Development of Techniques for the Automatic Extraction and Grade Detection of Glioma Tumors from Conventional Brain Magnetic Resonant Images

Cerebral glioma is the most prevalent primary brain tumor, which are classified broadly into low and high grades according to the degree of malignancy. High grade gliomas are highly malignant which possess a poor prognosis, and the patients survive less than eighteen months after diagnosis. Low grade gliomas are slow growing, least malignant and has better response to therapy. To date, histological grading is used as the standard technique for diagnosis, treatment planning and survival prediction. The main objective of this thesis is to propose novel methods for automatic extraction of low and high grade glioma and other brain tissues, grade detection techniques for glioma using conventional magnetic resonance imaging (MRI) modalities and 3D modelling of glioma from segmented tumor slices in order to assess the growth rate of tumors. Two new methods are developed for extracting tumor regions, of which the second method, named as Adaptive Gray level Algebraic set Segmentation Algorithm (AGASA) can also extract white matter and grey matter from T1 FLAIR an T2 weighted images. The methods were validated with manual Ground truth images, which showed promising results. The developed methods were compared with widely used Fuzzy c-means clustering technique and the robustness of the algorithm with respect to noise is also checked for different noise levels. Image texture can provide significant information on the (ab)normality of tissue, and this thesis expands this idea to tumour texture grading and detection. Based on the thresholds of discriminant first order and gray level cooccurrence matrix based second order statistical features three feature sets were formulated and a decision system was developed for grade detection of glioma from conventional T2 weighted MRI modality.The quantitative performance analysis using ROC curve showed 99.03% accuracy for distinguishing between advanced (aggressive) and early stage (non-aggressive) malignant glioma. The developed brain texture analysis techniques can improve the physician’s ability to detect and analyse pathologies leading to a more reliable diagnosis and treatment of disease. The segmented tumors were also used for volumetric modelling of tumors which can provide an idea of the growth rate of tumor; this can be used for assessing response to therapy and patient prognosis.

Network properties of folksonomies

Social resource sharing systems like YouTube and del.icio.us have acquired a large number of users within the last few years. They provide rich resources for data analysis, information retrieval, and knowledge discovery applications. A first step towards this end is to gain better insights into content and structure of these systems. In this paper, we will analyse the main network characteristics of two of these systems. We consider their underlying data structures – so-called folksonomies – as tri-partite hypergraphs, and adapt classical network measures like characteristic path length and clustering coefficient to them. Subsequently, we introduce a network of tag cooccurrence and investigate some of its statistical properties, focusing on correlations in node connectivity and pointing out features that reflect emergent semantics within the folksonomy. We show that simple statistical indicators unambiguously spot non-social behavior such as spam.

Plant Leaf Identification Using Gabor Wavelets

This article presents a novel method of plant classification using Gabor wavelet filters to extract texture filters in a foliar surface. The aim of this promising method is to add to the results obtained by other leaf attributes (such as shape, contour, color, among others), increasing, therefore, the percentage of classification of plant species. To corroborate the efficiency of the technique, an experiment using 20 species from Brazilian flora was done and discussed. The results are also compared with texture Fourier descriptors and cooccurrence matrices. (C) 2009 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 19, 236-243, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.20201

Ordinal Boltzmann machines for collaborative filtering

Collaborative filtering is an effective recommendation technique wherein the preference of an individual can potentially be predicted based on preferences of other members. Early algorithms often relied on the strong locality in the preference data, that is, it is enough to predict preference of a user on a particular item based on a small subset of other users with similar tastes or of other items with similar properties. More recently, dimensionality reduction techniques have proved to be equally competitive, and these are based on the co-occurrence patterns rather than locality. This paper explores and extends a probabilistic model known as Boltzmann Machine for collaborative filtering tasks. It seamlessly integrates both the similarity and cooccurrence in a principled manner. In particular, we study parameterisation options to deal with the ordinal nature of the preferences, and propose a joint modelling of both the user-based and item-based processes. Experiments on moderate and large-scale movie recommendation show that our framework rivals existing well-known methods.

Comorbidade em fobia social no transtorno obsessivo-compulsivo: prevalência e fatores associados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

RET haplotype, not linked to the C620R activating mutation, associated with Hirschsprung disease in a novel MEN2 family

Hirschsprung disease is a congenital form of aganglionic megacolon that results from cristopathy. Hirschsprung disease usually occurs as a sporadic disease, although it may be associated with several inherited conditions, such as multiple endocrine neoplasia type 2. The rearranged during transfection (RET) proto-oncogene is the major susceptibility gene for Hirschsprung disease, and germline mutations in RET have been reported in up to 50% of the inherited forms of Hirschsprung disease and in 15-20% of sporadic cases of Hirschsprung disease. The prevalence of Hirschsprung disease in multiple endocrine neoplasia type 2 cases was recently determined to be 7.5% and the cooccurrence of Hirschsprung disease and multiple endocrine neoplasia type 2 has been reported in at least 22 families so far. It was initially thought that Hirschsprung disease could be due to disturbances in apoptosis or due to a tendency of the mutated RET receptor to be retained in the Golgi apparatus. Presently, there is strong evidence favoring the hypothesis that specific inactivating haplotypes play a key role in the fetal development of congenital megacolon/Hirschsprung disease. In the present study, we report the genetic findings in a novel family with multiple endocrine neoplasia type 2: a specific RET haplotype was documented in patients with Hirschsprung disease associated with medullary thyroid carcinoma, but it was absent in patients with only medullary thyroid carcinoma. Despite the limited number of cases, the present data favor the hypothesis that specific haplotypes not linked to RET germline mutations are the genetic causes of Hirschsprung disease.

Characterising emergent semantics in Twitter lists

Twitter lists organise Twitter users into multiple, often overlapping, sets. We believe that these lists capture some form of emergent semantics, which may be useful to characterise. In this paper we describe an approach for such characterisation, which consists of deriving semantic relations between lists and users by analyzing the cooccurrence of keywords in list names. We use the vector space model and Latent Dirichlet Allocation to obtain similar keywords according to co-occurrence patterns. These results are then compared to similarity measures relying on WordNet and to existing Linked Data sets. Results show that co-occurrence of keywords based on members of the lists produce more synonyms and more correlated results to that of WordNet similarity measures.

Archaeological evidence of teosinte domestication from Guilá Naquitz, Oaxaca

Analysis of the three most ancient Zea mays inflorescence fragments from Guilá Naquitz, Oaxaca, Mexico shows they did not disarticulate naturally, indicating that agricultural selection of domesticated teosinte was underway by 5,400 14C years before the present (about 4,200 dendrocalibrated years B.C.). The cooccurrence of two-ranked specimens with two rows and four rows of grain and numerous additional morphological characteristics of these specimens support hypotheses based on molecular and quantitative genetic analyses that maize evolved from teosinte. Domestication of the wild ancestor of maize occurred before the end of the 5th millennium B.C.

Total organic carbon content and redox-sensitiv trace metal concentrations of selected late Cenoman claystones from DSDP Hole 93-603B

The Cenomanian/Turonian (C/T) intervals at DSDP Sites 105 and 603B from the northern part of the proto-North Atlantic show high amplitude, short-term cyclic variations in total organic carbon (TOC) content. The more pronounced changes in TOC are also reflected by changes in lithology from green claystones (TOC<1%) to black claystones (TOC>1%). Although their depositional history was different, the individual TOC cycles at Sites 105 and 603B can be correlated using stable carbon isotope stratigraphy. Sedimentation rates obtained from the isotope stratigraphy and spectral analyses indicate that these cycles were predominately precession controlled. The coinciding variations in HI, OI, delta13Corg and the abundance of marine relative to terrestrial biomarkers, as well as the low abundance of lignin pyrolysis products generated from the kerogen of the black claystones, indicate that these cyclic variations reflect changes in the contribution of marine organic matter (OM). The cooccurrence of lamination, enrichment of redox-sensitive trace metals and presence of molecular fossils of pigments from green sulfur bacteria indicate that the northern proto-North Atlantic Ocean water column was periodically euxinic from the bottom to at least the base of the photic zone (<150 m) during the deposition of the black claystones. In contrast, the green claystones are bioturbated, are enriched in Mn, do not show enrichments in redox-sensitive trace metals and show biomarker distributions indicative of long oxygen exposure times, indicating more oxic water conditions. At the same time, there is evidence (e.g., abundance of biogenic silica and significant 13C-enrichment for OC of phytoplanktic origin) for enhanced primary productivity during the deposition of the black claystones. We propose that increased primary productivity periodically overwhelmed the oxic OM remineralisation potential of the bottom waters resulting in the deposition of OM-rich black claystones. Because the amount of oxygen used for OM remineralisation exceeded the amount supplied by diffusion and deep-water circulation, the northern proto-North Atlantic became euxinic during these periods. Both Sites 105 and 603B show trends of continually increasing TOC contents and HI values of the black claystones up section, which most likely resulted from both enhanced preservation due to increased anoxia and increased production of marine OM during oceanic anoxic event 2 (OAE2).

Socioeconomic position, cognitive function, and clustering of cardiovascular risk factors in adolescence: Findings from the Mater University Study of Pregnancy and its outcomes

Objectives: The objectives of this study were to examine the extent of clustering of smoking, high levels of television watching, overweight, and high blood pressure among adolescents and whether this clustering varies by socioeconomic position and Cognitive function. Methods: This study was a cross-sectional analysis of 3613 (1742 females) participants of an Australian birth cohort who were examined at age 14. Results: Three hundred fifty-three (9.8%) of the participants had co-occurrence of three or four risk factors. Risk factors clustered in these adolescents with a greater number of participants than would be predicted by assumptions of independence having no risk factors and three or four risk factors. The extent of clustering tended to be greater in those from lower-income families and among those with lower cognitive function. The age-adjusted ratio of observed to expected cooccurrence of three or four risk factors was 2.70 (95% confidence interval [Cl], 1.80-4.06) among those from low-income families and 1.70 (95% Cl, 1.34-2.16) among those from more affluent families. The ratio among those with low Raven's scores (nonverbal reasoning) was 2.36 (95% Cl, 1.69-3.30) and among those with higher scores was 1.51 (95% Cl, 1.19-1.92); similar results for the WRAT 3 score (reading ability) were 2.69 (95% Cl, 1.85-3.94) and 1.68 (95% Cl, 1.34-2.11). Clustering did not differ by sex. Conclusion: Among adolescents, coronary heart disease risk factors cluster, and there is some evidence that this clustering is greater among those from families with low income and those who have lower cognitive function.

Padrões de organização das assembleias de aves florestais em uma paisagem fragmentada de Floresta Atlântica

Brazil is home to one of the richest avifaunas the world, which is subject to high levels of environmental degradation, in particular forest fragmentation. The Atlantic Forest biome depicts this history of devastation and today remains as small isolated fragments on highly degraded landscapes. This project aimed to evaluate the effects of forest fragmentation in an area with Atlantic Forest remnants in northern Paraná (Brazil) on the distribution and the organization of assemblage of forest birds and tested the hypothesis that the structure of the assembly in the fragments is different than expected by chance. We did four qualitative samplings of birds in three sets of forest fragments in the landscape, each with three fragments: large, medium and small. The method applied in the sampling was point counts along transects, traveled randomly for four hours in each fragment. Samples were taken in two periods: from September to November / 2013, and between March and May / 2014. The structure of the meeting was assessed by rates of co-occurring species (Checkerboard and CScore) and α diversity patterns (wealth) and β (turnover of species), while the landscape structure was analyzed from the parameters: area, distance between fragments, fractal dimension, edge density, fragment shape index and nuclear area index. The null hypothesis of no structure in the assembly of birds in the landscape was tested with null models from the co-occurrence indexes. The effects of landscape structure on the assembly of the structure were analyzed by the Mantel test and principal component analysis (PCA). The assembly of the structure in the landscape showed a pattern of spatiotemporal organization significantly different from that expected by chance, revealing a structure most influenced by segregation of the species. The fragments showed significant differences in richness, unlike sets of fragments, indicating relative homogeneity in the landscape structure. The differences between the size and the distance between the fragments significantly influenced the patterns of organization of the meeting of forest birds in the landscape and patterns of α and β diversity, indicating that the higher the fragment and smaller distances between them, more the standard of species cooccurrence is different than expected by chance. Thus, the fragmented landscape of remnants of the northern Paraná Atlantic Forest still has availability of environmental resources and physical characteristics that allow a persistent organizational structure of the assembly of forest birds in space over time.

Using niche modelling of indicator species to predict the distribution of xerophitic shrub dune communities in South-Western Portugal

Inland sand dune systems are amongst the most threatened habitat types of Europe. Affected by severe conditions, these habitats present distinct community compositions, which makes them excellent for studying possible interactions among their integrating species and the environment. We focus on understanding the distribution and cooccurrence of the species from dune plant assemblages as a key step for the adequate protection of these habitats. Using data from an extensive survey we identified the shrub species that could be considered indicators of the different xerophytic scrub dune communities in South West Portugal. Then, we modelled the responses of these species to the environmental conditions using Ecological Niche Factor Analysis. We present some preliminary results elucidating whether using species distribution models of indicator species at a regional scale is a valid approach to predict the distribution of the different types of communities inhabiting these endangered habitats.

Developmental, relational and situational characteristics of maritally abusive men

Rapport de stage présenté à la Faculté des Arts et Sciences en vue de l’obtention du grade de Maître des Sciences (M. Sc.) en Criminologie, Option Stage en Intervention

Developmental, relational and situational characteristics of maritally abusive men

Rapport de stage présenté à la Faculté des Arts et Sciences en vue de l’obtention du grade de Maître des Sciences (M. Sc.) en Criminologie, Option Stage en Intervention