Physical Sciences and Mathematics Commons^™

Information-Rich 6d Single-Molecule Imaging Design Using Optimization, Tingting Wu

McKelvey School of Engineering Theses & Dissertations

When studying biochemical processes, localizing the targets alone will not paint a complete picture. We also need techniques to probe how biomolecules interact with one another, including how molecules are organized into larger structures, how they are oriented with respect to surrounding molecules, and how local chemical parameters, like pH and hydrophobicity, vary spatially and temporally. My dissertation focuses on single-molecule orientation localization microscopy (SMOLM, Chapter 1). The objective is to develop imaging techniques for measuring how molecules are oriented with respect to their surrounding molecules, namely, 3D orientation. Achieving optimal imaging performance requires careful design of both the forward …

A Review Of Recent Gene Expression-Based And Dna Methylation-Based Mathematical Cell Type Deconvolution Methods, Chenxiao Tian

Arts & Sciences Electronic Theses and Dissertations

In recent years, many cell type deconvolution methods based on DNA methylation data and gene expression data have been developed. Both of these two methods have its special advantages and disadvantages, e.g., DNA methylation-based methods’ data source is usually more stable than gene expression and DNA methylation is easier to measure in FFPE tissues or formalin-fixed paraffin-embedded, while some gene-expression data like scRNA-seq data usually has high cost and complexity. On the other hand, gene expression-based deconvolution methods currently have many more available methods than DNA methylation-based deconvolution methods, which leads to DNA methylation-based methods in many cases can learn …

Lepton Flavor Violation And Lepton Flavor Universality Violation: Opportunity For New Physics Beyond The Standard Model, Fang Xu

Arts & Sciences Electronic Theses and Dissertations

The Standard Model (SM) of Particle Physics has been remarkably successful in explaining the fundamental forces and classifying elementary particles. However, there are various experimental and theoretical indications that suggest the need to go beyond the SM (BSM) and expand our understanding of the fundamental nature of the universe. From a theoretical perspective, there are several limitations of the SM that suggest the existence of a more fundamental theory. For example, the SM does not incorporate gravity, and it fails to explain the hierarchy problem. Additionally, the nature of dark matter and the origin of the mass hierarchy of elementary …

Non-Adjacent Anti Cyclobutane Pyrimidine Dimers As Intrinsic Probes Of Non-B Form Secondary Structures Of Dna, Natalia Eugenia Gutierrez Bayona

Arts & Sciences Electronic Theses and Dissertations

G-quadruplexes are four-stranded structures of DNA composed of G-quartets that have been proposed to play an extremely important role in replication, transcription, and translation. It has, however, been extremely difficult to unequivocally demonstrate that G-quadruplexes form in living cells due to the lack of probes that would allow for their unambiguous detection and location without disrupting the DNA or the cellular environment. To circumvent these problems, it was proposed that DNA itself could be used as an intrinsic photoprobe for certain classes of G-quadruplex structures and other non-B DNA conformations in vivo. Recently, we discovered that UVB irradiation of human …

An Assistive Interface For Displaying Novice's Code History, Ruiwei Xiao

McKelvey School of Engineering Theses & Dissertations

As Teaching Assistant (TA) programs grow in number and size in introductory CS courses, TAs play a significant role in novice programmers' experience and contribute to their success. However, many TAs are also relative beginners themselves and thus have limited experience in programming and teaching. Thus the effectiveness and consistency of their guidance can vary significantly. To improve interaction quality and assist TAs in providing better support, we examine the difficulties encountered by inexperienced TAs in previous literature and then identify the potential for the high cognitive load as an unaddressed difficulty that may prevent new TAs from initiating effective …

Feature Selection From Clinical Surveys Using Semantic Textual Similarity, Benjamin Warner

McKelvey School of Engineering Theses & Dissertations

Survey data collected from human subjects can contain a high number of features while having a comparatively low quantity of examples. Machine learning models that attempt to predict outcomes from survey data under these conditions can overfit and result in poor generalizability. One remedy to this issue is feature selection, which attempts to select an optimal subset of features to learn upon. A relatively unexplored source of information in the feature selection process is the usage of textual names of features, which may be semantically indicative of which features are relevant to a target outcome. The relationships between feature names …

Synthesis And Characterization Of Sodium Cathode Materials, He Zhou

McKelvey School of Engineering Theses & Dissertations

As sodium batteries hold great promise as a next-generation energy storage device to replace lithium batteries, the development of sodium battery materials has become increasingly urgent. The current study aims to investigate two potential sodium-ion battery cathode materials, Sodium Vanadium Phosphate, and Sodium Manganese Hexacyanoferrate, optimize the experimental procedures, conduct a systematic analysis of material properties and characterization, and ultimately determine the ideal synthesis conditions for these materials.

In the first part of the study, we focused on optimizing the synthesis of Sodium Vanadium Phosphate. By investigating various synthesis conditions, such as annealing temperature, pressure, ascorbic acid content, and material …

Understanding Societal Values Of Chatgpt, Yidan Tang

McKelvey School of Engineering Theses & Dissertations

As Large language models (LLMs) become increasingly pervasive in various domains, it is crucial to ensure that their outputs adhere to societal values and ethical considerations. In this thesis, we investigate the alignment of ChatGPT, a recent state-of-the-art large language model developed by OpenAI, with societal values. Specifically, we define the problem of societal values of LLMs and assemble a representative collection of 7 datasets covering 4 topics related to societal values. In-context learning techniques are applied and appropriate prompts are designed. The performance of each dataset is measured using a standardized evaluation system focused on accuracy. We then display …

Effects Of Functional Network Model Definition On Biomarker Outcome Prediction, Xinyang Feng

Arts & Sciences Electronic Theses and Dissertations

Machine learning (ML) models are widely used to investigate the human connectome and to predict and understand behavior, emotion, and cognition. Prior research has organized pediatric connectome data using adult functional network models. However, this assumes that adult functional network models are appropriate and useful for prediction developmental outcomes from pediatric connectome data. We hypothesize that the application of adult brain network models could result in poor model fit, limiting the generalizability of results. Here, we test whether prediction of biological age is improved by concordant brain network models matching underlying functional connectome data. To quantify the difference in age …

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

Evaluating The Problem Solving Abilities Of Chatgpt, Fankun Zeng

McKelvey School of Engineering Theses & Dissertations

This thesis addresses the need for a fair evaluation of language models' problem solving abilities by presenting a unified evaluation framework for ChatGPT on 16 problem solving datasets (e.g., NaturalQA, HellaSwag, MMLU, etc.). We evaluate the model's performance using F1, exact match, and quasi-exact match metrics and find that ChatGPT is highly accurate in solving tasks that require commonsense and knowledge. However, we also identify truncated text bias and few-shot scenarios as challenges that may impact ChatGPT's performance. Our research highlights the importance of standardizing datasets and developing a unified evaluation system for the fair evaluation of language models. Overall, …

The Quantitative Microanalysis Explorer: Introducing Web-Based Visualization For Optical, Electron, And Quantitative X-Ray Maps For Studying Lunar Samples, Angelina Minocha

Senior Honors Papers / Undergraduate Theses

Modern sample imaging techniques produce data in the form of large mosaics, wherein every pixel contains valuable mineralogical information. These heavy data files are challenging for most computers to load and process, furthermore access to lunar and other extraterrestrial samples is limited. We developed the QME Tool to display optical, electron, and quantitative x-ray maps in conjunction with one another to overcome these challenges and advance mineralogy data presentation and analysis. The images and quantitative data was collected using specialized techniques, followed by an extensive image co-registration process. The interface was developed using OpenSeadragon, “An open-source, web-based viewer for high-resolution …