Social-aware opportunistic routing

The increased capabilities (e.g., processing, storage) of portable devices along with the constant need of users to retrieve and send information have introduced a new form of communication. Users can seamlessly exchange data by means of opportunistic contacts among them and this is what characterizes the opportunistic networks (OppNets). OppNets allow users to communicate even when an end-to-end path may not exist between them. Since 2007, there has been a trend to improve the exchange of data by considering social similarity metrics. Social relationships, shared interests, and popularity are examples of such metrics that have been employed successfully: as users interact based on relationships and interests, this information can be used to decide on the best next forwarders of information. This Thesis work combines the features of today's devices found in the regular urban environment with the current social-awareness trend in the context of opportunistic routing. To achieve this goal, this work was divided into di erent tasks that map to a set of speci c objectives, leading to the following contributions: i) an up-to-date opportunistic routing taxonomy; ii) a universal evaluation framework that aids in devising and testing new routing proposals; iii) three social-aware utility functions that consider the dynamic user behavior and can be easily incorporated to other routing proposals; iv) two opportunistic routing proposals based on the users' daily routines and on the content traversing the network and interest of users in such content; and v) a structure analysis of the social-based network formed based on the approaches devised in this work.

Molecular study of cell degeneration and evolution induced by mRNA mistranslation

As proteínas existentes nas células são produzidas pelo mecanismo de tradução do mRNA, no qual a informação genética contida nos genes é descodificada em cadeias polipeptídicas. O código genético, que define as regras de descodificação do genoma, minimiza os erros de tradução do mRNA, garantindo a síntese de proteínas com elevada fidelidade. Esta é essencial para a estabilidade do proteoma e para a manutenção e funcionamento dos processos celulares. Em condições fisiológicas normais, os erros da tradução do mRNA ocorrem com frequências que variam de 10-3 a 10-5 erros por codão descodificado. Situações que aumentam este erro basal geralmente estão associadas ao envelhecimento, stresse e a doenças; no entanto, em certos organismos o código genético é traduzido naturalmente com elevado erro, indicando que a síntese de proteínas aberrantes pode de algum modo ser vantajosa. A fim de estudar a resposta celular aos erros de tradução do mRNA, construímos leveduras que incorporam serina no proteoma em resposta a um codão de leucina, usando a expressão constitutiva de um tRNASer mutante. Este fenómeno genético artificial provocou uma forte diminuição da esporulação, da viabilidade e da eficiência de mating, afectando imensamente a reprodução sexual da levedura. Observou-se também uma grande heterogeneidade no tamanho e na forma das células e elevada instabilidade genómica, com o aparecimento de populações poliplóides e aneuplóides. No sentido de clarificar as bases celulares e moleculares daqueles fenótipos e compreender melhor a biologia do erro de tradução do mRNA, construímos também células de levedura que inserem serina em resposta a um codão de leucina de modo indutível e controlado. Utilizaram-se perfis de mRNA total e de mRNA associado a polissomas para elucidar a resposta celular ao erro de tradução do mRNA. Observou-se a indução de genes envolvidos na resposta ao stresse geral, stresse oxidativo e na unfolded protein response (UPR). Um aumento significativo de espécies reactivas de oxigénio (ROS) e um forte impacto negativo na capacidade das células pós-mitóticas re-iniciarem o crescimento foram também observados. Este fenótipo de perda de viabilidade celular foi resgatado por scavangers de ROS, indicando que o stresse oxidativo é a principal causa de morte celular causada pelos erros de tradução. Este estudo levanta a hipótese de que o stresse oxidativo e a acumulação de ROS, ao invés do colapso súbito do proteoma, são as principais causas da degeneração celular e das doenças humanas associadas aos erros de tradução do genoma. ABSTRACT: Proteins are synthesized through the mechanism of translation, which uses the genetic code to transform the nucleic acids based information of the genome into the amino acids based information of the proteome. The genetic code evolved in such a manner that translational errors are kept to a minimum and even when they occur their impact is minimized by similar chemical properties of the amino acids. Protein synthesis fidelity is essential for proteome stability and for functional maintenance of cellular processes. Indeed, under normal physiological conditions, mistranslation occurs at frequencies that range from 10-3 to 10-5 errors per codon decoded. Situations where this basal error frequency increases are usually associated to aging and disease. However, there are some organisms where genetic code errors occur naturally at high level, suggesting that mRNA mistranslation can somehow be beneficial. In order to study the cellular response to mRNA mistranslation, we have engineered single codon mistranslation in yeast cells, using constitutive expression of mutant tRNASer genes. These mistranslating strains inserted serines at leucine-CUG sites on a proteome wide scale due to competition between the wild type tRNALeu with the mutant tRNASer. Such mistranslation event decreased yeast sporulation, viability and mating efficiencies sharply and affected sexual reproduction strongly. High heterogeneity in cell size and shape and high instability in the genome were also observed, with the appearance of some polyploid or aneuploid cell populations. To further study the cellular and molecular basis of those phenotypes and the biology of mRNA mistranslation, we have also engineered inducible mRNA misreading in yeast and used total mRNA and polysome associated mRNA profiling to determine whether codon misreading affects gene expression. Induced mistranslation up-regulated genes involved in the general stress response, oxidative stress and in the unfolded protein response (UPR). A significant increase in reactive oxygen species (ROS) and a strong negative impact on the capacity of post-mitotic cells to re-initiate growth in fresh media were also observed. This cell viability phenotype was rescued by scavengers of ROS, indicating that oxidative stress is the main cause of cell death caused by mRNA mistranslation. This study provides strong support for the hypothesis that oxidative stress and ROS accumulation, rather than sudden proteome collapse or major proteome disruption, are the main cause of the cellular degeneration observed in human diseases associated mRNA mistranslation.

A alimentação suplementar de aves necrófagas em comedouros

A alimentação artificial de aves necrófagas tem sido alvo de atenção e as suas vantagens e desvantagens ainda são discutidas. A habituação por parte dos abutres e a atracção de espécies oportunistas são vistas como um problema. Foi disponibilizado alimento em quatro comedouros durante três anos, de 2010 a 2012. Registaram-se todas as aves observadas nos comedouros, anotando-se a espécie, o número de indivíduos e o comportamento alimentar e/ou não alimentar a cada 5 minutos. Também foi monitorizado o número de casais e o sucesso reprodutor do Grifo e do Abutre do Egipto. Notou-se uma aparente relação positiva entre estas duas espécies. A frequência de alimentação e o número de indivíduos das duas espécies aumentou gradualmente ao longo dos três anos, enquanto os tempos de detecção e alimentação diminuíram. Uma tendência oposta foi obtida para espécies oportunistas como o Milhafre-preto e o Milhafre-real. Não foi possível concluir sobre o efeito da alimentação artificial na produtividade mas pode existir uma relação da frequência de alimentação com a fase da época de reprodução na qual as crias são um factor determinante. O máximo da frequência de alimentação e o mínimo geral de tempos coincidem com as primeiras semanas das crias, para o Abutre do Egipto, e com a fase de maior requerimento destas, para o Grifo. A evolução destes parâmetros pode definir habituação. Os nossos resultados mostram que esta habituação tornou a alimentação artificial mais eficaz, com pouca quantidade de alimento, maioritariamente obtido pelo Abutre do Egipto e pelo Grifo com menor presença de espécies oportunistas. As espécies que se alimentam nos comedouros apresentam diferentes estratégias na obtenção do alimento, contornando a monopolização apresentada pelo Grifo. Desta forma o Abutre do Egipto parece estar a conseguir tirar proveito do alimento que lhe é dirigido. A disponibilização de alimento regular em poucas quantidades, nas primeiras horas de luz do dia, alternando o local onde o alimento é colocado, podem ser estratégias acertadas na alimentação suplementar dirigida ao Abutre do Egipto e ao Grifo.

Design and performance of wireless cooperative relaying

In recent years, a new paradigm for communication called cooperative communications has been proposed for which initial information theoretic studies have shown the potential for improvements in capacity over traditional multi-hop wireless networks. Extensive research has been done to mitigate the impact of fading in wireless networks, being mostly focused on Multiple-Input Multiple-Output (MIMO) systems. Recently, cooperative relaying techniques have been investigated to increase the performance of wireless systems by using diversity created by different single antenna devices, aiming to reach the same level of performance of MIMO systems with low cost devices. Cooperative communication is a promising method to achieve high spectrum efficiency and improve transmission capacity for wireless networks. Cooperative communications is the general idea of pooling the resources of distributed nodes to improve the overall performance of a wireless network. In cooperative networks the nodes cooperate to help each other. A cooperative node offering help is acting like a middle man or proxy and can convey messages from source to destination. Cooperative communication involves exploiting the broadcast nature of the wireless medium to form virtual antenna arrays out of independent singleantenna network nodes for transmission. This research aims at contributing to the field of cooperative wireless networks. The focus of this research is on the relay-based Medium Access Control (MAC) protocol. Specifically, I provide a framework for cooperative relaying called RelaySpot which comprises on opportunistic relay selection, cooperative relay scheduling and relay switching. RelaySpot-based solutions are expected to minimize signaling exchange, remove estimation of channel conditions, and improve the utilization of spatial diversity, minimizing outage and increasing reliability.

Interactions of cetaceans with Spanish and Portuguese fisheries in Atlantic waters : costs, benefits and implications for management

With the aim to provide new insights into operational cetacean-fishery interactions in Atlantic waters, this thesis assesses interactions of cetaceans with Spanish and Portuguese fishing vessels operating in Iberian and South West Atlantic waters. Different opportunistic research methodologies were applied, including an interview survey with fishers (mainly skippers) and onboard observations by fisheries observers and skippers, to describe different types of interactions and to identify potential hotspots for cetacean-fishery interactions and the cetacean species most involved, and to quantify the extent and the consequences of these interactions in terms of benefits and costs for cetaceans and fisheries. In addition, the suitability of different mitigation strategies was evaluated and discussed. The results of this work indicate that cetaceans interact frequently with Spanish and Portuguese fishing vessels, sometimes in a beneficial way (e.g. cetaceans indicate fish schools in purse seine fisheries), but mostly with negative consequences (depredation on catch, gear damage and cetacean bycatch). Significant economic loss and high bycatch rates are, however, only reported for certain fisheries and associated with particular cetacean species. In Galician fisheries, substantial economic loss was reported as a result of bottlenose dolphins damaging artisanal coastal gillnets, while high catch loss may arise from common dolphins scattering fish in purse seine fisheries. High cetacean bycatch mortality arises in trawl fisheries, mainly of common dolphin and particularly during trawling in water depths below 350 m, and in coastal set gillnet fisheries (mainly common and bottlenose dolphins). In large-scale bottom-set longline fisheries in South West Atlantic waters, sperm whales may significantly reduce catch rates through depredation on catch. The high diversity of cetacean-fishery interactions observed in the study area indicates that case-specific management strategies are needed to reduce negative impacts on fisheries and cetaceans. Acoustic deterrent devices (pingers) may be used to prevent small cetaceans from approaching and getting entangled in purse seines and set gillnets, although possible problems include cetacean habituation to the pinger sounds, as well as negative side effects on non-target cetaceans (habitat exclusion) and fisheries target species (reduced catch rates). For sardine and horse mackerel, target species of Iberian Atlantic fisheries, no aversive reaction to pinger sounds was detected during tank experiments conducted in the scope of this thesis. Bycatch in trawls may be reduced by the implementation of time/area restrictions of fishing activity. In addition, the avoidance of fishing areas with high cetacean abundance combined with the minimization of fishery-specific sound cues that possibly attract cetaceans, may also help to decrease interactions. In large-scale bottom-set longline fisheries, cetacean depredation on catch may be reduced by covering hooked fish with net sleeves ("umbrellas") provided that catch rates are not negatively affected by this gear modification. Trap fishing, as an alternative fishing method to bottom-set gillnetting and longlining, also has the potential to reduce cetacean bycatch and depredation, given that fish catch rates are similar to the rates obtained by bottom-set gillnets and longlines, whereas cetacean by-catch is unlikely. Economic incentives, such as the eco-certification of dolphin-safe fishing methods, should be promoted in order to create an additional source of income for fishers negatively affected by interactions with cetaceans, which, in turn, may also increase fishers’ willingness to accept and adopt mitigation measures. Although the opportunistic sampling methods applied in this work have certain restrictions concerning their reliability and precision, the results are consistent with previous studies in the same area. Moreover, they allow for the active participation of fishers that can provide important complementary ecological and technical knowledge required for cetacean management and conservation.

Biology, ecology, population dynamics and distribution of metals in Sepia officinalis on a typical estuarine coastal lagoon - Ria de Aveiro

The common cuttlefish, Sepia officinalis, is a necto-benthic cephalopod that can live in coastal ecosystems, with high influence of anthropogenic pressures and thus be vulnerable to exposure to various types of contaminants. The cuttlefish is a species of great importance to the local economy of Aveiro, considering the global data of catches of this species in the Ria de Aveiro. However, studies on this species in Ria de Aveiro are scarce, so the present study aims to fill this information gap about the cuttlefish in the Ria de Aveiro. The cuttlefish enters Ria de Aveiro in the spring and summer to reproduce, returning to deeper waters in the winter. In terms of abundance, the eastern and center regions of the lagoon, closer to the sea, showed the highest values of abundance, while the northern and southern regions of the main channel had the lowest abundance. This fact may be related to abiotic factors, as well as depth, salinity and temperature. In the most southern point of the Ria de Aveiro (Areão) no cuttlefish was caught. This site had the lowest values of salinity and depth. The cuttlefish has an allometric the females being heavier than males to mantle lengths greater than 82.4 mm. Males reach sexual maturity first than females. In Ria de Aveiro in a generation of parents was found. The cuttlefish, presents itself as opportunistic predators, consuming a wide variety of prey from different taxa. The diet was similar in different sampling locations observing significant differences for the seasons. S. officinalis was captured at 10 sites in the Ria de Aveiro with different anthropogenic sources of contamination. Thus, levels of metals analyzed were similar at all sampling sites, with the exception of a restricted area, Laranjo, which showed higher values. The cuttlefish has the ability to accumulate metals in your body. The levels of Fe, Zn, Cu, Cd, Pb and Hg found in the digestive gland and mantle reflect a differential accumulation of metals in the tissues. This accumulation is related to the type and function of tissue analyzed and the type of metal analysis (essential and non-essential). The metal concentrations in the digestive gland are higher than in the mantle, with the exception of mercury. This may be due to the high affinity of the mantle for the incorporation of methylmercury (MeHg), the most abundant form of mercury. The accumulation of metals can vary over a lifetime, depending on the metal. The concentrations of Zn, Cd and Hg increases throughout life, while Pb decreases and essential metals such as Fe and Cu remain constant. The data collected suggest that the cuttlefish (Sepia officinalis) can be used as a bioindicator of environmental contamination for some metals.