer intervalo, pero solamente se actualiza en los demás intervalos según las dinámicas de la solución, aumentando de este modo la eficiencia del modelo de orden reducido resultante. Además, se aprovechan algunas propiedades asociadas a la dependencia débil de los modos DOP tanto en la variable temporal como en los posibles parámetros de que pueda depender el problema. De esta forma, se aumentan la flexibilidad y la eficiencia computacional del proceso. La aplicación de los métodos resultantes es muy prometedora, tanto en la simulación de transitorios en flujos laminares como en la construcción de diagramas de bifurcación en sistemas dependientes de parámetros. Las ideas y los algoritmos desarrollados en la tesis se ilustran en dos problemas test, la ecuación unidimensional compleja de Ginzburg-Landau y el problema bidimensional no estacionario de la cavidad. Abstract Various ideas and methods involving local proper orthogonal decomposition (POD) and Galerkin projection are presented aiming at accelerating the numerical integration of nonlinear time dependent parabolic problems. The proposed methods come from a new approach to the POD-based model reduction procedures, which combines short runs with a given numerical solver and a reduced order model constructed by expanding the solution of the problem into appropriate POD modes, which span a POD manifold, and Galerkin projecting some evolution equations onto that linear manifold. The POD manifold is completely constructed from the outset, but only updated as time proceeds according to the dynamics, which yields an adaptive and flexible procedure. In addition, some properties concerning the weak dependence of the POD modes on time and possible parameters in the problem are exploited in order to increase the flexibility and efficiency of the low dimensional model computation. Application of the developed techniques to the approximation of transients in laminar fluid flows and the simulation of attractors in bifurcation problems shows very promising results. The test problems considered to illustrate the various ideas and check the performance of the algorithms are the onedimensional complex Ginzburg-Landau equation and the two-dimensional unsteady liddriven cavity problem.

Polynomial approximation using particle swarm optimization of lineal enhanced neural networks with no hidden layers.

This paper presents some ideas about a new neural network architecture that can be compared to a Taylor analysis when dealing with patterns. Such architecture is based on lineal activation functions with an axo-axonic architecture. A biological axo-axonic connection between two neurons is defined as the weight in a connection in given by the output of another third neuron. This idea can be implemented in the so called Enhanced Neural Networks in which two Multilayer Perceptrons are used; the first one will output the weights that the second MLP uses to computed the desired output. This kind of neural network has universal approximation properties even with lineal activation functions. There exists a clear difference between cooperative and competitive strategies. The former ones are based on the swarm colonies, in which all individuals share its knowledge about the goal in order to pass such information to other individuals to get optimum solution. The latter ones are based on genetic models, that is, individuals can die and new individuals are created combining information of alive one; or are based on molecular/celular behaviour passing information from one structure to another. A swarm-based model is applied to obtain the Neural Network, training the net with a Particle Swarm algorithm.

The analytic hierarchy process to support decision-making processes in infrastructure projects with social impact

There is an increasing awareness among all kinds of organisations (in business,government and civil society) about the benefits of jointly working with stakeholders to satisfy both their goals and the social demands placed upon them. This is particularly the case within corporate social responsibility (CSR) frameworks. In this regard, multi-criteria tools for decision-making like the analytic hierarchy process (AHP) described in the paper can be useful for the building relationships with stakeholders. Since these tools can reveal decision-maker’s preferences, the integration of opinions from various stakeholders in the decision-making process may result in better and more innovative solutions with significant shared value. This paper is based on ongoing research to assess the feasibility of an AHP-based model to support CSR decisions in large infrastructure projects carried out by Red Electrica de España, the sole transmission agent and operator of the Spanishelectricity system.

Assessing urban mobility through participatory scenario building and combined utility-regret assessment

La planificación de la movilidad sostenible urbana es una tarea compleja que implica un alto grado de incertidumbre debido al horizonte de planificación a largo plazo, la amplia gama de paquetes de políticas posibles, la necesidad de una aplicación efectiva y eficiente, la gran escala geográfica, la necesidad de considerar objetivos económicos, sociales y ambientales, y la respuesta del viajero a los diferentes cursos de acción y su aceptabilidad política (Shiftan et al., 2003). Además, con las tendencias inevitables en motorización y urbanización, la demanda de terrenos y recursos de movilidad en las ciudades está aumentando dramáticamente. Como consecuencia de ello, los problemas de congestión de tráfico, deterioro ambiental, contaminación del aire, consumo de energía, desigualdades en la comunidad, etc. se hacen más y más críticos para la sociedad. Esta situación no es estable a largo plazo. Para enfrentarse a estos desafíos y conseguir un desarrollo sostenible, es necesario considerar una estrategia de planificación urbana a largo plazo, que aborde las necesarias implicaciones potencialmente importantes. Esta tesis contribuye a las herramientas de evaluación a largo plazo de la movilidad urbana estableciendo una metodología innovadora para el análisis y optimización de dos tipos de medidas de gestión de la demanda del transporte (TDM). La metodología nueva realizado se basa en la flexibilización de la toma de decisiones basadas en utilidad, integrando diversos mecanismos de decisión contrariedad‐anticipada y combinados utilidad‐contrariedad en un marco integral de planificación del transporte. La metodología propuesta incluye dos aspectos principales: 1) La construcción de escenarios con una o varias medidas TDM usando el método de encuesta que incorpora la teoría “regret”. La construcción de escenarios para este trabajo se hace para considerar específicamente la implementación de cada medida TDM en el marco temporal y marco espacial. Al final, se construyen 13 escenarios TDM en términos del más deseable, el más posible y el de menor grado de “regret” como resultado de una encuesta en dos rondas a expertos en el tema. 2) A continuación se procede al desarrollo de un marco de evaluación estratégica, basado en un Análisis Multicriterio de Toma de Decisiones (Multicriteria Decision Analysis, MCDA) y en un modelo “regret”. Este marco de evaluación se utiliza para comparar la contribución de los distintos escenarios TDM a la movilidad sostenible y para determinar el mejor escenario utilizando no sólo el valor objetivo de utilidad objetivo obtenido en el análisis orientado a utilidad MCDA, sino también el valor de “regret” que se calcula por medio del modelo “regret” MCDA. La función objetivo del MCDA se integra en un modelo de interacción de uso del suelo y transporte que se usa para optimizar y evaluar los impactos a largo plazo de los escenarios TDM previamente construidos. Un modelo de “regret”, llamado “referencedependent regret model (RDRM)” (modelo de contrariedad dependiente de referencias), se ha adaptado para analizar la contribución de cada escenario TDM desde un punto de vista subjetivo. La validación de la metodología se realiza mediante su aplicación a un caso de estudio en la provincia de Madrid. La metodología propuesta define pues un procedimiento técnico detallado para la evaluación de los impactos estratégicos de la aplicación de medidas de gestión de la demanda en el transporte, que se considera que constituye una herramienta de planificación útil, transparente y flexible, tanto para los planificadores como para los responsables de la gestión del transporte. Planning sustainable urban mobility is a complex task involving a high degree of uncertainty due to the long‐term planning horizon, the wide spectrum of potential policy packages, the need for effective and efficient implementation, the large geographical scale, the necessity to consider economic, social, and environmental goals, and the traveller’s response to the various action courses and their political acceptability (Shiftan et al., 2003). Moreover, with the inevitable trends on motorisation and urbanisation, the demand for land and mobility in cities is growing dramatically. Consequently, the problems of traffic congestion, environmental deterioration, air pollution, energy consumption, and community inequity etc., are becoming more and more critical for the society (EU, 2011). Certainly, this course is not sustainable in the long term. To address this challenge and achieve sustainable development, a long‐term perspective strategic urban plan, with its potentially important implications, should be established. This thesis contributes on assessing long‐term urban mobility by establishing an innovative methodology for optimizing and evaluating two types of transport demand management measures (TDM). The new methodology aims at relaxing the utility‐based decision‐making assumption by embedding anticipated‐regret and combined utilityregret decision mechanisms in an integrated transport planning framework. The proposed methodology includes two major aspects: 1) Construction of policy scenarios within a single measure or combined TDM policy‐packages using the survey method incorporating the regret theory. The purpose of building the TDM scenarios in this work is to address the specific implementation in terms of time frame and geographic scale for each TDM measure. Finally, 13 TDM scenarios are built in terms of the most desirable, the most expected and the least regret choice by means of the two‐round Delphi based survey. 2) Development of the combined utility‐regret analysis framework based on multicriteria decision analysis (MCDA). This assessment framework is used to compare the contribution of the TDM scenario towards sustainable mobility and to determine the best scenario considering not only the objective utility value obtained from the utilitybased MCDA, but also a regret value that is calculated via a regret‐based MCDA. The objective function of the utility‐based MCDA is integrated in a land use and transport interaction model and is used for optimizing and assessing the long term impacts of the constructed TDM scenarios. A regret based model, called referente dependent regret model (RDRM) is adapted to analyse the contribution of each TDM scenario in terms of a subjective point of view. The suggested methodology is implemented and validated in the case of Madrid. It defines a comprehensive technical procedure for assessing strategic effects of transport demand management measures, which can be useful, transparent and flexible planning tool both for planners and decision‐makers.

Linguistic linked data for sentiment analysis

In this paper we describe the specification of amodel for the semantically interoperable representation of language resources for sentiment analysis. The model integrates "lemon", an RDF-based model for the specification of ontology-lexica (Buitelaar et al. 2009), which is used increasinglyfor the representation of language resources asLinked Data, with Marl, an RDF-based model for the representation of sentiment annotations (West-erski et al., 2011; Sánchez-Rada et al., 2013)

Traffic sign detection and tracking using robust 3D analysis

In this paper we present an innovative technique to tackle the problem of automatic road sign detection and tracking using an on-board stereo camera. It involves a continuous 3D analysis of the road sign during the whole tracking process. Firstly, a color and appearance based model is applied to generate road sign candidates in both stereo images. A sparse disparity map between the left and right images is then created for each candidate by using contour-based and SURF-based matching in the far and short range, respectively. Once the map has been computed, the correspondences are back-projected to generate a cloud of 3D points, and the best-fit plane is computed through RANSAC, ensuring robustness to outliers. Temporal consistency is enforced by means of a Kalman filter, which exploits the intrinsic smoothness of the 3D camera motion in traffic environments. Additionally, the estimation of the plane allows to correct deformations due to perspective, thus easing further sign classification.

Enhancing iDynoMiCS framework with a plasmid conjugation module

Actualmente existen aplicaciones que permiten simular el comportamiento de bacterias en distintos hábitats y los procesos que ocurren en estos para facilitar su estudio y experimentación sin la necesidad de un laboratorio. Una de las aplicaciones de software libre para la simulación de poblaciones bacteriológicas mas usada es iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), un simulador basado en agentes que permite trabajar con varios modelos computacionales de bacterias en 2D y 3D. Este simulador permite una gran libertad al configurar una numerosa cantidad de variables con respecto al entorno, reacciones químicas y otros detalles importantes. Una característica importante es el poder simular de manera sencilla la conjugación de plásmidos entre bacterias. Los plásmidos son moléculas de ADN diferentes del cromosoma celular, generalmente circularles, que se replican, transcriben y conjugan independientemente del ADN cromosómico. Estas están presentes normalmente en bacterias procariotas, y en algunas ocasiones en eucariotas, sin embargo, en este tipo de células son llamados episomas. Dado el complejo comportamiento de los plásmidos y la gama de posibilidades que estos presentan como mecanismos externos al funcionamiento básico de la célula, en la mayoría de los casos confiriéndole distintas ventajas evolutivas, como por ejemplo: resistencia antibiótica, entre otros, resulta importante su estudio y subsecuente manipulación. Sin embargo, el marco operativo del iDynoMiCS, en cuanto a simulación de plásmidos se refiere, es demasiado sencillo y no permite realizar operaciones más complejas que el análisis de la propagación de un plásmido en la comunidad. El presente trabajo surge para resolver esta deficiencia de iDynomics. Aquí se analizarán, desarrollarán e implementarán las modificaciones necesarias para que iDynomics pueda simular satisfactoriamente y mas apegado a la realidad la conjugación de plásmidos y permita así mismo resolver distintas operaciones lógicas, como lo son los circuitos genéticos, basadas en plásmidos. También se analizarán los resultados obtenidos de acuerdo a distintos estudios relevantes y a la comparación de los resultados obtenidos con el código original de iDynomics. Adicionalmente se analizará un estudio comparando la eficiencia de detección de una sustancia mediante dos circuitos genéticos distintos. Asimismo el presente trabajo puede tener interés para el grupo LIA de la Facultad de Informática de la Universidad Politécnica de Madrid, el cual está participando en el proyecto europeo BACTOCOM que se centra en el estudio de la conjugación de plásmidos y circuitos genéticos. --ABSTRACT--Currently there are applications that simulate the behavior of bacteria in different habitats and the ongoing processes inside them to facilitate their study and experimentation without the need for an actual laboratory. One of the most used open source applications to simulate bacterial populations is iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), an agent-based simulator that allows working with several computer models of 2D and 3D bacteria in biofilms. This simulator allows great freedom by means of a large number of configurable variables regarding environment, chemical reactions and other important details of the simulation. Within these characteristics there exists a very basic framework to simulate plasmid conjugation. Plasmids are DNA molecules physically different from the cell’s chromosome, commonly found as small circular, double-stranded DNA molecules that are replicated, conjugated and transcribed independently of chromosomal DNA. These bacteria are normally present in prokaryotes and sometimes in eukaryotes, which in this case these cells are called episomes. Plasmids are external mechanisms to the cells basic operations, and as such, in the majority of the cases, confer to the host cell various evolutionary advantages, like antibiotic resistance for example. It is mperative to further study plasmids and the possibilities they present. However, the operational framework of the iDynoMiCS plasmid simulation is too simple, and does not allow more complex operations that the analysis of the spread of a plasmid in the community. This project was conceived to resolve this particular deficiency in iDynomics, moreover, in this paper is discussed, developed and implemented the necessary changes to iDynomics simulation software so it can satisfactorily and realistically simulate plasmid conjugation, and allow the possibility to solve various ogic operations, such as plasmid-based genetic circuits. Moreover the results obtained will be analyzed and compared with other relevant studies and with those obtained with the original iDynomics code. Conjointly, an additional study detailing the sensing of a substance with two different genetic circuits will be presented. This work may also be relevant to the LIA group of the Faculty of Informatics of the Polytechnic University of Madrid, which is participating in the European project BACTOCOM that focuses on the study of the of plasmid conjugation and genetic circuits.

Modelo de arquitectura para gestión cooperativa de sistemas y servicios distribuidos basado en agentes autónomos

La creciente complejidad, heterogeneidad y dinamismo inherente a las redes de telecomunicaciones, los sistemas distribuidos y los servicios avanzados de información y comunicación emergentes, así como el incremento de su criticidad e importancia estratégica, requieren la adopción de tecnologías cada vez más sofisticadas para su gestión, su coordinación y su integración por parte de los operadores de red, los proveedores de servicio y las empresas, como usuarios finales de los mismos, con el fin de garantizar niveles adecuados de funcionalidad, rendimiento y fiabilidad. Las estrategias de gestión adoptadas tradicionalmente adolecen de seguir modelos excesivamente estáticos y centralizados, con un elevado componente de supervisión y difícilmente escalables. La acuciante necesidad por flexibilizar esta gestión y hacerla a la vez más escalable y robusta, ha provocado en los últimos años un considerable interés por desarrollar nuevos paradigmas basados en modelos jerárquicos y distribuidos, como evolución natural de los primeros modelos jerárquicos débilmente distribuidos que sucedieron al paradigma centralizado. Se crean así nuevos modelos como son los basados en Gestión por Delegación, en el paradigma de código móvil, en las tecnologías de objetos distribuidos y en los servicios web. Estas alternativas se han mostrado enormemente robustas, flexibles y escalables frente a las estrategias tradicionales de gestión, pero continúan sin resolver aún muchos problemas. Las líneas actuales de investigación parten del hecho de que muchos problemas de robustez, escalabilidad y flexibilidad continúan sin ser resueltos por el paradigma jerárquico-distribuido, y abogan por la migración hacia un paradigma cooperativo fuertemente distribuido. Estas líneas tienen su germen en la Inteligencia Artificial Distribuida (DAI) y, más concretamente, en el paradigma de agentes autónomos y en los Sistemas Multi-agente (MAS). Todas ellas se perfilan en torno a un conjunto de objetivos que pueden resumirse en alcanzar un mayor grado de autonomía en la funcionalidad de la gestión y una mayor capacidad de autoconfiguración que resuelva los problemas de escalabilidad y la necesidad de supervisión presentes en los sistemas actuales, evolucionar hacia técnicas de control fuertemente distribuido y cooperativo guiado por la meta y dotar de una mayor riqueza semántica a los modelos de información. Cada vez más investigadores están empezando a utilizar agentes para la gestión de redes y sistemas distribuidos. Sin embargo, los límites establecidos en sus trabajos entre agentes móviles (que siguen el paradigma de código móvil) y agentes autónomos (que realmente siguen el paradigma cooperativo) resultan difusos. Muchos de estos trabajos se centran en la utilización de agentes móviles, lo cual, al igual que ocurría con las técnicas de código móvil comentadas anteriormente, les permite dotar de un mayor componente dinámico al concepto tradicional de Gestión por Delegación. Con ello se consigue flexibilizar la gestión, distribuir la lógica de gestión cerca de los datos y distribuir el control. Sin embargo se permanece en el paradigma jerárquico distribuido. Si bien continúa sin definirse aún una arquitectura de gestión fiel al paradigma cooperativo fuertemente distribuido, estas líneas de investigación han puesto de manifiesto serios problemas de adecuación en los modelos de información, comunicación y organizativo de las arquitecturas de gestión existentes. En este contexto, la tesis presenta un modelo de arquitectura para gestión holónica de sistemas y servicios distribuidos mediante sociedades de agentes autónomos, cuyos objetivos fundamentales son el incremento del grado de automatización asociado a las tareas de gestión, el aumento de la escalabilidad de las soluciones de gestión, soporte para delegación tanto por dominios como por macro-tareas, y un alto grado de interoperabilidad en entornos abiertos. A partir de estos objetivos se ha desarrollado un modelo de información formal de tipo semántico, basado en lógica descriptiva que permite un mayor grado de automatización en la gestión en base a la utilización de agentes autónomos racionales, capaces de razonar, inferir e integrar de forma dinámica conocimiento y servicios conceptualizados mediante el modelo CIM y formalizados a nivel semántico mediante lógica descriptiva. El modelo de información incluye además un “mapping” a nivel de meta-modelo de CIM al lenguaje de especificación de ontologías OWL, que supone un significativo avance en el área de la representación y el intercambio basado en XML de modelos y meta-información. A nivel de interacción, el modelo aporta un lenguaje de especificación formal de conversaciones entre agentes basado en la teoría de actos ilocucionales y aporta una semántica operacional para dicho lenguaje que facilita la labor de verificación de propiedades formales asociadas al protocolo de interacción. Se ha desarrollado también un modelo de organización holónico y orientado a roles cuyas principales características están alineadas con las demandadas por los servicios distribuidos emergentes e incluyen la ausencia de control central, capacidades de reestructuración dinámica, capacidades de cooperación, y facilidades de adaptación a diferentes culturas organizativas. El modelo incluye un submodelo normativo adecuado al carácter autónomo de los holones de gestión y basado en las lógicas modales deontológica y de acción.---ABSTRACT---The growing complexity, heterogeneity and dynamism inherent in telecommunications networks, distributed systems and the emerging advanced information and communication services, as well as their increased criticality and strategic importance, calls for the adoption of increasingly more sophisticated technologies for their management, coordination and integration by network operators, service providers and end-user companies to assure adequate levels of functionality, performance and reliability. The management strategies adopted traditionally follow models that are too static and centralised, have a high supervision component and are difficult to scale. The pressing need to flexibilise management and, at the same time, make it more scalable and robust recently led to a lot of interest in developing new paradigms based on hierarchical and distributed models, as a natural evolution from the first weakly distributed hierarchical models that succeeded the centralised paradigm. Thus new models based on management by delegation, the mobile code paradigm, distributed objects and web services came into being. These alternatives have turned out to be enormously robust, flexible and scalable as compared with the traditional management strategies. However, many problems still remain to be solved. Current research lines assume that the distributed hierarchical paradigm has as yet failed to solve many of the problems related to robustness, scalability and flexibility and advocate migration towards a strongly distributed cooperative paradigm. These lines of research were spawned by Distributed Artificial Intelligence (DAI) and, specifically, the autonomous agent paradigm and Multi-Agent Systems (MAS). They all revolve around a series of objectives, which can be summarised as achieving greater management functionality autonomy and a greater self-configuration capability, which solves the problems of scalability and the need for supervision that plague current systems, evolving towards strongly distributed and goal-driven cooperative control techniques and semantically enhancing information models. More and more researchers are starting to use agents for network and distributed systems management. However, the boundaries established in their work between mobile agents (that follow the mobile code paradigm) and autonomous agents (that really follow the cooperative paradigm) are fuzzy. Many of these approximations focus on the use of mobile agents, which, as was the case with the above-mentioned mobile code techniques, means that they can inject more dynamism into the traditional concept of management by delegation. Accordingly, they are able to flexibilise management, distribute management logic about data and distribute control. However, they remain within the distributed hierarchical paradigm. While a management architecture faithful to the strongly distributed cooperative paradigm has yet to be defined, these lines of research have revealed that the information, communication and organisation models of existing management architectures are far from adequate. In this context, this dissertation presents an architectural model for the holonic management of distributed systems and services through autonomous agent societies. The main objectives of this model are to raise the level of management task automation, increase the scalability of management solutions, provide support for delegation by both domains and macro-tasks and achieve a high level of interoperability in open environments. Bearing in mind these objectives, a descriptive logic-based formal semantic information model has been developed, which increases management automation by using rational autonomous agents capable of reasoning, inferring and dynamically integrating knowledge and services conceptualised by means of the CIM model and formalised at the semantic level by means of descriptive logic. The information model also includes a mapping, at the CIM metamodel level, to the OWL ontology specification language, which amounts to a significant advance in the field of XML-based model and metainformation representation and exchange. At the interaction level, the model introduces a formal specification language (ACSL) of conversations between agents based on speech act theory and contributes an operational semantics for this language that eases the task of verifying formal properties associated with the interaction protocol. A role-oriented holonic organisational model has also been developed, whose main features meet the requirements demanded by emerging distributed services, including no centralised control, dynamic restructuring capabilities, cooperative skills and facilities for adaptation to different organisational cultures. The model includes a normative submodel adapted to management holon autonomy and based on the deontic and action modal logics.

Modeling the shape hierarchy for visually guided grasping

The monkey anterior intraparietal area (AIP) encodes visual information about three-dimensional object shape that is used to shape the hand for grasping. We modeled shape tuning in visual AIP neurons and its relationship with curvature and gradient information from the caudal intraparietal area (CIP). The main goal was to gain insight into the kinds of shape parameterizations that can account for AIP tuning and that are consistent with both the inputs to AIP and the role of AIP in grasping. We first experimented with superquadric shape parameters. We considered superquadrics because they occupy a role in robotics that is similar to AIP , in that superquadric fits are derived from visual input and used for grasp planning. We also experimented with an alternative shape parameterization that was based on an Isomap dimension reduction of spatial derivatives of depth (i.e., distance from the observer to the object surface). We considered an Isomap-based model because its parameters lacked discontinuities between similar shapes. When we matched the dimension of the Isomap to the number of superquadric parameters, the superquadric model fit the AIP data somewhat more closely. However, higher-dimensional Isomaps provided excellent fits. Also, we found that the Isomap parameters could be approximated much more accurately than superquadric parameters by feedforward neural networks with CIP-like inputs. We conclude that Isomaps, or perhaps alternative dimension reductions of visual inputs to AIP, provide a promising model of AIP electrophysiology data. Further work is needed to test whether such shape parameterizations actually provide an effective basis for grasp control.

Context modelling for natural Human Computer Interaction applications in e-health

The conception of IoT (Internet of Things) is accepted as the future tendency of Internet among academia and industry. It will enable people and things to be connected at anytime and anyplace, with anything and anyone. IoT has been proposed to be applied into many areas such as Healthcare, Transportation，Logistics, and Smart environment etc. However, this thesis emphasizes on the home healthcare area as it is the potential healthcare model to solve many problems such as the limited medical resources, the increasing demands for healthcare from elderly and chronic patients which the traditional model is not capable of. A remarkable change in IoT in semantic oriented vision is that vast sensors or devices are involved which could generate enormous data. Methods to manage the data including acquiring, interpreting, processing and storing data need to be implemented. Apart from this, other abilities that IoT is not capable of are concluded, namely, interoperation, context awareness and security & privacy. Context awareness is an emerging technology to manage and take advantage of context to enable any type of system to provide personalized services. The aim of this thesis is to explore ways to facilitate context awareness in IoT. In order to realize this objective, a preliminary research is carried out in this thesis. The most basic premise to realize context awareness is to collect, model, understand, reason and make use of context. A complete literature review for the existing context modelling and context reasoning techniques is conducted. The conclusion is that the ontology-based context modelling and ontology-based context reasoning are the most promising and efficient techniques to manage context. In order to fuse ontology into IoT, a specific ontology-based context awareness framework is proposed for IoT applications. In general, the framework is composed of eight components which are hardware, UI (User Interface), Context modelling, Context fusion, Context reasoning, Context repository, Security unit and Context dissemination. Moreover, on the basis of TOVE (Toronto Virtual Enterprise), a formal ontology developing methodology is proposed and illustrated which consists of four stages: Specification & Conceptualization, Competency Formulation, Implementation and Validation & Documentation. In addition, a home healthcare scenario is elaborated by listing its well-defined functionalities. Aiming at representing this specific scenario, the proposed ontology developing methodology is applied and the ontology-based model is developed in a free and open-source ontology editor called Protégé. Finally, the accuracy and completeness of the proposed ontology are validated to show that this proposed ontology is able to accurately represent the scenario of interest.