Functional and expression analysis of the metal-inducible dmeRF system from Rhizobium legumionosarum bv. viciae

A gene encoding a homolog to the cation diffusion facilitator protein DmeF from Cupriavidus metallidurans has been identified in the genome of Rhizobium leguminosarum UPM791. The R. leguminosarum dmeF gene is located downstream of an open reading frame (designated dmeR) encoding a protein homologous to the nickel- and cobalt-responsive transcriptional regulator RcnR from Escherichia coli. Analysis of gene expression showed that the R. leguminosarum dmeRF genes are organized as a transcriptional unit whose expression is strongly induced by nickel and cobalt ions, likely by alleviating the repressor activity of DmeR on dmeRF transcription. An R. leguminosarum dmeRF mutant strain displayed increased sensitivity to Co(II) and Ni(II), whereas no alterations of its resistance to Cd(II), Cu(II), or Zn(II) were observed. A decrease of symbiotic performance was observed when pea plants inoculated with an R. leguminosarum dmeRF deletion mutant strain were grown in the presence of high concentrations of nickel and cobalt. The same mutant induced significantly lower activity levels of NiFe hydrogenase in microaerobic cultures. These results indicate that the R. leguminosarum DmeRF system is a metal-responsive efflux mechanism acting as a key element for metal homeostasis in R. leguminosarum under free-living and symbiotic conditions. The presence of similar dmeRF gene clusters in other Rhizobiaceae suggests that the dmeRF system is a conserved mechanism for metal tolerance in legume endosymbiotic bacteria.

Open Technologies for prototyping the Internet of Things

The worldwide "hyper-connection" of any object around us is the challenge that promises to cover the paradigm of the Internet of Things. If the Internet has colonized the daily life of more than 2000 million1 people around the globe, the Internet of Things faces of connecting more than 100000 million2 "things" by 2020. The underlying Internet of Things’ technologies are the cornerstone that promises to solve interrelated global problems such as exponential population growth, energy management in cities, and environmental sustainability in the average and long term. On the one hand, this Project has the goal of knowledge acquisition about prototyping technologies available in the market for the Internet of Things. On the other hand, the Project focuses on the development of a system for devices management within a Wireless Sensor and Actuator Network to offer some services accessible from the Internet. To accomplish the objectives, the Project will begin with a detailed analysis of various “open source” hardware platforms to encourage creative development of applications, and automatically extract information from the environment around them for transmission to external systems. In addition, web platforms that enable mass storage with the philosophy of the Internet of Things will be studied. The project will culminate in the proposal and specification of a service-oriented software architecture for embedded systems that allows communication between devices on the network, and the data transmission to external systems. Furthermore, it abstracts the complexities of hardware to application developers. RESUMEN. La “hiper-conexión” a nivel mundial de cualquier objeto que nos rodea es el desafío al que promete dar cobertura el paradigma de la Internet de las Cosas. Si la Internet ha colonizado el día a día de más de 2000 millones1 de personas en todo el planeta, la Internet de las Cosas plantea el reto de conectar a más de 100000 millones2 de “cosas” para el año 2020. Las tecnologías subyacentes de la Internet de las Cosas son la piedra angular que prometen dar solución a problemas globales interrelacionados como el crecimiento exponencial de la población, la gestión de la energía en las ciudades o la sostenibilidad del medioambiente a largo plazo. Este Proyecto Fin de Carrera tiene como principales objetivos por un lado, la adquisición de conocimientos acerca de las tecnologías para prototipos disponibles en el mercado para la Internet de las Cosas, y por otro lado el desarrollo de un sistema para la gestión de dispositivos de una red inalámbrica de sensores que ofrezcan unos servicios accesibles desde la Internet. Con el fin de abordar los objetivos marcados, el proyecto comenzará con un análisis detallado de varias plataformas hardware de tipo “open source” que estimulen el desarrollo creativo de aplicaciones y que permitan extraer de forma automática información del medio que les rodea para transmitirlo a sistemas externos para su posterior procesamiento. Por otro lado, se estudiarán plataformas web identificadas con la filosofía de la Internet de las Cosas que permitan el almacenamiento masivo de datos que diferentes plataformas hardware transfieren a través de la Internet. El Proyecto culminará con la propuesta y la especificación una arquitectura software orientada a servicios para sistemas empotrados que permita la comunicación entre los dispositivos de la red y la transmisión de datos a sistemas externos, así como facilitar el desarrollo de aplicaciones a los programadores mediante la abstracción de la complejidad del hardware.

UBURYO: open source software for managing microcredits in education

One of the major problems in developing countries is minority access to higher education. Traditional scholarships usually focus on paying tuition fees for bringing brilliant students to developed countries (from where they seldom return). But local grants seldom target the more needy students. We propose a system of student loans to pay tuition fees in exchange for technical work. This appears to be a satisfactory and sustainable solution. We also provide UBURYO (a Kirundi word meaning opportunity). UBURYO is the free open source software, that we have developed, to manage this loan system in a simple, trustworthy, fair and efficient way.

DmeRF system is required for nickel and cobalt resistance in Rhizobium leguminosarum bv. viciae.

A member of the Cation Diffusion Facilitator (CDF) family with high sequence similarity to DmeF (Divalent metal efflux) from Cupridavirus metallidurans was identified in Rhizobium leguminosarum bv. viciae UPM1137. The R. leguminosarum dmeF mutant strain was highly sensitive to Co2+ and moderately sensitive to Ni2+, but its tolerance to other metals such as Zn2+, Cu2+ or Mn2+ was unaffected. An open reading frame located upstream of R. leguminosarum dmeF, designated dmeR, encodes a protein homologous to the nickel and cobalt regulator RcnR from E.coli. Expression of the dmeRF operon was induced by nickel and cobalt ions in free-living cells, likely by alleviating DmeR-mediated transcriptional repression of the operon.

Agent-based modeling and simulation for the design of the future european Air Traffic Management system: the experience of CASSIOPEIA

The SESAR (Single European Sky ATM Research) program is an ambitious re-search and development initiative to design the future European air traffic man-agement (ATM) system. The study of the behavior of ATM systems using agent-based modeling and simulation tools can help the development of new methods to improve their performance. This paper presents an overview of existing agent-based approaches in air transportation (paying special attention to the challenges that exist for the design of future ATM systems) and, subsequently, describes a new agent-based approach that we proposed in the CASSIOPEIA project, which was developed according to the goals of the SESAR program. In our approach, we use agent models for different ATM stakeholders, and, in contrast to previous work, our solution models new collaborative decision processes for flow traffic management, it uses an intermediate level of abstraction (useful for simulations at larger scales), and was designed to be a practical tool (open and reusable) for the development of different ATM studies. It was successfully applied in three stud-ies related to the design of future ATM systems in Europe.

An agent-based approach for the design of the future european air traffic management system

This paper describes an agent-based approach for the simulation of air traffic management (ATM) in Europe that was designed to help analyze proposals for future ATM systems. This approach is able to represent new collaborative deci-sion processes for flow traffic management, it uses an intermediate level of ab-straction (useful for simulations at larger scales), and was designed to be a practi-cal tool (open and reusable) for the development of different ATM studies. It was successfully applied in three studies related to the design of future ATM systems in Europe.

Advanced system of planning and organization of classes at the university

This document is the result of a process of web development to create a tool that will allow to Cracow University of Technology consult, create and manage timetables. The technologies chosen for this purpose are Apache Tomcat Server, My SQL Community Server, JDBC driver, Java Servlets and JSPs for the server side. The client part counts on Javascript, jQuery, AJAX and CSS technologies to perform the dynamism. The document will justify the choice of these technologies and will explain some development tools that help in the integration and development of all this elements: specifically, NetBeans IDE and MySQL workbench have been used as helpful tools. After explaining all the elements involved in the development of the web application, the architecture and the code developed are explained through UML diagrams. Some implementation details related to security are also deeper explained through sequence diagrams. As the source code of the application is provided, an installation manual has been developed to run the project. In addition, as the platform is intended to be a beta that will be grown, some unimplemented ideas for future development are also exposed. Finally, some annexes with important files and scripts related to the initiation of the platform are attached. This project started through an existing tool that needed to be expanded. The main purpose of the project along its development has focused on setting the roots for a whole new platform that will replace the existing one. For this goal, it has been needed to make a deep inspection on the existing web technologies: a web server and a SQL database had to be chosen. Although the alternatives were a lot, Java technology for the server was finally selected because of the big community backwards, the easiness of modelling the language through UML diagrams and the fact of being free license software. Apache Tomcat is the open source server that can use Java Servlet and JSP technology. Related to the SQL database, MySQL Community Server is the most popular open-source SQL Server, with a big community after and quite a lot of tools to manage the server. JDBC is the driver needed to put in contact Java and MySQL. Once we chose the technologies that would be part of the platform, the development process started. After a detailed explanation of the development environment installation, we used UML use case diagrams to set the main tasks of the platform; UML class diagrams served to establish the existing relations between the classes generated; the architecture of the platform was represented through UML deployment diagrams; and Enhanced entity–relationship (EER) model were used to define the tables of the database and their relationships. Apart from the previous diagrams, some implementation issues were explained to make a better understanding of the developed code - UML sequence diagrams helped to explain this. Once the whole platform was properly defined and developed, the performance of the application has been shown: it has been proved that with the current state of the code, the platform covers the use cases that were set as the main target. Nevertheless, some requisites needed for the proper working of the platform have been specified. As the project is aimed to be grown, some ideas that could not be added to this beta have been explained in order not to be missed for future development. Finally, some annexes containing important configuration issues for the platform have been added after proper explanation, as well as an installation guide that will let a new developer get the project ready. In addition to this document some other files related to the project are provided: - Javadoc. The Javadoc containing the information of every Java class created is necessary for a better understanding of the source code. - database_model.mwb. This file contains the model of the database for MySQL Workbench. This model allows, among other things, generate the MySQL script for the creation of the tables. - ScheduleManager.war. The WAR file that will allow loading the developed application into Tomcat Server without using NetBeans. - ScheduleManager.zip. The source code exported from NetBeans project containing all Java packages, JSPs, Javascript files and CSS files that are part of the platform. - config.properties. The configuration file to properly get the names and credentials to use the database, also explained in Annex II. Example of config.properties file. - db_init_script.sql. The SQL query to initiate the database explained in Annex III. SQL statements for MySQL initialization. RESUMEN. Este proyecto tiene como punto de partida la necesidad de evolución de una herramienta web existente. El propósito principal del proyecto durante su desarrollo se ha centrado en establecer las bases de una completamente nueva plataforma que reemplazará a la existente. Para lograr esto, ha sido necesario realizar una profunda inspección en las tecnologías web existentes: un servidor web y una base de datos SQL debían ser elegidos. Aunque existen muchas alternativas, la tecnología Java ha resultado ser elegida debido a la gran comunidad de desarrolladores que tiene detrás, además de la facilidad que proporciona este lenguaje a la hora de modelarlo usando diagramas UML. Tampoco hay que olvidar que es una tecnología de uso libre de licencia. Apache Tomcat es el servidor de código libre que permite emplear Java Servlets y JSPs para hacer uso de la tecnología de Java. Respecto a la base de datos SQL, el servidor más popular de código libre es MySQL, y cuenta también con una gran comunidad detrás y buenas herramientas de modelado, creación y gestión de la bases de datos. JDBC es el driver que va a permitir comunicar las aplicaciones Java con MySQL. Tras elegir las tecnologías que formarían parte de esta nueva plataforma, el proceso de desarrollo tiene comienzo. Tras una extensa explicación de la instalación del entorno de desarrollo, se han usado diagramas de caso de UML para establecer cuáles son los objetivos principales de la plataforma; los diagramas de clases nos permiten realizar una organización del código java desarrollado de modo que sean fácilmente entendibles las relaciones entre las diferentes clases. La arquitectura de la plataforma queda definida a través de diagramas de despliegue. Por último, diagramas EER van a definir las relaciones entre las tablas creadas en la base de datos. Aparte de estos diagramas, algunos detalles de implementación se van a justificar para tener una mejor comprensión del código desarrollado. Diagramas de secuencia ayudarán en estas explicaciones. Una vez que toda la plataforma haya quedad debidamente definida y desarrollada, se va a realizar una demostración de la misma: se demostrará cómo los objetivos generales han sido alcanzados con el desarrollo actual del proyecto. No obstante, algunos requisitos han sido aclarados para que la plataforma trabaje adecuadamente. Como la intención del proyecto es crecer (no es una versión final), algunas ideas que se han podido llevar acabo han quedado descritas de manera que no se pierdan. Por último, algunos anexos que contienen información importante acerca de la plataforma se han añadido tras la correspondiente explicación de su utilidad, así como una guía de instalación que va a permitir a un nuevo desarrollador tener el proyecto preparado. Junto a este documento, ficheros conteniendo el proyecto desarrollado quedan adjuntos. Estos ficheros son: - Documentación Javadoc. Contiene la información de las clases Java que han sido creadas. - database_model.mwb. Este fichero contiene el modelo de la base de datos para MySQL Workbench. Esto permite, entre otras cosas, generar el script de iniciación de la base de datos para la creación de las tablas. - ScheduleManager.war. El fichero WAR que permite desplegar la plataforma en un servidor Apache Tomcat. - ScheduleManager.zip. El código fuente exportado directamente del proyecto de Netbeans. Contiene todos los paquetes de Java generados, ficheros JSPs, Javascript y CSS que forman parte de la plataforma. - config.properties. Ejemplo del fichero de configuración que permite obtener los nombres de la base de datos - db_init_script.sql. Las consultas SQL necesarias para la creación de la base de datos.

Sistema de simulación de escenarios de ciclos avanzados de combustible nuclear en transición = Simulation system for advanced fuel cycle transition scenarios

El estudio de los ciclos del combustible nuclear requieren de herramientas computacionales o "códigos" versátiles para dar respuestas al problema multicriterio de evaluar los actuales ciclos o las capacidades de las diferentes estrategias y escenarios con potencial de desarrollo en a nivel nacional, regional o mundial. Por otra parte, la introducción de nuevas tecnologías para reactores y procesos industriales hace que los códigos existentes requieran nuevas capacidades para evaluar la transición del estado actual del ciclo del combustible hacia otros más avanzados y sostenibles. Brevemente, esta tesis se centra en dar respuesta a las principales preguntas, en términos económicos y de recursos, al análisis de escenarios de ciclos de combustible, en particular, para el análisis de los diferentes escenarios del ciclo del combustible de relativa importancia para España y Europa. Para alcanzar este objetivo ha sido necesaria la actualización y el desarrollo de nuevas capacidades del código TR_EVOL (Transition Evolution code). Este trabajo ha sido desarrollado en el Programa de Innovación Nuclear del CIEMAT desde el año 2010. Esta tesis se divide en 6 capítulos. El primer capítulo ofrece una visión general del ciclo de combustible nuclear, sus principales etapas y los diferentes tipos utilizados en la actualidad o en desarrollo para el futuro. Además, se describen las fuentes de material nuclear que podrían ser utilizadas como combustible (uranio y otros). También se puntualizan brevemente una serie de herramientas desarrolladas para el estudio de estos ciclos de combustible nuclear. El capítulo 2 está dirigido a dar una idea básica acerca de los costes involucrados en la generación de electricidad mediante energía nuclear. Aquí se presentan una clasificación de estos costos y sus estimaciones, obtenidas en la bibliografía, y que han sido evaluadas y utilizadas en esta tesis. Se ha incluido también una breve descripción del principal indicador económico utilizado en esta tesis, el “coste nivelado de la electricidad”. El capítulo 3 se centra en la descripción del código de simulación desarrollado para el estudio del ciclo del combustible nuclear, TR_EVOL, que ha sido diseñado para evaluar diferentes opciones de ciclos de combustibles. En particular, pueden ser evaluados las diversos reactores con, posiblemente, diferentes tipos de combustibles y sus instalaciones del ciclo asociadas. El módulo de evaluaciones económica de TR_EVOL ofrece el coste nivelado de la electricidad haciendo uso de las cuatro fuentes principales de información económica y de la salida del balance de masas obtenido de la simulación del ciclo en TR_EVOL. Por otra parte, la estimación de las incertidumbres en los costes también puede ser efectuada por el código. Se ha efectuado un proceso de comprobación cruzada de las funcionalidades del código y se descrine en el Capítulo 4. El proceso se ha aplicado en cuatro etapas de acuerdo con las características más importantes de TR_EVOL, balance de masas, composición isotópica y análisis económico. Así, la primera etapa ha consistido en el balance masas del ciclo de combustible nuclear actual de España. La segunda etapa se ha centrado en la comprobación de la composición isotópica del flujo de masas mediante el la simulación del ciclo del combustible definido en el proyecto CP-ESFR UE. Las dos últimas etapas han tenido como objetivo validar el módulo económico. De este modo, en la tercera etapa han sido evaluados los tres principales costes (financieros, operación y mantenimiento y de combustible) y comparados con los obtenidos por el proyecto ARCAS, omitiendo los costes del fin del ciclo o Back-end, los que han sido evaluado solo en la cuarta etapa, haciendo uso de costes unitarios y parámetros obtenidos a partir de la bibliografía. En el capítulo 5 se analizan dos grupos de opciones del ciclo del combustible nuclear de relevante importancia, en términos económicos y de recursos, para España y Europa. Para el caso español, se han simulado dos grupos de escenarios del ciclo del combustible, incluyendo estrategias de reproceso y extensión de vida de los reactores. Este análisis se ha centrado en explorar las ventajas y desventajas de reprocesado de combustible irradiado en un país con una “relativa” pequeña cantidad de reactores nucleares. Para el grupo de Europa se han tratado cuatro escenarios, incluyendo opciones de transmutación. Los escenarios incluyen los reactores actuales utilizando la tecnología reactor de agua ligera y ciclo abierto, un reemplazo total de los reactores actuales con reactores rápidos que queman combustible U-Pu MOX y dos escenarios del ciclo del combustible con transmutación de actínidos minoritarios en una parte de los reactores rápidos o en sistemas impulsados por aceleradores dedicados a transmutación. Finalmente, el capítulo 6 da las principales conclusiones obtenidas de esta tesis y los trabajos futuros previstos en el campo del análisis de ciclos de combustible nuclear. ABSTRACT The study of the nuclear fuel cycle requires versatile computational tools or “codes” to provide answers to the multicriteria problem of assessing current nuclear fuel cycles or the capabilities of different strategies and scenarios with potential development in a country, region or at world level. Moreover, the introduction of new technologies for reactors and industrial processes makes the existing codes to require new capabilities to assess the transition from current status of the fuel cycle to the more advanced and sustainable ones. Briefly, this thesis is focused in providing answers to the main questions about resources and economics in fuel cycle scenario analyses, in particular for the analysis of different fuel cycle scenarios with relative importance for Spain and Europe. The upgrade and development of new capabilities of the TR_EVOL code (Transition Evolution code) has been necessary to achieve this goal. This work has been developed in the Nuclear Innovation Program at CIEMAT since year 2010. This thesis is divided in 6 chapters. The first one gives an overview of the nuclear fuel cycle, its main stages and types currently used or in development for the future. Besides the sources of nuclear material that could be used as fuel (uranium and others) are also viewed here. A number of tools developed for the study of these nuclear fuel cycles are also briefly described in this chapter. Chapter 2 is aimed to give a basic idea about the cost involved in the electricity generation by means of the nuclear energy. The main classification of these costs and their estimations given by bibliography, which have been evaluated in this thesis, are presented. A brief description of the Levelized Cost of Electricity, the principal economic indicator used in this thesis, has been also included. Chapter 3 is focused on the description of the simulation tool TR_EVOL developed for the study of the nuclear fuel cycle. TR_EVOL has been designed to evaluate different options for the fuel cycle scenario. In particular, diverse nuclear power plants, having possibly different types of fuels and the associated fuel cycle facilities can be assessed. The TR_EVOL module for economic assessments provides the Levelized Cost of Electricity making use of the TR_EVOL mass balance output and four main sources of economic information. Furthermore, uncertainties assessment can be also carried out by the code. A cross checking process of the performance of the code has been accomplished and it is shown in Chapter 4. The process has been applied in four stages according to the most important features of TR_EVOL. Thus, the first stage has involved the mass balance of the current Spanish nuclear fuel cycle. The second stage has been focused in the isotopic composition of the mass flow using the fuel cycle defined in the EU project CP-ESFR. The last two stages have been aimed to validate the economic module. In the third stage, the main three generation costs (financial cost, O&M and fuel cost) have been assessed and compared to those obtained by ARCAS project, omitting the back-end costs. This last cost has been evaluated alone in the fourth stage, making use of some unit cost and parameters obtained from the bibliography. In Chapter 5 two groups of nuclear fuel cycle options with relevant importance for Spain and Europe are analyzed in economic and resources terms. For the Spanish case, two groups of fuel cycle scenarios have been simulated including reprocessing strategies and life extension of the current reactor fleet. This analysis has been focused on exploring the advantages and disadvantages of spent fuel reprocessing in a country with relatively small amount of nuclear power plants. For the European group, four fuel cycle scenarios involving transmutation options have been addressed. Scenarios include the current fleet using Light Water Reactor technology and open fuel cycle, a full replacement of the initial fleet with Fast Reactors burning U-Pu MOX fuel and two fuel cycle scenarios with Minor Actinide transmutation in a fraction of the FR fleet or in dedicated Accelerator Driven Systems. Finally, Chapter 6 gives the main conclusions obtained from this thesis and the future work foreseen in the field of nuclear fuel cycle analysis.

Data consistency management in an open smart home management platform

In this paper, the authors introduce a novel mechanism for data management in a middleware for smart home control, where a relational database and semantic ontology storage are used at the same time in a Data Warehouse. An annotation system has been designed for instructing the storage format and location, registering new ontology concepts and most importantly, guaranteeing the Data Consistency between the two storage methods. For easing the data persistence process, the Data Access Object (DAO) pattern is applied and optimized to enhance the Data Consistency assurance. Finally, this novel mechanism provides an easy manner for the development of applications and their integration with BATMP. Finally, an application named "Parameter Monitoring Service" is given as an example for assessing the feasibility of the system.

Whole system approaches for managing land-use change to deliver multiple benefits from biodiversity in tropical forest landcapes

Presentamos en una sesión dedicada al proyecto ROBIN: Session No. 101: Whole system approaches for managing land-use change to deliver multiple benefits from biodiversity in tropical forest landcapes (Chairs: Terry Parr, Michael Schmidt, Kirsten Thonicke - Theme 3)

Characterizing chaos in a type of fractional duffing's equation

We characterize the chaos in a fractional Duffing’s equation computing the Lyapunov exponents and the dimension of the strange attractor in the effective phase space of the system. We develop a specific analytical method to estimate all Lyapunov exponents and check the results with the fiduciary orbit technique and a time series estimation method.

Loose Coupling Based Reference Scheme for Shop Floor-Control-System/Production-Equipment Integration.

Acoplamiento del sistema informático de control de piso de producción (SFS) con el conjunto de equipos de fabricación (SPE) es una tarea compleja. Tal acoplamiento involucra estándares abiertos y propietarios, tecnologías de información y comunicación, entre otras herramientas y técnicas. Debido a la turbulencia de mercados, ya sea soluciones personalizadas o soluciones basadas en estándares eventualmente requieren un esfuerzo considerable de adaptación. El concepto de acoplamiento débil ha sido identificado en la comunidad de diseño organizacional como soporte para la sobrevivencia de la organización. Su presencia reduce la resistencia de la organización a cambios en el ambiente. En este artículo los resultados obtenidos por la comunidad de diseño organizacional son identificados, traducidos y organizados para apoyar en la solución del problema de integración SFS-SPE. Un modelo clásico de acoplamiento débil, desarrollado por la comunidad de estudios de diseño organizacional, es resumido y trasladado al área de interés. Los aspectos claves son identificados para utilizarse como promotores del acoplamiento débil entre SFS-SPE, y presentados en forma de esquema de referencia. Así mismo, este esquema de referencia es presentado como base para el diseño e implementación de una solución genérica de acoplamiento o marco de trabajo (framework) de acoplamiento, a incluir como etapa de acoplamiento débil entre SFS y SPE. Un ejemplo de validación con varios conjuntos de equipos de fabricación, usando diferentes medios físicos de comunicación, comandos de controlador, lenguajes de programación de equipos y protocolos de comunicación es presentado, mostrando un nivel aceptable de autonomía del SFS. = Coupling shop floor software system (SFS) with the set of production equipment (SPE) becomes a complex task. It involves open and proprietary standards, information and communication technologies among other tools and techniques. Due to market turbulence, either custom solutions or standards based solutions eventually require a considerable effort of adaptation. Loose coupling concept has been identified in the organizational design community as a compensator for organization survival. Its presence reduces organization reaction to environment changes. In this paper the results obtained by the organizational de sign community are identified, translated and organized to support the SFS-SPE integration problem solution. A classical loose coupling model developed by organizational studies community is abstracted and translated to the area of interest. Key aspects are identified to be used as promoters of SFS-SPE loose coupling and presented in a form of a reference scheme. Furthermore, this reference scheme is proposed here as a basis for the design and implementation of a generic coupling solution or coupling framework, that is included as a loose coupling stage between SFS and SPE. A validation example with various sets of manufacturing equipment, using different physical communication media, controller commands, programming languages and wire protocols is presented, showing an acceptable level of autonomy gained by the SFS.

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

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

Lipidic cubic phases: A novel concept for the crystallization of membrane proteins

Understanding the mechanisms of action of membrane proteins requires the elucidation of their structures to high resolution. The critical step in accomplishing this by x-ray crystallography is the routine availability of well-ordered three-dimensional crystals. We have devised a novel, rational approach to meet this goal using quasisolid lipidic cubic phases. This membrane system, consisting of lipid, water, and protein in appropriate proportions, forms a structured, transparent, and complex three-dimensional lipidic array, which is pervaded by an intercommunicating aqueous channel system. Such matrices provide nucleation sites (“seeding”) and support growth by lateral diffusion of protein molecules in the membrane (“feeding”). Bacteriorhodopsin crystals were obtained from bicontinuous cubic phases, but not from micellar systems, implying a critical role of the continuity of the diffusion space (the bilayer) on crystal growth. Hexagonal bacteriorhodopsin crystals diffracted to 3.7 Å resolution, with a space group P63, and unit cell dimensions of a = b = 62 Å, c = 108 Å; α = β = 90° and γ = 120°.

Crystallization and identification of an assembly defect of recombinant antenna complexes produced in transgenic tobacco plants

A chimeric Lhcb gene encoding light-harvesting chlorophyll a/b-binding protein (LHCII) was expressed in transgenic tobacco plants. To separate native from recombinant LHCII, the protein was extended by six histidines at its C terminus. Recombinant LHCII was isolated by detergent-mediated monomerization of pure trimers followed by affinity-chromatography on Ni2+-NTA-agarose (NTA is nitrilotriacetic acid). Elution with imidazole yielded recombinant monomers that formed trimers readily after dilution of the detergent without further in vitro manipulations. LHCII subunits showed the typical chlorophyll a/b ratio at all steps of purification indicating no significant loss of pigments. Transgenic tobacco overexpressed amounts of recombinant protein that corresponded to about 0.7% of total LHCII. This yield suggested that expression in planta might be an alternative to the expression of eukaryotic membrane proteins in yeast. Recombinant LHCII was able to form two-dimensional crystals after addition of digalactolipids, which diffracted electrons to 3.6-Å resolution. LHCII carrying a replacement of Arg-21 with Gln accumulated to only 0.004% of total thylakoid proteins. This mutant was monomeric in the photosynthetic membrane probably due to the deletion of the phosphatidylglycerol binding site and was degraded by the plastidic proteolytic system. Exchange of Asn-183 with Leu impaired LHCII biogenesis in a similar way presumably due to the lack of a chlorophyll a binding site.