TITLE: Synchrony in a Boolean network model of the L-arabinose operon



ABSTRACT: In genetics, an operon is a segment of DNA that contains several co-transcribed genes, which together form a functional regulatory unit. Operons have primarily been studied in prokaryotes, with both the lactose and tryptophan operons in E. Coli having been classically modeled with differential equations and more recently, with Boolean networks. The L-arabinose operon in E. coli encodes proteins that function in the catabolism of arabinose. This operon has several complex features, such as a protein that acts both as an activator, a DNA looping repressing mechanism, and the lack of inducer exclusion by glucose. In this talk, I will propose a Boolean network model of the ara operon, and then show how computational algebra in Sage establishes that for 11 of the 12 choices of initial conditions, the state space contains a single fixed point that correctly predicts the biology. The final initial condition describes the case where there are medium levels of arabinose and no glucose, and it successfully predicts bistability of the system. Finally, I will compare the state space under synchronous and asynchronous update, and show how the former has several artificial cycles that go away under a general asynchronous update.

Title: Insight into Molecular through Subcellular Calcium Signaling via Multi-Scale Simulation

Abstract: Calcium is critical to a wide range of physiological processes, including neurological function, immune responses, and muscle contraction. Calcium-dependent signaling pathways enlist a variety of proteins and channels that must rapidly and selectively bind calcium against thousand-fold higher cationic concentrations. Frequently these pathways further require the co-localization of these proteins within specialized subcellular structures to function properly. Our lab has developed multi-scale simulation tools to elucidate how protein structure and co-localization facilitate intracellular calcium signaling. Developments include combining molecular simulations with a statistical mechanical model of ion binding, a homogenization theory to upscale molecular interactions into micron-scale diffusion models, and reaction-diffusion simulations that leverage sub-micron microscopy data. In this seminar, I will describe these tools and their applications toward molecular mechanisms of calcium-selective recognition and cross-talk between co-localized calcium binding proteins inside the cell.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Speaker: Devin Willmott

Title: Generative Neural Networks in Semi-Supervised Learning



Abstract: Semi-supervised learning is a relatively new machine learning concept that seeks to use both labeled and unlabeled data to perform supervised learning tasks. We will look at two network types with some promising applications to semi-supervised learning: ladder networks and adversarial networks. For each, we will discuss the motivations behind their architectures & training methods, and derive some favorable theoretical properties about their capabilities.