The effect of redundancy and neutrality in genetic search

An experimental study aimed at assessing the influence of redundancy and neutrality on the performance of an (1+1)-ES evolution strategy modeled using Markov chains and applied to NK fitness landscapes is presented. For the study, two families of redundant binary representations, one non-neutral family which is based on linear transformations and that allows the phenotypic neighborhoods to be designed in a simple and effective way, and the neutral family based on the mathematical formulation of error control codes are used. The results indicate whether redundancy or neutrality affects more strongly the behavior of the algorithm used.

Macrofauna spatial differences within clam dredge-tracks and their implications for short-term fishing effect studies

In situ observations of clam dredging showed that the effects of the dredge on the benthic macrofauna may not be constant during a tow. A sand buffer forms in front of the gear approximately 10m after the beginning of a tow, and this pushes the sediment partially aside.In this study, we analyse differences in abundance, the number of taxa present, diversity, and evenness within sections of dredge-tracks in a disturbed, fished area and a non-fished area along the southern coast of Portugal. These areas were sampled by divers before and after dredge-fishing activity. At each site, three dredge-tracks were produced. These tracks were divided in three longitudinal sections 1start, middle and end) and two transverse sections 1track and edge). Six quadrats were used to sample macrofauna in each section of every track and edge. Our results show differences exist in macro- faunal distribution and abundance across sections of a dredge-track. These differences should be considered in any assessment of the short-term ecological impact of dredges on benthic macrofauna

The effect of sucrose on protein stability and fibrillation of prion and S6 protein

Aggregation and fibrillation of proteins have a great importance in medicine and industry. Misfolding and aggregation are the basis of many neurodegenerative diseases like Alzheimer and Parkinson. Osmolytes are molecules that can accumulate within cells and act as protective agents and they can inclusively act as protein stabilizers when cells are exposed to stress conditions. Osmolytes can also act as protein stabilizers in vitro. In this work, two different proteins were studied, the ribosomal protein from Thermus thermophilus and the mouse prion protein. The existence of an unstructured N-terminal on the prion protein does not affect its stability. The effect of the osmolyte sucrose on the fibrillation and stabilization of these two proteins was studied through kinectic and equilibrium measurements. It was shown that sucrose is able to compact the native structure of S6 protein in fibrillization conditions. Sucrose affects also folding and unfolding kinetic of S6 protein, delaying unfolding and increasing folding rate constants. The mechanism of stabilization by sucrose is non-specific because it is distributed for all protein structure, as it was demonstrated by a protein engineering approach. Sucrose delays the process of formation and elongation of S6 and prion protein from mouse. This delay is the result of the compaction of the native structure refered above. However, cellular toxicity studies have shown that fibrils formed in the presence of sucrose are more toxic to neuronal cells.

The effect of conservation measures on the spatial and temporal variation of rocky fish assemblages in the Arrábida Marine Park

Marine protected areas (MPAs) have been widely proposed for conservation purposes and as a tool for fisheries management. The Arrábida Marine Park is the first MPA in continental Portugal having a management plan, fully implemented since 2009. The main objective of this study was to evaluate the effect of protection measures on rocky reef fish assemblages and target invertebrates through before-after and control-effect (no-take vs. fished areas) underwater visual surveys and analysis of landings trends. Second, we used surveys before, during and after implementation of the management plan to understand fishers‟ preferences for fishing grounds and adaptation to the new rules, and evaluated the reserve effect through analysis of both ecological responses and fishing effort density. Third, we identified the main oceanographic drivers influencing the structure of reef fish assemblages and predicted the community structure for the last 50 years, in light of climatic change. Overall results suggest positive responses in biomass but not yet in numbers of some commercial species, with no effects on non-target species. The reserve effect is reinforced by the increase in landings of commercial species, despite increased fishing effort density in some areas, especially with octopus traps. Fishing grounds are mainly chosen based on the distribution of target species and associated habitats, but distance to port, weather conditions and safety also influence fishers‟ choices. Moreover, different fisheries respond differently to the protection measures, and within each fishery, individual fishers show distinct strategies, with some operating in a broader area whereas others keep preferred territories. Our results also show that wind stress and temperature are the main oceanographic drivers for rocky reef fish assemblages, with tropicalization of assemblages and polewards movements of species over the last 50 years consistent with temperature trends. We believe this study provides significant lessons for marine conservation and management of coastal systems.

Electrical characterization of metal-oxide-polymer devices for non-volatile memory applications

The objective of this thesis is to study the properties of resistive switching effect based on bistable resistive memory which is fabricated in the form of Al2O3/polymer diodes and to contribute to the elucidation of resistive switching mechanisms. Resistive memories were characterized using a variety of electrical techniques, including current-voltage measurements, small-signal impedance, and electrical noise based techniques. All the measurements were carried out over a large temperature range. Fast voltage ramps were used to elucidate the dynamic response of the memory to rapid varying electric fields. The temperature dependence of the current provided insight into the role of trapped charges in resistive switching. The analysis of fast current fluctuations using electric noise techniques contributed to the elucidation of the kinetics involved in filament formation/rupture, the filament size and correspondent current capabilities. The results reported in this thesis provide insight into a number of issues namely: (i) The fundamental limitations on the speed of operation of a bi-layer resistive memory are the time and voltage dependences of the switch-on mechanism. (ii) The results explain the wide spread in switching times reported in the literature and the apparently anomalous behaviour of the high conductance state namely the disappearance of the negative differential resistance region at high voltage scan rates which is commonly attributed to a “dead time” phenomenon which had remained elusive since it was first reported in the ‘60s. (iii) Assuming that the current is filamentary, Comsol simulations were performed and used to explain the observed dynamic properties of the current-voltage characteristics. Furthermore, the simulations suggest that filaments can interact with each other. (iv) The current-voltage characteristics have been studied as a function of temperature. The findings indicate that creation and annihilation of filaments is controlled by filling and neutralizing traps localized at the oxide/polymer interface. (v) Resistive switching was also studied in small-molecule OLEDs. It was shown that the degradation that leads to a loss of light output during operation is caused by the presence of a resistive switching layer. A diagnostic tool that predicts premature failure of OLEDs was devised and proposed. Resistive switching is a property of oxides. These layers can grow in a number of devices including, organic light emitting diodes (OLEDs), spin-valve transistors and photovoltaic devices fabricated in different types of material. Under strong electric fields the oxides can undergo dielectric breakdown and become resistive switching layers. Resistive switching strongly modifies the charge injection causing a number of deleterious effects and eventually device failure. In this respect the findings in this thesis are relevant to understand reliability issues in devices across a very broad field.

The response of watercress (Nasturtium officinale) to vacuum impregnation: Effect of an antifreeze protein type I

The setting up of methodologies that reduce the size of ice crystals and reduce or inhibit the recrystalli- sation phenomena could have an extraordinary significance in the final quality of frozen products and consequently bring out new market opportunities. In this work, the effect of an antifreeze protein type I (AFP-I), by vacuum impregnation (VI), on frozen watercress was studied. The VI pressure, samples’ weight, Hunter Lab colour, scanning electron microscopy (SEM), and a wilting test were analysed in this work. The water intake of watercress samples augmented with vacuum pressure increase. The results also showed that, independently from the vacuum pressure used, the Lab colour parameters between raw and impregnated samples were maintained, showing no significant differences (P > 0.05). A VI of 58 kPa, during 5 min, allowed impregnating the AFP-I solution (0.01 mg ml-1) into the water- cress samples. The scanning electron microscopy (SEM) analysis showed the AFP-I impregnated frozen samples with better cell wall definition and rounded cell shape with smaller ice crystals compared with the control samples. The wilting test results corroborated that AFP-I is a valuable additive, since the leaves impregnated with AFP-I showed higher turgidity compared to the control samples. The present findings will help to better understand the effect of AFP-I, particularly, on frozen water- cress microstructure and its importance as valuable food additive in frozen foods and mainly in leafy vegetables.