Interdisciplinary – Page 37 – UROP Spring Symposium 2021

Interdisciplinary

Identification of novel genetic drivers of pediatric tumors

Acute lymphoblastic leukemia (ALL) is the most common cancer among pediatric patients and is characterized by fewer mutations than adult cancers, suggesting that aberrant gene expression is a critical factor in treatment and prognosis. Gene expression data can identify targeted therapy pathways by identifying more precise cancer profiles based on genetic expression. To assess effectiveness of RNA expression analysis at identifying target genes, mRNA copy counts from tumor samples of 32 pediatric ALL patients were gathered. Sample grouping was explored using principal component analysis, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. The samples were then split according to expression levels of known neuroblastoma driver ALK and then analyzed for differentially expressed genes using the DESeq2 and limma workflows. As part of the preliminary findings, differential expression analysis revealed differences within the group in expression of known neuroblastoma drivers MYCN, ALK, PHOX2B, and TERT. This also revealed limitations of RNAseq analysis due to noise at low expression levels and outliers that skewed mean expression data. Analysis of RNA expression data shows promising results by identifying groups of similar cancer profiles and identifying differentially expressed genes as therapeutic targets.

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Impact of a Web-Based Naloxone Training on First Responders

In the midst of the pandemic, the United States continues to experience an opioid epidemic. Fatal opioid overdoses have risen significantly during the pandemic. Naloxone is an opioid antagonist, and is an effective public health intervention to reduce opioid overdoses. Law enforcement officers are often first to arrive at the scene of an overdose. To equip law enforcement officers to respond to opioid overdoses, a web-based naloxone training program was developed in collaboration with our community partners (www.overdoseaction.org). The purpose of this study is to evaluate the impact of our First Responder web-based naloxone training program. We aim to use descriptive statistics and paired samples t-test to analyze pre-test and post-test data to assess the law enforcement officers’ improvements in knowledge, confidence, and attitudes towards naloxone and overdoses. We anticipate our results will show an increase in knowledge, confidence, and attitudes among law enforcement officers who participate in our web-based naloxone training.

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Consumer Response to Self-Sampling Methods for Cervical Cancer Screening

Cervical cancer is one of the most prominent cancers in the world, as it is the third most prevalent cancer in women across the globe. However, it is also deemed as one of the most treatable cancers as long as there is early detection and diagnosis because of the primary and secondary stages of prevention: “the HPV vaccine and cervical cancer screening have made it one of the most preventable cancers” (CDC.gov). The problem is that most people are unaware that they are infected with the Human Papillomavirus (HPV), and that many women between the recommended ages do not receive a Pap smear since it is not an accessible screening for everyone. Consequently, no treatment will be given to the patient, resulting in a greater risk of obtaining cervical cancer if the patient is infected with high-risk HPV. In this MISSH study, we observe the consumer response to two self-sampling kits used to detect the presence of high-risk HPV. One kit includes the urine sampling method (ColliPee), and the other includes the vaginal method (Eve brush). Women who volunteered to participate in this study were given the options of either using one method of their choice, or using both kits. These self-sampling kits are sent through the mail; and once the sampling is done, extensive phone interviews were conducted to inquire about the patient’s preferences. Through this, we were able to learn what adjustments/accommodations are needed to be made in order to make the self-sampling methods more widely accepted, taking into account that more women feel more comfortable and are more likely to get screened with a self-sampling method.

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Unravelling the organizing principles of bacterial chromosomes

Gene regulation in E. coli bacteria is determined primarily by transcriptional regulatory proteins and their interactions with DNA. These proteins, such as LER and H-NS, are vital to determining virulence in E. coli, and while much research has been done on the proteins themselves and the genes they express, work still needs to be done to determine which DNA structures and/or sequences are preferred by these proteins. We hypothesize that proteins like H-NS and LER prefer to bind to structures, rather than sequence, with an affinity for bent or elongated DNA. Using the molecular simulation software NAMD, and its analysis counterpart VMD, it is possible to simulate interactions between the proteins and DNA. Laboratory testing using Spect-seq and gel shift assays will work in conjunction with the simulations to test the findings of the computational side of this research, and provide additional insights into the reality of protein-DNA interaction in a laboratory setting. If we can better understand how these proteins regulate the bacterial genome, we will expand our knowledge of regulating virulence, and thus find better ways of treating bacterial infections without the harmful effects and risks of traditional antibiotics, as well as providing valuable insight on protein-DNA interaction of any form.

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Solidarity Not Charity’: Thematic Analysis of Definitions of Mutual Aid Activism in the COVID-19 Pandemic

As the COVID-19 pandemic continues in the US, many individuals have been unable to receive necessary resources due to economic struggles, concerns over contact with the virus, or a lack of governmental support in connecting with essential services. Mutual aid groups, who have played an active role in helping their communities for decades, have played an integral role in providing needed services with the knowledge that current systems and institutions have failed to provide these resources to Americans. This study analyzes the role of mutual aid and how different organizations have defined themselves during the pandemic. We examined and discussed academic literature on past and current mutual aid efforts and collected data, such as location, target populations, services, and self-definitions, about mutual aid organizations in 20 of the most populous metropolitan areas in the US. Data was collected through online research on organizations’ websites, social media pages, and newspaper articles and through thematic analysis. The analysis focuses on the definitions and agendas of mutual aid groups and how they differ from one another. By mapping the efforts of mutual aid groups and determining how they present themselves this study will increase discussions on community-level activism, inequalities within American society, and the flaws of established governance and institutions.

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The origins of human culture: tool use in wild chimpanzees

Over the last 50 years, there has been extensive research on the wide range of complex tool use behaviors exhibited by chimpanzees (Pan troglodyte) living in different locations across Africa. At some sites, like Gombe in Tanzania and Goualougo in Republic of Congo, chimpanzees exhibit elaborate tool sets. At other locations, chimpanzees exhibit fewer tool-related behaviors. This variation constitutes key evidence for potentially cultural behavior in nonhumans. To understand cultural differences in chimpanzees and the roots of individual variation in tool use, this study will examine multiple years of observational data of wild chimpanzees from the Kanyawara community at Kibale National Park, Uganda. Prior records of this community indicate that they have relatively simple tool use behaviors, but there has been little recent work on examining tool sets or more detailed information about individual variation. We will look for the types of tool use behaviors that exist in this population, and at what frequency these behaviors are exhibited. We will also investigate possible individual differences within this population, such as whether some chimpanzees tend to use certain tools more than others. Our findings will produce information on tool use in Ugandan chimpanzees, and the distribution of these behaviors across this community, to understand the roots of behavioral flexibility and human-like culture.

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Better Air Quality Outcomes in Southwest Detroit

Southwest Detroit Environmental Vision (SDEV) works to fulfill the needs of the community by empowering its residents to engage and by providing a connection to important resources. SDEV works with industrial corporations, businesses, and residents to address environmental pressures and concerns, specifically air pollution. Residents of Southwest Detroit live in the middle of industry and are exposed to bad air quality that leads to asthma, lead poisoning, strokes, heart attacks, and more. Even more significantly, these high impact areas correlate to more COVID fatalities as a result of these pre-existing conditions. SDEV recognizes that these high impact areas are primarily urban areas of color and that environmental and racial justice go hand in hand. To combat this issue, SDEV is working to propose a revised truck route to reduce truck traffic on residential streets and to increase enforcement of Detroit’s Anti-Idling Ordinance. SDEV has compiled a list of community members willing to host cameras and air-quality monitors at their residences collecting data relating to pollution levels. This data will be used in the proposal to revise the truck routes in order to better protect the health and wellbeing of the community. SDEV also fosters civic engagement and advocates for environmental policy. This is done by organizing residents to talk to their representatives who vote on the policies that affect them. Through these efforts, SDEV is able to engage the community and make deep and impactful changes that lessen environmental pressures. SDEV works to ensure that the residents come first and their concerns are being heard and met.

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Digital Dialogue

In the time of the COVID-19 pandemic, Americans find themselves depending on technology and virtual meeting tools more than ever. Though these resources are highly effective, their use tends to be more awkward when compared to face-to-face interaction. This project aims to evaluate the similarities and differences between in-person and virtual language processing. In order to do this, we utilized the Michigan SONA system to meet with 44 students over Zoom. We created a list of 56 yes/no audio questions (each one marked “predictable” or “unpredictable” depending on how easy or hard it would be to understand the question before it ends) and split them into two sets of 28. One set was to be played over Zoom from the experimenter to the student, while the other was to be played locally by the student. After having them answer the questions, we recorded the amount of time it took for participants to respond to each question. Data collection has been completed for this experiment, but the data is not yet fully organized. Though there are currently no reportable results, we hope to observe a significant difference in conversational flow and language comprehension depending on the medium of communication.

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Conversation

As the COVID-19 pandemic continues without a clear end in sight, a higher degree of conversation through digital means has risen. Often through online meetings there are technical boundaries that create odd disturbances within conversation that may make these meetings hesitant, awkward, and uncomfortable. Through preexisting literature on the turn-taking process in conversation, it is obvious that response times between two people conversing is very important in how one perceives the answer that will be given. Considering that technical delays in audio input may increase response time, it is imperative that digital conversations are examined. The basis of our study relies heavily on a similar project performed on non-digital conversation in the Cognition journal (Corps et al 2018). The project involved participants answering yes or no to questions considered either predictable or unpredictable with their response times recorded. This was replicated in the study with the addition of the variables “remote” and “local.” An unrelated member of the team prerecorded the questions from the Cognition journal to be used in data collection. The process involved one on one meetings with participants on Zoom where the audio recordings were played by the researcher through the share feature (remote) and later switched to the participant playing the audio through the share feature (local). The meeting was recorded in attempts to later derive the response times through manual transcription. Reflection on the raw data seems to suggest that response times were indeed larger though this process has yet to be completed. However, results will likely show an increase in response times which – taken with a grain of salt as there are many technical issues at play – can cause the hesitancy, awkwardness, and uncomfortableness that digital meetings may bring.

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The Promise of Free Tuition: The Case of Chile

During the last decade, different free-tuition initiatives have been discussed and implemented around the world. Although empirical research on this topic is emerging, little is known about the formation of such initiatives, and its impact on student’s access and persistence and on institutional outcomes. This study contributes to the literature about free college by analyzing the case of Chile, a country that implemented such a policy in 2016. This case study will be a valuable contribution to the international comparative discussion of free college. This study analyzes the formation of the free-tuition program in Chile through newspaper articles and policy documents. It analyzes the effect on institutions, by reviewing changes in institutional revenues and student composition. By examining these trends, we are able to evaluate whether the free-tuition program is able to diversify the student body in participating institutions and examine how these universities have adapted to this new policy. Preliminary results are presented and implications are discussed.

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