New strategies to detect and understand genotype-by-environment interactions and QTL-by-environment interactions

Dissertação para obtenção do Grau de Doutor em Estatística e Gestão do Risco, especialidade em Estatística

On an organizational level: How can the emergency department at Rouge Valley Centenary hospital improve their wait times?

The prolonged wait times may arguably put into question the Canadian Health Act of 1984. Statistics show throughput wait times are 5.5 hours and output wait times for admitted patients are 32.4 hours. After probing and analyzing best practices through a qualitative/quantitative Value Stream Mapping and a qualitative SWOT Analysis; Team Triage and an Overcapacity Protocol is suggested to improve non-admitted patients wait times by 1.89 hours and admitted patients wait times by 16 hours by eliminating wasteful steps in the patient process and upon overcapacity, effectively sharing already stabilized and admitted patients with all wards in the hospital.

Introducing mapping standards in the quality assessment of buildings extracted from very high resolution satellite imagery

Many municipal activities require updated large-scale maps that include both topographic and thematic information. For this purpose, the efficient use of very high spatial resolution (VHR) satellite imagery suggests the development of approaches that enable a timely discrimination, counting and delineation of urban elements according to legal technical specifications and quality standards. Therefore, the nature of this data source and expanding range of applications calls for objective methods and quantitative metrics to assess the quality of the extracted information which go beyond traditional thematic accuracy alone. The present work concerns the development and testing of a new approach for using technical mapping standards in the quality assessment of buildings automatically extracted from VHR satellite imagery. Feature extraction software was employed to map buildings present in a pansharpened QuickBird image of Lisbon. Quality assessment was exhaustive and involved comparisons of extracted features against a reference data set, introducing cartographic constraints from scales 1:1000, 1:5000, and 1:10,000. The spatial data quality elements subject to evaluation were: thematic (attribute) accuracy, completeness, and geometric quality assessed based on planimetric deviation from the reference map. Tests were developed and metrics analyzed considering thresholds and standards for the large mapping scales most frequently used by municipalities. Results show that values for completeness varied with mapping scales and were only slightly superior for scale 1:10,000. Concerning the geometric quality, a large percentage of extracted features met the strict topographic standards of planimetric deviation for scale 1:10,000, while no buildings were compliant with the specification for scale 1:1000.

The transformation of work? A quantitative evaluation of changes in work in Portugal

This report is made for the Work Package 15 of WORKS project and tries to develop more information on the Portuguese situation in the work structures changes in the recent years. It starts with an analysis of socio- economical indicators (Macro economical indicators, Employment indicators, Consumption, Technology at the workplace, Productivity), and then approaches the situation in terms of work flexibility in its dimensions of time use and New forms of work organisation. It traces employment in business functions with a sectoral and occupational approach, and analyses the occupational change in South Europe with particular relevance to Portugal (skill utilisation and job satisfaction, occupational and industrial mobility, quantitative evaluation of the shape of employment in Europe. Finaly are analysed the globalisation indicators.

Component-based software engineering: a quantitative approach

Dissertação apresentada para a obtenção do Grau de Doutor em Informática pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

The contribution of multitemporal information from multispectral satellite images for automatic land cover classification at the national scale

Thesis submitted to the Instituto Superior de Estatística e Gestão de Informação da Universidade Nova de Lisboa in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Information Management – Geographic Information Systems

Identification of mating type genes in the bipolar basidiomycetous yeast rhodosporidium toruloides: first insight into the MAT Locus structure of the sporidiobolales

Eukaryotic Cell, Vol.7, Nº6

Mapping and characterization of a green biofilm inside of Vilar de Frades Church (Portugal)

Vilar de Frades church is integrated in the Vilar de Frades Monastery, located in the North part of Portugal (Barcelos). The monastery, founded in 566, suffered several architectural modifications and restoration works, the most relevant was in the XVI century. The church, in granite, has one nave and six bays,holding ten chapels with vaults of crossed ribbings. Nowadays, the chapels present a severe biological colonization characterised by an intense green biofilm, which becoming apparent in other locations inside the church. In the course of a general survey concerning the conservation state of the church, an accurate campaign was planned in order to assess the main biodeterioration agents, map biological colonization and determine the environmental conditions. Laboratory analyses were accomplished with optical microscopy and spectrofluorometry. This study presents the results of this campaign. Details on conservation or preservation works that need to be implemented are also presented.

LADAR based mapping and obstacle detection system for service robots

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Mapping the quality of life experience in Alfama: a case study in Lisbon, Portugal.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Quantitative assessment of modularity of caesarJ components

Dissertação apresentada no âmbito do Mestrado em Engenharia Informática para obtenção do grau de Mestre em Engenharia Informática

Genetics of berry colour and anthocyanin content variation in grapevine (Vitis vinifera L.subsp. vinifera)

Dissertation presented in fulfillment of the requirements for the Degree of Doctor of Philosophy in Biology (Molecular Genetics) at the Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa

Manifesto para uma nova química: o discurso preliminar do Traité Elémentaire de Chimie de Antoine Laurent Lavoisier

Em 2011, ano internacional da química, parece ser pertinente a publicação de um dos textos que marcou o esforço de renovação desta disciplina nos finais do século xviii. O Discurso Preliminar do Tratado Elementar de Química (1789) de Antoine Laurent Lavoisier constituiu-se como um verdadeiro manifesto para uma nova forma de ensinar, entender e praticar esta disciplina. No âmbito de um processo com cariz revolucionário era imperativo mobilizar as jovens gerações de futuros químicos. Era ainda necessária a própria refundição da linguagem química. São estes os principais propósitos que Lavoisier apresenta neste documento inaugural, num modo claro e metódico característico do seu estilo.

Factores individuais que condicionam a Saúde : um estudo caso-controlo

RESUMO - O presente projecto enquadra-se no paradigma salutogénico e visa apurar alguns dos factores que determinam que algumas pessoas se apresentem mais saudáveis que a população em geral. Foi seleccionado um estudo, quantitativo, analítico tipo caso-controlo (1 caso para 3 controlos), em que os casos são constituídos por indivíduos integrando a Função Pública que se encontram acima do percentil 95 de assiduidade ao trabalho nos últimos dois anos e com uma auto-percepção de Saúde classificada como muito boa, os controlos são indivíduos que não obedecem à definição de caso. Os indivíduos serão emparelhados por idade, género, estado civil, carreira, categoria profissional e unidade funcional que integram. A assiduidade será calculada com recurso aos certificados de incapacidade temporária entregues nos respectivos serviços. Os factores a estudar são os mais citados na literatura como factores salutogénicos ou factores de protecção, são eles: - Sentido de Coerência de Antonowsky - Locus de controlo - Auto conceito -Auto Eficácia - Aptidão física nas três vertentes clássicas: Capacidade aeróbia, Composição corporal, Aptidão muscular. Todos estes factores serão estudados com recurso a questionários auto preenchidos devidamente testados e validados para o português de Portugal sendo a aptidão física apurada com recurso á bateria de testes "Fitness Gram" adoptada para Portugal pelo Instituto do Desporto de Portugal e pelo Ministério da Educação. Os resultados serão apurados com recurso ao software de análise epidemiológica EPIDAT. 3.1. ---------------- ABSTRACT - The present project follows the salutogénic paradigm and intends to identify some of the factors that determine why some people are healthier than the general population. It was selected a quantitative, analytic, case-control study type (1 case to 3 controls), in which the cases are constituted by individuals who are integrated in Public Services and find themselves above 95 percentile of assiduity in work in the last two years, and with a self-perception of Health classified as very good, the controls are individuals who don’t obey to the case definition. The individuals will be matched by age, gender, civil state, career, professional category and Functional Unity in the Health services. The assiduity will be calculated with the help of temporary incapacity certificates delivered in the respective services. The currently studying factors are the most cited in literature, like salutogenic factors or protection factors, are those: - Antonowsky’s Sense of Coherence - Locus Control - Self-concept - Self-Efficacy - The three classic strands of Physical Fitness: Aerobic Capacity, Corporal Composition, Muscular Fitness. All these factors will be studied with the resource of properly tested and validated self-filled questionnaires for Portugal Portuguese (language), with the Physical Fitness being determined with the resource of “Fitness Gram” test battery, adopted for Portugal by the Portuguese Sports Institute and the Education Ministry. The results will be determined with the resource of the epidemiologic analysis software EPIDAT. 3.1.

Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.