Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Regulatory T cells expressing the transcription factor Foxp3 have a critical role in the maintenance of tolerance to both self and innocuous exogenous antigens. Humans and mice die from overwhelming autoimmunity in the absence of Foxp3+ Treg whilst administration of regulatory T cells has shown promise therapeutically in ameliorating autoimmunity in several animal models. Regulatory T cells arise naturally in the thymus (nTreg) but may also be induced from naïve Foxp3- cells in the presence of TGF-β (iTreg), both in vitro and in vivo. This thesis focuses on in vitro generated mouse iTreg, testing the hypothesis that they are able to effect bystander suppression; iTreg activated by a given antigen are able to suppress other responding cells with different antigen reactivities. Chapter 3 details an in vitro assay system using iTreg and responder cells recognising different antigens (TCR transgenic cells). Evidence for bystander suppression is presented and that did not require the presence of iTreg-relevant antigen but did require iTreg-relevant MHC Class II. The kinetics of iTreg suppression are discussed, with evidence presented that iTreg exert their effects early in co-culture. Chapter 4 identifies the production of three pro-inflammatory cytokines by iTreg - IFN-γ, GM-CSF, and TNF. These were not involved in the in vitro suppressive mechanism, but early abrogation of TGF-β signalling did inhibit suppression. Chapter 5 describes the in vivo function of iTreg under various experimental protocols. iTreg did not limit initial proliferation of naïve T cells in response to antigen but did limit the development of effector cells producing pro-inflammatory cytokines. Exposure to a pro-inflammatory environment in vivo led to iTreg producing IFN-γ and TNF, but not GM-CSF. This could be replicated in vitro by exposure to IL-6, IL-12 or IL-27. Finally, evidence for bystander suppression by iTreg in vivo is presented, with a reduction in effector cells producing pro-inflammatory cytokines shown in an allergic airways diease model.

Master of Science / Department of Agronomy / Guorong Zhang / Guihua Bai / Wheat streak mosaic virus (WSMV) is a disease that causes significant yield losses in wheat (Triticum aestivum L.). Host resistance is the primary approach for control. KS06HW79 is a wheat line with WSMV resistance up to 21°C. To study the inheritance of resistance in KS06HW79, it was crossed with two WSMV-susceptible wheat genotypes, KS020638-M-5 and Brawl CL Plus. Parental lines, F₁, F₂, and check varieties were mechanically inoculated and evaluated for WSMV resistance at 21°C in growth chambers. The segregation pattern in two F₂ populations fit a one-recessive-gene model (1 resistant : 3 susceptible) and a dominant-suppression-epistasis model (3 resistant : 13 susceptible). To determine which model was a better fit, WSMV resistance was evaluated for F₂:₃ families generated from resistant F₂ plants in both crosses. Approximately two thirds of the F₂:₃ families in each cross showed segregation for WSMV resistance, suggesting that the dominant-suppression epistasis model better explained the WSMV resistance in KS06HW79. This model was also supported by two KS06HW79-derived doubled haploid populations, which had a segregation ratio of 1 resistant : 3 susceptible. Therefore, the WSMV resistance in KS06HW79 is likely controlled by two dominant genes, one of which is a suppressor.

As privacy concerns become more important, effective and efficient security techniques will become critical to those that are charged with the protection of sensitive information. Agencies that disseminate numerical data encounter a common disclosure control problem called the complementary cell suppression problem. In this problem, cell values that are considered sensitive in the statistical table must be suppressed before the table is made public. However, suppressing only these cells may not provide adequate protection since their values may be inferred using available marginal subtotals. In order to ensure that the values of the sensitive cells cannot be estimated within a specified degree of precision additional non-sensitive cells, called complementary cells, must also be suppressed. Since suppression of non-sensitive cells diminishes the utility of the released data, the objective in the complementary cell suppression problem is to minimize the information lost due to complementary suppression while guaranteeing that the sensitive cells are adequately protected. The resulting constrained optimization problem is known to be NP-hard and has been a major focus of research in statistical data security. Several heuristic methods have been developed to find good solutions for the complementary cell suppression problem. More recently, genetic algorithms have been used to improve upon these solutions. A problem with these GA-based approaches is that a vast majority of the solutions produced do not protect the sensitive cells. This is because the genetic operators used do not maintain the associations between cells that provide the protection. Consequently, the GA has to include an additional procedure for repairing the solutions. This dissertation details an improved GA-based method for the complementary cell suppression problem that addresses this limitation by designing more effective genetic operators. Specifically, it mitigated the problem of chromosomal repair by developing a crossover operator that maintains the necessary associations. The study also designed an improved mutation operator that exploits domain knowledge to increase the probability of finding good quality solutions. The proposed GA was evaluated by comparing it to extant methods based on the quality of its evolved solutions and its computational efficiency.

Master of Public Health - MPH / Background: Globally, it is estimated that about 1.8 million adolescents (aged 10–19 years) were living with HIV in 2015. In Kenya an estimated 133,455 adolescents were living with HIV in 2015, of which 75% (105,679) were in need of antiretroviral therapy (ART). Among adolescents on ART in 2016, 63% reported viral suppression; which is far below the UNAIDS targets of 90%. Viral suppression (having less than 1000 copies of viral RNA/ml of blood) is a key indicator of HIV treatment success, and is associated with better quality of life and reductions in HIV incidence at a population level. Homabay County recorded the highest HIV prevalence (26%) and the highest number of adolescents living with HIV in Kenya (15,323) in 2015. By the end of June 2017 5,709 adolescents were initiated on ART in Homabay County. Despite the successes in initiating HIV positive adolescents on ART, little is known about the factors that are associated with viral suppression. The current study investigated the factors associated with viral suppression among adolescents initiated on ART before November 30, 2017 in Homabay County, Kenya. Methods: A descriptive cross-sectional study was conducted among 925 adolescents registered on ART for at least 6 months and with at least one documented viral load in the last 12 months, in six health facilities in Homabay County. Data was extracted from the electronic medical records and exported into an excel spreadsheet. Bivariate and multivariate logistic regression analyses were conducted to identify factors associated to viral suppression using Stata 12.0.

Increases in agricultural intensification over the past century have resulted in significant alterations to the rural landscape across the Midwest. Pollinators are essential to sustain natural and managed ecosystems. They are vital for food production and their declines have been linked, in part, to a rise in intensive agricultural practices. There is a recognized need among numerous stakeholders to build sustainability into the management of agroecosystems to protect both the biotic and abiotic resources of these systems. The use of cover crops is gaining interest among agricultural producers for benefits such as improving water quality and soil health. Cover cropping systems have the potential to provide floral resources to pollinators and suppress problematic driver weeds. The overall objective of this study was to quantify the effects of cover crops on plant and pollinator biodiversity within agricultural systems. This study aimed to characterize the pollinator diversity indicative of the patchwork mosaic forest-agroecosystem of Crab Orchard National Wildlife Refuge; evaluate the roles cover crop treatments play in supporting pollinator diversity and weed suppression benefits in a conventionally managed system; and provide the basis of recommendations for sustainable weed suppression tactics and for enhancing the quality of pollinator habitat within agricultural systems.

MSc (Med), Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand / Three separate recent publications used genome-wide RNA interference (RNAi) to screen for novel host factors that are required for HIV-1 infection and replication. This was achieved using small interfering RNAs (siRNAs) to silence the expression of ~21 000 human genes and determining the effect of each gene’s loss of function on HIV-1 replication. Collectively, several hundred genes have now been implicated as novel HIV-1 host factors (termed HIV-1 Dependency Factors, HDFs). However, differences in study design resulted in little overlap and limited interpretive value from the three published datasets. To identify novel HDFs that are potential targets for anti-HIV therapy, five putative HDFs (SPTBN1, TMED2, KIAA1012, PRDM14 and SP110) were chosen for validation. RNAi effecters (both siRNAs and expressed short hairpin RNAs) were used to silence the selected genes. Gene suppression was measured by quantitative RT-PCR assay and two candidate genes were studied further (SPTBN1 and SP110) based on efficient mRNA inhibition (over 90%). As efforts to deliver the RNAi effecters to a T-cell line were unsuccessful, the effect of this knockdown on HIV-1 replication (both early- and late-stage) was assessed in cultured TZM-bl cells, a HeLa-derived cell line that expresses HIV-1 entry receptors and an integrated luciferase reporter for HIV-1 transcriptional activity (also used in the first genome-wide RNAi screen). An initial viral challenge assay with Subtype C-enveloped pseudovirus showed a 60% decrease in TZM-bl luciferase reporter activity in cells with suppressed SPTBN1 function, while knockdown of SP110 showed no effect on reporter activity. The final experiment, using fully-replicating Subtype B virus, showed a 75% decrease in late-stage viral replication when SPTBN1 expression was suppressed. In addition, SP110 suppression was confirmed to have no effect on TZM-bl reporter activity during any stage of HIV-1 replication. In conclusion, SPTBN1, but not SP110, is required for late-stage HIV-1 replication, though these results need to be confirmed in CD4+ T-cells. The absence of several important viral accessory factors from vi the virus used in the genome-wide screen may explain these findings and emphasises the need for using physiologically representative viral and cellular models to study the viral/cellular interactome.

MSc (Med), Epidemiology and Biostatistics, Faculty of Health Sciences, University of the Witwatersrand / Objectives: To evaluate differences in virologic outcomes between adolescents and pre-adolescents initiated on HAART and to determine the patient baseline variables associated with virologic suppression. Design: Retrospective cohort study using routinely collected clinic and outcome data. Setting: Public sector HIV paediatric facility at Harriet Shezi Children’s Clinic (Chris Hani Baragwanath Hospital) Soweto, South Africa. Patients: HIV infected pre-adolescents (5 to < 11 years) and adolescents (11 to <18 years) initiating HAART between 1 April 2004 and 31 December 2008. Main outcomes and measures: Primary: virologic suppression (HIV viral load ≤ 400 copies/ml) and viral rebound (single HIV viral load ≥ 400 copies/ml after initial suppression) at 24, 48, 72 and 96 week follow up intervals. Secondary: determination of baseline variables associated with virologic suppression. Survival analysis was performed using the Kaplan Meier method and modelling was based on Cox proportional hazards. Results: Both groups exhibited similar incidence rates of virologic suppression by the 24th week from HAART initiation. Adolescents had a slightly lower incidence rate of early virologic suppression in comparison to pre-adolescents (197/100 person years vs. 203/100 person years). However, the observed difference was not statistically significant at 5% significance level (IRR: 0.97, 95%CI: 0.81 - 1.15). In a sub-group of children who had not virologically suppressed by the 24th week (168 days) of follow up, adolescents were 42% less likely to achieve virologic suppression after this time point than pre-adolescents ([IRR: 0.58, 95%CI: 0.35, 0.93). In the sub-group of all female participants, lower hazards of virologic suppression by the 24th week (aHR 0.76, 95%CI 0.59-0.99) and 96th week (aHR 0.70, 0.55-0.90) of follow up were observed among female adolescents when compared with female pre-adolescents. Additionally, clinically advanced disease was observed as a risk factor for non-virologic suppression by the 96th week of follow up among participants of all ages (aHR 0.75, 95%CI 0.64 -0.87). After 60 weeks from the initial virologic suppression, adolescents were twice more likely to experience rebound after this point than pre-adolescents (IRR: 2.33, 95%CI: 1.00 - 5.13). Conclusion: Given the potential for resistant strains of the HIV virus and the public health threat this presents, health care teams face complicated dilemmas regarding initiation of HAART to adolescents, particularly female adolescent patients who are likely to be non-adherent. Findings from the study advocate for intensified adherence and treatment support for all adolescents initiated on HAART to achieve virologic suppression within the first 6 months of treatment, a time after which they have been shown to exhibit inferior virologic suppression rates. Once virologic suppression has been attained, adolescents require prolonged treatment support to maintain long term virologic suppression at levels observed among pre-adolescents. We recommend further research into the comparison of virologic outcomes between pre-adolescents and adolescents on HAART, through prospective study designs. Qualitative study designs are also important to bridge the knowledge gaps on the barriers to HAART encountered by female adolescents.

Childhood maltreatment predicts mental health problems and stress responses. To design better intervention/prevention programs, it is important to explore mechanisms that may mediate those relationships. Some evidence indicates that emotion regulation strategies (suppression and reappraisal) may play this role. Using self-report, observational, and biological measures and stress manipulation in female and male college students (Study 1: N=267; Study 2: U.S.= 264; Korean=211; Study 3: N=211), I tested the following hypotheses: Study (1) habitual suppression and reappraisal strategies will mediate the relation between childhood maltreatment and perceived stress; Study (2) parental emotional neglect will be positively associated with habitual suppression and internalizing problems, and negatively associated with habitual reappraisal, in both U.S. and Korean participants; Study (3) childhood maltreatment will be associated with heightened physio-emotional responses to the Trier Social Stress Test, mediated by spontaneous suppression and reappraisal. In Study 1, partially supporting my hypotheses, habitual suppression and reappraisal mediated the relationship between self-reported maternal/paternal emotional neglect and perceived stress, though in females only; habitual suppression also mediated the relationship between maternal psychological maltreatment and perceived stress in females. In Study 2, structural equation modeling revealed that, as hypothesized, in both countries parental emotional neglect was positively associated with internalizing problems and negatively associated with habitual reappraisal; habitual reappraisal was negatively associated and habitual suppression was positively associated with internalizing problems. The positive association between parental emotional neglect and suppression was significant only in U.S. participants. In Study 3, partially supporting hypotheses, childhood maltreatment was associated with lower spontaneous reappraisal, higher negative affect at stress-test baseline, and higher behavioral expression during recovery; spontaneous suppression and reappraisal were associated with reduced emotional responsivity. Contrary to hypothesis, no mediating roles for spontaneous suppression and reappraisal were found. Together, results showed that habitual use of some emotion regulation strategies can mediate the relation between childhood maltreatment and later perceived stress (at least in females) and internalizing problems; habitual suppression mediates the association between parental emotional neglect and internalizing problems in U.S. young adults; and childhood maltreatment is related to emotional and behavioral responses to stress and effectiveness of spontaneous reappraisal strategy use during stress. / 2022-02-28T00:00:00Z

Recent improvements in equipment used by firefighters has increased the value of manual suppression in buildings. However, because there is no evaluation method available, the effectiveness of manual suppression can not be incorporated into a fire safety analysis of a building. This thesis develops a method for evaluating manual suppression in buildings. he evaluation is done through an analysis of the paths through a building firefighters will use to attack a fire. The analysis considers the building, fire and fire department factors influencing progress towards teh fire. The fire attack path analysis yeilds a value relating the relative difficulty of a path.