Assembling models of embryo development: Image analysis and the construction of digital atlases

Digital atlases of animal development provide a quantitative description of morphogenesis, opening the path toward processes modeling. Prototypic atlases offer a data integration framework where to gather information from cohorts of individuals with phenotypic variability. Relevant information for further theoretical reconstruction includes measurements in time and space for cell behaviors and gene expression. The latter as well as data integration in a prototypic model, rely on image processing strategies. Developing the tools to integrate and analyze biological multidimensional data are highly relevant for assessing chemical toxicity or performing drugs preclinical testing. This article surveys some of the most prominent efforts to assemble these prototypes, categorizes them according to salient criteria and discusses the key questions in the field and the future challenges toward the reconstruction of multiscale dynamics in model organisms.

A Ground-Truth Video Dataset for the Development and Evaluation of Vision-based Sense-and-Avoid systems

The importance of vision-based systems for Sense-and-Avoid is increasing nowadays as remotely piloted and autonomous UAVs become part of the non-segregated airspace. The development and evaluation of these systems demand flight scenario images which are expensive and risky to obtain. Currently Augmented Reality techniques allow the compositing of real flight scenario images with 3D aircraft models to produce useful realistic images for system development and benchmarking purposes at a much lower cost and risk. With the techniques presented in this paper, 3D aircraft models are positioned firstly in a simulated 3D scene with controlled illumination and rendering parameters. Realistic simulated images are then obtained using an image processing algorithm which fuses the images obtained from the 3D scene with images from real UAV flights taking into account on board camera vibrations. Since the intruder and camera poses are user-defined, ground truth data is available. These ground truth annotations allow to develop and quantitatively evaluate aircraft detection and tracking algorithms. This paper presents the software developed to create a public dataset of 24 videos together with their annotations and some tracking application results.

Development and implementation of an air quality integrated assessment modelling system for the Iberian Peninsula

La mejora de la calidad del aire es una tarea eminentemente interdisciplinaria. Dada la gran variedad de ciencias y partes involucradas, dicha mejora requiere de herramientas de evaluación simples y completamente integradas. La modelización para la evaluación integrada (integrated assessment modeling) ha demostrado ser una solución adecuada para la descripción de los sistemas de contaminación atmosférica puesto que considera cada una de las etapas involucradas: emisiones, química y dispersión atmosférica, impactos ambientales asociados y potencial de disminución. Varios modelos de evaluación integrada ya están disponibles a escala continental, cubriendo cada una de las etapas antesmencionadas, siendo el modelo GAINS (Greenhouse Gas and Air Pollution Interactions and Synergies) el más reconocido y usado en el contexto europeo de toma de decisiones medioambientales. Sin embargo, el manejo de la calidad del aire a escala nacional/regional dentro del marco de la evaluación integrada es deseable. Esto sin embargo, no se lleva a cabo de manera satisfactoria con modelos a escala europea debido a la falta de resolución espacial o de detalle en los datos auxiliares, principalmente los inventarios de emisión y los patrones meteorológicos, entre otros. El objetivo de esta tesis es presentar los desarrollos en el diseño y aplicación de un modelo de evaluación integrada especialmente concebido para España y Portugal. El modelo AERIS (Atmospheric Evaluation and Research Integrated system for Spain) es capaz de cuantificar perfiles de concentración para varios contaminantes (NO2, SO2, PM10, PM2,5, NH3 y O3), el depósito atmosférico de especies de azufre y nitrógeno así como sus impactos en cultivos, vegetación, ecosistemas y salud como respuesta a cambios porcentuales en las emisiones de sectores relevantes. La versión actual de AERIS considera 20 sectores de emisión, ya sea equivalentes a sectores individuales SNAP o macrosectores, cuya contribución a los niveles de calidad del aire, depósito e impactos han sido modelados a través de matrices fuentereceptor (SRMs). Estas matrices son constantes de proporcionalidad que relacionan cambios en emisiones con diferentes indicadores de calidad del aire y han sido obtenidas a través de parametrizaciones estadísticas de un modelo de calidad del aire (AQM). Para el caso concreto de AERIS, su modelo de calidad del aire “de origen” consistió en el modelo WRF para la meteorología y en el modelo CMAQ para los procesos químico-atmosféricos. La cuantificación del depósito atmosférico, de los impactos en ecosistemas, cultivos, vegetación y salud humana se ha realizado siguiendo las metodologías estándar establecidas bajo los marcos internacionales de negociación, tales como CLRTAP. La estructura de programación está basada en MATLAB®, permitiendo gran compatibilidad con software típico de escritorio comoMicrosoft Excel® o ArcGIS®. En relación con los niveles de calidad del aire, AERIS es capaz de proveer datos de media anual y media mensual, así como el 19o valor horario más alto paraNO2, el 25o valor horario y el 4o valor diario más altos para SO2, el 36o valor diario más alto para PM10, el 26o valor octohorario más alto, SOMO35 y AOT40 para O3. En relación al depósito atmosférico, el depósito acumulado anual por unidad de area de especies de nitrógeno oxidado y reducido al igual que de azufre pueden ser determinados. Cuando los valores anteriormente mencionados se relacionan con características del dominio modelado tales como uso de suelo, cubiertas vegetales y forestales, censos poblacionales o estudios epidemiológicos, un gran número de impactos puede ser calculado. Centrándose en los impactos a ecosistemas y suelos, AERIS es capaz de estimar las superaciones de cargas críticas y las superaciones medias acumuladas para especies de nitrógeno y azufre. Los daños a bosques se calculan como una superación de los niveles críticos de NO2 y SO2 establecidos. Además, AERIS es capaz de cuantificar daños causados por O3 y SO2 en vid, maíz, patata, arroz, girasol, tabaco, tomate, sandía y trigo. Los impactos en salud humana han sido modelados como consecuencia de la exposición a PM2,5 y O3 y cuantificados como pérdidas en la esperanza de vida estadística e indicadores de mortalidad prematura. La exactitud del modelo de evaluación integrada ha sido contrastada estadísticamente con los resultados obtenidos por el modelo de calidad del aire convencional, exhibiendo en la mayoría de los casos un buen nivel de correspondencia. Debido a que la cuantificación de los impactos no es llevada a cabo directamente por el modelo de calidad del aire, un análisis de credibilidad ha sido realizado mediante la comparación de los resultados de AERIS con los de GAINS para un escenario de emisiones determinado. El análisis reveló un buen nivel de correspondencia en las medias y en las distribuciones probabilísticas de los conjuntos de datos. Las pruebas de verificación que fueron aplicadas a AERIS sugieren que los resultados son suficientemente consistentes para ser considerados como razonables y realistas. En conclusión, la principal motivación para la creación del modelo fue el producir una herramienta confiable y a la vez simple para el soporte de las partes involucradas en la toma de decisiones, de cara a analizar diferentes escenarios “y si” con un bajo coste computacional. La interacción con políticos y otros actores dictó encontrar un compromiso entre la complejidad del modeladomedioambiental con el carácter conciso de las políticas, siendo esto algo que AERIS refleja en sus estructuras conceptual y computacional. Finalmente, cabe decir que AERIS ha sido creado para su uso exclusivo dentro de un marco de evaluación y de ninguna manera debe ser considerado como un sustituto de los modelos de calidad del aire ordinarios. ABSTRACT Improving air quality is an eminently inter-disciplinary task. The wide variety of sciences and stakeholders that are involved call for having simple yet fully-integrated and reliable evaluation tools available. Integrated AssessmentModeling has proved to be a suitable solution for the description of air pollution systems due to the fact that it considers each of the involved stages: emissions, atmospheric chemistry, dispersion, environmental impacts and abatement potentials. Some integrated assessment models are available at European scale that cover each of the before mentioned stages, being the Greenhouse Gas and Air Pollution Interactions and Synergies (GAINS) model the most recognized and widely-used within a European policy-making context. However, addressing air quality at the national/regional scale under an integrated assessment framework is desirable. To do so, European-scale models do not provide enough spatial resolution or detail in their ancillary data sources, mainly emission inventories and local meteorology patterns as well as associated results. The objective of this dissertation is to present the developments in the design and application of an Integrated Assessment Model especially conceived for Spain and Portugal. The Atmospheric Evaluation and Research Integrated system for Spain (AERIS) is able to quantify concentration profiles for several pollutants (NO2, SO2, PM10, PM2.5, NH3 and O3), the atmospheric deposition of sulfur and nitrogen species and their related impacts on crops, vegetation, ecosystems and health as a response to percentual changes in the emissions of relevant sectors. The current version of AERIS considers 20 emission sectors, either corresponding to individual SNAP sectors or macrosectors, whose contribution to air quality levels, deposition and impacts have been modeled through the use of source-receptor matrices (SRMs). Thesematrices are proportionality constants that relate emission changes with different air quality indicators and have been derived through statistical parameterizations of an air qualitymodeling system (AQM). For the concrete case of AERIS, its parent AQM relied on the WRF model for meteorology and on the CMAQ model for atmospheric chemical processes. The quantification of atmospheric deposition, impacts on ecosystems, crops, vegetation and human health has been carried out following the standard methodologies established under international negotiation frameworks such as CLRTAP. The programming structure isMATLAB ® -based, allowing great compatibility with typical software such as Microsoft Excel ® or ArcGIS ® Regarding air quality levels, AERIS is able to provide mean annual andmean monthly concentration values, as well as the indicators established in Directive 2008/50/EC, namely the 19th highest hourly value for NO2, the 25th highest daily value and the 4th highest hourly value for SO2, the 36th highest daily value of PM10, the 26th highest maximum 8-hour daily value, SOMO35 and AOT40 for O3. Regarding atmospheric deposition, the annual accumulated deposition per unit of area of species of oxidized and reduced nitrogen as well as sulfur can be estimated. When relating the before mentioned values with specific characteristics of the modeling domain such as land use, forest and crops covers, population counts and epidemiological studies, a wide array of impacts can be calculated. When focusing on impacts on ecosystems and soils, AERIS is able to estimate critical load exceedances and accumulated average exceedances for nitrogen and sulfur species. Damage on forests is estimated as an exceedance of established critical levels of NO2 and SO2. Additionally, AERIS is able to quantify damage caused by O3 and SO2 on grapes, maize, potato, rice, sunflower, tobacco, tomato, watermelon and wheat. Impacts on human health aremodeled as a consequence of exposure to PM2.5 and O3 and quantified as losses in statistical life expectancy and premature mortality indicators. The accuracy of the IAM has been tested by statistically contrasting the obtained results with those yielded by the conventional AQM, exhibiting in most cases a good agreement level. Due to the fact that impacts cannot be directly produced by the AQM, a credibility analysis was carried out for the outputs of AERIS for a given emission scenario by comparing them through probability tests against the performance of GAINS for the same scenario. This analysis revealed a good correspondence in the mean behavior and the probabilistic distributions of the datasets. The verification tests that were applied to AERIS suggest that results are consistent enough to be credited as reasonable and realistic. In conclusion, the main reason thatmotivated the creation of this model was to produce a reliable yet simple screening tool that would provide decision and policy making support for different “what-if” scenarios at a low computing cost. The interaction with politicians and other stakeholders dictated that reconciling the complexity of modeling with the conciseness of policies should be reflected by AERIS in both, its conceptual and computational structures. It should be noted however, that AERIS has been created under a policy-driven framework and by no means should be considered as a substitute of the ordinary AQM.

Development and implementation of a virtual laboratory for training process improvement in the mechanics of continuous media

The project arises from the need to develop improved teaching methodologies in field of the mechanics of continuous media. The objective is to offer the student a learning process to acquire the necessary theoretical knowledge, cognitive skills and the responsibility and autonomy to professional development in this area. Traditionally the teaching of the concepts of these subjects was performed through lectures and laboratory practice. During these lessons the students attitude was usually passive, and therefore their effectiveness was poor. The proposed methodology has already been successfully employed in universities like University Bochum, Germany, University the South Australia and aims to improve the effectiveness of knowledge acquisition through use by the student of a virtual laboratory. This laboratory allows to adapt the curricula and learning techniques to the European Higher Education and improve current learning processes in the University School of Public Works Engineers -EUITOP- of the Technical University of Madrid -UPM-, due there are not laboratories in this specialization. The virtual space is created using a software platform built on OpenSim, manages 3D virtual worlds, and, language LSL -Linden Scripting Language-, which imprints specific powers to objects. The student or user can access this virtual world through their avatar -your character in the virtual world- and can perform practices within the space created for the purpose, at any time, just with computer with internet access and viewfinder. The virtual laboratory has three partitions. The virtual meeting rooms, where the avatar can interact with peers, solve problems and exchange existing documentation in the virtual library. The interactive game room, where the avatar is has to resolve a number of issues in time. And the video room where students can watch instructional videos and receive group lessons. Each audiovisual interactive element is accompanied by explanations framing it within the area of knowledge and enables students to begin to acquire a vocabulary and practice of the profession for which they are being formed. Plane elasticity concepts are introduced from the tension and compression testing of test pieces of steel and concrete. The behavior of reticulated and articulated structures is reinforced by some interactive games and concepts of tension, compression, local and global buckling will by tests to break articulated structures. Pure bending concepts, simple and composite torsion will be studied by observing a flexible specimen. Earthquake resistant design of buildings will be checked by a laboratory test video.

Continuum models of the mechanical behavior of rolled and die-cast magnesium alloys

En los últimos años ha habido una fuerte tendencia a disminuir las emisiones de CO2 y su negativo impacto medioambiental. En la industria del transporte, reducir el peso de los vehículos aparece como la mejor opción para alcanzar este objetivo. Las aleaciones de Mg constituyen un material con gran potencial para el ahorro de peso. Durante la última década se han realizado muchos esfuerzos encaminados a entender los mecanismos de deformación que gobiernan la plasticidad de estos materiales y así, las aleaciones de Mg de colada inyectadas a alta presión y forjadas son todavía objeto de intensas campañas de investigación. Es ahora necesario desarrollar modelos que contemplen la complejidad inherente de los procesos de deformación de éstos. Esta tesis doctoral constituye un intento de entender mejor la relación entre la microestructura y el comportamiento mecánico de aleaciones de Mg, y dará como resultado modelos de policristales capaces de predecir propiedades macro- y microscópicas. La deformación plástica de las aleaciones de Mg está gobernada por una combinación de mecanismos de deformación característicos de la estructura cristalina hexagonal, que incluye el deslizamiento cristalográfico en planos basales, prismáticos y piramidales, así como el maclado. Las aleaciones de Mg de forja presentan texturas fuertes y por tanto los mecanismos de deformación activos dependen de la orientación de la carga aplicada. En este trabajo se ha desarrollado un modelo de plasticidad cristalina por elementos finitos con el objetivo de entender el comportamiento macro- y micromecánico de la aleación de Mg laminada AZ31 (Mg-3wt.%Al-1wt.%Zn). Este modelo, que incorpora el maclado y tiene en cuenta el endurecimiento por deformación debido a las interacciones dislocación-dislocación, dislocación-macla y macla-macla, predice exitosamente las actividades de los distintos mecanismos de deformación y la evolución de la textura con la deformación. Además, se ha llevado a cabo un estudio que combina difracción de electrones retrodispersados en tres dimensiones y modelización para investigar el efecto de los límites de grano en la propagación del maclado en el mismo material. Ambos, experimentos y simulaciones, confirman que el ángulo de desorientación tiene una influencia decisiva en la propagación del maclado. Se ha observado que los efectos no-Schmid, esto es, eventos de deformación plástica que no cumplen la ley de Schmid con respecto a la carga aplicada, no tienen lugar en la vecindad de los límites de baja desorientación y se hacen más frecuentes a medida que la desorientación aumenta. Esta investigación también prueba que la morfología de las maclas está altamente influenciada por su factor de Schmid. Es conocido que los procesos de colada suelen dar lugar a la formación de microestructuras con una microporosidad elevada, lo cuál afecta negativamente a sus propiedades mecánicas. La aplicación de presión hidrostática después de la colada puede reducir la porosidad y mejorar las propiedades aunque es poco conocido su efecto en el tamaño y morfología de los poros. En este trabajo se ha utilizado un enfoque mixto experimentalcomputacional, basado en tomografía de rayos X, análisis de imagen y análisis por elementos finitos, para la determinación de la distribución tridimensional (3D) de la porosidad y de la evolución de ésta con la presión hidrostática en la aleación de Mg AZ91 (Mg- 9wt.%Al-1wt.%Zn) colada por inyección a alta presión. La distribución real de los poros en 3D obtenida por tomografía se utilizó como input para las simulaciones por elementos finitos. Los resultados revelan que la aplicación de presión tiene una influencia significativa tanto en el cambio de volumen como en el cambio de forma de los poros que han sido cuantificados con precisión. Se ha observado que la reducción del tamaño de éstos está íntimamente ligada con su volumen inicial. En conclusión, el modelo de plasticidad cristalina propuesto en este trabajo describe con éxito los mecanismos intrínsecos de la deformación de las aleaciones de Mg a escalas meso- y microscópica. Más especificamente, es capaz de capturar las activadades del deslizamiento cristalográfico y maclado, sus interacciones, así como los efectos en la porosidad derivados de los procesos de colada. ---ABSTRACT--- The last few years have seen a growing effort to reduce CO2 emissions and their negative environmental impact. In the transport industry more specifically, vehicle weight reduction appears as the most straightforward option to achieve this objective. To this end, Mg alloys constitute a significant weight saving material alternative. Many efforts have been devoted over the last decade to understand the main mechanisms governing the plasticity of these materials and, despite being already widely used, high pressure die-casting and wrought Mg alloys are still the subject of intense research campaigns. Developing models that can contemplate the complexity inherent to the deformation of Mg alloys is now timely. This PhD thesis constitutes an attempt to better understand the relationship between the microstructure and the mechanical behavior of Mg alloys, as it will result in the design of polycrystalline models that successfully predict macro- and microscopic properties. Plastic deformation of Mg alloys is driven by a combination of deformation mechanisms specific to their hexagonal crystal structure, namely, basal, prismatic and pyramidal dislocation slip as well as twinning. Wrought Mg alloys present strong textures and thus specific deformation mechanisms are preferentially activated depending on the orientation of the applied load. In this work a crystal plasticity finite element model has been developed in order to understand the macro- and micromechanical behavior of a rolled Mg AZ31 alloy (Mg-3wt.%Al-1wt.%Zn). The model includes twinning and accounts for slip-slip, slip-twin and twin-twin hardening interactions. Upon calibration and validation against experiments, the model successfully predicts the activity of the various deformation mechanisms and the evolution of the texture at different deformation stages. Furthermore, a combined three-dimensional electron backscatter diffraction and modeling approach has been adopted to investigate the effect of grain boundaries on twin propagation in the same material. Both experiments and simulations confirm that the misorientation angle has a critical influence on twin propagation. Non-Schmid effects, i.e. plastic deformation events that do not comply with the Schmid law with respect to the applied stress, are absent in the vicinity of low misorientation boundaries and become more abundant as misorientation angle increases. This research also proves that twin morphology is highly influenced by the Schmid factor. Finally, casting processes usually lead to the formation of significant amounts of gas and shrinkage microporosity, which adversely affect the mechanical properties. The application of hydrostatic pressure after casting can reduce the porosity and improve the properties but little is known about the effects on the casting’s pores size and morphology. In this work, an experimental-computational approach based on X-ray computed tomography, image analysis and finite element analysis is utilized for the determination of the 3D porosity distribution and its evolution with hydrostatic pressure in a high pressure diecast Mg AZ91 alloy (Mg-9wt.%Al-1wt.%Zn). The real 3D pore distribution obtained by tomography is used as input for the finite element simulations using an isotropic hardening law. The model is calibrated and validated against experimental stress-strain curves. The results reveal that the pressure treatment has a significant influence both on the volume and shape changes of individuals pores, which have been precisely quantified, and which are found to be related to the initial pore volume. In conclusion, the crystal plasticity model proposed in this work successfully describes the intrinsic deformation mechanisms of Mg alloys both at the mesoscale and the microscale. More specifically, it can capture slip and twin activities, their interactions, as well as the potential porosity effects arising from casting processes.

Design, development and evaluation of a portable recording system to capture dynamic presentations using the teacher's tablet PC

Computers and multimedia equipment have improved a lot in the last years. They have reduced their cost and size while at the same time increased their capabilities. These improvements allowed us to design and implement a portable recording system that also integrates the teacher´s tablet PC to capture what he/she writes on the slides and all that happens in it. This paper explains this system in detail and the validation of the recordings that we did after using it to record all the lectures the “Communications Software” course in our university. The results show that pupils used the recordings for different purposes and consider them useful for a variety of things, especially after missing a lecture.

Análisis de sistemas eléctricos en microsatélites. Desarrollo de módulos para una Concurrent Design Facility (CDF) para desarrollo y análisis de misiones espaciales = Analysis of microsatellites power subsystems (battery testing). Development and programming of a new Orbit Design Module for a space mission Concurrent Design Facility (CDF)

El presente proyecto se ha realizado durante las prácticas curriculares que han tenido lugar en el Instituto Universitario de Microgravedad “Ignacio Da Riva” (IDR/UPM). A lo largo de estas prácticas se han llevado a cabo trabajos en diversos campos, todos relacionados con el UPMSat-2, desde el subsistema de potencia (placas solares y baterías) hasta el desarrollo de módulos para la Sala de Diseño Concurrente (Concurrent Design Facility, CDF). En la realización de las mismas se ha trabajado en equipo, junto con otros dos alumnos. El objetivo del proyecto es recopilar las tareas realizadas, proporcionando el desarrollo teórico necesario para llevar a cabo todas ellas. Al ser un trabajo con varias partes claramente diferenciadas, se ha optado por comenzar con unas páginas dedicadas a las misiones espaciales. A continuación el trabajo se adentra en el subsistema de potencia de un satélite, particularizando para el UPMSat-2. Finalmente, se proporciona la teoría necesaria para el desarrollo del módulo de misión de la CDF del IDR/UPM, software que se ha desarrollado y tiene reservado un espacio al final, en el cual se describe el programa y se realizan comparaciones de los resultados que proporciona frente a casos reales.

Looking for the Holy Grail of Software Development

The history of Software Engineering has been marked by many famous project failures documented in papers, articles and books. This pattern of lack of success has prompted the creation of dozens of software analysis, requirements definition, and design methods, programming languages, software development environments and software development processes all promoted as solving ?the software problem.? What we hear less about are software projects that were successful. This article reports on the findings of an extensive analysis of successful software projects that have been reported in the literature. It discusses the different interpretations of success and extracts the characteristics that successful projects have in common. These characteristics provide Software Project Managers with an agenda of topics to be addressed that will help ensure, not guarantee, that their software project will be successful.