An Automatic Quantification and Registration Strategy to Create a Gene Expression Atlas of Zebrafish Embryogenesis

In order to properly understand and model the gene regulatory networks in animals development, it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains. In this paper, we propose a complete computational framework to fulfill this task and create a 3D Atlas of the early zebrafish embryogenesis annotated with both the cellular localizations and the level of expression of different genes at different developmental stages. The strategy to construct such an Atlas is described here with the expression pattern of 5 different genes at 6 hours of development post fertilization.

Tomas Lopez's Geographic Atlas of Spain in the Peninsular War: A methodology for determining errors

During the Peninsular War, Napoleon's and Wellington's armies were aware of the lack of precision in the maps of Spain and its provinces that appeared in Tomas Lopez \s Geographical Atlas of Spain. The errors were due to the non-topographical surveying method he used which he had learned from his teacher Jean Baptiste Bourguignon D 'Anville. To map all of the Spanish provinces, Tomas Lopez divided them into circles of three leagues in diameter (16,718 m), taking a particular town as the centre. He asked the town's priest to draw a map of the territory and to complete a questionnaire that Tomas Lopez sent to him. The priest was to return the two documents after he had completed them. Subsequently, at his desk, Tomas Lopez used the maps and reports as well as other graphic and written sources from various locations to make an outline of each map. Next, he made a mosaic that served as a pattern for drawing the final provincial map. We will see the way that this method was applied in two concrete cases: the villages ofChavaler and Monteagudo, situated in the Spanish province of Soria, and verify their degree of accuracy. We will use the maps drawn by the priests in 1767, the final map of the province which was published in 1804 by Tomás López, and a current map of the province showing the angular and linear errors in Lopez \s map.

Computational methods to create and analyze a digital gene expression atlas of embryo development from microscopy images

Abstract The creation of atlases, or digital models where information from different subjects can be combined, is a field of increasing interest in biomedical imaging. When a single image does not contain enough information to appropriately describe the organism under study, it is then necessary to acquire images of several individuals, each of them containing complementary data with respect to the rest of the components in the cohort. This approach allows creating digital prototypes, ranging from anatomical atlases of human patients and organs, obtained for instance from Magnetic Resonance Imaging, to gene expression cartographies of embryo development, typically achieved from Light Microscopy. Within such context, in this PhD Thesis we propose, develop and validate new dedicated image processing methodologies that, based on image registration techniques, bring information from multiple individuals into alignment within a single digital atlas model. We also elaborate a dedicated software visualization platform to explore the resulting wealth of multi-dimensional data and novel analysis algo-rithms to automatically mine the generated resource in search of bio¬logical insights. In particular, this work focuses on gene expression data from developing zebrafish embryos imaged at the cellular resolution level with Two-Photon Laser Scanning Microscopy. Disposing of quantitative measurements relating multiple gene expressions to cell position and their evolution in time is a fundamental prerequisite to understand embryogenesis multi-scale processes. However, the number of gene expressions that can be simultaneously stained in one acquisition is limited due to optical and labeling constraints. These limitations motivate the implementation of atlasing strategies that can recreate a virtual gene expression multiplex. The developed computational tools have been tested in two different scenarios. The first one is the early zebrafish embryogenesis where the resulting atlas constitutes a link between the phenotype and the genotype at the cellular level. The second one is the late zebrafish brain where the resulting atlas allows studies relating gene expression to brain regionalization and neurogenesis. The proposed computational frameworks have been adapted to the requirements of both scenarios, such as the integration of partial views of the embryo into a whole embryo model with cellular resolution or the registration of anatom¬ical traits with deformable transformation models non-dependent on any specific labeling. The software implementation of the atlas generation tool (Match-IT) and the visualization platform (Atlas-IT) together with the gene expression atlas resources developed in this Thesis are to be made freely available to the scientific community. Lastly, a novel proof-of-concept experiment integrates for the first time 3D gene expression atlas resources with cell lineages extracted from live embryos, opening up the door to correlate genetic and cellular spatio-temporal dynamics. La creación de atlas, o modelos digitales, donde la información de distintos sujetos puede ser combinada, es un campo de creciente interés en imagen biomédica. Cuando una sola imagen no contiene suficientes datos como para describir apropiadamente el organismo objeto de estudio, se hace necesario adquirir imágenes de varios individuos, cada una de las cuales contiene información complementaria respecto al resto de componentes del grupo. De este modo, es posible crear prototipos digitales, que pueden ir desde atlas anatómicos de órganos y pacientes humanos, adquiridos por ejemplo mediante Resonancia Magnética, hasta cartografías de la expresión genética del desarrollo de embrionario, típicamente adquiridas mediante Microscopía Optica. Dentro de este contexto, en esta Tesis Doctoral se introducen, desarrollan y validan nuevos métodos de procesado de imagen que, basándose en técnicas de registro de imagen, son capaces de alinear imágenes y datos provenientes de múltiples individuos en un solo atlas digital. Además, se ha elaborado una plataforma de visualization específicamente diseñada para explorar la gran cantidad de datos, caracterizados por su multi-dimensionalidad, que resulta de estos métodos. Asimismo, se han propuesto novedosos algoritmos de análisis y minería de datos que permiten inspeccionar automáticamente los atlas generados en busca de conclusiones biológicas significativas. En particular, este trabajo se centra en datos de expresión genética del desarrollo embrionario del pez cebra, adquiridos mediante Microscopía dos fotones con resolución celular. Disponer de medidas cuantitativas que relacionen estas expresiones genéticas con las posiciones celulares y su evolución en el tiempo es un prerrequisito fundamental para comprender los procesos multi-escala característicos de la morfogénesis. Sin embargo, el número de expresiones genéticos que pueden ser simultáneamente etiquetados en una sola adquisición es reducido debido a limitaciones tanto ópticas como del etiquetado. Estas limitaciones requieren la implementación de estrategias de creación de atlas que puedan recrear un multiplexado virtual de expresiones genéticas. Las herramientas computacionales desarrolladas han sido validadas en dos escenarios distintos. El primer escenario es el desarrollo embrionario temprano del pez cebra, donde el atlas resultante permite constituir un vínculo, a nivel celular, entre el fenotipo y el genotipo de este organismo modelo. El segundo escenario corresponde a estadios tardíos del desarrollo del cerebro del pez cebra, donde el atlas resultante permite relacionar expresiones genéticas con la regionalización del cerebro y la formación de neuronas. La plataforma computacional desarrollada ha sido adaptada a los requisitos y retos planteados en ambos escenarios, como la integración, a resolución celular, de vistas parciales dentro de un modelo consistente en un embrión completo, o el alineamiento entre estructuras de referencia anatómica equivalentes, logrado mediante el uso de modelos de transformación deformables que no requieren ningún marcador específico. Está previsto poner a disposición de la comunidad científica tanto la herramienta de generación de atlas (Match-IT), como su plataforma de visualización (Atlas-IT), así como las bases de datos de expresión genética creadas a partir de estas herramientas. Por último, dentro de la presente Tesis Doctoral, se ha incluido una prueba conceptual innovadora que permite integrar los mencionados atlas de expresión genética tridimensionales dentro del linaje celular extraído de una adquisición in vivo de un embrión. Esta prueba conceptual abre la puerta a la posibilidad de correlar, por primera vez, las dinámicas espacio-temporales de genes y células.

Citizens Interactive Behaviour in the Performance of the Urban Space of Cohabitacion. Interactive Atlas of Urban Habitability

The article shows a range of contemporary phenomena linked with urban space and the increasing citizens? interactivity in the network. The sources for theory and reflection are related to the ongoing research project ?Interactive Atlas of urban habitability" which is based on citizen participation in the sensitive description of the urban environment. It addresses a classification of variables related to the desires of urban habitability.

Tomas Lopez's Geographic Atlas of Spain (1787) and its Hydrographic Network: GIS analysis of the Reyno de Jaen

Knowledge of the development of hydrographic networks can be useful for a number of research works in hydraulic engineering. We thus, intend to analyse the cartography regarding the first work that systematically encompasses the entire hydrographic network: Tomas Lopez’s Geographic Atlas of Spain (1787). In order to achieve this goal, we will first analyze –by way of the Geographic Information System (GIS) – both the present and referred historical cartographies. In comparing them, we will use the then-existing population centres that correspond to modern ones. The aim is to compare the following research variables in the hydrographic network: former toponyms, length of riverbeds and distance to population centres. The results of this study will show the variation in the riverbeds and the probable change in their denomination.

Interactive Atlas of habitability. Urban data management for the improvement of habitability and coexistence

In this paper we approximate to the understanding of the hybrid city as a context of changes, produced in the perception and in the modes of inhabiting and coexisting in cities through new technologies of information and communication.

Fungal biodeterioration of colour cinematographic films of the cultural heritage of Cuba

Until recently, cinematographic film was largely cellulose-triacetate-based. However, this material is highly susceptible to biodeterioration, thus placing historic film collections, an important part of the cultural heritage of many countries, at risk. In the present study, samples taken from several biodeteriorated color cinematographic films belonging to the collection of the Cuban Institute for Cinematographic Industry and Arts (ICAIC) were investigated. Infrared spectroscopy showed that all films were of the same composition, i.e., a gelatin emulsion coating one side of a cellulose-triacetate-based film support. The films were analyzed by environmental scanning electron microscopy and scanning electron microscopy to determine the degree of biodeterioration and the type of colonizing microorganisms. Significant fungal colonization was found on both sides of the films in all samples, with a higher concentration of fungi on the gelatin emulsion side. Epifluorescence microscopy of fluorochrome-dyed films demonstrated that some of the fungi were still active, indicating that the films under study, and probably others at the ICAIC, are at risk of further deterioration. Fungi were identified by molecular biology techniques. The fungi mainly responsible for the observed biodeterioration were those belonging to the genera Aspergillus and Cladosporium, although other genera, such as Microascus and Penicillium, were identified as well. In accordance with the findings described herein, the existing guidelines for the prevention and control of film biodeterioration are discussed.

Modifying the atlas of low lunar orbits using inert tethers

For long enough tethers, the coupling of the attitude and orbital dynamics may show non-negligible effects in the orbital motion of a tethered satellite about a central body. In the case of fast rotating tethers the attitude remains constant, on average, up to second order effects. Besides, for a tether rotating in a plane parallel to the equatorial plane of the central body, the attitude?orbit coupling effect is formally equal to the perturbation of the Keplerian motion produced by the oblateness of the central body and, therefore, may have a stabilizing effect in the orbital dynamics. In the case of a tethered satellite in a low lunar orbit, it is demonstrated that feasible tether lengths can help in modifying the actual map of lunar frozen orbits