Metagenomic characterisation of the viral community of lough neagh, the largest freshwater lake in Ireland

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.

Integration of geochemical and biological modifications in mining areas: waters, sediments and diatoms

The development of mining activities over thousands of years in the region of Aljustrel is nowadays visible as a vast area of ore tailings, slag and host rocks of sulphides mineralization. The generation of acidic waters by the alteration of pyritic minerals - Acid Mine Drainage (AMD) - causes a significant impact on the river system both in the south of the village (Rib ª. Água Forte) and in the north of it (Rib ª. Água Azeda and Barranco do Farrobo), which is reflected in extremely low pH values (< 3) and high concentrations of As, Cd, Cu, Fe, Mn, Pb, Zn and sulphates. This study aimed to assess the environmental impacts extent, integrating geochemical (surface waters and stream sediments) and biological (diatoms) parameters. Three groups of sites were defined, based on sediments and water analysis, which integration with diatom data showed the same association of groups: Group 1- impacted, with acidic pH (1.9-5.1), high metal contents (0.4-1975 mg L-1) and Fe-Mg-sulphate waters, being metals more bioavailable in waters in cationic form (Me2+); mineralogically the sediments were characterized by phyllosilicates and sulphates/oxy-hydroxysulphate phases, easily solubilized, retaining a high amount of metals when precipitated; dominant taxon was Pinnularia aljustrelica (a new species); Group 2- slightly impacted, weak acid to neutral pH (5.0-6.8), metal contents not so high (0.2-25 mg L-1) and Fe-Mg-sulphate to Mg-chloride waters; dominant taxa were Brachysira neglectissima and Achnanthidium minutissimum; Group 3- unimpacted, alkaline pH (7.0-8.4), low metal contents (0-7 mg L-1) with Mg-chloride waters. In this group, metals were associated to the primary phases (e.g. sulphides), not so easily available; the existence of high chloride contents explained the presence of typical taxa of brackish/marine (e.g. Entomoneis paludosa) waters. Taxonomical aspects of the diatoms were studied (discovery of a new species: Pinnularia aljustrelica Luis, Almeida et Ector sp. nov.), as well as morphometric (size decrease of diatoms valves, as well as the appearance of deformed valves of Eunotia exigua in Group 1 and A. minutissimum in Group 2) and physiological (effective to assess the effects of metals/acidity in the photosynthetic efficiency through PAM Fluorometry) aspects. A study was carried out in an artificial river system (microcosm) that aimed to mimic Aljustrel’s extreme conditions in controlled laboratory conditions. The chronic effects of Fe, SO42- and acidity in field biofilms, inoculated in the artificial rivers, were evaluated as well as their contribution to the communities’ tolerance to metal toxicity, through acute tests with two metals (Cu and Zn). In general, the effects caused by low pH values and high concentrations of Fe and SO42- were reflected at the community level by the decrease in diversity, the predominance of acidophilic species, the decrease in photosynthetic efficiency and the increase of enzymatic (e.g. catalase, superoxide dismutase) and non-enzymatic activities (e.g. total glutathione and total phytochelatins). However, it was possible to verify that acidity performed a protective effect in the communities, upon Cu and Zn addition. A comparative study between Aljustrel mining area and New Brunswick mining area was carried out, both with similar mining and geological conditions, reflected in similar diatom communities in both mines, but in very different geographic and climatic areas.

Seamless integration of heterogeneous networks in multicast environments

Nowadays, communication environments are already characterized by a myriad of competing and complementary technologies that aim to provide an ubiquitous connectivity service. Next Generation Networks need to hide this heterogeneity by providing a new abstraction level, while simultaneously be aware of the underlying technologies to deliver richer service experiences to the end-user. Moreover, the increasing interest for group-based multimedia services followed by their ever growing resource demands and network dynamics, has been boosting the research towards more scalable and exible network control approaches. The work developed in this Thesis enables such abstraction and exploits the prevailing heterogeneity in favor of a context-aware network management and adaptation. In this scope, we introduce a novel hierarchical control framework with self-management capabilities that enables the concept of Abstract Multiparty Trees (AMTs) to ease the control of multiparty content distribution throughout heterogeneous networks. A thorough evaluation of the proposed multiparty transport control framework was performed in the scope of this Thesis, assessing its bene ts in terms of network selection, delivery tree recon guration and resource savings. Moreover, we developed an analytical study to highlight the scalability of the AMT concept as well as its exibility in large scale networks and group sizes. To prove the feasibility and easy deployment characteristic of the proposed control framework, we implemented a proof-of-concept demonstrator that comprehends the main control procedures conceptually introduced. Its outcomes highlight a good performance of the multiparty content distribution tree control, including its local and global recon guration. In order to endow the AMT concept with the ability to guarantee the best service experience by the end-user, we integrate in the control framework two additional QoE enhancement approaches. The rst employs the concept of Network Coding to improve the robustness of the multiparty content delivery, aiming at mitigating the impact of possible packet losses in the end-user service perception. The second approach relies on a machine learning scheme to autonomously determine at each node the expected QoE towards a certain destination. This knowledge is then used by di erent QoE-aware network management schemes that, jointly, maximize the overall users' QoE. The performance and scalability of the control procedures developed, aided by the context and QoE-aware mechanisms, show the advantages of the AMT concept and the proposed hierarchical control strategy for the multiparty content distribution with enhanced service experience. Moreover we also prove the feasibility of the solution in a practical environment, and provide future research directions that bene t the evolved control framework and make it commercially feasible.

Eliciting Security Requirements and Tracing them to Design: An Integration of Common Criteria, Heuristics, and UMLsec

Building secure systems is difficult for many reasons. This paper deals with two of the main challenges: (i) the lack of security expertise in development teams, and (ii) the inadequacy of existing methodologies to support developers who are not security experts. The security standard ISO 14508 (Common Criteria) together with secure design techniques such as UMLsec can provide the security expertise, knowledge, and guidelines that are needed. However, security expertise and guidelines are not stated explicitly in the Common Criteria. They are rather phrased in security domain terminology and difficult to understand for developers. This means that some general security and secure design expertise are required to fully take advantage of the Common Criteria and UMLsec. In addition, there is the problem of tracing security requirements and objectives into solution design,which is needed for proof of requirements fulfilment. This paper describes a security requirements engineering methodology called SecReq. SecReq combines three techniques: the Common Criteria, the heuristic requirements editorHeRA, andUMLsec. SecReqmakes systematic use of the security engineering knowledge contained in the Common Criteria and UMLsec, as well as security-related heuristics in the HeRA tool. The integrated SecReq method supports early detection of security-related issues (HeRA), their systematic refinement guided by the Common Criteria, and the ability to trace security requirements into UML design models. A feedback loop helps reusing experiencewithin SecReq and turns the approach into an iterative process for the secure system life-cycle, also in the presence of system evolution.

Brain responses and looking behavior during audiovisual speech integration in infants predict auditory speech comprehension in the second year of life

The use of visual cues during the processing of audiovisual (AV) speech is known to be less efficient in children and adults with language difficulties and difficulties are known to be more prevalent in children from low-income populations. In the present study, we followed an economically diverse group of thirty-seven infants longitudinally from 6–9 months to 14–16 months of age. We used eye-tracking to examine whether individual differences in visual attention during AV processing of speech in 6–9 month old infants, particularly when processing congruent and incongruent auditory and visual speech cues, might be indicative of their later language development. Twenty-two of these 6–9 month old infants also participated in an event-related potential (ERP) AV task within the same experimental session. Language development was then followed-up at the age of 14–16 months, using two measures of language development, the Preschool Language Scale and the Oxford Communicative Development Inventory. The results show that those infants who were less efficient in auditory speech processing at the age of 6–9 months had lower receptive language scores at 14–16 months. A correlational analysis revealed that the pattern of face scanning and ERP responses to audiovisually incongruent stimuli at 6–9 months were both significantly associated with language development at 14–16 months. These findings add to the understanding of individual differences in neural signatures of AV processing and associated looking behavior in infants.

Integration of numerical models in geographic databases: the case of Sado estuary management

Geographic information systems (GIS) are now widely applied in coastal resource management. Their ability to organise and interface information from a large range of public and private data sources, and their ability to combine this information, using management criteria, to develop a comprehensive picture of the system explains the success of GIS in this area. The use of numerical models as a tool to improve coastal management is also widespread. Less usual is a GIS-based management to ol implementing a comprehensive management model and integrating a numerical modelling system into itself. In this paper such a methodology is proposed. A GIS-based management tool based on the DPSIR model is presented. An overview of the MOHID numerical modelling system is given and the method of integrating this model in the management tool is described. This system is applied to the Sado Estuary (Portugal). Some preliminary results of the integration are presented, demonstrating the capabilities of the management system.

IP/optical integration in access network infrastructures: key issues on resource provisioning

This thesis contributes to the advancement of Fiber-Wireless (FiWi) access technologies, through the development of algorithms for resource allocation and energy efficient routing. FiWi access networks use both optical and wireless/cellular technologies to provide high bandwidth and ubiquity, required by users and current high demanding services. FiWi access technologies are divided in two parts. In one of the parts, fiber is brought from the central office to near the users, while in the other part wireless routers or base stations take over and provide Internet access to users. Many technologies can be used at both the optical and wireless parts, which lead to different integration and optimization problems to be solved. In this thesis, the focus will be on FiWi access networks that use a passive optical network at the optical section and a wireless mesh network at the wireless section. In such networks, two important aspects that influence network performance are: allocation of resources and traffic routing throughout the mesh section. In this thesis, both problems are addressed. A fair bandwidth allocation algorithm is developed, which provides fairness in terms of bandwidth and in terms of experienced delays among all users. As for routing, an energy efficient routing algorithm is proposed that optimizes sleeping and productive periods throughout the wireless and optical sections. To develop the stated algorithms, game theory and networks formation theory were used. These are powerful mathematical tools that can be used to solve problems involving agents with conflicting interests. Since, usually, these tools are not common knowledge, a brief survey on game theory and network formation theory is provided to explain the concepts that are used throughout the thesis. As such, this thesis also serves as a showcase on the use of game theory and network formation theory to develop new algorithms.

Integration von Nichtrationalität in die Praxis des Managements : ein zeitgemäßer unternehmensbezogener Erfolgsfaktor

Im Artikel wird Zunahme der Komplexität im Entscheidungsumfeld untersucht und auf zeitgemäße, auf Kreativität basierende Problemlösungsstrategien hingewiesen.

Integration der Klebflächenbehandlung in die Fertigung

In vielen Fällen muss vor dem Kleben eine Klebflächenbehandlung durchgeführt werden, da Klebverbindungen mit unvorbehandelten Teilen häufig zu geringe Klebfestigkeiten und/oder eine unzureichende Alterungsbeständigkeit aufweisen. Zur Klebflächenbehandlung stehen unterschiedliche Verfahren zur Verfügung. Wenn mit mehreren Behandlungen klebtechnisch einwandfreie Verbindungen hergestellt werden können, gilt es, das Verfahren zu ermitteln, welches am besten in den Fertigungsfluss integriert werden kann und die geringsten Kosten verursacht. Dabei muss auch die Arbeitssicherheit und der Umweltschutz mit beachtet werden. Zur Beurteilung der Verfahren werden Bewertungskriterien gegeben. Die Verfahren werden abschließend kurz charakterisiert.

Knowledge representation for data integration and exploration in translational medicine

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Environmental governance in China: weakness and potential from an environmental policy integration perspective

Interest in China’s capacity for environmental governance is growing, in line with its environmental woes and exponential economic growth. Environmental policy efforts have lacked effectiveness, confirming the persistence of a disjuncture between promise and performance. This article contributes to the debate through the analytical lens of Environmental Policy Integration (EPI): a normative concept and governance regime indispensable to sustainable development. It finds that China,like most OECD countries, falls short of the concept. Despite encouraging recent changes, driven by the Hu-Wen regime, and encapsulated in the idea of scientific development, the analysis reveals weaknesses in all three EPI-type responses: normative, organisational and procedural. The disjuncture is confirmed, but drawing on EPI’s normative perspective, it is suggested that the reasons for this lie as much in the framing of the promise, as in the performance, or implementation, itself. Based on this interpretation and on China’s unique extreme characteristics, it is recommended that environmental policy objectives be given principled priority status, as a condition for effective governance.

Miniaturization and Integration of Optoelectronics for Contact Lens Embedded Display and Wireless Communication

Thesis (Ph.D.)--University of Washington, 2013