Nanoinformatics approaches for information extraction and text mining in nanomedical research texts

La nanotecnología es un área de investigación de reciente creación que trata con la manipulación y el control de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. A escala nanométrica, los materiales exhiben fenómenos físicos, químicos y biológicos singulares, muy distintos a los que manifiestan a escala convencional. En medicina, los compuestos miniaturizados a nanoescala y los materiales nanoestructurados ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, así como una mejora en la focalización del medicamento hacia la diana terapéutica, revelando así nuevas propiedades diagnósticas y terapéuticas. A su vez, la complejidad de la información a nivel nano es mucho mayor que en los niveles biológicos convencionales (desde el nivel de población hasta el nivel de célula) y, por tanto, cualquier flujo de trabajo en nanomedicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Desafortunadamente, la informática biomédica todavía no ha proporcionado el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, ni ha adaptado sus métodos y herramientas a este nuevo campo de investigación. En este contexto, la nueva área de la nanoinformática pretende detectar y establecer los vínculos existentes entre la medicina, la nanotecnología y la informática, fomentando así la aplicación de métodos computacionales para resolver las cuestiones y problemas que surgen con la información en la amplia intersección entre la biomedicina y la nanotecnología. Las observaciones expuestas previamente determinan el contexto de esta tesis doctoral, la cual se centra en analizar el dominio de la nanomedicina en profundidad, así como en el desarrollo de estrategias y herramientas para establecer correspondencias entre las distintas disciplinas, fuentes de datos, recursos computacionales y técnicas orientadas a la extracción de información y la minería de textos, con el objetivo final de hacer uso de los datos nanomédicos disponibles. El autor analiza, a través de casos reales, alguna de las tareas de investigación en nanomedicina que requieren o que pueden beneficiarse del uso de métodos y herramientas nanoinformáticas, ilustrando de esta forma los inconvenientes y limitaciones actuales de los enfoques de informática biomédica a la hora de tratar con datos pertenecientes al dominio nanomédico. Se discuten tres escenarios diferentes como ejemplos de actividades que los investigadores realizan mientras llevan a cabo su investigación, comparando los contextos biomédico y nanomédico: i) búsqueda en la Web de fuentes de datos y recursos computacionales que den soporte a su investigación; ii) búsqueda en la literatura científica de resultados experimentales y publicaciones relacionadas con su investigación; iii) búsqueda en registros de ensayos clínicos de resultados clínicos relacionados con su investigación. El desarrollo de estas actividades requiere el uso de herramientas y servicios informáticos, como exploradores Web, bases de datos de referencias bibliográficas indexando la literatura biomédica y registros online de ensayos clínicos, respectivamente. Para cada escenario, este documento proporciona un análisis detallado de los posibles obstáculos que pueden dificultar el desarrollo y el resultado de las diferentes tareas de investigación en cada uno de los dos campos citados (biomedicina y nanomedicina), poniendo especial énfasis en los retos existentes en la investigación nanomédica, campo en el que se han detectado las mayores dificultades. El autor ilustra cómo la aplicación de metodologías provenientes de la informática biomédica a estos escenarios resulta efectiva en el dominio biomédico, mientras que dichas metodologías presentan serias limitaciones cuando son aplicadas al contexto nanomédico. Para abordar dichas limitaciones, el autor propone un enfoque nanoinformático, original, diseñado específicamente para tratar con las características especiales que la información presenta a nivel nano. El enfoque consiste en un análisis en profundidad de la literatura científica y de los registros de ensayos clínicos disponibles para extraer información relevante sobre experimentos y resultados en nanomedicina —patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.—, seguido del desarrollo de mecanismos para estructurar y analizar dicha información automáticamente. Este análisis concluye con la generación de un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento y de test anotados manualmente—, el cual ha sido aplicado a la clasificación de registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nanodrogas y nanodispositivos de aquellos enfocados a testear productos farmacéuticos tradicionales. El presente trabajo pretende proporcionar los métodos necesarios para organizar, depurar, filtrar y validar parte de los datos nanomédicos existentes en la actualidad a una escala adecuada para la toma de decisiones. Análisis similares para otras tareas de investigación en nanomedicina ayudarían a detectar qué recursos nanoinformáticos se requieren para cumplir los objetivos actuales en el área, así como a generar conjunto de datos de referencia, estructurados y densos en información, a partir de literatura y otros fuentes no estructuradas para poder aplicar nuevos algoritmos e inferir nueva información de valor para la investigación en nanomedicina. ABSTRACT Nanotechnology is a research area of recent development that deals with the manipulation and control of matter with dimensions ranging from 1 to 100 nanometers. At the nanoscale, materials exhibit singular physical, chemical and biological phenomena, very different from those manifested at the conventional scale. In medicine, nanosized compounds and nanostructured materials offer improved drug targeting and efficacy with respect to traditional formulations, and reveal novel diagnostic and therapeutic properties. Nevertheless, the complexity of information at the nano level is much higher than the complexity at the conventional biological levels (from populations to the cell). Thus, any nanomedical research workflow inherently demands advanced information management. Unfortunately, Biomedical Informatics (BMI) has not yet provided the necessary framework to deal with such information challenges, nor adapted its methods and tools to the new research field. In this context, the novel area of nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods to solve informational issues at the wide intersection between biomedicine and nanotechnology. The above observations determine the context of this doctoral dissertation, which is focused on analyzing the nanomedical domain in-depth, and developing nanoinformatics strategies and tools to map across disciplines, data sources, computational resources, and information extraction and text mining techniques, for leveraging available nanomedical data. The author analyzes, through real-life case studies, some research tasks in nanomedicine that would require or could benefit from the use of nanoinformatics methods and tools, illustrating present drawbacks and limitations of BMI approaches to deal with data belonging to the nanomedical domain. Three different scenarios, comparing both the biomedical and nanomedical contexts, are discussed as examples of activities that researchers would perform while conducting their research: i) searching over the Web for data sources and computational resources supporting their research; ii) searching the literature for experimental results and publications related to their research, and iii) searching clinical trial registries for clinical results related to their research. The development of these activities will depend on the use of informatics tools and services, such as web browsers, databases of citations and abstracts indexing the biomedical literature, and web-based clinical trial registries, respectively. For each scenario, this document provides a detailed analysis of the potential information barriers that could hamper the successful development of the different research tasks in both fields (biomedicine and nanomedicine), emphasizing the existing challenges for nanomedical research —where the major barriers have been found. The author illustrates how the application of BMI methodologies to these scenarios can be proven successful in the biomedical domain, whilst these methodologies present severe limitations when applied to the nanomedical context. To address such limitations, the author proposes an original nanoinformatics approach specifically designed to deal with the special characteristics of information at the nano level. This approach consists of an in-depth analysis of the scientific literature and available clinical trial registries to extract relevant information about experiments and results in nanomedicine —textual patterns, common vocabulary, experiment descriptors, characterization parameters, etc.—, followed by the development of mechanisms to automatically structure and analyze this information. This analysis resulted in the generation of a gold standard —a manually annotated training or reference set—, which was applied to the automatic classification of clinical trial summaries, distinguishing studies focused on nanodrugs and nanodevices from those aimed at testing traditional pharmaceuticals. The present work aims to provide the necessary methods for organizing, curating and validating existing nanomedical data on a scale suitable for decision-making. Similar analysis for different nanomedical research tasks would help to detect which nanoinformatics resources are required to meet current goals in the field, as well as to generate densely populated and machine-interpretable reference datasets from the literature and other unstructured sources for further testing novel algorithms and inferring new valuable information for nanomedicine.

Building ontologies from folksonomies and linked data: Data structures and Algorithms

We present the data structures and algorithms used in the approach for building domain ontologies from folksonomies and linked data. In this approach we extracts domain terms from folksonomies and enrich them with semantic information from the Linked Open Data cloud. As a result, we obtain a domain ontology that combines the emergent knowledge of social tagging systems with formal knowledge from Ontologies.

A Comparison of different Uncertainty Activation Cross-Section Data Libraries and collapsed values for different neutron spectra: ADS, FISSION and FUSION

PART I:Cross-section uncertainties under differentneutron spectra. PART II: Processing uncertainty libraries

Physical data acquisition and PWM signal generation using a microcontroller allowing control for DC motor rotation speed

El objetivo de este proyecto es diseñar un sistema capaz de controlar la velocidad de rotación de un motor DC en función del valor de temperatura obtenido de un sensor. Para ello se generará con un microcontrolador una señal PWM, cuyo ciclo de trabajo estará en función de la temperatura medida. En lo que respecta a la fase de diseño, hay dos partes claramente diferenciadas, relativas al hardware y al software. En cuanto al diseño del hardware puede hacerse a su vez una división en dos partes. En primer lugar, hubo que diseñar la circuitería necesaria para adaptar los niveles de tensión entregados por el sensor de temperatura a los niveles requeridos por ADC, requerido para digitalizar la información para su posterior procesamiento por parte del microcontrolador. Por tanto hubo que diseñar capaz de corregir el offset y la pendiente de la función tensión-temperatura del sensor, a fin de adaptarlo al rango de tensión requerido por el ADC. Por otro lado, hubo que diseñar el circuito encargado de controlar la velocidad de rotación del motor. Este circuito estará basado en un transistor MOSFET en conmutación, controlado mediante una señal PWM como se mencionó anteriormente. De esta manera, al variar el ciclo de trabajo de la señal PWM, variará de manera proporcional la tensión que cae en el motor, y por tanto su velocidad de rotación. En cuanto al diseño del software, se programó el microcontrolador para que generase una señal PWM en uno de sus pines en función del valor entregado por el ADC, a cuya entrada está conectada la tensión obtenida del circuito creado para adaptar la tensión generada por el sensor. Así mismo, se utiliza el microcontrolador para representar el valor de temperatura obtenido en una pantalla LCD. Para este proyecto se eligió una placa de desarrollo mbed, que incluye el microcontrolador integrado, debido a que facilita la tarea del prototipado. Posteriormente se procedió a la integración de ambas partes, y testeado del sistema para comprobar su correcto funcionamiento. Puesto que el resultado depende de la temperatura medida, fue necesario simular variaciones en ésta, para así comprobar los resultados obtenidos a distintas temperaturas. Para este propósito se empleó una bomba de aire caliente. Una vez comprobado el funcionamiento, como último paso se diseñó la placa de circuito impreso. Como conclusión, se consiguió desarrollar un sistema con un nivel de exactitud y precisión aceptable, en base a las limitaciones del sistema. SUMMARY: It is obvious that day by day people’s daily life depends more on technology and science. Tasks tend to be done automatically, making them simpler and as a result, user life is more comfortable. Every single task that can be controlled has an electronic system behind. In this project, a control system based on a microcontroller was designed for a fan, allowing it to go faster when temperature rises or slowing down as the environment gets colder. For this purpose, a microcontroller was programmed to generate a signal, to control the rotation speed of the fan depending on the data acquired from a temperature sensor. After testing the whole design developed in the laboratory, the next step taken was to build a prototype, which allows future improvements in the system that are discussed in the corresponding section of the thesis.

A Reuse-based Lightweight Method for Developing Linked Data Ontologies and Vocabularies

The uptake of Linked Data (LD) has promoted the proliferation of datasets and their associated ontologies for describing different domains. Par-ticular LD development characteristics such as agility and web-based architec-ture necessitate the revision, adaption, and lightening of existing methodologies for ontology development. This thesis proposes a lightweight method for ontol-ogy development in an LD context which will be based in data-driven agile de-velopments, existing resources to be reused, and the evaluation of the obtained products considering both classical ontological engineering principles and LD characteristics.

A note on data-parallelism and (and-parallel) prolog

Abstract is not available.

Combining data mining and ontology engineering to enrich ontologies and linked data

In this position paper, we claim that the need for time consuming data preparation and result interpretation tasks in knowledge discovery, as well as for costly expert consultation and consensus building activities required for ontology building can be reduced through exploiting the interplay of data mining and ontology engineering. The aim is to obtain in a semi-automatic way new knowledge from distributed data sources that can be used for inference and reasoning, as well as to guide the extraction of further knowledge from these data sources. The proposed approach is based on the creation of a novel knowledge discovery method relying on the combination, through an iterative ?feedbackloop?, of (a) data mining techniques to make emerge implicit models from data and (b) pattern-based ontology engineering to capture these models in reusable, conceptual and inferable artefacts.

Image and Identity. The experimental Housing of Schorlemerallee, Hans and Wassili Luckhardt, Alfons Anker, Berlin 1925-30

Proceedings of the 12th DOCOMOMO International Conference

A data-globe and immersive virtual reality environment for upper limb rehabilitation after spinal cord injury

While a number of virtual data-gloves have been used in stroke, there is little evidence about their use in spinal cord injury (SCI). A pilot clinical experience with nine SCI subjects was performed comparing two groups: one carried out a virtual rehabilitation training based on the use of a data glove, CyberTouch combined with traditional rehabilitation, during 30 minutes a day twice a week along two weeks; while the other made only conventional rehabilitation. Furthermore, two functional indexes were developed in order to assess the patient’s performance of the sessions: normalized trajectory lengths and repeatability. While differences between groups were not statistically significant, the data-glove group seemed to obtain better results in the muscle balance and functional parameters, and in the dexterity, coordination and fine grip tests. Related to the indexes that we implemented, normalized trajectory lengths and repeatability, every patient showed an improvement in at least one of the indexes, either along Y-axis trajectory or Z-axis trajectory. This study might be a step in investigating new ways of treatments and objective measures in order to obtain more accurate data about the patient’s evolution, allowing the clinicians to develop rehabilitation treatments, adapted to the abilities and needs of the patients.

Guidelines for Linked Data generation and publication: an example in building energy consumption

Linked Data is the key paradigm of the Semantic Web, a new generation of the World Wide Web that promises to bring meaning (semantics) to data. A large number of both public and private organizations have published their data following the Linked Data principles, or have done so with data from other organizations. To this extent, since the generation and publication of Linked Data are intensive engineering processes that require high attention in order to achieve high quality, and since experience has shown that existing general guidelines are not always sufficient to be applied to every domain, this paper presents a set of guidelines for generating and publishing Linked Data in the context of energy consumption in buildings (one aspect of Building Information Models). These guidelines offer a comprehensive description of the tasks to perform, including a list of steps, tools that help in achieving the task, various alternatives for performing the task, and best practices and recommendations. Furthermore, this paper presents a complete example on the generation and publication of Linked Data about energy consumption in buildings, following the presented guidelines, in which the energy consumption data of council sites (e.g., buildings and lights) belonging to the Leeds City Council jurisdiction have been generated and published as Linked Data.

On the economics of energy consumption in 4G networks: the case of Spain

Reducing energy consumption is one of the main challenges in most countries. For example, European Member States agreed to reduce greenhouse gas (GHG) emissions by 20% in 2020 compared to 1990 levels (EC 2008). Considering each sector separately, ICTs account nowadays for 2% of total carbon emissions. This percentage will increase as the demand of communication services and applications steps up. At the same time, the expected evolution of ICT-based developments - smart buildings, smart grids and smart transportation systems among others - could result in the creation of energy-saving opportunities leading to global emission reductions (Labouze et al. 2008), although the amount of these savings is under debate (Falch 2010). The main development required in telecommunication networks ?one of the three major blocks of energy consumption in ICTs together with data centers and consumer equipment (Sutherland 2009) ? is the evolution of existing infrastructures into ultra-broadband networks, the so-called Next Generation Networks (NGN). Fourth generation (4G) mobile communications are the technology of choice to complete -or supplement- the ubiquitous deployment of NGN. The risk and opportunities involved in NGN roll-out are currently in the forefront of the economic and policy debate. However, the issue of which is the role of energy consumption in 4G networks seems absent, despite the fact that the economic impact of energy consumption arises as a key element in the cost analysis of this type of networks. Precisely, the aim of this research is to provide deeper insight on the energy consumption involved in the usage of a 4G network, its relationship with network main design features, and the general economic impact this would have in the capital and operational expenditures related with network deployment and usage.

Diseño de un sistema networking audio para instalación audiovisual

Una vez presentada la tecnología de Networking audio (redes de datos, protocolos actuales, etc.) se realizará un diseño de la instalación del sistema de audio, en el que el punto de partida es la parte creativa de la actividad en dicha instalación: un juego en el que la comunicación auditiva es lo fundamental. La instalación se compondrá de una sala central, tres salas de grupos, tres salas de cabinas de actores y ocho salas de pasaje. Esta actividad tan particular hará plantearse configuraciones, equipamiento y formas de trabajar especiales que, mediante la tecnología de audio vía red de datos y el equipamiento auxiliar a esta red, podría realizarse de la una forma óptima cumpliendo con todos los objetivos de la actividad, tanto técnicos como relativos al juego. El libro se dividirá en dos partes: La primera parte consistirá en una explicación de lo que son las redes de datos y los aspectos básicos para entenderlas desde un punto de vista práctico: qué es Ethernet, los componentes de una red... Una vez explicada la terminología específica de redes, se expondrán los protocolos que se usan para transmitir audio profesional a día de hoy. En la segunda parte, se empezará presentando la actividad que se realizará en nuestra instalación: un juego de rol. A continuación se conocerá el flujo de señales existentes para después, poner en práctica lo aprendido en la primera parte: diseñaremos una instalación audiovisual mediante networking audio. Un sistema de estas características necesita además de dispositivos en red, sistemas convencionales de audio. Durante el diseño y debido a las necesidades tan específicas de la instalación, se verá que ha sido necesario pensar en sistemas especiales para hacer posible la actividad para la que ha sido ideada nuestra instalación. Los objetivos de este proyecto son, desarrollar los puntos que tendría que tener en cuenta un integrador que se proponga diseñar un sistema de audio networking para una instalación audiovisual para, a continuación, poner en práctica estos conocimientos con la exposición del diseño de una instalación en la que se llevará a cabo una actividad lúdica y de aprendizaje en la que una óptima transmisión de señal de audio a tiempo real, es lo fundamental. ABSTRACT. Once introduced the Networking technology (data networks, current protocols, etc.), the audio installation design is being done. In which the starting point is the creative part of the activity will be made: one game in which the auditory communication is fundamental. The installation will consist of a central room, three meeting groups, three actor cabins rooms and eight passage rooms. This particular activity will consider configurations, equipment and forms of special working that through audio technology via data network and auxiliary equipment to this network, it could be done in an optimal way to meet all the goals of the activity, both technical and relative to the game. The book is divided into two parts: The first part consists of an explanation of what the data networks and the basics to understand from a practical point of view: what Ethernet is, the network components... Once specific network terminology is explained, the current protocols used to transmit professional audio are being showed. In the second part, it is introducing the activity to be made in our installation: a game. Then, the flow of existing signals are being known, we practice what I learned in the first part: we will design an audiovisual installation by audio networking. A system like this besides networked devices, it needs conventional audio systems. During the design and due to the very specific needs of the installation, you will see that it was necessary to think of special systems for this special activity. The goals of this project are to develop the points that an system integrator would have to consider to design a system of networking audio for an audiovisual installation, then put this knowledge into practice with the installation design where it will take place a fun and learning activity in which an optimal transmission of audio signal in real time, is basic.

A set of canonical problems in sloshing. Part 0: Experimental setup and data processing

In a series of attempts to research and document relevant sloshing type phenomena, a series of experiments have been conducted. The aim of this paper is to describe the setup and data processing of such experiments. A sloshing tank is subjected to angular motion. As a result pressure registers are obtained at several locations, together with the motion data, torque and a collection of image and video information. The experimental rig and the data acquisition systems are described. Useful information for experimental sloshing research practitioners is provided. This information is related to the liquids used in the experiments, the dying techniques, tank building processes, synchronization of acquisition systems, etc. A new procedure for reconstructing experimental data, that takes into account experimental uncertainties, is presented. This procedure is based on a least squares spline approximation of the data. Based on a deterministic approach to the first sloshing wave impact event in a sloshing experiment, an uncertainty analysis procedure of the associated first pressure peak value is described.

Cloud Computing Service for Managing Large Medical Image Data-Sets Using Balanced Collaborative Agents

Managing large medical image collections is an increasingly demanding important issue in many hospitals and other medical settings. A huge amount of this information is daily generated, which requires robust and agile systems. In this paper we present a distributed multi-agent system capable of managing very large medical image datasets. In this approach, agents extract low-level information from images and store them in a data structure implemented in a relational database. The data structure can also store semantic information related to images and particular regions. A distinctive aspect of our work is that a single image can be divided so that the resultant sub-images can be stored and managed separately by different agents to improve performance in data accessing and processing. The system also offers the possibility of applying some region-based operations and filters on images, facilitating image classification. These operations can be performed directly on data structures in the database.