Comparative analysis of meta-analysis methods: when to use which?

Background: Several meta-analysis methods can be used to quantitatively combine the results of a group of experiments, including the weighted mean difference, statistical vote counting, the parametric response ratio and the non-parametric response ratio. The software engineering community has focused on the weighted mean difference method. However, other meta-analysis methods have distinct strengths, such as being able to be used when variances are not reported. There are as yet no guidelines to indicate which method is best for use in each case. Aim: Compile a set of rules that SE researchers can use to ascertain which aggregation method is best for use in the synthesis phase of a systematic review. Method: Monte Carlo simulation varying the number of experiments in the meta analyses, the number of subjects that they include, their variance and effect size. We empirically calculated the reliability and statistical power in each case Results: WMD is generally reliable if the variance is low, whereas its power depends on the effect size and number of subjects per meta-analysis; the reliability of RR is generally unaffected by changes in variance, but it does require more subjects than WMD to be powerful; NPRR is the most reliable method, but it is not very powerful; SVC behaves well when the effect size is moderate, but is less reliable with other effect sizes. Detailed tables of results are annexed. Conclusions: Before undertaking statistical aggregation in software engineering, it is worthwhile checking whether there is any appreciable difference in the reliability and power of the methods. If there is, software engineers should select the method that optimizes both parameters.

Estudio de las formas de aplicación de la fotografía sobre los materiales pétreos para la arquitectura = Study of photography application methods over architectural stony materials

Desde que el Hombre era morador de las cavernas ha sido manifiesto su deseo innato por grabar y reproducir "instantáneas con las que perpetuarse o sobre las que mirarse ". La aparición y desarrollo de la fotografía como medio para poder captar y fijar "la imagen directa de la realidad circundante " pronto se convierte en un nuevo lenguaje estético y poético que permite al artista la interpretación y reflexión de lo observado. Se imprime a la imagen el carácter de la mirada del fotógrafo, estableciendo un diálogo conceptual con el juego de luces. La presente Tesis plantea la creación de una nueva piel de arquitectura mediante la impresión fotográfica sobre materiales pétreos. La búsqueda de la expresividad de los materiales como soporte de expresión artística implica un cambio de escala al trasladar la instantánea fotográfica a la arquitectura y la aplicación de un nuevo soporte al imprimir la fotografía sobre materiales arquitectónicos. Se justifica la elección del dispositivo láser CO2 como sistema de impresión fotográfica sobre los materiales pétreos arquitectónicos, como la técnica que permite la unión física de la imagen y el proyecto arquitectónico, generando un valor añadido a través del arte de la fotografía. Se justifica la elección de los materiales investigados, Silestone® Blanco Zeus y GRC® con TX Active® Aria, de forma que la investigación de esta nueva piel de arquitectura abarca tanto la envolvente del edificio como su volumen interior, permitiendo cerrar el círculo arquitectónico "in&out" y dota al proyecto arquitectónico de un valor añadido al introducir conceptos sostenibles de carácter estético y medioambiental. Se realiza una consulta a las empresas del sector arquitectónico relacionadas directamente con la producción y distribución de los materiales Silestone® y GRC®, así como a las empresas especializadas en sistemas de impresión fotográfica sobre materiales, acerca del estado del arte. Se recorre la Historia de la fotografía desde sus orígenes hasta el desarrollo de la era digital y se analiza su condición artística. Se recopilan los sistemas de impresión fotográfica que han evolucionado en paralelo con los dispositivos de captura de la instantánea fotográfica y se describe en profundidad el sistema de impresión fotográfica mediante dispositivo láser CO2. Se describen los procesos de fabricación, las características técnicas, cualidades y aplicaciones de los materiales pétreos arquitectónicos Silestone® Blanco Zeus y GRC® con TX Active® Aria. Se explica la técnica utilizada para la captación de la imagen fotográfica, su justificación artística y su proceso de impresión mediante dispositivo láser CO2 bajo diferentes parámetros sobre muestras de los materiales arquitectónicos investigados. Se comprueba la viabilidad de desarrollo de la nueva piel de arquitectura sobre Silestone® Blanco Zeus y GRC® con TX Active® Aria sometiendo a las piezas impresas bajo diferentes parámetros a tres ensayos de laboratorio. En cada uno de ellos se concreta el objetivo y procedimiento del ensayo, la enumeración de las muestras ensayadas y los parámetros bajo los que han sido impresas, el análisis de los resultados del ensayo y las conclusiones del ensayo. Ensayo de amplitud térmica. Se determina el grado de afectación de las imágenes impresas bajo la acción de contrastes térmicos. Series de muestras de Silestone® Blanco Zeus y GRC® con TX Active® Aria impresas con láser CO2 se someten a ciclos de contraste frío-calor de 12 horas de duración para una amplitud térmica total de 102°C. Se realiza una toma sistemática de fotografías microscópicas con lupa de aumento de cada pieza antes y después de los ciclos frío-calor y la observación de las transformaciones que experimentan los materiales bajo la acción del láser CO2. Ensayo de exposición a la acción de la radiación ultravioleta (UV). Se determina el grado de afectación de las imágenes impresas al activar la capacidad autolimpiante de partículas orgánicas. Una serie de muestras de GRC® con TX Active® Aria impresa con láser CO2 se someten a ciclos de exposición de radiación ultravioleta de 26 horas de duración. Se somete la serie a un procedimiento de activación del aditivo TX Active®. Se simula la contaminación orgánica mediante la aplicación controlada de Rodamina B, tinte orgánico, y se simula la radiación UV mediante el empleo de una bombilla de emisión de rayos ultravioleta. Se realiza una toma sistemática de fotografías macroscópicas de la serie de muestras ensayadas: antes de aplicación de la Rodamina B, momento 00:00h, momento 04:00h y momento 26:00h del ensayo. Se procede a la descarga y análisis del histograma de las fotografías como registro de la actividad fotocatalítica. Ensayo de la capacidad autodescontaminante del GRC® con TX Active® impreso con láser CO2. Se comprueba si la capacidad autodescontaminante del GRC® con TX Active® se ve alterada como consecuencia de la impresión de la imagen fotográfica impresa con láser CO2. Serie de muestras de GRC® con TX Active® Aria impresa con láser CO2 se someten a test de capacidad autodescontaminante: atmósfera controlada y contaminada con óxidos de nitrógeno en los que se coloca cada pieza ensayada bajo la acción de una lámpara de emisión de radiación ultravioleta (UV). Se registra la actividad fotocatalítica en base a la variación de concentración de óxido de nitrógeno. Se recopila el análisis e interpretación de los resultados de los ensayos de laboratorio y se elaboran las conclusiones generales de la investigación. Se sintetizan las futuras líneas de investigación que, a partir de las investigaciones realizadas y de sus conclusiones generales, podrían desarrollarse en el ámbito de la impresión fotográfica sobre materiales arquitectónicos. Se describe el rendimiento tecnológico y artístico generado por las investigaciones previas que han dado origen y desarrollo a la Tesis Doctoral. ABSTRACT Since ancient time, humanity has been driven by an innate wish to reproduce and engrave "snapshots that could help to perpetúate or to look at one self". Photography's birth and its development as a mean to capture and fix "the direct image of the surrounding reality" quickly becomes a new aesthetical and poetical language allowing the artist to interpret and think over what has been observed. The photographer's eye is imprinted onto the image, and so the conceptual dialogue between the artist and the light beams begins. The current thesis suggests the creation of a new architectural skin through photography imprinting over stony materials. The search for material's expressiveness as a medium of artistic expression involves a change of scale as it transfers photographic snapshot into architecture and the use of a new photographic printing support over architectural materials. CO2 laser is the chosen printing system for this technique as it allows the physical union of the image and the architectonic project, generating an added value through the art of photography. The researched materials selected were Silestone®, Blanco Zeus and GRC® with TX Active® Aria. This new architectural skin contains the building surrounding as well as its interior volume, closing the architectonic "in & out" circle and adding a value to the project by introducing aesthetical and environmental sustainable concepts. Architecture companies related to the production and distribution of materials like Silestone® and GRC®, as well as companies specialized in photography printing over materials were consulted to obtain a State of the Art. A thorough analysis of photography's History from its origins to the digital era development was made and its artistic condition was studied in this thesis. In this study the author also makes a compilation of several photographic printing systems that evolved together with photographic snapshot devices. The CO2 laser-based photographic printing system is also described in depth. Regarding stony materials of architecture like Silestone®, Blanco Zeus and GRC® with TX Active® Aria, the present study also describes their manufacture processes as well as technical features, quality and application. There is also an explanation about the technique to capture the photographic image, its artistic justification and its CO2 laser-based printing system over the researched materials under different parameters. We also tested the feasibility of this new architectural skin over Silestone® Blanco Zeus and GRC® with TX Active® Aria. The pieces were tested under different parameters in three laboratory trials. Each trial comprises of an explanation of its objective and its process, the samples were numbered and the printing parameters were specified. Finally, with the analysis of the results some conclusions were drawn. In the thermal amplitude trial we tried to determine how printed images were affected as a result of the action of thermal contrasts. Series of samples of Silestone® Blanco Zeus and GRC® with TX Active® Aria printed with CO2 laser were subjected to several 12h warm-cold cycles for thermal total amplitude of 102oc. Each sample was captured systematically with microscopic enhanced lenses before and after cold-warm cycles. The changes experienced by these materials under the effect of CO2 laser were observed and recorded. Trial regarding the Ultraviolet Radiation (UR) effect on images. We determined to which extent printed images were affected once the self-cleaning organic particles were activated. This time GRC® with TX Active® Aria samples printed with CO2 laser were exposed to a 26h UR cycle. The samples were subjected to the activation of TX Active® additive. Through the controlled application of Rodamine B and organic dye we were able to simulate the organic contamination process. UR was simulated using an ultraviolet beam emission bulb. A systematic capture of macroscopic pictures of the tested sample series was performed at different time points: before Rodamine B application, at moment 00:00h, moment 04:00h and moment 26:00h of the trial. Picture's histogram was downloaded and analyzed as a log of photocatalytic activity. Trial regarding the self-decontaminating ability of GRC® with TX Active® printed with CO2 laser. We tested if this self-decontaminating ability is altered as a result of CO2 laser printed image. GRC® with TX Active® Aria samples printed with CO2 laser, were subject to self-decontaminating ability tests with controlled and nitrogen oxide contaminated atmosphere. Each piece was put under the action of an UR emission lamp. Photocatalytic activity was recorded according to the variation in nitrogen oxide concentration. The results of the trial and their interpretation as well as the general conclusions of the research are also compiled in the present study. Study conclusions enable to draw future research lines of potential applications of photographic printing over architecture materials. Previous research generated an artistic and technological outcome that led to the development of this doctoral thesis.

Systematic Approach for the selection of monitoring technologies in CO2 geological storage projects. Application of multicriteria decision making

Geologic storage of carbon dioxide (CO2) has been proposed as a viable means for reducing anthropogenic CO2 emissions. Once injection begins, a program for measurement, monitoring, and verification (MMV) of CO2 distribution is required in order to: a) research key features, effects and processes needed for risk assessment; b) manage the injection process; c) delineate and identify leakage risk and surface escape; d) provide early warnings of failure near the reservoir; and f) verify storage for accounting and crediting. The selection of the methodology of monitoring (characterization of site and control and verification in the post-injection phase) is influenced by economic and technological variables. Multiple Criteria Decision Making (MCDM) refers to a methodology developed for making decisions in the presence of multiple criteria. MCDM as a discipline has only a relatively short history of 40 years, and it has been closely related to advancements on computer technology. Evaluation methods and multicriteria decisions include the selection of a set of feasible alternatives, the simultaneous optimization of several objective functions, and a decision-making process and evaluation procedures that must be rational and consistent. The application of a mathematical model of decision-making will help to find the best solution, establishing the mechanisms to facilitate the management of information generated by number of disciplines of knowledge. Those problems in which decision alternatives are finite are called Discrete Multicriteria Decision problems. Such problems are most common in reality and this case scenario will be applied in solving the problem of site selection for storing CO2. Discrete MCDM is used to assess and decide on issues that by nature or design support a finite number of alternative solutions. Recently, Multicriteria Decision Analysis has been applied to hierarchy policy incentives for CCS, to assess the role of CCS, and to select potential areas which could be suitable to store. For those reasons, MCDM have been considered in the monitoring phase of CO2 storage, in order to select suitable technologies which could be techno-economical viable. In this paper, we identify techniques of gas measurements in subsurface which are currently applying in the phase of characterization (pre-injection); MCDM will help decision-makers to hierarchy the most suitable technique which fit the purpose to monitor the specific physic-chemical parameter.

Optimal boundary geometry in an elasticity problem: a systematic adjoint approach

In different problems of Elasticity the definition of the optimal gcometry of the boundary, according to a given objective function, is an issue of great interest. Finding the shape of a hole in the middle of a plate subjected to an arbitrary loading such that the stresses along the hole minimizes some functional or the optimal middle curved concrete vault for a tunnel along which a uniform minimum compression are two typical examples. In these two examples the objective functional depends on the geometry of the boundary that can be either a curve (in case of 2D problems) or a surface boundary (in 3D problems). Typically, optimization is achieved by means of an iterative process which requires the computation of gradients of the objective function with respect to design variables. Gradients can by computed in a variety of ways, although adjoint methods either continuous or discrete ones are the more efficient ones when they are applied in different technical branches. In this paper the adjoint continuous method is introduced in a systematic way to this type of problems and an illustrative simple example, namely the finding of an optimal shape tunnel vault immersed in a linearly elastic terrain, is presented.

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.