“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.

A Statistical Image-Based Shape Model for Visual Hull Reconstruction and 3D Structure Inference

We present a statistical image-based shape + structure model for Bayesian visual hull reconstruction and 3D structure inference. The 3D shape of a class of objects is represented by sets of contours from silhouette views simultaneously observed from multiple calibrated cameras. Bayesian reconstructions of new shapes are then estimated using a prior density constructed with a mixture model and probabilistic principal components analysis. We show how the use of a class-specific prior in a visual hull reconstruction can reduce the effect of segmentation errors from the silhouette extraction process. The proposed method is applied to a data set of pedestrian images, and improvements in the approximate 3D models under various noise conditions are shown. We further augment the shape model to incorporate structural features of interest; unknown structural parameters for a novel set of contours are then inferred via the Bayesian reconstruction process. Model matching and parameter inference are done entirely in the image domain and require no explicit 3D construction. Our shape model enables accurate estimation of structure despite segmentation errors or missing views in the input silhouettes, and works even with only a single input view. Using a data set of thousands of pedestrian images generated from a synthetic model, we can accurately infer the 3D locations of 19 joints on the body based on observed silhouette contours from real images.

On Degeneracy of Linear Reconstruction from Three Views: Linear Line Complex and Applications

This paper investigates the linear degeneracies of projective structure estimation from point and line features across three views. We show that the rank of the linear system of equations for recovering the trilinear tensor of three views reduces to 23 (instead of 26) in the case when the scene is a Linear Line Complex (set of lines in space intersecting at a common line) and is 21 when the scene is planar. The LLC situation is only linearly degenerate, and we show that one can obtain a unique solution when the admissibility constraints of the tensor are accounted for. The line configuration described by an LLC, rather than being some obscure case, is in fact quite typical. It includes, as a particular example, the case of a camera moving down a hallway in an office environment or down an urban street. Furthermore, an LLC situation may occur as an artifact such as in direct estimation from spatio-temporal derivatives of image brightness. Therefore, an investigation into degeneracies and their remedy is important also in practice.

Sparse Correlation Kernel Analysis and Reconstruction

This paper presents a new paradigm for signal reconstruction and superresolution, Correlation Kernel Analysis (CKA), that is based on the selection of a sparse set of bases from a large dictionary of class- specific basis functions. The basis functions that we use are the correlation functions of the class of signals we are analyzing. To choose the appropriate features from this large dictionary, we use Support Vector Machine (SVM) regression and compare this to traditional Principal Component Analysis (PCA) for the tasks of signal reconstruction, superresolution, and compression. The testbed we use in this paper is a set of images of pedestrians. This paper also presents results of experiments in which we use a dictionary of multiscale basis functions and then use Basis Pursuit De-Noising to obtain a sparse, multiscale approximation of a signal. The results are analyzed and we conclude that 1) when used with a sparse representation technique, the correlation function is an effective kernel for image reconstruction and superresolution, 2) for image compression, PCA and SVM have different tradeoffs, depending on the particular metric that is used to evaluate the results, 3) in sparse representation techniques, L_1 is not a good proxy for the true measure of sparsity, L_0, and 4) the L_epsilon norm may be a better error metric for image reconstruction and compression than the L_2 norm, though the exact psychophysical metric should take into account high order structure in images.

Desenvolupament d’un sistema de visió estereoscòpica per a la reconstrucció tridimensional d’objectes

El projecte consisteix en analitzar, dissenyar i desenvolupar un sistema estèreo binocular (format per dues càmeres) sobre un suport que ofereixi la mobilitat i portabilitat necessària per utilitzar-lo de forma independent, és a dir, sense necessitat de connexió a un ordinador, ja que normalment, els sistemes de visió per computador solen incorporar un ordinador amb un frame grabber (placa de captura d’imatges). Per a dur a terme el sistema estèreo més adient, s’analitzaran els requeriments necessaris, s’estudiaran diferents alternatives, i finalment, es desenvoluparà i es demostrarà el funcionament del sistema en qüestió

Laser stripe peak detector for 3D scanners: a FIR filter approach

The accuracy of a 3D reconstruction using laser scanners is significantly determined by the detection of the laser stripe. Since the energy pattern of such a stripe corresponds to a Gaussian profile, it makes sense to detect the point of maximum light intensity (or peak) by computing the zero-crossing point of the first derivative of such Gaussian profile. However, because noise is present in every physical process, such as electronic image formation, it is not sensitive to perform the derivative of the image of the stripe in almost any situation, unless a previous filtering stage is done. Considering that stripe scanning is an inherently row-parallel process, every row of a given image must be processed independently in order to compute its corresponding peak position in the row. This paper reports on the use of digital filtering techniques in order to cope with the scanning of different surfaces with different optical properties and different noise levels, leading to the proposal of a more accurate numerical peak detector, even at very low signal-to-noise ratios

Caracterización de dimensiones anatómicas de la válvula mitral en diferentes patologías cardiacas mediante ecocardiografía transesofágica tridimensional

Describir mediciones 3D y hallazgos estructurales de válvula mitral, en pacientes sanos, y con insuficiencia mitral grado 3 o 4, con enfermedad coronaria, patologías degenerativas o cardiopatía dilatada no isquémica, mediante uso de ecocardiografia transesofágica 3D en tiempo real.

Monocular-based 3-D seafloor reconstruction and ortho-mosaicing by piecewise planar representation

Photo-mosaicing techniques have become popular for seafloor mapping in various marine science applications. However, the common methods cannot accurately map regions with high relief and topographical variations. Ortho-mosaicing borrowed from photogrammetry is an alternative technique that enables taking into account the 3-D shape of the terrain. A serious bottleneck is the volume of elevation information that needs to be estimated from the video data, fused, and processed for the generation of a composite ortho-photo that covers a relatively large seafloor area. We present a framework that combines the advantages of dense depth-map and 3-D feature estimation techniques based on visual motion cues. The main goal is to identify and reconstruct certain key terrain feature points that adequately represent the surface with minimal complexity in the form of piecewise planar patches. The proposed implementation utilizes local depth maps for feature selection, while tracking over several views enables 3-D reconstruction by bundle adjustment. Experimental results with synthetic and real data validate the effectiveness of the proposed approach

A new optimised De Bruijn coding strategy for structured light patterns

Coded structured light is an optical technique based on active stereovision that obtains the shape of objects. One shot techniques are based on projecting a unique light pattern with an LCD projector so that grabbing an image with a camera, a large number of correspondences can be obtained. Then, a 3D reconstruction of the illuminated object can be recovered by means of triangulation. The most used strategy to encode one-shot patterns is based on De Bruijn sequences. In This work a new way to design patterns using this type of sequences is presented. The new coding strategy minimises the number of required colours and maximises both the resolution and the accuracy

Overview of coded light projection techniques for automatic 3D profiling

Obtaining automatic 3D profile of objects is one of the most important issues in computer vision. With this information, a large number of applications become feasible: from visual inspection of industrial parts to 3D reconstruction of the environment for mobile robots. In order to achieve 3D data, range finders can be used. Coded structured light approach is one of the most widely used techniques to retrieve 3D information of an unknown surface. An overview of the existing techniques as well as a new classification of patterns for structured light sensors is presented. This kind of systems belong to the group of active triangulation method, which are based on projecting a light pattern and imaging the illuminated scene from one or more points of view. Since the patterns are coded, correspondences between points of the image(s) and points of the projected pattern can be easily found. Once correspondences are found, a classical triangulation strategy between camera(s) and projector device leads to the reconstruction of the surface. Advantages and constraints of the different patterns are discussed

Modelo tridimensional del tendón del músculo supraespinoso

Introducción: Teniendo en cuenta el envejecimiento de la población y la alta prevalencia de las lesiones del manguito rotador no es de extrañar que esta patología se convierta en un problema de salud pública. Se sabe que el aumento en el tamaño de una lesión se asocia con la aparición de síntomas, pero no existen herramientas que permitan predecir la evolución del tamaño de una lesión. Con esto en mente se desarrollo una línea de investigación para estudiar el mecanismo de falla que inicia con la realización de un modelo tridimensional de un tendón del musculo supraespinoso sano. Materiales y métodos: Se caracterizo el tendón del músculo supraespinoso aplicando cargas uniaxiales a 7 complejos humero-tendón-escápula cadavéricos. Con los datos obtenidos se alimento un modelo tridimensional lineal isotrópico analizando la concentración de esfuerzos de von Misses Resultados: Del ensayo uniaxial se obtuvieron curvas esfuerzo-deformación homogéneas para el 20% de la deformación inicial, obteniendo un modulo de Young (14.4±2.3MPa) y un coeficiente de Poisson (0.14) con una concentración de esfuerzos de en la zona central de la cara articular del tendón, cercana a su inserción. Encontramos una disminución del 5% en los esfuerzos al retirar el acromion del modelo. Conclusiones: Se caracterizó de manera exitosa y se obtuvo un modelo tridimensional del tendón. La distribución de esfuerzos es compatible con la reportada en la literatura. El acromion no tiene mayor importancia en la magnitud de los esfuerzos en nuestro modelo. Este es el punto de partida para estudiar el mecanismo de falla.

Anatomia de la auriculilla izquierda: análisis comparativo por ecocardiografia transesofagica bidimensional y tridimensional

Introducción. La auriculilla izquierda es una estructura cardiaca que facilita la generación de trombos en su interior, favoreciendo la aparición de evento embolicos, por lo que su análisis a partir de imágenes bidimensionales y mas recientemente tridimensionales, adquieren cada vez mayor importancia Objetivo. Comparar los hallazgos anatómicos de la auriculilla izquierda obtenidos a través de la ecocardiografía tridimensional con respecto a los obtenidos por ecocardiografía bidimensional en un grupo de pacientes con ritmo sinusal y con fibrilación auricular. Métodos. Se trata de un estudio observacional analítico, transversal, en el que se compararan los resultados en las mediciones anatómicas obtenidas por ecocardiograma bidimensional en pacientes con rimo sinusal y fibrilación auricular, con los resultados de dichas mediciones obtenidas a través del ecocardiograma tridimensional en el mismo grupo de pacientes. Resultados. Se evaluaron 48 pacientes, 32 pacientes (66%) se encontraron en ritmo sinusal, la edad promedio fue de 58,2 años; 41,7% fueron mujeres y la mayoría, 32 pacientes (66,7%), tenían una o varias comorbilidades de importancia de riesgo cardiovascular, con evidencia de compromiso de la función sistólica en 20 paciente, encontrando una mayor homogeneidad en las variables área y profundidad de la auriculilla izquierda. Discusión. Los resultados nos permiten apoyar el concepto que las imágenes obtenidas por ecocardiografía tridimensional nos ofrecen una mejor evaluación de la auriculilla izquierda, observando una mayor homogeneidad con la ecocardiografía bidimensional en las variables área y profundidad, existiendo a su vez heterogeneidad en la variable longitud. Conclusión. El presente estudio demostró que la ecocardiografía tridimensional, es un aporte importante desde el punto de vista diagnostico tanto cualitativo como cuantitativo en el análisis de la auriculilla izquierda, permitiendo una fácil adquisición de imágenes en tiempo real y comparativas con las imágenes bidimensionales.

Evaluación de la vía aérea superior en pacientes con sahos mediante cefalometría 3D y multiplanar

Objetivo: determinar parámetros biométricos para evaluación y diagnóstico de pacientes con SAHOS por medio de Cefalometría Tridimensional y reconstrucción Multiplanar escanográfica. Materiales y Métodos: se realizó estudio observacional tipo cross-sectional, con 25 pacientes diagnosticados con SAHOS, a los cuales se les hizo TAC simple de cara con reconstrucción multiplanar y tridimensional, evaluando volumen de vía aérea, longitud, promedio del área en corte transversal, área retropalatal, área reglosal, espacio retrogloso lateral y anteroposterior. Resultados: se incluyeron 25 pacientes y realizaron medidas de volumen, longitud, promedio del área en corte transversal, área retropalatal, área retroglosal y espacios regloso lateral y anteroposterior, realizando análisis estadístico mediante el programa SPSS 17.0 reportando medidas de tendencia central como promedio, media, moda, rango, desviación estándar, y concordancia inter e intra observador. Conclusión: la Cefalometría tridimensional con reconstrucción multiplanar ha mostrado ser un excelente método de evaluación de vía aérea en pacientes con SAHOS, obteniendo propias clasificaciones dentro del estudio de estos pacientes. Sin embargo, ante la escasa literatura y difícil obtención de parámetros de referencia es necesario promover el estudio y la investigación de este método diagnostico en pacientes con SAHOS.

Proyecto cube : una introducción a la geometría tridimensional.

Se presenta el proyecto CUBE, propuesta de trabajo donde se desarrolla una serie de actividades de introducción a la geometría analítica. El proyecto se divide en 2 partes; una relativa al guión de la película y otra derivada dirigida al desarrollo del currículo de cuarto de ESO en Geometría.

Secondary education in Afghanistan : a portray of post-conflict education reconstruction. 'La educación secundaria en Afganistán : un retrato de la reconstrucción de la educación después del conflicto'.

Resumen tomado del autor. Resumen del autor también en inglés. Monográfico titulado: La REEC cumple 10 años. La Educación Comparada entre los siglos (1995-2005)