Bioinformatics Commons^™

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 …

Medical Device Alarm Systems: A Multi-Hospital Study Of Alarm-Related Events, Caregiver Alarm Response, And Their Contributing Factors, Colleen K. Lindell

Theses and Dissertations

Medical device alarm systems are expected to improve patient care by alerting clinicians about conditions that require attention. However, due to a variety of circumstances, including inadequate training, muting alarms, alarm fatigue, and staffing shortages, the effectiveness of alarm systems may be questionable. This research looked at the appropriateness of time- to-respond (TTR) to alarms, the alarm system configuration, policies and procedures regarding alarms, and the extent of alarm-specific training and education alarms. Using concepts from cognitive systems engineering, organization policy, and organizational learning, a research model was assembled to investigate these relationships.

Quantitative data analysis included an online survey …

Georac: An Rna-Seq Atlas Constructor For The Gene Expression Omnibus, Aurash A. Mohaimani

Theses and Dissertations

The meteoric rise of next-generation sequencing technologies over the past 15 years has resulted in a voluminous amount of data generated by modern biological and clinical studies. RNA sequencing, colloquially referred to as RNA-Seq, is a next-generation approach capable of surveying and quantifying whole organism transcriptomes. RNA-Seq methods are valued over microarray assays for their ability to avoid cross-hybridization signal noise, to quantify gene or transcript expression without assay-specific upper limits, to natively provide single-nucleotide genomic resolution, and to allow for de novo transcriptome assemblies. Many thousands of RNA-Seq studies have been published over the past seven years, and a …

Monitoring Expression Of Metabolic Genes During The Hypoxic Response Of S. Cerevisae, Nikkoli Lueder

Theses and Dissertations

All organisms appear to have the ability to sense and respond to changes in their environment. Hypoxia, or low oxygen, is experienced by many organisms at some point in their life cycle. Some organisms such as S. cerevisiae, a species of yeast, respond by dramatically altering gene expression. The result is that genes needed in the new environment are turned on and unneeded genes are turned off. S. cerevisiae has been used in our study because it shares many genes with other eukaryotes, including humans, so many of our findings are applicable to these organisms. Here, we tried to understand …

Discovering Driver Mutations In Biological Data, Yahya Bokhari

Theses and Dissertations

Background

Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. …

High-Throughput Prediction And Analysis Of Drug-Protein Interactions In The Druggable Human Proteome, Chen Wang

Theses and Dissertations

Drugs exert their (therapeutic) effects via molecular-level interactions with proteins and other biomolecules. Computational prediction of drug-protein interactions plays a significant role in the effort to improve our current and limited knowledge of these interactions. The use of the putative drug-protein interactions could facilitate the discovery of novel applications of drugs, assist in cataloging their targets, and help to explain the details of medicinal efficacy and side-effects of drugs. We investigate current studies related to the computational prediction of drug-protein interactions and categorize them into protein structure-based and similarity-based methods. We evaluate three representative structure-based predictors and develop a Protein-Drug …