Flow updating: fault-tolerant aggregation for dynamic networks

Documento submetido para revisão pelos pares. A publicar em Journal of Parallel and Distributed Computing. ISSN 0743-7315

Exploring chemical conversions in metabolic networks by tracing atoms transitions

Dissertação de mestrado em Bioinformática

Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Artificial neural networks in diagnosis of liver diseases

Liver diseases have severe patients’ consequences, being one of the main causes of premature death. These facts reveal the centrality of one`s daily habits, and how important it is the early diagnosis of these kind of illnesses, not only to the patients themselves, but also to the society in general. Therefore, this work will focus on the development of a diagnosis support system to these kind of maladies, built under a formal framework based on Logic Programming, in terms of its knowledge representation and reasoning procedures, complemented with an approach to computing grounded on Artificial Neural Networks.

Logic programming and artificial neural networks in breast cancer detection

About 90% of breast cancers do not cause or are capable of producing death if detected at an early stage and treated properly. Indeed, it is still not known a specific cause for the illness. It may be not only a beginning, but also a set of associations that will determine the onset of the disease. Undeniably, there are some factors that seem to be associated with the boosted risk of the malady. Pondering the present study, different breast cancer risk assessment models where considered. It is our intention to develop a hybrid decision support system under a formal framework based on Logic Programming for knowledge representation and reasoning, complemented with an approach to computing centered on Artificial Neural Networks, to evaluate the risk of developing breast cancer and the respective Degree-of-Confidence that one has on such a happening.

User expectations for media sharing practices in open display networks

Open Display Networks have the potential to allow many content creators to publish their media to an open-ended set of screen displays. However, this raises the issue of how to match that content to the right displays. In this study, we aim to understand how the perceived utility of particular media sharing scenarios is affected by three independent variables, more specifically: (a) the locativeness of the content being shared; (b) how personal that content is and (c) the scope in which it is being shared. To assess these effects, we composed a set of 24 media sharing scenarios embedded with different treatments of our three independent variables. We then asked 100 participants to express their perception of the relevance of those scenarios. The results suggest a clear preference for scenarios where content is both local and directly related to the person that is publishing it. This is in stark contrast to the types of content that are commonly found in public displays, and confirms the opportunity that open displays networks may represent a new media for self-expression. This novel understanding may inform the design of new publication paradigms that will enable people to share media across the display networks.

Portuguese publication in the aim of regional science: a study of articles published in RPER from 2003 to 2015

This paper is a study of the full content of articles published by RPER, the Portuguese Review of Regional Studies, from the time it was launched in 2003 until the first quarter of 2015. RPER is a journal edited by the Portuguese section of the European Regional Science Association, which was established in the first half of the 1980s. The Association (APDR) and the journal are the result of contributions by researchers and technicians from different scientific fields, including mainly Economics, Geography, Sociology, Engineering and Architecture. The main focus of these contributions is the socio-economic life of concrete sites, and the way this life is conditioned by resources and capabilities, the historical and cultural heritage and institutions. Content analysis was undertaken to identify the main subjects chosen during the total period under analysis, the nature of the articles published (theoretical or empirical) and the main analytical framework used. The analysis also covers sub-periods to investigate major trends found in terms of subjects chosen and analytical methods, questioning the rationale behind them. The paper concludes with a few notes regarding the social echo the research received and an identification of the main limitations of the research. In the first part of the article, we conduct a summary review of the genesis and evolution of Regional Science at international level to serve as a basis for the empirical approach developed.

A hybrid MAC Scheme to improve the transmission performance in body sensor networks

Wireless body sensor networks (WBSNs) constitute a key technology for closing the loop between patients and healthcare providers, as WBSNs provide sensing ability, as well as mobility and portability, essential characteristics for wide acceptance of wireless healthcare technology. However, one important and difficult aspect of WBSNs is to provide data transmissions with quality of service, among other factors due to the antennas being small size and placed close to the body. Such transmissions cannot be fully provided without the assumption of a MAC protocol that solves the problems of the medium sharing. A vast number of MAC protocols conceived for wireless networks are based on random or scheduled schemes. This paper studies firstly the suitability of two MAC protocols, one using CSMA and the other TDMA, to transmit directly to the base station the signals collected continuously from multiple sensor nodes placed on the human body. Tests in a real scenario show that the beaconed TDMA MAC protocol presents an average packet loss ratio lower than CSMA. However, the average packet loss ratio is above 1.0 %. To improve this performance, which is of vital importance in areas such as e-health and ambient assisted living, a hybrid TDMA/CSMA scheme is proposed and tested in a real scenario with two WBSNs and four sensor nodes per WBSN. An average packet loss ratio lower than 0.2 % was obtained with the hybrid scheme. To achieve this significant improvement, the hybrid scheme uses a lightweight algorithm to control dynamically the start of the superframes. Scalability and traffic rate variation tests show that this strategy allows approximately ten WBSNs operating simultaneously without significant performance degradation.

Concurrency detection on finish-to-start activity precedence networks

We explore the finish-to-start precedence relations of project activities used in scheduling problems. From these relations, we devise a method to identify groups of activities that could execute concurrently, i.e. activities in the same group can all execute in parallel. The method derives a new set of relations to describe the concurrency. Then, it is represented by an undirected graph and the maximal cliques problem identifies the groups. We provide a running example with a project from our previous studies in resource constrained project cost minimization together with an example application on the concurrency detection method: the evaluation of the resource stress.

Postcolonial co-ordinary literature and the Web 2.0/3.0: "Thinking Back" within transmediatic knowledge

Pedro Andrade destaca o papel que as literacias híbridas preenchem numa redefinição pós-colonial da Europa. Em sua opinião, as literacias híbridas constituem uma condição necessária para a desconstrução do discurso colonial e a posterior reconstrução de literacias e literaturas pós-coloniais. Como parte deste processo, o autor argumenta a necessidade de vários tipos de competências que enfatizem a leitura e escrita não apenas dentro de sua própria cultura, mas também nas culturas dos outros. A literacia digital desempenha um papel particularmente importante neste processo, o que nos permite enfatizar as multivocalidades desta alteridade, igualmente na interação entre diferentes tradições de literacia: Ocidental e Oriental, nacional e transnacional, verbal e mediática. Andrade exemplifica o conceito de literatura transmediática com uma série de projetos em que esteve envolvido, por exemplo a Web 3.0 Novel enquanto modalidade daquilo que ele nomeia "GeoNeoLogic Novel". Este género de novel experimental mistura a narrativa com a teoria e a recolha de dados no campo empírico, promovendo uma abordagem que se apresenta simultaneamente regional e global. Em suma, o autor sugere diversos conceitos em primeira mão que classifica de ‘origem Lusófona’, e que representam diversas estratégias pós-coloniais globais também visíveis na área social, política e cultural da Lusofonia: o ‘pensamento-réplica’ (thinking back); o 'conhecimento transmediático' (transmediatic knowledge); a ‘sociedade da escrita comum’ (common writing society); as ‘redes comuns de conflito/significado’ (common webs of conflict and meaning); a literatura co-ordinária (co-ordinary literature).

As imigrantes brasileiras no jornalismo impresso regional

O estudo sobre a representação das brasileiras nos media é revisto sob vários aspectos e nos diversos meios de comunicação. Alguns estudos aprofundam a imagem das imigrantes, enquanto outros se concentram nos meios (rádio, televisão e imprensa). Existe ainda uma linha de investigação que se centra nos estudos da recepção. Todavia, verificámos a escassez de um estudo específico sobre a representação deste grupo no jornalismo de proximidade. Esta comunicação tem por objectivo apresentar parte dos resultados sobre a representação dos imigrantes brasileiros nas notícias publicadas durante o ano de 2007 em dois jornais regionais (um português – Diário do Minho – e um italiano – L'Adige). A escolha de um jornal externo ao contexto português foi extremamente enriquecedora para identificar possíveis convergências no tratamento dos imigrantes brasileiros (homens e mulheres) em diferentes contextos sócioculturais. Além disso, tanto Portugal como Itália foram países de forte emigração, influenciando os processos migratórios de ambos. A investigação inicial mostrou uma acentuada assimetria de género, o que nos levou a aprofundar a análise sob este aspecto. Observámos que os jornais analisados, em relação ao tratamento informativo da imigrante brasileira, trabalham na mesma linha dos jornais de âmbito nacional e, mesmo que em escala inferior, continuam a representar estas mulheres com um baixo estatuto, associadas a temas e comportamentos socialmente conotados com a marginalidade. De salientar que as imigrantes brasileiras que têm visibilidade nas peças noticiosas dos dois jornais são geralmente conotadas com a prostituição, clandestinidade, crime e exploração.

Nonlinear behavior of gelatin networks reveals a hierarchical structure

We investigate the strain hardening behavior of various gelatin networks-namely physical gelatin gel, chemically cross-linked gelatin gel, and a hybrid gel made of a combination of the former two-under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillations shear protocols. Further, the internal structures of physical gelatin gels and chemically cross-linked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically cross-linked network whereas, in the physical gelatin gels, a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as the correlation length (ξ), the cross-sectional polymer chain radius (Rc) and the fractal dimension (df) of the gel networks. The fractal dimension df obtained from the SANS data of the physical and chemically cross-linked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized nonlinear elastic theory that has been used to fit the stress-strain curves. The chemical cross-linking that generates coils and aggregates hinders the free stretching of the triple helix bundles in the physical gels.

Quantifying, generating and mitigating radio interference in Low-Power Wireless Networks

Doctoral Programme in Telecommunication - MAP-tele

A cooperação transfronteiriça como oportunidade de desenvolvimento das regiões de fronteira. Da Raia Ibérica à euroregião Galiza-Norte de Portugal

Tese de Doutoramento em Geografia Humana.