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The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers.
Results
To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection.
Conclusions
While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.

Affective computing allows computers to monitor and influence people’s affects, in other words emotions. Currently, there is a lot of research exploring what can be done with this technology. There are many fields, such as education, healthcare, and marketing, that this technology can transform. However, it is important to question what should be done. There are unique ethical considerations in regards to affective computing that haven't been explored. The purpose of this study is to understand the user’s perspective of affective computing in regards to the Association of Computing Machinery (ACM) Code of Ethics, to ultimately start developing a better understanding of these ethical concerns. For this study, participants were required to watch three different videos and answer a questionnaire, all while wearing an Emotiv EPOC+ EEG headset that measures their emotions. Using the information gathered, the study explores the ethics of affective computing through the user’s perspective.
Cryptojacking is a process in which a program utilizes a user’s CPU to mine cryptocurrencies unknown to the user. Since cryptojacking is a relatively new problem and its impact is still limited, very little has been done to combat it. Multiple studies have been conducted where a cryptojacking detection system is implemented, but none of these systems have truly solved the problem. This thesis surveys existing studies and provides a classification and evaluation of each detection system with the aim of determining their pros and cons. The result of the evaluation indicates that it might be possible to bypass detection of existing systems by modifying the cryptojacking code. In addition to this classification, I developed an automatic code instrumentation program that replaces specific instructions with functionally similar sequences as a way to show how easy it is to implement simple obfuscation to bypass detection by existing systems.
This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a generator to attempt to satisfy the discriminator. The network design is described in further detail below; however there are several potential issues that arise including the averaging of a color for certain images such that small details in an image are not assigned unique colors leading to a neutral blend. We attempt to mitigate this issue as much as possible.
This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a generator to attempt to satisfy the discriminator. The network design is described in further detail below; however there are several potential issues that arise including the averaging of a color for certain images such that small details in an image are not assigned unique colors leading to a neutral blend. We attempt to mitigate this issue as much as possible.
The NCAA is changing the current rules and regulations around a student-athlete’s name, image, and likeness. Previously, student-athletes were not allowed to participate in business activities or noninstitutional promotional activities. With the new rule changes, student-athletes will be able to engage in business activities related to their own name, image, and likeness. The goal of the team was to help “prepare athletes to understand and properly navigate the evolving restrictions and guidelines around athlete name, image, and likeness”. In order to accomplish this, the team had to understand the problems student-athletes face with these changing rules and regulations. The team conducted basic market research to identify the problem. The problem discovered was the lack of communication between student-athletes and businesses. In order to verify this problem, the team conducted several interviews with Arizona State University Athletic Department personnel. From the interviews, the team identified that the user is the student-athletes and the buyer is the brands and businesses. Once the problem was verified and the user and buyer were identified, a solution that would best fit the customers was formulated. The solution is a platform that assists student-athletes navigate the changing rules of the NCAA by providing access to a marketplace optimized to working with student-athletes and offering an ease of maintaining relationships between student-athletes and businesses. The solution was validated through meetings with interested brands. The team used the business model and market potential to pitch the business idea to the brands. Finally, the team gained traction by initiating company partnerships.
Bermuda Land Snails make up a genus called Poecilozonites that is endemic to Bermuda and is extensively present in its fossil record. These snails were also integral to the creation of the theory of punctuated equilibrium. The DNA of mollusks is difficult to sequence because of a class of proteins called mucopolysaccharides that are present in high concentrations in mollusk tissue, and are not removed with standard DNA extraction methods. They inhibit Polymerase Chain Reactions (PCRs) and interfere with Next Generation Sequencing methods. This paper will discuss the DNA extraction methods that were designed to remove the inhibitory proteins that were tested on another gastropod species (Pomacea canaliculata). These were chosen because they are invasive and while they are not pulmonates, they are similar enough to Bermuda Land Snails to reliably test extraction methods. The methods that were tested included two commercially available kits: the Qiagen Blood and Tissue Kit and the Omega Biotek Mollusc Extraction Kit, and one Hexadecyltrimethylammonium Bromide (CTAB) Extraction method that was modified for use on mollusk tissue. The Blood and Tissue kit produced some DNA, the mollusk kit produced almost none, and the CTAB Extraction Method produced the highest concentrations on average, and may prove to be the most viable option for future extractions. PCRs attempted with the extracted DNA have all failed, though it is likely due to an issue with reagents. Further spectrographic analysis of the DNA from the test extractions has shown that they were successful at removing mucopolysaccharides. When the protocol is optimized, it will be used to extract DNA from the tissue from six individuals from each of the two extant species of Bermuda Land Snails. This DNA will be used in several experiments involving Next Generation Sequencing, with the goal of assembling a variety of genome data. These data will then be used to a construct reference genome for Bermuda Land Snails. The genomes generated by this project will be used in population genetic analyses between individuals of the same species, and between individuals of different species. These analyses will then be used to aid in conservation efforts for the species.
A project about developing software for learning turned into a project for learning about software development. The submission here only includes the journal. However, the journal has a link to the public GitHub repository containing the source code for the thesis. The source code implements a program to facilitate self-study by allowing the user to create quizzes. The journal contains my experience working on the project (both successes and failures).
Education has been at the forefront of many issues in Arizona over the past several years with concerns over lack of funding sparking the Red for Ed movement. However, despite the push for educational change, there remain many barriers to education including a lack of visibility for how Arizona schools are performing at a legislative district level. While there are sources of information released at a school district level, many of these are limited and can become obscure to legislators when such school districts lie on the boundary between 2 different legislative districts. Moreover, much of this information is in the form of raw spreadsheets and is often fragmented between government websites and educational organizations. As such, a visualization dashboard that clearly identifies schools and their relative performance within each legislative district would be an extremely valuable tool to legislative bodies and the Arizona public. Although this dashboard and research are rough drafts of a larger concept, they would ideally increase transparency regarding public information about these districts and allow legislators to utilize the dashboard as a tool for greater understanding and more effective policymaking.