Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Harmful algae and their potential impacts on the coastal ecosystem: growth and toxin production dynamics

The main goal of the present thesis was to study some harmful algal species which cause blooms in Italian coastal waters, leading to consequences for human health, coastal ecosystem, fishery and tourism. In particular, in the first part of this thesis the toxicity of Adriatic strains of the raphidophyte Fibrocapsa japonica was investigated. Despite several hypotheses have been proposed for the toxic mechanism of the raphidophytes, especially for the species Chattonella antiqua and C. marina, which have been studied more extensively, just a few studies on the toxic effects of these species for different organisms were reported. Moreover, a careful reading of the literature evidenced as any ichthyotoxic events reported worldwide can be linked to F. japonica blooms. Although recently several studies were performed on F. japonica strains from the USA, Japan, Australia, New Zealand, the Netherlands, Germany, and France in order to characterize their growth and toxicity features, the work reported in this thesis results one of the first investigation on the toxic effects of F. japonica for different organisms, such as bacteria, crustaceans and fish. Mortality effects, together with haemolysis of fish erythrocytes, probably due to the relatively high amount of PUFAs produced by this species, were observed. Mortality for fish, however, was reported only at a high cell density and after a long exposition period (9-10 days); moreover a significant increase of H2O2 obtained in the tanks where sea basses were exposed to F. japonica was also relevant. This result may justify the absence of ichthyotoxic events in the Italian coasts, despite F. japonica blooms detected in these areas were characterized by high cell densities. This work reports also a first complete characterization of the fatty acids produced and extracellularly released by the Adriatic F. japonica, and results were also compared with the fatty acid profile of other strains. The absence of known brevetoxins in F. japonica algal extracts was also highlighted, leading to the hypothesis that the toxicity of F. japonica may be due to a synergic effect of PUFAs and ROS. Another microalgae that was studied in this thesis is the benthic dinoflagellate Ostreopsis cf. ovata. This species was investigated with the aim to investigate the effect of environmental parameters on its growth and toxicity. O. cf. ovata, in fact, shows different blooming periods along the Italian coasts and even the reported toxic effects are variable. The results of this work confirmed the high variability in the growth dynamic and toxin content of several Italian strains which were isolated in recent years along the Adriatic and Tyrrhenian Seas. Moreover, the effects of temperature and salinity on the behaviour of the different isolates are in good agreement with the results obtained from field surveys, which evidence as the environmental parameters are important factors modulating O. cf. ovata proliferation. Another relevant result that was highlighted is the anomaly in the production of palytoxin-like compounds reported by one of the studied isolate, in particular the one isolated in 2008 in Ancona (Adriatic Sea). Only this strain reported the absence of two (ovatoxin-b and –c) of the five ovatoxins so far known in the toxin profile and a different relative abundance of the other toxins. The last aspect that was studied in this thesis regards the toxin biosythesis. In fact, toxins produced (palytoxin-like compounds) or supposed to be produced (brevetoxin-like compounds) by O. cf. ovata and F. japonica, respectively, are polyketides, which are highly oxygenated compounds synthesized by complex enzymes known as polyketide synthase (PKS) enzymes. These enzymes are multi-domain complexes that structurally and functionally resemble the fatty acid synthases (FASs). This work reports the first study of PKS proteins in the dinoflagellates O. cf. ovata, C. monotis and in the raphidophyte F. japonica. For the first time some PKSs were identified in these species, confirming the presence of PKS proteins predicted by the in silico translation of the transcripts found in K. brevis also in other species. The identification of O. cf. ovata PKSs and the localization of the palytoxin-like compounds produced by this dinoflagellate in a similar location (chloroplast) as that observed for other dinoflagellate and cyanobacterial toxins provides some indication that these proteins may be involved in polyketide biosynthesis. However, their potential function as fatty acid synthases cannot be ruled out, as plant fatty acid synthesis also occurs within chloroplasts. This last hypothesis is also supported by the fact that in all the investigated species, and in particular in F. japonica, PKS proteins were present. Therefore, these results provide an important contribution to the study of the polyketides and of the involvement of PKS proteins in the toxin biosynthesis.

A clustering method for robust and reliable large scale functional and structural protein sequence annotation

Bioinformatics, in the last few decades, has played a fundamental role to give sense to the huge amount of data produced. Obtained the complete sequence of a genome, the major problem of knowing as much as possible of its coding regions, is crucial. Protein sequence annotation is challenging and, due to the size of the problem, only computational approaches can provide a feasible solution. As it has been recently pointed out by the Critical Assessment of Function Annotations (CAFA), most accurate methods are those based on the transfer-by-homology approach and the most incisive contribution is given by cross-genome comparisons. In the present thesis it is described a non-hierarchical sequence clustering method for protein automatic large-scale annotation, called “The Bologna Annotation Resource Plus” (BAR+). The method is based on an all-against-all alignment of more than 13 millions protein sequences characterized by a very stringent metric. BAR+ can safely transfer functional features (Gene Ontology and Pfam terms) inside clusters by means of a statistical validation, even in the case of multi-domain proteins. Within BAR+ clusters it is also possible to transfer the three dimensional structure (when a template is available). This is possible by the way of cluster-specific HMM profiles that can be used to calculate reliable template-to-target alignments even in the case of distantly related proteins (sequence identity < 30%). Other BAR+ based applications have been developed during my doctorate including the prediction of Magnesium binding sites in human proteins, the ABC transporters superfamily classification and the functional prediction (GO terms) of the CAFA targets. Remarkably, in the CAFA assessment, BAR+ placed among the ten most accurate methods. At present, as a web server for the functional and structural protein sequence annotation, BAR+ is freely available at http://bar.biocomp.unibo.it/bar2.0.

Magnetic properties of ODP Hole 109-670A

Magnetic fabrics of serpentinized peridotites are related to anisomorphic magnetite formed during serpentinization. In the less serpentinized facies they are, however, mainly mimetic of the high temperature deformation prior to serpentinization. In more serpentinized peridotites, the magnetic fabrics, related to magnetite veins which are more developed in this case, are superimposed on mimetic fabrics. Remanent properties, hysteresis loop parameters, and Curie temperatures were measured. Natural remanent magnetizations (NRM) have crystallization remanent magnetic (CRM) origin. Measured magnetic parameters suggest that pseudo-single domain (PSD) grains of magnetite are present in samples with low degree of serpentinization. The samples with high degree of serpentinization contain mainly multi-domain (MD) magnetite grains.

Advanced Topics in Resource Analysis: Certification, Incrementality, Concurrency and Array-Sensitivity

El Análisis de Consumo de Recursos o Análisis de Coste trata de aproximar el coste de ejecutar un programa como una función dependiente de sus datos de entrada. A pesar de que existen trabajos previos a esta tesis doctoral que desarrollan potentes marcos para el análisis de coste de programas orientados a objetos, algunos aspectos avanzados, como la eficiencia, la precisión y la fiabilidad de los resultados, todavía deben ser estudiados en profundidad. Esta tesis aborda estos aspectos desde cuatro perspectivas diferentes: (1) Las estructuras de datos compartidas en la memoria del programa son una pesadilla para el análisis estático de programas. Trabajos recientes proponen una serie de condiciones de localidad para poder mantener de forma consistente información sobre los atributos de los objetos almacenados en memoria compartida, reemplazando éstos por variables locales no almacenadas en la memoria compartida. En esta tesis presentamos dos extensiones a estos trabajos: la primera es considerar, no sólo los accesos a los atributos, sino también los accesos a los elementos almacenados en arrays; la segunda se centra en los casos en los que las condiciones de localidad no se cumplen de forma incondicional, para lo cual, proponemos una técnica para encontrar las precondiciones necesarias para garantizar la consistencia de la información acerca de los datos almacenados en memoria. (2) El objetivo del análisis incremental es, dado un programa, los resultados de su análisis y una serie de cambios sobre el programa, obtener los nuevos resultados del análisis de la forma más eficiente posible, evitando reanalizar aquellos fragmentos de código que no se hayan visto afectados por los cambios. Los analizadores actuales todavía leen y analizan el programa completo de forma no incremental. Esta tesis presenta un análisis de coste incremental, que, dado un cambio en el programa, reconstruye la información sobre el coste del programa de todos los métodos afectados por el cambio de forma incremental. Para esto, proponemos (i) un algoritmo multi-dominio y de punto fijo que puede ser utilizado en todos los análisis globales necesarios para inferir el coste, y (ii) una novedosa forma de almacenar las expresiones de coste que nos permite reconstruir de forma incremental únicamente las funciones de coste de aquellos componentes afectados por el cambio. (3) Las garantías de coste obtenidas de forma automática por herramientas de análisis estático no son consideradas totalmente fiables salvo que la implementación de la herramienta o los resultados obtenidos sean verificados formalmente. Llevar a cabo el análisis de estas herramientas es una tarea titánica, ya que se trata de herramientas de gran tamaño y complejidad. En esta tesis nos centramos en el desarrollo de un marco formal para la verificación de las garantías de coste obtenidas por los analizadores en lugar de analizar las herramientas. Hemos implementado esta idea mediante la herramienta COSTA, un analizador de coste para programas Java y KeY, una herramienta de verificación de programas Java. De esta forma, COSTA genera las garantías de coste, mientras que KeY prueba la validez formal de los resultados obtenidos, generando de esta forma garantías de coste verificadas. (4) Hoy en día la concurrencia y los programas distribuidos son clave en el desarrollo de software. Los objetos concurrentes son un modelo de concurrencia asentado para el desarrollo de sistemas concurrentes. En este modelo, los objetos son las unidades de concurrencia y se comunican entre ellos mediante llamadas asíncronas a sus métodos. La distribución de las tareas sugiere que el análisis de coste debe inferir el coste de los diferentes componentes distribuidos por separado. En esta tesis proponemos un análisis de coste sensible a objetos que, utilizando los resultados obtenidos mediante un análisis de apunta-a, mantiene el coste de los diferentes componentes de forma independiente. Abstract Resource Analysis (a.k.a. Cost Analysis) tries to approximate the cost of executing programs as functions on their input data sizes and without actually having to execute the programs. While a powerful resource analysis framework on object-oriented programs existed before this thesis, advanced aspects to improve the efficiency, the accuracy and the reliability of the results of the analysis still need to be further investigated. This thesis tackles this need from the following four different perspectives. (1) Shared mutable data structures are the bane of formal reasoning and static analysis. Analyses which keep track of heap-allocated data are referred to as heap-sensitive. Recent work proposes locality conditions for soundly tracking field accesses by means of ghost non-heap allocated variables. In this thesis we present two extensions to this approach: the first extension is to consider arrays accesses (in addition to object fields), while the second extension focuses on handling cases for which the locality conditions cannot be proven unconditionally by finding aliasing preconditions under which tracking such heap locations is feasible. (2) The aim of incremental analysis is, given a program, its analysis results and a series of changes to the program, to obtain the new analysis results as efficiently as possible and, ideally, without having to (re-)analyze fragments of code that are not affected by the changes. During software development, programs are permanently modified but most analyzers still read and analyze the entire program at once in a non-incremental way. This thesis presents an incremental resource usage analysis which, after a change in the program is made, is able to reconstruct the upper-bounds of all affected methods in an incremental way. To this purpose, we propose (i) a multi-domain incremental fixed-point algorithm which can be used by all global analyses required to infer the cost, and (ii) a novel form of cost summaries that allows us to incrementally reconstruct only those components of cost functions affected by the change. (3) Resource guarantees that are automatically inferred by static analysis tools are generally not considered completely trustworthy, unless the tool implementation or the results are formally verified. Performing full-blown verification of such tools is a daunting task, since they are large and complex. In this thesis we focus on the development of a formal framework for the verification of the resource guarantees obtained by the analyzers, instead of verifying the tools. We have implemented this idea using COSTA, a state-of-the-art cost analyzer for Java programs and KeY, a state-of-the-art verification tool for Java source code. COSTA is able to derive upper-bounds of Java programs while KeY proves the validity of these bounds and provides a certificate. The main contribution of our work is to show that the proposed tools cooperation can be used for automatically producing verified resource guarantees. (4) Distribution and concurrency are today mainstream. Concurrent objects form a well established model for distributed concurrent systems. In this model, objects are the concurrency units that communicate via asynchronous method calls. Distribution suggests that analysis must infer the cost of the diverse distributed components separately. In this thesis we propose a novel object-sensitive cost analysis which, by using the results gathered by a points-to analysis, can keep the cost of the diverse distributed components separate.

Certificados electrónicos de servidor en administración y comercio electrónicos: garantías de seguridad

El uso de Internet por parte de los ciudadanos para relacionarse con las Administraciones Públicas o en relación con actividades de comercio electrónico crece día a día. Así lo evidencian los diferentes estudios realizados en esta materia, como los que lleva a cabo el Observatorio Nacional de las Telecomunicaciones y la Sociedad de la Información (http://www.ontsi.red.es/ontsi/). Se hace necesario, por tanto, identificar a las partes intervinientes en estas transacciones, además de dotarlas de la confidencialidad necesaria y garantizar el no repudio. Uno de los elementos que, junto con los mecanismos criptográficos apropiados, proporcionan estos requisitos, son los certificados electrónicos de servidor web. Existen numerosas publicaciones dedicadas a analizar esos mecanismos criptográficos y numerosos estudios de seguridad relacionados con los algoritmos de cifrado, simétrico y asimétrico, y el tamaño de las claves criptográficas. Sin embargo, la seguridad relacionada con el uso de los protocolos de seguridad SSL/TLS está estrechamente ligada a dos aspectos menos conocidos:  el grado de seguridad con el que se emiten los certificados electrónicos de servidor que permiten implementar dichos protocolos; y  el uso que hacen las aplicaciones software, y en especial los navegadores web, de los campos que contiene el perfil de dichos certificados. Por tanto, diferentes perfiles de certificados electrónicos de servidor y diferentes niveles de seguridad asociados al procedimiento de emisión de los mismos, dan lugar a diferentes tipos de certificados electrónicos. Si además se considera el marco jurídico que afecta a cada uno de ellos, se puede concluir que existe una tipología de certificados de servidor, con diferentes grados de seguridad o de confianza. Adicionalmente, existen otros requisitos que también pueden pasar desapercibidos tanto a los titulares de los certificados como a los usuarios de los servicios de comercio electrónico y administración electrónica. Por ejemplo, el grado de confianza que otorgan los navegadores web a las Autoridades de Certificación emisoras de los certificados y cómo estas adquieren tal condición, o la posibilidad de poder verificar el estado de revocación del certificado electrónico. El presente trabajo analiza todos estos requisitos y establece, en función de los mismos, la correspondiente tipología de certificados electrónicos de servidor web. Concretamente, las características a analizar para cada tipo de certificado son las siguientes:  Seguridad jurídica.  Normas técnicas.  Garantías sobre la verdadera identidad del dominio.  Verificación del estado de revocación.  Requisitos del Prestador de Servicios de Certificación. Los tipos de certificados electrónicos a analizar son:  Certificados de servidor web:  Certificados autofirmados y certificados emitidos por un Prestador de Servicios de Certificación.  Certificados de dominio simple y certificados multidominio (wildcard y SAN)  Certificados de validación extendida.  Certificados de sede electrónica. ABSTRACT Internet use by citizens to interact with government or with e-commerce activities is growing daily. This topic is evidenced by different studies in this area, such as those undertaken by the Observatorio Nacional de las Telecomunicaciones y la Sociedad de la Información (http://www.ontsi.red.es/ontsi/ ). Therefore, it is necessary to identify the parties involved in these transactions, as well as provide guaranties such as confidentiality and non-repudiation. One instrument which, together with appropriate cryptographic mechanisms, provides these requirements is SSL electronic certificate. There are numerous publications devoted to analyzing these cryptographic mechanisms and many studies related security encryption algorithms, symmetric and asymmetric, and the size of the cryptographic keys. However, the safety related to the use of security protocols SSL / TLS is closely linked to two lesser known aspects:  the degree of security used in issuing the SSL electronic certificates; and  the way software applications, especially web Internet browsers, work with the fields of the SSL certificates profiles. Therefore, the diversity of profiles and security levels of issuing SSL electronic certificates give rise to different types of certificates. Besides, some of these electronic certificates are affected by a specific legal framework. Consequently, it can be concluded that there are different types of SSL certificates, with different degrees of security or trustworthiness. Additionally, there are other requirements that may go unnoticed both certificate holders and users of e-commerce services and e-Government. For example, the degree of trustworthiness of the Certification Authorities and how they acquire such a condition by suppliers of Internet browsers, or the possibility to verify the revocation status of the SSL electronic certificate. This paper discusses these requirements and sets, according to them, the type of SSL electronic certificates. Specifically, the characteristics analyzed for each type of certificate are the following:  Legal security.  Technical standards.  Guarantees to the real identity of the domain.  Check the revocation status.  Requirements of the Certification Services Providers. The types of electronic certificates to be analyzed are the following:  SSL electronic certificates:  Self-signed certificates and certificates issued by a Certification Service Provider.  Single-domain certificates and multi-domain certificates (wildcard and SAN)  Extended Validation Certificates.  “Sede electrónica” certificates (specific certificates for web sites of Spanish Public Administrations).

Unified representation of monitoring information across federated cloud infrastructures

Nowadays one of the issues hindering the potential of federating cloud-based infrastructures to reach much larger scales is their standard management and monitoring. In particular, this is true in cases where these federated infrastructures provide emerging Future Internet and Smart Cities-oriented services, such as the Internet of Things (IoT), that benefit from cloud services. The contribution of this paper is the introduction of a unified monitoring architecture for federated cloud infrastructures accompanied by the adoption of a uniform representation of measurement data. The presented solution is capable of providing multi-domain compatibility, scalability, as well as the ability to analyze large amounts of monitoring data, collected from datacenters and offered through open and standardized APIs. The solution described herein has been deployed and is currently running on a community of 5 infrastructures within the framework of the European Project XIFI, to be extended to 12 more infrastructures.

A multidisciplinary reference framework to support innovative design, implementation and assessment of chronic care models

Hoy en día, por primera vez en la historia, la mayor parte de la población podrá vivir hasta los sesenta años y más (United Nations, 2015). Sin embargo, todavía existe poca evidencia que demuestre que las personas mayores, estén viviendo con mejor salud que sus padres, a la misma edad, ya que la mayoría de los problemas de salud en edades avanzadas están asociados a las enfermedades crónicas (WHO, 2015). Los sistemas sanitarios de los países desarrollados funcionan adecuadamente cuando se trata del cuidado de enfermedades agudas, pero no son lo suficientemente eficaces en la gestión de las enfermedades crónicas. Durante la última década, se han realizado esfuerzos para mejorar esta gestión, por medio de la utilización de estrategias de prevención y de reenfoque de la provisión de los servicios de atención para la salud (Kane et al. 2005). Según una revisión sistemática de modelos de cuidado de salud, comisionada por el sistema nacional de salud Británico, pocos modelos han conceptualizado cuáles son los componentes que hay que utilizar para proporcionar un cuidado crónico efectivo, y estos componentes no han sido suficientemente estructurados y articulados. Por lo tanto, no hay suficiente evidencia sobre el impacto real de cualquier modelo existente en la actualidad (Ham, 2006). Las innovaciones podrían ayudar a conseguir mejores diagnósticos, tratamientos y gestión de pacientes crónicos, así como a dar soporte a los profesionales y a los pacientes en el cuidado. Sin embargo, la forma en las que estas innovaciones se proporcionan no es lo suficientemente eficiente, efectiva y amigable para el usuario. Para mejorar esto, hace falta crear equipos de trabajo y estrategias multidisciplinares. En conclusión, hacen falta actividades que permitan conseguir que las innovaciones sean utilizadas en los sistemas de salud que quieren mejorar la gestión del cuidado crónico, para que sea posible: 1) traducir la “atención sanitaria basada en la evidencia” en “conocimiento factible”; 2) hacer frente a la complejidad de la atención sanitaria a través de una investigación multidisciplinaria; 3) identificar una aproximación sistemática para que se establezcan intervenciones innovadoras en el cuidado de salud. El marco de referencia desarrollado en este trabajo de investigación es un intento de aportar estas mejoras. Las siguientes hipótesis han sido propuestas: Hipótesis 1: es posible definir un proceso de traducción que convierta un modelo de cuidado crónico en una descripción estructurada de objetivos, requisitos e indicadores clave de rendimiento. Hipótesis 2: el proceso de traducción, si se ejecuta a través de elementos basados en la evidencia, multidisciplinares y de orientación económica, puede convertir un modelo de cuidado crónico en un marco descriptivo, que define el ciclo de vida de soluciones innovadoras para el cuidado de enfermedades crónicas. Hipótesis 3: es posible definir un método para evaluar procesos, resultados y capacidad de desarrollar habilidades, y asistir equipos multidisciplinares en la creación de soluciones innovadoras para el cuidado crónico. Hipótesis 4: es posible dar soporte al desarrollo de soluciones innovadoras para el cuidado crónico a través de un marco de referencia y conseguir efectos positivos, medidos en indicadores clave de rendimiento. Para verificar las hipótesis, se ha definido una aproximación metodológica compuesta de cuatro Fases, cada una asociada a una hipótesis. Antes de esto, se ha llevado a cabo una “Fase 0”, donde se han analizado los antecedentes sobre el problema (i.e. adopción sistemática de la innovación en el cuidado crónico) desde una perspectiva multi-dominio y multi-disciplinar. Durante la fase 1, se ha desarrollado un Proceso de Traducción del Conocimiento, elaborado a partir del JBI Joanna Briggs Institute (JBI) model of evidence-based healthcare (Pearson, 2005), y sobre el cual se han definido cuatro Bloques de Innovación. Estos bloques consisten en una descripción de elementos innovadores, definidos en la fase 0, que han sido añadidos a los cuatros elementos que componen el modelo JBI. El trabajo llevado a cabo en esta fase ha servido también para definir los materiales que el proceso de traducción tiene que ejecutar. La traducción que se ha llevado a cabo en la fase 2, y que traduce la mejor evidencia disponible de cuidado crónico en acción: resultado de este proceso de traducción es la parte descriptiva del marco de referencia, que consiste en una descripción de un modelo de cuidado crónico (se ha elegido el Chronic Care Model, Wagner, 1996) en términos de objetivos, especificaciones e indicadores clave de rendimiento y organizada en tres ciclos de innovación (diseño, implementación y evaluación). Este resultado ha permitido verificar la segunda hipótesis. Durante la fase 3, para demostrar la tercera hipótesis, se ha desarrollado un método-mixto de evaluación de equipos multidisciplinares que trabajan en innovaciones para el cuidado crónico. Este método se ha creado a partir del método mixto usado para la evaluación de equipo multidisciplinares translacionales (Wooden, 2013). El método creado añade una dimensión procedural al marco. El resultado de esta fase consiste, por lo tanto, en una primera versión del marco de referencia, lista para ser experimentada. En la fase 4, se ha validado el marco a través de un caso de estudio multinivel y con técnicas de observación-participante como método de recolección de datos. Como caso de estudio se han elegido las actividades de investigación que el grupo de investigación LifeStech ha desarrollado desde el 2008 para mejorar la gestión de la diabetes, actividades realizadas en un contexto internacional. Los resultados demuestran que el marco ha permitido mejorar las actividades de trabajo en distintos niveles: 1) la calidad y cantidad de las publicaciones; 2) se han conseguido dos contratos de investigación sobre diabetes: el primero es un proyecto de investigación aplicada, el segundo es un proyecto financiado para acelerar las innovaciones en el mercado; 3) a través de los indicadores claves de rendimiento propuestos en el marco, una prueba de concepto de un prototipo desarrollado en un proyecto de investigación ha sido transformada en una evaluación temprana de una intervención eHealth para el manejo de la diabetes, que ha sido recientemente incluida en Repositorio de prácticas innovadoras del Partenariado de Innovación Europeo en Envejecimiento saludable y activo. La verificación de las 4 hipótesis ha permitido demonstrar la hipótesis principal de este trabajo de investigación: es posible contribuir a crear un puente entre la atención sanitaria y la innovación y, por lo tanto, mejorar la manera en que el cuidado crónico sea procurado en los sistemas sanitarios. ABSTRACT Nowadays, for the first time in history, most people can expect to live into their sixties and beyond (United Nations, 2015). However, little evidence suggests that older people are experiencing better health than their parents, and most of the health problems of older age are linked to Chronic Diseases (WHO, 2015). The established health care systems in developed countries are well suited to the treatment of acute diseases but are mostly inadequate for dealing with CDs. Healthcare systems are challenging the burden of chronic diseases by putting more emphasis on the prevention of disease and by looking for new ways to reorient the provision of care (Kane et al., 2005). According to an evidence-based review commissioned by the British NHS Institute, few models have conceptualized effective components of care for CDs and these components have been not structured and articulated. “Consequently, there is limited evidence about the real impact of any of the existing models” (Ham, 2006). Innovations could support to achieve better diagnosis, treatment and management for patients across the continuum of care, by supporting health professionals and empowering patients to take responsibility. However, the way they are delivered is not sufficiently efficient, effective and consumer friendly. The improvement of innovation delivery, involves the creation of multidisciplinary research teams and taskforces, rather than just working teams. There are several actions to improve the adoption of innovations from healthcare systems that are tackling the epidemics of CDs: 1) Translate Evidence-Based Healthcare (EBH) into actionable knowledge; 2) Face the complexity of healthcare through multidisciplinary research; 3) Identify a systematic approach to support effective implementation of healthcare interventions through innovation. The framework proposed in this research work is an attempt to provide these improvements. The following hypotheses have been drafted: Hypothesis 1: it is possible to define a translation process to convert a model of chronic care into a structured description of goals, requirements and key performance indicators. Hypothesis 2: a translation process, if executed through evidence-based, multidisciplinary, holistic and business-oriented elements, can convert a model of chronic care in a descriptive framework, which defines the whole development cycle of innovative solutions for chronic disease management. Hypothesis 3: it is possible to design a method to evaluate processes, outcomes and skill acquisition capacities, and assist multidisciplinary research teams in the creation of innovative solutions for chronic disease management. Hypothesis 4: it is possible to assist the development of innovative solutions for chronic disease management through a reference framework and produce positive effects, measured through key performance indicators. In order to verify the hypotheses, a methodological approach, composed of four Phases that correspond to each one of the stated hypothesis, was defined. Prior to this, a “Phase 0”, consisting in a multi-domain and multi-disciplinary background analysis of the problem (i.e.: systematic adoption of innovation to chronic care), was carried out. During phase 1, in order to verify the first hypothesis, a Knowledge Translation Process (KTP) was developed, starting from the JBI Joanna Briggs Institute (JBI) model of evidence-based healthcare was used (Pearson, 2005) and adding Four Innovation Blocks. These blocks represent an enriched description, added to the JBI model, to accelerate the transformation of evidence-healthcare through innovation; the innovation blocks are built on top of the conclusions drawn after Phase 0. The background analysis gave also indication on the materials and methods to be used for the execution of the KTP, carried out during phase 2, that translates the actual best available evidence for chronic care into action: this resulted in a descriptive Framework, which is a description of a model of chronic care (the Chronic Care Model was chosen, Wagner, 1996) in terms of goals, specified requirements and Key Performance Indicators, and articulated in the three development cycles of innovation (i.e. design, implementation and evaluation). Thanks to this result the second hypothesis was verified. During phase 3, in order to verify the third hypothesis, a mixed-method to evaluate multidisciplinary teams working on innovations for chronic care, was created, based on a mixed-method used for the evaluation of Multidisciplinary Translational Teams (Wooden, 2013). This method adds a procedural dimension to the descriptive component of the Framework, The result of this phase consisted in a draft version of the framework, ready to be tested in a real scenario. During phase 4, a single and multilevel case study, with participant-observation data collection, was carried out, in order to have a complete but at the same time multi-sectorial evaluation of the framework. The activities that the LifeStech research group carried out since 2008 to improve the management of diabetes have been selected as case study. The results achieved showed that the framework allowed to improve the research activities in different directions: the quality and quantity of the research publications that LifeStech has issued, have increased substantially; 2 project grants to improve the management of diabetes, have been assigned: the first is a grant funding applied research while the second is about accelerating innovations into the market; by using the assessment KPIs of the framework, the proof of concept validation of a prototype developed in a research project was transformed into an early stage assessment of innovative eHealth intervention for Diabetes Management, which has been recently included in the repository of innovative practice of the European Innovation Partnership on Active and Health Ageing initiative. The verification of the 4 hypotheses lead to verify the main hypothesis of this research work: it is possible to contribute to bridge the gap between healthcare and innovation and, in turn, improve the way chronic care is delivered by healthcare systems.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

DdLIM Is a Cytoskeleton-associated Protein Involved in the Protrusion of Lamellipodia in Dictyostelium

DdLim, a multi-domain member of the cysteine-rich family of LIM domain proteins, was isolated from Dictyostelium cells where it localizes in lamellipodia and at sites of membrane ruffling. The transcription and expression of DdLim are developmentally regulated, and the timing of its increased association with the actin cytoskeleton coincides with the acquisition in starved cells of a motile, chemotactic behavior. Vegetative cells that overexpress DdLim contain large lamella and exhibit ruffling at the cortex. The high frequency of large, multinucleated mutant cells found in suspension culture suggests that excess DdLim interferes with cytokinesis. DdLim was also identified as a protein in a Dictyostelium cell lysate that associated indirectly, but in a guanosine triphosphate-dependent manner, with a GST-rac1 fusion protein. The data presented suggest that DdLim acts as an adapter protein at the cytoskeleton-membrane interface where it is involved in a receptor-mediated rac1-signaling pathway that leads to actin polymerization in lamellipodia and ultimately cell motility.

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Rock magnetism of pelagic sediments from DSDP Leg 85 sites

A detailed rock magnetic investigation has been carried out on Deep Sea Drilling Project (DSDP) pelagic sediments from the Central Equatorial Pacific. This comprises hysteresis and thermomagnetic measurements, Lowrie-Fuller test and, for the first time, ferromagnetic resonance (FMR). Nearly stochiometric magnetite in two grain size fractions, single domain (SD) and multi domain (MD), has been deduced to be the carrier of magnetic remanence. Comparatively strong paramagnetic contributions are carried by pyrite, being identified by X-ray analysis. The statistical analysis of paleomagnetic parameters (NRM, MDF, initial susceptibility, Königsberger ratio Q) from a large number (> 1000) of samples, supported by hysteresis measurements, indicates a latitude and sedimentation rate dependent ratio of SD/MD grains. Possible sources for the magnetic constituents are discussed in terms of bacterial, volcanic, meteoritic and authigenic origin.

Self-training from labeled features for sentiment analysis

Sentiment analysis concerns about automatically identifying sentiment or opinion expressed in a given piece of text. Most prior work either use prior lexical knowledge defined as sentiment polarity of words or view the task as a text classification problem and rely on labeled corpora to train a sentiment classifier. While lexicon-based approaches do not adapt well to different domains, corpus-based approaches require expensive manual annotation effort. In this paper, we propose a novel framework where an initial classifier is learned by incorporating prior information extracted from an existing sentiment lexicon with preferences on expectations of sentiment labels of those lexicon words being expressed using generalized expectation criteria. Documents classified with high confidence are then used as pseudo-labeled examples for automatical domain-specific feature acquisition. The word-class distributions of such self-learned features are estimated from the pseudo-labeled examples and are used to train another classifier by constraining the model's predictions on unlabeled instances. Experiments on both the movie-review data and the multi-domain sentiment dataset show that our approach attains comparable or better performance than existing weakly-supervised sentiment classification methods despite using no labeled documents.

Incorporating sentiment prior knowledge for weakly supervised sentiment analysis

This article presents two novel approaches for incorporating sentiment prior knowledge into the topic model for weakly supervised sentiment analysis where sentiment labels are considered as topics. One is by modifying the Dirichlet prior for topic-word distribution (LDA-DP), the other is by augmenting the model objective function through adding terms that express preferences on expectations of sentiment labels of the lexicon words using generalized expectation criteria (LDA-GE). We conducted extensive experiments on English movie review data and multi-domain sentiment dataset as well as Chinese product reviews about mobile phones, digital cameras, MP3 players, and monitors. The results show that while both LDA-DP and LDAGE perform comparably to existing weakly supervised sentiment classification algorithms, they are much simpler and computationally efficient, rendering themmore suitable for online and real-time sentiment classification on the Web. We observed that LDA-GE is more effective than LDA-DP, suggesting that it should be preferred when considering employing the topic model for sentiment analysis. Moreover, both models are able to extract highly domain-salient polarity words from text.