264 research outputs found

    Optimization techniques in respiratory control system models

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    One of the most complex physiological systems whose modeling is still an open study is the respiratory control system where different models have been proposed based on the criterion of minimizing the work of breathing (WOB). The aim of this study is twofold: to compare two known models of the respiratory control system which set the breathing pattern based on quantifying the respiratory work; and to assess the influence of using direct-search or evolutionary optimization algorithms on adjustment of model parameters. This study was carried out using experimental data from a group of healthy volunteers under CO2 incremental inhalation, which were used to adjust the model parameters and to evaluate how much the equations of WOB follow a real breathing pattern. This breathing pattern was characterized by the following variables: tidal volume, inspiratory and expiratory time duration and total minute ventilation. Different optimization algorithms were considered to determine the most appropriate model from physiological viewpoint. Algorithms were used for a double optimization: firstly, to minimize the WOB and secondly to adjust model parameters. The performance of optimization algorithms was also evaluated in terms of convergence rate, solution accuracy and precision. Results showed strong differences in the performance of optimization algorithms according to constraints and topological features of the function to be optimized. In breathing pattern optimization, the sequential quadratic programming technique (SQP) showed the best performance and convergence speed when respiratory work was low. In addition, SQP allowed to implement multiple non-linear constraints through mathematical expressions in the easiest way. Regarding parameter adjustment of the model to experimental data, the evolutionary strategy with covariance matrix and adaptation (CMA-ES) provided the best quality solutions with fast convergence and the best accuracy and precision in both models. CMAES reached the best adjustment because of its good performance on noise and multi-peaked fitness functions. Although one of the studied models has been much more commonly used to simulate respiratory response to CO2 inhalation, results showed that an alternative model has a more appropriate cost function to minimize WOB from a physiological viewpoint according to experimental data.Postprint (author's final draft

    Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

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    This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications

    Transformation Model With Constraints for High Accuracy of 2D-3D Building Registration in Aerial Imagery

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    This paper proposes a novel rigorous transformation model for 2D-3D registration to address the difficult problem of obtaining a sufficient number of well-distributed ground control points (GCPs) in urban areas with tall buildings. The proposed model applies two types of geometric constraints, co-planarity and perpendicularity, to the conventional photogrammetric collinearity model. Both types of geometric information are directly obtained from geometric building structures, with which the geometric constraints are automatically created and combined into the conventional transformation model. A test field located in downtown Denver, Colorado, is used to evaluate the accuracy and reliability of the proposed method. The comparison analysis of the accuracy achieved by the proposed method and the conventional method is conducted. Experimental results demonstrated that: (1) the theoretical accuracy of the solved registration parameters can reach 0.47 pixels, whereas the other methods reach only 1.23 and 1.09 pixels; (2) the RMS values of 2D-3D registration achieved by the proposed model are only two pixels along the x and y directions, much smaller than the RMS values of the conventional model, which are approximately 10 pixels along the x and y directions. These results demonstrate that the proposed method is able to significantly improve the accuracy of 2D-3D registration with much fewer GCPs in urban areas with tall buildings

    A Feature Point Based Image Registration Using Genetic Algorithms

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    Image registration has been widely applied in many fields such as remote sensing, medical image analysis, cartography, computer vision and pattern recognition. The key of image registration is to find the proper transformation of one image to another image so that each point of one image is spatially aligned with its corresponding point of the other. In this paper, we present a rigid feature point based image registration method integrating two techniques. The first is one in which we propose to extract the feature points by using efficiency of the multi-resolution representation data of the nonsubsampled contourlet transform. The second technique exploits the robustness of Genetic algorithms as an optimization method to find the best transformation parameters. The results show the effectiveness of this approach for registering the magnetic resonance images

    Pattern Recognition

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    A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

    Biomedical Image Registration by means of Bacterial Foraging Paradigm

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    Image registration (IR) is the process of geometric overlaying or alignment f two or more 2D/3D images of the same scene (unimodal registration), taken r not at different time slots, from different angles, and/or by different image acquisition ystems (multimodal registration). Technically, image registration implies  complex optimization of different parameters, performed at local or/and global evel. Local optimization methods often fail because functions of the involved metrics ith respect to transformation parameters are generally nonconvex and irregular, and lobal methods are required, at least at the beginning of the procedure. This paper resents a new evolutionary and bio-inspired robust approach for IR, Bacterial Foraging ptimization Algorithm (BFOA), which is adapted for PET-CT multimodal nd magnetic resonance image rigid registration. Results of optimizing the normalized utual information and normalized cross correlation similarity metrics validated he efficacy and precision of the proposed method by using a freely available medical mage database

    Medical Image Registration by means of a Bio-Inspired Optimization Strategy

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    Medical imaging mainly treats and processes missing, ambiguous, complementary, redundant and distorted data. Biomedical image registration is the process of geometric overlaying or alignment of two or more 2D/3D images of the same scene, taken at different time slots, from different angles, and/or by different acquisition systems. In medical practice, it is becoming increasingly important in diagnosis, treatment planning, functional studies, computer-guided therapies, and in biomedical research. Technically, image registration implies a complex optimization of different parameters, performed at local or/and global levels. Local optimization methods frequently fail because functions of the involved metrics with respect to transformation parameters are generally nonconvex and irregular. Therefore, global methods are often required, at least at the beginning of the procedure. In this paper, a new evolutionary and bio-inspired approach -- bacterial foraging optimization -- is adapted for single-slice to 3-D PET and CT multimodal image registration. Preliminary results of optimizing the normalized mutual information similarity metric validated the efficacy of the proposed method by using a freely available medical image database

    Ordered and deterministic cancer genome evolution after p53 loss

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    Although p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model of pancreatic ductal adenocarcinoma that reports sporadic p53 loss of heterozygosity before cancer onset, we find that malignant properties enabled by p53 inactivation are acquired through a predictable pattern of genome evolution. Single-cell sequencing and in situ genotyping of cells from the point of p53 inactivation through progression to frank cancer reveal that this deterministic behaviour involves four sequential phases-Trp53 (encoding mouse p53) loss of heterozygosity, accumulation of deletions, genome doubling, and the emergence of gains and amplifications-each associated with specific histological stages across the premalignant and malignant spectrum. Despite rampant heterogeneity, the deletion events that follow p53 inactivation target functionally relevant pathways that can shape genomic evolution and remain fixed as homogenous events in diverse malignant populations. Thus, loss of p53-the 'guardian of the genome'-is not merely a gateway to genetic chaos but, rather, can enable deterministic patterns of genome evolution that may point to new strategies for the treatment of TP53-mutant tumours

    Example Based Caricature Synthesis

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    The likeness of a caricature to the original face image is an essential and often overlooked part of caricature production. In this paper we present an example based caricature synthesis technique, consisting of shape exaggeration, relationship exaggeration, and optimization for likeness. Rather than relying on a large training set of caricature face pairs, our shape exaggeration step is based on only one or a small number of examples of facial features. The relationship exaggeration step introduces two definitions which facilitate global facial feature synthesis. The first is the T-Shape rule, which describes the relative relationship between the facial elements in an intuitive manner. The second is the so called proportions, which characterizes the facial features in a proportion form. Finally we introduce a similarity metric as the likeness metric based on the Modified Hausdorff Distance (MHD) which allows us to optimize the configuration of facial elements, maximizing likeness while satisfying a number of constraints. The effectiveness of our algorithm is demonstrated with experimental results
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