A clustering approach for vehicle routing problems with hard time windows

Dissertação para obtenção do Grau de Mestre em Logica Computicional

Functional and structural studies of a mini-ferritin protein

Dissertação para obtenção do Grau de Mestre em Bioquímica

Spiteful Strategies. The ontogeny and the practice of spite in human interaction: an experimental game theory approach and empirical applications

As estratégias de malevolência implicam que um indivíduo pague um custo para infligir um custo superior a um oponente. Como um dos comportamentos fundamentais da sociobiologia, a malevolência tem recebido menos atenção que os seus pares o egoísmo e a cooperação. Contudo, foi estabelecido que a malevolência é uma estratégia viável em populações pequenas quando usada contra indivíduos negativamente geneticamente relacionados pois este comportamento pode i) ser eliminado naturalmente, ou ii) manter-se em equilíbrio com estratégias cooperativas devido à disponibilidade da parte de indivíduos malevolentes de pagar um custo para punir. Esta tese propõe compreender se a propensão para a malevolência nos humanos é inerente ou se esta se desenvolve com a idade. Para esse efeito, considerei duas experiências de teoria de jogos em crianças em ambiente escolar com idades entre os 6 e os 22 anos. A primeira, um jogo 2x2 foi testada com duas variantes: 1) um prémio foi atribuído a ambos os jogadores, proporcionalmente aos pontos acumulados; 2), um prémio foi atribuído ao jogador com mais pontos. O jogo foi desenhado com o intuito de causar o seguinte dilema a cada jogador: i) maximizar o seu ganho e arriscar ter menos pontos que o adversário; ou ii) decidir não maximizar o seu ganho, garantindo que este não era inferior ao do seu adversário. A segunda experiência consistia num jogo do ditador com duas opções: uma escolha egoísta/altruísta (A), onde o ditador recebia mais ganho, mas o seu recipiente recebia mais que ele e uma escolha malevolente (B) que oferecia menos ganhos ao ditador que a A mas mais ganhos que o recipiente. O dilema era que se as crianças se comportassem de maneira egoísta, obtinham mais ganho para si, ao mesmo tempo que aumentavam o ganho do seu colega. Se fossem malevolentes, então prefeririam ter mais ganho que o seu colega ao mesmo tempo que tinham menos para eles próprios. As experiências foram efetuadas em escolas de duas áreas distintas de Portugal (continente e Açores) para perceber se as preferências malevolentes aumentavam ou diminuíam com a idade. Os resultados na primeira experiência sugerem que (1) os alunos compreenderam a primeira variante como um jogo de coordenação e comportaram-se como maximizadores, copiando as jogadas anteriores dos seus adversários; (2) que os alunos repetentes se comportaram preferencialmente como malevolentes, mais frequentemente que como maximizadores, com especial ênfase para os alunos de 14 anos; (3) maioria dos alunos comportou-se reciprocamente desde os 12 até aos 16 anos de idade, após os quais começaram a desenvolver uma maior tolerância às escolhas dos seus parceiros. Os resultados da segunda experiência sugerem que (1) as estratégias egoístas eram prevalentes até aos 6 anos de idade, (2) as tendências altruístas emergiram até aos 8 anos de idade e (3) as estratégias de malevolência começaram a emergir a partir dos 8 anos de idade. Estes resultados complementam a literatura relativamente escassa sobre malevolência e sugerem que este comportamento está intimamente ligado a preferências de consideração sobre os outros, o paroquialismo e os estágios de desenvolvimento das crianças.************************************************************Spite is defined as an act that causes loss of payoff to an opponent at a cost to the actor. As one of the four fundamental behaviours in sociobiology, it has received far less attention than its counterparts selfishness and cooperation. It has however been established as a viable strategy in small populations when used against negatively related individuals. Because of this, spite can either i) disappear or ii) remain at equilibrium with cooperative strategies due to the willingness of spiteful individuals to pay a cost in order to punish. This thesis sets out to understand whether propensity for spiteful behaviour is inherent or if it develops with age. For that effect, two game-theoretical experiments were performed with schoolboys and schoolgirls aged 6 to 22. The first, a 2 x 2 game, was tested in two variants: 1) a prize was awarded to both players, proportional to accumulated points; 2), a prize was given to the player with most points. Each player faced the following dilemma: i) to maximise pay-off risking a lower pay-off than the opponent; or ii) not to maximise pay-off in order to cut down the opponent below their own. The second game was a dictator experiment with two choices, (A) a selfish/altruistic choice affording more payoff to the donor than B, but more to the recipient than to the donor, and (B) a spiteful choice that afforded less payoff to the donor than A, but even lower payoff to the recipient. The dilemma here was that if subjects behaved selfishly, they obtained more payoff for themselves, while at the same time increasing their opponent payoff. If they were spiteful, they would rather have more payoff than their colleague, at the cost of less for themselves. Experiments were run in schools in two different areas in Portugal (mainland and Azores) to understand whether spiteful preferences varied with age. Results in the first experiment suggested that (1) students understood the first variant as a coordination game and engaged in maximising behaviour by copying their opponent’s plays; (2) repeating students preferentially engaged in spiteful behaviour more often than maximising behaviour, with special emphasis on 14 year-olds; (3) most students engaged in reciprocal behaviour from ages 12 to 16, as they began developing higher tolerance for their opponent choices. Results for the second experiment suggested that (1) selfish strategies were prevalent until the age of 6, (2) altruistic tendencies emerged since then, and (3) spiteful strategies began being chosen more often by 8 year-olds. These results add to the relatively scarce body of literature on spite and suggest that this type of behaviour is closely tied with other-regarding preferences, parochialism and the children’s stages of development.

First report of rabies infection in bats, Molossus molossus, Molossops neglectus and Myotis riparius in the city of São Paulo, State of São Paulo, southeastern Brazil

INTRODUCTION: This paper presents the first report of rabies in three bat species, Molossus molossus, Molossops neglectus and Myotis riparius in the city of São Paulo, Brazil. METHODS: Bats were diagnosed as positive for rabies using the fluorescent antibody test and mouse inoculation test. The isolates were characterized antigenically using a panel of eight monoclonal antibodies. The samples were also genetically analyzed by partial sequencing of the portion of nucleoprotein gene between positions 1157 and 1445nt. RESULTS: Analysis of the results verified that the sample isolated from the species M. molossus presented antigenic variant 6, while the other two samples showed a different profile from that established in the panel, one not previously reported in the literature. The results of genetic analysis revealed that the M. molossus sample segregated with Lasiurus sp. isolates, M. neglectus segregated with a subgroup of Eptesicus furinalis isolates and the Myotis riparius sample segregated with Myotis sp. isolates. CONCLUSIONS: The cases reported in this paper emphasize the need for clarification of the circumstances in which cases of rabies in wildlife occur, principally in urban areas.

A first case of protease codon 35 amino acid insertion in a HIV-1 subtype B sequence detected in the Bauru region, state of São Paulo, Brazil: case report

Amino acid insertions in the protease have rarely been described in HIVinfected patients. One of these insertions has recently been described in codon 35, although its impact on resistance remains unknown. This study presents a case of an HIV variant with an insertion in codon 35 of the protease, described for the first time in Bauru, State of Sao Paulo, Brazil, circulating in a 38-year-old caucasian male with asymptomatic HIV infection since 1997. The variant isolated showed a codon 35 insertion of two amino acids in the protease: a threonine and an aspartic acid, resulting in the amino acid sequence E35E_TD.

Molecular characterization of rabies virus isolated from non-haematophagous bats in Brazil

INTRODUCTION: Rabies is an important zoonosis that causes thousands of deaths worldwide each year. Although the terrestrial cycle, mainly transmitted by dogs, is controlled in Brazil, the aerial cycle remains a serious public health issue, besides the economic problem. In the aerial cycle, the haematophagous bat Desmodus rotundus is the main source of infection, where several different species of non-haematophagous bats can be infected and can transmit the virus. METHODS: The aim of this work was to study the epidemiological pattern of rabies using antigenic characterization with monoclonal antibodies and genetic characterization by reverse-transcriptase polymerase chain reaction followed by sequencing and phylogenetic analysis of non-haematophagous bats' and herbivorous animals' central nervous system samples from the western region of the State of São Paulo, Brazil. RESULTS: From 27 samples, 3 antigenic variants were identified: AgV-3, AgV-4, and AgV-6; and from 29 samples, 5 different clusters were identified, all belonging to the rabies virus species. CONCLUSIONS: Although only non-haematophagous bats were evaluated in the studied region, the majority of samples were from antigenic and genetic variants related to haematophagous bats Desmodus rotundus. Samples from the same antigenic variant were segregated in more than one genetic cluster. This study demonstrated the diversity of rabies virus genetic lineages presented and circulating in non-haematophagous bats in the studied region.

Circulation of the rabies virus in non-hematophagous bats in the city of Rio de Janeiro, Brazil, during 2001-2010

INTRODUCTION: Rabies is one of the most known lethal zoonosis, responsible for 55,000 human deaths per year. It is transmitted to humans mainly by the bite of domestic or wild animals infected with the virus. This paper shows the circulation of this virus in non-hematophagous bats in the City of Rio de Janeiro, Brazil. METHODS: A survey was performed on the number of bats that had been sent for diagnosis by the Seção de Virologia of the Instituto Municipal de Medicina Veterinária Jorge Vaitsman and were positive for rabies. The positive animals were identified, and the isolated viruses were sent for antigenic typification with indirect immunofluorescence. The results were compared with the antigenic panel of the Centers for Disease Control and Prevention. RESULTS: During 2001-2010, the laboratory received 555 non-hematophagous bats for rabies diagnosis, with 198 (35.7%) from Rio de Janeiro City. A total of 11 (5.5%) animals were positive for this disease. Antigenic typification revealed the predominance of variant 3 in 9 (81.8%) of the isolated viruses; 1 virus was classified as variant 4 and 1 variant was identified that segregated with the viruses in insectivorous bats. CONCLUSIONS: The data obtained in this study showed the presence of the rabies virus in synanthropic populations of non-hematophagous bats in the City of Rio de Janeiro. The circulation of this agent in these animals represents a serious risk to human and animal health and requires attention and control measures by the authorities.

Indicadores de prognóstico em utentes com disfunção do ombro submetidos a uma intervenção terapêutica direcionada para a estabilidade dinâmica da escápulo-torácica

RESUMO: Introdução/ Objetivo: Segundo a revisão sistemática de Chester e colaboradores (2013b)apenas dois fatores de prognóstico demonstraram uma associação consistente com o resultado que foram a duração dos sintomas e a funcionalidade na avaliação inicial. O objetivo do estudo é identificar indicadores de bom e mau prognóstico em utentes com disfunção do complexo articular do ombro (DCAO), tendo por base, aspetos da avaliação inicial do utente e critérios de alta de abolição da dor, aumento da funcionalidade e da estabilidade dinâmica considerando uma intervenção terapêutica direcionada para o aumento da estabilidade dinâmica da escápulo-torácica. Metodologia: Efetuou-se um estudo de coorte clínico retrospetivo. Para tal, aplicou-se um protocolo de intervenção terapêutica e analisou-se os resultados. A amostra foi constituída por 82 indivíduos com DCAO [53 com síndrome do conflito subacromial (SCSA) e 29 com instabilidade da glenoumeral (IGU)], residentes nos distritos de Lisboa, Setúbal e Santarém com o intuito de iniciar tratamento de fisioterapia. A análise dos dados foi efetuada tendo em consideração dois procedimentos: análise univariada (através do método de Kaplan-Meier para cada CVP) e análise multifatorial (pela análise de regressão de Cox e regressão logística nos grupos de utentes com SCSA, IGU e DCAO). Resultados: O tempo mediano de continuação no tratamento em fisioterapia foi de 7 semanas para os utentes com SCSA e 6 semanas para utentes com IGU. Segundo o teste de Logrank, na análise univariada, existem sete e oito covariáveis preditoras (CVP) com associação estatisticamente significativa (p<0,05) para o subgrupo SCSA e IGU, respectivamente. De acordo com estes resultados, a primeira parte da DASH e a SPADI são as únicas CVP com associação comuns às duas disfunções. Pela análise multifatorial e, em congruência com o teste de Wald, nenhuma das CVP contribui estatisticamente para o modelo preditivo de continuidade do tratamento de fisioterapia em qualquer um dos três modelos estudados: subgrupo SCSA, subgrupo IGU e utentes com DCAO. Conclusão: Por uma análise univariada verificou-se que existem CVP associadas à alta dos tratamentos em fisioterapia e estas não são as mesmas em ambas as DCAO. Contudo, a magnitude do efeito de cada CVP nos modelos multifatoriais definidos para os grupos de utentes com SCSA, IGU e DCAO não demonstraram valor estatisticamente significativo pelo que não foi possível determinar modelos de prognóstico em utentes com DCAO.-------------ABSTRACT: Background/ Purpose: According with the systematic review from Chester and collaborators (2013b) just two prognostic factors demonstrated a consistent association with the outcome: the duration of symptoms and functionality in the initial assessment. The purpose of the study is to identify indicators of good and poor prognosis in patients with shoulder’s dysfunctions, based on aspects of the initial assessment and discharge criteria of absence of pain, increased functionality and dynamic stability considering a therapeutic intervention used to increase the dynamic stability of scapulo-thoracic. Methodology: It was conducted a retrospective study of clinical cohort. For this purpose it was applied a protocol with therapeutic intervention and the results were analyzed. The sample consisted of 82 individuals with shoulder’s dysfunction (53 with subacromial impingement (SIMP) and 29 with shoulder instability (SINS) residing in the districts of Lisbon, Setúbal and Santarém in order to start physiotherapy. Data analysis was performed taking into account two procedures: univariate analysis [using the Kaplan-Meier method for each co-variant predictor variable (CVP)] and multifactorial analysis [analysis by Cox regression and logistic regression on groups of patients with SIMP, SINS and shoulder’s dysfunction (SD)]. Results: The median time of follow-up treatment at physical therapy was 7 weeks for patients with SIMP and 6 weeks for patients with SINS. According to the Logrank test in the univariate analysis, there are seven and eight CVP with a statistically significant association (p<0.05) for the patients with SIMP and SINS, respectively. According to these results, the first part of the DASH and SPADI are the only CVP common to both disorders association. By multifatorial analyses, and in agreement with the Wald test, none of the CVP contributes statistically to the predictive model of continuity of physiotherapy treatment in any of the three studied models: patients with SIMP, patients with SINS and patients with SD. Conclusion: In an univariate analysis, it was verified that there are CVP associated with discharge from treatments of physical therapy and these are not the same in both SD. However, the magnitude of effect of each CVP in multifactorial models for defined patients groups with SIMP, SINS and SD showed no statistically significant. Therefore, it was not possible to determine prognostic models for patients with SD.

Pandemic influenza A (H1N1) 2009: epidemiological analysis of cases in a tropical/semi-arid region of Brazil

IntroductionThe year 2009 marked the beginning of a pandemic caused by a new variant of influenza A (H1N1). After spreading through North America, the pandemic influenza virus (H1N1) 2009 spread rapidly throughout the world. The aim of this study was to describe the clinical and epidemiological characteristics of cases of pandemic influenza in a tropical/semi-arid region of Brazil.MethodsA retrospective study analyzed all suspected cases of pandemic influenza (H1N1) 2009 reported in the Ceará State through the National Information System for Notifiable Diseases during the pandemic period between 28 April, 2009 and November 25, 2010.ResultsA total of 616 suspected cases were notified, 58 (9.4%) in the containment phase and 558 (90.6%) in the mitigation phase. Most cases were of affected young people resident in the City of Fortaleza, the largest urban center in the State of Ceará. The most frequent symptoms presented by the cases with confirmed infection were fever, cough, myalgia, arthralgia, and nasal congestion. Mortality rate was 0.0009/1,000 inhabitants and lethality was 5.6%. Deaths were observed only in the mitigation phase. Mortality rates were similar for both sexes but were higher in the age group under 5 years.ConclusionsThe study suggests that the influenza A (H1N1) pandemic in this tropical/semi-arid region had a lower magnitude when compared to states in the Southern and Southeastern regions of Brazil.

A public transport bus assignment problem: parallel metaheuristics assessment

Combinatorial Optimization Problems occur in a wide variety of contexts and generally are NP-hard problems. At a corporate level solving this problems is of great importance since they contribute to the optimization of operational costs. In this thesis we propose to solve the Public Transport Bus Assignment problem considering an heterogeneous fleet and line exchanges, a variant of the Multi-Depot Vehicle Scheduling Problem in which additional constraints are enforced to model a real life scenario. The number of constraints involved and the large number of variables makes impracticable solving to optimality using complete search techniques. Therefore, we explore metaheuristics, that sacrifice optimality to produce solutions in feasible time. More concretely, we focus on the development of algorithms based on a sophisticated metaheuristic, Ant-Colony Optimization (ACO), which is based on a stochastic learning mechanism. For complex problems with a considerable number of constraints, sophisticated metaheuristics may fail to produce quality solutions in a reasonable amount of time. Thus, we developed parallel shared-memory (SM) synchronous ACO algorithms, however, synchronism originates the straggler problem. Therefore, we proposed three SM asynchronous algorithms that break the original algorithm semantics and differ on the degree of concurrency allowed while manipulating the learned information. Our results show that our sequential ACO algorithms produced better solutions than a Restarts metaheuristic, the ACO algorithms were able to learn and better solutions were achieved by increasing the amount of cooperation (number of search agents). Regarding parallel algorithms, our asynchronous ACO algorithms outperformed synchronous ones in terms of speedup and solution quality, achieving speedups of 17.6x. The cooperation scheme imposed by asynchronism also achieved a better learning rate than the original one.

Impact of chromossomal structure on the evolution of Schizosaccharomyces pombe undergoing Mutation Accumulation

Large chromosomal rearrangements are common in natural populations and thought to be involved in speciation events. In this project, we used experimental evolution to determine how the speed of evolution and the type of accumulated mutations depend on the ancestral chromosomal structure and genotype. We utilized two Wild Type strains and a set of genetically engineered Schizosaccharomyces pombe strains, different solely in the presence of a certain type of chromosomal variant (inversions or translocations), along with respective controls. Previous research has shown that these chromosomal variants have different fitness levels in several environments, probably due to changes in the gene expression along the genome. These strains were propagated in the laboratory at very low population sizes, in which we expect natural selection to be less efficient at purging deleterious mutations. We then measured these strains’ changes in fitness throughout this accumulation of deleterious mutations, comparing the evolutionary trajectories in the different rearrangements to understand if the chromosomal structure affected the speed of evolution. We also tested these mutations for possible epistatic effects and estimated their parameters: the number of arising deleterious mutations per generation (Ud) and each one’s mean effect (sd).

Quantitative Centromere Epigenetics

A PhD is like a box of chocolates, …… and in this thesis I will present what I got. My work has been focused on a cellular structure that is essential for accurate genome inheritance: the centromere. Centromeres are chromosomal domains that do not rely on the presence of any specific DNA sequence. Rather, they are determined by the presence of a histone variant called CENP-A. Stable transmission of CENP-A containing chromatin is accomplished through 1) an unusually high level of protein stability, 2) selfdirected recruitment of nascent CENP-A near existing molecules, and 3) strict cell cycle regulation of assembly. Together, these features lead to a self-sustaining loop that allows for epigenetic maintenance of centromeres.(...)

Contributions towards smart cities : exploring block level census data for the characterization of change in Lisbon

The interest in using information to improve the quality of living in large urban areas and its governance efficiency has been around for decades. Nevertheless, the improvements in Information and Communications Technology has sparked a new dynamic in academic research, usually under the umbrella term of Smart Cities. This concept of Smart City can probably be translated, in a simplified version, into cities that are lived, managed and developed in an information-saturated environment. While it makes perfect sense and we can easily foresee the benefits of such a concept, presently there are still several significant challenges that need to be tackled before we can materialize this vision. In this work we aim at providing a small contribution in this direction, which maximizes the relevancy of the available information resources. One of the most detailed and geographically relevant information resource available, for the study of cities, is the census, more specifically the data available at block level (Subsecção Estatística). In this work, we use Self-Organizing Maps (SOM) and the variant Geo-SOM to explore the block level data from the Portuguese census of Lisbon city, for the years of 2001 and 2011. We focus on gauging change, proposing ways that allow the comparison of the two time periods, which have two different underlying geographical bases. We proceed with the analysis of the data using different SOM variants, aiming at producing a two-fold portrait: one, of the evolution of Lisbon during the first decade of the XXI century, another, of how the census dataset and SOM’s can be used to produce an informational framework for the study of cities.

Continuous monitoring of concrete mechanical properties since an early age to support construction phasing

The assessment of concrete mechanical properties during construction of concrete structures is of paramount importance for many intrinsic operations. However many of the available non-destructive methods for mechanical properties have limitations for use in construction sites. One of such methodologies is EMM-ARM, which is a variant of classic resonant frequency methods. This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, as to provide real-time information about concrete mechanical properties such as E-modulus and compressive strength. To achieve the aforementioned objective, a set of adaptations to the method have been successfully implemented and tested: (i) the reduction of the beam span; (ii) the use of a different mould material and (iii) a new support system for the beams. Based on these adaptations, a reusable mould was designed to enable easier systematic use of EMMARM. A pilot test was successfully performed under in-situ conditions during a bridge construction.

Amazon landforms and soils in relation to biological diversity

Thirteen main landform units are distinguished for the whole of the forested Amazon region, each with its specific soil pattern and vegetation structure. These landform-soil-vegetation units are delineated on a small-scale map and illustrated by a schematic cross-section. Floristic diversity of the gamma type is to be highest on the steepland-and-valley complexes of the Andean fringe, on the crystalline shield uplands, on the inselberg complexes, and on the eutric variant of the western sedimentary plains. Endemism is expected to be highest on the sandy plains, and parts of the table lands and inselberg complexes. Speciation, linked to the concept of forest refuge areas, is likely to be highest on the sandstone table lands, on the stretches of Amazon planalto, and in the areas of relict valleys, in view of the prolonged geomorphological stability of these units.