A New Method to Retrieve, Cluster And Annotate Clinical Literature Related To Electronic Health Records

The access to medical literature collections such as PubMed, MedScape or Cochrane has been increased notably in the last years by the web-based tools that provide instant access to the information. However, more sophisticated methodologies are needed to exploit efficiently all that information. The lack of advanced search methods in clinical domain produce that even using well-defined questions for a particular disease, clinicians receive too many results. Since no information analysis is applied afterwards, some relevant results which are not presented in the top of the resultant collection could be ignored by the expert causing an important loose of information. In this work we present a new method to improve scientific article search using patient information for query generation. Using federated search strategy, it is able to simultaneously search in different resources and present a unique relevant literature collection. And applying NLP techniques it presents semantically similar publications together, facilitating the identification of relevant information to clinicians. This method aims to be the foundation of a collaborative environment for sharing clinical knowledge related to patients and scientific publications.

Service for the pseudonymization of electronic healthcare records based on ISO/EN 13606 for the secondary use of information

The availability of electronic health data favors scientific advance through the creation of repositories for secondary use. Data anonymization is a mandatory step to comply with current legislation. A service for the pseudonymization of electronic healthcare record (EHR) extracts aimed at facilitating the exchange of clinical information for secondary use in compliance with legislation on data protection is presented. According to ISO/TS 25237, pseudonymization is a particular type of anonymization. This tool performs the anonymizations by maintaining three quasi-identifiers (gender, date of birth and place of residence) with a degree of specification selected by the user. The developed system is based on the ISO/EN 13606 norm using its characteristics specifically favorable for anonymization. The service is made up of two independent modules: the demographic server and the pseudonymizing module. The demographic server supports the permanent storage of the demographic entities and the management of the identifiers. The pseudonymizing module anonymizes the ISO/EN 13606 extracts. The pseudonymizing process consists of four phases: the storage of the demographic information included in the extract, the substitution of the identifiers, the elimination of the demographic information of the extract and the elimination of key data in free-text fields. The described pseudonymizing system was used in three Telemedicine research projects with satisfactory results. A problem was detected with the type of data in a demographic data field and a proposal for modification was prepared for the group in charge of the drawing up and revision of the ISO/EN 13606 norm.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

Implementación del modelo RIM de HL7 v3 en orientación a objetos y su uso en procesos de interoperabilidad semántica

El trabajo ha sido realizado dentro del marco de los proyectos EURECA (Enabling information re-Use by linking clinical REsearch and Care) e INTEGRATE (Integrative Cancer Research Through Innovative Biomedical Infrastructures), en los que colabora el Grupo de Informática Biomédica de la UPM junto a otras universidades e instituciones sanitarias europeas. En ambos proyectos se desarrollan servicios e infraestructuras con el objetivo principal de almacenar información clínica, procedente de fuentes diversas (como por ejemplo de historiales clínicos electrónicos de hospitales, de ensayos clínicos o artículos de investigación biomédica), de una forma común y fácilmente accesible y consultable para facilitar al máximo la investigación de estos ámbitos, de manera colaborativa entre instituciones. Esta es la idea principal de la interoperabilidad semántica en la que se concentran ambos proyectos, siendo clave para el correcto funcionamiento del software del que se componen. El intercambio de datos con un modelo de representación compartido, común y sin ambigüedades, en el que cada concepto, término o dato clínico tendrá una única forma de representación. Lo cual permite la inferencia de conocimiento, y encaja perfectamente en el contexto de la investigación médica. En concreto, la herramienta a desarrollar en este trabajo también está orientada a la idea de maximizar la interoperabilidad semántica, pues se ocupa de la carga de información clínica con un formato estandarizado en un modelo común de almacenamiento de datos, implementado en bases de datos relacionales. El trabajo ha sido desarrollado en el periodo comprendido entre el 3 de Febrero y el 6 de Junio de 2014. Se ha seguido un ciclo de vida en cascada para la organización del trabajo realizado en las tareas de las que se compone el proyecto, de modo que una fase no puede iniciarse sin que se haya terminado, revisado y aceptado la fase anterior. Exceptuando la tarea de documentación del trabajo (para la elaboración de esta memoria), que se ha desarrollado paralelamente a todas las demás. ----ABSTRACT--- The project has been developed during the second semester of the 2013/2014 academic year. This Project has been done inside EURECA and INTEGRATE European biomedical research projects, where the GIB (Biomedical Informatics Group) of the UPM works as a partner. Both projects aim is to develop platforms and services with the main goal of storing clinical information (e.g. information from hospital electronic health records (EHRs), clinical trials or research articles) in a common way and easy to access and query, in order to support medical research. The whole software environment of these projects is based on the idea of semantic interoperability, which means the ability of computer systems to exchange data with unambiguous and shared meaning. This idea allows knowledge inference, which fits perfectly in medical research context. The tool to develop in this project is also "semantic operability-oriented". Its purpose is to store standardized clinical information in a common data model, implemented in relational databases. The project has been performed during the period between February 3rd and June 6th, of 2014. It has followed a "Waterfall model" of software development, in which progress is seen as flowing steadily downwards through its phases. Each phase starts when its previous phase has been completed and reviewed. The task of documenting the project‟s work is an exception; it has been performed in a parallel way to the rest of the tasks.

Diseño e implementación de un algoritmo para la detección de la negación de textos clínicos en español

Vivimos en una época en la que cada vez existe una mayor cantidad de información. En el dominio de la salud la historia clínica digital ha permitido digitalizar toda la información de los pacientes. Estas historias clínicas digitales contienen una gran cantidad de información valiosa escrita en forma narrativa que sólo podremos extraer recurriendo a técnicas de procesado de lenguaje natural. No obstante, si se quiere realizar búsquedas sobre estos textos es importante analizar que la información relativa a síntomas, enfermedades, tratamientos etc. se puede refererir al propio paciente o a sus antecentes familiares, y que ciertos términos pueden aparecer negados o ser hipotéticos. A pesar de que el español ocupa la segunda posición en el listado de idiomas más hablados con más de 500 millones de hispano hablantes, hasta donde tenemos de detección de la negación, probabilidad e histórico en textos clínicos en español. Por tanto, este Trabajo Fin de Grado presenta una implementación basada en el algoritmo ConText para la detección de la negación, probabilidad e histórico en textos clínicos escritos en español. El algoritmo se ha validado con 454 oraciones que incluían un total de 1897 disparadores obteniendo unos resultado de 83.5 %, 96.1 %, 96.9 %, 99.7% y 93.4% de exactitud con condiciones afirmados, negados, probable, probable negado e histórico respectivamente. ---ABSTRACT---We live in an era in which there is a huge amount of information. In the domain of health, the electronic health record has allowed to digitize all the information of the patients. These electronic health records contain valuable information written in narrative form that can only be extracted using techniques of natural language processing. However, if you want to search on these texts is important to analyze if the relative information about symptoms, diseases, treatments, etc. are referred to the patient or family casework, and that certain terms may appear negated or be hypothesis. Although Spanish is the second spoken language with more than 500 million speakers, there seems to be no method of detection of negation, hypothesis or historical in medical texts written in Spanish. Thus, this bachelor’s final degree presents an implementation based on the ConText algorithm for the detection of negation, hypothesis and historical in medical texts written in Spanish. The algorithm has been validated with 454 sentences that included a total of 1897 triggers getting a result of 83.5 %, 96.1 %, 96.9 %, 99.7% and 93.4% accuracy with affirmed, negated, hypothesis, negated hypothesis and historical respectively.

Diseño e implementación de un módulo para la estructuración de notas clínicas

El presente Trabajo Fin de Grado (TFG) surge de la necesidad de disponer de tecnologías que faciliten el Procesamiento de Lenguaje Natural (NLP) en español dentro del sector de la medicina. Centrado concretamente en la extracción de conocimiento de las historias clínicas electrónicas (HCE), que recogen toda la información relacionada con la salud del paciente y en particular, de los documentos recogidos en dichas historias, pretende la obtención de todos los términos relacionados con la medicina. El Procesamiento de Lenguaje Natural permite la obtención de datos estructurados a partir de información no estructurada. Estas técnicas permiten un análisis de texto que genera etiquetas aportando significado semántico a las palabras para la manipulación de información. A partir de la investigación realizada del estado del arte en NLP y de las tecnologías existentes para otras lenguas, se propone como solución un módulo de anotación de términos médicos extraídos de documentos clínicos. Como términos médicos se han considerado síntomas, enfermedades, partes del cuerpo o tratamientos obtenidos de UMLS, una ontología categorizada que agrega distintas fuentes de datos médicos. Se ha realizado el diseño y la implementación del módulo así como el análisis de los resultados obtenidos realizando una evaluación con treinta y dos documentos que contenían 1372 menciones de terminología médica y que han dado un resultado medio de Precisión: 70,4%, Recall: 36,2%, Accuracy: 31,4% y F-Measure: 47,2%.---ABSTRACT---This Final Thesis arises from the need for technologies that facilitate the Natural Language Processing (NLP) in Spanish in the medical sector. Specifically it is focused on extracting knowledge from Electronic Health Records (EHR), which contain all the information related to the patient's health and, in particular, it expects to obtain all the terms related to medicine from the documents contained in these records. Natural Language Processing allows us to obtain structured information from unstructured data. These techniques enable analysis of text generating labels providing semantic meaning to words for handling information. From the investigation of the state of the art in NLP and existing technologies in other languages, an annotation module of medical terms extracted from clinical documents is proposed as a solution. Symptoms, diseases, body parts or treatments are considered part of the medical terms contained in UMLS ontology which is categorized joining different sources of medical data. This project has completed the design and implementation of a module and the analysis of the results have been obtained. Thirty two documents which contain 1372 mentions of medical terminology have been evaluated and the average results obtained are: Precision: 70.4% Recall: 36.2% Accuracy: 31.4% and F-Measure: 47.2%.

PREDIRCAM eHealth platform for individualized telemedical assistance for lifestyle modification in the treatment of obesity, diabetes, and cardiometabolic risk prevention: a pilot study (PREDIRCAM 1)

Background: Healthy diet and regular physical activity are powerful tools in reducing diabetes and cardiometabolic risk. Various international scientific and health organizations have advocated the use of new technologies to solve these problems. The PREDIRCAM project explores the contribution that a technological system could offer for the continuous monitoring of lifestyle habits and individualized treatment of obesity as well as cardiometabolic risk prevention. Methods: PREDIRCAM is a technological platform for patients and professionals designed to improve the effectiveness of lifestyle behavior modifications through the intensive use of the latest information and communication technologies. The platform consists of a web-based application providing communication interface with monitoring devices of physiological variables, application for monitoring dietary intake, ad hoc electronic medical records, different communication channels, and an intelligent notification system. A 2-week feasibility study was conducted in 15 volunteers to assess the viability of the platform. Results: The website received 244 visits (average time/session: 17 min 45 s). A total of 435 dietary intakes were recorded (average time for each intake registration, 4 min 42 s ± 2 min 30 s), 59 exercises were recorded in 20 heart rate monitor downloads, 43 topics were discussed through a forum, and 11 of the 15 volunteers expressed a favorable opinion toward the platform. Food intake recording was reported as the most laborious task. Ten of the volunteers considered long-term use of the platform to be feasible. Conclusions: The PREDIRCAM platform is technically ready for clinical evaluation. Training is required to use the platform and, in particular, for registration of dietary food intake.

Integrated electronic system for ultrasonic structural health monitoring

A fully integrated on-board electronic system that can perform in-situ structural health monitoring (SHM) of aircraft?s structures using specifically designed equipment for SHM based on guided wave ultrasonic method or Lamb waves? method is introduced. This equipment is called Phased Array Monitoring for Enhanced Life Assessment (PAMELA III) and is an essential part of overall PAMELA SHM? system. PAMELA III can generate any kind of excitation signals, acquire the response signals that propagate throughout the structure being tested, and perform the signal processing for damage detection directly on the structure without need to send the huge amount of raw signals but only the final SHM maps. It monitors the structure by means of an array of integrated Phased Array (PhA) transducers preferably bonded onto the host structure. The PAMELA III hardware for SHM mapping has been designed, built and subjected to laboratory tests, using aluminum and CFRP structures. The 12 channel system has been designed to be low weight (265 grams only), to have a small form factor, to be directly mounted above the integrated PhA transducers without need for cables and to be EMI protected so that the equipment can be taken on board an aircraft to perform required SHM analyses by use of embedded SHM algorithms. Moreover, the autonomous, automatic and on real-time working procedure makes it suitable for the avionic field, sending the corresponding alerts, maps and reports to external equipment.

Structural health monitoring network system with wireless communications inside closed aerospace structures

Structural Health Monitoring (SHM) requires integrated "all in one" electronic devices capable of performing analysis of structural integrity and on-board damage detection in aircraft?s structures. PAMELA III (Phased Array Monitoring for Enhanced Life Assessment, version III) SHM embedded system is an example of this device type. This equipment is capable of generating excitation signals to be applied to an array of integrated piezoelectric Phased Array (PhA) transducers stuck to aircraft structure, acquiring the response signals, and carrying out the advanced signal processing to obtain SHM maps. PAMELA III is connected with a host computer in order to receive the configuration parameters and sending the obtained SHM maps, alarms and so on. This host can communicate with PAMELA III through an Ethernet interface. To avoid the use of wires where necessary, it is possible to add Wi-Fi capabilities to PAMELA III, connecting a Wi-Fi node working as a bridge, and to establish a wireless communication between PAMELA III and the host. However, in a real aircraft scenario, several PAMELA III devices must work together inside closed structures. In this situation, it is not possible for all PAMELA III devices to establish a wireless communication directly with the host, due to the signal attenuation caused by the different obstacles of the aircraft structure. To provide communication among all PAMELA III devices and the host, a wireless mesh network (WMN) system has been implemented inside a closed aluminum wingbox. In a WMN, as long as a node is connected to at least one other node, it will have full connectivity to the entire network because each mesh node forwards packets to other nodes in the network as required. Mesh protocols automatically determine the best route through the network and can dynamically reconfigure the network if a link drops out. The advantages and disadvantages on the use of a wireless mesh network system inside closed aerospace structures are discussed.

Integrated phased array transducer for on-board structural health monitoring

Permanently bonded onto a structure, an integrated Phased Array (PhA II) transducer that can provide reliable electromechanical connection with corresponding sophisticated miniaturized ?all in one? SHM electronic device installed directly above it, without need for any interface cabling, during all aerospace structure lifecycle phases and for a huge variety of real harsh service environments of structures to be monitored is presented. This integrated PhA II transducer [1], as a key component of the PAMELA SHM? (Phased Array Monitoring for Enhanced Life Assessment) system, has two principal tasks at the same time, reliably transceive elastic waves in real aerospace service environments and serves as a reliable sole carrier or support for associated integrated on-board SHM electronic device attached above. The PhA II transducer successfully accomplished both required task throughout extensive test campaigns which included low to high temperature tests, temperature cycling, mechanical loading, combined thermo- mechanical loading and vibration resistance, etc. both with and without SHM device attached above due to RTCA DO-160F.

A model to develop a platform for personalised health applications

Antecedentes Europa vive una situación insostenible. Desde el 2008 se han reducido los recursos de los gobiernos a raíz de la crisis económica. El continente Europeo envejece con ritmo constante al punto que se prevé que en 2050 habrá sólo dos trabajadores por jubilado [54]. A esta situación se le añade el aumento de la incidencia de las enfermedades crónicas, relacionadas con el envejecimiento, cuyo coste puede alcanzar el 7% del PIB de un país [51]. Es necesario un cambio de paradigma. Una nueva manera de cuidar de la salud de las personas: sustentable, eficaz y preventiva más que curativa. Algunos estudios abogan por el cuidado personalizado de la salud (pHealth). En este modelo las prácticas médicas son adaptadas e individualizadas al paciente, desde la detección de los factores de riesgo hasta la personalización de los tratamientos basada en la respuesta del individuo [81]. El cuidado personalizado de la salud está asociado a menudo al uso de las tecnologías de la información y comunicación (TICs) que, con su desarrollo exponencial, ofrecen oportunidades interesantes para la mejora de la salud. El cambio de paradigma hacia el pHealth está lentamente ocurriendo, tanto en el ámbito de la investigación como en la industria, pero todavía no de manera significativa. Existen todavía muchas barreras relacionadas a la economía, a la política y la cultura. También existen barreras puramente tecnológicas, como la falta de sistemas de información interoperables [199]. A pesar de que los aspectos de interoperabilidad están evolucionando, todavía hace falta un diseño de referencia especialmente direccionado a la implementación y el despliegue en gran escala de sistemas basados en pHealth. La presente Tesis representa un intento de organizar la disciplina de la aplicación de las TICs al cuidado personalizado de la salud en un modelo de referencia, que permita la creación de plataformas de desarrollo de software para simplificar tareas comunes de desarrollo en este dominio. Preguntas de investigación RQ1 >Es posible definir un modelo, basado en técnicas de ingeniería del software, que represente el dominio del cuidado personalizado de la salud de una forma abstracta y representativa? RQ2 >Es posible construir una plataforma de desarrollo basada en este modelo? RQ3 >Esta plataforma ayuda a los desarrolladores a crear sistemas pHealth complejos e integrados? Métodos Para la descripción del modelo se adoptó el estándar ISO/IEC/IEEE 42010por ser lo suficientemente general y abstracto para el amplio enfoque de esta tesis [25]. El modelo está definido en varias partes: un modelo conceptual, expresado a través de mapas conceptuales que representan las partes interesadas (stakeholders), los artefactos y la información compartida; y escenarios y casos de uso para la descripción de sus funcionalidades. El modelo fue desarrollado de acuerdo a la información obtenida del análisis de la literatura, incluyendo 7 informes industriales y científicos, 9 estándares, 10 artículos en conferencias, 37 artículos en revistas, 25 páginas web y 5 libros. Basándose en el modelo se definieron los requisitos para la creación de la plataforma de desarrollo, enriquecidos por otros requisitos recolectados a través de una encuesta realizada a 11 ingenieros con experiencia en la rama. Para el desarrollo de la plataforma, se adoptó la metodología de integración continua [74] que permitió ejecutar tests automáticos en un servidor y también desplegar aplicaciones en una página web. En cuanto a la metodología utilizada para la validación se adoptó un marco para la formulación de teorías en la ingeniería del software [181]. Esto requiere el desarrollo de modelos y proposiciones que han de ser validados dentro de un ámbito de investigación definido, y que sirvan para guiar al investigador en la búsqueda de la evidencia necesaria para justificarla. La validación del modelo fue desarrollada mediante una encuesta online en tres rondas con un número creciente de invitados. El cuestionario fue enviado a 134 contactos y distribuido en algunos canales públicos como listas de correo y redes sociales. El objetivo era evaluar la legibilidad del modelo, su nivel de cobertura del dominio y su potencial utilidad en el diseño de sistemas derivados. El cuestionario incluía preguntas cuantitativas de tipo Likert y campos para recolección de comentarios. La plataforma de desarrollo fue validada en dos etapas. En la primera etapa se utilizó la plataforma en un experimento a pequeña escala, que consistió en una sesión de entrenamiento de 12 horas en la que 4 desarrolladores tuvieron que desarrollar algunos casos de uso y reunirse en un grupo focal para discutir su uso. La segunda etapa se realizó durante los tests de un proyecto en gran escala llamado HeartCycle [160]. En este proyecto un equipo de diseñadores y programadores desarrollaron tres aplicaciones en el campo de las enfermedades cardio-vasculares. Una de estas aplicaciones fue testeada en un ensayo clínico con pacientes reales. Al analizar el proyecto, el equipo de desarrollo se reunió en un grupo focal para identificar las ventajas y desventajas de la plataforma y su utilidad. Resultados Por lo que concierne el modelo que describe el dominio del pHealth, la parte conceptual incluye una descripción de los roles principales y las preocupaciones de los participantes, un modelo de los artefactos TIC que se usan comúnmente y un modelo para representar los datos típicos que son necesarios formalizar e intercambiar entre sistemas basados en pHealth. El modelo funcional incluye un conjunto de 18 escenarios, repartidos en: punto de vista de la persona asistida, punto de vista del cuidador, punto de vista del desarrollador, punto de vista de los proveedores de tecnologías y punto de vista de las autoridades; y un conjunto de 52 casos de uso repartidos en 6 categorías: actividades de la persona asistida, reacciones del sistema, actividades del cuidador, \engagement" del usuario, actividades del desarrollador y actividades de despliegue. Como resultado del cuestionario de validación del modelo, un total de 65 personas revisó el modelo proporcionando su nivel de acuerdo con las dimensiones evaluadas y un total de 248 comentarios sobre cómo mejorar el modelo. Los conocimientos de los participantes variaban desde la ingeniería del software (70%) hasta las especialidades médicas (15%), con declarado interés en eHealth (24%), mHealth (16%), Ambient Assisted Living (21%), medicina personalizada (5%), sistemas basados en pHealth (15%), informática médica (10%) e ingeniería biomédica (8%) con una media de 7.25_4.99 años de experiencia en estas áreas. Los resultados de la encuesta muestran que los expertos contactados consideran el modelo fácil de leer (media de 1.89_0.79 siendo 1 el valor más favorable y 5 el peor), suficientemente abstracto (1.99_0.88) y formal (2.13_0.77), con una cobertura suficiente del dominio (2.26_0.95), útil para describir el dominio (2.02_0.7) y para generar sistemas más específicos (2_0.75). Los expertos también reportan un interés parcial en utilizar el modelo en su trabajo (2.48_0.91). Gracias a sus comentarios, el modelo fue mejorado y enriquecido con conceptos que faltaban, aunque no se pudo demonstrar su mejora en las dimensiones evaluadas, dada la composición diferente de personas en las tres rondas de evaluación. Desde el modelo, se generó una plataforma de desarrollo llamada \pHealth Patient Platform (pHPP)". La plataforma desarrollada incluye librerías, herramientas de programación y desarrollo, un tutorial y una aplicación de ejemplo. Se definieron cuatro módulos principales de la arquitectura: el Data Collection Engine, que permite abstraer las fuentes de datos como sensores o servicios externos, mapeando los datos a bases de datos u ontologías, y permitiendo interacción basada en eventos; el GUI Engine, que abstrae la interfaz de usuario en un modelo de interacción basado en mensajes; y el Rule Engine, que proporciona a los desarrolladores un medio simple para programar la lógica de la aplicación en forma de reglas \if-then". Después de que la plataforma pHPP fue utilizada durante 5 años en el proyecto HeartCycle, 5 desarrolladores fueron reunidos en un grupo de discusión para analizar y evaluar la plataforma. De estas evaluaciones se concluye que la plataforma fue diseñada para encajar las necesidades de los ingenieros que trabajan en la rama, permitiendo la separación de problemas entre las distintas especialidades, y simplificando algunas tareas de desarrollo como el manejo de datos y la interacción asíncrona. A pesar de ello, se encontraron algunos defectos a causa de la inmadurez de algunas tecnologías empleadas, y la ausencia de algunas herramientas específicas para el dominio como el procesado de datos o algunos protocolos de comunicación relacionados con la salud. Dentro del proyecto HeartCycle la plataforma fue utilizada para el desarrollo de la aplicación \Guided Exercise", un sistema TIC para la rehabilitación de pacientes que han sufrido un infarto del miocardio. El sistema fue testeado en un ensayo clínico randomizado en el cual a 55 pacientes se les dio el sistema para su uso por 21 semanas. De los resultados técnicos del ensayo se puede concluir que, a pesar de algunos errores menores prontamente corregidos durante el estudio, la plataforma es estable y fiable. Conclusiones La investigación llevada a cabo en esta Tesis y los resultados obtenidos proporcionan las respuestas a las tres preguntas de investigación que motivaron este trabajo: RQ1 Se ha desarrollado un modelo para representar el dominio de los sistemas personalizados de salud. La evaluación hecha por los expertos de la rama concluye que el modelo representa el dominio con precisión y con un balance apropiado entre abstracción y detalle. RQ2 Se ha desarrollado, con éxito, una plataforma de desarrollo basada en el modelo. RQ3 Se ha demostrado que la plataforma es capaz de ayudar a los desarrolladores en la creación de software pHealth complejos. Las ventajas de la plataforma han sido demostradas en el ámbito de un proyecto de gran escala, aunque el enfoque genérico adoptado indica que la plataforma podría ofrecer beneficios también en otros contextos. Los resultados de estas evaluaciones ofrecen indicios de que, ambos, el modelo y la plataforma serán buenos candidatos para poderse convertir en una referencia para futuros desarrollos de sistemas pHealth. ABSTRACT Background Europe is living in an unsustainable situation. The economic crisis has been reducing governments' economic resources since 2008 and threatening social and health systems, while the proportion of older people in the European population continues to increase so that it is foreseen that in 2050 there will be only two workers per retiree [54]. To this situation it should be added the rise, strongly related to age, of chronic diseases the burden of which has been estimated to be up to the 7% of a country's gross domestic product [51]. There is a need for a paradigm shift, the need for a new way of caring for people's health, shifting the focus from curing conditions that have arisen to a sustainable and effective approach with the emphasis on prevention. Some advocate the adoption of personalised health care (pHealth), a model where medical practices are tailored to the patient's unique life, from the detection of risk factors to the customization of treatments based on each individual's response [81]. Personalised health is often associated to the use of Information and Communications Technology (ICT), that, with its exponential development, offers interesting opportunities for improving healthcare. The shift towards pHealth is slowly taking place, both in research and in industry, but the change is not significant yet. Many barriers still exist related to economy, politics and culture, while others are purely technological, like the lack of interoperable information systems [199]. Though interoperability aspects are evolving, there is still the need of a reference design, especially tackling implementation and large scale deployment of pHealth systems. This thesis contributes to organizing the subject of ICT systems for personalised health into a reference model that allows for the creation of software development platforms to ease common development issues in the domain. Research questions RQ1 Is it possible to define a model, based on software engineering techniques, for representing the personalised health domain in an abstract and representative way? RQ2 Is it possible to build a development platform based on this model? RQ3 Does the development platform help developers create complex integrated pHealth systems? Methods As method for describing the model, the ISO/IEC/IEEE 42010 framework [25] is adopted for its generality and high level of abstraction. The model is specified in different parts: a conceptual model, which makes use of concept maps, for representing stakeholders, artefacts and shared information, and in scenarios and use cases for the representation of the functionalities of pHealth systems. The model was derived from literature analysis, including 7 industrial and scientific reports, 9 electronic standards, 10 conference proceedings papers, 37 journal papers, 25 websites and 5 books. Based on the reference model, requirements were drawn for building the development platform enriched with a set of requirements gathered in a survey run among 11 experienced engineers. For developing the platform, the continuous integration methodology [74] was adopted which allowed to perform automatic tests on a server and also to deploy packaged releases on a web site. As a validation methodology, a theory building framework for SW engineering was adopted from [181]. The framework, chosen as a guide to find evidence for justifying the research questions, imposed the creation of theories based on models and propositions to be validated within a scope. The validation of the model was conducted as an on-line survey in three validation rounds, encompassing a growing number of participants. The survey was submitted to 134 experts of the field and on some public channels like relevant mailing lists and social networks. Its objective was to assess the model's readability, its level of coverage of the domain and its potential usefulness in the design of actual, derived systems. The questionnaires included quantitative Likert scale questions and free text inputs for comments. The development platform was validated in two scopes. As a small-scale experiment, the platform was used in a 12 hours training session where 4 developers had to perform an exercise consisting in developing a set of typical pHealth use cases At the end of the session, a focus group was held to identify benefits and drawbacks of the platform. The second validation was held as a test-case study in a large scale research project called HeartCycle the aim of which was to develop a closed-loop disease management system for heart failure and coronary heart disease patients [160]. During this project three applications were developed by a team of programmers and designers. One of these applications was tested in a clinical trial with actual patients. At the end of the project, the team was interviewed in a focus group to assess the role the platform had within the project. Results For what regards the model that describes the pHealth domain, its conceptual part includes a description of the main roles and concerns of pHealth stakeholders, a model of the ICT artefacts that are commonly adopted and a model representing the typical data that need to be formalized among pHealth systems. The functional model includes a set of 18 scenarios, divided into assisted person's view, caregiver's view, developer's view, technology and services providers' view and authority's view, and a set of 52 Use Cases grouped in 6 categories: assisted person's activities, system reactions, caregiver's activities, user engagement, developer's activities and deployer's activities. For what concerns the validation of the model, a total of 65 people participated in the online survey providing their level of agreement in all the assessed dimensions and a total of 248 comments on how to improve and complete the model. Participants' background spanned from engineering and software development (70%) to medical specialities (15%), with declared interest in the fields of eHealth (24%), mHealth (16%), Ambient Assisted Living (21%), Personalized Medicine (5%), Personal Health Systems (15%), Medical Informatics (10%) and Biomedical Engineering (8%) with an average of 7.25_4.99 years of experience in these fields. From the analysis of the answers it is possible to observe that the contacted experts considered the model easily readable (average of 1.89_0.79 being 1 the most favourable scoring and 5 the worst), sufficiently abstract (1.99_0.88) and formal (2.13_0.77) for its purpose, with a sufficient coverage of the domain (2.26_0.95), useful for describing the domain (2.02_0.7) and for generating more specific systems (2_0.75) and they reported a partial interest in using the model in their job (2.48_0.91). Thanks to their comments, the model was improved and enriched with concepts that were missing at the beginning, nonetheless it was not possible to prove an improvement among the iterations, due to the diversity of the participants in the three rounds. From the model, a development platform for the pHealth domain was generated called pHealth Patient Platform (pHPP). The platform includes a set of libraries, programming and deployment tools, a tutorial and a sample application. The main four modules of the architecture are: the Data Collection Engine, which allows abstracting sources of information like sensors or external services, mapping data to databases and ontologies, and allowing event-based interaction and filtering, the GUI Engine, which abstracts the user interface in a message-like interaction model, the Workow Engine, which allows programming the application's user interaction ows with graphical workows, and the Rule Engine, which gives developers a simple means for programming the application's logic in the form of \if-then" rules. After the 5 years experience of HeartCycle, partially programmed with pHPP, 5 developers were joined in a focus group to discuss the advantages and drawbacks of the platform. The view that emerged from the training course and the focus group was that the platform is well-suited to the needs of the engineers working in the field, it allowed the separation of concerns among the different specialities and it simplified some common development tasks like data management and asynchronous interaction. Nevertheless, some deficiencies were pointed out in terms of a lack of maturity of some technological choices, and for the absence of some domain-specific tools, e.g. for data processing or for health-related communication protocols. Within HeartCycle, the platform was used to develop part of the Guided Exercise system, a composition of ICT tools for the physical rehabilitation of patients who suffered from myocardial infarction. The system developed using the platform was tested in a randomized controlled clinical trial, in which 55 patients used the system for 21 weeks. The technical results of this trial showed that the system was stable and reliable. Some minor bugs were detected, but these were promptly corrected using the platform. This shows that the platform, as well as facilitating the development task, can be successfully used to produce reliable software. Conclusions The research work carried out in developing this thesis provides responses to the three three research questions that were the motivation for the work. RQ1 A model was developed representing the domain of personalised health systems, and the assessment of experts in the field was that it represents the domain accurately, with an appropriate balance between abstraction and detail. RQ2 A development platform based on the model was successfully developed. RQ3 The platform has been shown to assist developers create complex pHealth software. This was demonstrated within the scope of one large-scale project, but the generic approach adopted provides indications that it would offer benefits more widely. The results of these evaluations provide indications that both the model and the platform are good candidates for being a reference for future pHealth developments.

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

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