An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Compêndio do clarinete: um contributo para a sistematização dos recursos técnicos e expressivos no nível secundário do ensino vocacional

Relatório de estágio de mestrado em Ensino da Música

Medir o impacto nas ciências sociais: pontos de referência teóricos

Os modos de fazer pesquisa científica têm vindo a alterar-se, em função das mudanças pelas quais passa o Ensino Superior, assim como os sistemas de ciência e tecnologia, no seu todo. Na Europa vivem-se tempos de grandes questionamentos acerca do modo de proceder relativamente à definição de metodologias de avaliação e/ou financiamento público à investigação individual e/ou coletiva. A tendência geral, neste contexto, é para aperfeiçoar as metodologias de avaliação, através da definição de indicadores que permitam medir as várias dimensões do trabalho científico. No campo específico da avaliação, prevê-se cada vez mais a avaliação do impacto das pesquisas. Ocorre que, apesar do número e da amplitude dos indicadores que vão sendo propostos, a definição de impacto resulta numa tarefa difícil. Não só porque a realidade medida nem toda é perfeitamente traduzível em algo tangível, mas também porque existem diferenças significativas nos modos como as diferentes áreas produzem conhecimento. Neste artigo, pretende-se refletir sobre esse conceito de impacto, nomeadamente ao nível das ciências sociais, evidenciando aquelas que são as principais conclusões e reflexões de estudos e escritos mais recentes.

Adoção e difusão de aplicações das tecnologias da informação: iniciativas lançadas no âmbito de processos de implantação de aplicações em organizações – estudo de práticas profissionais e proposta de ferramenta de suporte

Tese de Doutoramento Tecnologias e Sistemas de Informação

A soft computing approach to kidney diseases evaluation

Kidney renal failure means that one’s kidney have unexpectedly stopped functioning, i.e., once chronic disease is exposed, the presence or degree of kidney dysfunction and its progression must be assessed, and the underlying syndrome has to be diagnosed. Although the patient’s history and physical examination may denote good practice, some key information has to be obtained from valuation of the glomerular filtration rate, and the analysis of serum biomarkers. Indeed, chronic kidney sickness depicts anomalous kidney function and/or its makeup, i.e., there is evidence that treatment may avoid or delay its progression, either by reducing and prevent the development of some associated complications, namely hypertension, obesity, diabetes mellitus, and cardiovascular complications. Acute kidney injury appears abruptly, with a rapid deterioration of the renal function, but is often reversible if it is recognized early and treated promptly. In both situations, i.e., acute kidney injury and chronic kidney disease, an early intervention can significantly improve the prognosis.The assessment of these pathologies is therefore mandatory, although it is hard to do it with traditional methodologies and existing tools for problem solving. Hence, in this work, we will focus on the development of a hybrid decision support system, in terms of its knowledge representation and reasoning procedures based on Logic Programming, that will allow one to consider incomplete, unknown, and even contradictory information, complemented with an approach to computing centered on Artificial Neural Networks, in order to weigh the Degree-of-Confidence that one has on such a happening. The present study involved 558 patients with an age average of 51.7 years and the chronic kidney disease was observed in 175 cases. The dataset comprise twenty four variables, grouped into five main categories. The proposed model showed a good performance in the diagnosis of chronic kidney disease, since the sensitivity and the specificity exhibited values range between 93.1 and 94.9 and 91.9–94.2 %, respectively.

An assessment of chronic kidney diseases

Kidney renal failure means that one’s kidney have unexpectedlystoppedfunctioning,i.e.,oncechronicdiseaseis exposed, the presence or degree of kidney dysfunction and its progression must be assessed, and the underlying syndrome has to be diagnosed. Although the patient’s history and physical examination may denote good practice, some key information has to be obtained from valuation of the glomerular filtration rate, and the analysis of serum biomarkers. Indeed, chronic kidney sickness depicts anomalous kidney function and/or its makeup, i.e., there is evidence that treatment may avoid or delay its progression, either by reducing and prevent the development of some associated complications, namely hypertension, obesity, diabetes mellitus, and cardiovascular complications. Acute kidney injury appears abruptly, with a rapiddeteriorationoftherenalfunction,butisoftenreversible if it is recognized early and treated promptly. In both situations, i.e., acute kidney injury and chronic kidney disease, an early intervention can significantly improve the prognosis. The assessment of these pathologies is therefore mandatory, although it is hard to do it with traditional methodologies and existing tools for problem solving. Hence, in this work, we will focus on the development of a hybrid decision support system, in terms of its knowledge representation and reasoning procedures based on Logic Programming, that will allow onetoconsiderincomplete,unknown,and evencontradictory information, complemented with an approach to computing centered on Artificial Neural Networks, in order to weigh the Degree-of-Confidence that one has on such a happening. The present study involved 558 patients with an age average of 51.7 years and the chronic kidney disease was observed in 175 cases. The dataset comprise twenty four variables, grouped into five main categories. The proposed model showed a good performance in the diagnosis of chronic kidney disease, since the sensitivity and the specificity exhibited values range between 93.1 and 94.9 and 91.9–94.2 %, respectively.

An evaluation of parchments' degradation a hybrid approach

Parchment stands for a multifaceted material made from animal skin, which has been used for centuries as a writing support or as bookbinding. Due to the historic value of objects made of parchment, understanding their degradation and their condition is of utmost importance to archives, libraries and museums, i.e., the assessment of parchment degradation is mandatory, although it is hard to do with traditional methodologies and tools for problem solving. Hence, in this work we will focus on the development of a hybrid decision support system, in terms of its knowledge representation and reasoning procedures, under a formal framework based on Logic Programming, complemented with an approach to computing centered on Artificial Neural Networks, to evaluate Parchment Degradation and the respective Degree-of-Confidence that one has on such a happening.

Avaliação de competências de literacia mediática : o caso português

O que são e como se avaliam as competências de literacia mediática dos indivíduos? O que tem sido feito em Portugal em matéria de avaliação deste tipo competências? Este artigo reflete sobre estas questões e revela o caso português: pouco explorado, limitado, mas em notável crescimento. Aqui se apresentam os estudos portugueses de avaliação de competências de literacia mediática mais significativos, as suas metodologias e principais conclusões. Uma nota curiosa: todos foram desenvolvidos na última década.

Análise de tempos e métodos e implementação de ferramentas lean num sistema produtivo

Dissertação de mestrado em Engenharia Industrial

Influence of the hip joint modeling approaches on the kinematics of human gait

The influence of the hip joint formulation on the kinematic response of the model of human gait is investigated throughout this work. To accomplish this goal, the fundamental issues of the modeling process of a planar hip joint under the framework of multibody systems are revisited. In particular, the formulations for the ideal, dry, and lubricated revolute joints are described and utilized for the interaction of femur head inside acetabulum or the hip bone. In this process, the main kinematic and dynamic aspects of hip joints are analyzed. In a simple manner, the forces that are generated during human gait, for both dry and lubricated hip joint models, are computed in terms of the system’s state variables and subsequently introduced into the dynamics equations of motion of the multibody system as external generalized forces. Moreover, a human multibody model is considered, which incorporates the different approaches for the hip articulation, namely ideal joint, dry, and lubricated models. Finally, several computational simulations based on different approaches are performed, and the main results presented and compared to identify differences among the methodologies and procedures adopted in this work. The input conditions to the models correspond to the experimental data capture from an adult male during normal gait. In general, the obtained results in terms of positions do not differ significantly when the different hip joint models are considered. In sharp contrast, the velocity and acceleration plotted vary significantly. The effect of the hip joint modeling approach is clearly measurable and visible in terms of peaks and oscillations of the velocities and accelerations. In general, with the dry hip model, intra-joint force peaks can be observed, which can be associated with the multiple impacts between the femur head and the cup. In turn, when the lubricant is present, the system’s response tends to be smoother due to the damping effects of the synovial fluid.

Avaliação quantitativa da geodiversidade: desenvolvimento de instrumentos metodológicos com aplicação ao ordenamento do território

Tese de Doutoramento em Ciências (Especialidade de Geologia)

O currículo da formação em engenharia no âmbito do processo de bolonha: desenvolvimento de competências e perfil profissional na perspetiva dos docentes, dos estudantes e dos profissionais

Tese de Doutoramento em Ciências da Educação (área de especilização em Desenvolvimento Curricular).

Systems biology approaches for the design of novel Saccharomyces cerevisiae winemaking strains for enhanced flavour compounds synthesis

Tese de Doutoramento em Biologia Ambiental e Molecular

Análise do ciclo de vida usando Lourenço modelo: caso da cidade de Damasco (1960-2015)

Dissertação de mestrado Internacional em Ambiente Construído Sustentável

Remoção fotocatalítica de micropoluentes em meios porosos funcionalizados

Dissertação de mestrado integrado em Engenharia Civil