Life Sciences Commons^™

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 …

Facilitating And Enhancing Biomedical Knowledge Translation: An In Silico Approach To Patient-Centered Pharmacogenomic Outcomes Research, Kourosh Ravvaz

Theses and Dissertations

Current research paradigms such as traditional randomized control trials mostly rely on relatively narrow efficacy data which results in high internal validity and low external validity. Given this fact and the need to address many complex real-world healthcare questions in short periods of time, alternative research designs and approaches should be considered in translational research. In silico modeling studies, along with longitudinal observational studies, are considered as appropriate feasible means to address the slow pace of translational research. Taking into consideration this fact, there is a need for an approach that tests newly discovered genetic tests, via an in silico …

G-Quadruplex Dna Structures And Site Specific Genetic Instability, Jonathan David Williams

Theses and Dissertations

Repetitive DNA comprises a majority of the human genome yet functions and overall impacts on site-specific genetic instability are not fully defined. Repetitive G-rich sequences have the propensity to form G-quadruplex (G4), which are stable non-B form DNA structures. G4 structures are conspicuously found at regions of site-specific instability. Even so, human genomic loci capable of forming this structure and their connection to DNA rearrangements are just beginning to be elucidated. My dissertation focuses on G4 structures and their capacity to promote site-specific changes in the human genome, particularly at oncogenes. I identified and investigated new biologically relevant G4 loci …

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, …

Clinical And Genomic Characterization Of Two Vaginal Megasphaera Species, Abigail L. Glascock

Theses and Dissertations

Two vaginal phylotypes of the genus Megasphaera (phylotype 1 and phylotype 2) were recently associated with bacterial vaginosis (BV), an infection characterized by vaginal dysbiosis. Through an analysis of 16S rRNA profiles of 3,986 women enrolled in the Vaginal Human Microbiome Project, we confirmed that while both phylotypes were associated with BV, Megaspheara phylotype 1 had higher specificity for the condition. Megasphaera phylotype 2 was strongly associated with trichomoniasis. Previous studies have reported that BV-associated organisms are excluded in pregnancy. We observed that Megasphaera phylotype 1, which has been associated with adverse pregnancy outcomes, exhibited a trend of increased prevalence …

Prediction Of Protein-Protein Interactions In Escherichia Coli From Experimental Data In Treponema Pallidum, Marco A. Abreu

Theses and Dissertations

Protein – Protein interactions (PPIs) are thought to be conserved between species, although this has not been systematically investigated. This problem was explored in Escherichia coli from experimental data in Treponema pallidum by predicting PPIs, focusing on protein domains of little or unknown function. The comparison of T. pallidum to a model organism such as E. coli can not only reveal additional data about T. pallidum but also reveals how E. coli is similar to this distantly related, obligate parasite. A set of novel T. pallidum interactions, enriched for proteins of unknown function, were the basis of over 23,000 predicted …

Working Together: Using Protein Networks Of Bacterial Species To Compare Essentiality, Centrality, And Conservation In Escherichia Coli., Christopher Wimble

Theses and Dissertations

Proteins in Escherichia coli were compared in terms of essentiality, centrality, and conservation. The hypotheses of this study are: for proteins in Escherichia coli, (1) there is a positive, measureable correlation between protein conservation and essentiality, (2) there is a positive relationship between conservation and degree centrality, and (3) essentiality and centrality also have a positive correlation. The third hypothesis was supported by a moderate correlation, the first with a weak correlation, and the second hypotheis was not supported. When proteins that did not map to orthologous groups and proteins that had no interactions were removed, the relationship between essentality …

Dysregulation Of Micrornas In Blood As Biomarkers For Diagnosing Prostate Cancer, Rhonda W. Daniel

Theses and Dissertations

Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers.

Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such …

Mysteries Of The Trypanosomatid Maxicircles: Characterization Of The Maxicircle Genomes And The Evolution Of Rna Editing In The Order Kinetoplastida, Preethi Ranganathan Iyengar

Theses and Dissertations

The trypanosomatid protists belonging to Order Kinetoplastida are some of the most successful parasites ever known to mankind. Their extreme physiological diversity and adaptability to different environmental conditions and host systems make them some of the most widespread parasites, causing deadly diseases in humans and other vertebrates.

This project focuses on their unique mitochondrion, called the kinetoplast, and more specifically involves the characterization of a part of their mitochondrial DNA (also called kinetoplast DNA or kDNA), the maxicircles, which are functional homologs of eukaryotic mitochondrial DNA in the kinetoplastid protists. We have sequenced and characterized the maxicircle genomes of 20 …