Metadata assisted image segmentation

Tese de doutoramento. Engenharia Electrotécnica e de Computadores. 2006. Faculdade de Engenharia. Universidade do Port

Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing

Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease

Effective and efficient kernel-based image representations for classification and retrieval

Image representation is a challenging task. In particular, in order to obtain better performances in different image processing applications such as video surveillance, autonomous driving, crime scene detection and automatic inspection, effective and efficient image representation is a fundamental need. The performance of these applications usually depends on how accurately images are classified into their corresponding groups or how precisely relevant images are retrieved from a database based on a query. Accuracy in image classification and precision in image retrieval depend on the effectiveness of image representation. Existing image representation methods have some limitations. For example, spatial pyramid matching, which is a popular method incorporating spatial information in image-level representation, has not been fully studied to date. In addition, the strengths of pyramid match kernel and spatial pyramid matching are not combined for better image matching. Kernel descriptors based on gradient, colour and shape overcome the limitations of histogram-based descriptors, but suffer from information loss, noise effects and high computational complexity. Furthermore, the combined performance of kernel descriptors has limitations related to computational complexity, higher dimensionality and lower effectiveness. Moreover, the potential of a global texture descriptor which is based on human visual perception has not been fully explored to date. Therefore, in this research project, kernel-based effective and efficient image representation methods are proposed to address the above limitations. An enhancement is made to spatial pyramid matching in terms of improved rotation invariance. This is done by investigating different partitioning schemes suitable to achieve rotation-invariant image representation and the proposal of a weight function for appropriate level contribution in image matching. In addition, the strengths of pyramid match kernel and spatial pyramid are combined to enhance matching accuracy between images. The existing kernel descriptors are modified and improved to achieve greater effectiveness, minimum noise effects, less dimensionality and lower computational complexity. A novel fusion approach is also proposed to combine the information related to all pixel attributes, before the descriptor extraction stage. Existing kernel descriptors are based only on gradient, colour and shape information. In this research project, a texture-based kernel descriptor is proposed by modifying an existing popular global texture descriptor. Finally, all the contributions are evaluated in an integrated system. The performances of the proposed methods are qualitatively and quantitatively evaluated on two to four different publicly available image databases. The experimental results show that the proposed methods are more effective and efficient in image representation than existing benchmark methods.Doctor of Philosoph

Texture and Colour in Image Analysis

Research in colour and texture has experienced major changes in the last few years. This book presents some recent advances in the field, specifically in the theory and applications of colour texture analysis. This volume also features benchmarks, comparative evaluations and reviews

Fast mode decision in the HEVC Video coding standard by exploiting region with dominated motion and saliency features

The emerging High Efficiency Video Coding (HEVC) standard introduces a number of innovative and powerful coding tools to acquire better compression efficiency compared to its predecessor H.264. The encoding time complexities have also increased multiple times that is not suitable for realtime video coding applications. To address this limitation, this paper employs a novel coding strategy to reduce the time complexity in HEVC encoder by efficient selection of appropriate block-partitioning modes based on human visual features (HVF). The HVF in the proposed technique comprise with human visual attention modelling-based saliency feature and phase correlation-based motion features. The features are innovatively combined through a fusion process by developing a content-based adaptive weighted cost function to determine the region with dominated motion/saliency (RDMS)- based binary pattern for the current block. The generated binary pattern is then compared with a codebook of predefined binary pattern templates aligned to the HEVC recommended block-paritioning to estimate a subset of inter-prediction modes. Without exhaustive exploration of all modes available in the HEVC standard, only the selected subset of modes are motion estimated and motion compensated for a particular coding unit. The experimental evaluation reveals that the proposed technique notably down-scales the average computational time of the latest HEVC reference encoder by 34% while providing similar rate-distortion (RD) performance for a wide range of video sequences

Exploration of an anglerfish genome

Doctoral thesis (PhD) - Nord University, 2019The anglerfishes comprise an extremely diverse order of teleosts with unique adaptations. The most notable is sexually parasitism of reproduction where the male attaches to the female. This can result in fusion of two genetically distinct organisms, which would in most vertebrate species result in an immune rejection. However, in sexually parasitic anglerfish fusion occurs with no immune rejection. The mechanisms that have allowed the evolution of such adaptations are of interest not just to evolutionary biology, but perhaps also to biomedical research related to the prevention of allogenic rejection after transplantation. Nevertheless, anglerfishes remain poorly understood. In this project we have produced the first chromosome level assembly of an anglerfish (Lophius piscatorius). We also provide an annotation of this genome based on orthology inference and believe that this will provide a comprehensive genetic resource for the study of anglerfish biology facilitating research addressing the evolution of anglerfish specific properties. As part of an analysis of the initial contig level assembly we characterized the L. piscatorius mitochondrial genome and transcriptome. This identified low-level heteroplasmic sites, a species-specific control region indel, as well as a novel long non- coding RNA derived from the Cytochrome Oxidase I locus. Furthermore, we observed a remarkable sequence conservation of the mitochondrial-derived peptide Humanin. These findings contribute to our understanding of mitochondrial regulation and function, and are of interest not only to anglerfish research. It is thought that sexual parasitism has evolved independently multiple times within the Ceratioidei suborder, suggesting that they may share a common genetic predisposition that facilitates sexual parasitism. As the removal of immune rejection is a requirement for the fusion of two individuals it is possible that this predisposition arises from a modified immune system that may be shared with the non-parasitic anglerfish taxons. Given that two teleost taxons (Gadiformes and Syngnathus) have previously been reported to lack the MHC II arm of the adaptive immune system we made use of the initial draft genome assemblies to establish the absence or presence of MHC II in L. piscatorius. Surprisingly we found an absence of exactly the same five (of 30 assayed) genes absent in Gadiformes. This observation implies that these five genes (CD4, CD74 A/B, MHCIIα/β) comprise a core set of MHCII genes that have no essential functions external to MHC II, and suggests the possibility that loss of MHCII may have been one of the events that enabled the development of sexual parasitism in anglerfish. To annotate the final chromosome level assemblies, we made use of in silico gene predictions supported by evidence from RNA followed by an orthology based functional annotation. An analysis of the resulting annotation confirmed that L. piscatorius has a fairly typical teleost genome in terms of genome size, global gene repertoire and gene feature composition. We also observed a chromosomal orthology with several teleost species that argues that the scaffolds reported here do indeed represent physical chromosomes. These analyses also revealed a teleost specific bimodality in intron length distribution that could be correlated to genome size within the teleosts, suggesting a coupling between the mechanisms governing intron and genome size in teleosts. The work presented in this thesis not only provides new genome resources that should facilitate further research into the weird and wonderful world of the anglerfishes, but also confirms an unexpected plasticity in teleost adaptive immunity. Surprisingly we were also able to observe fundamental genome properties related to intron size that have not previously been reported. Our work thus touches not only on the specifics of teleost immunology but also on general mechanisms underlying genome evolution in the teleosts.publishedVersio

Towards locality aware de novo dna assembly of short reads in colour space

This thesis presents a new approach towards de novo DNA assembly for short reads. Its two main contributions are a novel, robust filtering scheme for noisy reads that outperforms the (accuracy of the) widely used Sasson’s filter, and a novel assembly algorithm that, minimizing space and maximizing locality of accesses, runs faster than all state-of-the-art algorithms even when on substantially cheaper hardwar

Image similarity in medical images

Recent experiments have indicated a strong influence of the substrate grain orientation on the self-ordering in anodic porous alumina. Anodic porous alumina with straight pore channels grown in a stable, self-ordered manner is formed on (001) oriented Al grain, while disordered porous pattern is formed on (101) oriented Al grain with tilted pore channels growing in an unstable manner. In this work, numerical simulation of the pore growth process is carried out to understand this phenomenon. The rate-determining step of the oxide growth is assumed to be the Cabrera-Mott barrier at the oxide/electrolyte (o/e) interface, while the substrate is assumed to determine the ratio β between the ionization and oxidation reactions at the metal/oxide (m/o) interface. By numerically solving the electric field inside a growing porous alumina during anodization, the migration rates of the ions and hence the evolution of the o/e and m/o interfaces are computed. The simulated results show that pore growth is more stable when β is higher. A higher β corresponds to more Al ionized and migrating away from the m/o interface rather than being oxidized, and hence a higher retained O:Al ratio in the oxide. Experimentally measured oxygen content in the self-ordered porous alumina on (001) Al is indeed found to be about 3% higher than that in the disordered alumina on (101) Al, in agreement with the theoretical prediction. The results, therefore, suggest that ionization on (001) Al substrate is relatively easier than on (101) Al, and this leads to the more stable growth of the pore channels on (001) Al