Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Conceptual-physical bridging – From BPMN models to physical implementations on kettle

Developing and implementing data-oriented workflows for data migration processes are complex tasks involving several problems related to the integration of data coming from different schemas. Usually, they involve very specific requirements - every process is almost unique. Having a way to abstract their representation will help us to better understand and validate them with business users, which is a crucial step for requirements validation. In this demo we present an approach that provides a way to enrich incrementally conceptual models in order to support an automatic way for producing their correspondent physical implementation. In this demo we will show how B2K (Business to Kettle) system works transforming BPMN 2.0 conceptual models into Kettle data-integration executable processes, approaching the most relevant aspects related to model design and enrichment, model to system transformation, and system execution.

Automatic generation of ETL physical systems from BPMN conceptual models

ETL conceptual modeling is a very important activity in any data warehousing system project implementation. Owning a high-level system representation allowing for a clear identification of the main parts of a data warehousing system is clearly a great advantage, especially in early stages of design and development. However, the effort to model conceptually an ETL system rarely is properly rewarded. Translating ETL conceptual models directly into something that saves work and time on the concrete implementation of the system process it would be, in fact, a great help. In this paper we present and discuss a hybrid approach to this problem, combining the simplicity of interpretation and power of expression of BPMN on ETL systems conceptualization with the use of ETL patterns to produce automatically an ETL skeleton, a first prototype system, which has the ability to be executed in a commercial ETL tool like Kettle.

Development of an integral viscoelastic flow solver in OpenFOAM®

The usual high cost of commercial codes, and some technical limitations, clearly limits the employment of numerical modelling tools in both industry and academia. Consequently, the number of companies that use numerical code is limited and there a lot of effort put on the development and maintenance of in-house academic based codes. Having in mind the potential of using numerical modelling tools as a design aid, of both products and processes, different research teams have been contributing to the development of open source codes/libraries. In this framework, any individual can take advantage of the available code capabilities and/or implement additional features based on his specific needs. These type of codes are usually developed by large communities, which provide improvements and new features in their specific fields of research, thus increasing significantly the code development process. Among others, OpenFOAM® multi-physics computational library, developed by a very large and dynamic community, nowadays comprises several features usually only available in their commercial counterparts; e.g. dynamic meshes, large diversity of complex physical models, parallelization, multiphase models, to name just a few. This computational library is developed in C++ and makes use of most of all language capabilities to facilitate the implementation of new functionalities. Concerning the field of computational rheology, OpenFOAM® solvers were recently developed to deal with the most relevant differential viscoelastic rheological models, and stabilization techniques are currently being verified. This work describes the implementation of a new solver in OpenFOAM® library, able to cope with integral viscoelastic models based on the deformation field method. The implemented solver is verified through the comparison of the predicted results with analytical solutions, results published in the literature and by using the Method of Manufactured Solutions.

Measuring university-to-work success: development of a new scale

Purpose – The purpose of this paper is to develop a subjective multidimensional measure of early career success during university-to-work transition. Design/methodology/approach – The construct of university-to-work success (UWS) was defined in terms of intrinsic and extrinsic career outcomes, and a three-stage study was conducted to create a new scale. Findings – A preliminary set of items was developed and tested by judges. Results showed the items had good content validity. Factor analyses indicated a four-factor structure and a second-order model with subscales to assess: career insertion and satisfaction, confidence in career future, income and financial independence, and adaptation to work. Third, the authors sought to confirm the hypothesized model examining the comparative fit of the scale and two alternative models. Results showed that fits for both the first- and second-order models were acceptable. Research limitations/implications – The proposed model has sound psychometric qualities, although the validated version of the scale was not able to incorporate all constructs envisaged by the initial theoretical model. Results indicated some direction for further refinement. Practical implications – The scale could be used as a tool for self-assessment or as an outcome measure to assess the efficacy of university-to-work programs in applied settings. Originality/value – This study provides a useful single measure to assess early career success during the university-to-work transition, and might facilitate testing of causal models which could help identify factors relevant for successful transition.

Development of a methodology to incorporate risk and uncertainty in electricity power planning

Dissertação de mestrado em Engenharia Industrial

Development of a thermoelectric generator for the exhaust of a vehicle

Dissertação de mestrado integrado em Engenharia Mecânica

Specification and testing of multiplicative time-varying GARCH models with applications

In this article, we develop a specification technique for building multiplicative time-varying GARCH models of Amado and Teräsvirta (2008, 2013). The variance is decomposed into an unconditional and a conditional component such that the unconditional variance component is allowed to evolve smoothly over time. This nonstationary component is defined as a linear combination of logistic transition functions with time as the transition variable. The appropriate number of transition functions is determined by a sequence of specification tests. For that purpose, a coherent modelling strategy based on statistical inference is presented. It is heavily dependent on Lagrange multiplier type misspecification tests. The tests are easily implemented as they are entirely based on auxiliary regressions. Finite-sample properties of the strategy and tests are examined by simulation. The modelling strategy is illustrated in practice with two real examples: an empirical application to daily exchange rate returns and another one to daily coffee futures returns.

Exploring the role of O-Mannosylation in the modulation of E-Cadherin function in Gastric Cancer cell line models

Dissertação de mestrado em Bioquímica Aplicada – Biomedicina

Single line for assembly just-in-sequence multiple models

Programa Doutoral em Líderes para as Indústrias Tecnológicas

Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

Development of hybrid composite plate (HCP) for strengthening and repair of RC structures

Tese de Doutoramento em Engenharia Civil

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

The electoral dynamics of human development

This paper analyses the impact of elections on the dynamics of human development in a panel of 82 countries over the period 1980-2013. The incidence of partisan and political support effects is also taken into account. A GMM estimator is employed in the empirical analysis and the results point out to the presence of an electoral cycle in the growth rate of human development. Majority governments also influence it, but no clear evidence is found regarding partisan effects. The electoral cycles have proved to be stronger in non-OECD countries, in countries with less frequent elections, with lower levels of income and human development, in presidential and non-plurality systems and in proportional representation regimes. They have also become more intense in this millennium.

Development of composite auxetic structures for civil engineering applications

Tese de Doutoramento em Engenharia Têxtil