Physical Sciences and Mathematics Commons^™

Leveraging Biomedical Ontological Knowledge To Improve Clinical Term Embeddings, Fuad Hatem Abuzahra

Theses and Dissertations

ABSTRACT Leveraging Biomedical Ontological Knowledge to Improve Clinical Term Embeddings by Fuad Abu Zahra The University of Wisconsin-Milwaukee, 2023 Under the Supervision of Dr. Rohit J. Kate This research is on obtaining and using word embeddings for natural language processing tasks in the biomedical domain. Word embeddings are vector representations of words commonly obtained from large text corpora. This research leverages the biomedical ontology of SNOMED CT as an alternate source for obtaining embeddings for clinical terms. The existing graph-based methods can only give embeddings for concepts (i.e., nodes of the graph) of an ontology, hence we developed a novel …

Dynamics Of Redox-Driven Molecular Processes In Local And Systemic Plant Immunity, Philip Berg

Theses and Dissertations

The work here presents two main parts. In the first part, chapters 1 – 3 focus on dynamical systems modeling in plant immunity, whereas chapters 4 – 6 describe contributions to computational modeling and analysis of proteomics and genomics data. Chapter 1 investigates dynamical and biochemical patterns of reversibly oxidized cysteines (RevOxCys) during effector-triggered immunity (ETI) in Arabidopsis, examines the regulatory patterns associated with Arabidopsis thimet oligopeptidase 1 and 2’s (TOP1 and TOP2), roles in the RevOxCys events during ETI, and analyzes the redox phenotype of the top1top2 mutant. The second chapter investigates the peptidome dynamics during ETI …

Evaluating Soil Health Changes Following Cover Crop And No-Till Integration Into A Soybean (Glycine Max) Cropping System In The Mississippi Alluvial Valley, Alexandra Gwin Firth

Theses and Dissertations

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, …

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee

Theses and Dissertations

Primary Care is on the frontlines of healthcare, thus they see the most diverse set of patients. In order to achieve high functioning primary care, a practice must establish empanelment, the pairing of patients to providers. Enumeration of empanelment, or estimating panel sizes, helps ensure that the demands of the patients demand the supply of providers and optimize the balance of primary care resources to improve quality of care. Further we can adjust panel sizes by using patient-level data on healthcare utilization and complexity extracted from the electronic medial record to determine the amount of care or burden of work …

Predicting Factors Of Re-Hospitalization After Medically Managed Intensive Inpatient Services In Opioid Use Disorder, Brian Kay

Theses and Dissertations

IntroductionOpioid use disorder has continued to rise in prevalence across the United States, with an estimated 2.5 million Americans ailing from the condition (NIDA, 2020). Medically managed detoxification incurs substantial costs and, when used independently, may not be effective in preventing relapse (Kosten & Baxter, 2019). While numerous studies have focused on predicting the factors of developing opioid use disorder, few have identified predictors of readmission to medically managed withdrawal at an inpatient level of care. Utilizing a high-fidelity dataset from a large multi-site behavioral health hospital, these predictors are explored.

MethodsPatients diagnosed with Opioid Use Disorder and hospitalized in …

Deep Learning For Multi-Tissue Cancer Classification Of Gene Expressions, Tarek Khorshed

Theses and Dissertations

We contribute in saving the lives of cancer patients through early detection and diagnosis, since one of the major challenges in cancer treatment is that patients are diagnosed at very late stages when appropriate medical interventions become less effective and full curative treatment is no longer achievable. Cancer classification using gene expressions is extremely challenging given the complexity and high dimensionality of the data. Current classification methods typically rely on samples collected from a single tissue type and perform a prerequisite of gene feature selection to avoid processing the full set of genes. These methods fall short in taking advantage …

Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield

Theses and Dissertations

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing …

A Discrete-Event Simulation Approach For Modeling Human Body Glucose Metabolism, Buket Aydas

Theses and Dissertations

This dissertation describes CarbMetSim (Carbohydrate Metabolism Simulator), a discrete-event simulator that tracks the blood glucose level of a person in response to a timed sequence of diet and exercise activities. CarbMetSim implements broader aspects of carbohydrate metabolism in human beings with the objective of capturing the average impact of various diet/exercise activities on the blood glucose level. Key organs (stomach, intestine, portal vein, liver, kidney, muscles, adipose tissue, brain and heart) are implemented to the extent necessary to capture their impact on the production and consumption of glucose. Key metabolic pathways (glucose oxidation, glycolysis and gluconeogenesis) are accounted for by …

Determining The Relationship Between Aging And Oxidative Stress In A Drosophila Melanogaster P38 Kb Framework, Aleksandra J. Majewski

Theses and Dissertations

Aging is inevitable for all organisms and can be characterized by degeneration of tissue, adecrease in motor function, and impaired stress response. In humans, it is often accompanied by an increased propensity for age related diseases. While all adults experience biological aging (senescence) not all adults experience age-associated disease. Thus, we claim these are not normal prospects of aging. Although the implications of aging are well understood, the molecular underpinnings for these processes remain elusive. As advances in medical science have been successful at prolonging lifespan, they concurrently extend the amount of time spend in diseased states. If we wish …

Unsupervised Biomedical Named Entity Recognition, Omid Ghiasvand

Theses and Dissertations

Named entity recognition (NER) from text is an important task for several applications, including in the biomedical domain. Supervised machine learning based systems have been the most successful on NER task, however, they require correct annotations in large quantities for training. Annotating text manually is very labor intensive and also needs domain expertise. The purpose of this research is to reduce human annotation effort and to decrease cost of annotation for building NER systems in the biomedical domain. The method developed in this work is based on leveraging the availability of resources like UMLS (Unified Medical Language System), that contain …

Stage-Specific Predictive Models For Cancer Survivability, Elham Sagheb Hossein Pour

Theses and Dissertations

Survivability of cancer strongly depends on the stage of cancer. In most previous works, machine learning survivability prediction models for a particular cancer, were trained and evaluated together on all stages of the cancer. In this work, we trained and evaluated survivability prediction models for five major cancers, together on all stages and separately for every stage. We named these models joint and stage-specific models respectively. The obtained results for the cancers which we investigated reveal that, the best model to predict the survivability of the cancer for one specific stage is the model which is specifically built for that …

Mhealth Technology: Towards A New Persuasive Mobile Application For Caregivers That Addresses Motivation And Usability, Suboh M. Alkhushayni

Theses and Dissertations

With the increasing use of mobile technologies and smartphones, new methods of promoting personal health have been developed. For example, there is now software for recording and tracking one's exercise activity or blood pressure. Even though there are already many of these services, the mobile health field still presents many opportunities for new research.

One apparent area of need would be software to support the efforts of caregivers for the elderly, especially those who suffer from multiple chronic conditions, such as cognitive impairment, chronic heart failure or diabetes. Very few mobile applications (apps) have been created that target caregivers of …

Evaluating And Improving The Efficiency Of Software And Algorithms For Sequence Data Analysis, Hugh L. Eaves

Theses and Dissertations

With the ever-growing size of sequence data sets, data processing and analysis are an increasingly large portion of the time and money spent on nucleic acid sequencing projects. Correspondingly, the performance of the software and algorithms used to perform that analysis has a direct effect on the time and expense involved. Although the analytical methods are widely varied, certain types of software and algorithms are applicable to a number of areas. Targeting improvements to these common elements has the potential for wide reaching rewards. This dissertation research consisted of several projects to characterize and improve upon the efficiency of several …

Three Essays On Enhancing Clinical Trial Subject Recruitment Using Natural Language Processing And Text Mining, Euisung Jung

Theses and Dissertations

Patient recruitment and enrollment are critical factors for a successful clinical trial; however, recruitment tends to be the most common problem in most clinical trials. The success of a clinical trial depends on efficiently recruiting suitable patients to conduct the trial. Every clinical trial research has a protocol, which describes what will be done in the study and how it will be conducted. Also, the protocol ensures the safety of the trial subjects and the integrity of the data collected. The eligibility criteria section of clinical trial protocols is important because it specifies the necessary conditions that participants have to …

Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz

Theses and Dissertations

Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of two …

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …

Disease Name Extraction From Clinical Text Using Conditional Random Fields, Omid Ghiasvand

Theses and Dissertations

The aim of the research done in this thesis was to extract disease and disorder names from clinical texts. We utilized Conditional Random Fields (CRF) as the main method to label diseases and disorders in clinical sentences. We used some other tools such as MetaMap and Stanford Core NLP tool to extract some crucial features. MetaMap tool was used to identify names of diseases/disorders that are already in UMLS Metathesaurus. Some other important features such as lemmatized versions of words, and POS tags were extracted using the Stanford Core NLP tool. Some more features were extracted directly from UMLS Metathesaurus, …

Identification Of Transcriptionally Quiescent Regions In The Neurospora Crassa Genome, Katie Marie Groskreutz

Theses and Dissertations

Sexual reproduction and genetic exchange via meiosis are important and highly conserved processes in many living organisms. Occasionally, complications occur during meiosis that can result in chromosome abnormalities. In humans, improper chromosome development can cause life altering disorders such as Down Syndrome, Edwards Syndrome, and Patau Syndrome. Unfortunately, despite its importance, gaps remain in our knowledge of how this process works. For instance, little is known about how homolog identification occurs and what proteins identify matching chromosomes during pairing. This fundamental process occurs early during meiosis and ensures proper development of gametes.

Understanding the proteins involved during homolog pairing may …

Methods For Integrative Analysis Of Genomic Data, Paul Manser

Theses and Dissertations

In recent years, the development of new genomic technologies has allowed for the investigation of many regulatory epigenetic marks besides expression levels, on a genome-wide scale. As the price for these technologies continues to decrease, study sizes will not only increase, but several different assays are beginning to be used for the same samples. It is therefore desirable to develop statistical methods to integrate multiple data types that can handle the increased computational burden of incorporating large data sets. Furthermore, it is important to develop sound quality control and normalization methods as technical errors can compound when integrating multiple genomic …

Health Care Informatics Support Of A Simulated Study, Zeinab Salari Far

Theses and Dissertations

The objective of this project is to assess the value of REDCap (Harris, 2009) by conducting a simulated breast cancer clinical trial and demonstration. REDCap is a free, secure, web-based application designed to support data capture for research studies. To assess REDCap's value, we conducted a simulation of a clinical trial study designed to compare the use of two new technologies for breast cancer diagnosis and treatment with current best practice breast cancer diagnosis and treatment. We call the trial, "Real-Time Operating Room BC Diagnostic Treatment (RORBCDT)". The RORBCDT clinical trial is designed to assess the value of a new …