Stochastic models for mainland-island metapopulations in static and dynamic landscapes

This paper has three primary aims: to establish an effective means for modelling mainland-island metapopulations inhabiting a dynamic landscape: to investigate the effect of immigration and dynamic changes in habitat on metapopulation patch occupancy dynamics; and to illustrate the implications of our results for decision-making and population management. We first extend the mainland-island metapopulation model of Alonso and McKane [Bull. Math. Biol. 64:913-958,2002] to incorporate a dynamic landscape. It is shown, for both the static and the dynamic landscape models, that a suitably scaled version of the process converges to a unique deterministic model as the size of the system becomes large. We also establish that. under quite general conditions, the density of occupied patches, and the densities of suitable and occupied patches, for the respective models, have approximate normal distributions. Our results not only provide us with estimates for the means and variances that are valid at all stages in the evolution of the population, but also provide a tool for fitting the models to real metapopulations. We discuss the effect of immigration and habitat dynamics on metapopulations, showing that mainland-like patches heavily influence metapopulation persistence, and we argue for adopting measures to increase connectivity between this large patch and the other island-like patches. We illustrate our results with specific reference to examples of populations of butterfly and the grasshopper Bryodema tuberculata.

Fish population dynamics in a seasonally varying wetland

Small fishes in seasonally flooded environments such as the Everglades are capable of spreading into newly flooded areas and building up substantial biomass. Passive drift cannot account for the rapidity of observed population expansions. To test the ‘reaction–diffusion’ mechanism for spread of the fish, we estimated their diffusion coefficient and applied a reaction–diffusion model. This mechanism was also too weak to account for the spatial dynamics. Two other hypotheses were tested through modeling. The first—the ‘refuge mechanism’—hypothesizes that small remnant populations of small fishes survive the dry season in small permanent bodies of water (refugia), sites where the water level is otherwise below the surface. The second mechanism, which we call the ‘dynamic ideal free distribution mechanism’ is that consumption by the fish creates a prey density gradient and that fish taxis along this gradient can lead to rapid population expansion in space. We examined the two alternatives and concluded that although refugia may play an important role in recolonization by the fish population during reflooding, only the second, taxis in the direction of the flooding front, seems capable of matching empirical observations. This study has important implications for management of wetlands, as fish biomass is an essential support of higher trophic levels.

Factors influencing movements and foraging ecology of American alligators (Alligator mississippiensis) in a dynamic subtropical coastal ecosystem

Top predators can have large effects on community and population dynamics but we still know relatively little about their roles in ecosystems and which biotic and abiotic factors potentially affect their behavioral patterns. Understanding the roles played by top predators is a pressing issue because many top predator populations around the world are declining rapidly yet we do not fully understand what the consequences of their potential extirpation could be for ecosystem structure and function. In addition, individual behavioral specialization is commonplace across many taxa, but studies of its prevalence, causes, and consequences in top predator populations are lacking. In this dissertation I investigated the movement, feeding patterns, and drivers and implications of individual specialization in an American alligator (Alligator mississippiensis ) population inhabiting a dynamic subtropical estuary. I found that alligator movement and feeding behaviors in this population were largely regulated by a combination of biotic and abiotic factors that varied seasonally. I also found that the population consisted of individuals that displayed an extremely wide range of movement and feeding behaviors, indicating that individual specialization is potentially an important determinant of the varied roles of alligators in ecosystems. Ultimately, I found that assuming top predator populations consist of individuals that all behave in similar ways in terms of their feeding, movements, and potential roles in ecosystems is likely incorrect. As climate change and ecosystem restoration and conservation activities continue to affect top predator populations worldwide, individuals will likely respond in different and possibly unexpected ways.

Dynamic Life Cycle Assessment Modeling Approaches for Transboundary Energy Feedstocks

The rise of the twenty-first century has seen the further increase in the industrialization of Earth’s resources, as society aims to meet the needs of a growing population while still protecting our environmental and natural resources. The advent of the industrial bioeconomy – which encompasses the production of renewable biological resources and their conversion into food, feed, and bio-based products – is seen as an important step in transition towards sustainable development and away from fossil fuels. One sector of the industrial bioeconomy which is rapidly being expanded is the use of biobased feedstocks in electricity production as an alternative to coal, especially in the European Union.

As bioeconomy policies and objectives increasingly appear on political agendas, there is a growing need to quantify the impacts of transitioning from fossil fuel-based feedstocks to renewable biological feedstocks. Specifically, there is a growing need to conduct a systems analysis and potential risks of increasing the industrial bioeconomy, given that the flows within it are inextricably linked. Furthermore, greater analysis is needed into the consequences of shifting from fossil fuels to renewable feedstocks, in part through the use of life cycle assessment modeling to analyze impacts along the entire value chain.

To assess the emerging nature of the industrial bioeconomy, three objectives are addressed: (1) quantify the global industrial bioeconomy, linking the use of primary resources with the ultimate end product; (2) quantify the impacts of the expaning wood pellet energy export market of the Southeastern United States; (3) conduct a comparative life cycle assessment, incorporating the use of dynamic life cycle assessment, of replacing coal-fired electricity generation in the United Kingdom with wood pellets that are produced in the Southeastern United States.

To quantify the emergent industrial bioeconomy, an empirical analysis was undertaken. Existing databases from multiple domestic and international agencies was aggregated and analyzed in Microsoft Excel to produce a harmonized dataset of the bioeconomy. First-person interviews, existing academic literature, and industry reports were then utilized to delineate the various intermediate and end use flows within the bioeconomy. The results indicate that within a decade, the industrial use of agriculture has risen ten percent, given increases in the production of bioenergy and bioproducts. The underlying resources supporting the emergent bioeconomy (i.e., land, water, and fertilizer use) were also quantified and included in the database.

Following the quantification of the existing bioeconomy, an in-depth analysis of the bioenergy sector was conducted. Specifically, the focus was on quantifying the impacts of the emergent wood pellet export sector that has rapidly developed in recent years in the Southeastern United States. A cradle-to-gate life cycle assessment was conducted in order to quantify supply chain impacts from two wood pellet production scenarios: roundwood and sawmill residues. For reach of the nine impact categories assessed, wood pellet production from sawmill residues resulted in higher values, ranging from 10-31% higher.

The analysis of the wood pellet sector was then expanded to include the full life cycle (i.e., cradle-to-grave). In doing to, the combustion of biogenic carbon and the subsequent timing of emissions were assessed by incorporating dynamic life cycle assessment modeling. Assuming immediate carbon neutrality of the biomass, the results indicated an 86% reduction in global warming potential when utilizing wood pellets as compared to coal for electricity production in the United Kingdom. When incorporating the timing of emissions, wood pellets equated to a 75% or 96% reduction in carbon dioxide emissions, depending upon whether the forestry feedstock was considered to be harvested or planted in year one, respectively.

Finally, a policy analysis of renewable energy in the United States was conducted. Existing coal-fired power plants in the Southeastern United States were assessed in terms of incorporating the co-firing of wood pellets. Co-firing wood pellets with coal in existing Southeastern United States power stations would result in a nine percent reduction in global warming potential.

RNA Virus Evolution: a Cross-scale, Disease Dynamic Perspective

RNA viruses are an important cause of global morbidity and mortality. The rapid evolutionary rates of RNA virus pathogens, caused by high replication rates and error-prone polymerases, can make the pathogens difficult to control. RNA viruses can undergo immune escape within their hosts and develop resistance to the treatment and vaccines we design to fight them. Understanding the spread and evolution of RNA pathogens is essential for reducing human suffering. In this dissertation, I make use of the rapid evolutionary rate of viral pathogens to answer several questions about how RNA viruses spread and evolve. To address each of the questions, I link mathematical techniques for modeling viral population dynamics with phylogenetic and coalescent techniques for analyzing and modeling viral genetic sequences and evolution. The first project uses multi-scale mechanistic modeling to show that decreases in viral substitution rates over the course of an acute infection, combined with the timing of infectious hosts transmitting new infections to susceptible individuals, can account for discrepancies in viral substitution rates in different host populations. The second project combines coalescent models with within-host mathematical models to identify driving evolutionary forces in chronic hepatitis C virus infection. The third project compares the effects of intrinsic and extrinsic viral transmission rate variation on viral phylogenies.

Essays in dynamic optimal taxation: working experience, unemployment scarring and poverty

This thesis investigates the design of optimal tax systems in dynamic environments. The first essay characterizes the optimal tax system where wages depend on stochastic shocks and work experience. In addition to redistributive and efficiency motives, the taxation of inexperienced workers depends on a second-best requirement that encourages work experience, a social insurance motive and incentive effects. Calibrations using U.S. data yield higher expected optimal marginal income tax rates for experienced workers for most of the inexperienced workers. They confirm that the average marginal income tax rate increases (decreases) with age when shocks and work experience are substitutes (complements). Finally, more variability in experienced workers' earnings prospects leads to increasing tax rates since income taxation acts as a social insurance mechanism. In the second essay, the properties of an optimal tax system are investigated in a dynamic private information economy where labor market frictions create unemployment that destroys workers' human capital. A two-skill type model is considered where wages and employment are endogenous. I find that the optimal tax system distorts the first-period wages of all workers below their efficient levels which leads to more employment. The standard no-distortion-at-the-top result no longer holds due to the combination of private information and the destruction of human capital. I show this result analytically under the Maximin social welfare function and confirm it numerically for a general social welfare function. I also investigate the use of a training program and job creation subsidies. The final essay analyzes the optimal linear tax system when there is a population of individuals whose perceptions of savings are linked to their disposable income and their family background through family cultural transmission. Aside from the standard equity/efficiency trade-off, taxes account for the endogeneity of perceptions through two channels. First, taxing labor decreases income, which decreases the perception of savings through time. Second, taxation on savings corrects for the misperceptions of workers and thus savings and labor decisions. Numerical simulations confirm that behavioral issues push labor income taxes upward to finance saving subsidies. Government transfers to individuals are also decreased to finance those same subsidies.

Implications de l’hétérogénéité comportementale et biologique pour la vaccination contre les virus du papillome humain au niveau de la population : modélisation mathématique, revue systématique et méta-analyse

Objectifs : Dans plusieurs pays la couverture vaccinale contre les virus du papillome humain (VPH) est associée aux déterminants sociaux des comportements sexuels et la participation au dépistage du cancer du col utérin. Ces vaccins protègent uniquement contre certains types de VPH, donc leur impact futur sur les VPH nonvaccinaux demeure incertain. L’hétérogénéité comportementale entre individus et biologique entre types de VPH affectera l’efficacité populationnelle de la vaccination contre les VPH. Les objectifs spécifiques de cette thèse étaient 1) de modéliser comment une couverture vaccinale inégale entre filles préadolescentes qui différeront selon leur activité sexuelle et leur participation au dépistage du cancer du col affectera l’efficacité populationnelle de la vaccination, 2) faire une synthèse et comparer les estimés d’efficacité croisée des vaccins contre les VPH dans des populations ADN-négatives aux VPH et 3) d’identifier, avec la modélisation, les devis d’étude épidémiologique qui réduisent les biais dans l’estimation des interactions biologiques entre types de VPH. Méthode : Nous avons utilisé des modèles de transmission dynamique et une revue systématique de la littérature pour répondre aux objectifs. 1) Nous avons modélisé une couverture vaccinale inégale entre filles qui différeront selon leur activité sexuelle et leur participation au dépistage, et examiné les changements postvaccination dans l’inégalité dans la prévalence des VPH et l’incidence des carcinomes malpighien (SCC) du col de l’utérus entre femmes ayant différents comportements. 2) Nous avons effectué une revue systématique et méta-analyse des efficacités croisées des vaccins contre les VPH estimées dans des populations ADNnégatives aux VPH. 3) Nous avons développé des modèles de transmission dynamique et d’interaction de deux types de VPH pour simuler les études épidémiologiques d’interactions entre les VPH. Résultats : Pour l’objectif 1), notre modèle de transmission prédit que l’efficacité populationnelle du vaccin dépendra de la distribution du vaccin dans la population. Après la vaccination, les inégalités absolues dans l’incidence de l’infection et des SCC entre groupes de femmes qui diffèrent selon leur activité sexuelle et leur participation au dépistage devraient diminuer. Inversement, les inégalités relatives pourraient augmenter si les femmes plus sexuellement actives et celles qui ne se font jamais dépister ont une couverture vaccinale moins élevée que les autres. Le taux d’incidence des SCC demeurera élevé chez les femmes qui ne sont jamais dépistées après la vaccination. L’efficacité croisée vaccinale et les interactions biologiques entre VPH ne sont pas encore assez bien caractérisées pour pouvoir prédire l’impact du vaccin sur les types de VPH nonvaccinaux. Pour l’objectif 2), notre méta-analyse des essais cliniques des vaccins suggère que le vaccin bivalent a une efficacité croisée significativement plus élevée que le quadrivalent contre les infections persistantes et lésions précancéreuses avec les VPH-31, 33 et 45. Les essais cliniques plus longs estiment une efficacité croisée plus faible. La modélisation des études épidémiologiques d’interactions pour l’objectif 3) montre que l’estimation des interactions biologiques entre types de VPH dans les études épidémiologiques est systématiquement biaisée par la corrélation entre le temps à risque d’infection avec un type de VPH et le temps à risque d’infection avec d’autres types de VPH. L’ajustement pour des marqueurs d’activité sexuelle ne réussit pas à contrôler ce biais. Une mesure valide des interactions biologiques entre types de VPH peut être obtenue uniquement avec des études épidémiologiques prospectives qui restreignent les analyses à des individus susceptibles ayant des partenaires sexuels infectés. Conclusion : L’hétérogénéité comportementale entre individus et l’hétérogénéité biologique entre VPH affecteront l’efficacité populationnelle du vaccin contre les VPH. Dans les contextes où les déterminants sociaux des comportements sexuels et la participation au dépistage sont aussi associés à la couverture vaccinale chez les préadolescentes, l’inégalité relative dans l’incidence des SCC risque d’augmenter. Ces comportements demeureront des facteurs de risque importants du cancer du col à l’avenir. L’effet à long terme du vaccin sur les types de VPH non-vaccinaux demeure incertain. Quoique nos résultats suggèrent que les vaccins offrent une efficacité croisée contre certains types de VPH, celle-ci pourrait diminuer après quelques années. Des interactions compétitives entre VPH pourraient exister malgré les associations observées entre les incidences des infections VPH, donc une augmentation post-vaccination de la prévalence des VPH non-vaccinaux demeure possible. Des devis d’analyse plus complexes sont nécessaires pour mesurer de façon valide les interactions biologiques entre les VPH dans les études épidémiologiques.

A two-fluid model for tissue growth within a dynamic flow environment

We study the growth of a tissue construct in a perfusion bioreactor, focussing on its response to the mechanical environment. The bioreactor system is modelled as a two-dimensional channel containing a tissue construct through which a flow of culture medium is driven. We employ a multiphase formulation of the type presented by G. Lemon, J. King, H. Byrne, O. Jensen and K. Shakesheff in their study (Multiphase modelling of tissue growth using the theory of mixtures. J. Math. Biol. 52(2), 2006, 571–594) restricted to two interacting fluid phases, representing a cell population (and attendant extracellular matrix) and a culture medium, and employ the simplifying limit of large interphase viscous drag after S. Franks in her study (Mathematical Modelling of Tumour Growth and Stability. Ph.D. Thesis, University of Nottingham, UK, 2002) and S. Franks and J. King in their study Interactions between a uniformly proliferating tumour and its surrounding: Uniform material properties. Math. Med. Biol. 20, 2003, 47–89). The novel aspects of this study are: (i) the investigation of the effect of an imposed flow on the growth of the tissue construct, and (ii) the inclusion of a chanotransduction mechanism regulating the response of the cells to the local mechanical environment. Specifically, we consider the response of the cells to their local density and the culture medium pressure. As such, this study forms the first step towards a general multiphase formulation that incorporates the effect of mechanotransduction on the growth and morphology of a tissue construct. The model is analysed using analytic and numerical techniques, the results of which illustrate the potential use of the model to predict the dominant regulatory stimuli in a cell population.

Population ageing and monetary policy

Mestrado em Economia Monetária e Financeira

Factors Influencing Movements and Foraging Ecology of American Alligators (Alligator mississippiensis) in a Dynamic Subtropical Coastal Ecosystem

Top predators can have large effects on community and population dynamics but we still know relatively little about their roles in ecosystems and which biotic and abiotic factors potentially affect their behavioral patterns. Understanding the roles played by top predators is a pressing issue because many top predator populations around the world are declining rapidly yet we do not fully understand what the consequences of their potential extirpation could be for ecosystem structure and function. In addition, individual behavioral specialization is commonplace across many taxa, but studies of its prevalence, causes, and consequences in top predator populations are lacking. In this dissertation I investigated the movement, feeding patterns, and drivers and implications of individual specialization in an American alligator (Alligator mississippiensis) population inhabiting a dynamic subtropical estuary. I found that alligator movement and feeding behaviors in this population were largely regulated by a combination of biotic and abiotic factors that varied seasonally. I also found that the population consisted of individuals that displayed an extremely wide range of movement and feeding behaviors, indicating that individual specialization is potentially an important determinant of the varied roles of alligators in ecosystems. Ultimately, I found that assuming top predator populations consist of individuals that all behave in similar ways in terms of their feeding, movements, and potential roles in ecosystems is likely incorrect. As climate change and ecosystem restoration and conservation activities continue to affect top predator populations worldwide, individuals will likely respond in different and possibly unexpected ways.

Balance ability of 7 and 10 year old children in the population:results from a large UK birth cohort study

OBJECTIVE: The literature contains many reports of balance function in children, but these are often on atypical samples taken from hospital-based clinics and may not be generalisable to the population as a whole. The purpose of the present study is to describe balance test results from a large UK-based birth cohort study. METHODS: Data from the Avon Longitudinal Study of Parents and Children (ALSPAC) were analysed. A total of 5402 children completed the heel-to-toe walking test at age 7 years. At age 10 years, 6915 children underwent clinical tests of balance including beam-walking, standing heel-to-toe on a beam and standing on one leg. A proportion of the children returned to the clinic for retesting within 3 months allowing test-retest agreement to be measured. RESULTS: Frequency distributions for each of the balance tests are given. Correlations between measures of dynamic balance at ages 7 and 10 years were weak. The static balance of 10 year old children was found to be poorer with eyes closed than with eyes open, and poorer in boys than in girls for all measures. Balance on one leg was poorer than heel-to-toe balance on a beam. A significant learning effect was found when first and second attempts of the tests were compared. Measures of static and dynamic balance appeared independent. Consistent with previous reports in the literature, test-retest reliability was found to be low. CONCLUSIONS: This study provides information about the balance ability of children aged 7 and 10 years and provides clinicians with reference data for balance tests commonly used in the paediatric clinic.

[diet Quality And Associated Factors Among The Elderly: A Population-based Study In Campinas, São Paulo State, Brazil].

The aim of this study was to assess the quality of diet among the elderly and associations with socio-demographic variables, health-related behaviors, and diseases. A population-based cross-sectional study was conducted in a representative sample of 1,509 elderly participants in a health survey in Campinas, São Paulo State, Brazil. Food quality was assessed using the Revised Diet Quality Index (DQI-R). Mean index scores were estimated and a multiple regression model was employed for the adjusted analyses. The highest diet quality scores were associated with age 80 years or older, Evangelical religion, diabetes mellitus, and physical activity, while the lowest scores were associated with home environments shared with three or more people, smoking, and consumption of soft drinks and alcoholic beverages. The findings emphasize a general need for diet quality improvements in the elderly, specifically in subgroups with unhealthy behaviors, who should be targeted with comprehensive strategies.

Falls Among The Elderly: Risk Factors In A Population-based Study.

The aim of the present study was to identify factors associated with the occurrence of falls among elderly adults in a population-based study (ISACamp 2008). A population-based cross-sectional study was carried out with two-stage cluster sampling. The sample was composed of 1,520 elderly adults living in the urban area of the city of Campinas, São Paulo, Brazil. The occurrence of falls was analyzed based on reports of the main accident occurred in the previous 12 months. Data on socioeconomic/demographic factors and adverse health conditions were tested for possible associations with the outcome. Prevalence ratios (PR) were estimated and adjusted for gender and age using the Poisson multiple regression analysis. Falls were more frequent, after adjustment for gender and age, among female elderly participants (PR = 2.39; 95% confidence interval (95% CI) 1.47 - 3.87), elderly adults (80 years old and older) (PR = 2.50; 95% CI 1.61 - 3.88), widowed (PR = 1.74; 95% CI 1.04 - 2.89) and among elderly adults who had rheumatism/arthritis/arthrosis (PR = 1.58; 95% CI 1.00 - 2.48), osteoporosis (PR = 1.71; 95% CI 1.18 - 2.49), asthma/bronchitis/emphysema (PR = 1,73; 95% CI 1.09 - 2.74), headache (PR = 1.59; 95% CI 1.07 - 2.38), mental common disorder (PR = 1.72; 95% CI 1.12 - 2.64), dizziness (PR = 2.82; 95% CI 1.98 - 4.02), insomnia (PR = 1.75; 95% CI 1.16 - 2.65), use of multiple medications (five or more) (PR = 2.50; 95% CI 1.12 - 5.56) and use of cane/walker (PR = 2.16; 95% CI 1.19 - 3,93). The present study shows segments of the elderly population who are more prone to falls through the identification of factors associated with this outcome. The findings can contribute to the planning of public health policies and programs addressed to the prevention of falls.

Clinicopathological And Immunohistochemical Evaluation Of Oral And Oropharyngeal Squamous Cell Carcinoma In Chilean Population.

In oral and oropharyngeal squamous cell carcinoma (OCSCC and OPSCC) exist an association between clinical and histopathological parameters with cell proliferation, basal lamina, connective tissue degradation and surrounding stroma markers. We evaluated these associations in Chilean patients. A convenience sample of 37 cases of OCSCC (n=16) and OPSCC (n=21) was analyzed clinically (TNM, clinical stage) and histologically (WHO grade of differentiation, pattern of tumor invasion). We assessed the expression of p53, Ki67, HOXA1, HOXB7, type IV collagen (ColIV) and carcinoma-associated fibroblast (α-SMA-positive cells). Additionally we conducted a univariate/bivariate analysis to assess the relationship of these variables with survival rates. Males were mostly affected (56.2% OCSCC, 76.2% OPSCC). Patients were mainly diagnosed at III/IV clinical stages (68.8% OCSCC, 90.5% OPSCC) with a predominantly infiltrative pattern invasion (62.9% OCSCC, 57.1% OPSCC). Significant association between regional lymph nodes (N) and clinical stage with OCSCC-HOXB7 expression (Chi-Square test P < 0.05) was observed. In OPSCC a statistically significant association exists between p53, Ki67 with gender (Chi-Square test P < 0.05). In OCSCC and OPSCC was statistically significant association between ki67 with HOXA1, HOXB7, and between these last two antigens (Pearson's Correlation test P < 0.05). Furthermore OPSCC-p53 showed significant correlation when it was compared with α-SMA (Kendall's Tau-c test P < 0.05). Only OCSCC-pattern invasion and OPSCC-primary tumor (T) pattern resulted associated with survival at the end of the follow up period (Chi-Square Likelihood Ratio, P < 0.05). Clinical, histological and immunohistochemical features are similar to seen in other countries. Cancer proliferation markers were associated strongly from each other. Our sample highlights prognostic value of T and pattern of invasion, but the conclusions may be limited and should be considered with caution (small sample). Many cases were diagnosed in the advanced stages of the disease, which suggests that the diagnosis of OCSCC and OPSCC is made late.

[access To Basic Health Services And Associated Factors: A Population-based Study].

This study sought to identify factors involved in access to the services of a basic health unit. It is a cross-sectional, population-based study involving 101 randomly-selected families residing in the area covered by the health unit. An adult resident of each household was interviewed. The response variable was whether or not the resident frequented the health unit if he/she or anyone in the family required assistance to resolve a health issue. The independent variables investigated were service provision aspects, demographic and socio-economic characteristics, individual habits, morbidities and use of the health unit. In addition to descriptive and univariate analysis, logistic regression was applied in the multivariate analysis. The results show that access to the basic health unit is associated with the treatment received previously (OR = 3,224) with accessibility (OR = 0,146) and micro-area of residence (OR = 10,918). These findings suggest that access is related to the impressions created by the care received at the health unit and is based on experiences with the service, but can also be strongly modulated by individual aspects and factors related to the territory.