O efeito da deposição salina nas características das escorrências rodoviárias em zonas costeiras

Tese de Doutoramento em Engenharia Civil.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Predicting SO2 pollution incidents by means of additive models with optimum variable selection

The aim of this paper is to predict time series of SO2 concentrations emitted by coal-fired power stations in order to estimate in advance emission episodes and analyze the influence of some meteorological variables in the prediction. An emission episode is said to occur when the series of bi-hourly means of SO2 is greater than a specific level. For coal-fired power stations it is essential to predict emission epi- sodes sufficiently in advance so appropriate preventive measures can be taken. We proposed a meth- odology to predict SO2 emission episodes based on using an additive model and an algorithm for variable selection. The methodology was applied to the estimation of SO2 emissions registered in sampling lo- cations near a coal-fired power station located in Northern Spain. The results obtained indicate a good performance of the model considering only two terms of the time series and that the inclusion of the meteorological variables in the model is not significant.

Transmission and progression to disease of Mycobacterium tuberculosis phylogenetic lineages in The Netherlands

The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference, Mycobacterium africanum showed significantly lower infectivity and clustering indices in the foreign-born population, while Mycobacterium bovis showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on M. tuberculosis control efforts.

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Introduction [to Contact force models for multibody dynamics]

"Series: Solid mechanics and its applications, vol. 226"

Pure elastic contact force models

"Series: Solid mechanics and its applications, vol. 226"

Dissipative contact force models

"Series: Solid mechanics and its applications, vol. 226"

Contact force models for multibody dynamics

"Series: Solid mechanics and its applications, vol. 226"

An evolutionary approach to the use of Petri net based models: from parallel controllers to HW/SW co-design

"A workshop within the 19th International Conference on Applications and Theory of Petri Nets - ICATPN’1998"

Real-Time models to predict the use of vasopressors in monitored patients

The needs of reducing human error has been growing in every field of study, and medicine is one of those. Through the implementation of technologies is possible to help in the decision making process of clinics, therefore to reduce the difficulties that are typically faced. This study focuses on easing some of those difficulties by presenting real-time data mining models capable of predicting if a monitored patient, typically admitted in intensive care, will need to take vasopressors. Data Mining models were induced using clinical variables such as vital signs, laboratory analysis, among others. The best model presented a sensitivity of 94.94%. With this model it is possible reducing the misuse of vasopressors acting as prevention. At same time it is offered a better care to patients by anticipating their treatment with vasopressors.

Electronic tongue: a versatile tool for mineral and fruit-flavored waters recognition

Natural mineral waters (still), effervescent natural mineral waters (sparkling) and aromatized waters with fruit-flavors (still or sparkling) are an emerging market. In this work, the capability of a potentiometric electronic tongue, comprised with lipid polymeric membranes, to quantitatively estimate routinely quality physicochemical parameters (pH and conductivity) as well as to qualitatively classify water samples according to the type of water was evaluated. The study showed that a linear discriminant model, based on 21 sensors selected by the simulated annealing algorithm, could correctly classify 100 % of the water samples (leave-one out cross-validation). This potential was further demonstrated by applying a repeated K-fold cross-validation (guaranteeing that at least 15 % of independent samples were only used for internal-validation) for which 96 % of correct classifications were attained. The satisfactory recognition performance of the E-tongue could be attributed to the pH, conductivity, sugars and organic acids contents of the studied waters, which turned out in significant differences of sweetness perception indexes and total acid flavor. Moreover, the E-tongue combined with multivariate linear regression models, based on sub-sets of sensors selected by the simulated annealing algorithm, could accurately estimate waters pH (25 sensors: R 2 equal to 0.99 and 0.97 for leave-one-out or repeated K-folds cross-validation) and conductivity (23 sensors: R 2 equal to 0.997 and 0.99 for leave-one-out or repeated K-folds cross-validation). So, the overall satisfactory results achieved, allow envisaging a potential future application of electronic tongue devices for bottled water analysis and classification.