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.

Primeiro registro de Phanoxyla hystrix (R. Felder, [1874]) (Lepidoptera, Sphingidae) para o estado de Rondônia, Brasil

Um macho de Phanoxyla hystrix (R. Felder, [1874]) foi coletado em Porto Velho, representando o primeiro registro para o estado de Rondônia, Brasil.

Acmella marajoensis G.A.R. Silva & J.U.M. Santos: uma nova espécie de Asteraceae para a Amazônia brasileira

Em decorrência dos estudos na subtribo Ecliptinae da Amazônia brasileira, é descrita uma nova espécie, Acmella marajoensis G.A.R. Silva & J.U.M. Santos. Até o presente momento, a espécie é considerada como endêmica da Ilha do Marajó. São apresentados diagnose em latim, descrição detalhada, comentários taxonômicos e ilustrações.

Organização e gestão da manutencão de ferramentas numa empresa de produção de peças metálicas

Dissertação de mestrado Engenharia e Gestão da Qualidade

Sistema reprodutivo e polinização de Lepidagathis sessilifolia (Pohl) Kameyama ex Wassh. & J.R.I. Wood (Acanthaceae), em remanescente florestal da região sudoeste de Mato Grosso, Brasil

O gênero Lepidagathis apresenta distribuição pantropical com cerca de 100 espécies. No Brasil ocorrem 16 espécies, a maioria nas regiões Centro - Oeste e Sudeste. O estudo foi realizado em sub - bosque de remanescente florestal do município de Tangará da Serra - MT e teve como objetivo analisar a fenologia de floração, descrever a morfologia e biologia floral, verificar os visitantes florais e avaliar o sistema e o sucesso reprodutivo por meio de polinizações manuais. Lepidagathis sessilifolia apresenta inflorescências espiciformes, terminais, com cálice de cor rósea vistosa e corola de coloração branco-rósea. A floração ficou restrita aos meses de março a abril, durante a estação chuvosa. A senescência floral ocorreu após 24 ou 48 horas. A viabilidade dos grãos de pólen foi elevada (92,5%). O único polinizador observado visitando as flores de L. sessilifolia foi a abelha Partamona nhambiquara (Apidae - Meliponini). O sistema reprodutivo misto da espécie é caracterizado pela formação de frutos por meio de agamospermia, autopolinização e polinização cruzada. Esse sistema reprodutivo flexível é vantajoso, pois, garante a manutenção da espécie na área de estudo mesmo na ausência de polinizadores.

Estudo e implementação de testes de software em desenvolvimento ágil

Dissertação de mestrado em Engenharia de Sistemas

Frameworks no desenvolvimento de software: o caso da Elevation da PRIMAVERA BSS

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Aplicação da metodologia ROC na avaliação de desempenho de índices de gravidade clínica em unidades de neonatologia de Portugal

Tese de Doutoramento em Engenharia Industrial e de Sistemas

Flexible gastrointestinal motility pressure sensors based on aluminum thin-film strain-gauge arrays

This paper reports on an innovative approach to measuring intraluminal pressure in the upper gastrointestinal (GI) tract, especially monitoring GI motility and peristaltic movements. The proposed approach relies on thin-film aluminum strain gauges deposited on top of a Kapton membrane, which in turn lies on top of an SU-8 diaphragm-like structure. This structure enables the Kapton membrane to bend when pressure is applied, thereby affecting the strain gauges and effectively changing their electrical resistance. The sensor, with an area of 3.4 mm2, is fabricated using photolithography and standard microfabrication techniques (wet etching). It features a linear response (R2 = 0.9987) and an overall sensitivity of 2.6 mV mmHg−1. Additionally, its topology allows a high integration capability. The strain gauges’ responses to pressure were studied and the fabrication process optimized to achieve high sensitivity, linearity, and reproducibility. The sequential acquisition of the different signals is carried out by a microcontroller, with a 10-bit ADC and a sample rate of 250 Hz. The pressure signals are then presented in a user-friendly interface, developed using the Integrated Development Environment software, QtCreator IDE, for better visualization by physicians.

Glazing daylighting performance and Trombe wall thermal performance of a modular façade system in four different Portuguese cities

This paper reports on a new façade system that uses passive solutions in the search for energy efficiency. The differentials are the versatility and flexibility of the modules, which are important advantages of the system. The thermal performance of Trombe walls and glazings and the daylighting performance of glazing were the key aspects analyzed in the results. Computational simulations were accomplished for the thermal performance of different arrangements of the modules with DesignBuilder software. The glazing daylighting performance was studied by means of Ecotect and Desktop Radiance programs and compared with the transmittance curves of glazings. Occupancy profile and internal gains were fixed according to the Portuguese reality for both studies. The main characteristics considered in this research were the use of two double glazings, four different climates in Portugal and one and two Trombe walls in the façade. The results show an important reduction in the energy consumption with the use of Trombe walls and double self-cleaning glazing in the façade, which also presented better daylighting performance.

From perfect strangers to research partners: a study of relationships, resource sharing and perceived benefits within R&D cooperation networks

Doctoral thesis in Marketing and Strategy.