Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Affordable prefabricated modular houses using cement and polymer based materials and advanced design tools

By taking advantage of the appropriate use of cement and polymer based materials and advanced computational tools, a pre-fabricated affordable house was built in a modular system. Modular system refers to the complete structure that is built-up by assembling pre-fabricated sandwich panels composed of steel fibre reinforced self-compacting concrete (SFRSCC) outer layers that are connected by innovative glass fibre reinforced polymer (GFRP) connectors, resulting in a panel with adequate structural, acoustic, and thermal insulation properties. The modular house was prepared for a typical family of six members, but its living area can be easily increased by assembling other pre-fabricated elements. The speed of construction and the cost of the constructive elements make these houses competitive when compared to traditional solutions. In this paper the relevant research subjacent to this project (LEGOUSE) is briefly described, as well as the construction process of the built real scale prototype.

Dispersion of fillers in viscoelastic polymer matrices using Eulerian-Lagrangian approaches

Understanding the behavior of c omplex composite materials using mixing procedures is fundamental in several industrial processes. For instance, polymer composites are usually manufactured using dispersion of fillers in polymer melt matrices. The success of the filler dispersion depends both on the complex flow patterns generated and on the polymer melt rheological behavior. Consequently, the availability of a numerical tool that allow to model both fluid and particle would be very useful to increase the process insight. Nowadays there ar e computational tools that allow modeling the behavior of filled systems, taking into account both the behavior of the fluid (Computational Rheology) and the particles (Discrete Element Method). One example is the DPMFoam solver of the OpenFOAM ® framework where the averaged volume fraction momentum and mass conservation equations are used to describe the fluid (continuous phase) rheology, and the Newton’s second law of motion is used to compute the particles (discrete phase) movement. In this work the refer red solver is extended to take into account the elasticity of the polymer melts for the continuous phase. The solver capabilities will be illustrated by studying the effect of the fluid rheology on the filler dispersion, taking into account different fluid types (generalized Newtonian or viscoelastic) and particles volume fraction and size. The results obtained are used to evaluate the relevance of considering the fluid complex rheology for the prediction of the composites morphology

An integrated model for simulation of construction phasing of arch concrete dams

Dissertação de mestrado integrado em Civil Engineering

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

Skin-derived cell-sheets as powerful tools to engineer skin analogues

Cell/cell-extracellular matrix (ECM) dynamic interactions appear to have a major role in regulating communication through soluble signaling, directing cell binding and activating substrates that participate in the highly organized wound healing process. Moreover, these interactions are also crucial for in vitro mimicking cutaneous physiology. Herein we explore cell sheet (CS) engineering to create cellular constructs formed by keratinocytes (hKC), fibroblasts (hDFB) and dermal microvascular endothelial cells (hDMEC), to target skin wound healing but also the in vitro recreation of relevant models. Taking advantage of temperature-responsive culture surfaces, which allow harvesting cultured cells as intact sheets along with the deposited native ECM, varied combinations of homotypic and heterotypic three-dimensional (3-D) CS-based constructs were developed. Constructs combining one CS of keratinocytes as an epidermis-like layer plus a vascularized dermis composed by hDFB and hDMECs were assembled as skin analogues for advancing in vitro testing. Simultaneously both hKC and hDMEC were shown to significantly contribute to the re-epithelialization of full-thickness mice skin wounds by promoting an early epithelial coverage, while hDMEC significantly lead to increased vessels density, incorporating the neovasculature. Thus, although determined by the cellular nature of the constructs, these outcomes demonstrated that CS engineering appear as an unique technology that open the possibility to create numerous combinations of 3D constructs to target defective wound healing as well as the construction of in vitro models to further mimic cutaneous functions crucial for drug screening and cosmetic testing assays.

Comparing standard and low-cost tools for gradient evaluation along potential cycling paths

Promoting the use of non-motorized modes of transport, such as cycling, is an important contribution to the improvement of mobility, accessibility and equity in cities. Cycling offers a fast and cheap transportation option for short distances, helping to lower pollutant emissions and contributing to a healthier way of life. In order to make the cycling mode more competitive in relation to motorized traffic, it is necessary to evaluate the potential of alternatives from the perspective of the physical effort. One way to do so consists of assessing the suitability of locations for implementing cycling infrastructures. In this work, four tools to determine the gradient along potential cycling paths are compared. Furthermore, an evaluation of the reliability of some low-cost tools to measure this parameter was conducted, by comparison with standard measurements using cartographic plans, on a field case study applied to the city of Braga, Portugal. These tools revealed a good level of accuracy for the planning stage, but proved to be less reliable for use in design.

Masonry macro-block analysis

The structural analysis involves the definition of the model and selection of the analysis type. The model should represent the stiffness, the mass and the loads of the structure. The structures can be represented using simplified models, such as the lumped mass models, and advanced models resorting the Finite Element Method (FEM) and Discrete Element Method (DEM). Depending on the characteristics of the structure, different types of analysis can be used such as limit analysis, linear and non-linear static analysis and linear and non-linear dynamic analysis. Unreinforced masonry structures present low tensile strength and the linear analyses seem to not be adequate for assessing their structural behaviour. On the other hand, the static and dynamic non-linear analyses are complex, since they involve large time computational requirements and advanced knowledge of the practitioner. The non-linear analysis requires advanced knowledge on the material properties, analysis tools and interpretation of results. The limit analysis with macro-blocks can be assumed as a more practical method in the estimation of maximum load capacity of structure. Furthermore, the limit analysis require a reduced number of parameters, which is an advantage for the assessment of ancient and historical masonry structures, due to the difficult in obtaining reliable data.

A novel approach for honey pollen profile assessment using an electronic tongue and chemometric tools

Nowadays the main honey producing countries require accurate labeling of honey before commercialization, including floral classification. Traditionally, this classification is made by melissopalynology analysis, an accurate but time-consuming task requiring laborious sample pre-treatment and high-skilled technicians. In this work the potential use of a potentiometric electronic tongue for pollinic assessment is evaluated, using monofloral and polyfloral honeys. The results showed that after splitting honeys according to color (white, amber and dark), the novel methodology enabled quantifying the relative percentage of the main pollens (Castanea sp., Echium sp., Erica sp., Eucaliptus sp., Lavandula sp., Prunus sp., Rubus sp. and Trifolium sp.). Multiple linear regression models were established for each type of pollen, based on the best sensors sub-sets selected using the simulated annealing algorithm. To minimize the overfitting risk, a repeated K-fold cross-validation procedure was implemented, ensuring that at least 10-20% of the honeys were used for internal validation. With this approach, a minimum average determination coefficient of 0.91 ± 0.15 was obtained. Also, the proposed technique enabled the correct classification of 92% and 100% of monofloral and polyfloral honeys, respectively. The quite satisfactory performance of the novel procedure for quantifying the relative pollen frequency may envisage its applicability for honey labeling and geographical origin identification. Nevertheless, this approach is not a full alternative to the traditional melissopalynologic analysis; it may be seen as a practical complementary tool for preliminary honey floral classification, leaving only problematic cases for pollinic evaluation.

Process simulation support in BPM tools: The case of BPMN

Due to the increasing acceptance of BPM, nowadays BPM tools are extensively used in organizations. Core to BPM are the process modeling languages, of which BPMN is the one that has been receiving most attention these days. Once a business process is described using BPMN, one can use a process simulation approach in order to find its optimized form. In this context, the simulation of business processes, such as those defined in BPMN, appears as an obvious way of improving processes. This paper analyzes the business process modeling and simulation areas, identifying the elements that must be present in the BPMN language in order to allow processes described in BPMN to be simulated. During this analysis a set of existing BPM tools, which support BPMN, are compared regarding their limitations in terms of simulation support.

Automated network resilience optimization using computational intelligence methods

This paper presents an automated optimization framework able to provide network administrators with resilient routing configurations for link-state protocols, such as OSPF or IS-IS. In order to deal with the formulated NP-hard optimization problems, the devised framework is underpinned by the use of computational in- telligence optimization engines, such as Multi-objective Evolutionary Algorithms (MOEAs). With the objective of demonstrating the framework capabilities, two il- lustrative Traffic Engineering methods are described, allowing to attain routing con- figurations robust to changes in the traffic demands and maintaining the network stable even in the presence of link failure events. The presented illustrative results clearly corroborate the usefulness of the proposed automated framework along with the devised optimization methods.

Implementation of integral viscoelastic constitutive models in OpenFOAM® computational library

This work reports the implementation and verification of a new so lver in OpenFOAM® open source computational library, able to cope with integral viscoelastic models based on the integral upper-convected Maxwell model. The code is verified through the comparison of its predictions with analytical solutions and numerical results obtained with the differential upper-convected Maxwell model