Characteristics of the turbulent/nonturbulent interface in boundary layers, jets and shear-free turbulence

The characteristics of turbulent/nonturbulent interfaces (TNTI) from boundary layers, jets and shear-free turbulence are compared using direct numerical simulations. The TNTI location is detected by assessing the volume of turbulent flow as function of the vorticity magnitude and is shown to be equivalent to other procedures using a scalar field. Vorticity maps show that the boundary layer contains a larger range of scales at the interface than in jets and shear-free turbulence where the change in vorticity characteristics across the TNTI is much more dramatic. The intermittency parameter shows that the extent of the intermittency region for jets and boundary layers is similar and is much bigger than in shear-free turbulence, and can be used to compute the vorticity threshold defining the TNTI location. The statistics of the vorticity jump across the TNTI exhibit the imprint of a large range of scales, from the Kolmogorov micro-scale to scales much bigger than the Taylor scale. Finally, it is shown that contrary to the classical view, the low-vorticity spots inside the jet are statistically similar to isotropic turbulence, suggesting that engulfing pockets simply do not exist in jets

Dinámicas de ocupación urbana del Anillo Verde metropolitano, desde sus orígenes en el Plan General del Área Metropolitana de Madrid de 1963 hasta el Plan General de Ordenación Urbana de 1997

El Anillo Verde metropolitano, definido por el Plan General de Ordenación Urbana del Área Metropolitana de Madrid en 1963 siguiendo los modelos planteados por la cultura urbanística internacional, como armadura de la estructura urbana del AMM, espacio protagonista dentro del sistema de espacios libres, lugar de uso público destinado al recreo y contacto con la naturaleza de la población madrileña, se convierte en realidad en una reserva de suelo que va entrando en juego motivado por las alianzas entre el poder institucional y la clase social dominante actuando al margen del planeamiento, poniendo en evidencia la escasez de recursos legales y culturales disponibles para la salvaguarda de los intereses comunes y, donde los condicionantes geográficos y naturales del territorio madrileño han influido decisivamente en la especialización funcional y espacial del Área Metropolitana de Madrid. Así pues considerando esta idea como HIPÓTESIS, el objetivo de la TESIS sería demostrarla, para lo cual se hace necesario primero, acotar espacial y temporalmente el objeto de estudio, es decir, del Anillo Verde metropolitano1, segundo, contextualizar histórica y disciplinarmente los presupuestos teóricos que conformaban la idea del Anillo Verde, tercero, reconocer, localizar y documentar las piezas que han ido materializando la ocupación urbana del Anillo Verde, clasificándolas según parámetros temporales, funcionales, urbanísticos y, formales, lo que permite analizar la geografía, uso, instrumentación y forma de su transformación a escala general metropolitana y, cuarto, profundizar a modo de comprobación a escala municipal y urbana en dos escenarios representativos del conjunto metropolitano: el municipio de Pozuelo de Alarcón y el distrito de Hortaleza-Barajas. El contenido del documento se divide en tres bloques, el bloque I, se centra en las bases teóricas, el bloque II sitúa el hilo argumental de la tesis a escala metropolitana y el bloque III comprueba el fenómeno a escala municipal y urbana. De esta forma, se comienza por la comprensión del significado del concepto del Anillo Verde, que va más allá de la dimensión instrumental asignada de límite y contención urbana frente al crecimiento de la ciudad industrial de principios del siglo XX, basada en la descentralización de la ciudad tradicional, para adquirir un significado más complejo, como gran espacio de reserva y salvaguarda de valores naturales y culturales que se expresaban en su territorio y que permitirían alcanzar el equilibrio entre la ciudad y sus habitantes, es decir, entre el hombre y el espacio que habita. Se hace un recorrido por las principales corrientes urbanísticas que se van nutriendo de distintas disciplinas (economía, sociología, geografía, biología, ecología) para plantear teorías que permitieran materializar un nuevo orden urbano según principios de equidad social, económica y ambiental, en una secuencia donde Europa y Estados Unidos realizaban un constante intercambio -el movimiento de la Ciudad Jardín o el Regionalismo, que dieron paso a propuestas como el Greater London o el Gran Berlín, donde la figura del Anillo Verde tenía un papel protagonista, y del que también participaría nuestro país y la ciudad de Madrid, con modelos regionales como el Plan Besteiro y urbanos como el Plan Bidagor, antecedentes directos del Plan General de Ordenación Urbana del Área Metropolitana de Madrid de 1963 que pone en marcha la ordenación del crecimiento metropolitano de Madrid. El hilo argumental de la tesis se organiza en una doble aproximación: un acercamiento a escala metropolitana a partir del reconocimiento del modelo de ciudad definido en los distintos planes generales que acompañaron el desarrollo metropolitano (municipio de Madrid y de los siete términos municipales que rodeaban a este y que tenían suelo destinado a Anillo Verde), haciendo referencia además a las relaciones con el planeamiento regional, concretando en una escala de aproximación municipal que avanza hasta la interpretación urbana detallada. El primer acercamiento tiene lugar en el bloque II y se organiza en tres capítulos. El capítulo 4 se dedica al punto obligado de partida de la geografía local, describiendo las características biofísicas de los terrenos que formaban parte del Anillo Verde, que han marcado históricamente la forma de aprovechamiento del territorio, desde las extensiones de bosques mediterráneos al norte y al oeste continuación del Monte del Pardo, a los distintos tipos de cultivo que se adaptaban al sustrato geológico y la forma del terreno (de las suaves ondulaciones de sedimentos arcósicos al norte a las extensas plataformas arenosas y yesíferas del sur), además de las zonas de huertos aprovechando las depresiones y los cursos de agua (arroyo del Monte Carmelo, arroyo de Valdebebas, arroyo del Quinto, arroyo del Santo, arroyo Butarque, arroyo Meaques y arroyo Pozuelo). Una vez reconocida la realidad física, el capítulo 5, avanza en la descripción de los distintos modelos de ciudad propuestos desde el planeamiento urbanístico, en sus distintas escalas, la regional y la municipal, como respuesta a la coyuntura social, económica y política que ha caracterizado el proceso de ocupación del Anillo Verde al compás de la construcción del AMM. Se han reunido las propuestas de planeamiento municipal de los distintos municipios que disponían de terreno calificado como Anillo Verde: Madrid, Coslada, Getafe, Leganés, Alcorcón, Boadilla del Monte y Pozuelo de Alarcón. Además se han incorporado las distintas propuestas de ordenación territorial que han servido de referencia al planeamiento municipal, en todas sus versiones, desde las sectoriales, de mayor éxito y apoyo institucional, a los distintos intentos de ordenación integral, de mayor complejidad pero de menor calado, precisamente por la dificultad de consenso entre la ordenación física y el desarrollo económico, entre los intereses privados y el beneficio público. El primer horizonte, comienza con la formulación del Plan General de Ordenación Urbana del Área Metropolitana de Madrid de 1963, su desarrollo y la puesta en marcha de los primeros planes municipales en la década de los años setenta, donde se comprueba la necesidad de un marco regional que “ordene” el territorio de forma integral y sirva de referencia a las actuaciones sectoriales que habían marcado el primer desarrollo metropolitano. El segundo, se sitúa dos décadas más tarde con la aprobación del Plan General de Ordenación Urbana de Madrid de 1985 y el conjunto de planes municipales de los términos limítrofes, que siguen su filosofía de austeridad en cuanto a crecimiento territorial. El tercero se inicia en 1997 con la siguiente generación de planes de corte neoliberal que imponen un modelo territorial basado en las grandes operaciones metropolitanas de centralidad, infraestructuras y equipamiento, que consumen de forma indiscriminada la totalidad del territorio madrileño. Será en el último capítulo del segundo bloque (capítulo 6) donde se represente gráficamente a escala metropolitana y se analicen las 229 piezas que han ido colmatando el espacio destinado a Anillo Verde, según los parámetros de estudio, en base a las cuales se plantean las primeras conclusiones generales de la tesis, poniendo de manifiesto que las alianzas entre los agentes soberanos en la construcción de la ciudad y su entorno han trasgredido sucesivamente las determinaciones del Planeamiento en su definición de modelo de ciudad y territorio, acusando la carencia de recursos instrumentales y jurídicos que alentaron el proceso de su desmantelamiento, y revelando la influencia de los condicionantes geográficos y naturales en la especialización funcional y segregación social en el conjunto del Área Metropolitana de Madrid. Se remata el discurso metropolitano con una batería de conclusiones que interpretan el fenómeno de ocupación del anillo de verdor metropolitano confirmando las hipótesis iniciales, reconociendo los valores medioambientales y culturales trasgredidos, sus diversos actores, las numerosas operaciones urbanísticas desarrolladas con distintos usos y envergadura, así como los instrumentos de planeamiento utilizados, en base a las cuales se materializa la construcción del AMM según un modelo extendido (spread), dibujando una mancha de aceite (o grase-spots según Geddes) que precisamente había querido evitarse desde el planeamiento urbanístico con la definición de un Anillo Verde, espacio inmune a la edificación, que se aleja de su papel estructurante (equilibrador entre la ciudad y sus habitantes) para convertirse en armadura de la estructura comunicativa, que una vez consolidada se convierte en la mejor aliada de la máquina inmobiliaria. El último paso, se desarrolla en el bloque III que se divide en los capítulo 7,8 y 9 y supone la comprobación de lo descrito en el conjunto de escala metropolitana, en dos aspectos fundamentales, la falta de consideración por los valores culturales y medioambientales que han modelado el territorio, imprimiéndole un carácter singular y específico y, la estructura del dominio del suelo, donde se reconoce de forma precisa el grupo social y los agentes encargados en cada momento de comercializar los suelos del anillo, que bajo el paraguas de la urgencia social y el engañoso beneficio popular, obtienen importantes beneficios económicos. Con esa intención, se da un salto hacia la escala municipal y urbana, seleccionando dos escenarios de estudio, el municipio de Pozuelo de Alarcón, que representa la materialización del crecimiento suburbano de la élite madrileña ocupando las zonas de mayor valor ecológico del anillo, y el distrito de Hortaleza-Barajas que ofrece su territorio a las grandes operaciones metropolitanas, apoyándose en el eje de actividad marcado por la conexión Madrid-Barcelona y el sistema aeroportuario de escala global, ambos situados al norte de la línea de borde entre la Sierra y la Mancha, ocupando por tanto los lugares más valiosos de la geografía madrileña (estructura funcional anticipada por Bidagor en 1946 en su modelo de ciudad adaptada al territorio madrileño) Una vez descrito este proceso trasgresor de límites, de normas, de conductas, y desde una perspectiva del fenómeno suficientemente documentada, en el capítulo 10, se realiza una reflexión sobre la incidencia real de la propuesta urbanística del Anillo Verde en la construcción del AMM, de la misma forma que se sugieren nuevos roles al planeamiento en un formato intencionado de largo recorrido en oposición a lo inmediato y circunstancial, que permita hacer una nueva lectura de los presupuestos teóricos que conformaban la idea del Anillo Verde, espacio articulador (medioambiental, social y cultural) del territorio madrileño. ABSTRACT The Metropolitan Greenbelt was defined by the 1963 Master Plan for the Madrid Metropolitan Area (MMA), following established international models of urban development, as the structural framework of the MMA, the principal open space within its network of open spaces and a public area of recreation and contact with nature for the residents of Madrid. In reality, however, it ha become a reserve of land in which various alliances between the institutional authorities and the dominant social class have been operating on the margin of the original plan, exposing a scarcity of legal and cultural resources for the safeguarding of common interests, and in which the geographical and natural characteristics of the territory itself have come to play an influential role in the functional specialization and spatial segregation of the MMA. With that idea as its HYPOTHESIS, the aim of this THESIS is to demonstrate its reality. The first step in this is to delineate, temporally and spatially, the object of study; i.e. the Metropolitan Greenbelt2. The second is to contextualize historically and disciplinarily those theoretical ideas which conform to the greenbelt concept. The third is to acknowledge, locate and document the elements which have characterized the urban occupation of the Greenbelt and classify these according to the parameters of time, function, urban development and form, which in turn would enable the geography, use, instrumentation and form of its transformation to be analysed on a general metropolitan scale. The fourth step, as a method of verification, is an in-depth analysis of two representative settings within the metropolitan network: the municipality of Pozuelo de Alarcón and the Hortaleza-Barajas district. The content of the document is divided into three parts. Part I focuses on the study’s theoretical foundations, Part II establishes a line of argument at the metropolitan level and Part III examines the phenomenon from a municipal and urban perspective. The thesis, then, begins with a study of the greenbelt concept itself and its meaning, which is far more complex than the accepted instrumental dimension of limiting and containing urbanization in response to the growth of the industrial city of the early 20th century, and which is based on a decentralization of the traditional city. This wider purpose is the setting aside of a large reserved space to safeguard the natural and cultural values of the region and thereby achieve a balance between the city and its residents; that is to say, between man and the space he inhabits. The principal currents of thought in urban planning will then be examined. These have drawn upon a variety of disciplines (economics, sociology, geography, biology, ecology) to develop theories for establishing a new urban order according to the principles of social, economic and environmental equity, and have involved a constant interchange between Europe and the United States. Thus, the City Garden and Regionalist movements would clear the way for proposals such as Greater London and Great Berlin, Chicago and Washington, in which the greenbelt would play a fundamental role. The participation of our own country and the city of Madrid is also discussed, through regional models such as the Besteiro Plan and urban ones like the Bidagor Plan, direct forerunners of 1963’s General Organizational Plan for the Madrid Metropolitan Area, which would set into motion the organization of Madrid’s metropolitan growth. The line of argument followed in this thesis is two-fold: first, an examination of metropolitan development in keeping with the city model as defined in the various General Plans for the development of both the municipality of Madrid and the seven surrounding municipalities which have land designated for its Greenbelt; and second, an examination of this growth in relation to Regional Planning measures, is detailed on a smaller scale (municipal and district), where the conditioning factors affecting the land property structure and the network of biophysical units may be analysed in depth. The first of these is dealt with in Part II and organized into three chapters (4, 5 and 6). Chapter 4 is dedicated to the obligatory starting point of the geographical setting itself. The biophysical characteristics of the territories set aside for the Greenbelt, and which historically have played a role in the area’s exploitation, are described here. These range from expanses of Mediterranean woodland to the north and west of Monte del Pardo to the various types of farmland that have been adapted to the geological substratum and the contours of the terrain (gentle undulations of arkosic sediment in the north, and wide sandy and gypsiferous tableland in the south), as well as orchards planted in low valleys and along watercourses (the creeks of Monte Carmelo, Valdebebas, Quinto, Santo, Butarque, Meaques and Pozuelo). Once this physical reality ha been detailed, in Chapter 5 will examine the various city models proposed by urban planners, both regionally and municipally, in response to the confluence of social, economic and political interests that have characterized the process of occupation in the Greenbelt area during the construction of the MMA. Municipal planning proposals will be collected and examined for the various municipalities which have land designated for the Greenbelt: Madrid, Coslada, Getafe, Leganés, Alcorcón, Boadilla del Monte and Pozuelo de Alarcón. Furthermore, the various territorial organization proposals which have served as references for municipal planning will also be addressed here, in all of their versions –from the sectorial, which have met with more success and institutional approval, to the many attempts at integration, which have been more complex but less influential, precisely for the difficulty of reconciling physical organization with economic development, and private interest with public benefit. The first period in this process was the development of the General Plan of 1963, followed by the first municipal development plans of the 1970s, in which the need for a regional framework that “organized” the territory in an integral fashion was defined. This would serve as a reference for the sectorial actions that marked the metropolitan area’s initial development. The second came two decades later with the approval of the General Plan of 1985, and the network of municipal plans for the surrounding communities, which followed the same philosophy of austerity with regard to territorial growth. The third would begin to take form in 1997, as a new generation of neo-liberal development plans imposed a territorial model based on centralized large-scale metropolitan operations of infrastructure and equipment, which would indiscriminately consume the totality of Madrid’s land. At the end of the Part II, in Chapter 6, the metropolitan area will be represented graphically and the 229 pieces that have been gradually encroaching upon land designated for the Greenbelt will be analysed. This analysis will be carried out according to the parameters defined for the study, and the first general conclusions of the thesis will be based on its findings. It will show how alliances between the various governing authorities in the construction of the city and its environment have successively violated established plans with regard to the definitions of city and territory, how shortages of instrumental and judicial resources have accentuated the dismantling process, and how natural and geographical factors have influenced functional specialization and social segregation in the Madrid Metropolitan Area. The final step, detailed in Part III, will address two fundamental aspects of what has just been described: the lack of consideration for the cultural and environmental values which have shaped this territory and imprinted upon it a specific and unique character; and the structure of land domination, with a precise identification of the social group and agents responsible at each stage of the Greenbelt’s commercialization, who, under an umbrella of social urgency and deceptive public benefit, have used it to obtain substantial financial rewards. For this purpose, a closer look is taken at two specific areas: the municipality of Pozuelo de Alarcón, representative of the suburban growth of an elite population which has occupied the Greenbelt areas of the greatest ecological value; and the Hortaleza-Barajas district, which has offered its territory to large metropolitan business interests, based on activities centred on the connection between Madrid and Barcelona and the system of international air travel. Both of these settings are located to the north of the line which divides the Sierra from La Mancha, and thus occupy the most valuable land in the Madrid region (a functional structure anticipated by Bidagor in 1946, with his city model adapted to the territory of Madrid). Finally, an attempt will be made to interpret the phenomenon of metropolitan Greenbelt occupation, confirming initial hypotheses, specifying the environmental and cultural values that have been violated, and identifying the various players involved, as well as numerous urbanization operations of varying sizes and interests, and the instruments of planning they have used. It will be seen from this that the construction of the MMA has in fact followed a “spread” model, a “grease spot” (as Geddes calls it) which, from the outset of the planning process and according to the definition of a greenbelt as a construction-free zone, was precisely to be avoided. This structural role (to provide a balance between a city and its residents) has thus been abandoned and the Greenbelt converted instead into a communicative framework which, once consolidated, has become the greatest ally of the real estate machine. After this process of violating limits, norms and established behaviour has been described and solidly documented, a reflection will be made on the real influence of the Greenbelt proposal in the construction of the MMA. At the same time, new roles will be suggested for future planning, roles which are deliberate and long term, in opposition to the immediate and circumstantial. This will enable a new interpretation of the theoretical principles behind the greenbelt concept, a space designed to connect the territory of Madrid environmentally, socially and culturally.

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

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

Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion–collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion–collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.

Protein kinase A activity is required for the budding of constitutive transport vesicles from the trans-Golgi network

We have examined the role played by protein kinase A (PKA) in vesicle-mediated protein transport from the trans-Golgi network (TGN) to the cell surface. In vivo this transport step was inhibited by inhibitors of PKA catalytic subunits (C-PKA) such as the compound known as H89 and a myristoylated form of the inhibitory peptide sequence contained in the thermostable PKA inhibitor. Inhibition by H89 occurred at an early stage during the transfer of vesicular stomatitis virus G glycoprotein from the TGN to the cell surface. Reversal from this inhibition correlated with a transient increase in the number of free coated vesicles in the Golgi area. Vesicle budding from the TGN was studied in vitro using vesicular stomatitis virus-infected, permeabilized cells. Addition to this assay of C-PKA stimulated vesicle release while it was suppressed by PKA inhibitory peptide, H89, and antibody against C-PKA. Furthermore, vesicle release was decreased when PKA-depleted cytosol was used and restored by addition of C-PKA. These results indicate a regulatory role for PKA activity in the production of constitutive transport vesicles from the TGN.

The EMBL nucleotide sequence database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

Folliculostellate cell network: A route for long-distance communication in the anterior pituitary

All higher life forms critically depend on hormones being rhythmically released by the anterior pituitary. The proper functioning of this master gland is dynamically controlled by a complex set of regulatory mechanisms that ultimately determine the fine tuning of the excitable endocrine cells, all of them heterogeneously distributed throughout the gland. Here, we provide evidence for an intrapituitary communication system by which information is transferred via the network of nonendocrine folliculostellate (FS) cells. Local electrical stimulation of FS cells in acute pituitary slices triggered cytosolic calcium waves, which propagated to other FS cells by signaling through gap junctions. Calcium wave initiation was because of the membrane excitability of FS cells, hitherto classified as silent cells. FS cell coupling could relay information between opposite regions of the gland. Because FS cells respond to central and peripheral stimuli and dialogue with endocrine cells, the form of large-scale intrapituitary communication described here may provide an efficient mechanism that orchestrates anterior pituitary functioning in response to physiological needs.

Metabolism of Alzheimer beta-amyloid precursor protein: regulation by protein kinase A in intact cells and in a cell-free system.

Various compounds that affect signal transduction regulate the relative utilization of alternative processing pathways for the beta-amyloid precursor protein (beta APP) in intact cells, increasing the production of nonamyloidogenic soluble beta APP (s beta APP) and decreasing that of amyloidogenic beta-amyloid peptide. In a recent study directed toward elucidating the mechanisms underlying phorbol ester-stimulated s beta APP secretion from cells, it was demonstrated that protein kinase C increases the formation from the trans-Golgi network (TGN) of beta APP-containing secretory vesicles. Here we present evidence that forskolin increases s beta APP production from intact PC12 cells, and protein kinase A stimulates formation from the TGN of beta APP-containing vesicles. Although protein kinase A and protein kinase C converge at the level of formation from the TGN of beta APP-containing vesicles, additional evidence indicates that the regulatory mechanisms involved are distinct.

Orchestration of energy efficiency capabilities for a sustainable network management

The energy demand for operating Information and Communication Technology (ICT) systems has been growing, implying in high operational costs and consequent increase of carbon emissions. Both in datacenters and telecom infrastructures, the networks represent a significant amount of energy spending. Given that, there is an increased demand for energy eficiency solutions, and several capabilities to save energy have been proposed. However, it is very dificult to orchestrate such energy eficiency capabilities, i.e., coordinate or combine them in the same network, ensuring a conflict-free operation and choosing the best one for a given scenario, ensuring that a capability not suited to the current bandwidth utilization will not be applied and lead to congestion or packet loss. Also, there is no way in the literature to do this taking business directives into account. In this regard, a method able to orchestrate diferent energy eficiency capabilities is proposed considering the possible combinations and conflicts among them, as well as the best option for a given bandwidth utilization and network characteristics. In the proposed method, the business policies specified in a high-level interface are refined down to the network level in order to bring highlevel directives into the operation, and a Utility Function is used to combine energy eficiency and performance requirements. A Decision Tree able to determine what to do in each scenario is deployed in a Software Defined Network environment. The proposed method was validated with diferent experiments, testing the Utility Function, checking the extra savings when combining several capabilities, the decision tree interpolation and dynamicity aspects. The orchestration proved to be valid to solve the problem of finding the best combination for a given scenario, achieving additional savings due to the combination, besides ensuring a conflict-free operation.

O idoso e sua participação - aspectos da vida urbana componentes da cidade amiga do idoso

Esta investigação teve por objetivo analisar a participação de idosos em direção à promoção da saúde considerando a articulação com oito aspectos da vida urbana do projeto cidade amiga do idoso (espaços abertos e prédios, transporte, moradia, participação social, respeito e inclusão social, participação cívica e emprego, comunicação e informação, e apoio comunitário e serviços de saúde) do bairro Vila Tibério, município de Ribeirão Preto, estado de São Paulo, Brasil. Trata-se de pesquisa descritiva de abordagem qualitativa sustentada pelos conceitos e princípios da promoção da saúde, a partir da perspectiva da participação social e do estabelecimento de ambientes saudáveis, motivo do alinhamento com os aspectos da vida urbana do Projeto Cidade Amiga do Idoso. A pesquisa atendeu aos preceitos éticos, sendo sua realização aprovada por Comitê de Ética em Pesquisa. A captação do empírico se deu por meio da realização de grupos focais com base no Protocolo de Vancouver, desenvolvido pelo Government of British Columbia, somando 32 idosos e 6 representantes de prestadores de serviços em 5 grupos focais. Adicionalmente, foi aplicado instrumento de avaliação funcional para verificar condição de independência ou dependência dos 32 idosos, sendo feita avaliação qualitativa da capacidade autorreferida pelos idosos, segundo a escala utilizada. Realizou-se análise de conteúdo na vertente temática para o material dos grupos, com a identificação de três temas: território: lugar de vida e cidadania, formação de redes de suporte social ao idoso e participação dos idosos na vida do bairro. A violência, o abandono presentes no território, em especial nos espaços coletivos, trazem preocupação e medo aos idosos, pois dificultam a livre circulação no território. Por outro lado, há no bairro certa tradição e possibilidade de serem construídas relações de amizade e apoio, que permitem ao idoso sentir-se acolhido, sendo enfatizado que as relações de amizade e mesmo as institucionalizadas, como por exemplo, o trabalho dos agentes comunitários de saúde, são necessárias às relações de convivência e sustentação na vida dos idosos. É trazida a importância dos jornais do bairro e de seu papel como elemento constitutivo da rede apoio na área de comunicação e informação dentro do território. A vinculação ao mundo do trabalho, com atividades remuneradas, ainda é uma forma que os idosos encontram de se manterem próximos aos amigos e participantes da vida em comunidade. Há dificuldade em ampliar a participação dos idosos por diferentes motivos que vão desde a dificuldade de mobilidade dentro do bairro, acesso à informação sobre as atividades disponíveis, ausência de canais mais ágeis de comunicação, baixa adesão aos processos de participação social no campo da saúde e assistência social, trabalho dos idosos como cuidadores de outros idosos familiares ou de netos. Situações que dificultam maior adesão aos processos de participação social, embora seja assinalada a importância destes processos para a melhoria do bairro. O conjunto dos resultados aponta que os idosos apresentam muitas dificuldades para ampliar sua participação nos processos coletivos no bairro, que por vezes se mostra hostil em suas condições a este grupo. Por outro lado se fazem presentes potencialidades, nas brechas e sugestões que indicam a possibilidade para se situarem no processo de construção da Promoção da Saúde no território em que estão inseridos, utilizando de suas características, perfis de vida e atuação para agir com autonomia e constituírem-se como protagonistas dos processos e de ações no território. Com a ciência dos limites, credita-se a esta investigação a possibilidade de que os elementos aqui discutidos possam oferecer subsídios para que as políticas voltadas ao envelhecimento saudável nos âmbitos da saúde, segurança, educação, assistência social, dentre outras possam se repensadas ou reestruturadas

EAST by Northeast

The Eastern Academic Scholars’ Trust (EAST) is a shared print initiative involving 48 libraries across the Northeast. Initiated in 2012 with a planning grant from the Andrew W. Mellon Foundation, EAST addresses directly the growing need for academic libraries to ensure that monographs and journals of scholarly value are not inadvertently discarded as they undertake weeding and deselection programs to free up space for other library services. EAST is currently completing a large-scale analysis of collections across 40 of the participating libraries. This analysis will provide insight into both uniqueness and overlap across the libraries’ holdings and will result in agreements by the libraries to retain circulating monographs in their local collections for an agreed upon time period and to make those materials available to researchers and scholars from other EAST libraries. In parallel to this collection analysis, EAST is implementing validation sampling across the libraries to better understand volume availability and condition and the role they may plan in retention decisions. The project team has developed an innovative sampling methodology and tools to support the study. As the largest shared print initiative to date, this project will secure a substantial portion of the scholarly record that is held in the Northeast and positions EAST as an important component of the growing network of shared print initiatives nationally.

Open educational resources: the role of OCW, blogs and videos in computer network classrooms

This paper analyzes the learning experiences and opinions obtained from a group of undergraduate students in their interaction with several on-line multimedia resources included in a free on-line course about Computer Networks. These new educational resources employed are based on the Web 2.0 approach such as blogs, videos and virtual labs which have been added in a web-site for distance self-learning.

A formal framework for modelling complex network management systems

Society today is completely dependent on computer networks, the Internet and distributed systems, which place at our disposal the necessary services to perform our daily tasks. Subconsciously, we rely increasingly on network management systems. These systems allow us to, in general, maintain, manage, configure, scale, adapt, modify, edit, protect, and enhance the main distributed systems. Their role is secondary and is unknown and transparent to the users. They provide the necessary support to maintain the distributed systems whose services we use every day. If we do not consider network management systems during the development stage of distributed systems, then there could be serious consequences or even total failures in the development of the distributed system. It is necessary, therefore, to consider the management of the systems within the design of the distributed systems and to systematise their design to minimise the impact of network management in distributed systems projects. In this paper, we present a framework that allows the design of network management systems systematically. To accomplish this goal, formal modelling tools are used for modelling different views sequentially proposed of the same problem. These views cover all the aspects that are involved in the system; based on process definitions for identifying responsible and defining the involved agents to propose the deployment in a distributed architecture that is both feasible and appropriate.

On Modeling an Innovative Monitoring Network for Protecting and Managing Cultural Heritage from Risk Events

In this paper the model of an Innovative Monitoring Network involving properly connected nodes to develop an Information and Communication Technology (ICT) solution for preventive maintenance of historical centres from early warnings is proposed. It is well known that the protection of historical centres generally goes from a large-scale monitoring to a local one and it could be supported by a unique ICT solution. More in detail, the models of a virtually organized monitoring system could enable the implementation of automated analyses by presenting various alert levels. An adequate ICT solution tool would allow to define a monitoring network for a shared processing of data and results. Thus, a possible retrofit solution could be planned for pilot cases shared among the nodes of the network on the basis of a suitable procedure utilizing a retrofit catalogue. The final objective would consist in providing a model of an innovative tool to identify hazards, damages and possible retrofit solutions for historical centres, assuring an easy early warning support for stakeholders. The action could proactively target the needs and requirements of users, such as decision makers responsible for damage mitigation and safeguarding of cultural heritage assets.

Direct Nucleophilic Substitution of Free Allylic Alcohols in Water Catalyzed by FeCl3⋅6 H2O: Which is the Real Catalyst?

The allylic substitution reaction, and particularly the direct allylic amination reaction, of free allylic alcohols in water catalyzed by FeCl3⋅6 H2O is described. This novel environmentally-friendly methodology allows the use of a wide variety of nitrogenated nucleophiles such as sulfonamides, carbamates, benzamides, anilines, benzotriazoles, and azides, generally giving good yields of the corresponding substitution products. The synthetic applicability of the process is also demonstrated because the reaction can be performed on gram-scale. Additionally, carbon nucleophiles such as silylated nucleophiles, aromatic compounds, and malonates also proved to be suitable for this transformation. Finally, the nature of the catalytic species present in aqueous media is unveiled, pointing towards the formation of hexaaquo iron(III) complexes.