Lidar uncertainty in complex terrain development of a bias correction methodology

El autor ha trabajado como parte del equipo de investigación en mediciones de viento en el Centro Nacional de Energías Renovables (CENER), España, en cooperación con la Universidad Politécnica de Madrid y la Universidad Técnica de Dinamarca. El presente reporte recapitula el trabajo de investigación realizado durante los últimos 4.5 años en el estudio de las fuentes de error de los sistemas de medición remota de viento, basados en la tecnología lidar, enfocado al error causado por los efectos del terreno complejo. Este trabajo corresponde a una tarea del paquete de trabajo dedicado al estudio de sistemas remotos de medición de viento, perteneciente al proyecto de intestigación europeo del 7mo programa marco WAUDIT. Adicionalmente, los datos de viento reales han sido obtenidos durante las campañas de medición en terreno llano y terreno complejo, pertenecientes al también proyecto de intestigación europeo del 7mo programa marco SAFEWIND. El principal objetivo de este trabajo de investigación es determinar los efectos del terreno complejo en el error de medición de la velocidad del viento obtenida con los sistemas de medición remota lidar. Con este conocimiento, es posible proponer una metodología de corrección del error de las mediciones del lidar. Esta metodología está basada en la estimación de las variaciones del campo de viento no uniforme dentro del volumen de medición del lidar. Las variaciones promedio del campo de viento son predichas a partir de los resultados de las simulaciones computacionales de viento RANS, realizadas para el parque experimental de Alaiz. La metodología de corrección es verificada con los resultados de las simulaciones RANS y validadas con las mediciones reales adquiridas en la campaña de medición en terreno complejo. Al inicio de este reporte, el marco teórico describiendo el principio de medición de la tecnología lidar utilizada, es presentado con el fin de familiarizar al lector con los principales conceptos a utilizar a lo largo de este trabajo. Posteriormente, el estado del arte es presentado en donde se describe los avances realizados en el desarrollo de la la tecnología lidar aplicados al sector de la energía eólica. En la parte experimental de este trabajo de investigación se ha estudiado los datos adquiridos durante las dos campañas de medición realizadas. Estas campañas has sido realizadas en terreno llano y complejo, con el fin de complementar los conocimiento adquiridos en casa una de ellas y poder comparar los efectos del terreno en las mediciones de viento realizadas con sistemas remotos lidar. La primer campaña experimental se desarrollo en terreno llano, en el parque de ensayos de aerogeneradores H0vs0re, propiedad de DTU Wind Energy (anteriormente Ris0). La segunda campaña experimental se llevó a cabo en el parque de ensayos de aerogeneradores Alaiz, propiedad de CENER. Exactamente los mismos dos equipos lidar fueron utilizados en estas campañas, haciendo de estos experimentos altamente relevantes en el contexto de evaluación del recurso eólico. Un equipo lidar está basado en tecnología de onda continua, mientras que el otro está basado en tecnología de onda pulsada. La velocidad del viento fue medida, además de con los equipos lidar, con anemómetros de cazoletas, veletas y anemómetros verticales, instalados en mástiles meteorológicos. Los sensores del mástil meteorológico son considerados como las mediciones de referencia en el presente estudio. En primera instancia, se han analizado los promedios diez minútales de las medidas de viento. El objetivo es identificar las principales fuentes de error en las mediciones de los equipos lidar causadas por diferentes condiciones atmosféricas y por el flujo no uniforme de viento causado por el terreno complejo. El error del lidar ha sido estudiado como función de varias propiedades estadísticas del viento, como lo son el ángulo vertical de inclinación, la intensidad de turbulencia, la velocidad vertical, la estabilidad atmosférica y las características del terreno. El propósito es usar este conocimiento con el fin de definir criterios de filtrado de datos. Seguidamente, se propone una metodología para corregir el error del lidar causado por el campo de viento no uniforme, producido por la presencia de terreno complejo. Esta metodología está basada en el análisis matemático inicial sobre el proceso de cálculo de la velocidad de viento por los equipos lidar de onda continua. La metodología de corrección propuesta hace uso de las variaciones de viento calculadas a partir de las simulaciones RANS realizadas para el parque experimental de Alaiz. Una ventaja importante que presenta esta metodología es que las propiedades el campo de viento real, presentes en las mediciones instantáneas del lidar de onda continua, puede dar paso a análisis adicionales como parte del trabajo a futuro. Dentro del marco del proyecto, el trabajo diario se realizó en las instalaciones de CENER, con supervisión cercana de la UPM, incluyendo una estancia de 1.5 meses en la universidad. Durante esta estancia, se definió el análisis matemático de las mediciones de viento realizadas por el equipo lidar de onda continua. Adicionalmente, los efectos del campo de viento no uniforme sobre el error de medición del lidar fueron analíticamente definidos, después de asumir algunas simplificaciones. Adicionalmente, durante la etapa inicial de este proyecto se desarrollo una importante trabajo de cooperación con DTU Wind Energy. Gracias a esto, el autor realizó una estancia de 1.5 meses en Dinamarca. Durante esta estancia, el autor realizó una visita a la campaña de medición en terreno llano con el fin de aprender los aspectos básicos del diseño de campañas de medidas experimentales, el estudio del terreno y los alrededores y familiarizarse con la instrumentación del mástil meteorológico, el sistema de adquisición y almacenamiento de datos, así como de el estudio y reporte del análisis de mediciones. ABSTRACT The present report summarizes the research work performed during last 4.5 years of investigation on the sources of lidar bias due to complex terrain. This work corresponds to one task of the remote sensing work package, belonging to the FP7 WAUDIT project. Furthermore, the field data from the wind velocity measurement campaigns of the FP7 SafeWind project have been used in this report. The main objective of this research work is to determine the terrain effects on the lidar bias in the measured wind velocity. With this knowledge, it is possible to propose a lidar bias correction methodology. This methodology is based on an estimation of the wind field variations within the lidar scan volume. The wind field variations are calculated from RANS simulations performed from the Alaiz test site. The methodology is validated against real scale measurements recorded during an eight month measurement campaign at the Alaiz test site. Firstly, the mathematical framework of the lidar sensing principle is introduced and an overview of the state of the art is presented. The experimental part includes the study of two different, but complementary experiments. The first experiment was a measurement campaign performed in flat terrain, at DTU Wind Energy H0vs0re test site, while the second experiment was performed in complex terrain at CENER Alaiz test site. Exactly the same two lidar devices, based on continuous wave and pulsed wave systems, have been used in the two consecutive measurement campaigns, making this a relevant experiment in the context of wind resource assessment. The wind velocity was sensed by the lidars and standard cup anemometry and wind vanes (installed on a met mast). The met mast sensors are considered as the reference wind velocity measurements. The first analysis of the experimental data is dedicated to identify the main sources of lidar bias present in the 10 minute average values. The purpose is to identify the bias magnitude introduced by different atmospheric conditions and by the non-uniform wind flow resultant of the terrain irregularities. The lidar bias as function of several statistical properties of the wind flow like the tilt angle, turbulence intensity, vertical velocity, atmospheric stability and the terrain characteristics have been studied. The aim of this exercise is to use this knowledge in order to define useful lidar bias data filters. Then, a methodology to correct the lidar bias caused by non-uniform wind flow is proposed, based on the initial mathematical analysis of the lidar measurements. The proposed lidar bias correction methodology has been developed focusing on the the continuous wave lidar system. In a last step, the proposed lidar bias correction methodology is validated with the data of the complex terrain measurement campaign. The methodology makes use of the wind field variations obtained from the RANS analysis. The results are presented and discussed. The advantage of this methodology is that the wind field properties at the Alaiz test site can be studied with more detail, based on the instantaneous measurements of the CW lidar. Within the project framework, the daily basis work has been done at CENER, with close guidance and support from the UPM, including an exchange period of 1.5 months. During this exchange period, the mathematical analysis of the lidar sensing of the wind velocity was defined. Furthermore, the effects of non-uniform wind fields on the lidar bias were analytically defined, after making some assumptions for the sake of simplification. Moreover, there has been an important cooperation with DTU Wind Energy, where a secondment period of 1.5 months has been done as well. During the secondment period at DTU Wind Energy, an important introductory learning has taken place. The learned aspects include the design of an experimental measurement campaign in flat terrain, the site assessment study of obstacles and terrain conditions, the data acquisition and processing, as well as the study and reporting of the measurement analysis.

New insights into the regulation of NADPH oxidase dependent reactive oxygen species signaling during the plant immune response

Las NADPH oxidasas de plantas, denominadas “respiratory burst oxidase homologues” (RBOHs), producen especies reactivas del oxígeno (ROS) que median un amplio rango de funciones. En la célula vegetal, el ajuste preciso de la producción de ROS aporta la especificidad de señal para generar una respuesta apropiada ante las amenazas ambientales. RbohD y RbohF, dos de los diez genes Rboh de Arabidopsis, son pleiotrópicos y median diversos procesos fisiológicos en respuesta a patógenos. El control espacio-temporal de la expresión de los genes RbohD y RbohF podría ser un aspecto crítico para determinar la multiplicidad de funciones de estas oxidasas. Por ello, generamos líneas transgénicas de Arabidopsis con fusiones de los promoters de RbohD y RbohF a los genes delatores de la B-glucuronidasa y la luciferasa. Estas líneas fueron empleadas para revelar el patrón de expresión diferencial de RbohD y RbohF durante la respuesta inmune de Arabidopsis a la bacteria patógena Pseudomonas syringae pv. tomato DC3000, el hongo necrótrofo Plectosphaerella cucumerina y en respuesta a señales relacionadas con la respuesta inmune. Nuestros experimentos revelan un patrón de expresión diferencial de los promotores de RbohD y RbohF durante el desarrollo de la planta y en la respuesta inmune de Arabidopsis. Además hemos puesto de manifiesto que existe una correlación entre el nivel de actividad de los promotores de RbohD y RbohF con la acumulación de ROS y el nivel de muerte celular en respuesta a patógenos. La expression de RbohD y RbohF también es modulada de manera diferencial en respuesta a patrones moleculares asociados a patógenos (PAMPs) y por ácido abscísico (ABA). Cabe destacar que, mediante una estrategia de intercambio de promotores, hemos revelado que la región promotora de RbohD, es necesaria para dirigir la producción de ROS en respuesta a P. cucumerina. Adicionalmente, la activación del promotor de RbohD en respuesta al aislado de P. cucumerina no adaptado a Arabidopsis 2127, nos llevó a realizar ensayos de susceptibilidad con el doble mutante rbohD rbohF que han revelado un papel desconocido de estas oxidasas en resistencia no-huesped. La interacción entre la señalización dependiente de las RBOHs y otros componentes de la respuesta inmune de plantas podría explicar también las distintas funciones que median estas oxidasas en relación con la respuesta inmune. Entre la gran cantidad de señales coordinadas con la actividad de las RBOHs, existen evidencias genéticas y farmacológicas que indican que las proteínas G heterotriméricas están implicadas en algunas de las rutas de señalización mediadas por ROS derivadas de los RBOHs en respuesta a señales ambientales. Por ello hemos estudiado la relación entre estas RBOH-NADPH oxidasas y AGB1, la subunidad β de las proteínas G heterotriméricas en la respuesta inmune de Arabidopsis. Análisis de epistasis indican que las proteínas G heterotriméricas están implicadas en distintas rutas de señalización en defensa mediadas por las RBOHs. Nuestros resultados ilustran la relación compleja entre la señalización mediada por las RBOHs y las proteínas G heterotriméricas, que varía en función de la interacción planta-patógeno analizada. Además, hemos explorado la posible asociación entre AGB1 con RBOHD y RBOHF en eventos tempranos de la respuesta immune. Cabe señalar que experimentos de coímmunoprecipitación apuntan a una posible asociación entre AGB1 y la kinasa citoplasmática reguladora de RBOHD, BIK1. Esto indica un posible mecanismo de control de la función de esta NADPH oxidase por AGB1. En conjunto, estos datos aportan nuevas perspectivas sobre cómo, a través del control transcripcional o mediante la interacción con las proteínas G heterotriméricas, las NADPH oxidases de plantas median la producción de ROS y la señalización por ROS en la respuesta inmune. Nuestro trabajo ejemplifica cómo la regulación diferencial de dos miembros de una familia multigénica, les permite realizar distintas funciones fisiológicas especializadas usando un mismo mecanismo enzimático. ABSTRACT The plant NADPH oxidases, termed respiratory burst oxidase homologues (RBOHs), produce reactive oxygen species (ROS) which mediate a wide range of functions. Fine tuning this ROS production provides the signaling specificity to the plant cell to produce the appropriate response to environmental threats. RbohD and RbohF, two of the ten Rboh genes present in Arabidopsis, are pleiotropic and mediate diverse physiological processes in response to pathogens. One aspect that may prove critical to determine the multiplicity of functions of RbohD and RbohF is the spatio-temporal control of their gene expression. Thus, we generated Arabidopsis transgenic lines with RbohD- and RbohF-promoter fusions to the β-glucuronidase and the luciferase reporter genes. These transgenics were employed to reveal RbohD and RbohF promoter activity during Arabidopsis immune response to the pathogenic bacterium Pseudomonas syringae pv tomato DC3000, the necrotrophic fungus Plectosphaerella cucumerina and in response to immunity-related cues. Our experiments revealed a differential expression pattern of RbohD and RbohF throughout plant development and during Arabidopsis immune response. Moreover, we observed a correlation between the level of RbohD and RbohF promoter activity, the accumulation of ROS and the amount of cell death in response to pathogens. RbohD and RbohF gene expression was also differentially modulated by pathogen associated molecular patterns and abscisic acid. Interestingly, a promoter-swap strategy revealed the requirement for the promoter region of RbohD to drive the production of ROS in response to P. cucumerina. Additionally, since the RbohD promoter was activated during Arabidopsis interaction with a non-adapted P. cucumerina isolate 2127, we performed susceptibility tests to this fungal isolate that uncovered a new role of these oxidases on non-host resistance. The interplay between RBOH-dependent signaling with other components of the plant immune response might also explain the different immunity-related functions mediated by these oxidases. Among the plethora of signals coordinated with RBOH activity, pharmacological and genetic evidence indicates that heterotrimeric G proteins are involved in some of the signaling pathways mediated by RBOH–derived ROS in response to environmental cues. Therefore, we analysed the interplay between these RBOH-NADPH oxidases and AGB1, the Arabidopsis β-subunit of heterotrimeric G proteins during Arabidopsis immune response. We carried out epistasis studies that allowed us to test the implication of AGB1 in different RBOH-mediated defense signaling pathways. Our results illustrate the complex relationship between RBOH and heterotrimeric G proteins signaling, that varies depending on the type of plant-pathogen interaction. Furthermore, we tested the potential association between AGB1 with RBOHD and RBOHF during early immunity. Interestingly, our co-immunoprecipitation experiments point towards an association of AGB1 and the RBOHD regulatory kinase BIK1, thus providing a putative mechanism in the control of the NADPH oxidase function by AGB1. Taken all together, these studies provide further insights into the role that transcriptional control or the interaction with heterotrimeric G-proteins have on RBOH-NADPH oxidase-dependent ROS production and signaling in immunity. Our work exemplifies how, through a differential regulation, two members of a multigenic family achieve specialized physiological functions using a common enzymatic mechanism.

Biometric authentication of users through iris by using key binding and similarity preserving hash functions = Autenticación biométrica de usuarios a través del iris mediante la ocultación de claves y funciones resumen que preservan la similitud

El extraordinario auge de las nuevas tecnologías de la información, el desarrollo de la Internet de las Cosas, el comercio electrónico, las redes sociales, la telefonía móvil y la computación y almacenamiento en la nube, han proporcionado grandes beneficios en todos los ámbitos de la sociedad. Junto a éstos, se presentan nuevos retos para la protección y privacidad de la información y su contenido, como la suplantación de personalidad y la pérdida de la confidencialidad e integridad de los documentos o las comunicaciones electrónicas. Este hecho puede verse agravado por la falta de una frontera clara que delimite el mundo personal del mundo laboral en cuanto al acceso de la información. En todos estos campos de la actividad personal y laboral, la Criptografía ha jugado un papel fundamental aportando las herramientas necesarias para garantizar la confidencialidad, integridad y disponibilidad tanto de la privacidad de los datos personales como de la información. Por otro lado, la Biometría ha propuesto y ofrecido diferentes técnicas con el fin de garantizar la autentificación de individuos a través del uso de determinadas características personales como las huellas dáctilares, el iris, la geometría de la mano, la voz, la forma de caminar, etc. Cada una de estas dos ciencias, Criptografía y Biometría, aportan soluciones a campos específicos de la protección de datos y autentificación de usuarios, que se verían enormemente potenciados si determinadas características de ambas ciencias se unieran con vistas a objetivos comunes. Por ello es imperativo intensificar la investigación en estos ámbitos combinando los algoritmos y primitivas matemáticas de la Criptografía con la Biometría para dar respuesta a la demanda creciente de nuevas soluciones más técnicas, seguras y fáciles de usar que potencien de modo simultáneo la protección de datos y la identificacíón de usuarios. En esta combinación el concepto de biometría cancelable ha supuesto una piedra angular en el proceso de autentificación e identificación de usuarios al proporcionar propiedades de revocación y cancelación a los ragos biométricos. La contribución de esta tesis se basa en el principal aspecto de la Biometría, es decir, la autentificación segura y eficiente de usuarios a través de sus rasgos biométricos, utilizando tres aproximaciones distintas: 1. Diseño de un esquema criptobiométrico borroso que implemente los principios de la biometría cancelable para identificar usuarios lidiando con los problemas acaecidos de la variabilidad intra e inter-usuarios. 2. Diseño de una nueva función hash que preserva la similitud (SPHF por sus siglas en inglés). Actualmente estas funciones se usan en el campo del análisis forense digital con el objetivo de buscar similitudes en el contenido de archivos distintos pero similares de modo que se pueda precisar hasta qué punto estos archivos pudieran ser considerados iguales. La función definida en este trabajo de investigación, además de mejorar los resultados de las principales funciones desarrolladas hasta el momento, intenta extender su uso a la comparación entre patrones de iris. 3. Desarrollando un nuevo mecanismo de comparación de patrones de iris que considera tales patrones como si fueran señales para compararlos posteriormente utilizando la transformada de Walsh-Hadarmard. Los resultados obtenidos son excelentes teniendo en cuenta los requerimientos de seguridad y privacidad mencionados anteriormente. Cada uno de los tres esquemas diseñados han sido implementados para poder realizar experimentos y probar su eficacia operativa en escenarios que simulan situaciones reales: El esquema criptobiométrico borroso y la función SPHF han sido implementados en lenguaje Java mientras que el proceso basado en la transformada de Walsh-Hadamard en Matlab. En los experimentos se ha utilizado una base de datos de imágenes de iris (CASIA) para simular una población de usuarios del sistema. En el caso particular de la función de SPHF, además se han realizado experimentos para comprobar su utilidad en el campo de análisis forense comparando archivos e imágenes con contenido similar y distinto. En este sentido, para cada uno de los esquemas se han calculado los ratios de falso negativo y falso positivo. ABSTRACT The extraordinary increase of new information technologies, the development of Internet of Things, the electronic commerce, the social networks, mobile or smart telephony and cloud computing and storage, have provided great benefits in all areas of society. Besides this fact, there are new challenges for the protection and privacy of information and its content, such as the loss of confidentiality and integrity of electronic documents and communications. This is exarcebated by the lack of a clear boundary between the personal world and the business world as their differences are becoming narrower. In both worlds, i.e the personal and the business one, Cryptography has played a key role by providing the necessary tools to ensure the confidentiality, integrity and availability both of the privacy of the personal data and information. On the other hand, Biometrics has offered and proposed different techniques with the aim to assure the authentication of individuals through their biometric traits, such as fingerprints, iris, hand geometry, voice, gait, etc. Each of these sciences, Cryptography and Biometrics, provides tools to specific problems of the data protection and user authentication, which would be widely strengthen if determined characteristics of both sciences would be combined in order to achieve common objectives. Therefore, it is imperative to intensify the research in this area by combining the basics mathematical algorithms and primitives of Cryptography with Biometrics to meet the growing demand for more secure and usability techniques which would improve the data protection and the user authentication. In this combination, the use of cancelable biometrics makes a cornerstone in the user authentication and identification process since it provides revocable or cancelation properties to the biometric traits. The contributions in this thesis involve the main aspect of Biometrics, i.e. the secure and efficient authentication of users through their biometric templates, considered from three different approaches. The first one is designing a fuzzy crypto-biometric scheme using the cancelable biometric principles to take advantage of the fuzziness of the biometric templates at the same time that it deals with the intra- and inter-user variability among users without compromising the biometric templates extracted from the legitimate users. The second one is designing a new Similarity Preserving Hash Function (SPHF), currently widely used in the Digital Forensics field to find similarities among different files to calculate their similarity level. The function designed in this research work, besides the fact of improving the results of the two main functions of this field currently in place, it tries to expand its use to the iris template comparison. Finally, the last approach of this thesis is developing a new mechanism of handling the iris templates, considering them as signals, to use the Walsh-Hadamard transform (complemented with three other algorithms) to compare them. The results obtained are excellent taking into account the security and privacy requirements mentioned previously. Every one of the three schemes designed have been implemented to test their operational efficacy in situations that simulate real scenarios: The fuzzy crypto-biometric scheme and the SPHF have been implemented in Java language, while the process based on the Walsh-Hadamard transform in Matlab. The experiments have been performed using a database of iris templates (CASIA-IrisV2) to simulate a user population. The case of the new SPHF designed is special since previous to be applied i to the Biometrics field, it has been also tested to determine its applicability in the Digital Forensic field comparing similar and dissimilar files and images. The ratios of efficiency and effectiveness regarding user authentication, i.e. False Non Match and False Match Rate, for the schemes designed have been calculated with different parameters and cases to analyse their behaviour.

Applications of Formal Languages to Management of Manned and Unmanned Aircraft

En el futuro, la gestión del tráfico aéreo (ATM, del inglés air traffic management) requerirá un cambio de paradigma, de la gestión principalmente táctica de hoy, a las denominadas operaciones basadas en trayectoria. Un incremento en el nivel de automatización liberará al personal de ATM —controladores, tripulación, etc.— de muchas de las tareas que realizan hoy. Las personas seguirán siendo el elemento central en la gestión del tráfico aéreo del futuro, pero lo serán mediante la gestión y toma de decisiones. Se espera que estas dos mejoras traigan un incremento en la eficiencia de la gestión del tráfico aéreo que permita hacer frente al incremento previsto en la demanda de transporte aéreo. Para aplicar el concepto de operaciones basadas en trayectoria, el usuario del espacio aéreo (la aerolínea, piloto, u operador) y el proveedor del servicio de navegación aérea deben negociar las trayectorias mediante un proceso de toma de decisiones colaborativo. En esta negociación, es necesaria una forma adecuada de compartir dichas trayectorias. Compartir la trayectoria completa requeriría un gran ancho de banda, y la trayectoria compartida podría invalidarse si cambiase la predicción meteorológica. En su lugar, podría compartirse una descripción de la trayectoria independiente de las condiciones meteorológicas, de manera que la trayectoria real se pudiese calcular a partir de dicha descripción. Esta descripción de la trayectoria debería ser fácil de procesar usando un programa de ordenador —ya que parte del proceso de toma de decisiones estará automatizado—, pero también fácil de entender para un operador humano —que será el que supervise el proceso y tome las decisiones oportunas—. Esta tesis presenta una serie de lenguajes formales que pueden usarse para este propósito. Estos lenguajes proporcionan los medios para describir trayectorias de aviones durante todas las fases de vuelo, desde la maniobra de push-back (remolcado hasta la calle de rodaje), hasta la llegada a la terminal del aeropuerto de destino. También permiten describir trayectorias tanto de aeronaves tripuladas como no tripuladas, incluyendo aviones de ala fija y cuadricópteros. Algunos de estos lenguajes están estrechamente relacionados entre sí, y organizados en una jerarquía. Uno de los lenguajes fundamentales de esta jerarquía, llamado aircraft intent description language (AIDL), ya había sido desarrollado con anterioridad a esta tesis. Este lenguaje fue derivado de las ecuaciones del movimiento de los aviones de ala fija, y puede utilizarse para describir sin ambigüedad trayectorias de este tipo de aeronaves. Una variante de este lenguaje, denominada quadrotor AIDL (QR-AIDL), ha sido desarrollada en esta tesis para permitir describir trayectorias de cuadricópteros con el mismo nivel de detalle. Seguidamente, otro lenguaje, denominado intent composite description language (ICDL), se apoya en los dos lenguajes anteriores, ofreciendo más flexibilidad para describir algunas partes de la trayectoria y dejar otras sin especificar. El ICDL se usa para proporcionar descripciones genéricas de maniobras comunes, que después se particularizan y combinan para formar descripciones complejas de un vuelo. Otro lenguaje puede construirse a partir del ICDL, denominado flight intent description language (FIDL). El FIDL especifica requisitos de alto nivel sobre las trayectorias —incluyendo restricciones y objetivos—, pero puede utilizar características del ICDL para proporcionar niveles de detalle arbitrarios en las distintas partes de un vuelo. Tanto el ICDL como el FIDL han sido desarrollados en colaboración con Boeing Research & Technology Europe (BR&TE). También se ha desarrollado un lenguaje para definir misiones en las que interactúan varias aeronaves, el mission intent description language (MIDL). Este lenguaje se basa en el FIDL y mantiene todo su poder expresivo, a la vez que proporciona nuevas semánticas para describir tareas, restricciones y objetivos relacionados con la misión. En ATM, los movimientos de un avión en la superficie de aeropuerto también tienen que ser monitorizados y gestionados. Otro lenguaje formal ha sido diseñado con este propósito, llamado surface movement description language (SMDL). Este lenguaje no pertenece a la jerarquía de lenguajes descrita en el párrafo anterior, y se basa en las clearances (autorizaciones del controlador) utilizadas durante las operaciones en superficie de aeropuerto. También proporciona medios para expresar incertidumbre y posibilidad de cambios en las distintas partes de la trayectoria. Finalmente, esta tesis explora las aplicaciones de estos lenguajes a la predicción de trayectorias y a la planificación de misiones. El concepto de trajectory language processing engine (TLPE) se usa en ambas aplicaciones. Un TLPE es una función de ATM cuya principal entrada y salida se expresan en cualquiera de los lenguajes incluidos en la jerarquía descrita en esta tesis. El proceso de predicción de trayectorias puede definirse como una combinación de TLPEs, cada uno de los cuales realiza una pequeña sub-tarea. Se le ha dado especial importancia a uno de estos TLPEs, que se encarga de generar el perfil horizontal, vertical y de configuración de la trayectoria. En particular, esta tesis presenta un método novedoso para la generación del perfil vertical. El proceso de planificar una misión también se puede ver como un TLPE donde la entrada se expresa en MIDL y la salida consiste en cierto número de trayectorias —una por cada aeronave disponible— descritas utilizando FIDL. Se ha formulado este problema utilizando programación entera mixta. Además, dado que encontrar caminos óptimos entre distintos puntos es un problema fundamental en la planificación de misiones, también se propone un algoritmo de búsqueda de caminos. Este algoritmo permite calcular rápidamente caminos cuasi-óptimos que esquivan todos los obstáculos en un entorno urbano. Los diferentes lenguajes formales definidos en esta tesis pueden utilizarse como una especificación estándar para la difusión de información entre distintos actores de la gestión del tráfico aéreo. En conjunto, estos lenguajes permiten describir trayectorias con el nivel de detalle necesario en cada aplicación, y se pueden utilizar para aumentar el nivel de automatización explotando esta información utilizando sistemas de soporte a la toma de decisiones. La aplicación de estos lenguajes a algunas funciones básicas de estos sistemas, como la predicción de trayectorias, han sido analizadas. ABSTRACT Future air traffic management (ATM) will require a paradigm shift from today’s mainly tactical ATM to trajectory-based operations (TBOs). An increase in the level of automation will also relieve humans —air traffic control officers (ATCOs), flight crew, etc.— from many of the tasks they perform today. Humans will still be central in this future ATM, as decision-makers and managers. These two improvements (TBOs and increased automation) are expected to provide the increase in ATM performance that will allow coping with the expected increase in air transport demand. Under TBOs, trajectories are negotiated between the airspace user (an airline, pilot, or operator) and the air navigation service provider (ANSP) using a collaborative decision making (CDM) process. A suitable method for sharing aircraft trajectories is necessary for this negotiation. Sharing a whole trajectory would require a high amount of bandwidth, and the shared trajectory might become invalid if the weather forecast changed. Instead, a description of the trajectory, decoupled from the weather conditions, could be shared, so that the actual trajectory could be computed from this trajectory description. This trajectory description should be easy to process using a computing program —as some of the CDM processes will be automated— but also easy to understand for a human operator —who will be supervising the process and making decisions. This thesis presents a series of formal languages that can be used for this purpose. These languages provide the means to describe aircraft trajectories during all phases of flight, from push back to arrival at the gate. They can also describe trajectories of both manned and unmanned aircraft, including fixedwing and some rotary-wing aircraft (quadrotors). Some of these languages are tightly interrelated and organized in a language hierarchy. One of the key languages in this hierarchy, the aircraft intent description language (AIDL), had already been developed prior to this thesis. This language was derived from the equations of motion of fixed-wing aircraft, and can provide an unambiguous description of fixed-wing aircraft trajectories. A variant of this language, the quadrotor AIDL (QR-AIDL), is developed in this thesis to allow describing a quadrotor aircraft trajectory with the same level of detail. Then, the intent composite description language (ICDL) is built on top of these two languages, providing more flexibility to describe some parts of the trajectory while leaving others unspecified. The ICDL is used to provide generic descriptions of common aircraft manoeuvres, which can be particularized and combined to form complex descriptions of flight. Another language is built on top of the ICDL, the flight intent description language (FIDL). The FIDL specifies high-level requirements on trajectories —including constraints and objectives—, but can use features of the ICDL to provide arbitrary levels of detail in different parts of the flight. The ICDL and FIDL have been developed in collaboration with Boeing Research & Technology Europe (BR&TE). Also, the mission intent description language (MIDL) has been developed to allow describing missions involving multiple aircraft. This language is based on the FIDL and keeps all its expressive power, while it also provides new semantics for describing mission tasks, mission objectives, and constraints involving several aircraft. In ATM, the movement of aircraft while on the airport surface also has to be monitored and managed. Another formal language has been designed for this purpose, denoted surface movement description language (SMDL). This language does not belong to the language hierarchy described above, and it is based on the clearances used in airport surface operations. Means to express uncertainty and mutability of different parts of the trajectory are also provided. Finally, the applications of these languages to trajectory prediction and mission planning are explored in this thesis. The concept of trajectory language processing engine (TLPE) is used in these two applications. A TLPE is an ATM function whose main input and output are expressed in any of the languages in the hierarchy described in this thesis. A modular trajectory predictor is defined as a combination of multiple TLPEs, each of them performing a small subtask. Special attention is given to the TLPE that builds the horizontal, vertical, and configuration profiles of the trajectory. In particular, a novel method for the generation of the vertical profile is presented. The process of planning a mission can also be seen as a TLPE, where the main input is expressed in the MIDL and the output consists of a number of trajectory descriptions —one for each aircraft available in the mission— expressed in the FIDL. A mixed integer linear programming (MILP) formulation for the problem of assigning mission tasks to the available aircraft is provided. In addition, since finding optimal paths between locations is a key problem to mission planning, a novel path finding algorithm is presented. This algorithm can compute near-shortest paths avoiding all obstacles in an urban environment in very short times. The several formal languages described in this thesis can serve as a standard specification to share trajectory information among different actors in ATM. In combination, these languages can describe trajectories with the necessary level of detail for any application, and can be used to increase automation by exploiting this information using decision support tools (DSTs). Their applications to some basic functions of DSTs, such as trajectory prediction, have been analized.

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

PREMISE OF THE STUDY: We conducted environmental niche modeling (ENM) of the Brachypodium distachyon s.l. complex, a model group of two diploid annual grasses ( B. distachyon , B. stacei ) and their derived allotetraploid ( B. hybridum) , native to the circum-Mediterranean region. We (1) investigated the ENMs of the three species in their native range based on present and past climate data; (2) identifi ed potential overlapping niches of the diploids and their hybrid across four Quaternary windows; (3) tested whether speciation was associated with niche divergence/conservatism in the complex species; and (4) tested for the potential of the polyploid outperforming the diploids in the native range. M ETHODS: Geo-referenced data, altitude, and 19 climatic variables were used to construct the ENMs. We used paleoclimate niche models to trace the potential existence of ancestral gene fl ow among the hybridizing species of the complex. KEY RESULTS: Brachypodium distachyon grows in higher, cooler, and wetter places, B. stacei in lower, warmer, and drier places, and B. hybridum in places with intermediate climatic features. Brachypodium hybridum had the largest niche overlap with its parent niches, but a similar distribution range and niche breadth. C ONCLUSIONS: Each species had a unique environmental niche though there were multiple niche overlapping areas for the diploids across time, suggesting the potential existence of several hybrid zones during the Pleistocene and the Holocene. No evidence of niche divergence was found, suggesting that species diversifi cation was not driven by ecological speciation but by evolutionary history, though it could be associated to distinct environmental adaptations.

Scar, a WASp-related protein, activates nucleation of actin filaments by the Arp2/3 complex

The Arp2/3 complex, a stable assembly of two actin-related proteins (Arp2 and Arp3) with five other subunits, caps the pointed end of actin filaments and nucleates actin polymerization with low efficiency. WASp and Scar are two similar proteins that bind the p21 subunit of the Arp2/3 complex, but their effect on the nucleation activity of the complex was not known. We report that full-length, recombinant human Scar protein, as well as N-terminally truncated Scar proteins, enhance nucleation by the Arp2/3 complex. By themselves, these proteins either have no effect or inhibit actin polymerization. The actin monomer-binding W domain and the p21-binding A domain from the C terminus of Scar are both required to activate Arp2/3 complex. A proline-rich domain in the middle of Scar enhances the activity of the W and A domains. Preincubating Scar and Arp2/3 complex with actin filaments overcomes the initial lag in polymerization, suggesting that efficient nucleation by the Arp2/3 complex requires assembly on the side of a preexisting filament—a dendritic nucleation mechanism. The Arp2/3 complex with full-length Scar, Scar containing P, W, and A domains, or Scar containing W and A domains overcomes inhibition of nucleation by the actin monomer-binding protein profilin, giving active nucleation over a low background of spontaneous nucleation. These results show that Scar and, likely, related proteins, such as the Cdc42 targets WASp and N-WASp, are endogenous activators of actin polymerization by the Arp2/3 complex.

Protein kinase mutants of human ATR increase sensitivity to UV and ionizing radiation and abrogate cell cycle checkpoint control

In fission yeast, the rad3 gene product plays a critical role in sensing DNA structure defects and activating damage response pathways. A structural homologue of rad3 in humans (ATR) has been identified based on sequence similarity in the protein kinase domain. General information regarding ATR expression, protein kinase activity, and cellular localization is known, but its function in human cells remains undetermined. In the current study, the ATR protein was examined by gel filtration of protein extracts and was found to exist predominantly as part of a large protein complex. A kinase-inactivated form of the ATR gene was prepared by site-directed mutagenesis and was used in transfection experiments to probe the function of this complex. Introduction of this kinase-dead ATR into a normal fibroblast cell line, an ATM-deficient fibroblast line derived from a patient with ataxia–telangiectasia, or a p53 mutant cell line all resulted in significant losses in cell viability. Clones expressing the kinase-dead ATR displayed increased sensitivity to x-rays and UV and a loss of checkpoint control. We conclude that ATR functions as a critical part of a protein complex that mediates responses to ionizing and UV radiation in human cells. These responses include effects on cell viability and cell cycle checkpoint control.

Opening of a monomer-monomer interface of the trimeric bacteriophage T4-coded GP45 sliding clamp is required for clamp loading onto DNA

The replication system of bacteriophage T4 uses a trimeric ring-shaped processivity clamp (gp45) to tether the replication polymerase (gp43) to the template-primer DNA. This ring is placed onto the DNA by an ATPase-driven clamp-loading complex (gp44/62) where it then transfers, in closed form, to the polymerase. It generally has been assumed that one of the functions of the loading machinery is to open the clamp to place it around the DNA. However, the mechanism by which this occurs has not been fully defined. In this study we design and characterize a double-mutant gp45 protein that contains pairs of cysteine residues located at each monomer-monomer interface of the trimeric clamp. This mutant protein is functionally equivalent to wild-type gp45. However, when all three monomer-monomer interfaces are tethered by covalent crosslinks formed (reversibly or irreversibly) between the cysteine pairs these closed clamps can no longer be loaded onto the DNA nor onto the polymerase, effectively eliminating processive strand-displacement DNA synthesis. Analysis of the individual steps of the clamp-loading process shows that the ATPase-dependent interactions between the clamp and the clamp loader that precede DNA binding are hyperstimulated by the covalently crosslinked ring, suggesting that binding of the closed ring induces a futile, ATP-driven, ring-opening cycle. These findings and others permit further characterization and ordering of the steps involved in the T4 clamp-loading process.

Characterization of human telomerase complex

Telomerase, a ribonucleoprotein complex, adds hexameric repeats called “telomeres” to the growing ends of chromosomal DNA. Characterization of mammalian telomerase has been elusive because of its low level of expression. We describe a bioinformatics approach to enrich and characterize the human telomerase complex. Using local sequence homology search methods, we detected similarity of the Tetrahymena p80 subunit of telomerase with the autoantigen Ro60. Antibodies to Ro60 immunoprecipitated the telomerase activity. Ro60 and p80 proteins were cross-recognizable by antibodies to either protein. Telomerase activity and the RNA component of telomerase complex were localized to a doublet in a native gel from the Ro60 antibody-precipitated material. The enriched material showed specific binding to a TTA GGG probe in vitro in an RNA template-dependent manner. Polyclonal antibodies to the doublet also immunoprecipitated the telomerase activity. These results suggest an evolutionary conservation of the telomerase proteins.

Use of intrinsic modes in biology: Examples of indicial response of pulmonary blood pressure to ± step hypoxia

Recently, a new method to analyze biological nonstationary stochastic variables has been presented. The method is especially suitable to analyze the variation of one biological variable with respect to changes of another variable. Here, it is illustrated by the change of the pulmonary blood pressure in response to a step change of oxygen concentration in the gas that an animal breathes. The pressure signal is resolved into the sum of a set of oscillatory intrinsic mode functions, which have zero “local mean,” and a final nonoscillatory mode. With this device, we obtain a set of “mean trends,” each of which represents a “mean” in a definitive sense, and together they represent the mean trend systematically with different degrees of oscillatory content. Correspondingly, the oscillatory content of the signal about any mean trend can be represented by a set of partial sums of intrinsic mode functions. When the concept of “indicial response function” is used to describe the change of one variable in response to a step change of another variable, we now have a set of indicial response functions of the mean trends and another set of indicial response functions to describe the energy or intensity of oscillations about each mean trend. Each of these can be represented by an analytic function whose coefficients can be determined by a least-squares curve-fitting procedure. In this way, experimental results are stated sharply by analytic functions.

Recruitment of IRAK to the interleukin 1 receptor complex requires interleukin 1 receptor accessory protein

The proinflammatory cytokine interleukin 1 (IL-1) activates the transcription of many genes encoding acute phase and proinflammatory proteins, a function mediated primarily by the transcription factor NF-κB. An early IL-1 signaling event is the recruitment of the Ser/Thr kinase IRAK to the type I IL-1 receptor (IL-1RI). Here we describe the function of a previously identified IL-1 receptor subunit designated IL-1 receptor accessory protein (IL-1RAcP). IL-1 treatment of cells induces the formation of a complex containing both IL-1RI and IL-1RAcP. IRAK is recruited to this complex through its association with IL-1RAcP. Overexpression of an IL-1RAcP mutant lacking its intracellular domain, the IRAK-binding domain, prevented the recruitment of IRAK to the receptor complex and blocked IL-1-induced NF-κB activation.

Negative regulation of mitosis in fission yeast by the Shk1interacting protein Skb1 and its human homolog, Skb1Hs

We previously provided evidence that the protein encoded by the highly conserved skb1 gene is a putative regulator of Shk1, a p21Cdc42/Rac-activated kinase (PAK) homolog in the fission yeast Schizosaccharomyces pombe. skb1 null mutants are viable and competent for mating but less elongate than wild-type S. pombe cells, whereas cells that overexpress skb1 are hyperelongated. These phenotypes suggest a possible role for Skb1 as a mitotic inhibitor. Here we show genetic interactions of both skb1 and shk1 with genes encoding key mitotic regulators in S. pombe. Our results indicate that Skb1 negatively regulates mitosis by a mechanism that is independent of the Cdc2-activating phosphatase Cdc25 but that is at least partially dependent on Shk1 and the Cdc2 inhibitory kinase Wee1. We provide biochemical evidence for association of Skb1 and Shk1 with Cdc2 in S. pombe, suggesting that Skb1 and Shk1 inhibit mitosis through interaction with the Cdc2 complex, rather than by an indirect mechanism. These results provide evidence of a previously undescribed role for PAK-related protein kinases as mitotic inhibitors. We also describe the cloning of a human homolog of skb1, SKB1Hs, and show that it can functionally replace skb1 in S. pombe. Thus, the molecular functions of Skb1-related proteins have likely been substantially conserved through evolution.

Cloning and characterization of a corepressor and potential component of the nuclear hormone receptor repression complex

Nuclear hormone receptors are potent repressors of transcription in the unliganded state. We describe here the cloning of a nuclear receptor corepressor that we call SUN-CoR (Small Unique Nuclear receptor CoRepressor), which shows no homology to previously described nuclear hormone receptor corepressors, N-CoR, or SMRT. SUN-CoR is a highly basic, 16-kDa nuclear protein that is expressed at high levels in adult tissues and is induced during adipocyte and myogenic differentiation. SUN-CoR potentiates transcriptional repression by thyroid hormone receptor and RevErb in vivo, represses transcription when fused to a heterologous DNA binding domain, and interacts with RevErb as well as with thyroid hormone receptor in vitro. SUN-CoR also interacts with N-CoR and SMRT in vitro and with endogenous N-CoR in cells. We conclude that SUN-CoR is a corepressor and may function as an additional component of the complex involved in transcriptional repression by unliganded and orphan nuclear hormone receptors.

Multiple Functions for Actin during Filamentous Growth of Saccharomyces cerevisiaeV⃞

Saccharomyces cerevisiae is dimorphic and switches from a yeast form to a pseudohyphal (PH) form when starved for nitrogen. PH cells are elongated, bud in a unipolar manner, and invade the agar substrate. We assessed the requirements for actin in mediating the dramatic morphogenetic events that accompany the transition to PH growth. Twelve “alanine scan” alleles of the single yeast actin gene (ACT1) were tested for effects on filamentation, unipolar budding, agar invasion, and cell elongation. Some act1 mutations affect all phenotypes, whereas others affect only one or two aspects of PH growth. Tests of intragenic complementation among specific act1 mutations support the phenotypic evidence for multiple actin functions in filamentous growth. We present evidence that interaction between actin and the actin-binding protein fimbrin is important for PH growth and suggest that association of different actin-binding proteins with actin mediates the multiple functions of actin in filamentous growth. Furthermore, characterization of cytoskeletal structure in wild type and act1/act1 mutants indicates that PH cell morphogenesis requires the maintenance of a highly polarized actin cytoskeleton. Collectively, this work demonstrates that actin plays a central role in fungal dimorphism.

Characterization of a Fourth Adaptor-related Protein Complex

Adaptor protein complexes (APs) function as vesicle coat components in different membrane traffic pathways; however, there are a number of pathways for which there is still no candidate coat. To find novel coat components related to AP complexes, we have searched the expressed sequence tag database and have identified, cloned, and sequenced a new member of each of the four AP subunit families. We have shown by a combination of coimmunoprecipitation and yeast two-hybrid analysis that these four proteins (ε, β4, μ4, and ς4) are components of a novel adaptor-like heterotetrameric complex, which we are calling AP-4. Immunofluorescence reveals that AP-4 is localized to ∼10–20 discrete dots in the perinuclear region of the cell. This pattern is disrupted by treating the cells with brefeldin A, indicating that, like other coat proteins, the association of AP-4 with membranes is regulated by the small GTPase ARF. Immunogold electron microscopy indicates that AP-4 is associated with nonclathrin-coated vesicles in the region of the trans-Golgi network. The μ4 subunit of the complex specifically interacts with a tyrosine-based sorting signal, indicating that, like the other three AP complexes, AP-4 is involved in the recognition and sorting of cargo proteins with tyrosine-based motifs. AP-4 is of relatively low abundance, but it is expressed ubiquitously, suggesting that it participates in a specialized trafficking pathway but one that is required in all cell types.