Barrett, The Honors College Thesis/Creative Project Collection

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.

The PPP Loan Program was created by the CARES Act and carried out by the Small Business Administration (SBA) to provide support to small businesses in maintaining their payroll during the Coronavirus pandemic. This program was approved for $350 billion, but this amount was expanded by an additional $320 billion to meet the demand by struggling businesses, since initial funding was exhausted under two weeks.<br/><br/>Significant controversy surrounds the program. In December 2020, the Department of Justice reported 90 individuals were charged for fraudulent use of funds, totaling $250 million. The loans, which were intended for small business, were actually approved for 450 public companies. Furthermore, the methods of approval are<br/>shrouded in mystery. In an effort to be transparent, the SBA has released information about loan recipients. Conveniently, the SBA has released information of all recipients. Detailed information was released for 661,218 recipients who have received a PPP loan in excess of $150,000. These recipients are the central point of this research.<br/><br/>This research sought to answer two primary questions: how did the SBA determine which loans, and therefore which industries are approved, and did the industries most affected by the pandemic receive the most in PPP loans, as intended by Congress? It was determined that, generally, PPP Loans were approved on the basis of employment percentages relative to the individual state. Furthermore, in general, the loans approved were approved fairly, with respect to the size of the industry. The loans, when adjusted for GDP and Employment factors, yielded a clear ranking that prioritized vulnerable industries first.<br/><br/>However, significant questions remain. The effectiveness of the PPP has been hindered by unclear incentives and negative outcomes, characterized by a government program that has essentially been rushed into service. Furthermore, limitations of available data to regress and compare the SBA's approved loans are not representative of small business.

The Covid-19 pandemic has made a significant impact on both the stock market and the<br/>global economy. The resulting volatility in stock prices has provided an opportunity to examine<br/>the Efficient Market Hypothesis. This study aims to gain insights into the efficiency of markets<br/>based on stock price performance in the Covid era. Specifically, it investigates the market’s<br/>ability to anticipate significant events during the Covid-19 timeline beginning November 1, 2019<br/><br/>and ending March 31, 2021. To examine the efficiency of markets, our team created a Stay-at-<br/>Home Portfolio, experiencing economic tailwinds from the Covid lockdowns, and a Pandemic<br/><br/>Loser Portfolio, experiencing economic headwinds from the Covid lockdowns. Cumulative<br/>returns of each portfolio are benchmarked to the cumulative returns of the S&P 500. The results<br/>showed that the Efficient Market Hypothesis is likely to be valid, although a definitive<br/>conclusion cannot be made based on the scope of the analysis. There are recommendations for<br/>further research surrounding key events that may be able to draw a more direct conclusion.

Robots are often used in long-duration scenarios, such as on the surface of Mars,where they may need to adapt to environmental changes. Typically, robots have been built specifically for single tasks, such as moving boxes in a warehouse or surveying construction sites. However, there is a modern trend away from human hand-engineering and toward robot learning. To this end, the ideal robot is not engineered,but automatically designed for a specific task. This thesis focuses on robots which learn path-planning algorithms for specific environments. Learning is accomplished via genetic programming. Path-planners are represented as Python code, which is optimized via Pareto evolution. These planners are encouraged to explore curiously and efficiently. This research asks the questions: “How can robots exhibit life-long learning where they adapt to changing environments in a robust way?”, and “How can robots learn to be curious?”.

Hundreds of thousands of people die annually from malaria; a protozoan of the genus Plasmodium is responsible for this mortality. The Plasmodium parasite undergoes several life stages within the mosquito vector, the transition between which require passage across the lumen of the mosquito midgut. It has been observed that in about 15% of parasites that develop ookinetes in the mosquito abdomen, sporozoites never develop in the salivary glands, indicating that passage across the midgut lumen is a significant barrier in parasite development (Gamage-Mendis et al., 1993). We aim to investigate a possible correlation between passage through the midgut lumen and drug-resistance trends in Plasmodium falciparum parasites. This study contains a total of 1024 Anopheles mosquitoes: 187 Anopheles gambiae and 837 Anopheles funestus samples collected in high malaria transmission areas of Mozambique between March and June of 2016. Sanger sequencing will be used to determine the prevalence of known resistance alleles for anti-malarial drugs: chloroquine resistance transporter (pfcrt), multidrug resistance (pfmdr1) gene, dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr). We compare prevalence of resistance between abdomen and head/thorax in order to determine whether drug resistant parasites are disproportionately hindered during their passage through the midgut lumen. A statistically significant difference between resistance alleles in the two studied body sections supports the efficacy of new anti-malarial gene surveillance strategies in areas of high malaria transmission.

Music streaming services have affected the music industry from both a financial and legal standpoint. Their current business model affects stakeholders such as artists, users, and investors. These services have been scrutinized recently for their imperfect royalty distribution model. Covid-19 has made these discussions even more relevant as touring income has come to a halt for musicians and the live entertainment industry. <br/>Under the current per-stream model, it is becoming exceedingly hard for artists to make a living off of streams. This forces artists to tour heavily as well as cut corners to create what is essentially “disposable art”. Rapidly releasing multiple projects a year has become the norm for many modern artists. This paper will examine the licensing framework, royalty payout issues, and propose a solution.

The COVID-19 pandemic has and will continue to radically shift the workplace. An increasing percentage of the workforce desires flexible working options and, as such, firms are likely to require less office space going forward. Additionally, the economic downturn caused by the pandemic provides an opportunity for companies to secure favorable rent rates on new lease agreements. This project aims to evaluate and measure Company X’s potential cost savings from terminating current leases and downsizing office space in five selected cities. Along with city-specific real estate market research and forecasts, we employ a four-stage model of Company X’s real estate negotiation process to analyze whether existing lease agreements in these cities should be renewed or terminated.

The COVID-19 pandemic has and will continue to radically shift the workplace. An increasing percentage of the workforce desires flexible working options and, as such, firms are likely to require less office space going forward. Additionally, the economic downturn caused by the pandemic provides an opportunity for companies to secure favorable rent rates on new lease agreements. This project aims to evaluate and measure Company X’s potential cost savings from terminating current leases and downsizing office space in five selected cities. Along with city-specific real estate market research and forecasts, we employ a four-stage model of Company X’s real estate negotiation process to analyze whether existing lease agreements in these cities should be renewed or terminated.

One of the largest problems facing modern medicine is drug resistance. Many classes of drugs can be rendered ineffective if their target is able to acquire beneficial mutations. While this is an excellent showcase of the power of evolution, it necessitates the development of increasingly stronger drugs to combat resistant pathogens. Not only is this strategy costly and time consuming, it is also unsustainable. To contend with this problem, many multi-drug treatment strategies are being explored. Previous studies have shown that resistance to some drug combinations is not possible, for example, resistance to a common antifungal drug, fluconazole, seems impossible in the presence of radicicol. We believe that in order to understand the viability of multi-drug strategies in combating drug resistance, we must understand the full spectrum of resistance mutations that an organism can develop, not just the most common ones. It is possible that rare mutations exist that are resistant to both drugs. Knowing the frequency of such mutations is important for making predictions about how problematic they will be when multi-drug strategies are used to treat human disease. This experiment aims to expand on previous research on the evolution of drug resistance in S. cerevisiae by using molecular barcodes to track ~100,000 evolving lineages simultaneously. The barcoded cells were evolved with serial transfers for seven weeks (200 generations) in three concentrations of the antifungal Fluconazole, three concentrations of the Hsp90 inhibitor Radicicol, and in four combinations of Fluconazole and Radicicol. Sequencing data was used to track barcode frequencies over the course of the evolution, allowing us to observe resistant lineages as they rise and quantify differences in resistance evolution across the different conditions. We were able to successfully observe over 100,000 replicates simultaneously, revealing many adaptive lineages in all conditions. Our results also show clear differences across drug concentrations and combinations, with the highest drug concentrations exhibiting distinct behaviors.