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- Creators: School of Life Sciences
- Creators: Ravel, Maurice, 1875-1937
Description
Aquatic macroinvertebrates are important for many ecological processes within river ecosystems and, as a result, their abundance and diversity are considered indicators of water quality and ecosystem health. Macroinvertebrates can be classified into functional feeding groups (FFG) based on morphological-behavioral adaptations. FFG ratios can shift due to changes in normal disturbance patterns, such as changes in precipitation, and from human impact. Due to their increased sensitivity to environmental changes, it has become more important to protect and monitor aquatic and riparian communities in arid regions as climate change continues to intensify. Therefore, the diversity and richness of macroinvertebrate FFGs before and after monsoon and winter storm seasons were analyzed to determine the effect of flow-related disturbances. Ecosystem size was also considered, as watershed area has been shown to affect macroinvertebrate diversity. There was no strong support for flow-related disturbance or ecosystem size on macroinvertebrate diversity and richness. This may indicate a need to explore other parameters of macroinvertebrate community assembly. Establishing how disturbance affects aquatic macroinvertebrate communities will provide a key understanding as to what the stream communities will look like in the future, as anthropogenic impacts continue to affect more vulnerable ecosystems.
ContributorsSainz, Ruby (Author) / Sabo, John (Thesis director) / Grimm, Nancy (Committee member) / Lupoli, Christina (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
RecyclePlus is an iOS mobile application that allows users to be knowledgeable in the realms of sustainability. It gives encourages users to be environmental responsible by providing them access to recycling information. In particular, it allows users to search up certain materials and learn about its recyclability and how to properly dispose of the material. Some searches will show locations of facilities near users that collect certain materials and dispose of the materials properly. This is a full stack software project that explores open source software and APIs, UI/UX design, and iOS development.
ContributorsTran, Nikki (Author) / Ganesh, Tirupalavanam (Thesis director) / Meuth, Ryan (Committee member) / Watts College of Public Service & Community Solut (Contributor) / Department of Information Systems (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
This study evaluates medical pluralism among 1.5 generation Indian American immigrants. 1.5 generation Indian Americans (N=16) were surveyed regarding their engagement in complementary and alternative medical systems (CAM), how immigration affected that, and reasons for and for not continuing the use of CAM. Results indicated most 1.5 Indian immigrants currently engage in CAM, given that their parents also engage in CAM. The top reasons respondents indicated continued engagement in CAM was that it has no side effects and is preventative. Reasons for not practicing CAM included feeling out of place, not living with parents or not believing in CAM. After immigration, most participants decreased or stopped their engagement in CAM. More women than men continued to practice CAM after immigration. From the results, it was concluded that CAM is still important to 1.5 generation Indian immigrants.
ContributorsMurugesh, Subhiksha (Author) / Stotts, Rhian (Thesis director) / Mubayi, Anuj (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Many factors are at play within the genome of an organism, contributing to much of the diversity and variation across the tree of life. While the genome is generally encoded by four nucleotides, A, C, T, and G, this code can be expanded. One particular mechanism that we examine in this thesis is modification of bases—more specifically, methylation of Adenine (m6A) within the GATC motif of Escherichia coli. These methylated adenines are especially important in a process called methyl-directed mismatch repair (MMR), a pathway responsible for repairing errors in the DNA sequence produced by replication. In this pathway, methylated adenines identify the parent strand and direct the repair proteins to correct the erroneous base in the daughter strand. While the primary role of methylated adenines at GATC sites is to direct the MMR pathway, this methylation has also been found to affect other processes, such as gene expression, the activity of transposable elements, and the timing of DNA replication. However, in the absence of MMR, the ability of these other processes to maintain adenine methylation and its targets is unknown.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
ContributorsBoyer, Gwyneth (Author) / Lynch, Michael (Thesis director) / Behringer, Megan (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
At present, the vast majority of human subjects with neurological disease are still diagnosed through in-person assessments and qualitative analysis of patient data. In this paper, we propose to use Topological Data Analysis (TDA) together with machine learning tools to automate the process of Parkinson’s disease classification and severity assessment. An automated, stable, and accurate method to evaluate Parkinson’s would be significant in streamlining diagnoses of patients and providing families more time for corrective measures. We propose a methodology which incorporates TDA into analyzing Parkinson’s disease postural shifts data through the representation of persistence images. Studying the topology of a system has proven to be invariant to small changes in data and has been shown to perform well in discrimination tasks. The contributions of the paper are twofold. We propose a method to 1) classify healthy patients from those afflicted by disease and 2) diagnose the severity of disease. We explore the use of the proposed method in an application involving a Parkinson’s disease dataset comprised of healthy-elderly, healthy-young and Parkinson’s disease patients.
ContributorsRahman, Farhan Nadir (Co-author) / Nawar, Afra (Co-author) / Turaga, Pavan (Thesis director) / Krishnamurthi, Narayanan (Committee member) / Electrical Engineering Program (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The current study investigated whether intermittent restraint stress (IRS) would impair fear extinction learning and lead to increased anxiety and depressive- like behaviors and then be attenuated when IRS ends and a post- stress rest period ensues for 6 weeks. Young adult, male Sprague Dawley rats underwent restraint stress using wire mesh (6hr/daily) for five days with two days off before restraint resumed for three weeks for a total of 23 restraint days. The groups consisted of control (CON) with no restraint other than food and water restriction yoked to the restrained groups, stress immediate (STR-IMM), which were restrained then fear conditioned soon after the end of the IRS paradigm, and stress given a rest for 6 weeks before fear conditioning commenced (STR-R6). Rats were fear conditioned by pairing a 20 second tone with a footshock, then given extinction training for two days (15 tone only on each day). On the first day of extinction, all groups discriminated well on the first trial, but then as trials progressed, STR-R6 discriminated between tone and context less than did CON. On the second day of extinction, STR- IMM froze more to context in the earlier trials than compared to STR-R6 and CON. As trials progressed STR-IMM and STR-R6 froze more to context than compared to CON. Together, CON discriminated between tone and context better than did STR-IMM and STR-R6. Sucrose preference, novelty suppressed feeding, and elevated plus maze was performed after fear extinction was completed. No statistical differences were observed among groups for sucrose preference or novelty suppressed feeding. For the elevated plus maze, STR-IMM entered the open arms and the sum of both open and closed arms fewer than did STR- R6 and CON. We interpret the findings to suggest that the stress groups displayed increased hypervigilance and anxiety with STR-R6 exhibiting a unique phenotype than that of STR-IMM and CON.
ContributorsShah, Vrishti Bimal (Author) / Conrad, Cheryl (Thesis director) / Newbern, Jason (Committee member) / Judd, Jessica (Committee member) / School of Life Sciences (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
After freelancing on my own for the past year and a half, I have realized that one of the biggest obstacles to college entrepreneurs is a fear or apprehension to sales. As a computer science major trying to sell my services, I discovered very quickly that I had not been prepared for the difficulty of learning sales. Sales get a bad rap and very often is the last thing that young entrepreneurs want to try, but the reality is that sales is oxygen to a company and a required skill for an entrepreneur. Due to this, I compiled all of my knowledge into an e-book for young entrepreneurs starting out to learn how to open up a conversation with a prospect all the way to closing them on the phone. Instead of starting from scratch like I did, college entrepreneurs can learn the bare basics of selling their own services, even if they are terrified of sales and what it entails. In this e-book, there are tips that I have learned to deal with my anxiety about sales such as taking the pressure off of yourself and prioritizing listening more than pitching. Instead of trying to teach sales expecting people to be natural sales people, this e-book takes the approach of helping entrepreneurs that are terrified of sales and show them how they can cope with this fear and still close a client. In the future, I hope young entrepreneurs will have access to more resources that handle this fear and make it much easier for them to learn it by themselves. This e-book is the first step.
ContributorsMead, Kevin Tyler (Author) / Sebold, Brent (Thesis director) / Kruse, Gabriel (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This thesis dives into the world of artificial intelligence by exploring the functionality of a single layer artificial neural network through a simple housing price classification example while simultaneously considering its impact from a data management perspective on both the software and hardware level. To begin this study, the universally accepted model of an artificial neuron is broken down into its key components and then analyzed for functionality by relating back to its biological counterpart. The role of a neuron is then described in the context of a neural network, with equal emphasis placed on how it individually undergoes training and then for an entire network. Using the technique of supervised learning, the neural network is trained with three main factors for housing price classification, including its total number of rooms, bathrooms, and square footage. Once trained with most of the generated data set, it is tested for accuracy by introducing the remainder of the data-set and observing how closely its computed output for each set of inputs compares to the target value. From a programming perspective, the artificial neuron is implemented in C so that it would be more closely tied to the operating system and therefore make the collected profiler data more precise during the program's execution. The program is designed to break down each stage of the neuron's training process into distinct functions. In addition to utilizing more functional code, the struct data type is used as the underlying data structure for this project to not only represent the neuron but for implementing the neuron's training and test data. Once fully trained, the neuron's test results are then graphed to visually depict how well the neuron learned from its sample training set. Finally, the profiler data is analyzed to describe how the program operated from a data management perspective on the software and hardware level.
ContributorsRichards, Nicholas Giovanni (Author) / Miller, Phillip (Thesis director) / Meuth, Ryan (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Due to artificial selection, dogs have high levels of phenotypic diversity, yet, there appears to be low genetic diversity within individual breeds. Through their domestication from wolves, dogs have gone through a series of population bottlenecks, which has resulted in a reduction in genetic diversity, with a large amount of linkage disequilibrium and the persistence of deleterious mutations. This has led to an increased susceptibility to a multitude of diseases, including cancer. To study the effects of artificial selection and life history characteristics on the risk of cancer mortality, we collected cancer mortality data from four studies as well as the percent of heterozygosity, body size, lifespan and breed group for 201 dog breeds. We also collected specific types of cancer breeds were susceptible to and compared the dog cancer mortality patterns to the patterns observed in other mammals. We found a relationship between cancer mortality rate and heterozygosity, body size, lifespan as well as breed group. Higher levels of heterozygosity were also associated with longer lifespan. These results indicate larger breeds, such as Irish Water Spaniels, Flat-coated Retrievers and Bernese Mountain Dogs, are more susceptible to cancer, with lower heterozygosity and lifespan. These breeds are also more susceptible to sarcomas, as opposed to carcinomas in smaller breeds, such as Miniature Pinschers, Chihuahuas, and Pekingese. Other mammals show that larger and long-lived animals have decreased cancer mortality, however, within dog breeds, the opposite relationship is observed. These relationships could be due to the trade-off between cellular maintenance and growing fast and large, with higher expression of growth factors, such as IGF-1. This study further demonstrates the relationships between cancer mortality, heterozygosity, and life history traits and exhibits dogs as an important model organism for understanding the relationship between genetics and health.
ContributorsBalsley, Cassandra Sierra (Author) / Maley, Carlo (Thesis director) / Wynne, Clive (Committee member) / Tollis, Marc (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
The need for automated / computational fact checking has grown substantially in recent times due to the high volume of false information and limited workforce of human fact checkers. This need has spawned research and new developments in this field and has created many different systems and approaches to this complex problem. This paper attempts to not just explain the most popular methods that are currently being used, but provide experimental results of the comparison of two different systems, the replication of results from their respective papers, and an annotated data-set of different test sentences to be used in these systems.
ContributorsRosenkilde, Trevor Curtis (Author) / Papotti, Paolo (Thesis director) / Candan, Kasim (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12