Embedded model discrepancy: A case study of Zika modeling

Mathematical models of epidemiological systems enable investigation of and predictions about potential disease outbreaks. However, commonly used models are often highly simplified representations of incredibly complex systems. Because of these simplifications, the model output, of say new cases of a disease over time, or when an epidemic will occur, may be inconsistent with available data. In this case, we must improve the model, especially if we plan to make decisions based on it that could affect human health and safety, but direct improvements are often beyond our reach. In this work, we explore this problem through a case study of the Zika outbreak in Brazil in 2016. We propose an embedded discrepancy operator---a modification to the model equations that requires modest information about the system and is calibrated by all relevant data. We show that the new enriched model demonstrates greatly increased consistency with real data. Moreover, the method is general enough to easily apply to many other mathematical models in epidemiology.Comment: 9 pages, 7 figure

Suicidal thinking and psychological distress: The role of personality and cognitive factors

Objectives. This thesis aimed to examine a series of personality and cognitive factors as prospective predictors of suicidal thinking and psychological distress. A secondary objective was to examine any causal relationship between rumination and attentional biases. Method. In order to achieve the above objectives, a series of four studies were conducted. Studies one and three were prospective studies, using analogue samples, to examine the role of personality and cognitive factors in distress and suicidal thinking. In addition, study one also investigated the effect on attentional bias of manipulating rumination. Study two was an experimental study in which two different methods of manipulating attentional bias were piloted. The final study in this thesis employed a clinical sample of general hospital parasuicide patients to investigate whether relationships between personality and cognitive factors were replicable in a clinical population. Results. The personality and cognitive factors understudy were investigated within a research framework to examine their interactive effects. Hierarchical regression analyses revealed a number of moderating and mediating relationships between these personality and cognitive factors to prospectively predict both suicidal thinking and psychological distress. In addition, rumination was found to have a causal influence on positive attentional bias. Conclusions. Evidence from this thesis links personality and cognitive factors to both suicidal thinking and psychological distress in a series of moderating and mediating relationships. These are discussed in relation to the possible theoretical and clinical implications

On the representation of model inadequacy : a stochastic operator approach

Mathematical models of physical systems are subject to many sources of uncertainty such as measurement errors and uncertain initial and boundary conditions. After accounting for these uncertainties, it is often revealed that there remains some discrepancy between the model output and the observations; if so, the model is said to be inadequate. In practice, the inadequate model may be the best that is available or tractable, and so despite its inadequacy the model may be used to make predictions of unobserved quantities. In this case, a representation of the inadequacy is necessary, so the impact of the observed discrepancy can be determined. We investigate this problem in the context of chemical kinetics and propose a new technique to account for model inadequacy that is both probabilistic and physically meaningful. Chemical reactions are generally modeled by a set of nonlinear ordinary differential equations (ODEs) for the concentrations of the species and temperature. In this work, a stochastic inadequacy operator S is introduced which includes three parts. The first is represented by a random matrix which is embedded within the ODEs of the concentrations. The matrix is required to satisfy several physical constraints, and its most general form exhibits some useful properties, such as having only non-positive eigenvalues. The second is a smaller but specific set of nonlinear terms that also modifies the species’ concentrations, and the third is an operator that properly accounts for changes to the energy equation due to the previous changes. The entries of S are governed by probability distributions, which in turn are characterized by a set of hyperparameters. The model parameters and hyperparameters are calibrated using high-dimensional hierarchical Bayesian inference, with data from a range of initial conditions. This allows the use of the inadequacy operator on a wide range of scenarios, rather than correcting any particular realization of the model with a corresponding data set. We apply the method to typical problems in chemical kinetics including the reaction mechanisms of hydrogen and methane combustion. We also study how the inadequacy representation affects an unobserved quantity of interest— the flamespeed of a one-dimensional hydrogen laminar flame.Computational Science, Engineering, and Mathematic

Purification of Feo proteins and analysis of residues important for Feo protein interactions

textIron is an essential element for virtually all forms of life. Complicating matters, it is present in the insoluble ferric form in aerobic environments, while the more soluble ferrous form is found in anaerobic or reducing environments. Vibrio cholerae, the causative agent of the disease cholera, requires iron to survive. In order to meet the need for iron, V. cholerae expresses a variety of iron acquisition systems. One of these systems, Feo, is highly conserved among bacterial species as well as archaea and transports ferrous iron. The Feo system consists of three proteins: FeoA, FeoB, and FeoC. Previous work using the bacterial adenylate cyclase two hybrid system has shown that FeoC interacts with the cytoplasmic N-terminal domain of FeoB. However, the significance of this interaction is not known. In this study, V. cholerae Feo system proteins were analyzed for residues important for the interaction between FeoB and FeoC. In addition, FeoA and FeoC were purified for antibody production. It was found that a residue in the G protein domain of FeoB was not necessary for interaction with FeoC. However, a conserved residue in FeoC did abolish the interaction with FeoB. These results indicate that there is at least one residue important in the interaction of FeoB and FeoC, although further characterization will most likely reveal more. Antibodies to FeoA and FeoC were generated to use them for further characterization of the Feo system.Microbiolog

Freedom through Education: The Sunflower County Freedom Project

The United States intelligence community is an integral part of the security of our\u27 nation. It has been continually growing and redesigning itself for the past 230 years to suit the needs of the people and of the nation. Inhibiting the American intelligence system, however, is the struggle for the U.S. to find a balance between the rights of the people and the security of the nation. This struggle has been at the basis of change in almost every instance of intelligence redesign. It is these changes that have become the study of this thesis. Major trends found in the redesign of the U.S. intelligence system can be categorized in three ways. First, early American intelligence history shows the common mindset that intelligence was needed only in times of war. Were intelligence used in peace time, it would be a breach of the people’s rights to privacy as well as a breach of trust among nations. Second, as the nation evolved and became embroiled in more and greater conflicts, the people realized that it was necessary to not only have intelligence during wars, but also, in order for war time intelligence to be most effective, it had to remain flmctioning during peace time. It was essential, however, that these new, full time intelligence units severely limit their capabilities and functions during peace time. Finally, it has only been in the last sixty years that intelligence units have existed and functioned both during times of war and of peace. Vitally important to the study of these changes in attitude towards intelligence are the three common threads which are found throughout history. These threads which bind the history of intelligence redesign include: 1) Change to the intelligence community V comes on the heels of intelligence failures; 2) Intelligence failures occur because of the lack of cohesion in the intelligence community; 3) The lack of cohesion stems from the inherent American struggle to find a balance between rights and security