Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Experimental analysis of the cyclic response of traditional timber joints and their influence on the seismic capacity of timber frame structures

Timber connections represent the crucial part of a timber structure and a great variability exists in terms of types of connections and mechanisms. Taking as case study the widespread traditional timber frame structures, in particular the Portuguese Pombalino buildings, one of the most common timber connection is the half-lap joint. Connections play a major role in the overall behaviour of a structure, particularly when assessing their seismic response, since damage is concentrated at the connections. For this reason, an experimental campaign was designed and distinct types of tests were carried out on traditional half-lap joints to assess their in-plane response. In particular, pull-out and in-plane cyclic tests were carried out on real scale unreinforced connections. Subsequently, the connections were retrofitted, using strengthening techniques such as self-tapping screws, steel plates and GFRP sheets. The tests chosen were meant to capture the hysteretic behaviour and dissipative capacity of the connections and characterise their response and, therefore, their influence on the seismic response of timber frame walls, particularly concerning their uplifting and rotation capacity, that could lead to rocking in the walls. In this paper, the results of the experimental campaign are presented in terms of hysteretic curves, dissipated energy and equivalent viscous damping ratio. Moreover, recommendations are provided on the most appropriate retrofitting solutions.

Aulas interativas com recurso à exposição: uma metodologia para o ensino da linguagem de programação Python

Relatório de estágio de mestrado em Ensino de Informática

Identifying finger postures when interacting with the touch screen of mobile devices

This study presents the results of preliminary test on the interaction between fingertip and touch screen. The objective of this study is to identify the fingertip posture when interacting with touch screen devices. Ten participants, 7 males and 3 females, participated in this study. The participants were asked to touch targets on the mobile devices screen by tapping them sequentially and connecting them. The participants performed the tasks in a sitting posture. A tablet with 10 inches screen and a mobile phone with 4 inches screen were used in the study. The results showed that all participants dominantly used their thumb to interact with the mobile phone in single and two hands postures. The common thumb posture adopted by the participants is the combination of the 60° pitch and 0° roll angles. While for interaction with tablet in various postures observed in the study, the participants commonly used their index fingers in the combination of 60° pitch and 0° roll angles. This study also observed the participant with long finger nails touched targets on the mobile devices screen by using her index or middle fingers very low pitch.

Desenvolvimento de um Range Extender para Veículo Elétrico

Dissertação de mestrado integrado em Engenharia Eletrónica Industrial e de Computadores

Layer-by-layer technique to developing functional nanolaminate films with antifungal activity

The layer-by-layer (LbL) deposition method was used to build up alternating layers (five) of different polyelectrolyte solutions (alginate, zein-carvacrol nanocapsules, chitosan and chitosan-carvacrol emulsions) on an aminolysed/charged polyethylene terephthalate (A/C PET) film. These nanolaminated films were characterised by contact angle measurements and through the determination of water vapour (WVTR) and oxygen (O2TR) transmission rates. The effect of active nanolaminated films against the Alternaria sp. and Rhizopus stolonifer was also evaluated. This procedure allowed developing optically transparent nanolaminated films with tuneable water vapour and gas properties and antifungal activity. The water and oxygen transmission rate values for the multilayer films were lower than those previously reported for the neat alginate or chitosan films. The presence of carvacrol and zein nanocapsules significantly decreased the water transmission rate (up to 40 %) of the nanolaminated films. However, the O2TR behaved differently and was only improved (up to 45 %) when carvacrol was encapsulated, i.e. nanolaminated films prepared by alternating alginate with nanocapsules of zein-carvacrol layers showed better oxygen barrier properties than those prepared as an emulsion of chitosan and carvacrol. These films containing zein-carvacrol nanocapsules also showed the highest antifungal activity (30 %), which did not significantly differ from those obtained with the highest amount of carvacrol, probably due to the controlled release of the active agent (carvacrol) from the zein-carvacrol nanocapsules. Thus, this work shows that nanolaminated films prepared with alternating layers of alginate and zein-carvacrol nanocapsules can be considered to improve the shelf-life of foodstuffs.

Hydrocarbonoclastic bacteria: from bioremediation to bioenergy feedstock

Tese de Doutoramento em Engenharia Química e Biológica.

Reforço de ligações tradicionais de madeira

Dissertação de mestrado integrado em Engenharia Civil

Experimental analysis of Maritime pine and Iroko single shear dowel-type connections

"Available online 21 March 2016"

Avaliação da comunicação expressiva em crianças dos 6 aos 41 meses de idade na região norte de Portugal: um estudo exploratório com o Early Communication Indicator

Dissertação de mestrado em Educação Especial (área de especialização em Intervenção Precoce)