In silico constraint-based strain optimization methods: the quest for optimal cell factories

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.

Kinematic constraint equations

This chapter presents a general methodology for the formulation of the kinematic constraint equations at position, velocity and acceleration levels. Also a brief characterization of the different type of constraints is offered, namely the holonomic and nonholonomic constraints. The kinematic constraints described here are formulated using generalized coordinates. The chapter ends with a general approach to deal with the kinematic analysis of multibody systems.

Study of the muscular activation in obese and non-obese subjects during lifting loads

The obesity prevalence is increasing among the workforce of the developed countries. However, obesity seems to negatively affect the individuals’ work performance. In occupational contexts, manual lifting tasks are frequent and can produce significant muscle loading. With the aim of analysing the possible effect of obesity on workers’ muscular activation, surface electromyography data were collected from six muscles recruited during these tasks. In the current study, 6 different tasks of manual lifting (3 loads × 2 lifting styles) were performed by 14 participants with different obesity levels. Electromyography data normalization was based on the percentage of maximum contraction during each task. The muscles’ activation times before each task were also calculated. The current study suggests that obesity can increase the maximum contraction during each task and the delays on muscles’ activation time. This study suggests that obese individuals can present some changes on their muscle activation during lifting, when comparing with non-obese individuals, and reinforces the need to develop further studies focused on obesity as a risk factor for musculoskeletal disorders development.

Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

Aplicação de metodologias Lean na secção de tecelagem de uma empresa têxtil

Dissertação de mestrado integrado em Engenharia e Gestão Industrial

Generating timed trajectories foran autonomous robot

Tese de Doutoramento Programa Doutoral em Engenharia Electrónica e Computadores

Otimização com restrições de complementaridade: algoritmos e aplicações

Tese de Doutoramento em Engenharia Industrial e de Sistemas (PDEIS)

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

Project management under uncertainty: a study on solution methods

Project Management involves onetime endeavors that demand for getting it right the first time. On the other hand, project scheduling, being one of the most modeled project management process stages, still faces a wide gap from theory to practice. Demanding computational models and their consequent call for simplification, divert the implementation of such models in project management tools from the actual day to day project management process. Special focus is being made to the robustness of the generated project schedules facing the omnipresence of uncertainty. An "easy" way out is to add, more or less cleverly calculated, time buffers that always result in project duration increase and correspondingly, in cost. A better approach to deal with uncertainty seems to be to explore slack that might be present in a given project schedule, a fortiori when a non-optimal schedule is used. The combination of such approach to recent advances in modeling resource allocation and scheduling techniques to cope with the increasing flexibility in resources, as can be expressed in "Flexible Resource Constraint Project Scheduling Problem" (FRCPSP) formulations, should be a promising line of research to generate more adequate project management tools. In reality, this approach has been frequently used, by project managers in an ad-hoc way.

Estudo e conceção de um sistema de encaixe rápido e simples para próteses de membros inferiores

Dissertação de mestrado integrado em Engenharia Biomédica

Modelação de governo electrónico para países emergentes: O caso de São Tomé e Príncipe

Tese de Doutoramento em Tecnologias e Sistemas de Informação

O ensino da flauta de bisel em grupo como inovação pedagógica: Uma investigação-ação no 2.º Ciclo do Ensino Básico

Tese de Doutoramento em Estudos da Criança (Especialidade em Educação Musical)

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Modelling and verifying smell-free architectures with the Archery language

Architectural (bad) smells are design decisions found in software architectures that degrade the ability of systems to evolve. This paper presents an approach to verify that a software architecture is smellfree using the Archery architectural description language. The language provides a core for modelling software architectures and an extension for specifying constraints. The approach consists in precisely specifying architectural smells as constraints, and then verifying that software architectures do not satisfy any of them. The constraint language is based on a propositional modal logic with recursion that includes: a converse operator for relations among architectural concepts, graded modalities for describing the cardinality in such relations, and nominals referencing architectural elements. Four architectural smells illustrate the approach.

Basic constraints between two vectors

This chapter deals with the characterization of the basic constraints between two vectors. This issue plays a crucial role in the formulation of constraint equations for mechanical joints. In particular, relations between two parallel and two perpendicular vectors are derived. Moreover, formulation for a vector that connects two generic points is presented. The material described here is developed under the framework of multibody systems formulation for spatial systems.