Sedimentation rate calculations and isotopic analysis on sediment cores along the IODP Expedition 311 transect

The oceanographic and tectonic conditions of accretionary margins are well-suited for several potential processes governing methane generation, storage and release. To identify the relevant methane evolution pathways in the northern Cascadia accretionary margin, a four-site transect was drilled during Integrated Ocean Drilling Program Expedition 311. The d13C values of methane range from a minimum value of -82.2 per mil on an uplifted ridge of accreted sediment near the deformation front (Site U1326, 1829 mbsl, meters below sea level) to a maximum value of -39.5 per mil at the most landward location within an area of steep canyons near the shelf edge (Site U1329, 946 mbsl). An interpretation based solely on methane isotope values might conclude the 13C-enrichment of methane indicates a transition from microbially- to thermogenically-sourced methane. However, the co-existing CO2 exhibits a similar trend of 13C-enrichment along the transect with values ranging from -22.5 per mil to +25.7 per mil. The magnitude of the carbon isotope separation between methane and CO2 (Ec = 63.8 ± 5.8) is consistent with isotope fractionation during microbially mediated carbonate reduction. These results, in conjunction with a transect-wide gaseous hydrocarbon content composed of > 99.8% (by volume) methane and uniform dDCH4 values (-172 per mil ± 8) that are distinct from thermogenic methane at a seep located 60 km from the Expedition 311 transect, suggest microbial CO2 reduction is the predominant methane source at all investigated sites. The magnitude of the intra-site downhole 13C-enrichment of CO2 within the accreted ridge (Site U1326) and a slope basin nearest the deformation front (Site U1325, 2195 mbsl) is ~ 5 per mil. At the mid-slope site (Site U1327, 1304 mbsl) the downhole 13C-enrichment of the CO2 is ~ 25 per mil and increases to ~ 40 per mil at the near-shelf edge Site U1329. This isotope fractionation pattern is indicative of more extensive diagenetic alteration at sites with greater 13C-enrichment. The magnitude of the 13C-enrichment of CO2 correlates with decreasing sedimentation rates and a diminishing occurrence of stratigraphic gas hydrate. We suggest the decreasing sedimentation rates increase the exposure time of sedimentary organic matter to aerobic and anaerobic degradation, during burial, thereby reducing the availability of metabolizable organic matter available for methane production. This process is reflected in the occurrence and distribution of gas hydrate within the northern Cascadia margin accretionary prism. Our observations are relevant for evaluating methane production and the occurrence of stratigraphic gas hydrate within other convergent margins.

Nonrigid Motion Compensation of Free Breathing Acquired Myocardial Perfusion Data

In this work, we present a novel method to compensate the movement in images acquired during free breathing using first-pass gadolinium enhanced, myocardial perfusion magnetic resonance imaging (MRI). First, we use independent component analysis (ICA) to identify the optimal number of independent components (ICs) that separate the breathing motion from the intensity change induced by the contrast agent. Then, synthetic images are created by recombining the ICs, but other then in previously published work (Milles et al. 2008), we omit the component related to motion, and therefore, the resulting reference image series is free of motion. Motion compensation is then achieved by using a multi-pass non-rigid image registration scheme. We tested our method on 15 distinct image series (5 patients) consisting of 58 images each and we validated our method by comparing manually tracked intensity profiles of the myocardial sections to automatically generated ones before and after registration. The average correlation to the manually obtained curves before registration 0:89 0:11 was increased to 0:98 0:02

Failure locus of polypropylene nonwoven fabrics under in-plane biaxial deformation

The failure locus, the characteristics of the stress–strain curve and the damage localization patterns were analyzed in a polypropylene nonwoven fabric under in-plane biaxial deformation. The analysis was carried out by means of a homogenization model developed within the context of the finite element method. It provides the constitutive response for a mesodomain of the fabric corresponding to the area associated to a finite element and takes into account the main deformation and damage mechanisms experimentally observed. It was found that the failure locus in the stress space was accurately predicted by the Von Mises criterion and failure took place by the localization of damage into a crack perpendicular to the main loading axis.

COMSOL Multyphisics Super Resolution Analysis of a Spherical Geodesic Waveguide Suitable for Manufacturing

Recently it has been proved theoretically (Miñano et al, 2011) that the super-resolution up to ?/500 can be achieved using an ideal metallic Spherical Geodesic Waveguide (SGW). This SGW is a theoretical design, in which the conductive walls are considered to be lossless conductors with zero thickness. In this paper, we study some key parameters that might influence the super resolution properties reported in (Miñano et al, 2011), such as losses, metal type, the thickness of conductive walls and the deformation from perfect sphere. We implement a realistic SGW in COMSOL multiphysics and analyze its super-resolution properties. The realistic model is designed in accordance with the manufacturing requirements and technological limitations.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole-brain suffers from distortions caused by the standard echo-planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a “theoretically correct” and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.

MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Simulation of the deformation of polycrystalline nanostructured Ti by computational homogenization

Computational homogenization by means of the finite element analysis of a representative volume element of the microstructure is used to simulate the deformation of nanostructured Ti. The behavior of each grain is taken into account using a single crystal elasto-viscoplastic model which includes the microscopic mechanisms of plastic deformation by slip along basal, prismatic and pyramidal systems. Two different representations of the polycrystal were used. Each grain was modeled with one cubic finite element in the first one while many cubic elements were used to represent each grain in the second one, leading to a model which includes the effect of grain shape and size in a limited number of grains due to the computational cost. Both representations were used to simulate the tensile deformation of nanostructured Ti processed by ECAP-C as well as the drawing process of nanostructured Ti billets. It was found that the first representation based in one finite element per grain led to a stiffer response in tension and was not able to predict the texture evolution during drawing because the strain gradient within each grain could not be captured. On the contrary, the second representation of the polycrystal microstructure with many finite elements per grain was able to predict accurately the deformation of nanostructured Ti.

Analysis of crystallographic slip and grain boundary sliding in a Ti-45Al-2Nb-2Mn (at%)-0.8 vol%TiB2 alloy by high temperature in situ mechanical testing

This work aims to contribute to a further understanding of the fundamentals of crystallographic slip and grain boundary sliding in the γ-TiAl Ti–45Al–2Nb–2Mn (at%)–0.8 vol%TiB2 intermetallic alloy, by means of in situ high-temperature tensile testing combined with electron backscatter diffraction (EBSD). Several microstructures, containing different fractions and sizes of lamellar colonies and equiaxed γ-grains, were fabricated by either centrifugal casting or powder metallurgy, followed by heat treatment at 1300 °C and furnace cooling. in situ tensile and tensile-creep experiments were performed in a scanning electron microscope (SEM) at temperatures ranging from 580 °C to 700 °C. EBSD was carried out in selected regions before and after straining. Our results suggest that, during constant strain rate tests, true twin γ/γ interfaces are the weakest barriers to dislocations and, thus, that the relevant length scale might be influenced by the distance between non-true twin boundaries. Under creep conditions both grain/colony boundary sliding (G/CBS) and crystallographic slip are observed to contribute to deformation. The incidence of boundary sliding is particularly high in γ grains of duplex microstructures. The slip activity during creep deformation in different microstructures was evaluated by trace analysis. Special emphasis was placed in distinguishing the compliance of different slip events with the Schmid law with respect to the applied stress.

Numerical methods in Nonlinear Analysis of shell structures

The design of shell and spatial structures represents an important challenge even with the use of the modern computer technology.If we concentrate in the concrete shell structures many problems must be faced,such as the conceptual and structural disposition, optimal shape design, analysis, construction methods, details etc. and all these problems are interconnected among them. As an example the shape optimization requires the use of several disciplines like structural analysis, sensitivity analysis, optimization strategies and geometrical design concepts. Similar comments can be applied to other space structures such as steel trusses with single or double shape and tension structures. In relation to the analysis the Finite Element Method appears to be the most extended and versatile technique used in the practice. In the application of this method several issues arise. First the derivation of the pertinent shell theory or alternatively the degenerated 3-D solid approach should be chosen. According to the previous election the suitable FE model has to be adopted i.e. the displacement,stress or mixed formulated element. The good behavior of the shell structures under dead loads that are carried out towards the supports by mainly compressive stresses is impaired by the high imperfection sensitivity usually exhibited by these structures. This last effect is important particularly if large deformation and material nonlinearities of the shell may interact unfavorably, as can be the case for thin reinforced shells. In this respect the study of the stability of the shell represents a compulsory step in the analysis. Therefore there are currently very active fields of research such as the different descriptions of consistent nonlinear shell models given by Simo, Fox and Rifai, Mantzenmiller and Buchter and Ramm among others, the consistent formulation of efficient tangent stiffness as the one presented by Ortiz and Schweizerhof and Wringgers, with application to concrete shells exhibiting creep behavior given by Scordelis and coworkers; and finally the development of numerical techniques needed to trace the nonlinear response of the structure. The objective of this paper is concentrated in the last research aspect i.e. in the presentation of a state-of-the-art on the existing solution techniques for nonlinear analysis of structures. In this presentation the following excellent reviews on this subject will be mainly used.

Analysis of the problems associated with dynamic interaction between train, track and structure at transition zones

El gran desarrollo experimentado por la alta velocidad en los principales países de la Unión Europea, en los últimos 30 años, hace que este campo haya sido y aún sea uno de los principales referentes en lo que a investigación se refiere. Por otra parte, la aparición del concepto super − alta velocidad hace que la investigación en el campo de la ingeniería ferroviaria siga adquiriendo importancia en los principales centros de investigación de los países en los que se desea implantar este modo de transporte, o en los que habiendo sido ya implantado, se pretenda mejorar. Las premisas de eficacia, eficiencia, seguridad y confort, que este medio de transporte tiene como razón de ser pueden verse comprometidas por diversos factores. Las zonas de transición, definidas en la ingeniería ferroviaria como aquellas secciones en las que se produce un cambio en las condiciones de soporte de la vía, pueden afectar al normal comportamiento para el que fue diseñada la infraestructura, comprometiendo seriamente los estándares de eficiencia en el tiempo de viaje, confort de los pasajeros y aumentando considerablemente los costes de mantenimiento de la vía, si no se toman las medidas oportunas. En esta tesis se realiza un estudio detallado de la zonas de transición, concretamente de aquellas en las que existe una cambio en la rigidez vertical de la vía debido a la presencia de un marco hidráulico. Para realizar dicho estudio se lleva a cabo un análisis numérico de interacción entre el vehículo y la estructura, con un modelo bidimensional de elemento finitos, calibrado experimentalmente, en estado de tensión plana. En este análisis se tiene en cuenta el efecto de las irregularidades de la vía y el comportamiento mecánico de la interfaz suelo-estructura, con el objetivo de reproducir de la forma más real posible el efecto de interacción entre el vehículo, la vía y la estructura. Otros efectos como la influencia de la velocidad del tren y los asientos diferenciales, debidos a deformaciones por consolidación de los terraplenes a ambos lados el marco hidráulico, son también analizados en este trabajo. En esta tesis, los cálculos de interacción se han llevado a cabo en dos fases diferentes. En la primera, se ha considerado una interacción sencilla debida al paso de un bogie de un tren Eurostar. Los cálculos derivados de esta fase se han denominado cálculos a corto plazo. En la segunda, se ha realizado un análisis considerando múltiples pasos de bogie del tren Eurostar, conformando un análisis de degradación en el que se tiene en cuenta, en cada ciclo, la deformación de la capa de balasto. Los cálculos derivados de esta fase, son denominados en el texto como cálculos a largo plazo. Los resultados analizados muestran que la utilización de los denominados elementos de contacto es fundamental cuando se desea estudiar la influencia de asientos diferenciales, especialmente en transiciones terraplén-estructura en las que la cuña de cimentación no llega hasta la base de cimentación de la estructura. Por otra parte, tener en cuenta los asientos del terraplén, es sumamente importante, cuando se desea realizar un análisis de degradación de la vía ya que su influencia en la interacción entre el vehículo y la vía es muy elevada, especialmente para valores altos de velocidad del tren. En cuanto a la influencia de las irregularidades de la vía, en los cálculos efectuados, se revela que su importancia es muy notable, siendo su influencia muy destacada cuanto mayor sea la velocidad del tren. En este punto cabe destacar la diferencia de resultados derivada de la consideración de perfiles de irregularidades de distinta naturaleza. Los resultados provenientes de considerar perfiles artificiales son en general muy elevados, siendo estos más apropiados para realizar estudios de otra índole, como por ejemplo de seguridad al descarrilamiento. Los resultados provenientes de perfiles reales, dados por diferentes Administradores ferroviarios, presentan resultados menos elevados y más propios del problema analizar. Su influencia en la interacción dinámica entre el vehículo y la vía es muy importante, especialmente para velocidades elevadas del tren. Además el fenómeno de degradación conocido como danza de traviesas, asociado a zonas de transición, es muy susceptible a la consideración de irregularidades de la vía, tal y como se desprende de los cálculos efectuados a largo plazo. The major development experienced by high speed in the main countries of the European Union, in the last 30 years, makes railway research one of the main references in the research field. It should also be mentioned that the emergence of the concept superhigh − speed makes research in the field of Railway Engineering continues to gain importance in major research centers in the countries in which this mode of transportation is already implemented or planned to be implemented. The characteristics that this transport has as rationale such as: effectiveness, efficiency, safety and comfort, may be compromised by several factors. The transition zones are defined in railway engineering as a region in which there is an abrupt change of track stiffness. This stiffness variation can affect the normal behavior for which the infrastructure has been designed, seriously compromising efficiency standards in the travel time, passenger comfort and significantly increasing the costs of track maintenance, if appropriate measures are not taken. In this thesis a detailed study of the transition zones has been performed, particularly of those in which there is a change in vertical stiffness of the track due to the presence of a reinforced concrete culvert. To perform such a study a numerical interaction analysis between the vehicle, the track and the structure has been developed. With this purpose a two-dimensional finite element model, experimentally calibrated, in a state of plane stress, has been used. The implemented numerical models have considered the effects of track irregularities and mechanical behavior of soil-structure interface, with the objective of reproducing as accurately as possible the dynamic interaction between the vehicle the track and the structure. Other effects such as the influence of train speed and differential settlement, due to secondary consolidation of the embankments on both sides of culvert, have also been analyzed. In this work, the interaction analysis has been carried out in two different phases. In the first part a simple interaction due to the passage of a bogie of a Eurostar train has been considered. Calculations derived from this phase have been named short-term analysis. In the second part, a multi-load assessment considering an Eurostar train bogie moving along the transition zone, has been performed. The objective here is to simulate a degradation process in which vertical deformation of the ballast layer was considered. Calculations derived from this phase have been named long-term analysis. The analyzed results show that the use of so-called contact elements is essential when one wants to analyze the influence of differential settlements, especially in embankment-structure transitions in which the wedge-shaped backfill does not reach the foundation base of the structure. Moreover, considering embankment settlement is extremely important when it is desired to perform an analysis of track degradation. In these cases the influence on the interaction behaviour between the vehicle and the track is very high, especially for higher values of speed train. Regarding the influence of the track irregularities, this study has proven that the track’s dynamic response is heavily influenced by the irregularity profile and that this influence is more important for higher train velocities. It should also be noted that the difference in results derived from consideration of irregularities profiles of different nature. The results coming from artificial profiles are generally very high, these might be more appropriate in order to study other effects, such as derailment safety. Results from real profiles, given by the monitoring works of different rail Managers, are softer and they fit better to the context of this thesis. The influence of irregularity profiles on the dynamic interaction between the train and the track is very important, especially for high-speeds of the train. Furthermore, the degradation phenomenon known as hanging sleepers, associated with transition zones, is very susceptible to the consideration of track irregularities, as it can be concluded from the long-term analysis.

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

The structural connectivity of the brain is considered to encode species-wise and subject-wise patterns that will unlock large areas of understanding of the human brain. Currently, diffusion MRI of the living brain enables to map the microstructure of tissue, allowing to track the pathways of fiber bundles connecting the cortical regions across the brain. These bundles are summarized in a network representation called connectome that is analyzed using graph theory. The extraction of the connectome from diffusion MRI requires a large processing flow including image enhancement, reconstruction, segmentation, registration, diffusion tracking, etc. Although a concerted effort has been devoted to the definition of standard pipelines for the connectome extraction, it is still crucial to define quality assessment protocols of these workflows. The definition of quality control protocols is hindered by the complexity of the pipelines under test and the absolute lack of gold-standards for diffusion MRI data. Here we characterize the impact on structural connectivity workflows of the geometrical deformation typically shown by diffusion MRI data due to the inhomogeneity of magnetic susceptibility across the imaged object. We propose an evaluation framework to compare the existing methodologies to correct for these artifacts including whole-brain realistic phantoms. Additionally, we design and implement an image segmentation and registration method to avoid performing the correction task and to enable processing in the native space of diffusion data. We release PySDCev, an evaluation framework for the quality control of connectivity pipelines, specialized in the study of susceptibility-derived distortions. In this context, we propose Diffantom, a whole-brain phantom that provides a solution to the lack of gold-standard data. The three correction methodologies under comparison performed reasonably, and it is difficult to determine which method is more advisable. We demonstrate that susceptibility-derived correction is necessary to increase the sensitivity of connectivity pipelines, at the cost of specificity. Finally, with the registration and segmentation tool called regseg we demonstrate how the problem of susceptibility-derived distortion can be overcome allowing data to be used in their original coordinates. This is crucial to increase the sensitivity of the whole pipeline without any loss in specificity.

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.

Multiscale analysis of the mechanical behavior of needle-punched nonwoven fabrics

Los fieltros son una familia de materiales textiles constituidos por una red desordenada de fibras conectadas por medio de enlaces térmicos, químicos o mecánicos. Presentan menor rigidez y resistencia (al igual que un menor coste de procesado) que sus homólogos tejidos, pero mayor deformabilidad y capacidad de absorción de energía. Los fieltros se emplean en diversas aplicaciones en ingeniería tales como aislamiento térmico, geotextiles, láminas ignífugas, filtración y absorción de agua, impacto balístico, etc. En particular, los fieltros punzonados fabricados con fibras de alta resistencia presentan una excelente resistencia frente a impacto balístico, ofreciendo las mismas prestaciones que los materiales tejidos con un tercio de la densidad areal. Sin embargo, se sabe muy poco acerca de los mecanismos de deformación y fallo a nivel microscópico, ni sobre como influyen en las propiedades mecánicas del material. Esta carencia de conocimiento dificulta la optimización del comportamiento mecánico de estos materiales y también limita el desarrollo de modelos constitutivos basados en mecanismos físicos, que puedan ser útiles en el diseño de componentes estructurales. En esta tesis doctoral se ha llevado a cabo un estudio minucioso con el fin de determinar los mecanismos de deformación y las propiedades mecánicas de fieltros punzonados fabricados con fibras de polietileno de ultra alto peso molecular. Los procesos de deformación y disipación de energía se han caracterizado en detalle por medio de una combinación de técnicas experimentales (ensayos mecánicos macroscópicos a velocidades de deformación cuasi-estáticas y dinámicas, impacto balístico, ensayos de extracción de una o múltiples fibras, microscopía óptica, tomografía computarizada de rayos X y difracción de rayos X de gran ángulo) que proporcionan información de los mecanismos dominantes a distintas escalas. Los ensayos mecánicos macroscópicos muestran que el fieltro presenta una resistencia y ductilidad excepcionales. El estado inicial de las fibras es curvado, y la carga se transmite por el fieltro a través de una red aleatoria e isótropa de nudos creada por el proceso de punzonamiento, resultando en la formación de una red activa de fibra. La rotación y el estirado de las fibras activas es seguido por el deslizamiento y extracción de la fibra de los puntos de anclaje mecánico. La mayor parte de la resistencia y la energía disipada es proporcionada por la extracción de las fibras activas de los nudos, y la fractura final tiene lugar como consecuencia del desenredo total de la red en una sección dada donde la deformación macroscópica se localiza. No obstante, aunque la distribución inicial de la orientación de las fibras es isótropa, las propiedades mecánicas resultantes (en términos de rigidez, resistencia y energía absorbida) son muy anisótropas. Los ensayos de extracción de múltiples fibras en diferentes orientaciones muestran que la estructura de los nudos conecta más fibras en la dirección transversal en comparación con la dirección de la máquina. La mejor interconectividad de las fibras a lo largo de la dirección transversal da lugar a una esqueleto activo de fibras más denso, mejorando las propiedades mecánicas. En términos de afinidad, los fieltros deformados a lo largo de la dirección transversal exhiben deformación afín (la deformación macroscópica transfiere directamente a las fibras por el material circundante), mientras que el fieltro deformado a lo largo de la dirección de la máquina presenta deformación no afín, y la mayor parte de la deformación macroscópica no es transmitida a las fibras. A partir de estas observaciones experimentales, se ha desarrollado un modelo constitutivo para fieltros punzonados confinados por enlaces mecánicos. El modelo considera los efectos de la deformación no afín, la conectividad anisótropa inducida durante el punzonamiento, la curvatura y re-orientación de la fibra, así como el desenredo y extracción de la fibra de los nudos. El modelo proporciona la respuesta de un mesodominio del material correspondiente al volumen asociado a un elemento finito, y se divide en dos bloques. El primer bloque representa el comportamiento de la red y establece la relación entre el gradiente de deformación macroscópico y la respuesta microscópica, obtenido a partir de la integración de la respuesta de las fibras en el mesodominio. El segundo bloque describe el comportamiento de la fibra, teniendo en cuenta las características de la deformación de cada familia de fibras en el mesodominio, incluyendo deformación no afín, estiramiento, deslizamiento y extracción. En la medida de lo posible, se ha asignado un significado físico claro a los parámetros del modelo, por lo que se pueden identificar por medio de ensayos independientes. Las simulaciones numéricas basadas en el modelo se adecúan a los resultados experimentales de ensayos cuasi-estáticos y balísticos desde el punto de vista de la respuesta mecánica macroscópica y de los micromecanismos de deformación. Además, suministran información adicional sobre la influencia de las características microstructurales (orientación de la fibra, conectividad de la fibra anisótropa, afinidad, etc) en el comportamiento mecánico de los fieltros punzonados. Nonwoven fabrics are a class of textile material made up of a disordered fiber network linked by either thermal, chemical or mechanical bonds. They present lower stiffness and strength (as well as processing cost) than the woven counterparts but much higher deformability and energy absorption capability and are used in many different engineering applications (including thermal insulation, geotextiles, fireproof layers, filtration and water absorption, ballistic impact, etc). In particular, needle-punched nonwoven fabrics manufactured with high strength fibers present an excellent performance for ballistic protection, providing the same ballistic protection with one third of the areal weight as compared to dry woven fabrics. Nevertheless, very little is known about their deformation and fracture micromechanisms at the microscopic level and how they contribute to the macroscopic mechanical properties. This lack of knowledge hinders the optimization of their mechanical performance and also limits the development of physically-based models of the mechanical behavior that can be used in the design of structural components with these materials. In this thesis, a thorough study was carried out to ascertain the micromechanisms of deformation and the mechanical properties of a needle-punched nonwoven fabric made up by ultra high molecular weight polyethylene fibers. The deformation and energy dissipation processes were characterized in detail by a combination of experimental techniques (macroscopic mechanical tests at quasi-static and high strain rates, ballistic impact, single fiber and multi fiber pull-out tests, optical microscopy, X-ray computed tomography and wide angle X-ray diffraction) that provided information of the dominant mechanisms at different length scales. The macroscopic mechanical tests showed that the nonwoven fabric presented an outstanding strength and energy absorption capacity. It was found that fibers were initially curved and the load was transferred within the fabric through the random and isotropic network of knots created by needlepunching, leading to the formation of an active fiber network. Uncurling and stretching of the active fibers was followed by fiber sliding and pull-out from the entanglement points. Most of the strength and energy dissipation was provided by the extraction of the active fibers from the knots and final fracture occurred by the total disentanglement of the fiber network in a given section at which the macroscopic deformation was localized. However, although the initial fiber orientation distribution was isotropic, the mechanical properties (in terms of stiffness, strength and energy absorption) were highly anisotropic. Pull-out tests of multiple fibers at different orientations showed that structure of the knots connected more fibers in the transverse direction as compared with the machine direction. The better fiber interconnection along the transverse direction led to a denser active fiber skeleton, enhancing the mechanical response. In terms of affinity, fabrics deformed along the transverse direction essentially displayed affine deformation {i.e. the macroscopic strain was directly transferred to the fibers by the surrounding fabric, while fabrics deformed along the machine direction underwent non-affine deformation, and most of the macroscopic strain was not transferred to the fibers. Based on these experimental observations, a constitutive model for the mechanical behavior of the mechanically-entangled nonwoven fiber network was developed. The model accounted for the effects of non-affine deformation, anisotropic connectivity induced by the entanglement points, fiber uncurling and re-orientation as well as fiber disentanglement and pull-out from the knots. The model provided the constitutive response for a mesodomain of the fabric corresponding to the volume associated to a finite element and is divided in two blocks. The first one was the network model which established the relationship between the macroscopic deformation gradient and the microscopic response obtained by integrating the response of the fibers in the mesodomain. The second one was the fiber model, which took into account the deformation features of each set of fibers in the mesodomain, including non-affinity, uncurling, pull-out and disentanglement. As far as possible, a clear physical meaning is given to the model parameters, so they can be identified by means of independent tests. The numerical simulations based on the model were in very good agreement with the experimental results of in-plane and ballistic mechanical response of the fabrics in terms of the macroscopic mechanical response and of the micromechanisms of deformation. In addition, it provided additional information about the influence of the microstructural features (fiber orientation, anisotropic fiber connectivity, affinity) on the mechanical performance of mechanically-entangled nonwoven fabrics.

A non-linear analysis of lying a floating pipeline on the seabed

In this article, a model for the determination of displacements, deformations and tensions of a submarine pipeline during the construction is presented. The process is carried out from an initial floating situation to the final laying position on the seabed. The existence of currents and small waves are also considered. Firstly, this technique, usually applied to polyethylene pipelines, is described in this paper as well as some real world examples, as well as the variables that can be modified to control the behavior of the structure. A detailed description of the actions in this process is considered, specially the ones related to marine environment, as Archimedes force, current and sea waves. The behavior of the pipeline is modeled with a non linear elasto dynamic model where geometric non linearities are taken into account. A 3-D beam model, without cross section deformation effects, is developed. Special care is taken in the numerical analysis, developed within an updated lagrangian formulation framework, with the sea bed contact, the follower forces due to the external water pressures and the dynamic actions. Finally, some subroutines are implemented into ANSYS to simulate the two dimensional case, where the whole construction process is achieved. With this software, a sensibility analysis of the bending moments, axial forces and stresses obtained with different values of the control variables in order to optimize the construction steps. These control variables are, the axial load in the pipe, the inundated inner length and the distance of the control barge from the coast.

A locus on chromosome 7 determines myocardial cell necrosis and calcification (dystrophic cardiac calcinosis) in mice.

Dystrophic cardiac calcinosis, an age-related cardiomyopathy that occurs among certain inbred strains of mice, involves myocardial injury, necrosis, and calcification. Using a complete linkage map approach and quantitative trait locus analysis, we sought to identify genetic loci determining dystrophic cardiac calcinosis in an F2 intercross of resistant C57BL/6J and susceptible C3H/HeJ inbred strains. We identified a single major locus, designated Dyscalc, located on proximal chromosome 7 in a region syntenic with human chromosomes 19q13 and 11p15. The statistical significance of Dyscalc (logarithm of odds score 14.6) was tested by analysis of permuted trait data. Analysis of BxH recombinant inbred strains confirmed the mapping position. The inheritance pattern indicated that this locus influences susceptibility of cells both to enter necrosis and to subsequently undergo calcification.