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.

Emigrantes portugueses low cost: as perspetivas de ontem e de hoje

Dissertação de mestrado em Sociologia (área de especialização em Organizações e Trabalho)

Hierarchical modelling of timber reference properties using probabilistic methods: Maximum Likelihood Method, Bayesian Methods and Probability Networks

In recent decades, an increased interest has been evidenced in the research on multi-scale hierarchical modelling in the field of mechanics, and also in the field of wood products and timber engineering. One of the main motivations for hierar-chical modelling is to understand how properties, composition and structure at lower scale levels may influence and be used to predict the material properties on a macroscopic and structural engineering scale. This chapter presents the applicability of statistic and probabilistic methods, such as the Maximum Likelihood method and Bayesian methods, in the representation of timber’s mechanical properties and its inference accounting to prior information obtained in different importance scales. These methods allow to analyse distinct timber’s reference properties, such as density, bending stiffness and strength, and hierarchically consider information obtained through different non, semi or destructive tests. The basis and fundaments of the methods are described and also recommendations and limitations are discussed. The methods may be used in several contexts, however require an expert’s knowledge to assess the correct statistic fitting and define the correlation arrangement between properties.

Integration of geometric consistency contributory factors in three-leg junctions collision prediction models of Portuguese two-lane national highways

This paper aims at developing a collision prediction model for three-leg junctions located in national roads (NR) in Northern Portugal. The focus is to identify factors that contribute for collision type crashes in those locations, mainly factors related to road geometric consistency, since literature is scarce on those, and to research the impact of three modeling methods: generalized estimating equations, random-effects negative binomial models and random-parameters negative binomial models, on the factors of those models. The database used included data published between 2008 and 2010 of 177 three-leg junctions. It was split in three groups of contributing factors which were tested sequentially for each of the adopted models: at first only traffic, then, traffic and the geometric characteristics of the junctions within their area of influence; and, lastly, factors which show the difference between the geometric characteristics of the segments boarding the junctionsâ area of influence and the segment included in that area were added. The choice of the best modeling technique was supported by the result of a cross validation made to ascertain the best model for the three sets of researched contributing factors. The models fitted with random-parameters negative binomial models had the best performance in the process. In the best models obtained for every modeling technique, the characteristics of the road environment, including proxy measures for the geometric consistency, along with traffic volume, contribute significantly to the number of collisions. Both the variables concerning junctions and the various national highway segments in their area of influence, as well as variations from those characteristics concerning roadway segments which border the already mentioned area of influence have proven their relevance and, therefore, there is a rightful need to incorporate the effect of geometric consistency in the three-leg junctions safety studies.

A bayesian approach for NDT data fusion: The Saint Torcato Church case study

This paper presents a methodology based on the Bayesian data fusion techniques applied to non-destructive and destructive tests for the structural assessment of historical constructions. The aim of the methodology is to reduce the uncertainties of the parameter estimation. The Young's modulus of granite stones was chosen as an example for the present paper. The methodology considers several levels of uncertainty since the parameters of interest are considered random variables with random moments. A new concept of Trust Factor was introduced to affect the uncertainty related to each test results, translated by their standard deviation, depending on the higher or lower reliability of each test to predict a certain parameter.

A GIS extension model to calculate urban heat island intensity based on urban geometry

This paper presents a simulation model, which was incorporated into a Geographic Information System (GIS), in order to calculate the maximum intensity of urban heat islands based on urban geometry data. The method-ology of this study stands on a theoretical-numerical basis (Okeâ s model), followed by the study and selection of existing GIS tools, the design of the calculation model, the incorporation of the resulting algorithm into the GIS platform and the application of the tool, developed as exemplification. The developed tool will help researchers to simulate UHI in different urban scenarios.

Safety classification using GIS in decision-making process to define priority road interventions

Given the current economic situation of the Portuguese municipalities, it is necessary to identify the priority investments in order to achieve a more efficient financial management. The classification of the road network of the municipality according to the occurrence of traffic accidents is fundamental to set priorities for road interventions. This paper presents a model for road network classification based on traffic accidents integrated in a geographic information system. Its practical application was developed through a case study in the municipality of Barcelos. An equation was defined to obtain a road safety index through the combination of the following indicators: severity, property damage only and accident costs. In addition to the road network classification, the application of the model allows to analyze the spatial coverage of accidents in order to determine the centrality and dispersion of the locations with the highest incidence of road accidents. This analysis can be further refined according to the nature of the accidents namely in collision, runoff and pedestrian crashes.

A TV do Mundial

No último ano da primeira década do século XXI, quase a entrar na era da televisão digital, importa saber que modelo de TV existe em Portugal. A análise da programação informativa destinada a acompanhar o Campeonato do Mundo de Futebol 2010 ajudará, decerto, a encontrar respostas. Neste artigo, apresentamos um estudo que incidiu em formatos informativos sobre este grande evento mediático, emitidos nos canais generalistas e temáticos entre os dias 11 de Junho e 11 de Julho de 2010 (datas de arranque e fecho do Mundial de Futebol da África do Sul). Essa análise, que incidiu em 604 emissões, procurou conhecer as formas de integração do telespectador nas emissões televisivas e quem foi chamado aos estúdios televisivos para participar nos debates aí promovidos. Os dados apurados demonstram claramente que esta TV do Mundial continua pouco aberta à participação do público e circunscrita a um grupo restrito de convidados, a maior parte dos quais oriundos da classe jornalística. Não é possível falar-se numa terceira fase do audiovisual. A hiper-televisão pode esperar.

Earthwork optimization system for sustainable highway construction

In highway construction, earthworks refer to the tasks of excavation, transportation, spreading and compaction of geomaterial (e.g. soil, rockfill and soil-rockfill mixture). Whereas relying heavily on machinery and repetitive processes, these tasks are highly susceptible to optimization. In this context Artificial Intelligent techniques, such as Data Mining and modern optimization can be applied for earthworks. A survey of these applications shows that they focus on the optimization of specific objectives and/or construction phases being possible to identify the capabilities and limitations of the analyzed techniques. Thus, according to the pinpointed drawbacks of these techniques, this paper describes a novel intelligent earthwork optimization system, capable of integrating DM, modern optimization and GIS technologies in order to optimize the earthwork processes throughout all phases of design and construction work. This integration system allows significant savings in time, cost and gas emissions contributing for a more sustainable construction.

Exploring chemical conversions in metabolic networks by tracing atoms transitions

Dissertação de mestrado em Bioinformática