Experimental investigation on box-wing configuration for UAS

The range for airframe configurations available for UAS is as diverse as those used for manned aircraft and more since the commercial risk in trying unorthodox solutions is less for the UAS manufacturer. This is principally because the UAS airframes are usually much smaller than the manned aircraft and operators are less likely to have a bias against unconventional configurations. One of these unconventional configurations is the box-wing, which is an unconventional solution for the design of the new UAS generation. The existence of two wings separated in different planes that are, however, significantly close together, means that the aerodynamic analysis by theoretical or computational methods is a difficult task, due to the considerable interference existing. Considering the fact that the flight of most UAS takes place at low Reynolds numbers, it is necessary to study the aerodynamics of the box wing configuration by testing different models in a wind tunnel to be able to obtain reasonable results. In the present work, the study is enhanced by varying not only the sweepback angles of the two wings, but also their position along the models’ fuselage. Certain models have shown being more efficient than others, pointing out that certain relative positions of wing exists that can improve the aerodynamics efficiency of the box wing configuration.

A method for incorporating residual stresses into patient-specific finite element simulations of arteries with an example on AAAs

Through progress in medical imaging, image analysis and finite element (FE) meshing tools it is now possible to extract patient-specific geometries from medical images of abdominal aortic aneurysms(AAAs), and thus to study clinically-relevant problems via FE simulations. Such simulations allow additional insight into human physiology in both healthy and diseased states. Medical imaging is most often performed in vivo, and hence the reconstructed model geometry in the problem of interest will represent the in vivo state, e.g., the AAA at physiological blood pressure. However, classical continuum mechanics and FE methods assume that constitutive models and the corresponding simulations begin from an unloaded, stress-free reference condition.

A fracture model for pearlitic steel bars using a cohesive model

The fracture of ductile materials, such as metals, is usually explained with the theory of nucleation, growth and coalescence of microvoids. Based on this theory, many numerical models have been developed, with a special mention to Gurson-type models. These models simulate mathematically the physical growth of microvoids, leading to a progressive development of the internal damage that takes place during a tensile test. In these models, the damage starts to develop in very early stages of the test. Tests carried out by the authors suggest that, in the case of some eutectoid steels such as those used for manufacturing prestressing steel wires, the internal damage that takes place as a result of the growth of microvoids is only noticeable in very late stages of the tensile test. In the authors’ opinion, using a cohesive model as a failure criterion may be interesting in this case; a cohesive model only requires two parameters to be defined, with the fracture energy being one of them, which can be obtained experimentally. In addition to this, given that it is known that the stress triaxiality has a strong influence on the fracture of ductile materials, a cohesive model whose parameters are affected by the value of the stress triaxiality can be considered. This work presents a fracture model for steel specimens in a tensile test, based on a cohesive behaviour and taking into account the effect of stress triaxiality, which is different at each point of the fracture plane.

A global Lagrangian descriptor applied to the Kuroshio current

A global Lagrangian descriptor applied to the Kuroshio current

Probabilistic Analysis of Tunnel Liners

The use of probabilistic methods to analyse reliability of structures is being applied to a variety of engineering problems due to the possibility of establishing the failure probability on rational grounds. In this paper we present the application of classical reliability theory to analyse the safety of underground tunnels.

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.

Benchmarking of calculation schemes in Apollo2 and COBAYA3 for VVER lattices

This paper presents solutions of the NURISP VVER lattice benchmark using APOLLO2, TRIPOLI4 and COBAYA3 pin-by-pin. The main objective is to validate MOC based calculation schemes for pin-by-pin cross-section generation with APOLLO2 against TRIPOLI4 reference results. A specific objective is to test the APOLLO2 generated cross-sections and interface discontinuity factors in COBAYA3 pin-by-pin calculations with unstructured mesh. The VVER-1000 core consists of large hexagonal assemblies with 2mm inter-assembly water gaps which require the use of unstructured meshes in the pin-by-pin core simulators. The considered 2D benchmark problems include 19-pin clusters, fuel assemblies and 7-assembly clusters. APOLLO2 calculation schemes with the step characteristic method (MOC) and the higher-order Linear Surface MOC have been tested. The comparison of APOLLO2 vs.TRIPOLI4 results shows a very close agreement. The 3D lattice solver in COBAYA3 uses transport corrected multi-group diffusion approximation with interface discontinuity factors of GET or Black Box Homogenization type. The COBAYA3 pin-by-pin results in 2, 4 and 8 energy groups are close to the reference solutions when using side-dependent interface discontinuity factors.

Statistical mechanics approaches to granular media: between micromechanics and macromechanics

The mechanical behavior of granular materials has been traditionally approached through two theoretical and computational frameworks: macromechanics and micromechanics. Macromechanics focuses on continuum based models. In consequence it is assumed that the matter in the granular material is homogeneous and continuously distributed over its volume so that the smallest element cut from the body possesses the same physical properties as the body. In particular, it has some equivalent mechanical properties, represented by complex and non-linear constitutive relationships. Engineering problems are usually solved using computational methods such as FEM or FDM. On the other hand, micromechanics is the analysis of heterogeneous materials on the level of their individual constituents. In granular materials, if the properties of particles are known, a micromechanical approach can lead to a predictive response of the whole heterogeneous material. Two classes of numerical techniques can be differentiated: computational micromechanics, which consists on applying continuum mechanics on each of the phases of a representative volume element and then solving numerically the equations, and atomistic methods (DEM), which consist on applying rigid body dynamics together with interaction potentials to the particles. Statistical mechanics approaches arise between micro and macromechanics. It tries to state which the expected macroscopic properties of a granular system are, by starting from a micromechanical analysis of the features of the particles and the interactions. The main objective of this paper is to introduce this approach.

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.

Performance-based seismic design of a retaining wall

The design of containment walls suffering seismic loads traditionally has been realized with methods based on pseudoanalitic procedures such as Mononobe-Okabe's method, which it has led in certain occasions to insecure designs, that they have produced the ruin of many containment walls suffering the action of an earthquake. The recommendations gathered in Mononobe-Okabe's theory have been included in numerous Codes of Seismic Design. It is clear that a revision of these recommendations must be done. At present there is taking place an important review of the design methods of anti-seismic structures such as containment walls placed in an area of numerous earthquakes, by means of the introduction at the beginning of the decade of 1990 the Displacement Response Spectrum (DRS) and the Capacity Demand Diagram (CDD) that suppose an important change in the way of presenting the Elastic Response Spectrum (ERS). On the other hand in case of action of an earthquake, the dynamic characteristics of a soil have been referred traditionally to the speed of the shear waves that can be generated in a site, together with the characteristics of plasticity and damping of the soil. The Principle of the energy conservation explains why a shear upward propagating seismic wave can be amplified when travelling from a medium with high shear wave velocity (rock) to other medium with lower velocity (soil deposit), as it happened in the earthquake of Mexico of 1985. This amplification is a function of the speed gradient or of the contrast of impedances in the border of both types of mediums. A method is proposed in this paper for the design of containment walls in different soils, suffering to the action of an earthquake, based on the Performance-Based Seismic Design.

Nonlinear models for lateral dynamics of railway vehicles on bridges subject to wind action

The study of lateral dynamics of running trains on bridges is of importance mainly for the safety of the traffic, and may be relevant for laterally compliant bridges. These studies require threedimensional coupled vehicle-bridge models, wheree consideration of wheel to rail contact is a key aspect. Furthermore, an adequate evaluation of safety of rail traffic requires nonlinear models. A nonlinear coupled model is proposed here for vehicle-structure vertical and lateral dynamics. Vehicles are considered as fully three-dimensional multibody systems including gyroscopic terms and large rotation effects. The bridge structure is modeled by means of finite elements which may be of beam, shell or continuum type and may include geometric or material nonlinearities. The track geometry includes distributed track alignment irregularities. Both subsystems (bridge and vehicles) are described with coordinates in absolute reference frames, as opposed to alternative approaches which describe the multibody system with coordinates relative to the base bridge motion. The wheelrail contact employed is a semi-Hertzian model based on realistic wheel-rail profiles. It allows a detailed geometrical description of the contact patch under each wheel including multiple-point contact, flange contact and uplift. Normal and tangential stresses in each contact are integrated at each time-step to obtain the resultant contact forces. The models have been implemented within an existing finite element analysis software with multibody capabilities, Abaqus (Simulia Ltd., 2010). Further details of the model are presented in Antolín et al. (2012). Representative applications are presented for railway vehicles under lateral wind action on laterally compliant viaducts, showing the relevance of the nonlinear wheel-rail contact model as well as the interaction between bridge and vehicle.

A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

Uso de técnicas de minería de texto para la identificación de ensayos clínicos en nanomedicina

La nanotecnología es el estudio que la mayoría de veces es tomada como una meta tecnológica que nos ayuda en el área de investigación para tratar con la manipulación y el control en forma precisa de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. Recordando que el prefijo nano proviene del griego vavoc que significa enano y corresponde a un factor de 10^-9, que aplicada a las unidades de longitud corresponde a una mil millonésima parte de un metro. Ahora sabemos que esta ciencia permite trabajar con estructuras moleculares y sus átomos, obteniendo materiales que exhiben fenómenos físicos, químicos y biológicos, muy distintos a los que manifiestan los materiales usados con una longitud mayor. Por ejemplo en medicina, los compuestos manométricos y los materiales nano estructurados muchas veces ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, ya que muchas veces llegan a combinar los antiguos compuestos con estos nuevos para crear nuevas terapias e inclusive han llegado a reemplazarlos, 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 y, por tanto, cualquier flujo de trabajo en nano medicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Muchos investigadores en la nanotecnología están buscando la manera de obtener información acerca de estos materiales nanométricos, para mejorar sus estudios que muchas veces lleva a probar estos métodos o crear nuevos compuestos para ayudar a la medicina actual, contra las enfermedades más poderosas como el cáncer. Pero en estos días es muy difícil encontrar una herramienta que les brinde la información específica que buscan en los miles de ensayos clínicos que se suben diariamente en la web. Actualmente, la informática biomédica trata de proporcionar el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, en este contexto, la nueva área de la nano informática 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. Otro caso en la actualidad es que muchos investigadores de biomedicina desean saber y comparar la información dentro de los ensayos clínicos que contiene temas de nanotecnología en las diferentes paginas en la web por todo el mundo, obteniendo en si ensayos clínicos que se han creado en Norte América, y ensayos clínicos que se han creado en Europa, y saber si en este tiempo este campo realmente está siendo explotado en los dos continentes. El problema es que no se ha creado una herramienta que estime un valor aproximado para saber los porcentajes del total de ensayos clínicos que se han creado en estas páginas web. En esta tesis de fin de máster, el autor utiliza un mejorado pre-procesamiento de texto y un algoritmo que fue determinado como el mejor procesamiento de texto en una tesis doctoral, que incluyo algunas pruebas con muchos de estos para obtener una estimación cercana que ayudaba a diferenciar cuando un ensayo clínico contiene información sobre nanotecnología y cuando no. En otras palabras aplicar un análisis de la literatura científica y de los registros de ensayos clínicos disponibles en los dos continentes para extraer información relevante sobre experimentos y resultados en nano medicina (patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.), seguido el mecanismo de procesamiento para estructurar y analizar dicha información automáticamente. Este análisis concluye con la estimación antes mencionada necesaria para comparar la cantidad de estudios sobre nanotecnología en estos dos continentes. Obviamente usamos un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento anotados manualmente—, y el conjunto de datos para el test es toda la base de datos de estos registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nano drogas, nano dispositivos y nano métodos de aquellos enfocados a testear productos farmacéuticos tradicionales.---ABSTRACT---Nanotechnology is the scientific study that usually is seen as a technological goal that helps us in the investigation field to deal with the manipulation and precise control of the matter with dimensions that range from 1 to 100 nanometers. Remembering that the prefix nano comes from the Greek word νᾶνος, meaning dwarf and denotes a factor of 10^-9, that applyied the longitude units is equal to a billionth of a meter. Now we know that this science allows us to work with molecular structures and their atoms, obtaining material that exhibit physical, chemical and biological phenomena very different to those manifesting in materials with a bigger longitude. As an example in medicine, the nanometric compounds and the materials in nano structures are often offered with more effectiveness regarding to the traditional chemical formulas. This is due to the fact that many occasions combining these old compounds with the new ones, creates new therapies and even replaced them, reveling new diagnostic and therapeutic properties. Even though the complexity of the information at nano level is greater than that in conventional biologic level and, thus, any work flow in nano medicine requires, in an inherent way, advance information management strategies. Many researchers in nanotechnology are looking for a way to obtain information about these nanometric materials to improve their studies that leads in many occasions to prove these methods or to create a new compound that helps modern medicine against powerful diseases, such as cancer. But in these days it is difficult to find a tool that searches and provides a specific information in the thousands of clinic essays that are uploaded daily on the web. Currently, the bio medic informatics tries to provide the work frame that will allow to deal with these information challenge in nano level. In this context, the new area of nano informatics pretends to detect and establish the existing links between medicine, nanotechnology and informatics, encouraging the usage of computational methods to resolve questions and problems that surge with the wide information intersection that is between biomedicine and nanotechnology. Another present case, is that many biomedicine researchers want to know and be able to compare the information inside those clinic essays that contains subjects of nanotechnology on the different webpages across the world, obtaining the clinic essays that has been done in North America and the essays done in Europe, and thus knowing if in this time, this field is really being exploited in both continents. In this master thesis, the author will use an enhanced text pre-processor with an algorithm that was defined as the best text processor in a doctoral thesis, that included many of these tests to obtain a close estimation that helps to differentiate when a clinic essay contains information about nanotechnology and when it does not. In other words, applying an analysis to the scientific literature and clinic essay available in both continents, in order to extract relevant information about experiments and the results in nano-medicine (textual patterns, common vocabulary, experiments descriptors, characterization parameters, etc.), followed by the mechanism process to structure and analyze said information automatically. This analysis concludes with the estimation, mentioned before, needed to compare the quantity of studies about nanotechnology in these two continents. Obviously we use a data reference model (Gold standard) – a set of training data manually annotated –, and the set of data for the test conforms the entire database of these clinic essay registers, allowing to distinguish automatically the studies centered on nano drugs, nano devices and nano methods of those focus on testing traditional pharmaceutical products.

Mining Abstractions in Scientific Workows

Los flujos de trabajo científicos han sido adoptados durante la última década para representar los métodos computacionales utilizados en experimentos in silico, así como para dar soporte a sus publicaciones asociadas. Dichos flujos de trabajo han demostrado ser útiles para compartir y reproducir experimentos científicos, permitiendo a investigadores visualizar, depurar y ahorrar tiempo a la hora de re-ejecutar un trabajo realizado con anterioridad. Sin embargo, los flujos de trabajo científicos pueden ser en ocasiones difíciles de entender y reutilizar. Esto es debido a impedimentos como el gran número de flujos de trabajo existentes en repositorios, su heterogeneidad o la falta generalizada de documentación y ejemplos de uso. Además, dado que normalmente es posible implementar un mismo método utilizando algoritmos o técnicas distintas, flujos de trabajo aparentemente distintos pueden estar relacionados a un determinado nivel de abstracción, basándose, por ejemplo, en su funcionalidad común. Esta tesis se centra en la reutilización de flujos de trabajo y su abstracción mediante la exploración de relaciones entre los flujos de trabajo de un repositorio y la extracción de abstracciones que podrían ayudar a la hora de reutilizar otros flujos de trabajo existentes. Para ello, se propone un modelo simple de representación de flujos de trabajo y sus ejecuciones, se analizan las abstracciones típicas que se pueden encontrar en los repositorios de flujos de trabajo, se exploran las prácticas habituales de los usuarios a la hora de reutilizar flujos de trabajo existentes y se describe un método para descubrir abstracciones útiles para usuarios, basadas en técnicas existentes de teoría de grafos. Los resultados obtenidos exponen las abstracciones y prácticas comunes de usuarios en términos de reutilización de flujos de trabajo, y muestran cómo las abstracciones que se extraen automáticamente tienen potencial para ser reutilizadas por usuarios que buscan diseñar nuevos flujos de trabajo. Abstract Scientific workflows have been adopted in the last decade to represent the computational methods used in in silico scientific experiments and their associated research products. Scientific workflows have demonstrated to be useful for sharing and reproducing scientific experiments, allowing scientists to visualize, debug and save time when re-executing previous work. However, scientific workflows may be difficult to understand and reuse. The large amount of available workflows in repositories, together with their heterogeneity and lack of documentation and usage examples may become an obstacle for a scientist aiming to reuse the work from other scientists. Furthermore, given that it is often possible to implement a method using different algorithms or techniques, seemingly disparate workflows may be related at a higher level of abstraction, based on their common functionality. In this thesis we address the issue of reusability and abstraction by exploring how workflows relate to one another in a workflow repository, mining abstractions that may be helpful for workflow reuse. In order to do so, we propose a simple model for representing and relating workflows and their executions, we analyze the typical common abstractions that can be found in workflow repositories, we explore the current practices of users regarding workflow reuse and we describe a method for discovering useful abstractions for workflows based on existing graph mining techniques. Our results expose the common abstractions and practices of users in terms of workflow reuse, and show how our proposed abstractions have potential to become useful for users designing new workflows.