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Introduction
Texas ScholarWorks was established to provide open, online access to the products of the University's research and scholarship, to preserve these works for future generations, to promote new models of scholarly communication, and to help deepen community understanding of the value of higher education.
UT Tower and campus image credit: Earl McGehee, CC-BY, https://www.flickr.com/photos/ejmc/7452145850
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Motif-informed analysis of phenotype heterogeneity in cancer
(2023-12) Xu, Qi, Ph. D.; Ehrlich, Lauren; Kowalski, Jeanne; Yankeelov, Thomas E; Marcotte, Edward M; DiGiovanni, John; Vasquez, Karen M
The landscape of cancer genomics harbors a wealth of DNA motifs, whose thorough analysis and integration provide a pivotal method to decipher the complex molecular interactions underlying cancer. This dissertation delineates novel computational methodologies for robust DNA motif analysis and data integration, aiming to elucidate the implications of DNA motifs on cancer heterogeneity and clinical outcomes. Chapter 1 lays the groundwork by showing the significance of DNA motifs in the genomic framework and delineating the current biomarkers in cancer. It highlights the opportunity that DNA motif analysis presents in unveiling a nuanced understanding of genomic interactions. It also indicates the motivations and specific aims of the study of both DNA motif quantification and co-localization analysis. In Chapter 2, a foundational marker for quantifying the prevalence of DNA repetitive motifs, termed as “Non-B DNA Burden”, is introduced. A user-centric platform is also developed to facilitate the efficient computation and visualization of this metric across various genomic scales. Together, they are offering a novel perspective for analyzing DNA motif heterogeneity. Transitioning to Chapter 3, the focus evolves toward an integrated marker approach. By integrating the prevalence analysis of DNA motifs in conjunction with the frequency of co-localized mutations, novel markers mlTNB (mutation-localized total non-B burden) and nbTMB (non-B informed tumor mutation burden) are proposed. Their potential in predicting cancer prognosis and treatment responses is specifically explored. Chapter 4 broadens the analytical foundation by defining MoCoLo (Motif Co-Localization), a robust statistical framework for testing multi-modal DNA motif co-localization. Through this framework, we are able to explore the complex interplay of genomic features and provide a methodical approach to investigate their co-localization in a multi-modal data integration context. Case studies are employed to showcase the utility of MoCoLo in examining the co-localization of genomic features, thus facilitating the understanding of genomic interactions that are pivotal to cancer biology. Chapter 5 synthesizes the findings from the preceding explorations, outlining the contributions of the developed methodologies to the field of cancer genomics and bioinformatics. It demonstrates the potential impact of DNA motif analysis and data integration on understanding phenotype heterogeneity in cancer and shows the prospective avenues it provides for impactful future research. Overall, this work is structured to contribute to the bioinformatics community by weaving together innovative tools and analyses focused on DNA motif analysis and data integration. It strives to pave a beneficial way forward to a deeper understanding of the cancer genome, thereby enhancing potential diagnostic and therapeutic strategies.
Automated drill bit forensics : enhancing efficiency and accuracy through image processing and machine learning
(2023-12) Chu, Jian, Ph. D.; Chen, Dongmei, Ph. D.; Oort, Eric van; Sha, Zhenghui; Ashok, Preadeepkumar; Li, Wei; Hasenbein, John
In recent years, the automation of drilling has garnered considerable attention within both the upstream oil and gas companies and the drilling research community. Drill bit forensics, being integral to the enhancement of efficiencies and profits in the oil and gas industries, promises heightened drilling efficiency, augmented consistency, and a refined comprehension of bit damage mechanisms through automation. Nevertheless, the adoption rate of drilling automation remains sluggish, largely due to the intricate nature of drilling operations. At present, the conventional inspection and grading of bit damage by human operators is labor-intensive and susceptible to human biases. This underscores the imperative for an automated system in drill bit forensics, which would aid drilling operators and specialists in processing and analyzing bit damage data.
In this dissertation, a novel systematic framework is introduced, amalgamating computer vision and machine learning techniques with domain-specific knowledge of drill bits. This framework streamlines the evaluation process from identifying various drill bit components, quantifying and categorizing cutter damage, collating positional data, to ultimately forecasting the primary causes of damage.
The methodologies devised are applied to visual data of drill bits, encompassing images and videos from hundreds of different bit runs. This work delves into several innovative contributions: (1) The industry's first bit detection model that segments distinct parts of the bit; (2) A pioneering proposition to utilize video data of drill bits to expedite the automation of bit forensics; (3) A comprehensive workflow tailored for diverse bit data sources; (4) An adaptable analytical methodology for discerning the root causes of bit damage. The outcomes underscore the potential of an automated system in drill bit forensics to bolster the precision and uniformity of drill bit assessments, offering invaluable insights into drilling operations. This groundbreaking methodology lays the foundation for further advancements in the realm of automated drill bit forensics, targeting the enhancement of the overall efficacy and cost-efficiency of drilling operations.
Do you still find me attractive? : partners’ daily perceptions of attractiveness across the transition to parenthood
(2023-12) Blickman, Rachel Sherak; Gleason, Marci Elizabeth Joy; Neff, Lisa Hassig
The transition to parenthood is often characterized by physical changes and altered sexual dynamics that can increase new parents’ insecurity regarding their own attractiveness. Drawing from theories of risk regulation, this insecurity may lead individuals to underestimate their partner’s attraction to them and become more attentive to daily changes in their partner’s regard. To investigate this possibility, the current study examined bias and accuracy in new parents’ perceptions of their partner’s daily attraction to them. Sixty-one couples completed 21-day daily diary tasks during pregnancy, immediately after childbirth, and again when their child was approximately four months old (i.e., up to 63 days of data). On average, parents did not exhibit significant bias in their perception of their partner’s attraction across the three phases. Further analyses examined whether bias and accuracy would be stronger for those experiencing (1) higher appearance insecurity, (2) lower sexual frequency, and (3) lower sexual satisfaction. Results indicated that, for both mothers and fathers, those who experienced higher appearance insecurity and lower sexual satisfaction were more likely to underestimate their partner’s level of attraction to them. These findings underscore the notion that fathers, as well as mothers, experience sensitivities that can impact how they perceive their partner’s attraction during this pivotal and often challenging life transition.
Research and development of high voltage SiC bipolar junction transistor
(2023-12) Luo, Xixi; Huang, Alex Q.; Li, Xiuling; Agarwal, Anant; Dodabalapur, Ananth; Banerjee, Sanjay K.
In this Dissertation, a 3kV level 4H-SiC Bipolar Junction Transistor (BJT) was designed, simulated, fabricated, and characterized. The epi layers were selected with a theoretical vertical breakdown voltage of about 4.1kV, which was verified both by hand calculation and Sentaurus TCAD simulation. With a four step Junction Termination Extension (JTE) structure with total width longer than 40μm, the BJT simulated and measured collector-base breakdown voltage and collector-emitter breakdown voltage were both higher than 3kV. The BJT base layer was designed to be as thin and lightly doped as possible to guarantee the current gain, giving a record light base charge density of 1.2×10¹³cm⁻². According to measurement results, the current gain of the BJT was dependent mostly on the minority carrier lifetime. Therefore, the minority carrier lifetime enhancement process was conducted and studied. Different cell geometries of BJTs were fabricated, with variations include circular/finger device, finger length, finger width and finger numbers. Among all available devices, a minimal specific on-resistance of about 6.7mΩ*cm² was achieved, which was smaller than the calculated epi resistance and indicated the existence of conduction modulation. With help of TCAD simulation, the impact of cell geometries on BJT conduction performances was summarized.
Nitrogen bases from pyrolysis of cottonseed meal
(1935) Parker, Ivy May; Bailey, James Robinson