Automatic Classification of Human Epithelial Type 2 Cell Indirect Immunofluorescence Images using Cell Pyramid Matching

This paper describes a novel system for automatic classification of images obtained from Anti-Nuclear Antibody (ANA) pathology tests on Human Epithelial type 2 (HEp-2) cells using the Indirect Immunofluorescence (IIF) protocol. The IIF protocol on HEp-2 cells has been the hallmark method to identify the presence of ANAs, due to its high sensitivity and the large range of antigens that can be detected. However, it suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg. speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. We propose a novel automatic cell image classification method termed Cell Pyramid Matching (CPM), which is comprised of regional histograms of visual words coupled with the Multiple Kernel Learning framework. We present a study of several variations of generating histograms and show the efficacy of the system on two publicly available datasets: the ICPR HEp-2 cell classification contest dataset and the SNPHEp-2 dataset.Comment: arXiv admin note: substantial text overlap with arXiv:1304.126

The effectiveness of face detection algorithms in unconstrained crowd scenes

The 2013 Boston Marathon bombing represents a case where automatic facial biometrics tools could have proven invaluable to law enforcement officials, yet the lack of ro-bustness of current tools in unstructured environments lim-ited their utility. In this work, we focus on complications that confound face detection algorithms. We first present a simple multi-pose generalization of the Viola-Jones al-gorithm. Our results on the Face Detection Data set and Benchmark (FDDB) show that it makes a significant im-provement over the state of the art for published algorithms. Conversely, our experiments demonstrate that the improve-ments attained by accommodating multiple poses can be negligible compared to the gains yielded by normalizing scores and using the most appropriate classifier for uncon-trolled data. We conclude with a qualitative evaluation of the proposed algorithm on publicly available images of the Boston Marathon crowds. Although the results of our evalu-ations are encouraging, they confirm that there is still room for improvement in terms of robustness to out-of-plane ro-tation, blur and occlusion. 1

Un environnement de spécification et de découverte pour la réutilisation des composants logiciels dans le développement des logiciels distribués

Notre travail vise à élaborer une solution efficace pour la découverte et la réutilisation des composants logiciels dans les environnements de développement existants et couramment utilisés. Nous proposons une ontologie pour décrire et découvrir des composants logiciels élémentaires. La description couvre à la fois les propriétés fonctionnelles et les propriétés non fonctionnelles des composants logiciels exprimées comme des paramètres de QoS. Notre processus de recherche est basé sur la fonction qui calcule la distance sémantique entre la signature d'un composant et la signature d'une requête donnée, réalisant ainsi une comparaison judicieuse. Nous employons également la notion de " subsumption " pour comparer l'entrée-sortie de la requête et des composants. Après sélection des composants adéquats, les propriétés non fonctionnelles sont employées comme un facteur distinctif pour raffiner le résultat de publication des composants résultats. Nous proposons une approche de découverte des composants composite si aucun composant élémentaire n'est trouvé, cette approche basée sur l'ontologie commune. Pour intégrer le composant résultat dans le projet en cours de développement, nous avons développé l'ontologie d'intégration et les deux services " input/output convertor " et " output Matching ".Our work aims to develop an effective solution for the discovery and the reuse of software components in existing and commonly used development environments. We propose an ontology for describing and discovering atomic software components. The description covers both the functional and non functional properties which are expressed as QoS parameters. Our search process is based on the function that calculates the semantic distance between the component interface signature and the signature of a given query, thus achieving an appropriate comparison. We also use the notion of "subsumption" to compare the input/output of the query and the components input/output. After selecting the appropriate components, the non-functional properties are used to refine the search result. We propose an approach for discovering composite components if any atomic component is found, this approach based on the shared ontology. To integrate the component results in the project under development, we developed the ontology integration and two services " input/output convertor " and " output Matching "

Mathematical modeling of evolutionary changes of oligonucleotide frequency patterns of bacterial genomes for genome-scale phylogenetic inferences

Modern phylogenetic studies from the advancement of next generation sequencing can benefit from an analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome scale analysis were believed to be more accurate than gene-based ones. However, the computational complexity of current phylogenomic procedures and lack of reliable annotation and alignment free evolutionary models keep microbiologists from wider use of these opportunities. For example, the super-matrix approach of phylogenomics requires identification of clusters of orthologous genes in compared genomes followed by alignment of numerous sequences to proceed with reconciliation of multiple trees inferred by traditional phylogenetic tools. In fact, the approach potentially multiplies the problems of gene annotation and sequence alignment, not mentioning the computational difficulties and laboriousness of the methods. For this research, we identified that the alignment and annotation-free method based on comparison of oligonucleotide usage patterns (OUP) calculated for genome-scale DNA sequences allowed fast inferring of phylogenetic trees. These were also congruent with the corresponding whole genome supermatrix trees in terms of tree topology and branch lengths. Validation and benchmarking tests for OUP phylogenomics were done based on comparisons to current literature and artificially created sequences with known phylogeny. It was demonstrated that the OUP diversification between taxa was driven by global adjustments of codon usage to fit fluctuating tRNA concentrations that were well aligned to the species evolution. A web-based program to perform OUP-based phylogenomics was released on http://swphylo.bi.up.ac.za/. Applicability of the tool was proven for different taxa from species to family levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, e.g. gyrA.Thesis (PhD)--University of Pretoria, 2018.BiochemistryPhDUnrestricte

Chromosome Architecture and Evolution in Bacteria

Inferences of organismal molecular evolution have been dominated by comparisons of their constituent genes. Yet the evolutionary histories of genes within Bacterial genomes are not necessarily congruent. Here, Horizontal Gene Transfer (HGT) of sequences across species boundaries can confound these analyses. There does appear to be phylogenetic cohesion, where members of higher taxonomic groups share genotypic similarity despite gene transfer. Herein I examine the rules for governing HGT to determine the impact this process has played in the evolution of Bacteria and Archaea. Bacterial chromosomes are more than simple lists of genes. Genomes must maintain information beyond component genes to direct efficient replication and segregation of their chromosomes. I propose that this structure constrains the process of HGT so that transfer among certain pairs of donors and recipients is favored. I present methods to detect this structure and new theories of bacterial cell biology and evolution based on what this structure reveals. I present evidence that bacterial chromosomes are structured by repetitive sequences termed Architecture IMparting Sequences (AIMS). AIMS are found primarily on leading strands and increase in abundance towards the replication terminus. Bacteria with robustly-identified replication origins and termini all have AIMS, and related AIMS are conserved amongst families of bacteria. We propose that AIMS are under selection to provide DNA binding proteins with polarity information, facilitating identification of the location of the replication terminus. Although AIMS evolved to direct the biology of cell division and replication, the conservation of AIMS among related taxa leads to a secondary effect. Because AIMS are counterselected when in nonpermissive orientations, AIMS constrain both intragenomic and intergenomic rearrangements. Thus HGT frequency will depend on AIMS compatibility between different species. We predict that HGT is most common between bacterial genomes which are more closely related and will impede transfer between species which have dissimilar genome architecture. The additional level of selection reflected by AIMS has resulted in cohesive bacterial groups that reflect common gene pools as a result of biased rates of gene transfer

Perception systems for robust autonomous navigation in natural environments

2022 Spring.Includes bibliographical references.As assistive robotics continues to develop thanks to the rapid advances of artificial intelligence, smart sensors, Internet of Things, and robotics, the industry began introducing robots to perform various functions that make humans' lives more comfortable and enjoyable. While the principal purpose of deploying robots has been productivity enhancement, their usability has widely expanded. Examples include assisting people with disabilities (e.g., Toyota's Human Support Robot), providing driver-less transportation (e.g., Waymo's driver-less cars), and helping with tedious house chores (e.g., iRobot). The challenge in these applications is that the robots have to function appropriately under continuously changing environments, harsh real-world conditions, deal with significant amounts of noise and uncertainty, and operate autonomously without the intervention or supervision of an expert. To meet these challenges, a robust perception system is vital. This dissertation casts light on the perception component of autonomous mobile robots and highlights their major capabilities, and analyzes the factors that affect their performance. In short, the developed approaches in this dissertation cover the following four topics: (1) learning the detection and identification of objects in the environment in which the robot is operating, (2) estimating the 6D pose of objects of interest to the robot, (3) studying the importance of the tracking information in the motion prediction module, and (4) analyzing the performance of three motion prediction methods, comparing their performances, and highlighting their strengths and weaknesses. All techniques developed in this dissertation have been implemented and evaluated on popular public benchmarks. Extensive experiments have been conducted to analyze and validate the properties of the developed methods and demonstrate this dissertation's conclusions on the robustness, performance, and utility of the proposed approaches for intelligent mobile robots

Development of an automated identification system for nanocrystal encoded microspheres in flow cytometry

Aim: This work sets out to use haplotype-based tagSNP selection and a systematic in silico analysis for design of multiplex-compatible PCR primer and SAT probe sets to capture maximum variation with minimum tests across candidate genes IGF1, IGFBP1 and IGFBP3. Additionally, the work aims to develop a number of robust, high-efficiency, high-specificity multiplex PCR constructs for amplification of these targets and to demonstrate the applicability of these target types to suspension array genotyping for non-insulin-dependant diabetes mellitus association facilitation. Methods: Haplotypes for predominantly European Caucasian populations were constructed and tagSNP selection performed using Haploview to capture maximum variation across candidate genes IGF1, IGFBP1 and IGFBP3. Extensive in silico analysis was performed for design, evaluation and selection of robust high-specificity primer and probe pairs, suitable for downstream multiplex PCR and SAT analysis. Singleplex endpoint and real-time PCR was performed for primer pair profile determination which informed multiplex PCR set construction and optimisation. The applicability of this complex target type to suspension array-based genotyping was investigated using a model probe pair using both quantum dot-encoded and fluorophore-encoded microspheres. Results: Haploview was used for haplotype construction and linkage disequilibriumbased tagSNP selection across candidate genes, reducing the number of SNP targets from 292 to 32 with minimal information loss. Extensive evaluation of potential tagSNPs was performed and 29 SNPs, representing 29 bins across target genes were designed for multiplex analysis. Singleplex end-point and real-time PCR was performed for primer pair profile determination which allowed four multiplex PCR sets to be constructed and optimised for simultaneous amplification of 14, six, five and two targets. The applicability of this complex target type (14-plex) to suspension array-based genotyping was demonstrated using a model probe pair. Conclusion: In silico analysis techniques have been applied for successful development of four robust multiplex PCR sets (14-plex, 6-plex, 5-plex and 2-plex) which display high-efficiency and target-specific amplification of tagSNPs, capturing maximum assaycompatible variation across candidate genes IGF1, IGFBP1 and IGFBP3 for European Caucasian populations. The applicability of these multiplex PCR constructs to suspension array-based genotyping has been demonstrated, thus paving the way for development of large multiplex suspension array-based genotyping assays using probes designed during the course of this work. This work offers the potential for comprehensive association analyses to become more accessible to the wider-scientific community by facilitating reduced genotyping burdens which allow increased accessibility for powerful association.EThOS - Electronic Theses Online ServiceGBUnited Kingdo