Human activity recognition with accelerometry: novel time and frequency features

Human Activity Recognition systems require objective and reliable methods that can be used in the daily routine and must offer consistent results according with the performed activities. These systems are under development and offer objective and personalized support for several applications such as the healthcare area. This thesis aims to create a framework for human activities recognition based on accelerometry signals. Some new features and techniques inspired in the audio recognition methodology are introduced in this work, namely Log Scale Power Bandwidth and the Markov Models application. The Forward Feature Selection was adopted as the feature selection algorithm in order to improve the clustering performances and limit the computational demands. This method selects the most suitable set of features for activities recognition in accelerometry from a 423th dimensional feature vector. Several Machine Learning algorithms were applied to the used accelerometry databases – FCHA and PAMAP databases - and these showed promising results in activities recognition. The developed algorithm set constitutes a mighty contribution for the development of reliable evaluation methods of movement disorders for diagnosis and treatment applications.

Diagnosis of hantavirus infection in humans and rodents in Ribeirão Preto, State of São Paulo, Brazil

INTRODUCTION: Hantavirus pulmonary and cardiovascular syndrome (HPCS) is an emerging serious disease in the Americas. Hantaviruses (Bunyaviridae) are the causative agents of this syndrome and are mainly transmitted through inhalation of aerosols containing the excreta of wild rodents. In the Ribeirão Preto region (state of São Paulo, Brazil), HPCS has been reported since 1998, caused by the Araraquara virus (ARAV), for which Necromys lasiurus is the rodent reservoir. This study aimed to show diagnostic results relating to infection in humans and rodents, obtained at the Virology Research Center of the Ribeirão Preto School of Medicine, University of São Paulo, between 2005 and 2008. METHODS: HPCS was diagnosed by means of ELISA and/or RT-PCR in 11 (21.2%) out of 52 suspected cases, and 54.4% of these were fatal. Furthermore, 595 wild rodents (Necromys lasiurus, Akodon sp, Calomys tener and Oligoryzomys sp) were caught between 2005 and 2008. RESULTS: Fifteen (2.5%) of these rodents presented antibodies for hantavirus, as follows: Necromys lasiurus (4%), Calomys tener (1.9%) and Akodon sp (1.5%). Nucleotide sequences obtained through RT-PCR from one HPCS patient and one Calomys tener rodent were compared with hantavirus sequences from GenBank, which showed that both were homologous with ARAV. CONCLUSIONS: This work corroborates previous studies showing that ARAV is the hantavirus causing HPCS in the Ribeirão Preto region. It also shows that rodents infected with hantavirus represent a constant risk of transmission of this virus to man.

Real-time collaborative editing of OutSystems DSL models

Real-time collaborative editing systems are common nowadays, and their advantages are widely recognized. Examples of such systems include Google Docs, ShareLaTeX, among others. This thesis aims to adopt this paradigm in a software development environment. The OutSystems visual language lends itself very appropriate to this kind of collaboration, since the visual code enables a natural flow of knowledge between developers regarding the developed code. Furthermore, communication and coordination are simplified. This proposal explores the field of collaboration on a very structured and rigid model, where collaboration is made through the copy-modify-merge paradigm, in which a developer gets its own private copy from the shared repository, modifies it in isolation and later uploads his changes to be merged with modifications concurrently produced by other developers. To this end, we designed and implemented an extension to the OutSystems Platform, in order to enable real-time collaborative editing. The solution guarantees consistency among the artefacts distributed across several developers working on the same project. We believe that it is possible to achieve a much more intense collaboration over the same models with a low negative impact on the individual productivity of each developer.

Glomerulonephritis in schistosomiasis mansoni: a time to reappraise

INTRODUCTION: The current prevalence of glomerulonephritis in patients with hepatosplenic schistosomiasis mansoni in Brazil was evaluated. METHODS: Sixty three patients (mean age 45.5±11 years) attending the outpatient infectious disease clinic of a University Hospital in Belo Horizonte, Brazil, from 2007 to 2009, were consecutively examined and enrolled in the present investigation. Diagnosis of hepatosplenic schistosomiasis was based on epidemiological, clinical and parasitological data and imaging techniques. Eight patients, who presented >30mg/day albuminuria, were submitted to percutaneous ultrasound guided renal biopsy. Kidney tissue fragments were examined under light, direct immunofluorescence and electron microscopy. RESULTS: All patients showed mesangial enlargement. In five, mesangial hypercellularity was observed and four presented duplication of the glomerular basement membrane. Areas of glomerular sclerosis were diagnosed in four. Deposits of immunoglobulin M and C3 were present in six samples; deposits of IgG in four, IgA in three and C1q in two samples. In all patients, immunoglobulin A was reported in the lumen of renal tubules. Deposits of kappa and lambda were observed in six samples. Electron microscopy revealed dense deposits in the glomerular tissue of three patients. Arterial hypertension, small esophageal varices, slight increases in serum creatinine and decreases in serum albumin were associated with glomerular disease. CONCLUSIONS: Renal disease associated with hepatosplenic schistosomiasis was verified in 12.7% of patients and type I membranoproliferative glomerulonephritis was observed in 50% of them. Schistosomal glomerulopathy still is an important problem in patients with hepatosplenic schistosomiasis in Brazil.

Caracterização do papel dos genes TYMS e MTR no desenvolvimento de Cancro Colo-Rectal

RESUMO: O cancro colo-rectal (CCR) é um dos cancros que possui maior taxa de mortalidade a nível mundial. Em Portugal esta patologia é responsável pela morte de cerca de 3700 pessoas por ano, sendo que estes números aumentam de ano para ano. Ao longo das últimas décadas o papel das alterações genéticas na etiologia das patologias oncológicas tem vindo a ter cada vez mais um maior destaque. O número de estudos que avaliam a importância de polimorfismos, mutações, alterações na regulação génica e interacções entre genes no desenvolvimento destas patologias tem aumentado exponencialmente. Com o aumento do conhecimento da forma como estas alterações influenciam o desenvolvimento do cancro surgiram os primeiros meios de diagnóstico genético, levando assim a uma alteração da forma como são encarados o diagnóstico e a prevenção destas doenças. No CCR as formas hereditárias com alterações genéticas inequivocamente identificadas representam apenas 5% dos casos. Existem cerca de 25% que representam formas hereditárias para as quais ainda não foram estabelecidos os padrões de alterações genéticas subjacentes. Desta forma, estudos que venham contribuir para um maior conhecimento dos mecanismos moleculares responsáveis pelo aumento da susceptibilidade dos indivíduos para o desenvolvimento de CCR são extremamente importantes. O CCR é uma patologia multifactorial, onde factores genéticos interagem com factores ambientais no surgimento e desenvolvimento da doença. Assim, torna-se essencial integrar o estudo das alterações genéticas no contexto ambiental onde os indivíduos em estudo se encontram. No caso desta patologia um dos principais factores ambientais estudado é a nutrição. Vários estudos têm sido realizados ao longo dos últimos anos de forma a compreender como pode a ingestão dos nutrientes influenciar o desenvolvimento de CCR e de que forma interage com as alterações genéticas individuais. O ciclo do folato é um dos processos metabólicos onde o papel da nutrição em interacção com alterações genéticas mais tem sido estudado nos últimos anos. Deste cruzamento entre o estudo das alterações genéticas e ambientais surge a Nutrigenética. O conjunto de estudos da presente tese tem como objectivo aumentar o conhecimento do papel das alterações em genes do ciclo do folato, em interacção com factores nutricionais e de estilo de vida, não só no desenvolvimento de CCR, mas também de outra patologia do tracto gastrointestinal, a Doença de Crohn (DC), uma doença inflamatória muitas vezes associada como factor de risco para o desenvolvimento de CCR. Este estudo debruçou-se essencialmente no estudo dos genes timidilato sintetase (TYMS) e metionina sintetase (MTR) em populações com CCR e DC, bem como no padrão nutricional destas populações com particular incidência nos nutrientes envolvidos no ciclo do folato (folato, metionina, vitamina B6, vitamina B12). Analisando o conjunto de resultados obtidos para os estudos do CCR podemos concluir que quer a TYMS quer a MTR possuem um papel relevante na susceptibilidade para desenvolver esta patologia, assim como têm destaque no funcionamento do ciclo celular durante o processo oncogénico. Os resultados demonstram que os factores que levam a uma menor disponibilidade de grupos metil no ciclo de folato (baixos níveis de folato, alteração da actividade de MTR, elevada expressão de TYMS) constituem factores de risco, muito provavelmente por contribuírem para uma desregulação dos níveis de metionina disponível para a metilação do DNA da célula. Demonstram ainda que em células tumorais ocorrem alterações na regulação do ciclo do folato de forma a favorecer a síntese de DNA em detrimento da metilação do mesmo, alterando para isso a expressão dos genes de forma a que o fluxo de grupos metil provenientes do folato sejam encaminhados para a enzima TYMS. O polimorfismo de deleção 6pb da TYMS surge como um factor de diagnóstico e de prognóstico de CCR para a população portuguesa. Dos factores nutricionais analisados apenas o folato aparenta ter um papel relevante na modelação do risco de desenvolver CCR. Na doença de Crohn (DC) podemos verificar que a homocisteína e o seu metabolismo poderão contribuir para o aparecimento e desenvolvimento da patologia. O aumento da homocisteína poderá ser o responsável por um aumento da resposta auto-imune do organismo, promovendo o aparecimento da DC. O polimorfismo A2756G MTR desempenha um papel preponderante como factor de diagnóstico da DC, tendo sido associado pela primeira vez a esta patologia. Tem também um papel importante no desenvolvimento da doença, uma vez que está associado a uma idade de diagnóstico mais baixa, sugerindo assim que o desenvolvimento da doença ocorre de forma mais precoce. Concluindo, com este estudo pensamos ter contribuído para um melhor entendimento do papel do ciclo do folato no desenvolvimento de CCR e DC, sendo um ponto de partida para futuras investigações que possam revelar cada vez melhor as complexas interacções metabólicas desta via e a sua influência nas patologias estudadas. Do nosso estudo destacamos a importância de uma análise global das várias etapas do ciclo do folato para que se possa compreender a dinâmica que se estabelece no desenvolvimento destas patologias, podendo diversas alterações, quer a nível genético quer a nível nutricional, exercerem efeitos diferentes consoante o estado dos restantes intervenientes do ciclo do folato. Acreditamos que no futuro este estudo permitirá que o conhecimento do ciclo do folato tenha cada vez mais uma relevância fundamental a nível de diagnóstico e terapêutica destas patologias.------------ ABSTRACT: Colorectal Cancer (CRC) is one of the cancers that have a higher rate of mortality worldwide. In Portugal this pathology is responsible for the deaths of about 3700 people per year, and these numbers increase each year. Over the past few decades the role of genetic changes in the etiology of oncological pathologies has had an increasingly greater emphasis. The number of studies that evaluate the importance of polymorphisms, mutations, changes in gene regulation and gene interactions in the development of these diseases has increased exponentially. With the increased knowledge of how these changes influence the development of cancer, appeared the first means for genetic diagnostic, leading to a change in the way diagnosis is seen and in the prevention of these diseases. In CRC the hereditary forms with clearly identified genetic changes represent only 5% of cases. There are about 25% representing hereditary forms for which the patterns of genetic changes haven’t been established. In this way, studies that will contribute to a greater understanding of the molecular mechanisms responsible for increased susceptibility of individuals to the CRC development are extremely important. CRC is a multifactorial pathology, where genetic factors interact with environmental factors in the emergence and development of the disease.Thus, it is essential to integrate the study of genetic changes in the environmental context of the individuals under study. In the case of this pathology one of the main environmental factors studied is nutrition. Several studies have been conducted over the past few years in order to understand how the intake of nutrients can influence the development of CRC and how nutrients interact with the individual genetic changes. The folate cycle is one of the metabolic processes where the role of nutrition in interaction with genetic alterations has been studied in recent years. This cross between the study of genetic and environmental changes developed Nutrigenetics. The set of studies of this thesis aims to increase awareness of the role of changes in genes of the folate cycle, in interaction with nutritional factors and lifestyle, not only in the development of CRC, but also of another pathology of the gastrointestinal tract, Crohn's disease (CD), an inflammatory disease often associated as a risk factor for the development of CRC. This study dealt mainly in the study of genes thymidylate synthase (TYMS) and methionine synthase (MTR) in populations with CRC and CD, as well as in the nutritional pattern of these populations with particular focus on nutrients involved in the folate cycle (folate, methionine, vitamin B6, vitamin B12). Analyzing the results obtained for the CRC studies we conclude that either the MTR TYMS have a relevant role in susceptibility to develop this pathology, and have an important role in the functioning of the cell cycle during oncogenesis. The results show that the factors that lead to a lower availability of methyl groups in folate cycle (low levels of folate, change the activity of MTR, high expression of TYMS) constitute risk factors, most likely by contribute to a dysregulation of methionine levels available for DNA methylation of the cell. Our results also demonstrate that in tumor cells occur changes in the regulation of the folate cycle in order to promote the synthesis of DNA, to the detriment of methylation of the same by changing the expression of genes so that the methyl groups from folate are forwarded to the TYMS enzyme reaction. The deletion polymorphism 6bp of TYMS emerges as a diagnostic and prognostic factor of CCR for the Portuguese population. Nutritional factors analyzed only folate appears to have a major role in modulating the risk of developing CCR.In Crohn’s disease (CD) we can check that homocysteine and its metabolism may contribute to the emergence and development of this pathology. Increased homocysteine may be responsible for an increase in the body's autoimmune response, promoting the emergence of CD. The polymorphism A2756G MTR plays a leading role as a factor of diagnosis of DC, having been associated with this pathology for the first time. It also has an important role in the development of the disease, since it is associated with a lower diagnostic age, suggesting that the development of the disease occurs earlier. In conclusion, our study has contributed to a better understanding of the role of folate cycle in the development of CRC and CD, being a starting point for future research that may prove increasingly complex metabolic interactions in this via and its influence on the pathologies studied. In our study we highlight the importance of a comprehensive analysis of the various steps of the folate cycle in order to understand the dynamics that settles in the development of these pathologies, and a number of amendments, whether at the genetic level or at the nutritional level, exercise different effects depending on the stage of the remaining participants in the folate cycle. We believe that in the future this study will allow the knowledge of folate cycle to have increasingly a fundamental relevance at the level of diagnosis and treatment of these diseases.

Métodos estatísticos aplicados à modelação de dados oncológicos

RESUMO: A estrutura demográfica portuguesa é marcada por baixas taxas de natalidade e mortalidade, onde a população idosa representa uma fatia cada vez mais representativa, fruto de uma maior longevidade. A incidência do cancro, na sua generalidade, é maior precisamente nessa classe etária. A par de outras doenças igualmente lesivas (e.g. cardiovasculares, degenerativas) cuja incidência aumenta com a idade, o cancro merece relevo. Estudos epidemiológicos apresentam o cancro como líder mundial na mortalidade. Em países desenvolvidos, o seu peso representa 25% do número total de óbitos, percentagem essa que mais que duplica noutros países. A obesidade, a baixa ingestão de frutas e vegetais, o sedentarismo, o consumo de tabaco e a ingestão de álcool, configuram-se como cinco dos fatores de risco presentes em 30% das mortes diagnosticadas por cancro. A nível mundial e, em particular no Sul de Portugal, os cancros do estômago, recto e cólon apresentam elevadas taxas de incidência e de mortalidade. Do ponto de vista estritamente económico, o cancro é a doença que mais recursos consome enquanto que do ponto de vista físico e psicológico é uma doença que não limita o seu raio de ação ao doente. O cancro é, portanto, uma doença sempre atual e cada vez mais presente, pois reflete os hábitos e o ambiente de uma sociedade, não obstante as características intrínsecas a cada indivíduo. A adoção de metodologia estatística aplicada à modelação de dados oncológicos é, sobretudo, valiosa e pertinente quando a informação é oriunda de Registos de Cancro de Base Populacional (RCBP). A pertinência é justificada pelo fato destes registos permitirem aferir numa população específica, o risco desta sofrer e/ou vir a sofrer de uma dada neoplasia. O peso que as neoplasias do estômago, cólon e recto assumem foi um dos elementos que motivou o presente estudo que tem por objetivo analisar tendências, projeções, sobrevivências relativas e a distribuição espacial destas neoplasias. Foram considerados neste estudo todos os casos diagnosticados no período 1998-2006, pelo RCBP da região sul de Portugal (ROR-Sul). O estudo descritivo inicial das taxas de incidência e da tendência em cada uma das referidas neoplasias teve como base uma única variável temporal - o ano de diagnóstico - também designada por período. Todavia, uma metodologia que contemple apenas uma única variável temporal é limitativa. No cancro, para além do período, a idade à data do diagnóstico e a coorte de nascimento, são variáveis temporais que poderão prestar um contributo adicional na caracterização das taxas de incidência. A relevância assumida por estas variáveis temporais justificou a sua inclusão numaclasse de modelos designada por modelos Idade-Período-Coorte (Age-Period-Cohort models - APC), utilizada na modelação das taxas de incidência para as neoplasias em estudo. Os referidos modelos permitem ultrapassar o problema de relações não lineares e/ou de mudanças súbitas na tendência linear das taxas. Nos modelos APC foram consideradas a abordagem clássica e a abordagem com recurso a funções suavizadoras. A modelação das taxas foi estratificada por sexo. Foram ainda estudados os respectivos submodelos (apenas com uma ou duas variáveis temporais). Conhecido o comportamento das taxas de incidência, uma questão subsequente prende-se com a sua projeção em períodos futuros. Porém, o efeito de mudanças estruturais na população, ao qual Portugal não é alheio, altera substancialmente o número esperado de casos futuros com cancro. Estimativas da incidência de cancro a nível mundial obtidas a partir de projeções demográficas apontam para um aumento de 25% dos casos de cancro nas próximas duas décadas. Embora a projeção da incidência esteja associada a alguma incerteza, as projeções auxiliam no planeamento de políticas de saúde para a afetação de recursos e permitem a avaliação de cenários e de intervenções que tenham como objetivo a redução do impacto do cancro. O desconhecimento de projeções da taxa de incidência destas neoplasias na área abrangida pelo ROR-Sul, levou à utilização de modelos de projeção que diferem entre si quanto à sua estrutura, linearidade (ou não) dos seus coeficientes e comportamento das taxas na série histórica de dados (e.g. crescente, decrescente ou estável). Os referidos modelos pautaram-se por duas abordagens: (i)modelos lineares no que concerne ao tempo e (ii) extrapolação de efeitos temporais identificados pelos modelos APC para períodos futuros. Foi feita a projeção das taxas de incidência para os anos de 2007 a 2010 tendo em conta o género, idade e neoplasia. É ainda apresentada uma estimativa do impacto económico destas neoplasias no período de projeção. Uma questão pertinente e habitual no contexto clínico e a que o presente estudo pretende dar resposta, reside em saber qual a contribuição da neoplasia em si para a sobrevivência do doente. Nesse sentido, a mortalidade por causa específica é habitualmente utilizada para estimar a mortalidade atribuível apenas ao cancro em estudo. Porém, existem muitas situações em que a causa de morte é desconhecida e, mesmo que esta informação esteja disponível através dos certificados de óbito, não é fácil distinguir os casos em que a principal causa de morte é devida ao cancro. A sobrevivência relativa surge como uma medida objetiva que não necessita do conhecimento da causa específica da morte para o seu cálculo e dar-nos-á uma estimativa da probabilidade de sobrevivência caso o cancro em análise, num cenário hipotético, seja a única causa de morte. Desconhecida a principal causa de morte nos casos diagnosticados com cancro no registo ROR-Sul, foi determinada a sobrevivência relativa para cada uma das neoplasias em estudo, para um período de follow-up de 5 anos, tendo em conta o sexo, a idade e cada uma das regiões que constituem o registo. Foi adotada uma análise por período e as abordagens convencional e por modelos. No epílogo deste estudo, é analisada a influência da variabilidade espaço-temporal nas taxas de incidência. O longo período de latência das doenças oncológicas, a dificuldade em identificar mudanças súbitas no comportamento das taxas, populações com dimensão e riscos reduzidos, são alguns dos elementos que dificultam a análise da variação temporal das taxas. Nalguns casos, estas variações podem ser reflexo de flutuações aleatórias. O efeito da componente temporal aferida pelos modelos APC dá-nos um retrato incompleto da incidência do cancro. A etiologia desta doença, quando conhecida, está associada com alguma frequência a fatores de risco tais como condições socioeconómicas, hábitos alimentares e estilo de vida, atividade profissional, localização geográfica e componente genética. O “contributo”, dos fatores de risco é, por vezes, determinante e não deve ser ignorado. Surge, assim, a necessidade em complementar o estudo temporal das taxas com uma abordagem de cariz espacial. Assim, procurar-se-á aferir se as variações nas taxas de incidência observadas entre os concelhos inseridos na área do registo ROR-Sul poderiam ser explicadas quer pela variabilidade temporal e geográfica quer por fatores socioeconómicos ou, ainda, pelos desiguais estilos de vida. Foram utilizados os Modelos Bayesianos Hierárquicos Espaço-Temporais com o objetivo de identificar tendências espaço-temporais nas taxas de incidência bem como quantificar alguns fatores de risco ajustados à influência simultânea da região e do tempo. Os resultados obtidos pela implementação de todas estas metodologias considera-se ser uma mais valia para o conhecimento destas neoplasias em Portugal.------------ABSTRACT: mortality rates, with the elderly being an increasingly representative sector of the population, mainly due to greater longevity. The incidence of cancer, in general, is greater precisely in that age group. Alongside with other equally damaging diseases (e.g. cardiovascular,degenerative), whose incidence rates increases with age, cancer is of special note. In epidemiological studies, cancer is the global leader in mortality. In developed countries its weight represents 25% of the total number of deaths, with this percentage being doubled in other countries. Obesity, a reduce consumption of fruit and vegetables, physical inactivity, smoking and alcohol consumption, are the five risk factors present in 30% of deaths due to cancer. Globally, and in particular in the South of Portugal, the stomach, rectum and colon cancer have high incidence and mortality rates. From a strictly economic perspective, cancer is the disease that consumes more resources, while from a physical and psychological point of view, it is a disease that is not limited to the patient. Cancer is therefore na up to date disease and one of increased importance, since it reflects the habits and the environment of a society, regardless the intrinsic characteristics of each individual. The adoption of statistical methodology applied to cancer data modelling is especially valuable and relevant when the information comes from population-based cancer registries (PBCR). In such cases, these registries allow for the assessment of the risk and the suffering associated to a given neoplasm in a specific population. The weight that stomach, colon and rectum cancers assume in Portugal was one of the motivations of the present study, that focus on analyzing trends, projections, relative survival and spatial distribution of these neoplasms. The data considered in this study, are all cases diagnosed between 1998 and 2006, by the PBCR of Portugal, ROR-Sul.Only year of diagnosis, also called period, was the only time variable considered in the initial descriptive analysis of the incidence rates and trends for each of the three neoplasms considered. However, a methodology that only considers one single time variable will probably fall short on the conclusions that could be drawn from the data under study. In cancer, apart from the variable period, the age at diagnosis and the birth cohort are also temporal variables and may provide an additional contribution to the characterization of the incidence. The relevance assumed by these temporal variables justified its inclusion in a class of models called Age-Period-Cohort models (APC). This class of models was used for the analysis of the incidence rates of the three cancers under study. APC models allow to model nonlinearity and/or sudden changes in linear relationships of rate trends. Two approaches of APC models were considered: the classical and the one using smoothing functions. The models were stratified by gender and, when justified, further studies explored other sub-models where only one or two temporal variables were considered. After the analysis of the incidence rates, a subsequent goal is related to their projections in future periods. Although the effect of structural changes in the population, of which Portugal is not oblivious, may substantially change the expected number of future cancer cases, the results of these projections could help planning health policies with the proper allocation of resources, allowing for the evaluation of scenarios and interventions that aim to reduce the impact of cancer in a population. Worth noting that cancer incidence worldwide obtained from demographic projections point out to an increase of 25% of cancer cases in the next two decades. The lack of projections of incidence rates of the three cancers under study in the area covered by ROR-Sul, led us to use a variety of forecasting models that differ in the nature and structure. For example, linearity or nonlinearity in their coefficients and the trend of the incidence rates in historical data series (e.g. increasing, decreasing or stable).The models followed two approaches: (i) linear models regarding time and (ii) extrapolation of temporal effects identified by the APC models for future periods. The study provide incidence rates projections and the numbers of newly diagnosed cases for the year, 2007 to 2010, taking into account gender, age and the type of cancer. In addition, an estimate of the economic impact of these neoplasms is presented for the projection period considered. This research also try to address a relevant and common clinical question in these type of studies, regarding the contribution of the type of cancer to the patient survival. In such studies, the primary cause of death is commonly used to estimate the mortality specifically due to the cancer. However, there are many situations in which the cause of death is unknown, or, even if this information is available through the death certificates, it is not easy to distinguish the cases where the primary cause of death is the cancer. With this in mind, the relative survival is an alternative measure that does not need the knowledge of the specific cause of death to be calculated. This estimate will represent the survival probability in the hypothetical scenario of a certain cancer be the only cause of death. For the patients with unknown cause of death that were diagnosed with cancer in the ROR-Sul, the relative survival was calculated for each of the cancers under study, for a follow-up period of 5 years, considering gender, age and each one of the regions that are part the registry. A period analysis was undertaken, considering both the conventional and the model approaches. In final part of this study, we analyzed the influence of space-time variability in the incidence rates. The long latency period of oncologic diseases, the difficulty in identifying subtle changes in the rates behavior, populations of reduced size and low risk are some of the elements that can be a challenge in the analysis of temporal variations in rates, that, in some cases, can reflect simple random fluctuations. The effect of the temporal component measured by the APC models gives an incomplete picture of the cancer incidence. The etiology of this disease, when known, is frequently associated to risk factors such as socioeconomic conditions, eating habits and lifestyle, occupation, geographic location and genetic component. The "contribution"of such risk factors is sometimes decisive in the evolution of the disease and should not be ignored. Therefore, there was the need to consider an additional approach in this study, one of spatial nature, addressing the fact that changes in incidence rates observed in the ROR-Sul area, could be explained either by temporal and geographical variability or by unequal socio-economic or lifestyle factors. Thus, Bayesian hierarchical space-time models were used with the purpose of identifying space-time trends in incidence rates together with the the analysis of the effect of the risk factors considered in the study. The results obtained and the implementation of all these methodologies are considered to be an added value to the knowledge of these neoplasms in Portugal.

Diagnosis of Leishmania (Leishmania) chagasi infection in dogs and the relationship with environmental and sanitary aspects in the municipality of Palmas, state of Tocantins, Brazil

INTRODUCTION: The aim of the present study was to identify the presence of Leishmania (Leishmania) chagasi infection in dogs in the City of Palmas, Tocantins, Brazil, using the PCR technique to list the hot spots of infected dogs in the city and associate their occurrence to significant environmental changes at capture sites. METHODS: DNA was extracted from blood of dogs, and the PCR were performed with primers RV1/RV2. After screening the population studied, the regions of the city that had the highest occurrence of canine infection were detected. These sites were visited, and ecological parameters denoting anthropogenic disturbance were evaluated. RESULTS: Some important features were listed in the regions visited, such as low urbanization, lack of public collection of sewage, limited garbage collection, vacant lots with tall vegetation, decaying organic matter, and, most importantly, the occurrence of stray dogs and poultry in homes. CONCLUSIONS: The methodology for screening the population was very efficient, especially in evaluating a large number of individuals in a short time, with a high degree of automation. The results indicate an association between the observed parameters and the occurrence of infection in dogs. The model presented in the city is ideal for studies of disease progression and expansion and for the evaluation of control measures adopted for canine VL.

The performance of four molecular methods for the laboratory diagnosis of congenital toxoplasmosis in amniotic fluid samples

Introduction Toxoplasmosis may be life-threatening in fetuses and in immune-deficient patients. Conventional laboratory diagnosis of toxoplasmosis is based on the presence of IgM and IgG anti-Toxoplasma gondii antibodies; however, molecular techniques have emerged as alternative tools due to their increased sensitivity. The aim of this study was to compare the performance of 4 PCR-based methods for the laboratory diagnosis of toxoplasmosis. One hundred pregnant women who seroconverted during pregnancy were included in the study. The definition of cases was based on a 12-month follow-up of the infants. Methods Amniotic fluid samples were submitted to DNA extraction and amplification by the following 4 Toxoplasma techniques performed with parasite B1 gene primers: conventional PCR, nested-PCR, multiplex-nested-PCR, and real-time PCR. Seven parameters were analyzed, sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), negative likelihood ratio (NLR) and efficiency (Ef). Results Fifty-nine of the 100 infants had toxoplasmosis; 42 (71.2%) had IgM antibodies at birth but were asymptomatic, and the remaining 17 cases had non-detectable IgM antibodies but high IgG antibody titers that were associated with retinochoroiditis in 8 (13.5%) cases, abnormal cranial ultrasound in 5 (8.5%) cases, and signs/symptoms suggestive of infection in 4 (6.8%) cases. The conventional PCR assay detected 50 cases (9 false-negatives), nested-PCR detected 58 cases (1 false-negative and 4 false-positives), multiplex-nested-PCR detected 57 cases (2 false-negatives), and real-time-PCR detected 58 cases (1 false-negative). Conclusions The real-time PCR assay was the best-performing technique based on the parameters of Se (98.3%), Sp (100%), PPV (100%), NPV (97.6%), PLR (∞), NLR (0.017), and Ef (99%).

Laboratory diagnosis of amebiasis in a sample of students from southeastern Brazil and a comparison of microscopy with enzyme-linked immunosorbent assay for screening of infections with Entamoeba sp.

Introduction: Epidemiological studies on amebiasis have been reassessed since Entamoeba histolytica and E. dispar were first recognized as distinct species. Because the morphological similarity of these species renders microscopic diagnosis unreliable, additional tools are required to discriminate between Entamoeba species. The objectives of our study were to compare microscopy with ELISA kit (IVD®) results, to diagnose E. histolytica infection, and to determine the prevalence of amebiasis in a sample of students from southeastern Brazil. Methods: In this study, diagnosis was based on microscopy due to its capacity for revealing potential cysts/trophozoites and on two commercial kits for antigen detection in stool samples. Results: For 1,403 samples collected from students aged 6 to 14 years who were living in Divinópolis, Minas Gerais, Brazil, microscopy underestimated the number of individuals infected with E. histolytica/E. dispar (5.7% prevalence) compared with the ELISA kit (IVD®)-based diagnoses (15.7% for E. histolytica/E. dispar). A comparison of the ELISA (IVD®) and light microscopy results returned a 20% sensitivity, 97% specificity, low positive predictive value, and high negative predictive value for microscopy. An ELISA kit (TechLab®) that was specific for E. histolytica detected a 3.1% (43/1403) prevalence for E. histolytica infection. Conclusions: The ELISA kit (IVD®) can be used as an alternative screening tool. The high prevalence of E. histolytica infection detected in this study warrants the implementation of actions directed toward health promotion and preventive measures.

Perfil imunológico de grávidas atópicas versus grávidas saudáveis

RESUMO: A prevalência das doenças atópicas tem vindo a aumentar, em especial ao nível dos países ocidentalizados. Vários fatores têm sido apontados para justificar este aumento de prevalência,destacando-se o reduzido tamanho das famílias, o elevado uso de antibióticos, a melhoria das condições sanitárias, bem como a diminuição quer das infeções de helmintas, quer da contaminação orofecal. Alguns estudos têm também avaliado a influência do ambiente pré-natal no desenvolvimento de atopia e asma. Da análise da literatura, parece inegável a importância deste período para o desenvolvimento do sistema imunitário. Neste âmbito, a transmissão de atopia à descendência em mulheres atópicas, e concretamente com asma alérgica, poderá ser moldada desde este período. A possibilidade de identificar marcadores de risco precoces para o desenvolvimento de atopia poderá ser o primeiro passo para o desenvolvimento de estratégias de prevenção para os indivíduos em risco. Este trabalho pretendeu abordar o sistema imunitário materno de forma a enriquecer a sua caraterização desde o terceiro trimestre da gravidez até ao fim do puerpério. Para além da exploração de perfis celulares e citocínicos maternos (nos quais se incluiu sobretudo a avaliação de diferentes populações de células T e B, com funções efetoras e reguladoras), foi também considerada a sua eventual relação com o desenvolvimento de atopia nas crianças. Foram recrutadas 135 mulheres com critérios para serem incluídas num dos 4 grupos do estudo: grávidas atópicas – GA (n=24), não grávidas atópicas – NGA (n=32), grávidas saudáveis – GS (n=44) e não grávidas saudáveis – NGS (n=35). Foram caraterizadas por Citometria de Fluxo populações de leucócitos e linfócitos, com particular interesse nos perfis maturativos de linfócitos T e B, bem como nas subpopulações de células T e B reguladoras. Foi ainda efetuada uma análise funcional, para avaliar a capacidade de produção de citocinas pelos linfócitos T e B. Foram igualmente avaliadas as concentrações de citocinas séricas por ensaios imunoenzimáticos. Estes parâmetros imunológicos maternos foram acompanhados desde o terceiro trimestre de gestação, até depois do puerpério (primeiras 6 semanas pós parto), e aos seis meses de idade, foi efetuada uma avaliação clínica das crianças. As mulheres não grávidas atópicas apresentaram contagens celulares mais elevadas para a generalidade das populações leucocitárias e linfocitárias (em relação a mulheres não grávidas saudáveis). Destaca-se ainda uma maior presença de eosinófilos nas mulheres NGA (p=0,0009; teste de Mann-Whitney U), que tinham igualmente os seus compartimentos linfocitários T e B mais ricos em células de memória, em relação às mulheres NGS. Para os perfis de regulação, verificou-se que as células T reguladoras se encontravam percentualmente aumentadas (p≤0,003; teste de Mann-Whitney U), tal omo as células T produtoras de IL10 após estimulação (p≤0,03; teste de Mann-Whitney U) em mulheres NGA. Também se observou uma maior expressão de Foxp3 (p=0,0002; teste de Mann-Whitney U), e ainda a diminuição dos níveis séricos de IFN-γ nas mulheres NGA (p=0,0019; teste de Mann-Whitney U), em relação a mulheres NGS. De um modo geral, as alterações verificadas nos parâmetros imunológicos de mulheres grávidas atópicas no terceiro trimestre da gravidez foram semelhantes às observadas em mulheres grávidas saudáveis. Comparadas com mulheres NGA, nas mulheres grávidas atópicas ocorreu uma alteração substancial da fórmula leucocitária, com um importante incremento de neutrófilos (p<0,0001; teste de Mann-Whitney U) e diminuição dos valores das restantes populações leucocitárias. A diminuição nas contagens de linfócitos totais estendeu-se a grande parte das subpopulações linfocitárias caraterizadas. Nos compartimentos linfocitários T e B foi possível observar uma diminuição das subpopulações de células de memória. Verificou-se igualmente na gravidez uma menor expressão de Foxp3 em mulheres GA (p<0,0001; teste de Mann-Whitney U) e ainda menos células B CD24HiCD38Hi circulantes (p=0,0012; teste de Mann-Whitney U). Ocrreu ainda uma diminuição relativa das células T CD4 produtoras de IFN-γ em mulheres GA (p≤0,024; teste de Mann-Whitney U), e uma maior presença de células T CD8 produtoras de IL17 (p=0,0172; teste de Mann-Whitney U), em relação ao observado em mulheres NGA. Depois do puerpério, no compartimento T de mulheres do grupo GA, verificou-se um aumento das populações de células de memória. Em comparação com a gravidez, após o puerpério o compartimento B, apresentou nas mulheres GA um aumento significativo da subpopulação de células B de transição (p<0,0001; teste de Wilcoxon). Verificou-se, igualmente em mulheres GA após o puerpério, uma maior expressão de Foxp3 nas células T reguladoras (p<0,0001; teste de Wilcoxon) e o aumento das populações de células T circulantes produtoras de IFN-γ (p≤0,0234; teste de Wilcoxon). As modulações das populações T e B desde a gravidez até depois do puerpério ocorreram de forma semelhante nas mulheres dos grupos GA e GS. Apesar de as mulheres GA manterem um perfil imunológico próximo do das mulheres GS depois do puerpério, aconteceu também neste período um processo de reaproximação ao perfil observado nas mulheres NGA. As mulheres GA com manifestações de risco para atopia na descendência (comparadas com mulheres GA sem manifestações de risco para atopia na descendência até aos 6 meses de vida) apresentaram uma maior proporção de células T e menor proporção de células B, percentagens mais elevadas de células T CD8 de memória efetoras, de células B de transição e de células B CD24HiCD38Hi, e contagens mais baixas de células B de memória. Na avaliação destes parâmetros como marcadores de risco para o desenvolvimento de atopia verificou-se que o parâmetro com melhor desempenho foi a percentagem de células B de transição, com uma Odds-Ratio de 54,0 [IC 95%: 4,2-692,9; (p=0,0005)], sensibilidade de 90,0% [IC 95%: 55,5 – 99,8] e especificidade de 85,7% [IC 95%: 57,2 – 98,2]. Este estudo foi pioneiro em Portugal, e no mundo, no que se refere ao acompanhamento do compartimento linfocitário B circulante, abordando o seu perfil de maturação, e em particular as células B com funções reguladoras, desde a gravidez até ao fim do puerpério, em mulheres atópicas e não atópicas. A este nível, encontram-se estudos na literatura a documentar a alteração do compartimento B durante a gravidez. O presente trabalho reporta agora que alterações, como a diminuição do número de células B em circulação, são impostas também na mulher atópica. Em suma, demonstrou-se a existência de um perfil imunológico caraterístico em mulheres atópicas, que sofre alterações significativas durante a gravidez, tendendo os parâmetros imunológicos a normalizar após o puerpério. O compartimento T, para o qual a literatura é mais rica em estudos e abordagens, demonstrou também neste trabalho oscilações caraterísticas entre o período pré e pós-natal. Verificaram-se sobretudo variações nos compartimentos de células T de memória, sem grandes alterações ao nível das células Treg no que se refere à sua presença em circulação. Apenas a registar a menor expressão de Foxp3 nas células Treg durante a gestação observada em mulheres atópicas, tal como em mulheres saudáveis (como também já foi relatado em estudos anteriores). Apesar de muitos dos dados se encontrarem em concordância com a literatura, quer no que se refere às subpopulações de células de memória, quer no que se refere às células Treg, também se encontram resultados discordantes, por exemplo documentando variações numéricas nas células Treg em circulação em mulheres atópicas e mulheres atópicas grávidas. A importância de harmonizar protocolos e fenótipos, parece crucial na abordagem de estudos futuros. Ao nível do risco para a atopia na descendência de mulheres atópicas, acrescentou-se ainda a possibilidade de definir marcadores não invasivos para a criança, em particular as células B de transição. Estas células, cuja maior presença em circulação no recém-nascido foi recentemente associada com manifestações alérgicas subsequentes, são agora apontadas já na mulher atópica, grávida do terceiro trimestre, como um elemento de risco para o desenvolvimento de atopia. Os marcadores de risco descritos, para além de facilmente poderem vir a ser englobados no âmbito dos normais rastreios maternos durante a gravidez, apresentam ainda a vantagem da precocidade do diagnóstico, permitindo não só a possibilidade de prevenção pós-natal, mas estendendo esta possibilidade ao período gestacional.----------------------------ABSTRACT: The prevalence of atopic diseases has been increasing, especially in Westernized countries. Several factors have been suggested to justify this increase in prevalence, as the small size of families, the high use of antibiotics, the improvement in sanitation conditions, as well as the reduction of both helminth infections, and orofecal contamination. A few studies have adressed the influence of prenatal environment on the development of atopy and asthma. From literature, it seems undeniable the importance of the prenatal period for the development of the immune system. In this context, the transmission of atopy to the progeny in atopic women, and specifically in women with allergic asthma, can be modulated from this period on. The ability to detect early risk markers for the development of atopic diseases may be the first step in the development of prevention strategies for individuals at risk. This study aimed to approach the maternal immune system in order to enrich its characterization from the third trimester of pregnancy until the end of the puerperium period. In addition to the evaluation of the maternal cellular profiles (in which, mostly, diferente populations of T and B cells with effector and regulatory functions were included) and citokines, the relation between these profiles and the development of atopy in the progeny was also assessed. 135 women were recruited for this study, and fullfiled the inclusion criteria necessary to be included in one of the four groups preset: atopic pregnant women - GA (n = 24), atopic nonpregnant women - NGA (n = 32), healthy pregnant women - GS (n = 44) and healthy nonpregnant women - NGS (n = 35). Populations of leukocytes and lymphocytes, and particularty maturation profiles of T and B lymphocytes, as well as subpopulations of T and B cells with regulatory functions, were characterized by flow cytometry. Functional assays were also performed, to assess the ability of cytokine production by T and B lymphocytes. Serum cytokine concentrations were assessed as well by enzymatic immunoassays. These maternal imune parameters were monitored since the third trimester of pregnancy until the end of the puerperium period (first six weeks after delivery). A clinical evaluation of all the newborn children was performed at the age of six months. Non-atopic pregnant women presented higher cell counts for most leukocyte and lymphocyte populations (compared to healthy non-pregnant women). We should also highlight the increased presence of eosinophils in NGA women (p = 0,0009; Mann-Whitney U test). Again compared to NGS women, NGA women showed increased memory cells within the circulating T and B lymphocyte compartments. Considering the regulatory profiles, NGA women presented higher percentages of regulatory T cells (p≤0,003; Mann-Whitney U test) and IL10 producing T cells after stimulation (p≤0,03; Mann Whitney U), as well as increased expression of Foxp3 (p = 0,0002; Mann-Whitney U test), and also decreased serum levels of IFN-γ (p = 0,0019; test Mann-Whitney U test) compared to NGS women. In general, the changes observed in immune parameters of atopic pregnant women in the third trimester of gestation were similar to those observed in healthy pregnant women. Comparing pregnant and non-pregnant atopic women, an important change in leukocyte subsets was observed, with a significant increase of neutrophils (p <0,0001; Mann-Whitney U test) and the consequent diminution of the remaining leukocyte populations in the GA group. The decrease in total lymphocyte counts was extended to most of the lymphocyte subsets characterized. It was possible to detect a decrease in memory cell subsets within the T and B lymphocyte compartments, also. During pregnancy, a lower expression of Foxp3 was reported in GA women (p <0,0001; Mann-Whitney U test) and, besides, lesser CD24HiCD38Hi B cells were present in circulation in these women, compared to NGA women (p = 0,0012; Mann-Whitney U test). There was still a decrease in the percentages of IFN-γ-producing CD4 T cells in GA women (p≤0,024; Mann-Whitney U test) and a greater presence of IL17-producing CD8 T cells (p = 0,0172; Mann-Whitney U test), compared to the levels observed in NGA women. At the end of the puerperium, there was an increase in memory cell subpopulations within the T cell compartment of GA women. Compared with the pregnancy evaluation, after puerperium, the B cell compartment showed a significant increase in the transitional subpopulation (p<0,0001; Wilcoxon test), in GA women. Moreover, after puerperium, GA women exhibited a greater expression of Foxp3 in Treg cells (p <0,0001; Wilcoxon test) and there was an increase in circulating IFN-γ-producing T cells (p≤0,0234; Test Wilcoxon). The modulations of T and B cell subpopulations from pregnancy until the end of puerperium were similar in women of GA and GS groups. Although at the end of puerperium, GA women still kept an immune profile close the one observed in GS women, at this time point, there were also signs of rapprochement between the immune profiles observed in women of GA and NGA groups. GA women with atopic manifestations in the offspring (compared to GA women without atopic manifestations in the offspring at the age of 6 months) presented higher proportions of T cells and lower proportions of B cells, higher percentages of effector memory CD8 T cells, transitional B cells and CD24HiCD38Hi B cells, and, finally, lower absolute counts of memory B cells. In the evaluation of these parameters as risk markers for the development of atopy, the parameter which presented the best performance was the percentage of transitional B cells, with an Oddsratio of 54,0 [95% CI: 4,2 to 692,9; (p = 0,0005)], sensitivity of 90,0% [95% CI: 55,5 to 99,8] and a specificity of 85,7% [95% CI: 57,2 to 98,2]. This study was a pioneer in Portugal, and in the world, in what concerns the monitoring of the circulating B cell compartment, addressing not only the maturation profile, but, in particular, B cells with regulatory functions, from pregnancy untill after puerperium, in atopic and non-atopic women. Literature presents evidence of a typical change in circulating B cells during pregnancy. This study now reports that changes, such as the decrease in the number of circulating B cells,/ are also imposed by pregnancy in atopic woman. In brief, it demonstrated the existence of a characteristic immune profile in atopic women, which undergoes significant alterations during pregnancy, tending to normalize after the puerperium. As for the T cell compartment, for which the literature is richer in studies and approaches, this study also showed characteristic fluctuations between the pre- and postnatal periods. There were variations mostly in the memory subsets within the T cell compartment, without major changes in regulatory T cells regarding their presence in circulation. Only the expression of Foxp3 in Treg cells presented lower levels during pregnancy, in both atopic and healthy women (as previously reported in other studies). Although much of the data now reported are in agreement with literature, regarding either memory cell subsets or regulatory T cells, there are also conflicting results, for example documenting changes in the numbers of regulatory T cells circulating in atopic pregnant and atopic non-pregnant women. The importance of harmonizing protocols and phenotypes seems crucial for the establishement of future studies. Considering the risk for atopy in the offspring of atopic women, this study added the possibility to define non-invasive markers for the child, in particular transitional B cells. These cells, whose greater presence in circulation in newborns has recently been associated with subsequent allergy development, are here identified in atopic pregnant women in the third trimester of gestation as a risk factor in the development of atopy in their progeny. The risk factors described, besides having the capacity to easily become integrated within the normal maternal screening protocols during pregnancy, also have the advantage of an early diagnosis, allowing not only the possibility of postnatal prevention but extending this possibility to the prenatal period.

Malaria in the State of Amazonas: a typical Brazilian tropical disease influenced by waves of economic development

In Brazil, more than 99% of malaria cases are reported in the Amazon, and the State of Amazonas accounts for 40% of this total. However, the accumulated experience and challenges in controlling malaria in this region in recent decades have not been reported. Throughout the first economic cycle during the rubber boom (1879 to 1912), malaria was recorded in the entire state, with the highest incidence in the villages near the Madeira River in the Southern part of the State of Amazonas. In the 1970s, during the second economic development cycle, the economy turned to the industrial sector and demanded a large labor force, resulting in a large migratory influx to the capital Manaus. Over time, a gradual increase in malaria transmission was observed in peri-urban areas. In the 1990s, the stimulation of agroforestry, particularly fish farming, led to the formation of permanent Anopheline breeding sites and increased malaria in settlements. The estimation of environmental impacts and the planning of measures to mitigate them, as seen in the construction of the Coari-Manaus gas pipeline, proved effective. Considering the changes occurred since the Amsterdam Conference in 1992, disease control has been based on early diagnosis and treatment, but the development of parasites that are resistant to major antimalarial drugs in Brazilian Amazon has posed a new challenge. Despite the decreased lethality and the gradual decrease in the number of malaria cases, disease elimination, which should be associated with government programs for economic development in the region, continues to be a challenge.

Hydronephrosis in Schinzel-Giedion syndrome: an important clue for the diagnosis

Schinzel-Giedion syndrome is a rare autosomal recessive disorder characterized by coarse facies, midface retraction, hypertrichosis, multiple skeletal anomalies, and cardiac and renal malformations. Craniofacial abnormalities of this syndrome sometimes resemble a storage or metabolic disease. The pathogenesis of the disease remains unknown. The objective of this report was to emphasize the importance of congenital bilateral hydronephrosis for the diagnosis of Schinzel-Giedion syndrome. We describe the first Brazilian case of a newborn with typical facies, generalized hypertrichosis, cardiac and skeletal anomalies, and bilateral hydronephrosis detected during pregnancy and confirmed later by abdominal ultrasonography. Chromosomal constitution was normal. Of the 35 cases already reported in the literature, 31 presented hydronephrosis, which is considered an important clue in diagnosis. If Schinzel-Giedion syndrome were indexed as a cause of congenital hydronephrosis, its identification would be greatly facilitated, since the majority of the other findings in Schinzel-Giedion syndrome are nonspecific and common to many genetic syndromes.

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.

Changes in population and land use over time in the Ecuadorian Amazon

This paper draws upon a detailed longitudinal survey of households living on agricultural plots in the northern three provinces of the Ecuadorian Amazon, the principal region of colonization by migrants in Ecuador since the 1970s. Following the discovery of petroleum in 1967 near what has subsequently come to be the provincial capital and largest Amazonian city of Lago Agrio, oil companies built roads to lay pipelines to extract and pump oil across the Andes for export. As a result, for the past 30 years over half of both Ecuador's export earnings and government revenues have come from petroleum extracted from this region. But the roads also facilitated massive spontaneous in-migration of families from origin areas in the Ecuadorian Sierra, characterized by minifundia and rural poverty. This paper is about those migrants and their effects on the Amazonian landscape. We discuss the data collection methodology and summarize key results on settler characteristics and changes in population, land use, land ownership, technology, labor allocation, and living conditions, as well as the relationships between changes in population and changes in land use over time. The population in the study region has been growing rapidly due to both natural population growth (high fertility) and in-migration. This has led to a dramatic process of subdivision and fragmentation of plots in the 1990's, which contrasts with the consolidation of plots that has occurred in most of the mature frontier areas of the Brazilian Amazon. This fragmentation has led to important changes in land tenure and land use, deforestation, cattle raising, labor allocation, and settler welfare.

Methodology for real-time adaptation of tunnels support using the observational method

The observational method in tunnel engineering allows the evaluation in real time of the actual conditions of the ground and to take measures if its behavior deviates considerably from predictions. However, it lacks a consistent and structured methodology to use the monitoring data to adapt the support system in real time. The definition of limit criteria above which adaptation is required are not defined and complex inverse analysis procedures (Rechea et al. 2008, Levasseur et al. 2010, Zentar et al. 2001, Lecampion et al. 2002, Finno and Calvello 2005, Goh 1999, Cui and Pan 2012, Deng et al. 2010, Mathew and Lehane 2013, Sharifzadeh et al. 2012, 2013) may be needed to consistently analyze the problem. In this paper a methodology for the real time adaptation of the support systems during tunneling is presented. In a first step limit criteria for displacements and stresses are proposed. The methodology uses graphics that are constructed during the project stage based on parametric calculations to assist in the process and when these graphics are not available, since it is not possible to predict every possible scenario, inverse analysis calculations are carried out. The methodology is applied to the “Bois de Peu” tunnel which is composed by two tubes with over 500 m long. High uncertainty levels existed concerning the heterogeneity of the soil and consequently in the geomechanical design parameters. The methodology was applied in four sections and the results focus on two of them. It is shown that the methodology has potential to be applied in real cases contributing for a consistent approach of a real time adaptation of the support system and highlight the importance of the existence of good quality and specific monitoring data to improve the inverse analysis procedure.