This report is an exploration of theoretical and applied aspects of form-based coding. First, it presents an in-depth look at conventional zoning, conditions surrounding its origins around the turn of the twentieth century, the system of legal precedents that supports zoning, the evolution of the zoning “toolkit”, and the scope of zoning policies which are prevalent today. Second, form-based codes are defined and differentiated from conventional codes as well as design guidelines. The organizing principles on which FBCs are based are explained and the components of FBCs are described. Issues and controversy surrounding FBCs are discussed. Third, diverse case studies from around the country are carried out in order to examine how form-based codes are developed and applied in various real-world contexts. Case studies are presented in two different tiers, primary and secondary. Primary case studies involve in-depth research, whereas secondary case studies receive a brief, overview-style treatment. Primary case studies are: St. Lucie County, Florida and Sarasota County, Florida. Secondary case studies are: Leander, Texas; Peoria, Illinois; Montgomery, Alabama; Arlington County, Virginia; Hercules, California; and Miami, Florida. Fourth, conclusions are drawn from the research and point towards best practices in form-based coding. The report concludes that form-based codes are not a cure-all, should be developed in the context of a visioning process, and should strike a balance in terms of regulation. Additionally, market factors play a major role. The high cost of coding is a major concern. Furthermore, code writers should be prepared to educate the public as part of their profession. / text

Despite adolescence and emerging adulthood being a time of peak physical ability, it is marked by a dramatic increase in morbidity and mortality, primarily driven by poor behavioral and emotional control (Dahl, 2004). Multiple lines of recent research are now focusing on how maturation of decision-making impacts risk-taking, and more specifically, what role emotion regulation plays (Weinberger et al., 2005; Steinberg, 2007). Rather than avoiding risk factors, a call is made for strength and skills-based approaches to risk-taking interventions. The purpose of the current exploratory study was to assess the efficacy of an experiential learning (EL) intervention designed to increase participants’ emotion regulation skills and decrease risk-taking. Twenty-eight emerging adults participated; 15 were assigned to the experimental group and presented with two separate sessions on emotional regulation and risk-taking using EL methodology (low and high element activities). The control group’s 13 participants were presented with two separate powerpoint lectures on emotion regulation and risk-taking. Participants’ difficulty with emotion regulation and risk-taking were assessed prior to the first session, between sessions, and one week following the second session. Qualitative interviews assessed participants’ understanding of how emotions and risk-taking are connected and process measures assessed the emotional impact of the intervention activities. While hypotheses were not confirmed, results revealed a significant decline in difficulty with emotion regulation across time for all participants. Unexpectedly, however, there were no significant differences between the groups on emotional regulation and the group x time interaction was also not significant. Additionally, risk-taking significantly increased across time. The control group reported more risk-taking across the three time periods than the experimental group. The time x group interaction approached significance [F(2,56) =2.68, p =.07], showing consistent increases for the control group but relatively low levels for the experimental group. Qualitative data revealed that participants had clear notions of how emotions drive risk-taking, how the thrill of risk- taking can be used to displace negative feelings, and how one’s need to connect to others can lead to risk-taking. Experimental group participants demonstrated a shift from global thinking about emotions and risk-taking to more specific thoughts about emotional awareness as a key skill. / text

The dopamine transporter (DAT) is a plasma membrane-bound protein, localized on peri-synaptic terminals of dopaminergic (DA) neurons. DAT is responsible for terminating DA signaling by rapid removal of the transmitter from the synaptic cleft region. DA signaling relies on a critical balance between release and removal of the neurotransmitter within synaptic clefts. Recycling of DAT between intracellular endosomal compartments and the plasma membrane regulates DAT function. This dynamic trafficking occurs in both a constitutive and regulated manner to increase or decrease the number of transporters on the cell surface available for transmitter reuptake. Therapeutic drugs and/or drugs of abuse, including psychostimulants and ethanol, cause maladaptive changes in DA signaling in mesolimbic areas of the brain, leading to addictive behaviors. DAT is the primary site of action for psychostimulants such as, cocaine, methylphenidate, and amphetamine. These drugs can alter the function and/or regulation of the transporter. Ethanol, one of the most widely abused drugs in society, is known to activate DA pathways in reward and reinforcement areas of the brain. However, the effect of ethanol on DAT function and regulation is less clear. The studies presented here explore the action of ethanol on DAT function in mammalian cell systems, and the subcellular trafficking mechanisms that regulate the transporter. To delineate mechanisms of ethanol action on DAT, several lines of HEK-293 cells stably expressing DAT or ethanol-insensitive DAT mutants were generated. Short-term ethanol exposure was found to potentiate DAT function, and ethanol sensitivity is mediated by specific amino acids in the first intracellular loop. This increase in function was accompanied by an enhancement of DAT expressed on the cell surface. The changes in DAT localization and the absence of consensus phosphorylation sites in the ethanol sensitive regions of the transporter, led to the hypothesis that ethanol modulates DAT uptake by altering the dynamic trafficking of the transporter. In the present studies, we found ethanol directly regulates DAT function by altering specific step of the endosomal recycling pathway. Further analysis of the ethanol-sensitive first intracellular loop revealed this region might also play a role in conformational changes required for substrate binding. The findings presented in these studies describe a novel molecular mechanism of ethanol action on DAT, and provide a framework to further understand the action of ethanol on synaptic dopamine regulation. / text

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

 As a neuropeptide, both secretin and secretin receptor are expressed in the central nervous system (CNS). It has been revealed that the activities of secretin on hypothalamic cells of rodents are important for osmoregulation and food intake. In the present study, embryonic mouse hypothalamic cell line N42 was used to study the promoter activity of mouse secretin receptor (mSR). By 5′ deletion analysis, a promoter element was identified within ?282 to ?443, relative to the ATG codon, and it contains a GC-box (-297 to -286), a ras responsive element (RRE) (-289 to -276) and an E-box (-416 to -411). Electrophoretic mobility shift assay (EMSA) and supershift analyses showed that Sp1 interacted with the GC-box, another zinc finger As a neuropeptide, both secretin and secretin receptor are expressed in the central nervous system (CNS). It has been revealed that the activities of secretin on hypothalamic cells of rodents are important for osmoregulation and food intake. In the present study, embryonic mouse hypothalamic cell line N42 was used to study the promoter activity of mouse secretin receptor (mSR). By 5′ deletion analysis, a promoter element was identified within ?282 to ?443, relative to the ATG codon, and it contains a GC-box (-297 to -286), a ras responsive element (RRE) (-289 to -276) and an E-box (-416 to -411). Electrophoretic mobility shift assay (EMSA) and supershift analyses showed that Sp1 interacted with the GC-box, another zinc finger / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Reconstruction of Transcription Regulatory Network (TRN) and Transcription Factor Activity (TFA) from gene expression data is an important problem in systems biology. Currently, there exist various factor analysis methods for TRN reconstruction, but most approaches have specific assumptions not satisfied by real biological data. Network Component Analysis (NCA) can handle such limitations and is considered to be one of the most effective methods. The prerequisite for NCA is knowledge of the structure of TRN. Such structure can be obtained from ChIP-chip or ChIP-seq experiments, which however have quite limited applications. In order to cope with the difficulty, we resort to heuristic optimization algorithm such as Particle Swarm Optimization (PSO), in order to explore the possible structures of TRN and choose the most plausible one. Regarding the structure estimation problem, we extend classical PSO and propose a novel Probabilistic binary PSO. Furthermore, an improved NCA called FastNCA is adopted to compute the objective function accurately and fast, which enables PSO to run efficiently. Since heuristic optimization cannot guarantee global convergence, we run PSO multiple times and integrate the results. Then GCV-LASSO (Generalized Cross Validation - Least Absolute Shrinkage and Selection Operator) is performed to estimate TRN. We apply our approach and other factor analysis methods on the synthetic data. The results indicate that the proposed PSOFastNCA-GCV-LASSO algorithm gives better estimation. In order to incorporate more prior information on TRN structure and gene expression dynamics in the linear factor analysis model for improved estimation of TRN and TFAs, a linear Bayesian framework is adopted. Under the unified Bayesian framework, Bayesian Linear Sparse Factor Analysis Model (BLSFM) and Bayesian Linear State Space Model (BLSSM) are developed for instantaneous and dynamic TRN, respectively. Various approaches to incorporate partial and ambiguous prior network structure information in the Bayesian framework are proposed to improve performance in practical applications. Furthermore, we propose a novel mechanism for estimating the hyper-parameters of the distribution priors in our BLSFM and BLSSM models, which can significantly improve the estimation compared to traditional ways of hyper-parameter setting. With this development, reasonably good estimation of TFAs and TRN can be obtained even without use of any structure prior of TRN. Extensive numerical experiments are performed to investigate our developed methods under various settings, with comparison to some existing alternative approaches. It is demonstrated that our hyper-parameter estimation method improves the estimation of TFA and TRN in most settings and has superior performance, and that structure priors in general leads to improved estimation performance. Regarding application to real biological data, we execute the PSO-FastNCAGCV-LASSO algorithm developed in the thesis using E. Coli microarray data and obtain sensible estimation of TFAs and TRN. We apply BLSFM without structure priors of TRN, BLSSM without structure priors as well as with partial structure priors to Yeast S. cerevisiae microarray data and obtain a reasonable estimation of TFAs and TRN. / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

Bacterial dehalogenase is a key enzyme involved in bioremediation of halogenated organic compounds. A dehalogenase, Deh4a, was isolated from the Gram-negative bacterium Burkholderia caribensis MBA4, which can utilize haloacetic acids as carbon source. The haloacid operon in MBA4 was identified and characterized. It is composed of the structural genes forDeh4a and a transporter Deh4p. Transcription of this operon is negatively regulated, but the mechanism and the relevant regulator are still poorly understood. In this study, magnetic DNA affinity chromatography and Tn5transposon mutagenesis were employed to explore the regulatory factors that affected the expression of this haloacid operon. A process that uses lysates from glycolate-grown cells, magnetic DNA affinity chromatography and LC-MS/MS has identified a TetR family transcriptional regulator, TetR8620, which binds to the promoter region of deh4a. Disruption of the TetR8620 gene in mutant Ins8620 abolished the formation of a slow migrating complex in electrophoretic mobility shift assay (EMSA) using lysates from glycolate-grown cells. Moreover, expressions of deh4a were enhanced in bothglycolate- and MCA- grown Ins8620. The addition of recombinant histidine-tagged TetR8620 to lysates of Ins8620 resumed the formation of a retardation complex, but different from that using purified His-tagged TetR8620.This suggested that TetR8620 is responsible for formation of retardation complexes, and an additional protein might be involved. To investigate other putative factors that interact with TetR8620, purified His-tagged TetR8620 was immobilized with Ni-NTA agarose and used for isolation of interacting proteins. Chemical cross-linking of the purified fraction with BS3established that TetR8620 interacts with a proteinof30 kDa. Separation of the cross-linked complex in SDS-PAGE gel also showed that a protein with similar MW was specifically pulled down. These results suggest that TetR8620 was interacting with a ~30 kDa protein. Protein identification using mass spectrometry assay proposed that this protein is probably a universal stress protein UspA encoding by peg.3485 or acetyl-glutamate kinase (EC 2.7.2.8) encoding by peg.714 in MBA4. Tn5transposon mutagenesis was also employed to explore the factors that regulate the haloacid operon ofMBA4. A derivative of MBA4, MK06, which contains a kanamycin resistant gene (kan) with a deh4apromoter was constructed. Kanamycin resistancy of this derivative was MCA inducible. Transposon mutagenesis was conducted on this derivative, and Tn-containing mutants were isolated as tetracycline resistant colonies on pyruvate plates. These colonies were further selected on their resistance tokanamycin in pyruvate plates. Gene peg.6589 encoding a putative transcriptional regulator, DehR1, was disrupted by Tn insertion. While the production of dehalogenase was still MCA-inducible, this mutant has partially relieved the repression of the haloacid operon in media containing pyruvate. Moreover, constitutive production of DehR1 in MBA4 decreased the transcript levels of deh4ain medium containing pyruvate or MCA. This study has identified two transcription factors, TetR8620 and DehR1, which regulate the expression of Deh4a negatively. TetR8620 is a DNA-binding protein that interacts with the deh4apromoter. Results from this study imply that the regulation of the haloacid operon in MBA4 is likely to be under the control of multiple factors. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

This study examines the readiness of suburban towns in Austin for the potential development of affordable and low-income housing through their comprehensive plans and land use policies. The study consists of four sections: an overview of the greater Austin MSA and the developing poverty in the suburban areas, a literature review of the effects of local land use policies on affordable housing production and development, the establishment of a “best practices” metric for local land use policies amenable to affordable housing production, and application of the metric to four localities in the Austin MSA, including Elgin, Dripping Springs, Kyle, and Georgetown. The findings reveal primarily low scores overall for the four localities, and expose the challenges suburban jurisdictions in a high-growth MSA in Texas face when addressing the needs of increasing low-income residents, and display best practices that localities with successful methods use to address those needs. / text

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