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Cancer rates vary between people, between cultures, and between tissue types, driven by clinically relevant distinctions in the risk factors that lead to different cancer types. Despite the importance of cancer location in human health, little is known about tissue-specific cancers in non-human animals. We can gain significant insight into

Cancer rates vary between people, between cultures, and between tissue types, driven by clinically relevant distinctions in the risk factors that lead to different cancer types. Despite the importance of cancer location in human health, little is known about tissue-specific cancers in non-human animals. We can gain significant insight into how evolutionary history has shaped mechanisms of cancer suppression by examining how life history traits impact cancer susceptibility across species. Here, we perform multi-level analysis to test how species-level life history strategies are associated with differences in neoplasia prevalence, and apply this to mammary neoplasia within mammals. We propose that the same patterns of cancer prevalence that have been reported across species will be maintained at the tissue-specific level. We used a combination of factor analysis and phylogenetic regression on 13 life history traits across 90 mammalian species to determine the correlation between a life history trait and how it relates to mammary neoplasia prevalence. The factor analysis presented ways to calculate quantifiable underlying factors that contribute to covariance of entangled life history variables. A greater risk of mammary neoplasia was found to be correlated most significantly with shorter gestation length. With this analysis, a framework is provided for how different life history modalities can influence cancer vulnerability. Additionally, statistical methods developed for this project present a framework for future comparative oncology studies and have the potential for many diverse applications.

ContributorsFox, Morgan Shane (Author) / Maley, Carlo C. (Thesis director) / Boddy, Amy (Committee member) / Compton, Zachary (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Despite the 40-year war on cancer, very limited progress has been made in developing a cure for the disease. This failure has prompted the reevaluation of the causes and development of cancer. One resulting model, coined the atavistic model of cancer, posits that cancer is a default phenotype of the

Despite the 40-year war on cancer, very limited progress has been made in developing a cure for the disease. This failure has prompted the reevaluation of the causes and development of cancer. One resulting model, coined the atavistic model of cancer, posits that cancer is a default phenotype of the cells of multicellular organisms which arises when the cell is subjected to an unusual amount of stress. Since this default phenotype is similar across cell types and even organisms, it seems it must be an evolutionarily ancestral phenotype. We take a phylostratigraphical approach, but systematically add species divergence time data to estimate gene ages numerically and use these ages to investigate the ages of genes involved in cancer. We find that ancient disease-recessive cancer genes are significantly enriched for DNA repair and SOS activity, which seems to imply that a core component of cancer development is not the regulation of growth, but the regulation of mutation. Verification of this finding could drastically improve cancer treatment and prevention.
ContributorsOrr, Adam James (Author) / Davies, Paul (Thesis director) / Bussey, Kimberly (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Glioblastoma Multiforme (GBM) is an aggressive and deadly form of brain cancer with a median survival time of about a year with treatment. Due to the aggressive nature of these tumors and the tendency of gliomas to follow white matter tracks in the brain, each tumor mass has a unique

Glioblastoma Multiforme (GBM) is an aggressive and deadly form of brain cancer with a median survival time of about a year with treatment. Due to the aggressive nature of these tumors and the tendency of gliomas to follow white matter tracks in the brain, each tumor mass has a unique growth pattern. Consequently it is difficult for neurosurgeons to anticipate where the tumor will spread in the brain, making treatment planning difficult. Archival patient data including MRI scans depicting the progress of tumors have been helpful in developing a model to predict Glioblastoma proliferation, but limited scans per patient make the tumor growth rate difficult to determine. Furthermore, patient treatment between scan points can significantly compound the challenge of accurately predicting the tumor growth. A partnership with Barrow Neurological Institute has allowed murine studies to be conducted in order to closely observe tumor growth and potentially improve the current model to more closely resemble intermittent stages of GBM growth without treatment effects.
ContributorsSnyder, Lena Haley (Author) / Kostelich, Eric (Thesis director) / Frakes, David (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Harrington Bioengineering Program (Contributor)
Created2014-05
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Mr. Green has stage 4 prostate cancer which has spread to the bones and liver and has become resistant to radiation and standard chemotherapy treatment. After 3 rounds of chemotherapy, his primary oncologist recommends that he participate in a clinical trial. He went to Dr. Red at the Saguaro Clinic

Mr. Green has stage 4 prostate cancer which has spread to the bones and liver and has become resistant to radiation and standard chemotherapy treatment. After 3 rounds of chemotherapy, his primary oncologist recommends that he participate in a clinical trial. He went to Dr. Red at the Saguaro Clinic after reading on the internet about a new Phase 1 clinical trial that the clinic is hosting, which is designed to target a specific receptor called AB-111 that may be present in malignant prostate, cervical, ovarian, and breast cells. After signing consent and completing the blood screens in the morning at the clinic, Mr. Green is told his liver enzymes are too high and the ranges specified in the protocol prohibit him from enrolling. Mr. Green is noticeably affected and distressed at this news, and Dr. Red recommends end-of-life care. Behind the scenes, this event is noted on official medical documents and trial study rosters as a "screen fail." This narrative, while fictional, is realistic because similar events occur in cancer clinical trial sites on a regular basis. I look at the inner "world" and mental journey of possible clinical trial candidates as they seek out information about clinical trials and gain understanding of their function \u2014 specifically in the context of Phase 1 cancer clinical trials. To whom is the language of the term "screen failure" useful? How does excluding individuals from clinical trials protect their health and does the integrity of the trial data supersede the person's curative goals? What is the message that cancer patients (potential research subjects) receive regarding clinical trials from sources outside their oncologists?
ContributorsMcKane, Alexandra (Author) / Maienschein, Jane (Thesis director) / Ellison, Karin (Committee member) / Foy, Joseph (Committee member) / Barrett, The Honors College (Contributor)
Created2013-12
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Description

Over time, tumor treatment resistance inadvertently develops when androgen de-privation therapy (ADT) is applied to metastasized prostate cancer (PCa). To combat tumor resistance, while reducing the harsh side effects of hormone therapy, the clinician may opt to cyclically alternates the patient’s treatment on and off. This method,known as intermittent ADT,

Over time, tumor treatment resistance inadvertently develops when androgen de-privation therapy (ADT) is applied to metastasized prostate cancer (PCa). To combat tumor resistance, while reducing the harsh side effects of hormone therapy, the clinician may opt to cyclically alternates the patient’s treatment on and off. This method,known as intermittent ADT, is an alternative to continuous ADT that improves the patient’s quality of life while testosterone levels recover between cycles. In this paper,we explore the response of intermittent ADT to metastasized prostate cancer by employing a previously clinical data validated mathematical model to new clinical data from patients undergoing Abiraterone therapy. This cell quota model, a system of ordinary differential equations constructed using Droop’s nutrient limiting theory, assumes the tumor comprises of castration-sensitive (CS) and castration-resistant (CR)cancer sub-populations. The two sub-populations rely on varying levels of intracellular androgen for growth, death and transformation. Due to the complexity of the model,we carry out sensitivity analyses to study the effect of certain parameters on their outputs, and to increase the identifiability of each patient’s unique parameter set. The model’s forecasting results show consistent accuracy for patients with sufficient data,which means the model could give useful information in practice, especially to decide whether an additional round of treatment would be effective.

ContributorsBennett, Justin Klark (Author) / Kuang, Yang (Thesis director) / Kostelich, Eric (Committee member) / Phan, Tin (Committee member) / School of Mathematical and Statistical Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

This thesis attempts to explain Everettian quantum mechanics from the ground up, such that those with little to no experience in quantum physics can understand it. First, we introduce the history of quantum theory, and some concepts that make up the framework of quantum physics. Through these concepts, we reveal

This thesis attempts to explain Everettian quantum mechanics from the ground up, such that those with little to no experience in quantum physics can understand it. First, we introduce the history of quantum theory, and some concepts that make up the framework of quantum physics. Through these concepts, we reveal why interpretations are necessary to map the quantum world onto our classical world. We then introduce the Copenhagen interpretation, and how many-worlds differs from it. From there, we dive into the concepts of entanglement and decoherence, explaining how worlds branch in an Everettian universe, and how an Everettian universe can appear as our classical observed world. From there, we attempt to answer common questions about many-worlds and discuss whether there are philosophical ramifications to believing such a theory. Finally, we look at whether the many-worlds interpretation can be proven, and why one might choose to believe it.

ContributorsSecrest, Micah (Author) / Foy, Joseph (Thesis director) / Hines, Taylor (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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The purpose of this paper is to provide an analysis of entanglement and the particular problems it poses for some physicists. In addition to looking at the history of entanglement and non-locality, this paper will use the Bell Test as a means for demonstrating how entanglement works, which measures the

The purpose of this paper is to provide an analysis of entanglement and the particular problems it poses for some physicists. In addition to looking at the history of entanglement and non-locality, this paper will use the Bell Test as a means for demonstrating how entanglement works, which measures the behavior of electrons whose combined internal angular momentum is zero. This paper will go over Dr. Bell's famous inequality, which shows why the process of entanglement cannot be explained by traditional means of local processes. Entanglement will be viewed initially through the Copenhagen Interpretation, but this paper will also look at two particular models of quantum mechanics, de-Broglie Bohm theory and Everett's Many-Worlds Interpretation, and observe how they explain the behavior of spin and entangled particles compared to the Copenhagen Interpretation.

ContributorsWood, Keaten Lawrence (Author) / Foy, Joseph (Thesis director) / Hines, Taylor (Committee member) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description
Immunotherapy is an effective treatment for cancer which enables the patient's immune system to recognize tumor cells as pathogens. In order to design an individualized treatment, the t cell receptors (TCR) which bind to a tumor's unique antigens need to be determined. We created a convolutional neural network to predict

Immunotherapy is an effective treatment for cancer which enables the patient's immune system to recognize tumor cells as pathogens. In order to design an individualized treatment, the t cell receptors (TCR) which bind to a tumor's unique antigens need to be determined. We created a convolutional neural network to predict the binding affinity between a given TCR and antigen to enable this.
ContributorsCai, Michael Ray (Author) / Lee, Heewook (Thesis director) / Meuth, Ryan (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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Description
Magnetic resonance imaging (MRI) data of metastatic brain cancer patients at the Barrow Neurological Institute sparked interest in the radiology department due to the possibility that tumor size distributions might mimic a power law or an exponential distribution. In order to consider the question regarding the growth trends of metastatic

Magnetic resonance imaging (MRI) data of metastatic brain cancer patients at the Barrow Neurological Institute sparked interest in the radiology department due to the possibility that tumor size distributions might mimic a power law or an exponential distribution. In order to consider the question regarding the growth trends of metastatic brain tumors, this thesis analyzes the volume measurements of the tumor sizes from the BNI data and attempts to explain such size distributions through mathematical models. More specifically, a basic stochastic cellular automaton model is used and has three-dimensional results that show similar size distributions of those of the BNI data. Results of the models are investigated using the likelihood ratio test suggesting that, when the tumor volumes are measured based on assuming tumor sphericity, the tumor size distributions significantly mimic the power law over an exponential distribution.
ContributorsFreed, Rebecca (Co-author) / Snopko, Morgan (Co-author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / WPC Graduate Programs (Contributor) / School of Accountancy (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
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Description
Cancer is the second leading cause of death in the United States. Cancer is a serious, complex disease which causes cells to grow uncontrollably, causing millions of deaths per year [1]. Cancer is usually caused by a combination of environmental variables and biological pathways. The pathways have a very robust

Cancer is the second leading cause of death in the United States. Cancer is a serious, complex disease which causes cells to grow uncontrollably, causing millions of deaths per year [1]. Cancer is usually caused by a combination of environmental variables and biological pathways. The pathways have a very robust structure normally, but are altered because of cancer, resulting in a loss of connectivity between pathways. In order detect these pathways, a PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) was created, which measures the relative rankings of the genes in each pathway. Applying this algorithm will allow us to figure out what pathways differed significantly in areas with cancer and areas without cancer. This would allow scientists to focus on specific pathways in order to learn more about the cancer and find more effective ways to treat it. So far, analysis using PoTRA has been successfully conducted on hepatocellular carcinoma (HCC) and its subtypes, resulting in all significant pathways found being cancer-associated. Now, using the TCGA data stored in Google Cloud's BigQuery, we created a pipeline to apply PoTRA to other cancer data sets and see how well it cross-applies to other cancers. The results show that even though some modification may need to be made to adapt to other datasets, many significant pathways were found for both HCC and breast cancer.
ContributorsMahesh, Sunny Nishant (Author) / Valentin, Dinu (Thesis director) / Liu, Li (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05