Prognostic modelling of breast cancer patients: a benchmark of predictive models with external validation

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores – Sistemas Digitais e Percepcionais pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Development of regional spatial data infrastructure (SDI) case study in hearth of Borneo

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

Oil, foreign aid and FDI flows: The missing link?

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Economics from the NOVA – School of Business and Economics

Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work.

Environmental data management in the Sado Estuary

Estuaries are perhaps the most threatened environments in the coastal fringe; the coincidence of high natural value and attractiveness for human use has led to conflicts between conservation and development. These conflicts occur in the Sado Estuary since its location is near the industrialised zone of Peninsula of Setúbal and at the same time, a great part of the Estuary is classified as a Natural Reserve due to its high biodiversity. These facts led us to the need of implementing a model of environmental management and quality assessment, based on methodologies that enable the assessment of the Sado Estuary quality and evaluation of the human pressures in the estuary. These methodologies are based on indicators that can better depict the state of the environment and not necessarily all that could be measured or analysed. Sediments have always been considered as an important temporary source of some compounds or a sink for other type of materials or an interface where a great diversity of biogeochemical transformations occur. For all this they are of great importance in the formulation of coastal management system. Many authors have been using sediments to monitor aquatic contamination, showing great advantages when compared to the sampling of the traditional water column. The main objective of this thesis was to develop an estuary environmental management framework applied to Sado Estuary using the DPSIR Model (EMMSado), including data collection, data processing and data analysis. The support infrastructure of EMMSado were a set of spatially contiguous and homogeneous regions of sediment structure (management units). The environmental quality of the estuary was assessed through the sediment quality assessment and integrated in a preliminary stage with the human pressure for development. Besides the earlier explained advantages, studying the quality of the estuary mainly based on the indicators and indexes of the sediment compartment also turns this methodology easier, faster and human and financial resource saving. These are essential factors to an efficient environmental management of coastal areas. Data management, visualization, processing and analysis was obtained through the combined use of indicators and indices, sampling optimization techniques, Geographical Information Systems, remote sensing, statistics for spatial data, Global Positioning Systems and best expert judgments. As a global conclusion, from the nineteen management units delineated and analyzed three showed no ecological risk (18.5 % of the study area). The areas of more concern (5.6 % of the study area) are located in the North Channel and are under strong human pressure mainly due to industrial activities. These areas have also low hydrodynamics and are, thus associated with high levels of deposition. In particular the areas near Lisnave and Eurominas industries can also accumulate the contamination coming from Águas de Moura Channel, since particles coming from that channel can settle down in that area due to residual flow. In these areas the contaminants of concern, from those analyzed, are the heavy metals and metalloids (Cd, Cu, Zn and As exceeded the PEL guidelines) and the pesticides BHC isomers, heptachlor, isodrin, DDT and metabolits, endosulfan and endrin. In the remain management units (76 % of the study area) there is a moderate impact potential of occurrence of adverse ecological effects and in some of these areas no stress agents could be identified. This emphasizes the need for further research, since unmeasured chemicals may be causing or contributing to these adverse effects. Special attention must be taken to the units with moderate impact potential of occurrence of adverse ecological effects, located inside the natural reserve. Non-point source pollution coming from agriculture and aquaculture activities also seem to contribute with important pollution load into the estuary entering from Águas de Moura Channel. This pressure is expressed in a moderate impact potential for ecological risk existent in the areas near the entrance of this Channel. Pressures may also came from Alcácer Channel although they were not quantified in this study. The management framework presented here, including all the methodological tools may be applied and tested in other estuarine ecosystems, which will also allow a comparison between estuarine ecosystems in other parts of the globe.

Miocene lithological, foraminiferal and palynological data from the Belverde borehole (Portugal)

XVIII Jornadas de Paleontología, 2002

Spatial data infrastructures model for developing countries: A case study of Nigeria

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

Discovery and retrieval of Geographic data using Google

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

Visualization of clusters in geo-referenced data using three-dimensional self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Adaption of the Creative Commons approach and the roaming concept to spatial data infrastructures (SDI)

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

Estimation of vegetation carbon stock in Portugal using land use/ land cover data

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

Exploratory geospatial data analysis using self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Ciência e Sistemas de Informação Geográfica

Integrated ecological-economic modelling and assessment aproach for coastal ecosystem management

Thesis submitted to the Faculty of Sciences and Technology, New University of Lisbon, for the degree of Doctor of Philosophy in Environmental Sciences

Neural correlations during brain activation in arithmetical tasks – an approach using electroencephalographic data

Dissertação apresentada na Faculdade de Ciências e Tecnologiea da Universidade Nova de Lisboa, para obtenção do Grau de Mestre em Engenharia Biomédica

Quaternary elephants in Portugal: new data

In this paper, a synopsis on the already known data, and the study of further specimens either new (*) or hither to undescribed are presented. The specimens dealt with have been collected at the Condeixa travertines; in the Tagus terraces near Carregado(*) and at Foz do Enxarrique(*); in the mousterian, about 31000 BP infilling from the Figueira Brava cave(*); and at Algar de Joao Ramos(*). Some specimens are ascribed to Elephas antiquus, the best represented form. Material from Figueira Brava cave and Algar de João Ramos is ascribed to Mammuthus primigenius, a species recognized here for the first time in Portugal.