<p>Dengue is an important vector-borne virus that infects on the order of 400 million individuals per year. Infection with one of the virus's four serotypes (denoted DENV-1 to 4) may be silent, result in symptomatic dengue 'breakbone' fever, or develop into the more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Extensive research has therefore focused on identifying factors that influence dengue infection outcomes. It has been well-documented through epidemiological studies that DHF is most likely to result from a secondary heterologous infection, and that individuals experiencing a DENV-2 or DENV-3 infection typically are more likely to present with more severe dengue disease than those individuals experiencing a DENV-1 or DENV-4 infection. However, a mechanistic understanding of how these risk factors affect disease outcomes, and further, how the virus's ability to evolve these mechanisms will affect disease severity patterns over time, is lacking. In the second chapter of my dissertation, I formulate mechanistic mathematical models of primary and secondary dengue infections that describe how the dengue virus interacts with the immune response and the results of this interaction on the risk of developing severe dengue disease. I show that only the innate immune response is needed to reproduce characteristic features of a primary infection whereas the adaptive immune response is needed to reproduce characteristic features of a secondary dengue infection. I then add to these models a quantitative measure of disease severity that assumes immunopathology, and analyze the effectiveness of virological indicators of disease severity. In the third chapter of my dissertation, I then statistically fit these mathematical models to viral load data of dengue patients to understand the mechanisms that drive variation in viral load. I specifically consider the roles that immune status, clinical disease manifestation, and serotype may play in explaining viral load variation observed across the patients. With this analysis, I show that there is statistical support for the theory of antibody dependent enhancement in the development of severe disease in secondary dengue infections and that there is statistical support for serotype-specific differences in viral infectivity rates, with infectivity rates of DENV-2 and DENV-3 exceeding those of DENV-1. In the fourth chapter of my dissertation, I integrate these within-host models with a vector-borne epidemiological model to understand the potential for virulence evolution in dengue. Critically, I show that dengue is expected to evolve towards intermediate virulence, and that the optimal virulence of the virus depends strongly on the number of serotypes that co-circulate. Together, these dissertation chapters show that dengue viral load dynamics provide insight into the within-host mechanisms driving differences in dengue disease patterns and that these mechanisms have important implications for dengue virulence evolution.</p> / Dissertation

A distribuição beta é apropriada para analisar dados de variáveis medidas no intervalo (0, 1), como taxas e proporções, como por exemplo a proporção de severidade de doenças em plantas. Portanto, dados que são pares observações de taxas e proporções, naturalmente pensa-se numa distribuição beta bivariada com suporte (0, 1)2. O objetivo deste trabalho constitui-se em encontrar a melhor distribuição beta bivariada na literatura para este caso e, além disso, tentar encontrar estimadores para seus parâmetros, a fim de verificar se esta distribuição escolhida se ajusta bem aos dados. Foi criada uma metodologia para a estimação dos parâmetros, utilizando aquela distribuição que consideramos a mais adequada. Posteriormente foram feitas simulações para avaliar a qualidade desses estimadores e, por fim, foram utilizados três bancos de dados com a finalidade de exemplificar esta metodologia. / Beta distribution is suitable for analyzing variable data measured in the range (0, 1), as rates and proportions, such as the proportion of disease severity in plants. Therefore, data that are paired observations rates and proportions naturally thinks in a bivariate distribution beta supported (0, 1)2. The objective of this work is on finding the best beta bivariate distribution in the literature for this case and, furthermore, try to find estimators for its parameters in order to verify that this chosen distribution fits the data well. A methodology was created for the estimation of parameters using that distribution we consider the most appropriate. Later simulations were performed to evaluate the quality of these estimators and, finally, we use three databases in order to illustrate this methodology.

Chronic pulmonary diseases include a wide range of illnesses that differ in etiology, prevalence, symptomatology and available therapy. A common link among these illnesses is their impact on patients’ vital function of breathing, high symptom burden and significantly impaired quality of life. This dissertation research evaluates disease severity, symptom burden and health behaviors of patients with three different chronic pulmonary conditions. First, alpha-1 antitrypsin deficiency (AATD) is an inherited condition that typically is associated with an increased risk of early onset pulmonary emphysema. This study examines differences in demographic, health, and behavioral characteristics and compares clinical outcomes and health related behaviors and attitudes between two severe genotypes of AATD - ZZ and SZ. The findings of the study suggest that patients with SZ genotype and less severe form of deficiency report higher number of exacerbations, comorbidities, as well as unhealthy behaviors such as lack of exercise and current smoking. In addition, individuals with the more severely deficient ZZ genotype are more adherent to disease management and prevention program recommendations and maintain a healthier lifestyle than individuals with SZ genotype. Second chronic lung disease examined in this research was chronic obstructive pulmonary disease (COPD), the fourth leading cause of death and second leading cause of disability in the United States. Prevalence and burden of cough and phlegm, two of the most common symptoms of the COPD, were assessed among participants of the COPD Foundation’s Patient-Powered Research Network (COPD PPRN). In addition, association between patient-reported levels of phlegm and cough, clinical outcomes and patients’ quality of life were evaluated. Participants’ quality of life was assessed using Patient Reported Outcome Measurement Information System instrument PROMIS-29. Association between changes in symptom severity over time and patient-reported quality of life were examined. Findings of this study indicated that severity of cough and phlegm were associated with higher number of exacerbations, greater dyspnea, and worsened patient-reported quality of life including physical and social functioning. Improvement in cough and phlegm severity over time was associated with better patient-reported quality of life. Third pulmonary illness described in this dissertation is non-cystic fibrosis bronchiectasis (NCFB), a rare and etiologically diverse condition characterized by dilated bronchi, poor mucus clearance and susceptibility to bacterial infection. Association between presence of Pseudomonas aeruginosa (PA), one of the most frequently isolated pathogens in patients with NCFFB, and disease severity was assessed utilizing enrollment data from the Bronchiectasis and NTM Research Registry (BRR). NCFB disease severity was evaluated using modified versions of validated in large international cohorts instruments, the Bronchiectasis Severity Index (BSI) and FACED. The findings of this study indicate that PA infection is common in NCFB patients, and presence of PA in patients’ sputum is associated with having moderate and high severity of bronchiectasis. In addition, the results of this study suggest that the two severity assessment instruments classify patients with NCFB differently which may be attributed to a greater number of severity markers utilized in the calculation of the BSI compared to FACED. In conclusion, the proposed dissertation aims to enhance understanding of differences in health outcomes between genotypes of AATD within AlphaNet registry, and to guide future health-promoting behaviors. It highlights the burden of common symptoms such as cough and phlegm in patients with COPD within COPD PPRN and their association with patients’ quality of life. In addition, it introduces modified indices of NCFB severity and emphasizes high burden of the disease in patients with presence of PA within the US BRR.

Hantaviruses can cause two severe human diseases: hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). Hantaviruses are spread to humans mainly through inhalation of infectious virions, secreted from infected rodents. The human diseases are characterized by an increased capillary leakage syndrome. Hantaviruses are known to infect endothelial cells, but they are non-cytopathogenic. The mechanism behind human disease is not well understood, but an overactive immune response is implicated in the pathogenesis. The aim of my thesis has been to investigate parts of innate and adaptive immune responses in Puumala virus-infected patients. In paper I we found a sex difference in the cytokine profile during acute infection. Females had significantly higher plasma levels of IL-9, FGF-2, GM-CSF and lower levels of IL-8 and IP-10 compared to males. These differences may affect the activation and function of the immune response. In paper II we studied the phenotype and kinetics of NK cells. We observed that CD56dim NK cells were elevated during acute infection and that these, predominantly NKG2C+ NK cells, remained elevated for at least two months after symptom debut. Our novel finding of a prolonged NK cell response, implicates that NK cells may possess adaptive immunity features.  In paper III we observed a vigorous cytotoxic T cell (CTL) response during acute infection, which contracted in parallel with decrease in viral load. The CTL response was not balanced by an increase in regulatory T cells. The T cells expressed inhibitory immunoregulatory receptors, known to dampen intrinsic T cell activity.  In paper IV, we found that a low IgG response in patients was significantly associated with more severe disease, while the viral load did not affect the outcome. Our findings support the use of passive immunization as a treatment alternative for hantavirus-infected patients. In conclusion, my thesis contributes to an increased knowledge about the immune response in hantavirus-infected patients. The findings, combined with future studies, will hopefully lead to a better understanding of the pathogenesis and possible treatment alternatives.

A distribuição beta é apropriada para analisar dados de variáveis medidas no intervalo (0, 1), como taxas e proporções, como por exemplo a proporção de severidade de doenças em plantas. Portanto, dados que são pares observações de taxas e proporções, naturalmente pensa-se numa distribuição beta bivariada com suporte (0, 1)2. O objetivo deste trabalho constitui-se em encontrar a melhor distribuição beta bivariada na literatura para este caso e, além disso, tentar encontrar estimadores para seus parâmetros, a fim de verificar se esta distribuição escolhida se ajusta bem aos dados. Foi criada uma metodologia para a estimação dos parâmetros, utilizando aquela distribuição que consideramos a mais adequada. Posteriormente foram feitas simulações para avaliar a qualidade desses estimadores e, por fim, foram utilizados três bancos de dados com a finalidade de exemplificar esta metodologia. / Beta distribution is suitable for analyzing variable data measured in the range (0, 1), as rates and proportions, such as the proportion of disease severity in plants. Therefore, data that are paired observations rates and proportions naturally thinks in a bivariate distribution beta supported (0, 1)2. The objective of this work is on finding the best beta bivariate distribution in the literature for this case and, furthermore, try to find estimators for its parameters in order to verify that this chosen distribution fits the data well. A methodology was created for the estimation of parameters using that distribution we consider the most appropriate. Later simulations were performed to evaluate the quality of these estimators and, finally, we use three databases in order to illustrate this methodology.

Background: Generating evidence to inform care for pediatric medium-chain acyl-CoA dehydrogenase (MCAD) deficiency requires sustainable and integrated measurement of priority outcomes. Methods: From an existing Canadian cohort study, we evaluated the quality of metabolic clinic chart-abstracted data for measuring core outcomes for pediatric MCAD deficiency. We then modelled variation in emergency department (ED) use, in association with disease severity, child age, and distance to care. Results: Children with MCAD deficiency visit the metabolic clinic at least annually on average but we identified data quality challenges related to inconsistent definitions of core outcomes and missing information in patient charts. Rates of ED use were highest among children aged 6 to 12 months, with more severe disease, and living closest to care. Conclusion: While measuring core outcomes through the metabolic clinic for children with MCAD deficiency is feasible, harmonized data collection is needed to evaluate care and further understand ED use.

We conducted a cross-sectional survey to assess the anxiety, distress, and turnover intention (likelihood to leave their current job) of healthcare workers in Peru during the COVID-19 pandemic. Our results reported that 21.7% healthcare workers in Peru experienced severe anxiety, whereas 26.1% of them experienced severe mental distress. A higher level of education related with a lower level of anxiety. Younger workers had a higher level of turnover intention than their older colleagues did. Healthcare workers in the private sector had a higher turnover intention than those in the public sector. Most importantly, people who were geographically far from Lima, the epicenter in Peru, during the outbreak experienced less anxiety and mental distress, corroborating the ripple effect and disconfirming the typhoon eye theory. However, the direction of these relationships can change depending on the type of institutions (public versus private) and the type of employees' contract (full time versus part time). Our research helps provide insights for clinical professionals in identifying the vulnerable groups to mental disorders in Peru. This is the first study to assess anxiety, mental distress, and turnover intention in healthcare workers in Peru during the COVID-19 pandemic. Copyright

Bipolar affective disorder is a very dynamic disease, which is influenced by numerous factors. One of these factors is the age at onset. The age at onset of bipolar affective disorder may play a major role in its course, severity and number of relapses, number of hospitalizations or response to mood stabilizers. Other factors influenced by the age at onset are suicide thoughts or attempted suicide. The aim of this work is to investigate and demonstrate the effect of age of the first symptom on the course of bipolar disorder. In the framework of quantitative research, 116 respondents completed a questionnaire on the course of bipolar affective disorder. Early age at onset (≤ 19 years) correlated significantly with the longer interval between the first symptom and the visit to the doctor, the first symptom and the first diagnosis and the first symptom and the diagnosis of bipolar affective disorder. There were no statistically significant relationships between the age at onset and the number of hospitalizations or the severity of the disease. Although the effect of age at onset on the course and severity of the disease has not been proven, this area should be further explored as it may help to better management the treatment of the disorder.

Background: Investigators are often interested in using population-level health administrative data in inflammatory bowel disease (IBD) patients to study disease outcomes, risk factors and treatment effects to enhance knowledge, shape clinical practice and influence health care policy. A major limitation of using health administrative data for these purposes is the lack of detailed clinical data to adjust for the confounding effects of differential disease severity on observed associations. Methods to account for disease severity using administrative variables would offer a major advance to population-level studies in IBD patients. Thus, in this study we aimed to use a cohort of IBD patients from The Ottawa Hospital (TOH) to validate a model that was originally developed in Manitoba for estimating clinical disease course in IBD patients through healthcare utilization measures. Objectives: The objectives of this thesis are: 1) To identify and characterize a reference cohort of IBD patients in the ambulatory clinics of four gastroenterologists from TOH on clinical disease course in the preceding year (reference cohort), based on a Manitoba definition of clinical disease course; 2) To fit a partial proportional odds (PPO) model for predicting IBD course, derived using Manitoba health administrative data, to the reference cohort of IBD patients using Ontario health administrative data; 3) To derive new PPO models of IBD disease course for the reference cohort using Ontario administrative variables and compare model performance; and 4) To apply the models to the Ontario Crohn’s and Colitis cohort (OCCC) to estimate IBD course in Ontario, and compare the distribution to that of the Manitoba IBD population.Methods: We first identified a reference cohort of IBD patients in Ontario from the outpatient clinics at TOH during fiscal year 2015. Through chart review, we classified these patients into one of four clinical disease categories (remission, mild, moderate, or severe) using the Manitoba definition. We linked these patients to Ontario health administrative datasets. Given slight differences in data structure and coding between Manitoba and Ontario, we were unable to directly test the Manitoba model and instead fit a PPO model to the Ontario cohort using analogous administrative variables to those used in the final Manitoba model (“adapted model”). We subsequently derived new PPO models using unique Ontario administrative variables under three strategies: 1) Stepwise variable selection (“stepwise model”); 2) Forced fitting of all variables (“all-variables model”); and 3) Using a two-step modelling algorithm that considered IBD-related hospitalizations separate from other administrative variables (“two-step model”). We then compared model performance from the four strategies. Finally, we applied the models to the Ontario IBD population from 2004 to 2016 and compared model estimates to those from Manitoba. Results: We identified 963 patients with IBD from TOH outpatient clinics, of which 52.3% (n=504) were males, 64.6% (n=622) had Crohn's Disease, and 89.2% (n=859) resided in an urban setting. Based on the Manitoba definition, 64.9% of patients within our reference cohort were classified as remission, while 11.4%, 14.1%, and 9.6% were classified as mild, moderate, and severe disease course, respectively. The adapted model (c-statistic 0.77, goodness-fit p-value 0.28) performed comparably to the other models: the stepwise model (c-statistic 0.77, goodness-fit p-value 0.50), the all-variables model (c-statistic 0.77, goodness-fit p-value 0.53), and the two-step model (c-statistic 0.78, goodness-fit p-value 0.75). The adapted model also resulted in overall similar estimates with regards to the disease course distribution among the Ontario IBD population. However, on closer inspection, our two-step model, in which individuals who had been hospitalized for an IBD-related indication within the past year were assumed to have severe disease, performed better with respect to accurately classifying individuals with moderate or severe disease, without sacrificing discriminative ability. Based on the two-step model, from 2004 to 2016, 89.2-91.2% of the Ontario IBD population was in remission, 0% had mild disease, 2.4-3.2% had moderate disease, and 5.9-8.4% had severe disease. Distribution of disease course among IBD patients in Ontario differed considerably than that in Manitoba. Conclusion: In the absence of clinical information within health administrative data, we present and compare four different models that can be used to partially account for the confounding effect of disease course among IBD patients in future population-based studies using Ontario health administrative data. Given that our models did not perform as originally expected, especially with regards to accurately identifying individuals with more active disease states, we advise researchers to use these models at their own discretion.

Thesis (M. Agricultural Management (Plant Production)) -- University of Limpopo, 2020 / Tomato is a major vegetable crop produced in Limpopo province by subsistence and commercial farmers. Biotic and abiotic factors such as diseases and drought affect its productivity and yield negatively. The most economically important tomato disease in Limpopo is early blight, caused by Alternaria solani. Early blight affects tomato growing under stressful conditions such as drought. The main aim of this study was to evaluate water management in tomato production and its effect on tomato yield, early blight occurrence and severity under smallholder farming systems in Giyani. A survey study and field experiments on early blight occurrence and severity were conducted in the Greater Giyani municipality in Limpopo province. Firstly, a survey of early blight was conducted in tomato fields selected from three service centres namely Guwela, Hlaneki and Mhlava Willem. Twenty five potential tomato grower’s farms were randomly selected for survey based on the location and production management strategies. A second study was carried out by establishing field experiments at two farms in the same area, namely: A hi tirheni Mqekwa and Duvadzi farms. The experiments were laid out in a randomized complete block design (RCBD) in a split plot arrangement, with irrigation as the main plot treatment and tomato variety as the subplot treatment. Each treatment was replicated four times. The irrigation treatments consisted of full irrigation up to field capacity and deficit irrigation. The tomato varieties planted were HTX14, Rodade, STAR9006 and Commander, and were irrigated with a drip irrigation system. The overall survey results showed that Guwela s/c had high disease incidence and the lowest disease severity as compared to the other two service centers. The lowest disease incidence was observed at Hlaneki s/c whilst Mhlava willem s/c had the highest disease severity. The two water treatments (full and deficit irrigation) in both farms have shown no significant pairwise differences among xx the volumetric water content means. There was no significant difference (P≥0.05) in early blight disease severity in both farms. Results shows that, all tomato varieties did not differ significantly (P≥0.05) in yield observed between treatments at Duvadzi and A hi tirheni Mqekwa Farm. Deficit irrigation can be used effectively to produce high yields in tomato production provided the cropping season window does not coincide with the hottest time of the year. Full and deficit irrigation did not have influence on the early blight disease incidence on tomato plants. Key words: Alternaria solani; disease incidence; disease severity and drip irrigation