There are approximately 2.5 million cases of multiple sclerosis [MS] in the world. Each year, around 10,000 new cases of MS are diagnosed. There are approximately 0.1%. in the Czech Republic and that means that there are approximately 15,000 people with this disease. Multiple sclerosis is a progressive neurological inflammatory disease of the central nervous system in pathogenesis. The auto-immune mechanisms are appliedinvolves; both the affect the myelin and damaged axons. This damage is responsible for the permanent disability of MS. The main objective of this thesis was to use quantitative research to describe the occurrence of MS in the Regions of South Bohemia and Usti, and within objective to estimate the true prevalence of multiple sclerosis in the South and the Usti Regions. MUDr. Príkaszký and I used the method of descriptive epidemiological studies on the technique of data collection, as well as the analysis and the comparison of two sources using the double-capture method. As a research area, we used a set of patients with multiple sclerosis. The data were gathered in two regions of the Czech Republic: Usti nad Labem Region and South Bohemia. We investigated the number of patients from neurologists and MS centers in both regions.There is also the data on health insurance included with the Ústí Region in this research. According to the data, we estimated the prevalence of neurologists in South Bohemia to be 79.20 per 100,000 people. The MS Center at the hospital in Ceske Budejovice has registered 512 patients: 388 women and 124 men. The values of the MS Centre in Ceske Budejovice received from the neurologists are a total of 882 patients, which is a prevalence of 138.6 patients per 100,000 of the population. Regarding the Usti Region, the prevalence reported by neurologists is 208.2 per 100 000 people. The MS Center at the hospital in Teplice, has registered 1139 sick 730 women and 409 men. According to health insurance data in their database, of 1187 people listed with a diagnosis of G.35, 333 are men and 854 are women. This represents an estimate of the prevalence 305/100000 of the people who are registered in the NGA. We calculated the prevalence of illnesses from those sources in both of these regions is higher than the general estimates. When comparing the data source of health insurance and the model file from the MS center of Ústí Region, we calculated the overall sensitivity of 91.7% within a health insurance group. The calculation of the estimated prevalence has been reached by using the method of double-capture of those sources that provided an estimate of 2,681 patients in the Usti Region. The models of this data are mainly demonstrated as a possible approach to the estimate of the prevalence of this chronic disease in the case of multiple sclerosis. The information has been obtained from the collection of data. The results of this study can be used by other workers who have the same objective as this study.

Longitudinal data are common in biological research. However, real data sets vary considerably in terms of their structure and complexity and present many challenges for statistical modelling. This thesis proposes a series of methods using random coefficients for modelling two broad types of longitudinal response: normally distributed measurements and binary recapture data. Biased inference can occur in linear mixed-effects modelling if subjects are drawn from a number of unknown sub-populations, or if the residual covariance is poorly specified. To address some of the shortcomings of previous approaches in terms of model selection and flexibility, this thesis presents methods for: (i) determining the presence of latent grouping structures using a two-step approach, involving regression splines for modelling functional random effects and mixture modelling of the fitted random effects; and (ii) flexible of modelling of the residual covariance matrix using regression splines to specify smooth and potentially non-monotonic variance and correlation functions. Spatially explicit capture-recapture methods for estimating the density of animal populations have shown a rapid increase in popularity over recent years. However, further refinements to existing theory and fitting software are required to apply these methods in many situations. This thesis presents: (i) an analysis of recapture data from an acoustic survey of gibbons using supplementary data in the form of estimated angles to detections, (ii) the development of a multi-occasion likelihood including a model for stochastic availability using a partially observed random effect (interpreted in terms of calling behaviour in the case of gibbons), and (iii) an analysis of recapture data from a population of radio-tagged skates using a conditional likelihood that allows the density of animal activity centres to be modelled as functions of time, space and animal-level covariates.

RESUMO Introdução - Estima-se que 2 por cento da população mundial esteja infectada pelo Vírus da Hepatite C e assim, a hepatite C é considerada importante problema de saúde pública por sua magnitude e gravidade. O uso de bancos de dados, originados pelos serviços de saúde, pode ser uma alternativa aos tradicionais inquéritos epidemiológicos de base populacional. Conjugar o desenvolvimento na área dos sistemas de informação com a necessidade de avançar no conhecimento das doenças importantes para a saúde pública é o desafio que se coloca no cenário da pesquisa epidemiológica. Objetivos - Estimar a subnotificação e a prevalência da hepatite C, no município de São Paulo, no período de 2003 a 2008, usando o método de captura-recaptura e descrever o perfil dos casos registrados em quatro Sistemas de Informação em Saúde. Método - Estudo transversal usando dados secundários registrados no Sistema de Informação de Agravos de Notificação (SINAN), no Sistema de Informação de Mortalidade (SIM), no Sistema de Informação Hospitalar (SIH) e no Sistema de Comunicação Hospitalar (CIH), empregando o método de captura e recaptura. Os bancos SIH e CIH foram unificados para o cálculo da estimativa de casos de hepatite C usando o método de capturarecaptura com a aplicação do modelo log-linear. Resultados O SINAN permitiu detectar características importantes dos portadores da hepatite C, como o uso de drogas injetáveis e inaláveis, a co-infecção com o VHB e com o HIV. A subnotificação estimada de casos de hepatite C no SINAN, em relação ao SIH, SIM e CIH, separadamente, foi de 60,3 por cento (IC95 por cento: 58,3 por cento;62,1 por cento), 73,7 por cento (IC95 por cento: 71,9;75,3 por cento) e 83,1 por cento (IC95 por cento: 66,9 por cento;84,9 por cento), respectivamente. O número estimado de casos de hepatite C utilizando três fontes de dados e com a aplicação do modelo log-linear foi de 56.935 (IC95 por cento por cento: 53.154;61.192).Com este resultado estimou-se a subnotificação de 75,5 por cento (IC95 por cento: 73,7 por cento;77,2) e a prevalência da hepatite C de 0,5 por cento (IC95 por cento: 0,50;0,57 por cento). Conclusões A elevada subnotificação encontrada deve desencadear medidas que tornem o Sistema de Vigilância Epidemiológica da hepatite C mais ativo na captação de casos da doença. O método de captura-recaptura é útil para a prática dos serviços de vigilância epidemiológica e a prevalência encontrada neste estudo refere-se aos casos mais graves de hepatite C / Summary Introduction It has been estimated that 2 per cent of the worlds population are infected with Hepatitis C Virus and, thus, hepatitis C is considered a major public health problem due to its magnitude and severity. The use of datasets, originated from health services, can be an alternative to traditional population-based surveys. Combining information systems development with the need of enhanced knowledge of diseases of public health importance is the challenge that is put forward in the epidemiological research scenario. Objectives To estimate the under-reporting and the prevalence of hepatitis C, in the city of São Paulo, in the period 2003 to 2008, using the capture-recapture method and to describe the cases recorded in four Health Information Systems. Method Cross-sectional study using secondary data from: the Information System for Notifiable Diseases (ISND), the Mortality Information System (MIS), the Hospital Information System (HIS), and from the Hospital Communication Information System (HCIS) employing the capture-recapture method. The HIS and HCIS datasets were merged together to estimate the total number of hepatitis C cases using the capture-recapture method with log-linear modeling. Results The ISND dataset allowed detecting important characteristics of the hepatitis C carriers, as the use of injecting and inhaled drugs and the co-infection with the HBV and HIV. The estimated under-reporting of hepatitis C cases in the ISND, when comparing with the HIS, MIS and CHIS, separately, was 60.3 per cent (CI95 per cent: 58.3 per cent;62.1 per cent), 73.7 per cent (CI95 per cent: 71.9;75.3 per cent) e 83.1 per cent (CI95 per cent: 66.9 per cent;84.9 per cent), respectively. The estimated number of hepatitis C cases using three data sources and log-linear modeling was 56,935 (CI95 per cent: 53,154;61,192). With this result it was estimated an under-reporting of 75.5 per cent (CI95 per cent: 73.7 per cent;77.2 per cent) and a prevalence of hepatitis C of 0.53 per cent (CI95 per cent: 0.50 per cent;0.57 per cent). Conclusions The elevated underreporting found must lead to measures that make the Epidemiologic Surveillance System of hepatitis C more active in the capture of cases of the disease. The capture-recapture method is useful for the practice of epidemiological surveillance services and the prevalence found in this study refers to the severer cases of hepatitis C

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Aims: To estimate the number of street children and adolescents in Maceió and Arapiraca, northeast Brazil, describe the characteristics of this population. Methods: The number of children and adolescents in street situation in Maceió and Arapiraca was estimated using the Capture-Recapture method and calculated with log-linear method. Three independent lists of children and adolescents in street situation of each municipality were constructed. In each municipality in was obtained on official list and two other lists from surveys. Each survey took the entire day, the first in a week day (Wednesday) and the other in the following Saturday. The characteristics of the children were recorded during the street surveys. Results: The estimated number of children and adolescents in street situation was 4965 in Maceió and 466 in Arapiraca. The population estimated before was 565 in Maceió and 158 in Arapiraca. In Maceió most street children and adolescents were male (71,4%) and (71,80%), who maintain contact with their families (85,3%) and (89,60%) and frequent the school (43,4% and (49,70%), drug use was referred for 47,00% of the children and adolescents in Maceió and (26,6%) in Arapiraca glue associated on not with other drug was the most cited one. Conclusion: children and adolescents in street situation is a common event in Maceió and Arapiraca and individuals envolved have similiar characteristics to street children from other countries and other cities in Brazil. The estimated number of street children and adolescents, calculated by Capture-Recapture method is coherent to the cities socioeconomic and demographic status. The method of Capture-Recapture seems to be suited to study mobile populations such as street children and adolescent good reproducibility. / Objetivo - Estimar o número de crianças e adolescentes em situação de rua em Maceió e Arapiraca, nordeste do Brasil, usando o método Captura-Recaptura, descrever suas características. Metodologia - O número de crianças e adolescentes em situação de rua em Maceió e Arapiraca dois municípios do estado de Alagoas, foi estimado usando o método Captura-Recaptura, calculado pelo método log linear. Três listas independentes de crianças e adolescentes em situação de rua de cada município foram construídas, através de uma lista de registro de uma organização governamental e de duas pesquisas realizadas em cada município estudado, em um dia de semana (quarta-feira) e no sábado. As características destas crianças foram registradas durante as pesquisas de rua. Resultados - A estimativa do número de crianças de rua foi de Maceió foi de 4965 e de Arapiraca foi de 466. A estimativa oficial desta população antes da pesquisa era de 565 em Maceió e de 158 em Arapiraca. Em Maceió e Arapiraca a maioria das crianças e adolescentes são do sexo masculino (71,4%) e (71,80%), preserva contato com seus familiares (85,4%) e (89,60%) e ainda freqüenta a escola (43,6%) e (49,70%). O uso de drogas em Maceió foi referido por 47,0% das crianças e adolescentes de Maceió e 26,6% de Arapiraca, sendo a cola a droga mais usada, associada ou não a outras drogas. Conclusão - Crianças e adolescentes em situação de rua em Maceió e Arapiraca é um evento muito constante e as crianças envolvidas têm características similares às de crianças de rua de outros países e cidades do Brasil. A estimativa do número de crianças e adolescentes em situação de rua pelo método Captura-Recaptura, reflete o esperado quando comparado através de indicadores socioeconômicos, com cidades de porte semelhante (Aracaju). O Método Captura-Recaptura é adaptável e adequado para estudar populações móveis como crianças e adolescentes em situação de rua, possuindo boa reprodutibilidade.

I confronted empirical habitat data (1994-2004) and population data (1988-2005) with ecological theory on habitat dynamics, recruitment, survival, and dispersal to develop predictive relationships between landcover variation and population dynamics. I focus on Florida Scrub-Jays, although one chapter presents a model for the potential influence of habitat restoration on viability of the Florida Grasshopper Sparrow. Both species are unique to Florida landscapes that are dominated by shrubs and grasses and maintained by frequent fires. Both species are declining, even in protected areas, despite their protected status. I mapped habitat for both species using grid polygon cells to quantify population potential and habitat quality. A grid cell was the average territory size and the landcover unit in which habitat-specific recruitment and survival occurred. I measured habitat-specific recruitment and survival of Florida Scrub-Jays from 1988-2008. Data analyses included multistate analysis, which was developed for capture-recapture data but is useful for analyzing many ecological processes, such as habitat change. I relied on publications by other investigators for empirical Florida Grasshopper Sparrow data. The amount of potential habitat was greatly underestimated by landcover mapping not specific to Florida Scrub-Jays. Overlaying east central Florida with grid polygons was an efficient method to map potential habitat and monitor habitat quality directly related to recruitment, survival, and management needs. Most habitats for both species were degraded by anthropogenic reductions in fire frequency. Degradation occurred across large areas. Florida Scrub-Jay recruitment and survival were most influenced by shrub height states. Multistate modeling of shrub heights showed that state transitions were influenced by vegetation composition, edges, and habitat management. Measured population declines of 4% per year corroborated habitat-specific modeling predictions. Habitat quality improved over the study period but not enough to recover precariously small populations. The degree of landcover fragmentation influenced mean Florida Scrub-Jay dispersal distances but not the number of occupied territories between natal and breeding territories. There was little exchange between populations, which were usually further apart than mean dispersal distances. Florida Scrub-Jays bred or delayed breeding depending on age, sex, and breeding opportunities. I show an urgent need also for Florida Grasshopper Sparrow habitat restoration given that the endangered bird has declined to only two sizeable populations and there is a high likelihood for continued large decline. A major effect of habitat fragmentation identified in this dissertation that should apply to many organisms in disturbance prone systems is that fragmentation disrupts natural processes, reducing habitat quality across large areas. Humans have managed wildland fire for > 40,000 years, so it should be possible to manage habitat for many endangered species that make Florida's biodiversity unique. This dissertation provides methods to quantify landscape units into potential source and sink territories and provides a basis for applying adaptive management to reach population and conservation goals.

Significant efforts in conservation are devoted to the management and study of ungulates, due to their significant roles in ecosystems as well as their potential economic value. This is especially true for species considered exotic, such as mouflon sheep (Ovis musimon) in Hawaii. Effective management of an exotic species requires an understanding of ecological metrics such as space use, survival, and population size. We provided these metrics for a population of mouflon that have hybridized with feral sheep (Ovis aries) on the island of Hawaii. In Chapter 1, we quantified space use and annual survival of sheep in an area where sheep are managed for hunting opportunity. We determined that sheep have relatively small home-ranges and high rates of annual survival (>90%). In Chapter 2, we provided the first estimate of population size for the same study area while simultaneously testing the viability of a novel method of estimating population size, currently known as Instantaneous Sampling. Using photographic capture recapture as a comparison method, we compared estimates derived from both techniques and provided support for Instantaneous Sampling as an alternative method for estimating population size.

We studied the dynamic of nine populations of Alpine ibex ( Capra ibex ibex ) in five protected areas. We showed a strong effect of age on demographic parameters, with a marked decrease of survival after 10-12 years of age. We also found a high variability of old females' reproduction between populations. Contrary to what is expected for a highly dimorphic species like ibex, males survived as well as females except for old individuals. Winter harshness had a negative impact on survival of old individuals but not on reproduction and survival of young. We conclude that ibex have evolved a highly conservative life-history tactic compared to other ungulates studied to now. From a management viewpoint we also showed that under some circumstances ground counts might provide reliable estimates of ibex population trends.

En Europe, la présence de grands carnivores dans des paysages anthropisés entraîne une forte compétition avec l'homme et alimente d'importantes polémiques concernant leur protection légale. La perception antagoniste de ces espèces à la fois emblématiques pour certains et sources de conflits pour d'autres, rend la gestion de leurs populations très délicate. Depuis la recolonisation spontanée du loup (Canis lupus) dans les Alpes françaises au début des années 1990, la population s'est accrue numériquement et spatialement. Parallèlement, les dégâts occasionnés par le loup sur la filière élevage ont suivi la même tendance. L'Etat met en place aujourd'hui un contrôle raisonné de la population, sous réserve que les objectifs de conservation, exigés par la Directive Habitat, soient respectés. En s'inspirant du cas d'étude du loup en France, nous proposons dans cette thèse un cadre de prise de décision structurée adapté pour la gestion et la conservation d'espèces rares et difficilement observables, protégées par des accords législatifs mais qui, dans un contexte social conflictuel, peuvent être régulées. La modélisation séquentielle du processus décisionnel s'est déroulée dans un contexte de forte incertitude selon plusieurs étapes : 1) appréhender les objectifs de conservation et/ou contrôle du loup en France pour les formaliser sous forme mathématique via une fonction d'utilité, 2) suivre la population par une méthode non-invasive pour définir des indicateurs de gestion fiables et évaluer le statut de conservation de la population, 3) coupler les mesures létales adoptées actuellement à un modèle démographique décrivant la dynamique du loup et intégrant sa structure sociale, 4) et déterminer la décision. Cette dernière étape est réalisée à l'aide d'une méthode d'optimisation qui calcule la stratégie optimale de gestion en fonction de la structure sociale de la population et des différentes sources d'incertitude accumulées à chaque étape du processus décisionnel. Nous avons choisi comme indicateur de gestion le taux de croissance, à partir duquel nous avons défini l'utilité. Cet indicateur était robuste à l'incertitude d'échantillonnage émergeant de la détection partielle et hétérogène des individus. Des analyses de sensibilité de la décision ont montré une forte influence de la fonction d'utilité sur la stratégie optimale, soulignant ainsi l'importance de définir correctement les objectifs. Nous avons également montré que la stratégie optimale était sensible aux variations des paramètres démographiques, montrant ainsi l'intérêt des méthodes de capture-marquage-recapture pour les estimer correctement. Nous discutons enfin de l'extension de notre approche à un cadre décisionnel de gestion adaptative pour traiter des problèmes de conservation dans un contexte conflictuel. / Large carnivore management in Europe is controversial because of conflictive objectives arising from the legal protection of threatened species vs. the possible necessity of culling individuals to prevent severe damages on human activities. Since the wolf recovery in the French Alps in the early 90's, the population has been numerically and spatially increasing. In parallel, livestock depredations have been following the same trend. As an EU member state, France is bound to the European Habitat Directive, which provides full protection of wolf populations and their habitat. Nevertheless, derogatory killings are allowed for individuals causing problems on livestock and some lethal control is now incorporated into the national management plan, as long as the population growth and its distribution range are not being threatened. Illustrating with the case study of the wolf in France, my dissertation proposes a structured decision making framework for the management and the conservation of elusive species that are legally protected but, in a conflictive context, are subject to population control. The sequential modeling of our decision process occurred in the following steps: 1) define the multiple objectives and formulate them in terms of a utility function, 2) monitor the population through a non-invasive approach in order to define the population conservation status, 3) build a demographic model to predict the consequences of harvesting on population dynamics and social structure, 4) obtain optimal state-dependent decisions. The last step is done with stochastic dynamic programming (SDP), acknowledged to be one of the most useful optimization methods in decision making. We provide an optimal solution for wolf management that gives the highest chance of meeting objectives, defined on population growth rate. This demographic indicator was found to be robust to sampling uncertainty arising from partial and heterogeneous detection of individuals. We ran decision sensibility analyses and found a strong effect of the utility function on the optimal strategy, highlighting the importance of defining explicit objectives. We also found that the optimal strategy was sensitive to demographic parameters, which demonstrate the general need of using solid statistical approaches to estimate them properly. This structured decision making framework can further be extended to adaptive management, acknowledged as being a convenient framework for wildlife management.

La perte d’habitat et la fragmentation sont les principales causes de déclin des amphibiens en Europe de l’ouest. Malgré les réglementations mises en place concernant la construction de nouvelles infrastructures, le manque de connaissances fondamentales concernant les espèces et leurs habitats rendent difficiles l’évaluation des impacts ainsi que la mise en place de solutions efficaces pour conserver la biodiversité. En se basant sur l’exemple du triton marbré (Triturus marmoratus), espèce protégée présente dans l’ouest de la France, ce travail vise à évaluer la pertinence des méthodes de terrain et de modélisation disponibles pour la récolte des données nécessaires à la caractérisation de la dynamique des populations chez cette espèce. Pour ce faire, deux populations de tritons marbrés (Loire Atlantique et Vendée) ont été étudiées grâce à des techniques de comptages à la lampe, piégeage, utilisation d’épuisettes avec un suivi intensif par capture-marquage-recapture (CMR), complété par la méthode de l’ADN environnemental (ADNe). Dans une première partie ce travail a permis de montrer que dans le cadre de la caractérisation quantitative de la dynamique d’une population, les informations apportées par la CMR sont les plus fiables. Ceci est notamment dû au taux de détection faible et hétérogène dans l’espace et dans le temps du triton marbré, qui ne permet pas aux autres méthodes s’en affranchissant de produire des résultats reproductibles et transposables. L’ADNe est la méthode permettant d’estimer l’occurrence le plus efficacement mais la possibilité d’une utilisation pour estimer des abondances absolues voire des abondances relatives reste du domaine des perspectives prometteuses mais non abouties à ce jour. Dans un second chapitre, nous avons montré comment les récentes avancées méthodologiques dans les approches de modélisation permettent de déterminer le temps passé par une espèce sur un site grâce aux données de CMR. Ces méthodes ont été appliquées au triton marbré pour mettre en évidence une phénologie particulière avec des individus arrivant et repartant du site de reproduction de manière non simultanée et n’occupant chacun la mare qu’une partie de la période de reproduction. L’ensemble de ces résultats permettent de définir un cadre méthodologique adapté pour développer un suivi dans le temps des mesures de compensation envisagées dans le cadre du projet de construction, mais aussi pour le suivi des populations d’urodèles en général. / Habitat loss and fragmentation are the main causes of amphibian decline in Western Europe. In spite of regulations concerning the construction of new infrastructures, the lack of knowledge concerning species and their habitat make difficult to evaluate the impact as well as the implementation of effective solutions to preserve biodiversity. Using the example of marbled newt (Triturus marmoratus), a protected species presents in Western France, this works aims at estimating the relevance of the fieldwork and modeling methods available to obtain data necessary for characterizing the dynamic of population for this species. To do so, two populations of marbled newts (situated in Loire Atlantique and Vendée) were studied using torch counts, traps, dip nets, with an intensive capture recapture (CR) protocol, and environmental DNA (eDNA) method. In the first part, this work allowed us to show that within the framework of quantitative characterization of the dynamics of a population, the information gathered by CR is the most reliable. This is especially due to the low and heterogeneous detection rate in space and time for marbled newt, which does not allow traditional methods to get reproducible and transposable results. eDNA is the most accurate method when it comes to estimating occurence but the possibility to use it to estimate absolute or even relative abundances stays a promising perspective that did not succeed yet. In a second chapter, we showed how recent methodological advances in modeling approaches allow estimating time spent by a species in a site thanks to CR data. These methods were applied to marbled newts to highlight a particular phenology, with arriving and leaving individuals being not simultaneous but progressive and each individual occupying the pond only for a part of the breeding season. These results allows to define a methodological frame adapted to develop long term studies of compensation measures within the framework of the construction project, but also more generally for future studies of urodele species.

Made available in DSpace on 2016-06-02T20:06:11Z (GMT). No. of bitstreams: 1 DissMP.pdf: 748309 bytes, checksum: b6a638a5f9ec09f6622480b42f13d699 (MD5) Previous issue date: 2006-02-22 / Financiadora de Estudos e Projetos / This work has as main objective to insert covariates in the capture probability of the multiple capture-recapture method for closed animal population. Factors like climate, seasons of the year, animal size, could a¤ect the animal capture probability. We revise the methodology concepts, we make a study about the posteriori parameters sensibility, we present new parameters for the capture probability in specific situations and we insert covariates in the model used by Castledine (1981) through bayesian methods. The bayesian analysis was made through several studies of stochastic simulation through MCMC (Monte Carlo Markov Chain) with simulated and real data to obtain the population size posteriori results. / Este trabalho tem como objetivo principal a inserção de covariáveis nas probabilidades de captura do método de captura-recaptura múltipla para população fechada. No caso de população animal, por exemplo, fatores como clima, época do ano, tamanho do animal, podem afetar a probabilidade de captura do animal. Revisamos os conceitos da metodologia, fazemos um breve estudo sobre a sensibilidade das estimativas a posteriori em relação a escolha dos hiperparâmetros, apresentamos uma reparametrização para a probabilidade de captura em situações específicas e, motivados nessa reparametrização, inserimos covariáveis no modelo proposto por Castledine (1981) por meio de métodos bayesianos. A análise bayesiana foi feita através de vários estudos de simulação estocástica via MCMC (Monte Carlo Markov Chain) com dados simulados e reais para obter os resultados a posteriori do tamanho populacional.