Lithologic Control on the Scaling Properties of the First-Order Streams of Drainage Networks: A Monofractal Analysis

The movement of water through the landscape can be investigated at different scales. This study dealt with the interrelation between bedrock lithology and the geometry of the overlying drainage systems. Parameters of fractal analysis, such as fractal dimension and lacunarity, were used to measure and quantify this relationship. The interrelation between bedrock lithology and the geometry of the drainage systems has been widely studied in the last decades. The quantification of this linkage has not yet been clearly established. Several studies have selected river basins or regularly shaped areas as study units, assuming them to be lithologically homogeneous. This study considered irregular distributions of rock types, establishing areas of the soil map (1:25,000) with the same lithologic information as study units. The tectonic stability and the low climatic variability of the study region allowed effective investigation of the lithologic controls on the drainage networks developed on the plutonic rocks, the metamorphic rocks, and the sedimentary materials existing in the study area. To exclude the effect of multiple in- and outflows in the lithologically homogeneous units, we focused this study on the first-order streams of the drainage networks. The geometry of the hydrologic features was quantified through traditional metrics of fluvial geomorphology and scaling parameters of fractal analysis, such as the fractal dimension, the reference density, and the lacunarity. The results demonstrate the scale invariance of both the drainage networks and the set of first-order streams at the study scale and a relationship between scaling in the lithology and the drainage network.

Towards an abstract domain for resource analysis of logic programs using sized types

We present a novel general resource analysis for logic programs based on sized types.Sized types are representations that incorporate structural (shape) information and allow expressing both lower and upper bounds on the size of a set of terms and their subterms at any position and depth. They also allow relating the sizes of terms and subterms occurring at different argument positions in logic predicates. Using these sized types, the resource analysis can infer both lower and upper bounds on the resources used by all the procedures in a program as functions on input term (and subterm) sizes, overcoming limitations of existing analyses and enhancing their precision. Our new resource analysis has been developed within the abstract interpretation framework, as an extension of the sized types abstract domain, and has been integrated into the Ciao preprocessor, CiaoPP. The abstract domain operations are integrated with the setting up and solving of recurrence equations for both, inferring size and resource usage functions. We show that the analysis is an improvement over the previous resource analysis present in CiaoPP and compares well in power to state of the art systems.

Sized Type Analysis for Logic Programs (Technical Communication)

We present a novel analysis for relating the sizes of terms and subterms occurring at diferent argument positions in logic predicates. We extend and enrich the concept of sized type as a representation that incorporates structural (shape) information and allows expressing both lower and upper bounds on the size of a set of terms and their subterms at any position and depth. For example, expressing bounds on the length of lists of numbers, together with bounds on the values of all of their elements. The analysis is developed using abstract interpretation and the novel abstract operations are based on setting up and solving recurrence relations between sized types. It has been integrated, together with novel resource usage and cardinality analyses, in the abstract interpretation framework in the Ciao preprocessor, CiaoPP, in order to assess both the accuracy of the new size analysis and its usefulness in the resource usage estimation application. We show that the proposed sized types are a substantial improvement over the previous size analyses present in CiaoPP, and also benefit the resource analysis considerably, allowing the inference of equal or better bounds than comparable state of the art systems.

Resource usage analysis of logic programs via abstract interpretation using sized types

We present a novel general resource analysis for logic programs based on sized types. Sized types are representations that incorporate structural (shape) information and allow expressing both lower and upper bounds on the size of a set of terms and their subterms at any position and depth. They also allow relating the sizes of terms and subterms occurring at different argument positions in logic predicates. Using these sized types, the resource analysis can infer both lower and upper bounds on the resources used by all the procedures in a program as functions on input term (and subterm) sizes, overcoming limitations of existing resource analyses and enhancing their precision. Our new resource analysis has been developed within the abstract interpretation framework, as an extension of the sized types abstract domain, and has been integrated into the Ciao preprocessor, CiaoPP. The abstract domain operations are integrated with the setting up and solving of recurrence equations for inferring both size and resource usage functions. We show that the analysis is an improvement over the previous resource analysis present in CiaoPP and compares well in power to state of the art systems.

Non uniform embedding based on relevance analysis with reduced computational complexity: application to the detection of pathologies from biosignal recordings

Nonlinear analysis tools for studying and characterizing the dynamics of physiological signals have gained popularity, mainly because tracking sudden alterations of the inherent complexity of biological processes might be an indicator of altered physiological states. Typically, in order to perform an analysis with such tools, the physiological variables that describe the biological process under study are used to reconstruct the underlying dynamics of the biological processes. For that goal, a procedure called time-delay or uniform embedding is usually employed. Nonetheless, there is evidence of its inability for dealing with non-stationary signals, as those recorded from many physiological processes. To handle with such a drawback, this paper evaluates the utility of non-conventional time series reconstruction procedures based on non uniform embedding, applying them to automatic pattern recognition tasks. The paper compares a state of the art non uniform approach with a novel scheme which fuses embedding and feature selection at once, searching for better reconstructions of the dynamics of the system. Moreover, results are also compared with two classic uniform embedding techniques. Thus, the goal is comparing uniform and non uniform reconstruction techniques, including the one proposed in this work, for pattern recognition in biomedical signal processing tasks. Once the state space is reconstructed, the scheme followed characterizes with three classic nonlinear dynamic features (Largest Lyapunov Exponent, Correlation Dimension and Recurrence Period Density Entropy), while classification is carried out by means of a simple k-nn classifier. In order to test its generalization capabilities, the approach was tested with three different physiological databases (Speech Pathologies, Epilepsy and Heart Murmurs). In terms of the accuracy obtained to automatically detect the presence of pathologies, and for the three types of biosignals analyzed, the non uniform techniques used in this work lightly outperformed the results obtained using the uniform methods, suggesting their usefulness to characterize non-stationary biomedical signals in pattern recognition applications. On the other hand, in view of the results obtained and its low computational load, the proposed technique suggests its applicability for the applications under study.

Improved static analysis and verification of energy consumption and other resources via abstract interpretation

Resource analysis aims at inferring the cost of executing programs for any possible input, in terms of a given resource, such as the traditional execution steps, time ormemory, and, more recently energy consumption or user defined resources (e.g., number of bits sent over a socket, number of database accesses, number of calls to particular procedures, etc.). This is performed statically, i.e., without actually running the programs. Resource usage information is useful for a variety of optimization and verification applications, as well as for guiding software design. For example, programmers can use such information to choose different algorithmic solutions to a problem; program transformation systems can use cost information to choose between alternative transformations; parallelizing compilers can use cost estimates for granularity control, which tries to balance the overheads of task creation and manipulation against the benefits of parallelization. In this thesis we have significatively improved an existing prototype implementation for resource usage analysis based on abstract interpretation, addressing a number of relevant challenges and overcoming many limitations it presented. The goal of that prototype was to show the viability of casting the resource analysis as an abstract domain, and howit could overcome important limitations of the state-of-the-art resource usage analysis tools. For this purpose, it was implemented as an abstract domain in the abstract interpretation framework of the CiaoPP system, PLAI.We have improved both the design and implementation of the prototype, for eventually allowing an evolution of the tool to the industrial application level. The abstract operations of such tool heavily depend on the setting up and finding closed-form solutions of recurrence relations representing the resource usage behavior of program components and the whole program as well. While there exist many tools, such as Computer Algebra Systems (CAS) and libraries able to find closed-form solutions for some types of recurrences, none of them alone is able to handle all the types of recurrences arising during program analysis. In addition, there are some types of recurrences that cannot be solved by any existing tool. This clearly constitutes a bottleneck for this kind of resource usage analysis. Thus, one of the major challenges we have addressed in this thesis is the design and development of a novel modular framework for solving recurrence relations, able to combine and take advantage of the results of existing solvers. Additionally, we have developed and integrated into our novel solver a technique for finding upper-bound closed-form solutions of a special class of recurrence relations that arise during the analysis of programs with accumulating parameters. Finally, we have integrated the improved resource analysis into the CiaoPP general framework for resource usage verification, and specialized the framework for verifying energy consumption specifications of embedded imperative programs in a real application, showing the usefulness and practicality of the resulting tool.---ABSTRACT---El Análisis de recursos tiene como objetivo inferir el coste de la ejecución de programas para cualquier entrada posible, en términos de algún recurso determinado, como pasos de ejecución, tiempo o memoria, y, más recientemente, el consumo de energía o recursos definidos por el usuario (por ejemplo, número de bits enviados a través de un socket, el número de accesos a una base de datos, cantidad de llamadas a determinados procedimientos, etc.). Ello se realiza estáticamente, es decir, sin necesidad de ejecutar los programas. La información sobre el uso de recursos resulta muy útil para una gran variedad de aplicaciones de optimización y verificación de programas, así como para asistir en el diseño de los mismos. Por ejemplo, los programadores pueden utilizar dicha información para elegir diferentes soluciones algorítmicas a un problema; los sistemas de transformación de programas pueden utilizar la información de coste para elegir entre transformaciones alternativas; los compiladores paralelizantes pueden utilizar las estimaciones de coste para realizar control de granularidad, el cual trata de equilibrar el coste debido a la creación y gestión de tareas, con los beneficios de la paralelización. En esta tesis hemos mejorado de manera significativa la implementación de un prototipo existente para el análisis del uso de recursos basado en interpretación abstracta, abordando diversos desafíos relevantes y superando numerosas limitaciones que éste presentaba. El objetivo de dicho prototipo era mostrar la viabilidad de definir el análisis de recursos como un dominio abstracto, y cómo se podían superar las limitaciones de otras herramientas similares que constituyen el estado del arte. Para ello, se implementó como un dominio abstracto en el marco de interpretación abstracta presente en el sistema CiaoPP, PLAI. Hemos mejorado tanto el diseño como la implementación del mencionado prototipo para posibilitar su evolución hacia una herramienta utilizable en el ámbito industrial. Las operaciones abstractas de dicha herramienta dependen en gran medida de la generación, y posterior búsqueda de soluciones en forma cerrada, de relaciones recurrentes, las cuales modelizan el comportamiento, respecto al consumo de recursos, de los componentes del programa y del programa completo. Si bien existen actualmente muchas herramientas capaces de encontrar soluciones en forma cerrada para ciertos tipos de recurrencias, tales como Sistemas de Computación Algebraicos (CAS) y librerías de programación, ninguna de dichas herramientas es capaz de tratar, por sí sola, todos los tipos de recurrencias que surgen durante el análisis de recursos. Existen incluso recurrencias que no las puede resolver ninguna herramienta actual. Esto constituye claramente un cuello de botella para este tipo de análisis del uso de recursos. Por lo tanto, uno de los principales desafíos que hemos abordado en esta tesis es el diseño y desarrollo de un novedoso marco modular para la resolución de relaciones recurrentes, combinando y aprovechando los resultados de resolutores existentes. Además de ello, hemos desarrollado e integrado en nuestro nuevo resolutor una técnica para la obtención de cotas superiores en forma cerrada de una clase característica de relaciones recurrentes que surgen durante el análisis de programas lógicos con parámetros de acumulación. Finalmente, hemos integrado el nuevo análisis de recursos con el marco general para verificación de recursos de CiaoPP, y hemos instanciado dicho marco para la verificación de especificaciones sobre el consumo de energía de programas imperativas embarcados, mostrando la viabilidad y utilidad de la herramienta resultante en una aplicación real.

Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

A Comparative Analysis of Hedging in a Corpus of Two Written Legal Discourse Genres

Esta tesis doctoral, que es la culminación de mis estudios de doctorado impartidos por el Departamento de Lingüística Aplicada a la Ciencia y a la Tecnología de la Universidad Politécnica de Madrid, aborda el análisis del uso de la matización (hedging) en el lenguaje legal inglés siguiendo los postulados y principios de la análisis crítica de género (Bhatia, 2004) y empleando las herramientas de análisis de córpora WordSmith Tools versión 6 (Scott, 2014). Como refleja el título, el estudio se centra en la descripción y en el análisis contrastivo de las variedades léxico-sintácticas de los matizadores del discurso (hedges) y las estrategias discursivas que con ellos se llevan a cabo, además de las funciones que éstas desempeñan en un corpus de sentencias del Tribunal Supremo de EE. UU., y de artículos jurídicos de investigación americanos, relacionando, en la medida posible, éstas con los rasgos determinantes de los dos géneros, desde una perspectiva socio-cognitiva. El elemento innovador que ofrece es que, a pesar de los numerosos estudios que se han podido realizar sobre los matizadores del discurso en el inglés general (Lakoff, 1973; Hübler, 1983; Clemen, 1997; Markkanen and Schröder, 1997; Mauranen, 1997; Fetzer 2010; y Finnegan, 2010 entre otros) académico (Crompton, 1997; Meyer, 1997; Skelton, 1997; Martín Butragueňo, 2003) científico (Hyland, 1996a, 1996c, 1998c, 2007; Grabe and Kaplan, 1997; Salager-Meyer, 1997 Varttala, 2001) médico (Prince, 1982; Salager-Meyer, 1994; Skelton, 1997), y, en menor medida el inglés legal (Toska, 2012), no existe ningún tipo de investigación que vincule los distintos usos de la matización a las características genéricas de las comunicaciones profesionales. Dentro del lenguaje legal, la matización confirma su dependencia tanto de las expectativas a macro-nivel de la comunidad de discurso, como de las intenciones a micro-nivel del escritor de la comunicación, variando en función de los propósitos comunicativos del género ya sean éstos educativos, pedagógicos, interpersonales u operativos. El estudio pone de relieve el uso predominante de los verbos modales epistémicos y de los verbos léxicos como matizadores del discurso, estos últimos divididos en cuatro tipos (Hyland 1998c; Palmer 1986, 1990, 2001) especulativos, citativos, deductivos y sensoriales. La realización léxico-sintáctica del matizador puede señalar una de cuatro estrategias discursivas particulares (Namsaraev, 1997; Salager-Meyer, 1994), la indeterminación, la despersonalización, la subjectivisación, o la matización camuflada (camouflage hedging), cuya incidencia y función varia según género. La identificación y cuantificación de los distintos matizadores y estrategias empleados en los diferentes géneros del discurso legal puede tener implicaciones pedagógicos para los estudiantes de derecho no nativos que tienen que demostrar una competencia adecuada en su uso y procesamiento. ABSTRACT This doctoral thesis, which represents the culmination of my doctoral studies undertaken in the Department of Linguistics Applied to Science and Technology of the Universidad Politécnica de Madrid, focusses on the analysis of hedging in legal English following the principles of Critical Genre Analysis (Bhatia, 2004), and using WordSmith Tools version 6 (Scott, 2014) corpus analysis tools. As the title suggests, this study centers on the description and contrastive analysis of lexico-grammatical realizations of hedges and the discourse strategies which they can indicate, as well as the functions they can carry out, in a corpus of U.S. Supreme Court opinions and American law review articles. The study relates realization, incidence and function of hedging to the predominant generic characteristics of the two genres from a socio-cognitive perspective. While there have been numerous studies on hedging in general English (Lakoff, 1973; Hübler, 1983; Clemen, 1997; Markkanen and Schröder, 1997; Mauranen, 1997; Fetzer 2010; and Finnegan, 2010 among others) academic English (Crompton, 1997; Meyer, 1997; Skelton, 1997; Martín Butragueňo, 2003) scientific English (Hyland, 1996a, 1996c, 1998c, 2007; Grabe and Kaplan, 1997; Salager-Meyer, 1997 Varttala, 2001) medical English (Prince, 1982; Salager-Meyer, 1994; Skelton, 1997), and, to a lesser degree, legal English (Toska, 2012), this study is innovative in that it links the different realizations and functions of hedging to the generic characteristics of a particular professional communication. Within legal English, hedging has been found to depend on not only the macro-level expectations of the discourse community for a specific genre, but also on the micro-level intentions of the author of a communication, varying according to the educational, pedagogical, interpersonal or operative purposes the genre may have. The study highlights the predominance of epistemic modal verbs and lexical verbs as hedges, dividing the latter into four types (Hyland, 1998c; Palmer, 1986, 1990, 2001): speculative, quotative, deductive and sensorial. Lexical-grammatical realizations of hedges can signal one of four discourse strategies (Namsaraev, 1997; Salager-Meyer, 1994), indetermination, depersonalization, subjectivization and camouflage hedging, as well as fulfill a variety of functions. The identification and quantification of the different hedges and hedging strategies and functions in the two genres may have pedagogical implications for non-native law students who must demonstrate adequate competence in the production and interpretation of hedged discourse.

A methodology to estimate uncertainty for emission projections through sensitivity analysis

Air pollution abatement policies must be based on quantitative information on current and future emissions of pollutants. As emission projections uncertainties are inevitable and traditional statistical treatments of uncertainty are highly time/resources consuming, a simplified methodology for nonstatistical uncertainty estimation based on sensitivity analysis is presented in this work. The methodology was applied to the “with measures” scenario for Spain, concretely over the 12 highest emitting sectors regarding greenhouse gas and air pollutants emissions. Examples of methodology application for two important sectors (power plants, and agriculture and livestock) are shown and explained in depth. Uncertainty bands were obtained up to 2020 by modifying the driving factors of the 12 selected sectors and the methodology was tested against a recomputed emission trend in a low economic-growth perspective and official figures for 2010, showing a very good performance. Implications: A solid understanding and quantification of uncertainties related to atmospheric emission inventories and projections provide useful information for policy negotiations. However, as many of those uncertainties are irreducible, there is an interest on how they could be managed in order to derive robust policy conclusions. Taking this into account, a method developed to use sensitivity analysis as a source of information to derive nonstatistical uncertainty bands for emission projections is presented and applied to Spain. This method simplifies uncertainty assessment and allows other countries to take advantage of their sensitivity analyses.

RNA analysis by ion-pair reversed-phase high performance liquid chromatography

Ion-pair reversed-phase high performance liquid chromatography (IP RP HPLC) is presented as a new, superior method for the analysis of RNA. IP RP HPLC provides a fast and reliable alternative to classical methods of RNA analysis, including separation of different RNA species, quantification and purification. RNA is stable under the analysis conditions used; degradation of RNA during the analyses was not observed. The versatility of IP RP HPLC for RNA analysis is demonstrated. Components of an RNA ladder, ranging in size from 155 to 1770 nt, were resolved. RNA transcripts of up to 5219 nt were analyzed, their integrity determined and they were quantified and purified. Purification of mRNA from total RNA is described, separating mouse rRNA from poly(A)+ mRNA. IP RP HPLC is also suitable for the separation and purification of DIG-labeled from unlabeled RNA. RNA purified by IP RP HPLC exhibits improved stability.

Do socioeconomic inequalities in mortality vary between different Spanish cities? a pooled cross-sectional analysis

Background: The relationship between deprivation and mortality in urban settings is well established. This relationship has been found for several causes of death in Spanish cities in independent analyses (the MEDEA project). However, no joint analysis which pools the strength of this relationship across several cities has ever been undertaken. Such an analysis would determine, if appropriate, a joint relationship by linking the associations found. Methods: A pooled cross-sectional analysis of the data from the MEDEA project has been carried out for each of the causes of death studied. Specifically, a meta-analysis has been carried out to pool the relative risks in eleven Spanish cities. Different deprivation-mortality relationships across the cities are considered in the analysis (fixed and random effects models). The size of the cities is also considered as a possible factor explaining differences between cities. Results: Twenty studies have been carried out for different combinations of sex and causes of death. For nine of them (men: prostate cancer, diabetes, mental illnesses, Alzheimer’s disease, cerebrovascular disease; women: diabetes, mental illnesses, respiratory diseases, cirrhosis) no differences were found between cities in the effect of deprivation on mortality; in four cases (men: respiratory diseases, all causes of mortality; women: breast cancer, Alzheimer’s disease) differences not associated with the size of the city have been determined; in two cases (men: cirrhosis; women: lung cancer) differences strictly linked to the size of the city have been determined, and in five cases (men: lung cancer, ischaemic heart disease; women: ischaemic heart disease, cerebrovascular diseases, all causes of mortality) both kinds of differences have been found. Except for lung cancer in women, every significant relationship between deprivation and mortality goes in the same direction: deprivation increases mortality. Variability in the relative risks across cities was found for general mortality for both sexes. Conclusions: This study provides a general overview of the relationship between deprivation and mortality for a sample of large Spanish cities combined. This joint study allows the exploration of and, if appropriate, the quantification of the variability in that relationship for the set of cities considered.

Blood markers and recurrence of stroke in patients with transient ischemic attack

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Macroeconomic Scenarios for the Euro-Mediterranean Area Quantification based on the GEM-E3 Model. MEDPRO Report No. 7, July 2013

Four alternative macroeconomic scenarios for southern Mediterranean countries are quantified in this study with the use of GEM-E3, a general equilibrium model. These are i) the continuation of current policies (business-as-usual scenario), ii) southern Mediterranean–EU cooperation (Euro-Mediterranean Union scenario), iii) a global opening of the southern Mediterranean countries and cooperation with the rest of the Middle East and other developing countries like China (Euro-Mediterranean alliance scenario), and iv) a deterioration in the regional political climate and a failure of cooperation (Euro-Mediterranean under threat scenario). Explicit assumptions on trade integration, infrastructure upgrade, population and governance developments are adopted in each scenario. The simulation results indicate that an infrastructure upgrade and governance improvements in the context of southern Mediterranean–EU cooperation could benefit most of the countries under consideration. The analysis remains important in light of ongoing regional developments and the need to design the best policies to pursue in the aftermath of the Arab spring.

Analysis of Protein Turnover by Quantitative SNAP-Based Pulse-Chase Imaging

Assessment of protein dynamics in living cells is crucial for understanding their biological properties and functions. The SNAP-tag, a self labeling suicide enzyme, presents a tool with unique features that can be adopted for determining protein dynamics in living cells. Here we present detailed protocols for the use of SNAP in fluorescent pulse-chase and quench-chase-pulse experiments. These time-slicing methods provide powerful tools to assay and quantify the fate and turnover rate of proteins of different ages. We cover advantages and pitfalls of SNAP-tagging in fixed- and live-cell studies and evaluate the recently developed fast-acting SNAPf variant. In addition, to facilitate the analysis of protein turnover datasets, we present an automated algorithm for spot recognition and quantification.

Predictors of Nasal Obstruction: Quantification and Assessment Using Multiple Grading Scales

Objective. To evaluate the association between nasal obstruction and (1) demographic factors, (2) medical history, (3) physical tests, and (4) nasal exam findings. Study Design. CASE SERIES: Methods. Chart review at a tertiary medical center. Results. Two hundred-forty consecutive patients (52.1 ± 17.5 years old, with a Nasal Obstruction Symptom Evaluation (NOSE) score of 32.0 ± 24.1) were included. Demographic factors and inferior turbinate sizes were not associated with NOSE score or Nasal Obstruction Visual Analog Scale (NO-VAS). A significant association was found between higher NOSE score on univariate analysis and positive history of nasal trauma (p = 0.0136), allergic rhinitis (p < 0.0001), use of nasal steroids (p = 0.0108), higher grade of external nasal deformity (p = 0.0149), higher internal nasal septal deviation grade (p = 0.0024), and narrow internal nasal valve angle (p < 0.0001). Multivariate analysis identified the following as independent predictors of high NOSE score: NO-VAS: ≥50 (Odds Ratio (OR) = 17.6 (95% CI 5.83-61.6), p < 0.0001), external nasal deformity: grades 2-4 (OR = 4.63 (95% CI 1.14-19.9), p = 0.0339), and allergic rhinitis: yes (OR = 5.5 (95% CI 1.77-18.7), p = 0.0041). Conclusion. Allergic rhinitis, NO-VAS score ≥ 50, and external nasal deformity (grades 2-4) were statistically significant independent predictors of high NOSE scores on multivariate analysis. Inferior turbinate size was not associated with NOSE scores or NO-VAS.