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.

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.

Underwater acoustic modem with streaming video capabilities

Oceans have shown tremendous importance and impact on our lives. Thus the need for monitoring and protecting the oceans has grown exponentially in recent years. On the other hand, oceans have economical and industrial potential in areas such as pharmaceutical, oil, minerals and biodiversity. This demand is increasing and the need for high data rate and near real-time communications between submerged agents became of paramount importance. Among the needs for underwater communications, streaming video (e.g. for inspecting risers or hydrothermal vents) can be seen as the top challenge, which when solved will make all the other applications possible. Presently, the only reliable approach for underwater video streaming relies on wired connections or tethers (e.g. from ROVs to the surface) which presents severe operational constraints that makes acoustic links together with AUVs and sensor networks strongly appealing. Using new polymer-based acoustic transducers, which in very recent works have shown to have bandwidth and power efficiency much higher than the usual ceramics, this article proposes the development of a reprogrammable acoustic modem for operating in underwater communications with video streaming capabilities. The results have shown a maximum data-rate of 1Mbps with a simple modulation scheme such as OOK, at a distance of 20 m.

Optimization of magnetoelectric composites based on electroactive polymers for energy harvesting and sensor application

Tese de Doutoramento em Engenharia de Materiais.