Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners

1. The spatial distribution of individual plants within a population and the population’s genetic structure are determined by several factors, like dispersal, reproduction mode or biotic interactions. The role of interspecific interactions in shaping the spatial genetic structure of plant populations remains largely unknown. 2. Species with a common evolutionary history are known to interact more closely with each other than unrelated species due to the greater number of traits they share. We hypothesize that plant interactions may shape the fine genetic structure of closely related congeners. 3. We used spatial statistics (georeferenced design) and molecular techniques (ISSR markers) to understand how two closely related congeners, Thymus vulgaris (widespread species) and T. loscosii (narrow endemic) interact at the local scale. Specific cover, number of individuals of both study species and several community attributes were measured in a 10 × 10 m plot. 4. Both species showed similar levels of genetic variation, but differed in their spatial genetic structure. Thymus vulgaris showed spatial aggregation but no spatial genetic structure, while T. loscosii showed spatial genetic structure (positive genetic autocorrelation) at short distances. The spatial pattern of T. vulgaris’ cover showed significant dissociation with that of T. loscosii. The same was true between the spatial patterns of the cover of T. vulgaris and the abundance of T. loscosii and between the abundance of each species. Most importantly, we found a correlation between the genetic structure of T. loscosii and the abundance of T. vulgaris: T. loscosii plants were genetically more similar when they were surrounded by a similar number of T. vulgaris plants. 5. Synthesis. Our results reveal spatially complex genetic structures of both congeners at small spatial scales. The negative association among the spatial patterns of the two species and the genetic structure found for T. loscosii in relation to the abundance of T. vulgaris indicate that competition between the two species may account for the presence of adapted ecotypes of T. loscosii to the abundance of a competing congeneric species. This suggests that the presence and abundance of close congeners can influence the genetic spatial structure of plant species at fine scales.

Oscillatory genetic circuits: new designs and mathematical models

Introduction and motivation: A wide variety of organisms have developed in-ternal biomolecular clocks in order to adapt to cyclic changes of the environment. Clock operation involves genetic networks. These genetic networks have to be mod¬eled in order to understand the underlying mechanism of oscillations and to design new synthetic cellular clocks. This doctoral thesis has resulted in two contributions to the fields of genetic clocks and systems and synthetic biology, generally. The first contribution is a new genetic circuit model that exhibits an oscillatory behav¬ior through catalytic RNA molecules. The second and major contribution is a new genetic circuit model demonstrating that a repressor molecule acting on the positive feedback of a self-activating gene produces reliable oscillations. First contribution: A new model of a synthetic genetic oscillator based on a typical two-gene motif with one positive and one negative feedback loop is pre¬sented. The originality is that the repressor is a catalytic RNA molecule rather than a protein or a non-catalytic RNA molecule. This catalytic RNA is a ribozyme that acts post-transcriptionally by binding to and cleaving target mRNA molecules. This genetic clock involves just two genes, a mRNA and an activator protein, apart from the ribozyme. Parameter values that produce a circadian period in both determin¬istic and stochastic simulations have been chosen as an example of clock operation. The effects of the stochastic fluctuations are quantified by a period histogram and autocorrelation function. The conclusion is that catalytic RNA molecules can act as repressor proteins and simplify the design of genetic oscillators. Second and major contribution: It is demonstrated that a self-activating gene in conjunction with a simple negative interaction can easily produce robust matically validated. This model is comprised of two clearly distinct parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the oscillator dynamics are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this study is that a simple and usual negative interaction, such as degradation, se¬questration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. At the genetic level, this means that an explicit negative feedback loop is not necessary. Unlike many genetic oscillators, this model needs neither cooperative binding reactions nor the formation of protein multimers. Applications and future research directions: Recently, RNA molecules have been found to play many new catalytic roles. The first oscillatory genetic model proposed in this thesis uses ribozymes as repressor molecules. This could provide new synthetic biology design principles and a better understanding of cel¬lular clocks regulated by RNA molecules. The second genetic model proposed here involves only a repression acting on a self-activating gene and produces robust oscil¬lations. Unlike current two-gene oscillators, this model surprisingly does not require a second repressor gene. This result could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators. Possible follow-on research directions are: validate models in vivo and in vitro, research the potential of second model as a genetic memory, investigate new genetic oscillators regulated by non-coding RNAs and design a biosensor of positive feedbacks in genetic networks based on the operation of the second model Resumen Introduccion y motivacion: Una amplia variedad de organismos han desarro-llado relojes biomoleculares internos con el fin de adaptarse a los cambios ciclicos del entorno. El funcionamiento de estos relojes involucra redes geneticas. El mo delado de estas redes geneticas es esencial tanto para entender los mecanismos que producen las oscilaciones como para diseiiar nuevos circuitos sinteticos en celulas. Esta tesis doctoral ha dado lugar a dos contribuciones dentro de los campos de los circuitos geneticos en particular, y biologia de sistemas y sintetica en general. La primera contribucion es un nuevo modelo de circuito genetico que muestra un comportamiento oscilatorio usando moleculas de ARN cataliticas. La segunda y principal contribucion es un nuevo modelo de circuito genetico que demuestra que una molecula represora actuando sobre el lazo de un gen auto-activado produce oscilaciones robustas. Primera contribucion: Es un nuevo modelo de oscilador genetico sintetico basado en una tipica red genetica compuesta por dos genes con dos lazos de retroa-limentacion, uno positivo y otro negativo. La novedad de este modelo es que el represor es una molecula de ARN catalftica, en lugar de una protefna o una molecula de ARN no-catalitica. Este ARN catalitico es una ribozima que actua despues de la transcription genetica uniendose y cortando moleculas de ARN mensajero (ARNm). Este reloj genetico involucra solo dos genes, un ARNm y una proteina activadora, aparte de la ribozima. Como ejemplo de funcionamiento, se han escogido valores de los parametros que producen oscilaciones con periodo circadiano (24 horas) tanto en simulaciones deterministas como estocasticas. El efecto de las fluctuaciones es-tocasticas ha sido cuantificado mediante un histograma del periodo y la función de auto-correlacion. La conclusion es que las moleculas de ARN con propiedades cataliticas pueden jugar el misnio papel que las protemas represoras, y por lo tanto, simplificar el diseno de los osciladores geneticos. Segunda y principal contribucion: Es un nuevo modelo de oscilador genetico que demuestra que un gen auto-activado junto con una simple interaction negativa puede producir oscilaciones robustas. Este modelo ha sido estudiado y validado matematicamente. El modelo esta compuesto de dos partes bien diferenciadas. La primera parte es un lazo de retroalimentacion positiva creado por una proteina que se une al promotor de su propio gen activando la transcription. La segunda parte es una interaction negativa en la que una molecula represora evita la union de la proteina con el promotor. Un estudio estocastico muestra que el sistema es robusto al ruido. Un estudio determinista muestra que la dinamica del sistema es debida principalmente a dos tipos de biomoleculas: la proteina, y el complejo formado por el represor y esta proteina. La conclusion principal de este estudio es que una simple y usual interaction negativa, tal como una degradation, un secuestro o una inhibition, actuando sobre el lazo de retroalimentacion positiva de un solo gen es una condition suficiente para producir oscilaciones robustas. Un gen es suficiente y el lazo de retroalimentacion positiva no necesita activar a un segundo gen represor, tal y como ocurre en los relojes actuales con dos genes. Esto significa que a nivel genetico un lazo de retroalimentacion negativa no es necesario de forma explicita. Ademas, este modelo no necesita reacciones cooperativas ni la formation de multimeros proteicos, al contrario que en muchos osciladores geneticos. Aplicaciones y futuras lineas de investigacion: En los liltimos anos, se han descubierto muchas moleculas de ARN con capacidad catalitica. El primer modelo de oscilador genetico propuesto en esta tesis usa ribozimas como moleculas repre¬soras. Esto podria proporcionar nuevos principios de diseno en biologia sintetica y una mejor comprension de los relojes celulares regulados por moleculas de ARN. El segundo modelo de oscilador genetico propuesto aqui involucra solo una represion actuando sobre un gen auto-activado y produce oscilaciones robustas. Sorprendente-mente, un segundo gen represor no es necesario al contrario que en los bien conocidos osciladores con dos genes. Este resultado podria ayudar a clarificar los principios de diseno de los relojes celulares naturales y constituir una nueva y eficiente he-rramienta para crear osciladores geneticos sinteticos. Algunas de las futuras lineas de investigation abiertas tras esta tesis son: (1) la validation in vivo e in vitro de ambos modelos, (2) el estudio del potential del segundo modelo como circuito base para la construction de una memoria genetica, (3) el estudio de nuevos osciladores geneticos regulados por ARN no codificante y, por ultimo, (4) el rediseno del se¬gundo modelo de oscilador genetico para su uso como biosensor capaz de detectar genes auto-activados en redes geneticas.

Estrategias innovadoras para la gestión del riesgo de sequía en sistemas ganaderos extensivos

La vulnerabilidad de los sistemas ganaderos de pastoreo pone en evidencia la necesidad de herramientas para evaluar y mitigar los efectos de la sequía. El avance en la teledetección ha despertado el interés por explotar potenciales aplicaciones, y está dando lugar a un intenso desarrollo de innovaciones en distintos campos. Una de estas áreas es la gestión del riesgo climático, en donde la utilización de índices de vegetación permite la evaluación de la sequía. En esta investigación, se analiza el impacto de la sequía y se evalúa el potencial de nuevas tecnologías como la teledetección para la gestión del riesgo de sequía en sistemas de ganadería extensiva. Para ello, se desarrollan tres aplicaciones: (i) evaluar el impacto económico de la sequía en una explotación ganadera extensiva de la dehesa de Andalucía, (ii) elaborar mapas de vulnerabilidad a la sequía en pastos de Chile y (iii) diseñar y evaluar el potencial de un seguro indexado para sequía en pastos en la región de Coquimbo en Chile. En la primera aplicación, se diseña un modelo dinámico y estocástico que integra aspectos climáticos, ecológicos, agronómicos y socioeconómicos para evaluar el riesgo de sequía. El modelo simula una explotación ganadera tipo de la dehesa de Andalucía para el período 1999-2010. El método de Análisis Histórico y la simulación de MonteCarlo se utilizan para identificar los principales factores de riesgo de la explotación, entre los que destacan, los periodos de inicios del verano e inicios de invierno. Los resultados muestran la existencia de un desfase temporal entre el riesgo climático y riesgo económico, teniendo este último un periodo de duración más extenso en el tiempo. También, revelan que la intensidad, frecuencia y duración son tres atributos cruciales que determinan el impacto económico de la sequía. La estrategia de reducción de la carga ganadera permite aminorar el riesgo, pero conlleva una disminución en el margen bruto de la explotación. La segunda aplicación está dedicada a la elaboración de mapas de vulnerabilidad a la sequia en pastos de Chile. Para ello, se propone y desarrolla un índice de riesgo económico (IRESP) sencillo de interpretar y replicable, que integra factores de riesgo y estrategias de adaptación para obtener una medida del Valor en Riesgo, es decir, la máxima pérdida esperada en un año con un nivel de significación del 5%.La representación espacial del IRESP pone en evidencia patrones espaciales y diferencias significativas en la vulnerabilidad a la sequía a lo largo de Chile. Además, refleja que la vulnerabilidad no siempre esta correlacionada con el riesgo climático y demuestra la importancia de considerar las estrategias de adaptación. Las medidas de autocorrelación espacial revelan que el riesgo sistémico es considerablemente mayor en el sur que en el resto de zonas. Los resultados demuestran que el IRESP transmite información pertinente y, que los mapas de vulnerabilidad pueden ser una herramienta útil en el diseño de políticas y toma de decisiones para la gestión del riesgo de sequía. La tercera aplicación evalúa el potencial de un seguro indexado para sequía en pastos en la región de Coquimbo en Chile. Para lo cual, se desarrolla un modelo estocástico para estimar la prima actuarialmente justa del seguro y se proponen y evalúan pautas alternativas para mejorar el diseño del contrato. Se aborda el riesgo base, el principal problema de los seguros indexados identificado en la literatura y, que está referido a la correlación imperfecta del índice con las pérdidas de la explotación. Para ello, se sigue un enfoque bayesiano que permite evaluar el impacto en el riesgo base de las pautas de diseño propuestas: i) una zonificación por clúster que considera aspectos espacio-temporales, ii) un período de garantía acotado a los ciclos fenológicos del pasto y iii) umbral de garantía. Los resultados muestran que tanto la zonificación como el periodo de garantía reducen el riesgo base considerablemente. Sin embargo, el umbral de garantía tiene un efecto ambiguo sobre el riesgo base. Por otra parte, la zonificación por clúster contribuye a aminorar el riesgo sistémico que enfrentan las aseguradoras. Estos resultados han puesto de manifiesto que un buen diseño de contrato puede tener un doble dividendo, por un lado aumentar su utilidad y, por otro, reducir el coste del seguro. Un diseño de contrato eficiente junto con los avances en la teledetección y un adecuado marco institucional son los pilares básicos para el buen funcionamiento de un programa de seguro. Las nuevas tecnologías ofrecen un importante potencial para la innovación en la gestión del riesgo climático. Los avances en este campo pueden proporcionar importantes beneficios sociales en los países en desarrollo y regiones vulnerables, donde las herramientas para gestionar eficazmente los riesgos sistémicos como la sequía pueden ser de gran ayuda para el desarrollo. The vulnerability of grazing livestock systems highlights the need for tools to assess and mitigate the adverse impact of drought. The recent and rapid progress in remote sensing has awakened an interest for tapping into potential applications, triggering intensive efforts to develop innovations in a number of spheres. One of these areas is climate risk management, where the use of vegetation indices facilitates assessment of drought. This research analyzes drought impacts and evaluates the potential of new technologies such as remote sensing to manage drought risk in extensive livestock systems. Three essays in drought risk management are developed to: (i) assess the economic impact of drought on a livestock farm in the Andalusian Dehesa, (ii) build drought vulnerability maps in Chilean grazing lands, and (iii) design and evaluate the potential of an index insurance policy to address the risk of drought in grazing lands in Coquimbo, Chile. In the first essay, a dynamic and stochastic farm model is designed combining climate, agronomic, socio-economic and ecological aspects to assess drought risk. The model is developed to simulate a representative livestock farm in the Dehesa of Andalusia for the time period 1999-2010. Burn analysis and MonteCarlo simulation methods are used to identify the significance of various risk sources at the farm. Most notably, early summer and early winter are identified as periods of peak risk. Moreover, there is a significant time lag between climate and economic risk and this later last longer than the former. It is shown that intensity, frequency and duration of the drought are three crucial attributes that shape the economic impact of drought. Sensitivity analysis is conducted to assess the sustainability of farm management strategies and demonstrates that lowering the stocking rate reduces farmer exposure to drought risk but entails a reduction in the expected gross margin. The second essay, mapping drought vulnerability in Chilean grazing lands, proposes and builds an index of economic risk (IRESP) that is replicable and simple to interpret. This methodology integrates risk factors and adaptation strategies to deliver information on Value at Risk, maximum expected losses at 5% significance level. Mapping IRESP provides evidence about spatial patterns and significant differences in drought vulnerability across Chilean grazing lands. Spatial autocorrelation measures reveal that systemic risk is considerably larger in the South as compared to Northern or Central Regions. Furthermore, it is shown that vulnerability is not necessarily correlated with climate risk and that adaptation strategies do matter. These results show that IRESP conveys relevant information and that vulnerability maps may be useful tools to assess policy design and decision-making in drought risk management. The third essay develops a stochastic model to estimate the actuarially fair premium and evaluates the potential of an indexed insurance policy to manage drought risk in Coquimbo, a relevant livestock farming region of Chile. Basis risk refers to the imperfect correlation of the index and farmer loses and is identified in the literature as a main limitation of index insurance. A Bayesian approach is proposed to assess the impact on basis risk of alternative guidelines in contract design: i) A cluster zoning that considers space-time aspects, ii) A guarantee period bounded to fit phenological cycles, and iii) the triggering index threshold. Results show that both the proposed zoning and guarantee period considerably reduces basis risk. However, the triggering index threshold has an ambiguous effect on basis risk. On the other hand, cluster zoning contributes to ameliorate systemic risk faced by the insurer. These results highlighted that adequate contract design is important and may result in double dividend. On the one hand, increasing farmers’ utility and, secondly, reducing the cost of insurance. An efficient contract design coupled with advances in remote sensing and an appropriate institutional framework are the basis for an efficient operation of an insurance program. The new technologies offer significant potential for innovation in climate risk managements. Progress in this field is capturing increasing attention and may provide important social gains in developing countries and vulnerable regions where the tools to efficiently manage systemic risks, such as drought, may be a means to foster development.

Análisis y clasificación de maderas mediante técnicas no invasivas de baja energía

El estudio de materiales, especialmente biológicos, por medios no destructivos está adquiriendo una importancia creciente tanto en las aplicaciones científicas como industriales. Las ventajas económicas de los métodos no destructivos son múltiples. Existen numerosos procedimientos físicos capaces de extraer información detallada de las superficie de la madera con escaso o nulo tratamiento previo y mínima intrusión en el material. Entre los diversos métodos destacan las técnicas ópticas y las acústicas por su gran versatilidad, relativa sencillez y bajo coste. Esta tesis pretende establecer desde la aplicación de principios simples de física, de medición directa y superficial, a través del desarrollo de los algoritmos de decisión mas adecuados basados en la estadística, unas soluciones tecnológicas simples y en esencia, de coste mínimo, para su posible aplicación en la determinación de la especie y los defectos superficiales de la madera de cada muestra tratando, en la medida de lo posible, no alterar su geometría de trabajo. Los análisis desarrollados han sido los tres siguientes: El primer método óptico utiliza las propiedades de la luz dispersada por la superficie de la madera cuando es iluminada por un laser difuso. Esta dispersión produce un moteado luminoso (speckle) cuyas propiedades estadísticas permiten extraer propiedades muy precisas de la estructura tanto microscópica como macroscópica de la madera. El análisis de las propiedades espectrales de la luz laser dispersada genera ciertos patrones mas o menos regulares relacionados con la estructura anatómica, composición, procesado y textura superficial de la madera bajo estudio que ponen de manifiesto características del material o de la calidad de los procesos a los que ha sido sometido. El uso de este tipo de láseres implica también la posibilidad de realizar monitorizaciones de procesos industriales en tiempo real y a distancia sin interferir con otros sensores. La segunda técnica óptica que emplearemos hace uso del estudio estadístico y matemático de las propiedades de las imágenes digitales obtenidas de la superficie de la madera a través de un sistema de scanner de alta resolución. Después de aislar los detalles mas relevantes de las imágenes, diversos algoritmos de clasificacion automatica se encargan de generar bases de datos con las diversas especies de maderas a las que pertenecían las imágenes, junto con los márgenes de error de tales clasificaciones. Una parte fundamental de las herramientas de clasificacion se basa en el estudio preciso de las bandas de color de las diversas maderas. Finalmente, numerosas técnicas acústicas, tales como el análisis de pulsos por impacto acústico, permiten complementar y afinar los resultados obtenidos con los métodos ópticos descritos, identificando estructuras superficiales y profundas en la madera así como patologías o deformaciones, aspectos de especial utilidad en usos de la madera en estructuras. La utilidad de estas técnicas esta mas que demostrada en el campo industrial aun cuando su aplicación carece de la suficiente expansión debido a sus altos costes y falta de normalización de los procesos, lo cual hace que cada análisis no sea comparable con su teórico equivalente de mercado. En la actualidad gran parte de los esfuerzos de investigación tienden a dar por supuesto que la diferenciación entre especies es un mecanismo de reconocimiento propio del ser humano y concentran las tecnologías en la definición de parámetros físicos (módulos de elasticidad, conductividad eléctrica o acústica, etc.), utilizando aparatos muy costosos y en muchos casos complejos en su aplicación de campo. Abstract The study of materials, especially the biological ones, by non-destructive techniques is becoming increasingly important in both scientific and industrial applications. The economic advantages of non-destructive methods are multiple and clear due to the related costs and resources necessaries. There are many physical processes capable of extracting detailed information on the wood surface with little or no previous treatment and minimal intrusion into the material. Among the various methods stand out acoustic and optical techniques for their great versatility, relative simplicity and low cost. This thesis aims to establish from the application of simple principles of physics, surface direct measurement and through the development of the more appropriate decision algorithms based on statistics, a simple technological solutions with the minimum cost for possible application in determining the species and the wood surface defects of each sample. Looking for a reasonable accuracy without altering their work-location or properties is the main objetive. There are three different work lines: Empirical characterization of wood surfaces by means of iterative autocorrelation of laser speckle patterns: A simple and inexpensive method for the qualitative characterization of wood surfaces is presented. it is based on the iterative autocorrelation of laser speckle patterns produced by diffuse laser illumination of the wood surfaces. The method exploits the high spatial frequency content of speckle images. A similar approach with raw conventional photographs taken with ordinary light would be very difficult. A few iterations of the algorithm are necessary, typically three or four, in order to visualize the most important periodic features of the surface. The processed patterns help in the study of surface parameters, to design new scattering models and to classify the wood species. Fractal-based image enhancement techniques inspired by differential interference contrast microscopy: Differential interference contrast microscopy is a very powerful optical technique for microscopic imaging. Inspired by the physics of this type of microscope, we have developed a series of image processing algorithms aimed at the magnification, noise reduction, contrast enhancement and tissue analysis of biological samples. These algorithms use fractal convolution schemes which provide fast and accurate results with a performance comparable to the best present image enhancement algorithms. These techniques can be used as post processing tools for advanced microscopy or as a means to improve the performance of less expensive visualization instruments. Several examples of the use of these algorithms to visualize microscopic images of raw pine wood samples with a simple desktop scanner are provided. Wood species identification using stress-wave analysis in the audible range: Stress-wave analysis is a powerful and flexible technique to study mechanical properties of many materials. We present a simple technique to obtain information about the species of wood samples using stress-wave sounds in the audible range generated by collision with a small pendulum. Stress-wave analysis has been used for flaw detection and quality control for decades, but its use for material identification and classification is less cited in the literature. Accurate wood species identification is a time consuming task for highly trained human experts. For this reason, the development of cost effective techniques for automatic wood classification is a desirable goal. Our proposed approach is fully non-invasive and non-destructive, reducing significantly the cost and complexity of the identification and classification process.

Environmental variables modeling based on remote sensing data using time series analysis: forestry and agricultural applications

En la actualidad, el seguimiento de la dinámica de los procesos medio ambientales está considerado como un punto de gran interés en el campo medioambiental. La cobertura espacio temporal de los datos de teledetección proporciona información continua con una alta frecuencia temporal, permitiendo el análisis de la evolución de los ecosistemas desde diferentes escalas espacio-temporales. Aunque el valor de la teledetección ha sido ampliamente probado, en la actualidad solo existe un número reducido de metodologías que permiten su análisis de una forma cuantitativa. En la presente tesis se propone un esquema de trabajo para explotar las series temporales de datos de teledetección, basado en la combinación del análisis estadístico de series de tiempo y la fenometría. El objetivo principal es demostrar el uso de las series temporales de datos de teledetección para analizar la dinámica de variables medio ambientales de una forma cuantitativa. Los objetivos específicos son: (1) evaluar dichas variables medio ambientales y (2) desarrollar modelos empíricos para predecir su comportamiento futuro. Estos objetivos se materializan en cuatro aplicaciones cuyos objetivos específicos son: (1) evaluar y cartografiar estados fenológicos del cultivo del algodón mediante análisis espectral y fenometría, (2) evaluar y modelizar la estacionalidad de incendios forestales en dos regiones bioclimáticas mediante modelos dinámicos, (3) predecir el riesgo de incendios forestales a nivel pixel utilizando modelos dinámicos y (4) evaluar el funcionamiento de la vegetación en base a la autocorrelación temporal y la fenometría. Los resultados de esta tesis muestran la utilidad del ajuste de funciones para modelizar los índices espectrales AS1 y AS2. Los parámetros fenológicos derivados del ajuste de funciones permiten la identificación de distintos estados fenológicos del cultivo del algodón. El análisis espectral ha demostrado, de una forma cuantitativa, la presencia de un ciclo en el índice AS2 y de dos ciclos en el AS1 así como el comportamiento unimodal y bimodal de la estacionalidad de incendios en las regiones mediterránea y templada respectivamente. Modelos autorregresivos han sido utilizados para caracterizar la dinámica de la estacionalidad de incendios y para predecir de una forma muy precisa el riesgo de incendios forestales a nivel pixel. Ha sido demostrada la utilidad de la autocorrelación temporal para definir y caracterizar el funcionamiento de la vegetación a nivel pixel. Finalmente el concepto “Optical Functional Type” ha sido definido, donde se propone que los pixeles deberían ser considerados como unidades temporales y analizados en función de su dinámica temporal. ix SUMMARY A good understanding of land surface processes is considered as a key subject in environmental sciences. The spatial-temporal coverage of remote sensing data provides continuous observations with a high temporal frequency allowing the assessment of ecosystem evolution at different temporal and spatial scales. Although the value of remote sensing time series has been firmly proved, only few time series methods have been developed for analyzing this data in a quantitative and continuous manner. In the present dissertation a working framework to exploit Remote Sensing time series is proposed based on the combination of Time Series Analysis and phenometric approach. The main goal is to demonstrate the use of remote sensing time series to analyze quantitatively environmental variable dynamics. The specific objectives are (1) to assess environmental variables based on remote sensing time series and (2) to develop empirical models to forecast environmental variables. These objectives have been achieved in four applications which specific objectives are (1) assessing and mapping cotton crop phenological stages using spectral and phenometric analyses, (2) assessing and modeling fire seasonality in two different ecoregions by dynamic models, (3) forecasting forest fire risk on a pixel basis by dynamic models, and (4) assessing vegetation functioning based on temporal autocorrelation and phenometric analysis. The results of this dissertation show the usefulness of function fitting procedures to model AS1 and AS2. Phenometrics derived from function fitting procedure makes it possible to identify cotton crop phenological stages. Spectral analysis has demonstrated quantitatively the presence of one cycle in AS2 and two in AS1 and the unimodal and bimodal behaviour of fire seasonality in the Mediterranean and temperate ecoregions respectively. Autoregressive models has been used to characterize the dynamics of fire seasonality in two ecoregions and to forecasts accurately fire risk on a pixel basis. The usefulness of temporal autocorrelation to define and characterized land surface functioning has been demonstrated. And finally the “Optical Functional Types” concept has been proposed, in this approach pixels could be as temporal unities based on its temporal dynamics or functioning.

The trade credit in the Spanish agrofood industry

Selling on credit is rather frequent in Mediterranean countries. Its generalized use can lead to excessive enlargements of the payment periods and consequently can deteriorate the profitability of firms. In spite of the relevance of this problem there are few empirical researches. This work intends to fill this gap and to shed light on the factors related to the extension of trade credit. In the theoretical and empirical literature, different motives have been proposed to explain this issue: a mechanism to reduce transaction costs, a financial alternative to the bank system and an additional tool to improve commercial activities. To contrast these ideas a panel of 388 firms of the Spanish agrofood industry has been taken, and static and dynamic regression models have been estimated by using robust methods to heteroskedasticity, autocorrelation and endogeneity of the explanatory variables. The results confirm that trade credit receivable is associated with more active firms and with cheaper bank financing. Other factors with positive relationships are short-term bank debts and accounts payable. These findings are consistent with commercial motives, rather than a pure financial view, in the sense that financial distressed producers extend trade credit as a way of promoting their products and in turn increasing their sales.

Economic analysis of drought risks: an application to irrigated agriculture in Spain

Abstract This paper describes a two-part methodology for managing the risk posed by water supply variability to irrigated agriculture. First, an econometric model is used to explain the variation in the production value of irrigated agriculture. The explanatory variables include an index of irrigation water availability (surface storage levels), a price index representative of the crops grown in each geographical unit, and a time variable. The model corrects for autocorrelation and it is applied to 16 representative Spanish provinces in terms of irrigated agriculture. In the second part, the fitted models are used for the economic evaluation of drought risk. In flow variability in the hydrological system servicing each province is used to perform ex-ante evaluations of economic output for the upcoming irrigation season. The model?s error and the probability distribution functions (PDFs) of the reservoirs? storage variations are used to generate Monte Carlo (Latin Hypercube) simulations of agricultural output 7 and 3 months prior to the irrigation season. The results of these simulations illustrate the different risk profiles of each management unit, which depend on farm productivity and on the probability distribution function of water in flow to reservoirs. The potential for ex-ante drought impact assessments is demonstrated. By complementing hydrological models, this method can assist water managers and decisionmakers in managing reservoirs.

Modelling the spatio-temporal pattern of primary dispersal in stone pine (Pinus pinea L.) stands in the Northern Plateau (Spain)

Natural regeneration in stone pine (Pinus pinea L.) managed forests in the Spanish Northern Plateau is not achieved successfully under current silviculture practices, constituting a main concern for forest managers. We modelled spatio-temporal features of primary dispersal to test whether (a) present low stand densities constrain natural regeneration success and (b) seed release is a climate-controlled process. The present study is based on data collected from a 6 years seed trap experiment considering different regeneration felling intensities. From a spatial perspective, we attempted alternate established kernels under different data distribution assumptions to fit a spatial model able to predict P. pinea seed rain. Due to P. pinea umbrella-like crown, models were adapted to account for crown effect through correction of distances between potential seed arrival locations and seed sources. In addition, individual tree fecundity was assessed independently from existing models, improving parameter estimation stability. Seed rain simulation enabled to calculate seed dispersal indexes for diverse silvicultural regeneration treatments. The selected spatial model of best fit (Weibull, Poisson assumption) predicted a highly clumped dispersal pattern that resulted in a proportion of gaps where no seed arrival is expected (dispersal limitation) between 0.25 and 0.30 for intermediate intensity regeneration fellings and over 0.50 for intense fellings. To describe the temporal pattern, the proportion of seeds released during monthly intervals was modelled as a function of climate variables – rainfall events – through a linear model that considered temporal autocorrelation, whereas cone opening took place over a temperature threshold. Our findings suggest the application of less intensive regeneration fellings, to be carried out after years of successful seedling establishment and, seasonally, subsequent to the main rainfall period (late fall). This schedule would avoid dispersal limitation and would allow for a complete seed release. These modifications in present silviculture practices would produce a more efficient seed shadow in managed stands.

Detecting periodicity with horizontal visibility graphs

The horizontal visibility algorithm was recently introduced as a mapping between time series and networks. The challenge lies in characterizing the structure of time series (and the processes that generated those series) using the powerful tools of graph theory. Recent works have shown that the visibility graphs inherit several degrees of correlations from their associated series, and therefore such graph theoretical characterization is in principle possible. However, both the mathematical grounding of this promising theory and its applications are in its infancy. Following this line, here we address the question of detecting hidden periodicity in series polluted with a certain amount of noise. We first put forward some generic properties of horizontal visibility graphs which allow us to define a (graph theoretical) noise reduction filter. Accordingly, we evaluate its performance for the task of calculating the period of noisy periodic signals, and compare our results with standard time domain (autocorrelation) methods. Finally, potentials, limitations and applications are discussed.

Mapa preliminar de períodos predominantes del suelo en Puerto Príncipe (Haití) a partir de medidas de ruido ambiental.

The 2010 Haiti earthquake, occurred on January 12th at 16:53:09 local time (21:53:09 UTC) with epicentral distance of 15 km from the capital Port au Prince, MW 7.0 and 13 km hypocenter deep, was the strongest event in the area since happened in 1770. The maximum macroseismic intensity was estimated as X (MMI scale). The aim of this research is to obtain a preliminary zonation of Port-au-Prince in terms of predominant resonance periods of ground. A total of 36 short-period ambient noise records have been carried out on a grid of about 500x500m. H/V spectral ratio method (HVSR) has been applied to determine the predominant period at each point. The lowest values (<0.2s) predominate in the southern part of the city, composed by Miocene conglomerates, while highest values (> 0.45s) correspond to the center and western parts, composed of Pleistocene-Holocene alluvial deposits and anthropogenic land reclaimed from the sea. We have determined the ground VS30 structure inside National Palace garden, using simultaneous ambient noise measurements. An array made up of 6 sensors were used, with 5 of them uniformly distributed along a circumference and a sixth one placed in its centre. The records were analyzed by using the spatial autocorrelation method (SPAC). The VS 30 value obtained was 331m/sec, in good agreement with the average values obtained for this area by other authors, using prospecting techniques.

Spatial distribution of the soil carbon pool in a Holm oak dehesa in Spain

Aims Dehesas are agroforestry systems characterized by scattered trees among pastures, crops and/or fallows. A study at a Spanish dehesa has been carried out to estimate the spatial distribution of the soil organic carbon stock and to assess the influence of the tree cover. Methods The soil organic carbon stock was estimated from the five uppermost cm of themineral soil with high spatial resolution at two plots with different grazing intensities. The Universal Kriging technique was used to assess the spatial distribution of the soil organic carbon stocks, using tree coverage within a buffering area as an auxiliary variable. Results A significant positive correlation between tree presence and soil organic carbon stocks up to distances of around 8 m from the trees was found. The tree crown cover within a buffer up to a distance similar to the crown radius around the point absorbed 30 % of the variance in the model for both grazing intensities, but residual variance showed stronger spatial autocorrelation under regular grazing conditions. Conclusions Tree cover increases soil organic carbon stocks, and can be satisfactorily estimated by means of crown parameters. However, other factors are involved in the spatial pattern of the soil organic carbon distribution. Livestock plays an interactive role together with tree presence in soil organic carbon distribution.

Codificador de voz MIDI

El presente proyecto tiene el objetivo de facilitar la composición de canciones mediante la creación de las distintas pistas MIDI que la forman. Se implementan dos controladores. El primero, con objeto de transcribir la parte melódica, convierte la voz cantada o tarareada a eventos MIDI. Para ello, y tras el estudio de las distintas técnicas del cálculo del tono (pitch), se implementará una técnica con ciertas variaciones basada en la autocorrelación. También se profundiza en el segmentado de eventos, en particular, una técnica basada en el análisis de la derivada de la envolvente. El segundo, dedicado a la base rítmica de la canción, permite la creación de la percusión mediante el golpe rítmico de objetos que disponga el usuario, que serán asignados a los distintos elementos de percusión elegidos. Los resultados de la grabación de estos impactos serán señales de corta duración, no lineales y no armónicas, dificultando su discriminación. La herramienta elegida para la clasificación de los distintos patrones serán las redes neuronales artificiales (RNA). Se realizara un estudio de la metodología de diseño de redes neuronales especifico para este tipo de señales, evaluando la importancia de las variables de diseño como son el número de capas ocultas y neuronas en cada una de ellas, algoritmo de entrenamiento y funciones de activación. El estudio concluirá con la implementación de dos redes de diferente naturaleza. Una red de Elman, cuyas propiedades de memoria permiten la clasificación de patrones temporales, procesará las cualidades temporales analizando el ataque de su forma de onda. Una red de propagación hacia adelante feed-forward, que necesitará de robustas características espectrales y temporales para su clasificación. Se proponen 26 descriptores como los derivados de los momentos del espectro: centroide, curtosis y simetría, los coeficientes cepstrales de la escala de Mel (MFCCs), y algunos temporales como son la tasa de cruces por cero y el centroide de la envolvente temporal. Las capacidades de discriminación inter e intra clase de estas características serán evaluadas mediante un algoritmo de selección, habiéndose elegido RELIEF, un método basado en el algoritmo de los k vecinos mas próximos (KNN). Ambos controladores tendrán función de trabajar en tiempo real y offline, permitiendo tanto la composición de canciones, como su utilización como un instrumento más junto con mas músicos. ABSTRACT. The aim of this project is to make song composition easier by creating each MIDI track that builds it. Two controllers are implemented. In order to transcribe the melody, the first controler converts singing voice or humming into MIDI files. To do this a technique based on autocorrelation is implemented after having studied different pitch detection methods. Event segmentation has also been dealt with, to be more precise a technique based on the analysis of the signal's envelope and it's derivative have been used. The second one, can be used to make the song's rhythm . It allows the user, to create percussive patterns by hitting different objects of his environment. These recordings results in short duration, non-linear and non-harmonic signals. Which makes the classification process more complicated in the traditional way. The tools to used are the artificial neural networks (ANN). We will study the neural network design to deal with this kind of signals. The goal is to get a design methodology, paying attention to the variables involved, as the number of hidden layers and neurons in each, transfer functions and training algorithm. The study will end implementing two neural networks with different nature. Elman network, which has memory properties, is capable to recognize sequences of data and analyse the impact's waveform, precisely, the attack portion. A feed-forward network, needs strong spectral and temporal features extracted from the hit. Some descriptors are proposed as the derivates from the spectrum moment as centroid, kurtosis and skewness, the Mel-frequency cepstral coefficients, and some temporal features as the zero crossing rate (zcr) and the temporal envelope's centroid. Intra and inter class discrimination abilities of those descriptors will be weighted using the selection algorithm RELIEF, a Knn (K-nearest neighbor) based algorithm. Both MIDI controllers can be used to compose, or play with other musicians as it works on real-time and offline.

Improving parameters selection of a seeded region growing method for multiband image segmentation

In the last decade, Object Based Image Analysis (OBIA) has been accepted as an effective method for processing high spatial resolution multiband images. This image analysis method is an approach that starts with the segmentation of the image. Image segmentation in general is a procedure to partition an image into homogenous groups (segments). In practice, visual interpretation is often used to assess the quality of segmentation and the analysis relies on the experience of an analyst. In an effort to address the issue, in this study, we evaluate several seed selection strategies for an automatic image segmentation methodology based on a seeded region growing-merging approach. In order to evaluate the segmentation quality, segments were subjected to spatial autocorrelation analysis using Moran's I index and intra-segment variance analysis. We apply the algorithm to image segmentation using an aerial multiband image.

Análisis de sistemas dinámicos y complejos en la Liga Profesional de Balonmano de España = Complex and dynamical systems analysis in Spanish Professional Handball League

El propósito de esta tesis fue estudiar el rendimiento ofensivo de los equipos de balonmano de élite cuando se considera el balonmano como un sistema dinámico complejo no lineal. La perspectiva de análisis dinámica dependiente del tiempo fue adoptada para evaluar el rendimiento de los equipos durante el partido. La muestra general comprendió los 240 partidos jugados en la temporada 2011-2012 de la liga profesional masculina de balonmano de España (Liga ASOBAL). En el análisis posterior solo se consideraron los partidos ajustados (diferencia final de goles ≤ 5; n = 142). El estado del marcador, la localización del partido, el nivel de los oponentes y el periodo de juego fueron incorporados al análisis como variables situacionales. Tres estudios compusieron el núcleo de la tesis. En el primer estudio, analizamos la coordinación entre las series temporales que representan el proceso goleador a lo largo del partido de cada uno de los dos equipos que se enfrentan. Autocorrelaciones, correlaciones cruzadas, doble media móvil y transformada de Hilbert fueron usadas para el análisis. El proceso goleador de los equipos presentó una alta consistencia a lo largo de todos los partidos, así como fuertes modos de coordinación en fase en todos los contextos de juego. Las únicas diferencias se encontraron en relación al periodo de juego. La coordinación en los procesos goleadores de los equipos fue significativamente menor en el 1er y 2º periodo (0–10 min y 10–20 min), mostrando una clara coordinación creciente a medida que el partido avanzaba. Esto sugiere que son los 20 primeros minutos aquellos que rompen los partidos. En el segundo estudio, analizamos los efectos temporales (efecto inmediato, a corto y a medio plazo) de los tiempos muertos en el rendimiento goleador de los equipos. Modelos de regresión lineal múltiple fueron empleados para el análisis. Los resultados mostraron incrementos de 0.59, 1.40 y 1.85 goles para los periodos que comprenden la primera, tercera y quinta posesión de los equipos que pidieron el tiempo muerto. Inversamente, se encontraron efectos significativamente negativos para los equipos rivales, con decrementos de 0.50, 1.43 y 2.05 goles en los mismos periodos respectivamente. La influencia de las variables situacionales solo se registró en ciertos periodos de juego. Finalmente, en el tercer estudio, analizamos los efectos temporales de las exclusiones de los jugadores sobre el rendimiento goleador de los equipos, tanto para los equipos que sufren la exclusión (inferioridad numérica) como para los rivales (superioridad numérica). Se emplearon modelos de regresión lineal múltiple para el análisis. Los resultados mostraron efectos negativos significativos en el número de goles marcados por los equipos con un jugador menos, con decrementos de 0.25, 0.40, 0.61, 0.62 y 0.57 goles para los periodos que comprenden el primer, segundo, tercer, cuarto y quinto minutos previos y posteriores a la exclusión. Para los rivales, los resultados mostraron efectos positivos significativos, con incrementos de la misma magnitud en los mismos periodos. Esta tendencia no se vio afectada por el estado del marcador, localización del partido, nivel de los oponentes o periodo de juego. Los incrementos goleadores fueron menores de lo que se podría esperar de una superioridad numérica de 2 minutos. Diferentes teorías psicológicas como la paralización ante situaciones de presión donde se espera un gran rendimiento pueden ayudar a explicar este hecho. Los últimos capítulos de la tesis enumeran las conclusiones principales y presentan diferentes aplicaciones prácticas que surgen de los tres estudios. Por último, se presentan las limitaciones y futuras líneas de investigación. ABSTRACT The purpose of this thesis was to investigate the offensive performance of elite handball teams when considering handball as a complex non-linear dynamical system. The time-dependent dynamic approach was adopted to assess teams’ performance during the game. The overall sample comprised the 240 games played in the season 2011-2012 of men’s Spanish Professional Handball League (ASOBAL League). In the subsequent analyses, only close games (final goal-difference ≤ 5; n = 142) were considered. Match status, game location, quality of opposition, and game period situational variables were incorporated into the analysis. Three studies composed the core of the thesis. In the first study, we analyzed the game-scoring coordination between the time series representing the scoring processes of the two opposing teams throughout the game. Autocorrelation, cross-correlation, double moving average, and Hilbert transform were used for analysis. The scoring processes of the teams presented a high consistency across all the games as well as strong in-phase modes of coordination in all the game contexts. The only differences were found when controlling for the game period. The coordination in the scoring processes of the teams was significantly lower for the 1st and 2nd period (0–10 min and 10–20 min), showing a clear increasing coordination behavior as the game progressed. This suggests that the first 20 minutes are those that break the game-scoring. In the second study, we analyzed the temporal effects (immediate effect, short-term effect, and medium-term effect) of team timeouts on teams’ scoring performance. Multiple linear regression models were used for the analysis. The results showed increments of 0.59, 1.40 and 1.85 goals for the periods within the first, third and fifth timeout ball possessions for the teams that requested the timeout. Conversely, significant negative effects on goals scored were found for the opponent teams, with decrements of 0.59, 1.43 and 2.04 goals for the same periods, respectively. The influence of situational variables on the scoring performance was only registered in certain game periods. Finally, in the third study, we analyzed the players’ exclusions temporal effects on teams’ scoring performance, for the teams that suffer the exclusion (numerical inferiority) and for the opponents (numerical superiority). Multiple linear regression models were used for the analysis. The results showed significant negative effects on the number of goals scored for the teams with one less player, with decrements of 0.25, 0.40, 0.61, 0.62, and 0.57 goals for the periods within the previous and post one, two, three, four and five minutes of play. For the opponent teams, the results showed positive effects, with increments of the same magnitude in the same game periods. This trend was not affected by match status, game location, quality of opposition, or game period. The scoring increments were smaller than might be expected from a 2-minute numerical playing superiority. Psychological theories such as choking under pressure situations where good performance is expected could contribute to explain this finding. The final chapters of the thesis enumerate the main conclusions and underline the main practical applications that arise from the three studies. Lastly, limitations and future research directions are described.

Vector Boolean Functions: Applications in Symmetric Cryptography

Esta tesis establece los fundamentos teóricos y diseña una colección abierta de clases C++ denominada VBF (Vector Boolean Functions) para analizar funciones booleanas vectoriales (funciones que asocian un vector booleano a otro vector booleano) desde una perspectiva criptográfica. Esta nueva implementación emplea la librería NTL de Victor Shoup, incorporando nuevos módulos que complementan a las funciones de NTL, adecuándolas para el análisis criptográfico. La clase fundamental que representa una función booleana vectorial se puede inicializar de manera muy flexible mediante diferentes estructuras de datas tales como la Tabla de verdad, la Representación de traza y la Forma algebraica normal entre otras. De esta manera VBF permite evaluar los criterios criptográficos más relevantes de los algoritmos de cifra en bloque y de stream, así como funciones hash: por ejemplo, proporciona la no-linealidad, la distancia lineal, el grado algebraico, las estructuras lineales, la distribución de frecuencias de los valores absolutos del espectro Walsh o del espectro de autocorrelación, entre otros criterios. Adicionalmente, VBF puede llevar a cabo operaciones entre funciones booleanas vectoriales tales como la comprobación de igualdad, la composición, la inversión, la suma, la suma directa, el bricklayering (aplicación paralela de funciones booleanas vectoriales como la empleada en el algoritmo de cifra Rijndael), y la adición de funciones coordenada. La tesis también muestra el empleo de la librería VBF en dos aplicaciones prácticas. Por un lado, se han analizado las características más relevantes de los sistemas de cifra en bloque. Por otro lado, combinando VBF con algoritmos de optimización, se han diseñado funciones booleanas cuyas propiedades criptográficas son las mejores conocidas hasta la fecha. ABSTRACT This thesis develops the theoretical foundations and designs an open collection of C++ classes, called VBF, designed for analyzing vector Boolean functions (functions that map a Boolean vector to another Boolean vector) from a cryptographic perspective. This new implementation uses the NTL library from Victor Shoup, adding new modules which complement the existing ones making VBF better suited for cryptography. The fundamental class representing a vector Boolean function can be initialized in a flexible way via several alternative types of data structures such as Truth Table, Trace Representation, Algebraic Normal Form (ANF) among others. This way, VBF allows the evaluation of the most relevant cryptographic criteria for block and stream ciphers as well as for hash functions: for instance, it provides the nonlinearity, the linearity distance, the algebraic degree, the linear structures, the frequency distribution of the absolute values of the Walsh Spectrum or the Autocorrelation Spectrum, among others. In addition, VBF can perform operations such as equality testing, composition, inversion, sum, direct sum, bricklayering (parallel application of vector Boolean functions as employed in Rijndael cipher), and adding coordinate functions of two vector Boolean functions. This thesis also illustrates the use of VBF in two practical applications. On the one hand, the most relevant properties of the existing block ciphers have been analysed. On the other hand, by combining VBF with optimization algorithms, new Boolean functions have been designed which have the best known cryptographic properties up-to-date.