Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.

Validity of the Brazilian version of WHOQOL-BREF in depressed patients using Rasch modelling

OBJECTIVE: To assess the validity of the Brazilian version of the World Health Organization Quality of Life Instrument - Abbreviated version (WHOQOL-BREF) in adults with major depression, using Rasch modelling. METHODS: Study analyzing data from the baseline sample of the Longitudinal Investigation of Depression Outcomes in Brazil, including a total of 208 patients with major depression recruited in a primary care service in Porto Alegre (Southern Brazil), in 1999. The Center for Epidemiological Studies Depression Scale was used to assess intensity of depression; the WHOQOL-BREF to assess generic quality of life; and the Composite International Diagnostic Interview version 2.1 for the diagnosis of depression. RESULTS: In the Rasch analysis, the four domains of WHOQOL-BREF showed appropriate fit to this model. Some items needed adjustments: four items were rescored (pain, finances, services, and transport); two items (work and activity) were identified as having dependency of responses, and one item was deleted (sleep) due to multidimensionality. CONCLUSIONS: The validation of the WHOQOL-BREF Brazilian version using Rasch analysis complements previous validation studies, evidencing the robustness of this instrument as a generic cross-cultural quality of life measure.

Modelling and aerodynamic simulation of a vehicle and failure analysis of a laminated front fender

Master Thesis in Mechanical Engineering field of Maintenance and Production

Modelling and segmentation of the vocal tract during speech production by using deformable models in magnetic resonance images

The first and second authors would like to thank the support of the PhD grants with references SFRH/BD/28817/2006 and SFRH/PROTEC/49517/2009, respectively, from Fundação para a Ciência e Tecnol ogia (FCT). This work was partially done in the scope of the project “Methodologies to Analyze Organs from Complex Medical Images – Applications to Fema le Pelvic Cavity”, wi th reference PTDC/EEA- CRO/103320/2008, financially supported by FCT.

Removal of Cd(II), Zn(II) and Pb(II) from aqueous solutions by brown marine macro algae: kinetic modelling

Specific marine macro algae species abundant at the Portuguese coast (Laminaria hyperborea, Bifurcaria bifurcata, Sargassum muticum and Fucus spiralis) were shown to be effective for removing toxic metals (Cd(II), Zn(II) and Pb(II)) from aqueous solutions. The initial metal concentrations in solution were about 75–100 mg L−1. The observed biosorption capacities for cadmium, zinc and lead ions were in the ranges of 23.9–39.5, 18.6–32.0 and 32.3–50.4 mg g−1, respectively. Kinetic studies revealed that the metal uptake rate was rather fast, with 75% of the total amount occurring in the first 10 min for all algal species. Experimental data were well fitted by a pseudo-second order rate equation. The contribution of internal diffusion mechanism was significant only to the initial biosorption stage. Results indicate that all the studied macro algae species can provide an efficient and cost-effective technology for eliminating heavy metals from industrial effluents.

Feature selection for clustering categorical data with an embedded modelling approach

Research on the problem of feature selection for clustering continues to develop. This is a challenging task, mainly due to the absence of class labels to guide the search for relevant features. Categorical feature selection for clustering has rarely been addressed in the literature, with most of the proposed approaches having focused on numerical data. In this work, we propose an approach to simultaneously cluster categorical data and select a subset of relevant features. Our approach is based on a modification of a finite mixture model (of multinomial distributions), where a set of latent variables indicate the relevance of each feature. To estimate the model parameters, we implement a variant of the expectation-maximization algorithm that simultaneously selects the subset of relevant features, using a minimum message length criterion. The proposed approach compares favourably with two baseline methods: a filter based on an entropy measure and a wrapper based on mutual information. The results obtained on synthetic data illustrate the ability of the proposed expectation-maximization method to recover ground truth. An application to real data, referred to official statistics, shows its usefulness.

Modelling adhesive joints with cohesive zone models: effect of the cohesive law shape of the adhesive layer

Adhesively-bonded joints are extensively used in several fields of engineering. Cohesive Zone Models (CZM) have been used for the strength prediction of adhesive joints, as an add-in to Finite Element (FE) analyses that allows simulation of damage growth, by consideration of energetic principles. A useful feature of CZM is that different shapes can be developed for the cohesive laws, depending on the nature of the material or interface to be simulated, allowing an accurate strength prediction. This work studies the influence of the CZM shape (triangular, exponential or trapezoidal) used to model a thin adhesive layer in single-lap adhesive joints, for an estimation of its influence on the strength prediction under different material conditions. By performing this study, guidelines are provided on the possibility to use a CZM shape that may not be the most suited for a particular adhesive, but that may be more straightforward to use/implement and have less convergence problems (e.g. triangular shaped CZM), thus attaining the solution faster. The overall results showed that joints bonded with ductile adhesives are highly influenced by the CZM shape, and that the trapezoidal shape fits best the experimental data. Moreover, the smaller is the overlap length (LO), the greater is the influence of the CZM shape. On the other hand, the influence of the CZM shape can be neglected when using brittle adhesives, without compromising too much the accuracy of the strength predictions.

Modellus: Learning Physics with Mathematical Modelling

Tese de doutoramento em Ciências da Educação, área de Teoria Curricular e Ensino das Ciências

Fractional order modelling of zero length column desorption response for adsorbents with variable particle sizes

This manuscript analyses the data generated by a Zero Length Column (ZLC) diffusion experimental set-up, for 1,3 Di-isopropyl benzene in a 100% alumina matrix with variable particle size. The time evolution of the phenomena resembles those of fractional order systems, namely those with a fast initial transient followed by long and slow tails. The experimental measurements are best fitted with the Harris model revealing a power law behavior.

Fractional order modelling of fractional-order holds

Discrete time control systems require sample- and-hold circuits to perform the conversion from digital to analog. Fractional-Order Holds (FROHs) are an interpolation between the classical zero and first order holds and can be tuned to produce better system performance. However, the model of the FROH is somewhat hermetic and the design of the system becomes unnecessarily complicated. This paper addresses the modelling of the FROHs using the concepts of Fractional Calculus (FC). For this purpose, two simple fractional-order approximations are proposed whose parameters are estimated by a genetic algorithm. The results are simple to interpret, demonstrating that FC is a useful tool for the analysis of these devices.

Wind resource modelling in complex terrain using different mesoscale–microscale coupling techniques

Wind resource evaluation in two sites located in Portugal was performed using the mesoscale modelling system Weather Research and Forecasting (WRF) and the wind resource analysis tool commonly used within the wind power industry, the Wind Atlas Analysis and Application Program (WAsP) microscale model. Wind measurement campaigns were conducted in the selected sites, allowing for a comparison between in situ measurements and simulated wind, in terms of flow characteristics and energy yields estimates. Three different methodologies were tested, aiming to provide an overview of the benefits and limitations of these methodologies for wind resource estimation. In the first methodology the mesoscale model acts like “virtual” wind measuring stations, where wind data was computed by WRF for both sites and inserted directly as input in WAsP. In the second approach, the same procedure was followed but here the terrain influences induced by the mesoscale model low resolution terrain data were removed from the simulated wind data. In the third methodology, the simulated wind data is extracted at the top of the planetary boundary layer height for both sites, aiming to assess if the use of geostrophic winds (which, by definition, are not influenced by the local terrain) can bring any improvement in the models performance. The obtained results for the abovementioned methodologies were compared with those resulting from in situ measurements, in terms of mean wind speed, Weibull probability density function parameters and production estimates, considering the installation of one wind turbine in each site. Results showed that the second tested approach is the one that produces values closest to the measured ones, and fairly acceptable deviations were found using this coupling technique in terms of estimated annual production. However, mesoscale output should not be used directly in wind farm sitting projects, mainly due to the mesoscale model terrain data poor resolution. Instead, the use of mesoscale output in microscale models should be seen as a valid alternative to in situ data mainly for preliminary wind resource assessments, although the application of mesoscale and microscale coupling in areas with complex topography should be done with extreme caution.

A simple approach to numerical modelling of propane combustion in fluidized beds

A mathematical model is proposed for the evolution of temperature, chemical composition, and energy release in bubbles, clouds, and emulsion phase during combustion of gaseous premixtures of air and propane in a bubbling fluidized bed. The analysis begins as the bubbles are formed at the orifices of the distributor, until they explode inside the bed or emerge at the free surface of the bed. The model also considers the freeboard region of the fluidized bed until the propane is thoroughly burned. It is essentially built upon the quasi-global mechanism of Hautman et al. (1981) and the mass and heat transfer equations from the two-phase model of Davidson and Harrison (1963). The focus is not on a new modeling approach, but on combining the classical models of the kinetics and other diffusional aspects to obtain a better insight into the events occurring inside a fluidized bed reactor. Experimental data are obtained to validate the model by testing the combustion of commercial propane, in a laboratory-scale fluidized bed, using four sand particle sizes: 400–500, 315–400, 250–315, and 200–250 µm. The mole fractions of CO2, CO, and O2 in the flue gases and the temperature of the fluidized bed are measured and compared with the numerical results.

Fractional calculus: application in modelling and control

This contribution introduces the fractional calculus (FC) fundamental mathematical aspects and discuses some of their consequences. Based on the FC concepts, the chapter reviews the main approaches for implementing fractional operators and discusses the adoption of FC in control systems. Finally are presented some applications in the areas of modeling and control, namely fractional PID, heat diffusion systems, electromagnetism, fractional electrical impedances, evolutionary algorithms, robotics, and nonlinear system control.

Strength prediction of single- and double-lap joints by standard and extended finite element modelling

The structural integrity of multi-component structures is usually determined by the strength and durability of their unions. Adhesive bonding is often chosen over welding, riveting and bolting, due to the reduction of stress concentrations, reduced weight penalty and easy manufacturing, amongst other issues. In the past decades, the Finite Element Method (FEM) has been used for the simulation and strength prediction of bonded structures, by strength of materials or fracture mechanics-based criteria. Cohesive-zone models (CZMs) have already proved to be an effective tool in modelling damage growth, surpassing a few limitations of the aforementioned techniques. Despite this fact, they still suffer from the restriction of damage growth only at predefined growth paths. The eXtended Finite Element Method (XFEM) is a recent improvement of the FEM, developed to allow the growth of discontinuities within bulk solids along an arbitrary path, by enriching degrees of freedom with special displacement functions, thus overcoming the main restriction of CZMs. These two techniques were tested to simulate adhesively bonded single- and double-lap joints. The comparative evaluation of the two methods showed their capabilities and/or limitations for this specific purpose.

A theoretical study on modelling the respiratory tract with ladder networks by means of intrinsic fractal geometry

Fractional order modeling of biological systems has received significant interest in the research community. Since the fractal geometry is characterized by a recurrent structure, the self-similar branching arrangement of the airways makes the respiratory system an ideal candidate for the application of fractional calculus theory. To demonstrate the link between the recurrence of the respiratory tree and the appearance of a fractional-order model, we develop an anatomically consistent representation of the respiratory system. This model is capable of simulating the mechanical properties of the lungs and we compare the model output with in vivo measurements of the respiratory input impedance collected in 20 healthy subjects. This paper provides further proof of the underlying fractal geometry of the human lungs, and the consequent appearance of constant-phase behavior in the total respiratory impedance.