Life-patterns on the periphery : a humanities base for development imperatives and their application in the Chicago city-region

Life-Patterns on the Periphery: A Humanities Base for Development Imperatives and their Application in the Chicago City-Region is informed by the need to bring diverse fields together in order to tackle issues related to the contemporary city-region. By honouring the long-term economic, social, political, and ecological imperatives that form the fabric of healthy, productive, sustainable communities, it becomes possible to setup political structures and citizen will to develop distinct places that result in the overlapping of citizen life patterns, setting the stage for citizen action and interaction. Based in humanities scholarship, the four imperatives act as checks on each other so that no one imperative is solely honoured in development. Informed by Heidegger, Arendt, deCerteau, Casey, and others, their foundation in the humanities underlines their importance, while at the same time creating a stage where all fields can contribute to actualizing this balance in practice. For this project, theoretical assistance has been greatly borrowed from architecture, planning theory, urban theory, and landscape urbanism, including scholarship from Saskia Sassen, John Friedmann, William Cronon, Jane Jacobs, Joel Garreau, Alan Berger, and many others. This project uses the Chicago city-region as a site, specifically the Interstate 80 and 88 corridors extending west from Chicago. Both transportation corridors are divided into study regions, providing the opportunity to examine a broad variety of population and development densities. Through observational research, a picture of each study region can be extrapolated, analyzed, and understood with respect to the four imperatives. This is put to use in this project by studying region-specific suggestions for future development moves, culminating in some universal steps that can be taken to develop stronger communities and set both the research site specifically and North American city-regions in general on a path towards healthy, productive, sustainable development.

Water and sanitation accessibility and the health of rural Ugandans

The lack of access to sufficient water and sanitation facilities is one of the largest hindrances towards the sustainable development of the poorest 2.2 billion people in the world. Rural Uganda is one of the areas where such inaccessibility is seriously hampering their efforts at development. Many rural Ugandans must travel several kilometers to fetch adequate water and many still do not have adequate sanitation facilities. Such poor access to clean water forces Ugandans to spend an inordinate amount of time and energy collecting water - time and energy that could be used for more useful endeavors. Furthermore, the difficulty in getting water means that people use less water than they need to for optimal health and well-being. Access to other sanitation facilities can also have a large impact, particularly on the health of young children and the elderly whose immune systems are less than optimal. Hand-washing, presence of a sanitary latrine, general household cleanliness, maintenance of the safe water chain and the households’ knowledge about and adherence to sound sanitation practices may be as important as access to clean water sources. This report investigates these problems using the results from two different studies. It first looks into how access to water affects peoples’ use of it. In particular it investigates how much water households use as a function of perceived effort to fetch it. Operationally, this was accomplished by surveying nearly 1,500 residents in three different districts around Uganda about their water usage and the time and distance they must travel to fetch it. The study found that there is no statistically significant correlation between a family’s water usage and the perceived effort they must put forth to have to fetch it. On average, people use around 15 liters per person per day. Rural Ugandan residents apparently require a certain amount of water and will travel as far or as long as necessary to collect it. Secondly, a study entitled “What Works Best in Diarrheal Disease Prevention?” was carried out to study the effectiveness of five different water and sanitation facilities in reducing diarrheal disease incidences amongst children under five. It did this by surveying five different communities before and after the implementation of improvements to find changes in diarrheal disease incidences amongst children under five years of age. It found that household water treatment devices provide the best means of preventing diarrheal diseases. This is likely because water often becomes contaminated before it is consumed even if it was collected from a protected source.

Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.

Using a Prediction and Option Generation Paradigm to Understand Decision Making

In many complex and dynamic domains, the ability to generate and then select the appropriate course of action is based on the decision maker's "reading" of the situation--in other words, their ability to assess the situation and predict how it will evolve over the next few seconds. Current theories regarding option generation during the situation assessment and response phases of decision making offer contrasting views on the cognitive mechanisms that support superior performance. The Recognition-Primed Decision-making model (RPD; Klein, 1989) and Take-The-First heuristic (TTF; Johnson & Raab, 2003) suggest that superior decisions are made by generating few options, and then selecting the first option as the final one. Long-Term Working Memory theory (LTWM; Ericsson & Kintsch, 1995), on the other hand, posits that skilled decision makers construct rich, detailed situation models, and that as a result, skilled performers should have the ability to generate more of the available task-relevant options. The main goal of this dissertation was to use these theories about option generation as a way to further the understanding of how police officers anticipate a perpetrator's actions, and make decisions about how to respond, during dynamic law enforcement situations. An additional goal was to gather information that can be used, in the future, to design training based on the anticipation skills, decision strategies, and processes of experienced officers. Two studies were conducted to achieve these goals. Study 1 identified video-based law enforcement scenarios that could be used to discriminate between experienced and less-experienced police officers, in terms of their ability to anticipate the outcome. The discriminating scenarios were used as the stimuli in Study 2; 23 experienced and 26 less-experienced police officers observed temporally-occluded versions of the scenarios, and then completed assessment and response option-generation tasks. The results provided mixed support for the nature of option generation in these situations. Consistent with RPD and TTF, participants typically selected the first-generated option as their final one, and did so during both the assessment and response phases of decision making. Consistent with LTWM theory, participants--regardless of experience level--generated more task-relevant assessment options than task-irrelevant options. However, an expected interaction between experience level and option-relevance was not observed. Collectively, the two studies provide a deeper understanding of how police officers make decisions in dynamic situations. The methods developed and employed in the studies can be used to investigate anticipation and decision making in other critical domains (e.g., nursing, military). The results are discussed in relation to how they can inform future studies of option-generation performance, and how they could be applied to develop training for law enforcement officers.

Oligodeoxynucleotide synthesis using protecting groups and a linker cleavable under non-nucleophilic conditions

Oligodeoxynucleotides (ODNs) containing latent electrophilic groups can be highly useful in antisense drug development and many other applications such as chemical biology and medicine, where covalent cross-linking of ODNs with mRNA, protein and ODN is required. However, such ODN analogues cannot be synthesized using traditional technologies due to the strongly nucleophilic conditions used in traditional deprotection/cleavage process. To solve this long lasting and highly challenging problem in nucleic acid chemistry, I used the 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) function to protect the exo-amino groups on the nucleobases dA, dC and dG, and to design the linker between the nascent ODN and solid support. These protecting groups and linker are completely stable under all ODN synthesis conditions, but can be readily cleaved under non-nucleophilic and nearly neutral conditions. As a result, the new ODN synthesis technology is universally useful for the synthesis of electrophilic ODNs. The dissertation is mainly comprised of two portions. In the first portion, the development of the Dmoc-based linker for ODN synthesis will be described. The construction of the dT-Dmoc-linker required a total of seven steps to synthesize. The linker was then anchored to the solid support―controlled pore glass (CPG). In the second portion, the syntheses of Dmoc-protected phosphoramidites ODN synthesis monomers including Dmoc-dC-amidite, Dmoc-dA-amidite, Dmoc-dG-amidite are described. The protection of dC and dA with 1,3-dithian-2-yl-methyl 4-nitrophenyl carbonate proceeded smoothly giving Dmoc-dC and Dmoc-dA in good yields. However, when the same acylation procedure was applied for the synthesis of Dmoc-dG, very low yield was obtained. This problem was later solved using a highly innovative and environmentally benign procedure, which is expected to be widely useful for the acylation of the exo-amino groups on nucleoside bases. The reactions to convert the Dmoc-protected nucleosides to phosphoramidite monomers proceeded smoothly with high yields. Using the Dmoc phosphoramidite monomers dA, dC, dG and the commercially available dT, and the Dmoc linker, four ODN sequences were synthesized. In all cases, excellent coupling yields were obtained. ODN deprotection/cleavage was achieved by using non-nucleophilic oxidative conditions. The new technology is predicted to be universally useful for the synthesis of ODNs containing one or more electrophilic functionalities.