There are a huge number of pathogens with multi-component transmission cycles, involving ampli_er hosts, vectors, complex pathogen life cycles and particular environmental conditions. These complex systems present challenges in terms of modeling and policy development. The deadliest tick-borne infectious disease in the world, the Brazilian Spotted Fever (BSF), is a relevant example of that. The current increase of human cases of BSF has been associated with the presence and expansion of capybaras Hydrochoerus hydrochaeris, amplifer host for the agent Rickettsia rickettsii and primary host for the tick vector Amblyomma sculptum. The objective of this thesis was to analyze the dynamics of the FMB with the purpose of providing bases for the planning of strategies focused on the prevention of human cases. We proposed diferent approaches to evaluating: i) the contribution of hosts and vectors in the transmission of BSF, ii) potential risk areas and anthropogenic parameters associated with the occurrence of human cases, iii) the pattern and the spatial propagation velocity of BSF, and iv) climatic and landscape factors that could be related to the distribution of the vector. The proposed approaches elucidated how BSF control and prevention strategies can be focused on the management of amplifier hosts populations. We found that geographical barriers generated, for example, by areas of riparian reforestation, could prevent the spatial spread of BSF, since a positive association between the occurrence of human cases and the increment of sugarcane crop was determined, as well as a higher propagation velocity of BSF in places with higher carrying capacity. This thesis was interdisciplinary and required, on one hand, expertise in biology, computational epidemiology, mathematics and statistics and on the other hand, a datarich environment such as the Laboratory of Parasitology of the VPS/FMVZ/USP. The results of this thesis can be usefulness in the planning of public health policies related to the prevention of BSF. Furthermore, this work will open the path to further mathematical and computational studies focused on the dynamics and prevention of other vector-borne infectious diseases. / Existe um grande número de agentes patogênicos com ciclos de transmissão complexos, envolvendo hospedeiros amplificadores, vetores e condições ambientais particulares. Esses sistemas complexos apresentam desafios quanto a modelagem e desenvolvimento de políticas públicas. A Febre Maculosa Brasileira (FMB) é a doença transmitida por carrapatos mais letal do mundo e é um claro exemplo de um sistema complexo. O aumento atual de casos humanos de BSF tem sido associado à presença e expansão de capivaras Hydrochoerus hydrochaeris, hospedeiros amplificadores do agente Rickettsia rickettsii e hospedeiros primários do carrapato vetor Amblyomma sculptum. O objetivo desta tese foi analisar a dinâmica da FMB com o propósito de fornecer bases para o delineamento de estratégias de prevenção de casos em humanos. Diferentes abordagens foram propostas para avaliar: i) a contribuição específica de hospedeiros e vetores na transmissão da FMB, ii) os parâmetros antropogênicos associados com a ocorrência dos casos e potenciais áreas de risco, iii) o padrão e a velocidade de propagação espacial e da doença, e iv) os fatores climáticos e paisagísticos que poderiam estar relacionados à distribuição do vetor. Os modelos propostos elucidaram que as estratégias de controle e prevenção da FMB podem estar focadas em práticas de manejo das populações de hospedeiros amplificadores. Uma vez que uma associação positiva entre ocorrência de casos humanos e o incremento de cultura de cana-de-açúcar foi determinada, assim como uma maior velocidade de propagação da FMB em locais com alta quantidade desta cultura, barreiras geográficas geradas, por exemplo, por zonas de reflorestamento ciliar, poderiam impedir a disseminação da FMB. Esta tese foi interdisciplinar e exigiu, por um lado, conhecimentos em biologia, epidemiologia computacional, matemática e estatística e, em contrapartida, um ambiente rico em dados biológicos como o Laboratório de Parasitologia do VPS/USP. Os resultados desta tese poderão ser utilizados na planificação de políticas de saúde pública enfocadas à prevenção da FMB. Complementarmente, este trabalho abrirá o caminho para futuros estudos matemáticos e computacionais orientados no estudo da dinâmica e prevenção de outras doenças infecciosas transmitidas por vetores.

Foi estruturado um modelo de servidor de mapas, na plataforma MapGuide, capaz de disseminar eletrônicamente os dados geoespaciais gerados pela Prefeitura de Taboão da Serra SP. O projeto de servidor visou duas finalidades principais: implementar este tipo de tecnologia ao analista responsável pelo projeto, no âmbito da Prefeitura, e; tornar a dissertação um guia teóricometodológico introdutório a profissionais da Cartografia e Geociências, não especializados com este ramo das geotecnologias. O serviço de disseminação foi configurado para servir dados geoespaciais diretamente a navegadores de rede, servidores FTP e Sistemas de Informação Geográfica (SIG). Para estes últimos, foram utilizados recursos de acesso a dados localizados em servidores de mapas remotos, por meio dos serviços de Web Mapping Service (WMS) e Web Feature Service (WFS). Enquanto a disseminação em navegador de rede pode alcançar usuários não especializados com este campo das geotecnologias, a utilização de servidores FTP, serviços WMS e WFS remotos, favorece usuários técnicos das Geociências e Cartografia. Comparou-se as funcionalidades do MapGuide, a SIG de primeira e segunda geração, com funções topológicas completas. Concluiu-se que o servidor de mapas não possuía a mesma capacidade de análise espacial dos SIG topológicos. / A Web Mapping application built on MapGuide was designed to digitally serve the municipal government of Taboão da Serra SP geospatial data. There were two aims related to the application project: to implement the technology to the analyst responsible for the project, and; to develop the project content as an introdutory theoretical-methodological guide to geoscientists and cartographers not specialized in the internet mapping field. The geospatial data dissemination services were configured to web browsers, FTP servers and Geographic Information Systems (GIS). For these lasts, data access resources to remote spatial servers were used, via Web Mapping Services (WMS) and Web Feature Services (WFS). While the web browser data dissemination is suitable for non-technicians, the FTP server, WMS and WFS resources, are best suitable for GIS analysts. A comparison between MapGuide functionalities with other first and second generation topological GIS softwares was performed. The conclusion revealed the web mapping application didn\'t have the same spatial analysis capabilities as the topological GIS.

Neste trabalho foram utilizados modelos de regressão espaço-temporais bayesianos para estimar a incidência de TB em Ribeirão Preto (anos de 2006 a 2009) por área de abrangência de unidades de saúde, associando-a a covariáveis de interesse (IPVS, Renda e Educação predominantes naquelas áreas). O método baseia-se em simulações MCMC para estimar as distribuições a posteriori das incidências de TB em Ribeirão Preto. Como resultado, temos mapas que mostram mais claramente um padrão espacial, com estimativas mais suavizadas e com menos flutuações aleatórias. Observamos que as áreas com as mais altas taxas de incidência também possuem índice de vulnerabilidade social médio e alto. Em relação à renda, a faixa salarial predominante dos responsáveis pelo domicílio nestas regiões é entre 0 e 3 salários mínimos e o nível de escolaridade predominante dos chefes do domicílio nestas regiões é o ensino fundamental. Os resultados dos modelos bayesianos analisados nos evidenciam que com o aumento da vulnerabilidade social aumentamos significativamente a incidência de TB em Ribeirão Preto. Nas áreas onde a vulnerabilidade é alta a incidência de TB chega a quase 15 vezes a incidência das áreas sem vulnerabilidade. Houve um aumento significativo em relação à incidência de tuberculose em Ribeirão Preto durante os anos estudados, sendo as maiores incidências registradas no ano de 2009. O uso de mapas facilitou a visualização de áreas que merecem uma atenção especial no controle da TB, além disso, a associação da doença com renda, escolaridade e vulnerabilidade social trazem subsídios para que os gestores responsáveis pelo planejamento do município planejem intervenções com uma atenção especial a estas áreas, reunindo esforços para a redução da pobreza e da desigualdade social, alternativas para uma melhor distribuição de renda e melhorar o acesso ao saneamento básico dentre outras prioridades. / In this study we used Bayesian space-temporal regression models to estimate the incidence of TB in Ribeirão Preto, SP (years 2006 to 2009) by the coverage area of health units, associating it with the covariates of interest (IPVS, Income and Education predominant those areas). The method is based on MCMC simulations for estimate the posterior distributions of TB incidence in Ribeirão Preto. As a result, we have maps that show a spatial pattern more clearly, with estimates smoother and less random fluctuations. We observed that the areas with the highest incidence rates also have medium and high social vulnerability index. Concerning income, the prevailing salary range of household heads in these regions is between 0 and 3 minimum wages and the prevailing level of education of household heads in these regions is the elementary school. The results of the models in Bayesian analysis show that with increasing social vulnerability significantly increased the incidence of TB in Ribeirao Preto. In areas where vulnerability is high incidence of TB is nearly 15 times the incidence of areas without vulnerability. There was a significant increase in the incidence of tuberculosis in Ribeirão Preto during the years studied, the highest incidence recorded in 2009. The use of maps improved visualization of areas that deserve special attention for TB control, in addition, the association of disease with income, education and social vulnerability that bring benefits to the managers responsible for planning the municipality to plan interventions with special attention these areas, uniting efforts to reduce poverty and social inequality, alternatives to improve income distribution and improve access to basic sanitation among other priorities.

Orientador: Luiz Fernando Costa Nascimento / Resumo: O ecossistema amazônico é impactado fortemente pelas queimadas no período da estação seca com as emissões de poluentes na atmosfera. Os efeitos sobre a saúde das populações, especialmente na região do arco do desmatamento, tem sido objeto de recentes estudos. O objetivo do presente estudo é avaliar a distribuição espacial dos focos de queimadas, da morbidade por doenças cardiovasculares, e das concentrações dos poluentes PM2,5 e CO, no estado do Tocantins. Foi desenvolvido estudo ecológico com ferramentas da análise espacial. A análise utilizou o estimador de Kernel e índice de Moran (Im), além de mapas temáticos e correlação de Spearman (rs) entre as variáveis. O geoprocessamento utilizou o programa TerraView 4.2.2. Foram encontradas altas taxas de queimadas no estado e forte associação entre as queimadas e o coeficiente de Gini (rs = 0,30 e p-valor < 0,01). Foi encontrada correlação significativa entre concentrações de monóxido de carbono e internações por doenças do aparelho circulatório (rs = 0,18 e p-valor < 0,05). O índice de Moran para focos de queimadas foi Im = 0,28 com p-valor = 0,01. Foram identificadas cidades que necessitam de prioridade de intervenções. Conclui-se que é necessária uma maior fiscalização ambiental quanto ao controle de queimadas, inclusive nas áreas de preservação ambiental. / Abstract: The Amazonian ecosystem is strongly impacted by the forest fires in the dry season with emissions of pollutants into the atmosphere. The effects on population health, especially in the deforestation arc region, have been the subject of recent studies. The goal of the present study is to evaluate the spatial distribution of forest fires, cardiovascular disease morbidity, and PM2,5and CO pollutant concentrations in the state of Tocantins. An ecological study was developed with spatial analysis tools. The Kernel estimator and the Moran index (Im) were used as spatial analysis techniques, as well as thematic maps and Spearman correlation (rs) between the variables for the analysis of the results. The geoprocessing was development through the program TerraView 4.2.2. High forest fires rates in the state and strong association with the Gini coefficient (rs = 0.30 and p-value <0.01) were found. A significant correlation was found between carbon monoxide concentrations and hospitalizations for circulatory diseases (rs = 0.18 and p-value <0.05). The Moran index for forest fires was Im = 0.28 with p-value = 0.01. Cities that need priority interventions have been identified. It is concluded that a greater environmental inspection is necessary regarding the control of forest fires, including in the areas of environmental preservation. / Mestre

Because urban areas comprise a variety of biotic (e.g. people, trees) and abiotic (e.g. streets, water) components that interact and are often interdependent upon one another, it is helpful to study urban areas as urban ecosystems. Our goal in Chapter 2 is to measure and quantify the spatial and demographic structure of the urbanized portion of Salt Lake County, Utah. We use 18 metrics from four broad categories (density, centrality, accessibility, and neighborhood mix) to measure urban form for three age-based residential neighborhood types. Using analysis of variance (ANOVA) we test for differences in mean values for the 18 urban form metrics. We find measureable differences in the spatial and demographic characteristics of these neighborhoods, suggesting that the rate of urban sprawl in Salt Lake County has been holding steady, if not increasing, during the last 20 years. Chapter 3 seeks to better understand how spatial heterogeneity in urban tree canopy is related to household characteristics, urban form, and the geophysical landscape of residential neighborhoods. We consider neighborhood age a factor that moderates the relationship between these determinants of tree canopy, and the abundance of tree canopy observed. Using linear regression analysis with neighborhood age as interaction term, we assess the relationship between tree canopy and 15 determinants of tree canopy abundance at three neighborhood ages. We find that neighborhood age has a significant moderating effect on the relationship between several determinants of canopy cover and the abundance of canopy cover observed. While the urban forest provides many benefits to human well-being, it also consumes considerable quantities of water. An important question in Chapter 4 is to determine whether a growing urban forest increases overall residential irrigation demand, decreases demand, or has no apparent effect. Using a water demand model borrowed from agronomy, we estimate irrigation water demand based on the area of three residential landscape types and climatic factors. We project future residential water demand by generating residential landscape scenarios based on predicted urban forest canopy growth. We find that urban forest growth has the effect of stabilizing or potentially decreasing overall residential irrigation water demand.

Activities and production among ethnographic Arctic peoples were primarily divided by gender. This gendered division of labor also extended to a spatial segregated pattern of the household in some Arctic cultures. Other cultures had a more gender-integrated spatial pattern of the household. There have been very few archaeological studies of gender in the Arctic, and even fewer studies of gendered use of space. In this thesis, I evaluated the existence of this gendered use of space in pre-contact Northwest Alaska. I also evaluated the existence of discrete activity spaces. I drew from both ethnoarchaeology and gender/feminist archaeology to both construct my hypotheses and interpret my results. I used ceramics, which were likely primarily made by and used by women, as a proxy for women's movement within the house. Ceramics are abundant and well-preserved in many Northwestern Alaskan sites, and are well suited for a robust spatial analysis. In addition to ceramics, I also evaluated the spatial density of other female artifacts, like ulus or scrapers, and male artifacts, like harpoon points or adzes, in order to further test the existence of gender specific use of space. I tested this using the HDBSCAN (Hierarchical Density Based Spatial Clustering of Applications with Noise) algorithm in Python, a programming language. HDBSCAN identifies discrete clusters of artifacts, as well as the persistence, or stability, of the cluster. Birnirk and Thule era (1300-150 BP) house features from Cape Espenberg, Alaska, were used to test these expectations. Based on the results of my spatial analysis, I did not find any evidence of gender specific use of space, nor did I find specific activity areas within the house. My findings are not necessarily an indication that gender-segregated use of space does not exist among pre-contact Northwest Alaskan people: I just did not find evidence supporting it. This could be, in part, due to issues of sample size, house size, and the role of secondary and post deposition processes in shaping the ceramic assemblage and distribution. While ceramics did cluster, they mostly clustered in the entrance tunnel of the house. This is likely the result of cleaning, storage, or other depositional processes. When ceramics did cluster in the main rooms, clustering was idiosyncratic. Male and female artifacts were not spatially segregated. Female artifacts were slightly more likely to cluster than male artifacts. Both sets of artifacts were generally in the same area as the ceramic clusters. While this study did not find evidence of gendered use of space, it still is an important contribution of addressing questions of gender in the Arctic. In addition, it is a valuable methodological contribution, using a clustering algorithm that previously has not been frequently used by archaeologists.

In northwest Alaska, archaeologists hypothesize that environmental variability was a major factor in both growing coastal population density, with large aggregated villages and large houses, between 1000 and 500 years ago (ya), and subsequent decreasing population density between 500 ya and the contact era. After 500 ya people are thought to have dispersed to smaller settlements with smaller house sizes in coastal areas, and perhaps, upriver. This settlement pattern was identified through research at four site locations over 30 years ago. The changing geographic distribution of sites, associated settlement size, and house size has not been examined in detail. A more careful examination of changing northwest Alaskan settlement patterns is needed before larger questions about socio-economic organization can be addressed. I use Geographic Information Systems (GIS) to evaluate the evidence for a geographic redistribution of Arctic peoples during the Late Holocene. The author constructed a database of settlement location and site attribute information, specifically the number of houses within each settlement and the size (m2). Data were collected from a dataset of Western Arctic National Parklands (WEAR), the Alaska Heritage Resource Survey (AHRS) database of archaeological sites in Alaska, 409 unpublished site reports and field notes curated by the National Park Service (NPS) and Bureau of Indian Affairs (BIA), and the results of recent fieldwork in northwest Alaska. A total of 486 settlements were identified within the northwest Alaska with 128 settlements having temporal and site attribute data. The author incorporated settlement size data into a GIS database and then carried out global, Moran's I, local Moran's I, and local Getis-Ord spatial analyses to test whether settlement redistribution occurred and if key settlement locations shifted after 500 ya. The site attribute data (number of houses and average size of houses) are used to test the additional aspects of the proposed settlement pattern change after 500 ya. A total of 83 settlements with 465 houses are used to test if the average size of settlements and average house size changed after 500 ya. The results of the spatial analyses indicate no statistically significant patterns in the spatial distribution of settlements. Site attribute analysis shows no statistical difference in the average number of houses per village or the average size of houses before or after 500 ya. The results of this work build our understanding of regional settlement patterns during the late Holocene. By testing settlement pattern change, i.e. settlement distribution, settlement size, and house size, future research into settlement pattern change can begin to evaluate likely causes for the observed changes. My method, specifically the use of GIS as a method for testing settlement pattern change, can be applied to other regions and temporal scales.

This thesis reports on research that examines the early stage invasion process of Asparagus asparagoides (L.) W. Wight (bridal creeper), primarily a bird-dispersed weed, in a remnant vegetation patch. The study site is on Phillip Island, approximately 100 kilometres south east of Melbourne, Victoria. Asparagus asparagoides invasion of the remnant vegetation reserve is a relatively recent phenomenon. Landscape elements that affect bird dispersal and vegetation types that affect seedling establishment may be important factors that limit or enhance the spread of A. asparagoides. A systematic sampling strategy was adopted and data collected for a variety of landscape and vegetative variables including cover and abundance of A. asparagoides and the data were presented in a Geographic Information System (GIS). Preliminary results show that the distribution of A. asparagoides within a remnant vegetation patch is not random. It appears to have entered the reserve from two boundaries, spreading toward the centre, which to date remains sparsely colonised despite the capacity of this weed to spread rapidly over long distances by birds. A number of other outcomes are noted. Asparagus asparagoides establishment is prevented in pasture where sheep and cattle graze, and paddocks subjected to tillage practices. The exclusion of grazing in fenced off vegetation in pastures demonstrates rapid weed establishment and colonisation several hundred metres from main infestation. Field observation and visual inspection of temporal progress of invasion (using above ground weed density with tuber appearance to infer age) appear to suggest that invasion into remnant is associated with the track network. This age/density assumption is strengthened when spatial distribution is examined using a data set where low-density values for A. asparagoides are removed and compared with a data set using all A. asparagoides density values. The mapping of A. asparagoides in fenced off farm remnants suggests that velocity of spread at 191m/yr is a considerable underestimate. Subsequent analysis shows that the spatial distribution of A. asparagoides is not completely spatially random while intensity surface analysis highlights regions of low and high intensity located near track network. Mapping a density surface within GIS provided confirmatory evidence for the establishment of satellite clusters along the track network. The change in the intensity surface observed using the two data sets (lowdensity values and all density values) is also consistent with an expanding invasion occurring between two time periods. Spatial point pattern analysis using K-function statistics shows that xxii the clustering observed using GIS appears to be occurring at two scales or distances (130m- 160m and 195m-205m). The association between tracks and the invasion process observed in the initial stages of the study is examined. There is a change in density as a function of distance from a track where the density of A. asparagoides appears to reduce the further away from the track a site is and this relationship holds regardless of track width. The final stages of the study look at the development of a predictive model. Visual exploration of the data through mapping in a GIS and field observation made during data collection provide the starting point for the development of logistic models to estimate the probability of A. asparagoides presence. Finally the best overall logistic model is applied to a second independent site to determine the general applicability of the model. A number of variables that impact on the presence of A. asparagoides, particularly during the initial stages of the invasion process, are identified. While all the identified variables and the overall model are statistically significant, the model is found to correctly predict presence/absence in only 67% of cases overall. The model however could be expected to correctly predict the presence of A. asparagoides in 74% of cases and has a false positive rate of 40%. The model is applied at a second independent site and found to have an overall percent correct rate of 80% and correctly predicted A. asparagoides presence in 94% of cases. The variables identified as influential in the early stage of invasion are relatively easy to acquire by simple field survey that does not require specialist skills. When considering the model as a tool for the management of remnant vegetation communities, high false positive rates may lead to limited resources being spent on searching sites where there is no weed. However, a high false negative rate would have a larger impact on the management of the weed since the undetected infestations would form sources for new propagules. The model performs well from this point of view in that it provided low false negative rates at both sites. The value of the predictive model is its ability to provide managers with information regarding specific areas to target for weed eradication and management can use the model to assess the effectiveness of any control measures by going back to obtain new cover density data, then using the model to examine the changes over time. The model also provides a starting point for the development of a generic model of A. asparagoides invasion at sites outside of Phillip Island and could also provide the starting point for developing models that could be used for other bird-dispersed fleshy-fruited weed species.

Filamentous fungal colonies show a remarkable diversity of different mycelial branching patterns. To date, the characterization of this biostructural complexity has been based on subjective descriptions. Here, computerized image analysis in conjunction with video microscopy has been used to quantify several aspects of fungal growth and differentiation. This was accomplished by applying the new branch of mathematics called Fractal Geometry to this biological system, to provide an objective description of morphological and biochemical complexity. The fractal dimension is useful for describing irregularity and shape complexity in systems that appear to display scaling correlations (between structural units) over several orders of length or size. The branching dynamics of Pycnoporus cinnabarinus have been evaluated using fractals in order to determine whether there was a correlation between branching complexity and the amount of extracellular phenol-oxidase that accumulated during growth. A non-linear branching response was observed when colonies were grown in the presence of the aminoanthraquinone dye, Remazol Brilliant Blue R. Branching complexity could be used to predict the generalized yield of phenol-oxidase that accumulated in submerged culture, or identify paramorphogens that could be used to improve yield. A method to optimize growth of discrete fungal colonies for microscopy and image analysis on microporous membranes revealed secretion sites of the phenoloxidase, laccase as well as the intracellular enzyme, acid phosphatase. This method was further improved using microwave-accelerated heating to detect tip and sheath bound enzyme. The spatial deposition of secreted laccase and acid phosphatase displayed antipersistent scaling in deposition and/or secretion pattern. To overcome inherent statistical limitations of existing methods, a new signal processing tool, called wavelets were applied to analyze both one and two-dimensional data to measure fractal scaling. Two-dimensional wavelet packet analysis (2-d WPA) measured the (i) mass fractal dimension of binary images, or the (ii) self-affine dimension of grey-scale images. Both 1- and 2-d WPA showed comparative accuracy with existing methods yet offered improvements in computational efficiency that were inherent with this multiresolution technique. The fractal dimension was shown to be a sensitive indicator of shape complexity. The discovery of power law scaling was a hallmark of fractal geometry and in many cases returned values that were indicative of a self-organized critical state. This meant that the dynamics of fungal colony branching equilibrium. Hence there was potential for biostructural changes of all sizes, which would allow the system to efficiently adapt to environmental change at both the macro and micro levels.

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Susan J. Elliott. Includes bibliographical references (leaves 166-171).