Estimating Particle Shape and Orientation Using Volume Tensors

We develop statistical procedures for estimating shape and orientation of arbitrary three-dimensional particles. We focus on the case where particles cannot be observed directly, but only via sections. Volume tensors are used for describing particle shape and orientation, and we derive stereological estimators of the tensors. These estimators are combined to provide consistent estimators of the moments of the so-called particle cover density. The covariance structure associated with the particle cover density depends on the orientation and shape of the particles. For instance, if the distribution of the typical particle is invariant under rotations, then the covariance matrix is proportional to the identity matrix. We develop a non-parametric test for such isotropy. A flexible Lévy-based particle model is proposed, which may be analysed using a generalized method of moments in which the volume tensors enter. The developed methods are used to study the cell organization in the human brain cortex.

Stereological estimation of particle shape and orientation from volume tensors

In the present paper, we describe new robust methods of estimating cell shape and orientation in 3D from sections. The descriptors of 3D cell shape and orientation are based on volume tensors which are used to construct an ellipsoid, the Miles ellipsoid, approximating the average cell shape and orientation in 3D. The estimators of volume tensors are based on observations in several optical planes through sampled cells. This type of geometric sampling design is known as the optical rotator. The statistical behaviour of the estimator of the Miles ellipsoid is studied under a flexible model for 3D cell shape and orientation. In a simulation study, the lengths of the axes of the Miles ellipsoid can be estimated with CVs of about 2% if 100 cells are sampled. Finally, we illustrate the use of the developed methods in an example, involving neurons in the medial prefrontal cortex of rat.

The association between uterus shape and development of chronic conditions in a retrospective corhort of diethylstilbestrol-exposed women in Minnesota and Texas

Diethylstilbestrol (DES) exposed women are well known to be at increased risk of gynecologic cancers and infertility. Infertility may result from DES associated abnormalities in the shape of women's uteri, yet little research has addressed the effect of uterine abnormalities on risk of infertility and reproductive tract infection. Changes in uterine shape may also influence the risk of autoimmune disease and women's subsequent mental health. A sample of consenting women exposed in utero to hormone who were recruited into the DESAD project, underwent hysterosalpingogram (HSG) from 1978 to 1984. These women also completed a comprehensive health questionnaire in 1994 which included women's self-reports of chronic conditions. HSG data were used to categorize uterine shape abnormalities as arcuate shape, hypoplastic, wide lower segment, and constricted. Women were recruited from two of the four DESAD study sites in Houston (Baylor) and Minnesota (Mayo). All women were DES-exposed. Adjusted relative risk estimates were calculated comparing the range of abnormal uterine shaped to women with normal shaped uteri for each of the four outcomes: infertility, reproductive tract infection, autoimmune disease and depressive symptoms. Only the arcuate shape (n=80) was associated with a higher risk of infertility (relative risk [RR]= 1.53, 95% CI = 1.09, 2.15) as well as reproductive tract infection (RR= 1.74, 95% CI = 1.11, 2.73). In conclusion, DES-associated arcuate shaped uteri appeared to be associated with the higher risk of a reproductive tract infection and infertility while no other abnormal uterine shapes were associated with these two outcomes.^

Grain shape and mineralogy of loess on New Zealands South Island

Infilled fissures are described from the interface between two loess deposits on Banks Peninsula, South Island, New Zealand. Both loesses differ from the other loesses by having a solifluction deposit at their base consisting of angular basalt fragments of the same angularity as fresh frost shattered basalt mixed with the loess. Typically, the fissures are narrow and up to 160 cm deep while the infilling of the overlying loess shows no obvious structure. They occur mainly at higher elevations on south (poleward) facing slopes, and the host loess forms a fragipan of high density. They are most readily explained as being seasonal frost fissures or more probably ice-wedge casts, which would have required either permafrost or deep seasonal frost for their formation. If permafrost had existed, this would imply a cooling of the mean annual temperatures by at least 16 to 18°C.

Level Set Segmentation with Shape and Appearance Models Using Affine Moment Descriptors

We propose a level set based variational approach that incorporates shape priors into edge-based and region-based models. The evolution of the active contour depends on local and global information. It has been implemented using an efficient narrow band technique. For each boundary pixel we calculate its dynamic according to its gray level, the neighborhood and geometric properties established by training shapes. We also propose a criterion for shape aligning based on affine transformation using an image normalization procedure. Finally, we illustrate the benefits of the our approach on the liver segmentation from CT images.

A static heap analysis for shape and connectivity: Unified memory analysis: The base framework

Modeling the evolution of the state of program memory during program execution is critical to many parallehzation techniques. Current memory analysis techniques either provide very accurate information but run prohibitively slowly or produce very conservative results. An approach based on abstract interpretation is presented for analyzing programs at compile time, which can accurately determine many important program properties such as aliasing, logical data structures and shape. These properties are known to be critical for transforming a single threaded program into a versión that can be run on múltiple execution units in parallel. The analysis is shown to be of polynomial complexity in the size of the memory heap. Experimental results for benchmarks in the Jolden suite are given. These results show that in practice the analysis method is efflcient and is capable of accurately determining shape information in programs that créate and manipúlate complex data structures.

Detection and Isolation of Simultaneous Additive and Parametric Faults in Nonlinear Stochastic Dynamical Systems

This paper presents a new fault detection and isolation scheme for dealing with simultaneous additive and parametric faults. The new design integrates a system for additive fault detection based on Castillo and Zufiria, 2009 and a new parametric fault detection and isolation scheme inspired in Munz and Zufiria, 2008 . It is shown that the so far existing schemes do not behave correctly when both additive and parametric faults occur simultaneously; to solve the problem a new integrated scheme is proposed. Computer simulation results are presented to confirm the theoretical studies.

Instability and topology bifurcations on a hemisphere-cylinder at high angle of attack

La configuración de un cilindro acoplado a una semi-esfera, conocida como ’hemispherecylinder’, se considera como un modelo simplificado para numerosas aplicaciones industriales tales como fuselaje de aviones o submarinos. Por tanto, el estudio y entendimiento de los fenómenos fluidos que ocurren alrededor de dicha geometría presenta gran interés. En esta tesis se muestra la investigación del origen y evolución de los, ya conocidos, patrones de flujo (burbuja de separación, vórtices ’horn’ y vórtices ’leeward’) que se dan en esta geometría bajo condiciones de flujo separado. Para ello se han llevado a cabo simulaciones numéricas (DNS) y ensayos experimentales usando la técnica de Particle Image Velocimetry (PIV), para una variedad de números de Reynolds (Re) y ángulos de ataque (AoA). Se ha aplicado sobre los resultados numéricos la teoría de puntos críticos obteniendo, por primera vez para esta geometría, un diagrama de bifurcaciones que clasifica los diferentes regímenes topológicos en función del número de Reynolds y del ángulo de ataque. Se ha llevado a cabo una caracterización completa sobre el origen y la evolución de los patrones estructurales característicos del cuerpo estudiado. Puntos críticos de superficie y líneas de corriente tridimensionales han ayudado a describir el origen y la evolución de las principales estructuras presentes en el flujo hasta alcanzar un estado de estabilidad desde el punto de vista topológico. Este estado se asocia con el patrón de los vórtices ’horn’, definido por una topología característica que se encuentra en un rango de números de Reynolds muy amplio y en regímenes compresibles e incompresibles. Por otro lado, con el objeto de determinar las estructuras presentes en el flujo y sus frecuencias asociadas, se han usado distintas técnicas de análisis: Proper Orthogonal Decomposition (POD), Dynamic Mode Decomposition (DMD) y análisis de Fourier. Dichas técnicas se han aplicado sobre los datos experimentales y numéricos, demostrándose la buena concordancia entre ambos resultados. Finalmente, se ha encontrado en ambos casos, una frecuencia dominante asociada con una inestabilidad de los vórtices ’leeward’. ABSTRACT The hemisphere-cylinder may be considered as a simplified model for several geometries found in industrial applications such as aircrafts’ fuselages or submarines. Understanding the complex flow phenomena that surrounds this particular geometry is therefore of major industrial interest. This thesis presents an investigation of the origin and evolution of the complex flow pattern; i.e. separation bubbles, horn vortices and leeward vortices, around the hemisphere-cylinder under separated flow conditions. To this aim, threedimensional Direct Numerical Simulations (DNS) and experimental tests, using Particle Image Velocimetry (PIV) techniques, have been performed for a variety of Reynolds numbers (Re) and angles of attack (AoA). Critical point theory has been applied to the numerical simulations to provide, for the first time for this geometry, a bifurcation diagram that classifies the different flow topology regimes as a function of the Reynolds number and the angle of attack. A complete characterization about the origin and evolution of the complex structural patterns of this geometry has been put in evidence. Surface critical points and surface and volume streamlines were able to describe the main flow structures and their strong dependence with the flow conditions up to reach the structurally stable state. This state was associated with the pattern of the horn vortices, found on ranges from low to high Reynolds numbers and from incompressible to compressible regimes. In addition, different structural analysis techniques have been employed: Proper Orthogonal Decomposition (POD), Dynamic Mode Decomposition (DMD) and Fourier analysis. These techniques have been applied to the experimental and numerical data to extract flow structure information (i.e. modes and frequencies). Experimental and numerical modes are shown to be in good agreement. A dominant frequency associated with an instability of the leeward vortices has been identified in both, experimental and numerical results.

Numerical study of ultrasound induced non-linear shape and size bubble oscillations in viscoelastic media

The theoretical study of forced bubble oscillations is motivated by the importance of cavitation bubbles and oscillating encapsulated microbubbles (i.e. contrast agents) in medical sciences. In more details,theoretical studies on bubble dynamics addressing the sound-bubble interaction phenomenon provide the basis for understanding the dynamics of contrast agent microbubbles used in medical diagnosis and of non-linearly oscillating cavitation bubbles in the case of high-intensity ultrasound therapy. Moreover, the inclusion of viscoelasticity is of vital importance for an accurate theoretical analysis since most biological tissues and fluids exhibit non-Newtonian behavior.

Control of Cyclin D1, p27Kip1, and Cell Cycle Progression in Human Capillary Endothelial Cells by Cell Shape and Cytoskeletal Tension

The extracellular matrix (ECM) plays an essential role in the regulation of cell proliferation during angiogenesis. Cell adhesion to ECM is mediated by binding of cell surface integrin receptors, which both activate intracellular signaling cascades and mediate tension-dependent changes in cell shape and cytoskeletal structure. Although the growth control field has focused on early integrin and growth factor signaling events, recent studies suggest that cell shape may play an equally critical role in control of cell cycle progression. Studies were carried out to determine when cell shape exerts its regulatory effects during the cell cycle and to analyze the molecular basis for shape-dependent growth control. The shape of human capillary endothelial cells was controlled by culturing cells on microfabricated substrates containing ECM-coated adhesive islands with defined shape and size on the micrometer scale or on plastic dishes coated with defined ECM molecular coating densities. Cells that were prevented from spreading in medium containing soluble growth factors exhibited normal activation of the mitogen-activated kinase (erk1/erk2) growth signaling pathway. However, in contrast to spread cells, these cells failed to progress through G1 and enter S phase. This shape-dependent block in cell cycle progression correlated with a failure to increase cyclin D1 protein levels, down-regulate the cell cycle inhibitor p27Kip1, and phosphorylate the retinoblastoma protein in late G1. A similar block in cell cycle progression was induced before this same shape-sensitive restriction point by disrupting the actin network using cytochalasin or by inhibiting cytoskeletal tension generation using an inhibitor of actomyosin interactions. In contrast, neither modifications of cell shape, cytoskeletal structure, nor mechanical tension had any effect on S phase entry when added at later times. These findings demonstrate that although early growth factor and integrin signaling events are required for growth, they alone are not sufficient. Subsequent cell cycle progression and, hence, cell proliferation are controlled by tension-dependent changes in cell shape and cytoskeletal structure that act by subjugating the molecular machinery that regulates the G1/S transition.

The effect of cultivation on the size, shape, and persistence of disease patches in fields

Epidemics of soil-borne plant disease are characterized by patchiness because of restricted dispersal of inoculum. The density of inoculum within disease patches depends on a sequence comprising local amplification during the parasitic phase followed by dispersal of inoculum by cultivation during the intercrop period. The mechanisms that control size, shape, and persistence have received very little rigorous attention in epidemiological theory. Here we derive a model for dispersal of inoculum in soil by cultivation that takes account into the discrete stochastic nature of the system in time and space. Two parameters, probability of movement and mean dispersal distance, characterize lateral dispersal of inoculum by cultivation. The dispersal parameters are used in combination with the characteristic area and dimensions of host plants to identify criteria that control the shape and size of disease patches. We derive a critical value for the probability of movement for the formation of cross-shaped patches and show that this is independent of the amount of inoculum. We examine the interaction between local amplification of inoculum by parasitic activity and subsequent dilution by dispersal and identify criteria whereby asymptomatic patches may persist as inoculum falls below a threshold necessary for symptoms to appear in the subsequent crop. The model is motivated by the spread of rhizomania, an economically important soil-borne disease of sugar beet. However, the results have broad applicability to a very wide range of diseases that survive as discrete units of inoculum. The application of the model to patch dynamics of weed seeds and local introductions of genetically modified seeds is also discussed.