A new module system for prolog

It is now widely accepted that separating programs into modules is useful in program development and maintenance. While many Prolog implementations include useful module systems, we argüe that these systems can be improved in a number of ways, such as, for example, being more amenable to effective global analysis and transformation and allowing sepárate compilation or sensible creation of standalone executables. We discuss a number of issues related to the design of such an improved module system for Prolog and propose some novel solutions. Based on this, we present the choices made in the Ciao module system, which has been designed to meet a number of objectives: allowing sepárate compilation, extensibility in features and in syntax, amenability to modular global analysis and transformation, enhanced error detection, support for meta-programming and higher-order, compatibility to the extent possible with official and de-facto standards, etc.

A new module system for prolog

It is now widely accepted that separating programs into modules has proven very useful in program development and maintenance. While many Prolog implementations include useful module systems, we feel that these systems can be improved in a number of ways, such as, for example, being more amenable to effective global analysis and allowing sepárate compilation or sensible creation of standalone executables. We discuss a number of issues related to the design of such an improved module system for Prolog. Based on this, we present the choices made in the Ciao module system, which has been designed to meet a number of objectives: allowing sepárate compilation, extensibility in features and in syntax, amenability to modular global analysis, etc.

Sequential origin in the high performance properties of spider dragline silk

Major ampullate (MA) dragline silk supports spider orb webs, combining strength and extensibility in the toughest biomaterial. MA silk evolved ~376 MYA and identifying how evolutionary changes in proteins influenced silk mechanics is crucial for biomimetics, but is hindered by high spinning plasticity. We use supercontraction to remove that variation and characterize MA silk across the spider phylogeny. We show that mechanical performance is conserved within, but divergent among, major lineages, evolving in correlation with discrete changes in proteins. Early MA silk tensile strength improved rapidly with the origin of GGX amino acid motifs and increased repetitiveness. Tensile strength then maximized in basal entelegyne spiders, ~230 MYA. Toughness subsequently improved through increased extensibility within orb spiders, coupled with the origin of a novel protein (MaSp2). Key changes in MA silk proteins therefore correlate with the sequential evolution high performance orb spider silk and could aid design of biomimetic fibers.

ARGoS: a modular, multi-engine simulator for heterogeneous swarm robotics

We present ARGoS, a novel open source multi-robot simulator. The main design focus of ARGoS is the real-time simulation of large heterogeneous swarms of robots. Existing robot simulators obtain scalability by imposing limitations on their extensibility and on the accuracy of the robot models. By contrast, in ARGoS we pursue a deeply modular approach that allows the user both to easily add custom features and to allocate computational resources where needed by the experiment. A unique feature of ARGoS is the possibility to use multiple physics engines of different types and to assign them to different parts of the environment. Robots can migrate from one engine to another transparently. This feature enables entirely novel classes of optimizations to improve scalability and paves the way for a new approach to parallelism in robotics simulation. Results show that ARGoS can simulate about 10,000 simple wheeled robots 40% faster than real-time.

Xyloglucan endotransglucosylase/hydrolase (XTH) overexpression affects growth and cell wall mechanics in etiolated Arabidopsis hypocotyls.

Growth and biomechanics of etiolated hypocotyls from Arabidopsis thaliana lines overexpressing xyloglucan endotransglucosylase/hydrolase AtXTH18, AtXTH19, AtXTH20, and PttXET16-34 were studied. Overexpression of AtXTH18, AtXTH19, and AtXTH20 stimulated growth of hypocotyls, while PttXET16-34 overexpression did not show this effect. In vitro extension of frozen/thawed hypocotyls measured by a constant-load extensiometer started from a high-amplitude initial deformation followed by a slow time-dependent creep. Creep of growing XTH-overexpressing (OE) hypocotyls was more linear in time compared with the wild type at pH 5.0, reflecting their higher potential for long-term extension. XTH-OE plants deposited 65?84% more cell wall material per hypocotyl cross-sectional area than wild-type plants. As a result, their wall stress under each external load was lower than in the wild-type. Growing XTH-OE hypocotyls had higher values of initial deformation·stress?1 compared with the wild type. Plotting creep rates for each line under different loads against the respective wall stress values gave straight lines. Their slopes and intercepts with the abscissa correspond to ? (in vitro cell wall extensibility) and y (in vitro cell wall yield threshold) values characterizing cell wall material properties. The wall material in XTH-OE lines was more pliant than in the wild type due to lower y values. In contrast, the acid-induced wall extension in vitro resulted from increasing ? values. Thus, three factors contributed to the XTH-OE-stimulated growth in Arabidopsis hypocotyls: their more linear creep, higher values of initial deformation·stress?1, and lower y values.

Advances in global instability computations: from incompressible to hypersonic flow

Esta tesis constituye un gran avance en el conocimiento del estudio y análisis de inestabilidades hidrodinámicas desde un punto de vista físico y teórico, como consecuencia de haber desarrollado innovadoras técnicas para la resolución computacional eficiente y precisa de la parte principal del espectro correspondiente a los problemas de autovalores (EVP) multidimensionales que gobiernan la inestabilidad de flujos con dos o tres direcciones espaciales inhomogéneas, denominados problemas de estabilidad global lineal. En el contexto del trabajo de desarrollo de herramientas computacionales presentado en la tesis, la discretización mediante métodos de diferencias finitas estables de alto orden de los EVP bidimensionales y tridimensionales que se derivan de las ecuaciones de Navier-Stokes linealizadas sobre flujos con dos o tres direcciones espaciales inhomogéneas, ha permitido una aceleración de cuatro órdenes de magnitud en su resolución. Esta mejora de eficiencia numérica se ha conseguido gracias al hecho de que usando estos esquemas de diferencias finitas, técnicas eficientes de resolución de problemas lineales son utilizables, explotando el alto nivel de dispersión o alto número de elementos nulos en las matrices involucradas en los problemas tratados. Como más notable consecuencia cabe destacar que la resolución de EVPs multidimensionales de inestabilidad global, que hasta la fecha necesitaban de superordenadores, se ha podido realizar en ordenadores de sobremesa. Además de la solución de problemas de estabilidad global lineal, el mencionado desarrollo numérico facilitó la extensión de las ecuaciones de estabilidad parabolizadas (PSE) lineales y no lineales para analizar la inestabilidad de flujos que dependen fuertemente en dos direcciones espaciales y suavemente en la tercera con las ecuaciones de estabilidad parabolizadas tridimensionales (PSE-3D). Precisamente la capacidad de extensión del novedoso algoritmo PSE-3D para el estudio de interacciones no lineales de los modos de estabilidad, desarrollado íntegramente en esta tesis, permite la predicción de transición en flujos complejos de gran interés industrial y por lo tanto extiende el concepto clásico de PSE, el cuál ha sido empleado exitosamente durante las pasadas tres décadas en el mismo contexto para problemas de capa límite bidimensional. Típicos ejemplos de flujos incompresibles se han analizado en este trabajo sin la necesidad de recurrir a restrictivas presuposiciones usadas en el pasado. Se han estudiado problemas vorticales como es el caso de un vórtice aislado o sistemas de vórtices simulando la estela de alas, en los que la homogeneidad axial no se impone y así se puede considerar la difusión viscosa del flujo. Además, se ha estudiado el chorro giratorio turbulento, cuya inestabilidad se utiliza para mejorar las características de funcionamiento de combustores. En la tesis se abarcan adicionalmente problemas de flujos compresibles. Se presenta el estudio de inestabilidad de flujos de borde de ataque a diferentes velocidades de vuelo. También se analiza la estela formada por un elemento rugoso aislado en capa límite supersónica e hipersónica, mostrando excelentes comparaciones con resultados obtenidos mediante simulación numérica directa. Finalmente, nuevas inestabilidades se han identificado en el flujo hipersónico a Mach 7 alrededor de un cono elíptico que modela el vehículo de pruebas en vuelo HIFiRE-5. Los resultados comparan favorablemente con experimentos en vuelo, lo que subraya aún más el potencial de las metodologías de análisis de estabilidad desarrolladas en esta tesis. ABSTRACT The present thesis constitutes a step forward in advancing the frontiers of knowledge of fluid flow instability from a physical point of view, as a consequence of having been successful in developing groundbreaking methodologies for the efficient and accurate computation of the leading part of the spectrum pertinent to multi-dimensional eigenvalue problems (EVP) governing instability of flows with two or three inhomogeneous spatial directions. In the context of the numerical work presented in this thesis, the discretization of the spatial operator resulting from linearization of the Navier-Stokes equations around flows with two or three inhomogeneous spatial directions by variable-high-order stable finite-difference methods has permitted a speedup of four orders of magnitude in the solution of the corresponding two- and three-dimensional EVPs. This improvement of numerical performance has been achieved thanks to the high-sparsity level offered by the high-order finite-difference schemes employed for the discretization of the operators. This permitted use of efficient sparse linear algebra techniques without sacrificing accuracy and, consequently, solutions being obtained on typical workstations, as opposed to the previously employed supercomputers. Besides solution of the two- and three-dimensional EVPs of global linear instability, this development paved the way for the extension of the (linear and nonlinear) Parabolized Stability Equations (PSE) to analyze instability of flows which depend in a strongly-coupled inhomogeneous manner on two spatial directions and weakly on the third. Precisely the extensibility of the novel PSE-3D algorithm developed in the framework of the present thesis to study nonlinear flow instability permits transition prediction in flows of industrial interest, thus extending the classic PSE concept which has been successfully employed in the same context to boundary-layer type of flows over the last three decades. Typical examples of incompressible flows, the instability of which was analyzed in the present thesis without the need to resort to the restrictive assumptions used in the past, range from isolated vortices, and systems thereof, in which axial homogeneity is relaxed to consider viscous diffusion, as well as turbulent swirling jets, the instability of which is exploited in order to improve flame-holding properties of combustors. The instability of compressible subsonic and supersonic leading edge flows has been solved, and the wake of an isolated roughness element in a supersonic and hypersonic boundary-layer has also been analyzed with respect to its instability: excellent agreement with direct numerical simulation results has been obtained in all cases. Finally, instability analysis of Mach number 7 ow around an elliptic cone modeling the HIFiRE-5 flight test vehicle has unraveled flow instabilities near the minor-axis centerline, results comparing favorably with flight test predictions.

CloudRoom: módulo de gestión de cursos online, abiertos y masivos

La razón de este proyecto, es la de desarrollar el módulo de cursos de la plataforma de Massive Online Open Courses (MOOCs), CloudRoom. Dicho módulo está englobado en una arquitectura orientada a servicios (SOA) y en una infraestructura de Cloud Computing utilizando Amazon Web Services (AWS). Nuestro objetivo es el de diseñar un Software as a Service (SaaS) robusto con las cualidades que a un producto de este tipo se le estiman: alta disponibilidad, alto rendimiento, gran experiencia de usuario y gran extensibilidad del sistema. Para lograrlo, se llevará a cabo la integración de las últimas tendencias tecnológicas dentro del desarrollo de sistemas distribuidos como Neo4j, Node.JS, Servicios RESTful, CoffeeScript. Todo esto siguiendo un estrategia de desarrollo PLAN-DO-CHECK utilizando Scrum y prácticas de metodologías ágiles. ---ABSTRACT---The reason of this Project is to develop the courses‟ module of CloudRoom, a Massive Online Open Courses platform. This module is encapsulated in a service-oriented architecture (SOA) based on a Cloud Computing infrastructure built on Amazon Web Services (AWS). Our goal is to design a robust Software as a Service (SaaS) with the qualities that are estimated in a product of this type: high availability, high performance, great user experience and great extensibility of the system. In order to address this, we carry out the integration of the latest technology trends in the development of distributed systems: Neo4j, Node.JS, RESTful Services and CoffeeScript. All of this, following a development strategy PLAN-DO-CHECK, using Scrum and practices of agile methodologies.

Análisis del software ImageJ para el análisis científico de imágenes

ImageJ es un programa informático de tratamiento digital de imagen orientado principalmente hacia el ámbito de las ciencias de la salud. Se trata de un software de dominio público y de código abierto desarrollado en lenguaje Java en las instituciones del National Institutes of Health de Estados Unidos. Incluye por defecto potentes herramientas para editar, procesar y analizar imágenes de casi cualquier tipo y formato. Sin embargo, su mayor virtud reside en su extensibilidad: las funcionalidades de ImageJ pueden ampliarse hasta resolver casi cualquier problema de tratamiento digital de imagen mediante macros, scripts y, especialmente, plugins programables en lenguaje Java gracias a la API que ofrece. Además, ImageJ cuenta con repositorios oficiales en los que es posible obtener de forma gratuita macros, scripts y plugins aplicables en multitud de entornos gracias a la labor de la extensa comunidad de desarrolladores de ImageJ, que los depura, mejora y amplia frecuentemente. Este documento es la memoria de un proyecto que consiste en el análisis detallado de las herramientas de tratamiento digital de imagen que ofrece ImageJ. Tiene por objetivo determinar si ImageJ, a pesar de estar más enfocado a las ciencias de la salud, puede resultar útil en el entorno de la Escuela Técnica Superior de Ingeniería y Sistemas de Telecomunicación de la Universidad Politécnica de Madrid, y en tal caso, resaltar las características que pudieran resultar más beneficiosas en este ámbito y servir además como guía introductoria. En las siguientes páginas se examinan una a una las herramientas de ImageJ (versión 1.48q), su funcionamiento y los mecanismos subyacentes. Se sigue el orden marcado por los menús de la interfaz de usuario: el primer capítulo abarca las herramientas destinadas a la manipulación de imágenes en general (menú Image); el segundo, las herramientas de procesado (menú Process); el tercero, las herramientas de análisis (menú Analyze); y el cuarto y último, las herramientas relacionadas con la extensibilidad de ImageJ (menú Plugins). ABSTRACT. ImageJ is a digital image processing computer program which is mainly focused at the health sciences field. It is a public domain, open source software developed in Java language at the National Institutes of Health of the United States of America. It includes powerful built-in tools to edit, process and analyze almost every type of image in nearly every format. However, its main virtue is its extensibility: ImageJ functionalities can be widened to solve nearly every situation found in digital image processing through macros, scripts and, specially, plugins programmed in Java language thanks to the ImageJ API. In addition, ImageJ has official repositories where it is possible to freely get many different macros, scripts and plugins thanks to the work carried out by the ImageJ developers community, which continuously debug, improve and widen them. This document is a report which explains a detailed analysis of all the digital image processing tools offered by ImageJ. Its final goal is to determine if ImageJ can be useful to the environment of Escuela Tecnica Superior de Ingenierfa y Sistemas de Telecomunicacion of Universidad Politecnica de Madrid, in spite of being focused at the health sciences field. In such a case, it also aims to highlight the characteristics which could be more beneficial in this field, and serve as an introductory guide too. In the following pages, all of the ImageJ tools (version 1.48q) are examined one by one, as well as their work and the underlying mechanics. The document follows the order established by the menus in ImageJ: the first chapter covers all the tools destined to manipulate images in general (menu Image); the second one covers all the processing tools (menu Process); the third one includes analyzing tools (menu Analyze); and finally, the fourth one contains all those tools related to ImageJ extensibility (menu Plugins).

Application of Agent Technology for Fault Diagnosis of Telecommunication Networks

La presente tesis doctoral contribuye al problema del diagnóstico autonómico de fallos en redes de telecomunicación. En las redes de telecomunicación actuales, las operadoras realizan tareas de diagnóstico de forma manual. Dichas operaciones deben ser llevadas a cabo por ingenieros altamente cualificados que cada vez tienen más dificultades a la hora de gestionar debidamente el crecimiento exponencial de la red tanto en tamaño, complejidad y heterogeneidad. Además, el advenimiento del Internet del Futuro hace que la demanda de sistemas que simplifiquen y automaticen la gestión de las redes de telecomunicación se haya incrementado en los últimos años. Para extraer el conocimiento necesario para desarrollar las soluciones propuestas y facilitar su adopción por los operadores de red, se propone una metodología de pruebas de aceptación para sistemas multi-agente enfocada en simplificar la comunicación entre los diferentes grupos de trabajo involucrados en todo proyecto de desarrollo software: clientes y desarrolladores. Para contribuir a la solución del problema del diagnóstico autonómico de fallos, se propone una arquitectura de agente capaz de diagnosticar fallos en redes de telecomunicación de manera autónoma. Dicha arquitectura extiende el modelo de agente Belief-Desire- Intention (BDI) con diferentes modelos de diagnóstico que gestionan las diferentes sub-tareas del proceso. La arquitectura propuesta combina diferentes técnicas de razonamiento para alcanzar su propósito gracias a un modelo estructural de la red, que usa razonamiento basado en ontologías, y un modelo causal de fallos, que usa razonamiento Bayesiano para gestionar debidamente la incertidumbre del proceso de diagnóstico. Para asegurar la adecuación de la arquitectura propuesta en situaciones de gran complejidad y heterogeneidad, se propone un marco de argumentación que permite diagnosticar a agentes que estén ejecutando en dominios federados. Para la aplicación de este marco en un sistema multi-agente, se propone un protocolo de coordinación en el que los agentes dialogan hasta alcanzar una conclusión para un caso de diagnóstico concreto. Como trabajos futuros, se consideran la extensión de la arquitectura para abordar otros problemas de gestión como el auto-descubrimiento o la auto-optimización, el uso de técnicas de reputación dentro del marco de argumentación para mejorar la extensibilidad del sistema de diagnóstico en entornos federados y la aplicación de las arquitecturas propuestas en las arquitecturas de red emergentes, como SDN, que ofrecen mayor capacidad de interacción con la red. ABSTRACT This PhD thesis contributes to the problem of autonomic fault diagnosis of telecommunication networks. Nowadays, in telecommunication networks, operators perform manual diagnosis tasks. Those operations must be carried out by high skilled network engineers which have increasing difficulties to properly manage the growing of those networks, both in size, complexity and heterogeneity. Moreover, the advent of the Future Internet makes the demand of solutions which simplifies and automates the telecommunication network management has been increased in recent years. To collect the domain knowledge required to developed the proposed solutions and to simplify its adoption by the operators, an agile testing methodology is defined for multiagent systems. This methodology is focused on the communication gap between the different work groups involved in any software development project, stakeholders and developers. To contribute to overcoming the problem of autonomic fault diagnosis, an agent architecture for fault diagnosis of telecommunication networks is defined. That architecture extends the Belief-Desire-Intention (BDI) agent model with different diagnostic models which handle the different subtasks of the process. The proposed architecture combines different reasoning techniques to achieve its objective using a structural model of the network, which uses ontology-based reasoning, and a causal model, which uses Bayesian reasoning to properly handle the uncertainty of the diagnosis process. To ensure the suitability of the proposed architecture in complex and heterogeneous environments, an argumentation framework is defined. This framework allows agents to perform fault diagnosis in federated domains. To apply this framework in a multi-agent system, a coordination protocol is defined. This protocol is used by agents to dialogue until a reliable conclusion for a specific diagnosis case is reached. Future work comprises the further extension of the agent architecture to approach other managements problems, such as self-discovery or self-optimisation; the application of reputation techniques in the argumentation framework to improve the extensibility of the diagnostic system in federated domains; and the application of the proposed agent architecture in emergent networking architectures, such as SDN, which offers new capabilities of control for the network.

Nepfix: on-demand cloud elastic simulation of networks of evolutionary processors

Una Red de Procesadores Evolutivos o NEP (por sus siglas en ingles), es un modelo computacional inspirado por el modelo evolutivo de las celulas, específicamente por las reglas de multiplicación de las mismas. Esta inspiración hace que el modelo sea una abstracción sintactica de la manipulation de information de las celulas. En particu¬lar, una NEP define una maquina de cómputo teorica capaz de resolver problemas NP completos de manera eficiente en tóerminos de tiempo. En la praóctica, se espera que las NEP simuladas en móaquinas computacionales convencionales puedan resolver prob¬lemas reales complejos (que requieran ser altamente escalables) a cambio de una alta complejidad espacial. En el modelo NEP, las cóelulas estóan representadas por palabras que codifican sus secuencias de ADN. Informalmente, en cualquier momento de cómputo del sistema, su estado evolutivo se describe como un coleccion de palabras, donde cada una de ellas representa una celula. Estos momentos fijos de evolucion se denominan configuraciones. De manera similar al modelo biologico, las palabras (celulas) mutan y se dividen en base a bio-operaciones sencillas, pero solo aquellas palabras aptas (como ocurre de forma parecida en proceso de selection natural) seran conservadas para la siguiente configuracióon. Una NEP como herramienta de computation, define una arquitectura paralela y distribuida de procesamiento simbolico, en otras palabras, una red de procesadores de lenguajes. Desde el momento en que el modelo fue propuesto a la comunidad científica en el año 2001, múltiples variantes se han desarrollado y sus propiedades respecto a la completitud computacional, eficiencia y universalidad han sido ampliamente estudiadas y demostradas. En la actualidad, por tanto, podemos considerar que el modelo teórico NEP se encuentra en el estadio de la madurez. La motivación principal de este Proyecto de Fin de Grado, es proponer una aproxi-mación práctica que permita dar un salto del modelo teórico NEP a una implantación real que permita su ejecucion en plataformas computacionales de alto rendimiento, con el fin de solucionar problemas complejos que demanda la sociedad actual. Hasta el momento, las herramientas desarrolladas para la simulation del modelo NEP, si bien correctas y con resultados satisfactorios, normalmente estón atadas a su entorno de ejecucion, ya sea el uso de hardware específico o implementaciones particulares de un problema. En este contexto, el propósito fundamental de este trabajo es el desarrollo de Nepfix, una herramienta generica y extensible para la ejecucion de cualquier algo¬ritmo de un modelo NEP (o alguna de sus variantes), ya sea de forma local, como una aplicación tradicional, o distribuida utilizando los servicios de la nube. Nepfix es una aplicacion software desarrollada durante 7 meses y que actualmente se encuentra en su segunda iteration, una vez abandonada la fase de prototipo. Nepfix ha sido disenada como una aplicacion modular escrita en Java 8 y autocontenida, es decir, no requiere de un entorno de ejecucion específico (cualquier maquina virtual de Java es un contenedor vólido). Nepfix contiene dos componentes o móodulos. El primer móodulo corresponde a la ejecución de una NEP y es por lo tanto, el simulador. Para su desarrollo, se ha tenido en cuenta el estado actual del modelo, es decir, las definiciones de los procesadores y filtros mas comunes que conforman la familia del modelo NEP. Adicionalmente, este componente ofrece flexibilidad en la ejecucion, pudiendo ampliar las capacidades del simulador sin modificar Nepfix, usando para ello un lenguaje de scripting. Dentro del desarrollo de este componente, tambióen se ha definido un estóandar de representacióon del modelo NEP basado en el formato JSON y se propone una forma de representation y codificación de las palabras, necesaria para la comunicación entre servidores. Adicional-mente, una característica importante de este componente, es que se puede considerar una aplicacion aislada y por tanto, la estrategia de distribution y ejecución son total-mente independientes. El segundo moódulo, corresponde a la distribucióon de Nepfix en la nube. Este de-sarrollo es el resultado de un proceso de i+D, que tiene una componente científica considerable. Vale la pena resaltar el desarrollo de este modulo no solo por los resul-tados prócticos esperados, sino por el proceso de investigation que se se debe abordar con esta nueva perspectiva para la ejecución de sistemas de computación natural. La principal característica de las aplicaciones que se ejecutan en la nube es que son gestionadas por la plataforma y normalmente se encapsulan en un contenedor. En el caso de Nepfix, este contenedor es una aplicacion Spring que utiliza el protocolo HTTP o AMQP para comunicarse con el resto de instancias. Como valor añadido, Nepfix aborda dos perspectivas de implementation distintas (que han sido desarrolladas en dos iteraciones diferentes) del modelo de distribution y ejecucion, que tienen un impacto muy significativo en las capacidades y restricciones del simulador. En concreto, la primera iteration utiliza un modelo de ejecucion asincrono. En esta perspectiva asincrona, los componentes de la red NEP (procesadores y filtros) son considerados como elementos reactivos a la necesidad de procesar una palabra. Esta implementation es una optimization de una topologia comun en el modelo NEP que permite utilizar herramientas de la nube para lograr un escalado transparente (en lo ref¬erente al balance de carga entre procesadores) pero produce efectos no deseados como indeterminacion en el orden de los resultados o imposibilidad de distribuir eficiente-mente redes fuertemente interconectadas. Por otro lado, la segunda iteration corresponde al modelo de ejecucion sincrono. Los elementos de una red NEP siguen un ciclo inicio-computo-sincronizacion hasta que el problema se ha resuelto. Esta perspectiva sincrona representa fielmente al modelo teórico NEP pero el proceso de sincronizacion es costoso y requiere de infraestructura adicional. En concreto, se requiere un servidor de colas de mensajes RabbitMQ. Sin embargo, en esta perspectiva los beneficios para problemas suficientemente grandes superan a los inconvenientes, ya que la distribuciín es inmediata (no hay restricciones), aunque el proceso de escalado no es trivial. En definitiva, el concepto de Nepfix como marco computacional se puede considerar satisfactorio: la tecnología es viable y los primeros resultados confirman que las carac-terísticas que se buscaban originalmente se han conseguido. Muchos frentes quedan abiertos para futuras investigaciones. En este documento se proponen algunas aproxi-maciones a la solucion de los problemas identificados como la recuperacion de errores y la division dinamica de una NEP en diferentes subdominios. Por otra parte, otros prob-lemas, lejos del alcance de este proyecto, quedan abiertos a un futuro desarrollo como por ejemplo, la estandarización de la representación de las palabras y optimizaciones en la ejecucion del modelo síncrono. Finalmente, algunos resultados preliminares de este Proyecto de Fin de Grado han sido presentados recientemente en formato de artículo científico en la "International Work-Conference on Artificial Neural Networks (IWANN)-2015" y publicados en "Ad-vances in Computational Intelligence" volumen 9094 de "Lecture Notes in Computer Science" de Springer International Publishing. Lo anterior, es una confirmation de que este trabajo mas que un Proyecto de Fin de Grado, es solo el inicio de un trabajo que puede tener mayor repercusion en la comunidad científica. Abstract Network of Evolutionary Processors -NEP is a computational model inspired by the evolution of cell populations, which might model some properties of evolving cell communities at the syntactical level. NEP defines theoretical computing devices able to solve NP complete problems in an efficient manner. In this model, cells are represented by words which encode their DNA sequences. Informally, at any moment of time, the evolutionary system is described by a collection of words, where each word represents one cell. Cells belong to species and their community evolves according to mutations and division which are defined by operations on words. Only those cells are accepted as surviving (correct) ones which are represented by a word in a given set of words, called the genotype space of the species. This feature is analogous with the natural process of evolution. Formally, NEP is based on an architecture for parallel and distributed processing, in other words, a network of language processors. Since the date when NEP was pro¬posed, several extensions and variants have appeared engendering a new set of models named Networks of Bio-inspired Processors (NBP). During this time, several works have proved the computational power of NBP. Specifically, their efficiency, universality, and computational completeness have been thoroughly investigated. Therefore, we can say that the NEP model has reached its maturity. The main motivation for this End of Grade project (EOG project in short) is to propose a practical approximation that allows to close the gap between theoretical NEP model and a practical implementation in high performing computational platforms in order to solve some of high the high complexity problems society requires today. Up until now tools developed to simulate NEPs, while correct and successful, are usu¬ally tightly coupled to the execution environment, using specific software frameworks (Hadoop) or direct hardware usage (GPUs). Within this context the main purpose of this work is the development of Nepfix, a generic and extensible tool that aims to execute algorithms based on NEP model and compatible variants in a local way, similar to a traditional application or in a distributed cloud environment. Nepfix as an application was developed during a 7 month cycle and is undergoing its second iteration once the prototype period was abandoned. Nepfix is designed as a modular self-contained application written in Java 8, that is, no additional external dependencies are required and it does not rely on an specific execution environment, any JVM is a valid container. Nepfix is made of two components or modules. The first module corresponds to the NEP execution and therefore simulation. During the development the current state of the theoretical model was used as a reference including most common filters and processors. Additionally extensibility is provided by the use of Python as a scripting language to run custom logic. Along with the simulation a definition language for NEP has been defined based on JSON as well as a mechanisms to represent words and their possible manipulations. NEP simulator is isolated from distribution and as mentioned before different applications that include it as a dependency are possible, the distribution of NEPs is an example of this. The second module corresponds to executing Nepfix in the cloud. The development carried a heavy R&D process since this front was not explored by other research groups until now. It's important to point out that the development of this module is not focused on results at this point in time, instead we focus on feasibility and discovery of this new perspective to execute natural computing systems and NEPs specifically. The main properties of cloud applications is that they are managed by the platform and are encapsulated in a container. For Nepfix a Spring application becomes the container and the HTTP or AMQP protocols are used for communication with the rest of the instances. Different execution perspectives were studied, namely asynchronous and synchronous models were developed for solving different kind of problems using NEPs. Different limitations and restrictions manifest in both models and are explored in detail in the respective chapters. In conclusion we can consider that Nepfix as a computational framework is suc-cessful: Cloud technology is ready for the challenge and the first results reassure that the properties Nepfix project pursued were met. Many investigation branches are left open for future investigations. In this EOG implementation guidelines are proposed for some of them like error recovery or dynamic NEP splitting. On the other hand other interesting problems that were not in the scope of this project were identified during development like word representation standardization or NEP model optimizations. As a confirmation that the results of this work can be useful to the scientific com-munity a preliminary version of this project was published in The International Work- Conference on Artificial Neural Networks (IWANN) in May 2015. Development has not stopped since that point and while Nepfix in it's current state can not be consid¬ered a final product the most relevant ideas, possible problems and solutions that were produced during the seven months development cycle are worthy to be gathered and presented giving a meaning to this EOG work.

Rapid Regulation by Acid pH of Cell Wall Adjustment and Leaf Growth in Maize Plants Responding to Reversal of Water Stress1

The role of acid secretion in regulating short-term changes in growth rate and wall extensibility was investigated in emerging first leaves of intact, water-stressed maize (Zea mays L.) seedlings. A novel approach was used to measure leaf responses to injection of water or solutions containing potential regulators of growth. Both leaf elongation and wall extensibility, as measured with a whole-plant creep extensiometer, increased dramatically within minutes of injecting water, 0.5 mm phosphate, or strong (50 mm) buffer solutions with pH ≤ 5.0 into the cell-elongation zone of water-stressed leaves. In contrast, injecting buffer solutions at pH ≥ 5.5 inhibited these fast responses. Solutions containing 0.5 mm orthovanadate or erythrosin B to inhibit wall acidification by plasma membrane H+-ATPases were also inhibitory. Thus, cell wall extensibility and leaf growth in water-stressed plants remained inhibited, despite the increased availability of (injected) water when accompanying increases in acid-induced wall loosening were prevented. However, growth was stimulated when pH 4.5 buffers were included with the vanadate injections. These findings suggest that increasing the availability of water to expanding cells in water-stressed leaves signals rapid increases in outward proton pumping by plasma membrane H+-ATPases. Resultant increases in cell wall extensibility participate in the regulation of water uptake, cell expansion, and leaf growth.

Efeito da adição de amido resistente de milho e enzimas sobre as propriedades da massa de pão e as propriedades físicas do pão de forma.

O amido resistente de milho (ARM) não é digerido em humanos fornecendo benefícios para a saúde tais como redução do colesterol, do índice glicêmico e fermentação no cólon. Porém, a substituição parcial de farinha de trigo (FT) por ARM em massa de pão resulta na diluição do glúten prejudicando a qualidade do produto. Massa de pão foi produzida com 12,5 g/100g de ARM e os efeitos das enzimas glicose-oxidase (Gox), tranglutaminase (TG) e xilanase (HE) na massa foram estudados. Massa produzida sem ARM e sem enzimas foi considerada padrão e massa produzida com ARM e sem enzimas foi considerada controle para comparação. Uma metodologia foi desenvolvida para medir o torque durante o amassamento em grande escala, utilizando um reômetro dinâmico adaptado. As propriedades reológicas foram avaliadas nos testes de medidas descritivas de textura, adesividade Chen-Hoseney, extensão uniaxial Kieffer, extensão biaxial e testes oscilatórios em reômetro. Pão produzido de acordo com as formulações padrão, controle e ótima foi avaliado com relação ao volume específico (VEP), firmeza do miolo, cor e análise sensorial para o atributo preferência. As três enzimas testadas influenciaram positivamente o torque máximo atingido durante o amassamento que variou entre (8,36 e 9,38) N m. Gox e TG apresentaram efeito positivo na altura máxima desenvolvida pela massa medida em reofermentógrafo enquanto que o efeito da HE foi negativo. Uma formulação com ARM e enzimas apresentou desempenho de panificação similar a massa padrão (altura máxima ajustada igual a (45,5 ± 3,9) mm), correspondente a adição de (4, 2,5 e 0,5) mg/100g de TG, Gox e HE respectivamente (ótima). A formulação ótima apresentou adesividade, trabalho de adesão, coesividade, dureza, resiliência, resistência à extensão e extensibilidade similares a massa padrão e diferentes da massa controle. As enzimas aumentaram o índice de strain hardening reduzido pela adição de ARM. Para o pão de forma, o VEP variou entre (3,16 e 3,64) cm3/g (diferença não significativa) e o pão produzido com a formulação ótima foi o mais escolhido como preferido. Durante o armazenamento por até 7 dias, o ARM diminuiu a taxa de envelhecimento do pão enquanto que as enzimas apresentaram efeito oposto. Em geral, a substituição parcial de FT por ARM reduziu a elasticidade da massa diminuindo a qualidade do pão enquanto que as enzimas minimizaram esse efeito.

Approaches and Strategy for Cancer Research and Surveillance Data: Integration, Information Pipeline, Data Models, and Informatics Opportunities

Thesis (Ph.D.)--University of Washington, 2016-04

Mechanical effects of plant cell wall enzymes on cellulose/xyloglucan composites

Xyloglucan-acting enzymes are believed to have effects on type I primary plant cell wall mechanical properties. In order to get a better understanding of these effects, a range of enzymes with different in vitro modes of action were tested against cell wall analogues (bio-composite materials based on Acetobacter xylinus cellulose and xyloglucan). Tomato pericarp xyloglucan endo transglycosylase (tXET) and nasturtium seed xyloglucanase (nXGase) were produced heterologously in Pichia pastoris. Their action against the cell wall analogues was compared with that of a commercial preparation of Trichoderma endo-glucanase (EndoGase). Both 'hydrolytic' enzymes (nXGase and EndoGase) were able to depolymerise not only the cross-link xyloglucan fraction but also the surface-bound fraction. Consequent major changes in cellulose fibril architecture were observed. In mechanical terms, removal of xyloglucan cross-links from composites resulted in increased stiffness (at high strain) and decreased visco-elasticity with similar extensibility. On the other hand, true transglycosylase activity (tXET) did not affect the cellulose/xyloglucan ratio. No change in composite stiffness or extensibility resulted, but a significant increase in creep behaviour was observed in the presence of active tXET. These results provide direct in vitro evidence for the involvement of cell wall xyloglucan-specific enzymes in mechanical changes underlying plant cell wall re-modelling and growth processes. Mechanical consequences of tXET action are shown to be complimentary to those of cucumber expansin.

Obstacles to a totally functional programming style

"Totally functional programming" (TFP) advocates the complete replacement of symbolic representations for data by functions. TFP is motivated by observations from practice in language extensibility and functional programming. Its technical essence extends the role of "fold" functions in structuring functional programs to include methods that make comparisons on elements of data structures. The obstacles that currently prevent the immediate uptake of TFP as a style within functional programming equally indicate future research directions in the areas of theoretical foundations, supporting technical infrastructure, demonstrated practical applicability, and relationship to OOP.