Surface plasmon resonance as a tool in the functional analisys of an immunodominant site in foot-and-mouth disease virus

A fast and direct surface plasmon resonance (SPR) method for the kinetic analysis of the interactions between peptide antigens and immobilised monoclonal antibodies (mAb) has been established. Protocols have been developed to overcome the problems posed by the small size of the analytes (< 1600 Da). The interactions were well described by a simple 1:1 bimolecular interaction and the rate constants were self-consistent and reproducible. The key features for the accuracy of the kinetic constants measured were high buffer flow rates, medium antibody surface densities and high peptide concentrations. The method was applied to an extensive analysis of over 40 peptide analogues towards two distinct anti-FMDV antibodies, providing data in total agreement with previous competition ELISA experiments. Eleven linear 15-residue synthetic peptides, reproducing all possible combinations of the four replacements found in foot-and-mouth disease virus (FMDV) field isolate C-S30, were evaluated. The direct kinetic SPR analysis of the interactions between these peptides and three anti-site A mAbs suggested additivity in all combinations of the four relevant mutations, which was confirmed by parallel ELISA analysis. The four-point mutant peptide (A15S30) reproducing site A from the C-S30 strain was the least antigenic of the set, in disagreement with previously reported studies with the virus isolate. Increasing peptide size from 15 to 21 residues did not significantly improve antigenicity. Overnight incubation of A15S30 with mAb 4C4 in solution showed a marked increase in peptide antigenicity not observed for other peptide analogues, suggesting that conformational rearrangement could lead to a stable peptide-antibody complex. In fact, peptide cyclization clearly improved antigenicity, confirming an antigenic reversion in a multiply substituted peptide. Solution NMR studies of both linear and cyclic versions of the antigenic loop of FMDV C-S30 showed that structural features previously correlated with antigenicity were more pronounced in the cyclic peptide. Twenty-six synthetic peptides, corresponding to all possible combinations of five single-point antigenicity-enhancing replacements in the GH loop of FMDV C-S8c1, were also studied. SPR kinetic screening of these peptides was not possible due to problems mainly related to the high mAb affinities displayed by these synthetic antigens. Solution affinity SPR analysis was employed and affinities displayed were generally comparable to or even higher than those corresponding to the C-S8c1 reference peptide A15. The NMR characterisation of one of these multiple mutants in solution showed that it had a conformational behaviour quite similar to that of the native sequence A15 and the X-ray diffraction crystallographic analysis of the peptide ? mAb 4C4 complex showed paratope ? epitope interactions identical to all FMDV peptide ? mAb complexes studied so far. Key residues for these interactions are those directly involved in epitope ? paratope contacts (141Arg, 143Asp, 146His) as well as residues able to stabilise a particular peptide global folding. A quasi-cyclic conformation is held up by a hydrophobic cavity defined by residues 138, 144 and 147 and by other key intrapeptide hydrogen bonds, delineating an open turn at positions 141, 142 and 143 (corresponding to the Arg-Gly-Asp motif).

Concepção de uma pequena turbina eólica destinada ao segmento doméstico (simplificação e análise aerodinâmica das pás)

O trabalho que se apresenta incide sobre o estudo aerodinâmico das pás de uma turbina eólica de pequeno porte, com vista à simplificação geométrica, de forma a que estas sejam baratas e de fácil concepção. A teoria da quantidade de movimento do elemento de pá (BEMT), que é o modelo de referência para o projecto e análise aerodinâmica das pás das turbinas eólicas, foi utilizada neste trabalho de forma a projectar e analisar aerodinamicamente as pás da turbina. Sendo assim, desenvolveu-se um programa computacional em MATLAB, denominado de “Turbina”, de forma a implementar a teoria BEM. Introduzindo os dados dos parâmetros de projecto no programa (potência requerida, o número de pás, velocidade do vento, a TSR e o tipo de perfil alar), obtêm-se os parâmetros geométricos das pás (distribuição da corda ao longo da envergadura, o raio da pá e a distribuição da torção da pá), os parâmetros aerodinâmicos e de desempenho. Uma pá ideal foi calculada e de seguida foi modificada de forma a obter-se uma pá simples e menos carregada aerodinamicamente. Introduzidas as modificações na geometria da pá ideal, obtiveram-se duas configurações distintas. Uma configuração linear, onde a distribuição da corda e do ângulo de torção se tornam lineares, e outra configuração bi-linear, onde a distribuição da corda continua linear mas o ângulo de torção se torna bi-linear, isto é, a pá é composta por dois troços onde cada troço apresenta uma distribuição linear do ângulo de torção geométrica. As conclusões demonstram que a configuração bi-linear é uma boa alternativa a configuração ideal, apresentando uma redução do desempenho do rotor de 2.8% para um aumento do raio da pá em 1.41%, para se obter a mesma potência da configuração ideal. A análise aos perfis alares, utilizados neste trabalho, foi efectuada a partir dos programas comerciais ICEM e FLUENT. De forma a automatizar a análise de CFD, três programas foram desenvolvidos utilizando a linguagem de programação “C”. Os programas são denominados de “Malha2D”, “Calcula_Coeficientes” e “Plot_Graficos”. Finalmente, um estudo paramétrico foi feito de forma a avaliar a influências das variáveis de projecto no desempenho geral da turbina.

A distributed system for learning programming on-line

Several Web-based on-line judges or on-line programming trainers have been developed in order to allow students to train their programming skills. However, their pedagogical functionalities in the learning of programming have not been clearly defined. EduJudge is a project which aims to integrate the “UVA On-line Judge”, an existing on-line programming trainer with an important number of problems and users, into an effective educational environment consisting of the e-learning platform Moodle and the competitive learning tool QUESTOURnament. The result is the EduJudge system which allows teachers to apply different pedagogical approaches using a proven e-learning platform, makes problems easy to search through an effective search engine, and provides an automated evaluation of the solutions submitted to these problems. The final objective is to provide new learning strategies to motivate students and present programming as an easy and attractive challenge. EduJudge has been tried and tested in three algorithms and programming courses in three different Engineering degrees. The students’ motivation and satisfaction levels were analysed alongside the effects of the EduJudge system on students’ academic outcomes. Results indicate that both students and teachers found that among other multiple benefits the EduJudge system facilitates the learning process. Furthermore, the experi- ment also showed an improvement in students’ academic outcomes. It must be noted that the students’ level of satisfaction did not depend on their computer skills or their gender.

Social capital, social participation and life satisfaction among Chilean older adults

OBJECTIVE To examine factors associated with social participation and their relationship with self-perceived well-being in older adults. METHODS This study was based on data obtained from the National Socioeconomic Characterization (CASEN) Survey conducted in Chile, in 2011, on a probability sample of households. We examined information of 31,428 older adults living in these households. Descriptive and explanatory analyses were performed using linear and multivariate logistic regression models. We assessed the respondents’ participation in different types of associations: egotropic, sociotropic, and religious. RESULTS Social participation increased with advancing age and then declined after the age of 80. The main finding of this study was that family social capital is a major determinant of social participation of older adults. Their involvement was associated with high levels of self-perceived subjective well-being. We identified four settings as sources of social participation: home-based; rural community-based; social policy programs; and religious. Older adults were significantly more likely to participate when other members of the household were also involved in social activities evidencing an intergenerational transmission of social participation. Rural communities, especially territorial associations, were the most favorable setting for participation. There has been a steady increase in the rates of involvement of older adults in social groups in Chile, especially after retirement. Religiosity remains a major determinant of associativism. The proportion of participation was higher among older women than men but these proportions equaled after the age of 80. CONCLUSIONS Self-perceived subjective well-being is not only dependent upon objective factors such as health and income, but is also dependent upon active participation in social life, measured as participation in associations, though its effects are moderate.

Tetranuclear COPPER(II) complexes with macrocyclic and open-chain disiloxane ligands as catalyst precursors for hydrocarboxylation and oxidation of alkanes and 1-phenylethanol

Two new tetranuclear complexes [Cu-4(mu-O)(L-1)-Cl-4] and [Cu-4(mu(4)-O)(L-2)(2)Cl-4] (2), where H2L1 is a macrocyclic ligand resulting from [2+2] condensation of 2,6-diformy1-4-methylphanol (DFF) and 1,3-bis(aminopropy1)tetramethyldisiloxane, and HL2 is a 1:2 condensation product: of DFF with trimethylsilyl p-aminobenzoate, have been prepared. The structures of the products were established by Xray diffraction. The complexes have been characterised by FTIR, UV/Vis spectroscopy, ES1 mass-spectrometry and magnetic susceptibility measurements. The latter revealed that the letrftriuclear complexes can be descr bed as two ferromagnetically coupled dinuclear units, in which the two copper(II) ions interact antiferromacinetically. The ccimpi.iunds act as homogeneous catalyst precursors for a number of single-pot reactions, including (I) hydrocarbaxylation, with CO, H2O and K2S2O8, of a variety of linear and cyclic (n = 5-8) alkanes into the corresponding Cn+1 carboxylic acids, (ii) peroxidative oxidation of cyclohexane, and (iii) solvent-free microwave-assisted oxidation of 1-phenyletha.nol.

Trits(Pyrazol-1-YL)methane metal complexes for catalytic mild oxidative functionalizations of alkanes, alkanes and ketones

This work concerns recent advances (since 2005) in the oxidative functionalization of alkanes, alkenes and ketones, under mild conditions, catalyzed by homoscorpionate tris(pyrazol-1-yl)methane metal complexes. The main types of such homogeneous or supported catalysts are classified, and the critical analysis of the most efficient catalytic systems in the different reactions is presented. These reactions include the mild oxidation of alkanes (typically cyclohexane as a model substrate) with hydrogen peroxide (into alkyl hydroperoxides, alcohols, and ketones), the hydrocarboxylation of gaseous alkanes (with carbon monoxide and potassium peroxodisulfate) into the corresponding Cn+1 carboxylic acids, as well as the epoxidation of alkenes and the Baeyer-Villiger oxidation of linear and cyclic ketones with hydrogen peroxide into the corresponding esters and lactones. Effects of various reaction parameters are highlighted and the preferable requirements for a prospective homogeneous or supported C-scorpionate-M-based catalyst in oxidative transformations of those substrates are identified. (C) 2014 Elsevier B.V. All rights reserved.

Visual programming of XSLT from examples

Vishnu is a tool for XSLT visual programming in Eclipse - a popular and extensible integrated development environment. Rather than writing the XSLT transformations, the programmer loads or edits two document instances, a source document and its corresponding target document, and pairs texts between then by drawing lines over the documents. This form of XSLT programming is intended for simple transformations between related document types, such as HTML formatting or conversion among similar formats. Complex XSLT programs involving, for instance, recursive templates or second order transformations are out of the scope of Vishnu. We present the architecture of Vishnu composed by a graphical editor and a programming engine. The editor is an Eclipse plug-in where the programmer loads and edits document examples and pairs their content using graphical primitives. The programming engine receives the data collected by the editor and produces an XSLT program. The design of the engine and the process of creation of an XSLT program from examples are also detailed. It starts with the generation of an initial transformation that maps source document to the target document. This transformation is fed to a rewrite process where each step produces a refined version of the transformation. Finally, the transformation is simplified before being presented to the programmer for further editing.

Specifying a programming exercises evaluation service on the e-Framework

The e-Framework is arguably the most prominent e-learning framework currently in use. For this reason it was selected as basis for modelling a programming exercises evaluation service. The purpose of this type of evaluator is to mark and grade exercises in computer programming courses and in programming contests. By exposing its functions as services a programming exercise evaluator is able to participate in business processes integrating different system types, such as Programming Contest Management Systems, Learning Management Systems, Integrated Development Environments and Learning Object Repositories. This paper formalizes the approaches to be used in the implementation of a programming exercise evaluator as a service on the e-Framework.

PETCHA: a Programming Exercises Teaching Assistant

This paper presents a tool called Petcha that acts as an automated Teaching Assistant in computer programming courses. The ultimate objective of Petcha is to increase the number of programming exercises effectively solved by students. Petcha meets this objective by helping both teachers to author programming exercises and students to solve them. It also coordinates a network of heterogeneous systems, integrating automatic program evaluators, learning management systems, learning object repositories and integrated programming environments. This paper presents the concept and the design of Petcha and sets this tool in a service oriented architecture for managing learning processes based on the automatic evaluation of programming exercises. The paper presents also a case study that validates the use of Petcha and of the proposed architecture.

Assessing the balance between biodiversity conservation and coastal and estuarine management of the Sado Estuary Natural Reserve, Portugal, using BIO-SAFE

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia do Ambiente, perfil de Engenharia Ecológica

A Review of Operational Matrices and Spectral Techniques for Fractional Calculus

Recently, operational matrices were adapted for solving several kinds of fractional differential equations (FDEs). The use of numerical techniques in conjunction with operational matrices of some orthogonal polynomials, for the solution of FDEs on finite and infinite intervals, produced highly accurate solutions for such equations. This article discusses spectral techniques based on operational matrices of fractional derivatives and integrals for solving several kinds of linear and nonlinear FDEs. More precisely, we present the operational matrices of fractional derivatives and integrals, for several polynomials on bounded domains, such as the Legendre, Chebyshev, Jacobi and Bernstein polynomials, and we use them with different spectral techniques for solving the aforementioned equations on bounded domains. The operational matrices of fractional derivatives and integrals are also presented for orthogonal Laguerre and modified generalized Laguerre polynomials, and their use with numerical techniques for solving FDEs on a semi-infinite interval is discussed. Several examples are presented to illustrate the numerical and theoretical properties of various spectral techniques for solving FDEs on finite and semi-infinite intervals.

System Modeling and Control Through Fractional-Order Algorithms

The theory of fractional calculus goes back to the beginning of thr throry of differential calculus but its inherent complexity postponed the applications of the associated concepts. In the last decade the progress in the areas of chaos and fractals revealed subtle relationships with the fractional calculus leading to an increasing interest in the development of the new paradigm. In the area of automaticcontrol preliminary work has already been carried out but the proposed algorithms are restricted to the frequency domain. The paper discusses the design of fractional-order discrete-time controllers. The algorithms studied adopt the time domein, which makes them suited for z-transform analusis and discrete-time implementation. The performance of discrete-time fractional-order controllers with linear and non-linear systems is also investigated.

Skin lesions in envenoming by cnidarians (Portuguese man-of-war and jellyfish): etiology and severity of accidents on the Brazilian coast

This work attempts to establish dermatological identification patterns for Brazilian cnidarian species and a probable correlation with envenoming severity. In an observational prospective study, one hundred and twenty-eight patients from the North Coast region of São Paulo State, Brazil were seen between 2002 and 2008. About 80% of these showed only local effects (erythema, edema, and pain) with small, less than 20 cm, oval or round skin marks and impressions from small tentacles. Approximately 20% of the victims had long, more than 20 cm, linear and crossed marks with frequent systemic phenomena, such as malaise, vomiting, dyspnea, and tachycardia. The former is compatible with the common hydromedusa from Southeast and Southern Brazil (Olindias sambaquiensis). The long linear marks with intense pain and systemic phenomena are compatible with envenoming by the box jellyfish Tamoya haplonema and Chiropsalmus quadrumanus and the hydrozoan Portuguese man-of-war (Physalis physalis). There was an association between skin marks and probable accident etiology. This simple observation rule can be indicative of severity, as the Cubozoa Class (box jellyfish) and Portuguese man-of-war cause the most severe accidents. In such cases, medical attention, including intensive care, is important, as the systemic manifestations can be associated with death.

Oral Contraceptive Use and Clinical Outcomes in Patients with Multiple Sclerosis

Experimental and clinical data suggest a role of sex steroids in the pathogenesis of multiple sclerosis (MS). Scant information is available about the potential effect of oral contraceptive (OC) use on the prognosis of the disease. We aimed to evaluate this. The study population consisted of 132 women with relapsing-remitting MS before receiving disease modifying treatment and a mean disease duration 6.2 (SD 5.1) years. Three groups of patients were distinguished according to their OC behavior: [1] never-users, patients who never used OC [2] past-users, patients who stopped OC use before disease onset, and [3] after-users, those who used these drugs after disease onset. Multiple linear and logistic regression models were used to analyze the association between oral contraceptive use and annualized relapse rates, disability accumulation and severity of the disease. After-user patients had lower Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Severity Score (MSSS) values than never users (p<0.001 and p=0.002, respectively) and past users (p=0.010 and p=0.002, respectively). These patients were also more likely to have a benign disease course (MSSS<2.5) than never and past users together (OR: 4.52, 95%CI: 2.13-9.56, p<0.001). This effect remained significant after adjustment for confounders, including smoking and childbirths (OR: 2.97, 95%CI: 1.24, 6.54, p=0.011 and for MSSS β: -1.04; 95% C.I. -1.78, -0.30, p=0.006). These results suggest that OC use in women with relapsing-remitting MS is possible associated with a milder disabling disease course.

Effects of UV radiation exposure on DNA and DNA repair enzymes

Dissertação para obtenção do Grau de Mestre em Biotecnologia