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.

Arsenic speciation in edible alga samples by microwave-assisted extraction and high performance liquid chromatography coupled to atomic fluorescence spectrometry

Twelve commercially available edible marine algae from France, Japan and Spain and the certified reference material (CRM) NIES No. 9 Sargassum fulvellum were analyzed for total arsenic and arsenic species. Total arsenic concentrations were determined by inductively coupled plasma atomic emission spectrometry (ICP-AES) after microwave digestion and ranged from 23 to 126 μg g−1. Arsenic species in alga samples were extracted with deionized water by microwave-assisted extraction and showed extraction efficiencies from 49 to 98%, in terms of total arsenic. The presence of eleven arsenic species was studied by high performance liquid chromatography–ultraviolet photo-oxidation–hydride generation atomic–fluorescence spectrometry (HPLC–(UV)–HG–AFS) developed methods, using both anion and cation exchange chromatography. Glycerol and phosphate sugars were found in all alga samples analyzed, at concentrations between 0.11 and 22 μg g−1, whereas sulfonate and sulfate sugars were only detected in three of them (0.6-7.2 μg g−1). Regarding arsenic toxic species, low concentration levels of dimethylarsinic acid (DMA) (<0.9 μg g−1) and generally high arsenate (As(V)) concentrations (up to 77 μg g−1) were found in most of the algae studied. The results obtained are of interest to highlight the need to perform speciation analysis and to introduce appropriate legislation to limit toxic arsenic species content in these food products.

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.

Determination of selected pharmaceutical compounds in biosolids bysupported liquid extraction and gas chromatography?tandem massspectrometry

In this work, an analytical method was developed for the determination of pharmaceutical drugs inbiosolids. Samples were extracted with an acidic mixture of water and acetone (1:2, v/v) and supportedliquid extraction was used for the clean-up of extracts, eluting with ethyl acetate:methanol (90:10, v/v).The compounds were determined by gas chromatography?tandem mass spectrometry using matrix-match calibration after silylation to form their t-butyldimethylsilyl derivatives. This method presentsvarious advantages, such as a fairly simple operation for the analysis of complex matrices, the use ofinexpensive glassware and low solvent volumes. Satisfactory mean recoveries were obtained with thedeveloped method ranging from 70 to 120% with relative standard deviations (RSDs) ? 13%, and limitsof detection between 0.5 and 3.6 ng g?1. The method was then successfully applied to biosolids samplescollected in Madrid and Catalonia (Spain). Eleven of the sixteen target compounds were detected in thestudied samples, at levels up to 1.1 ?g g?1(salicylic acid). Ibuprofen, caffeine, paracetamol and fenofibratewere detected in all of the samples analyzed.

Facing the climate change challenges in the mining and mineral industry as providers of a sustainable manufacturing process

A sustainable manufacturing process must rely on an also sustainable raw materials and energy supply. This paper is intended to show the results of the studies developed on sustainable business models for the minerals industry as a fundamental previous part of a sustainable manufacturing process. As it has happened in other economic activities, the mining and minerals industry has come under tremendous pressure to improve its social, developmental, and environmental performance. Mining, refining, and the use and disposal of minerals have in some instances led to significant local environmental and social damage. Nowadays, like in other parts of the corporate world, companies are more routinely expected to perform to ever higher standards of behavior, going well beyond achieving the best rate of return for shareholders. They are also increasingly being asked to be more transparent and subject to third-party audit or review, especially in environmental aspects. In terms of environment, there are three inter-related areas where innovation and new business models can make the biggest difference: carbon, water and biodiversity. The focus in these three areas is for two reasons. First, the industrial and energetic minerals industry has significant footprints in each of these areas. Second, these three areas are where the potential environmental impacts go beyond local stakeholders and communities, and can even have global impacts, like in the case of carbon. So prioritizing efforts in these areas will ultimately be a strategic differentiator as the industry businesses continues to grow. Over the next forty years, world?s population is predicted to rise from 6.300 million to 9.500 million people. This will mean a huge demand of natural resources. Indeed, consumption rates are such that current demand for raw materials will probably soon exceed the planet?s capacity. As awareness of the actual situation grows, the public is demanding goods and services that are even more environmentally sustainable. This means that massive efforts are required to reduce the amount of materials we use, including freshwater, minerals and oil, biodiversity, and marine resources. It?s clear that business as usual is no longer possible. Today, companies face not only the economic fallout of the financial crisis; they face the substantial challenge of transitioning to a low-carbon economy that is constrained by dwindling natural resources easily accessible. Innovative business models offer pioneering companies an early start toward the future. They can signal to consumers how to make sustainable choices and provide reward for both the consumer and the shareholder. Climate change and carbon remain major risk discontinuities that we need to better understand and deal with. In the absence of a global carbon solution, the principal objective of any individual country should be to reduce its global carbon emissions by encouraging conservation. The mineral industry internal response is to continue to focus on reducing the energy intensity of our existing operations through energy efficiency and the progressive introduction of new technology. Planning of the new projects must ensure that their energy footprint is minimal from the start. These actions will increase the long term resilience of the business to uncertain energy and carbon markets. This focus, combined with a strong demand for skills in this strategic area for the future requires an appropriate change in initial and continuing training of engineers and technicians and their awareness of the issue of eco-design. It will also need the development of measurement tools for consistent comparisons between companies and the assessments integration of the carbon footprint of mining equipments and services in a comprehensive impact study on the sustainable development of the Economy.

Adapting autonomously classification data mining algorithms for ubiquitous devices

Abstract Due to recent scientific and technological advances in information sys¬tems, it is now possible to perform almost every application on a mobile device. The need to make sense of such devices more intelligent opens an opportunity to design data mining algorithm that are able to autonomous execute in local devices to provide the device with knowledge. The problem behind autonomous mining deals with the proper configuration of the algorithm to produce the most appropriate results. Contextual information together with resource information of the device have a strong impact on both the feasibility of a particu¬lar execution and on the production of the proper patterns. On the other hand, performance of the algorithm expressed in terms of efficacy and efficiency highly depends on the features of the dataset to be analyzed together with values of the parameters of a particular implementation of an algorithm. However, few existing approaches deal with autonomous configuration of data mining algorithms and in any case they do not deal with contextual or resources information. Both issues are of particular significance, in particular for social net¬works application. In fact, the widespread use of social networks and consequently the amount of information shared have made the need of modeling context in social application a priority. Also the resource consumption has a crucial role in such platforms as the users are using social networks mainly on their mobile devices. This PhD thesis addresses the aforementioned open issues, focusing on i) Analyzing the behavior of algorithms, ii) mapping contextual and resources information to find the most appropriate configuration iii) applying the model for the case of a social recommender. Four main contributions are presented: - The EE-Model: is able to predict the behavior of a data mining algorithm in terms of resource consumed and accuracy of the mining model it will obtain. - The SC-Mapper: maps a situation defined by the context and resource state to a data mining configuration. - SOMAR: is a social activity (event and informal ongoings) recommender for mobile devices. - D-SOMAR: is an evolution of SOMAR which incorporates the configurator in order to provide updated recommendations. Finally, the experimental validation of the proposed contributions using synthetic and real datasets allows us to achieve the objectives and answer the research questions proposed for this dissertation.

Enhancing web-based learning resources with quizzes through an Authoring Tool and an Audience Response System

Quizzes are among the most widely used resources in web-based education due to their many benefits. However, educators need suitable authoring tools that can be used to create reusable quizzes and to enhance existing materials with them. On the other hand, if teachers use Audience Response Systems (ARSs) they can get instant feedback from their students and thereby enhance their instruction. This paper presents an online authoring tool for creating reusable quizzes and enhancing existing learning resources with them, and a web-based ARS that enables teachers to launch the created quizzes and get instant feedback from the class. Both the authoring tool and the ARS were evaluated. The evaluation of the authoring tool showed that educators can effectively enhance existing learning resources in an easy way by creating and adding quizzes using that tool. Besides, the different factors that assure the reusability of the created quizzes are also exposed. Finally, the evaluation of the developed ARS showed an excellent acceptance of the system by teachers and students, and also it indicated that teachers found the system easy to set up and use in their classrooms.

Aprovechamiento térmico de residuos estériles de carbón para generación eléctrica mediante tecnologías de combustión y gasificación eficientes y con mínimo impacto ambiental

La presente tesis doctoral, “Aprovechamiento térmico de residuos estériles de carbón para generación eléctrica mediante tecnologías de combustión y gasificación eficientes y con mínimo impacto ambiental”, desarrolla la valorización energética de los residuos del carbón, estériles de carbón, producidos durante las etapas de extracción y lavado del carbón. El sistema energético se encuentra en una encrucijada, estamos asistiendo a un cambio en el paradigma energético y, en concreto, en el sector de la generación eléctrica. Se precipita un cambio en la generación y el consumo eléctricos. Una mayor concienciación por la salud está forzando la contención y eliminación de agentes contaminantes que se generan por la utilización de combustibles fósiles de la forma en la que se viene haciendo. Aumenta la preocupación por el cambio climático y por contener en 2°C el aumento de la temperatura de la Tierra para final de este siglo, circunstancia que está impulsando el desarrollo e implantación definitiva de tecnología de control y reducción de emisiones CO2. Generar electricidad de una manera sostenible se está convirtiendo en una obligación. Esto se materializa en generar electricidad respetando el medioambiente, de una forma eficiente en la utilización de los recursos naturales y a un coste competitivo, pensando en el desarrollo de la sociedad y en el beneficio de las personas. En la actualidad, el carbón es la principal fuente de energía utilizada para generar electricidad, y su empleo presenta la forma de energía más barata para mejorar el nivel de vida de cualquier grupo y sociedad. Además, se espera que el carbón siga presente en el mix de generación eléctrica, manteniendo una significativa presencia y extrayéndose en elevadas cantidades. Pero la producción de carbón lleva asociada la generación de un residuo, estéril, que se produce durante la extracción y el lavado del mineral de carbón. Durante décadas se ha estudiado la posibilidad de utilizar el estéril y actualmente se utiliza, en un limitado porcentaje, en la construcción de carreteras, terraplenes y rellenos, y en la producción de algunos materiales de construcción. Esta tesis doctoral aborda la valorización energética del estéril, y analiza el potencial aprovechamiento del residuo para generar electricidad, en una instalación que integre tecnología disponible para minimizar el impacto medioambiental. Además, persigue aprovechar el significativo contenido en azufre que presenta el estéril para producir ácido sulfúrico (H2SO4) como subproducto de la instalación, un compuesto químico muy demandado por la industria de los fertilizantes y con multitud de aplicaciones en otros mercados. Se ha realizado el análisis de caracterización del estéril, los parámetros significativos y los valores de referencia para su empleo como combustible, encontrándose que su empleo como combustible para generar electricidad es posible. Aunque en España se lleva extrayendo carbón desde principios del siglo XVIII, se ha evaluado para un período más reciente la disponibilidad del recurso en España y la normativa existente que condiciona su aplicación en el territorio nacional. Para el período evaluado, se ha calculado que podrían estar disponibles más de 68 millones de toneladas de estéril susceptibles de ser valorizados energéticamente. Una vez realizado el análisis de la tecnología disponible y que podría considerarse para emplear el estéril como combustible, se proponen cuatro configuraciones posibles de planta, tres de ellas basadas en un proceso de combustión y una de ellas en un proceso de gasificación. Tras evaluar las cuatro configuraciones por su interés tecnológico, innovador y económico, se desarrolla el análisis conceptual de una de ellas, basada en un proceso de combustión. La instalación propuesta tiene una capacidad de 65 MW y emplea como combustible una mezcla de carbón y estéril en relación 20/80 en peso. La instalación integra tecnología para eliminar en un 99,8% el SO2 presente en el gas de combustión y en más de un 99% las partículas generadas. La instalación incorpora una unidad de producción de H2SO4, capaz de producir 18,5 t/h de producto, y otra unidad de captura para retirar un 60% del CO2 presente en la corriente de gases de combustión, produciendo 48 tCO2/h. La potencia neta de la planta es 49,7 MW. Se ha calculado el coste de inversión de la instalación, y su cálculo resulta en un coste de inversión unitario de 3.685 €/kW. ABSTRACT The present doctoral thesis, “Thermal utilisation of waste coal for electricity generation by deployment of efficient combustion and gasification technologies with minimum environmental impact”, develops an innovative waste-to-energy concept of waste coals produced during coal mining and washing. The energy system is at a dilemma, we are witnessing a shift in the energy paradigm and specifically in the field of electricity generation. A change in the generation and electrical consumption is foreseen. An increased health consciousness is forcing the containment and elimination of pollutants that are generated by the use of fossil fuels in the way that is being done. Increasing concern about climate change and to contain the rise of global temperature by 2°C by the end of this century, is promoting the development and final implementation of technology to control and reduce the CO2 emission. Electricity generation in a sustainable manner is becoming an obligation. This concept materialised in generating electricity while protecting the environment and deployment of natural resources at a competitive cost, considering the development of society and people´s benefit. Currently, coal is the main source of energy employ to generate electricity, and its use represents the most cost competitive form of energy to increase the standard of living of any group or society. Moreover, coal will keep playing a key role in the global electricity generation mix, maintaining a significant presence and being extracting in large amounts. However, coal production implies the production of waste, termed waste coal or culm in Pennsylvania anthracite extraction, produced during coal mining and coal washing activities. During the last decades, the potential use of waste coal has been studied, and currently, in a limited amount, waste coal is used in roads construction, embankments and fillings, and to produce some construction materials. This doctoral thesis evaluates the waste to energy of waste coals and assesses its potential use to generate electricity, implementing available technology to minimise the environment impact. Additionally, it pursues the significant advantage that presents sulphur content in waste coal to produce sulphuric acid (H2SO4) as a byproduct of the waste-to-energy process, a chemical compound highly demanded by the fertiliser industry and many applications in other markets. It analyses the characteristics of waste coal, and assesses the significant parameters and reference values for its use as fuel, being its fuel use for electricity generation very possible. While mining coal is taking place in Spain since the 1700s, it has been evaluated for a more recent period the waste coal available in Spain and the existing legislation that affects its application and deploy to generate electricity in the country. For the evaluation period has been calculated that may be available more than 68 million tons of waste coal that can be waste-toenergy. The potential available technology to deploy waste coal as fuel has been evaluated and assessed. After considering this, the doctoral thesis proposes four innovative alternatives of facility configuration, three of them based on a combustion process and one in a gasification process. After evaluating the four configurations for its technological, innovative and economic interest, the conceptual analysis of one of alternatives, based on a combustion process, takes place. The proposed alternative facility developed has a capacity of 65 MW, using as fuel a mixture of coal and waste coal 80/20 by weight. The facility comprises technology to remove 99.8% SO2 present in the flue gas and more than 99% of the particles. The facility includes a unit capable of producing 18.5 t/h of H2SO4, and another capture facility, removing 60% of CO2 present in the flue gas stream, producing 48 tCO2/h. The net capacity of the power station is 49.7 MW. The facility unitary cost of investment is 3,685 €/kW.