Computer Sciences Commons^™

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

An Automatic Framework For Embryonic Localization Using Edges In A Scale Space, Zachary Bessinger

Masters Theses & Specialist Projects

Localization of Drosophila embryos in images is a fundamental step in an automatic computational system for the exploration of gene-gene interaction on Drosophila. Contour extraction of embryonic images is challenging due to many variations in embryonic images. In the thesis work, we develop a localization framework based on the analysis of connected components of edge pixels in a scale space. We propose criteria to select optimal scales for embryonic localization. Furthermore, we propose a scale mapping strategy to compress the range of a scale space in order to improve the efficiency of the localization framework. The effectiveness of the proposed …

Effect Of Step Rate On Foot Strike Pattern And Running Economy In Novice Runners, Janae Lynn Richardson

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Purpose—The objective was to examine if step rates ±5% or ±10% of a novice runner's preferred step rate (SR) is sufficient enough to shift a novice runner’s foot strike pattern (FSP) (rear-foot, mid-foot, forefoot) and whether these SR changes produce changes in the rate of submaximal oxygen consumption (VO2). Methods—Foot strike angle (FSA) was recorded using sagittal plane video images and VO2 was measured for novice runners while running on a treadmill at a constant speed during increased and decreased (±5% and ±10%) SR conditions. Foot strike angle was used to predict strike index (SI) (predicted strike index = [FSA …

A Semantic Situation Awareness Framework For Indoor Cyber-Physical Systems, Pratikkumar Desai

Kno.e.sis Publications

Recently, the domain of cyber-physical systems (CPSs) has emerged as a successor to the traditional embedded systems and the wireless sensor networks. The relatively new cyber-physical domain offers tight integration of control, communication and computation components to develop advanced web based application in various heterogeneous domains such as health care, disaster management, automation and environment monitoring. The applications of indoor CPSs include remote patient monitoring, smart home, etc. with focus on situation awareness via event identification from context information. The principal challenges associated with the development of situation awareness applications include uncertainty in contextual data, incomplete domain knowledge, interoperability between …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Diffusion Of Mobile Payment Systems Among Microentrepreneurs In Kenya And Tanzania, Dionne Nickerson

Annual Celebration of Student Scholarship and Creativity

The rapid rise of Kenya's mobile payment system, M-PESA , has grasped the attention of policy makers and private enterprise alike. In just six years M-PESA has transformed how money flows throughout Kenya, and similar systems are gaining traction elsewhere in Africa. This project examines the impact of mobile payment system adoption on the economic advancement of Kenyan and Tanzanian microentrepreneurs. This work will further the understanding of mobile payment systems’ contribution to the economic growth of microenterprises, which may have implications for poverty reduction in these two nations.

Volume 05, Ian Karamarkovich, Jessica Cox, Kyle Fowlkes, Allison Pawlowski, Kaitlin Major, Carrie Dunham, Kelsey Scheitlin, Kathryn Grayson, Ashley Johnson, Jennifer Nehrt, Kelsey Stolzenbach, Kristin Mcquarrie, Sara Nelson, Melisa Michelle, Jessica Sudlow, Perry Bason, Danielle Dmuchawski, Mariah Asbell, Matthew Sakach, Timothy Smith Jr., Annaliese Troxell, T. Dane Summerell, Sarah Ganrude, Malina Rutherford, Hannah Hopper, John Berry Jr., James Early, Colleen Festa, Chelsea D. Taylor, Michelle Maddox, Kaitlyn Smith, Sarah Schu, Cabell Edmunds, Katherine Grayson, Kayla Tornai

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

The Tallis House as an Extension of Emily Tallis in McEwan's Atonement by Ian Karamarkovich

Graphic Design by Jessica Cox

Graphic Design by Kyle Fowlkes

Graphic Design by Allison Pawlowski

Incorporating Original Research in The Classroom: A Case Study Analyzing the Influence of the Chesapeake Bay on Local Temperatures by Kaitlin Major, Carrie Dunham and Dr. Kelsey Scheitlin

Graphic Design by Kathryn Grayson

Graphic Design by Ashley Johnson

Facing the Music: Environmental Impact Assessment of Building A Concert Hall on North Campus by Jennifer Nehrt, Kelsey Stolzenbach And Dr. Kelsey Scheitlin

Art by Kristin …

Beta Atomic Contacts: Identifying Critical Specific Contacts In Protein Binding Interfaces, Qian Lu, Chee Keong Kwoh, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the …

Broad Vision: The Art & Science Of Looking, Heather Barnett, John R. A. Smith

The Transdisciplinary STEAM+ Journal

Undergraduate students and academic staff from diverse disciplines in the arts and sciences investigated questions of mediated vision through a year-long interdisciplinary research project at the University of Westminster, London, United Kingdom. The Broad Vision project explored the perception and interpretation of microscopic worlds, and investigated the benefits and challenges of working across disciplinary divides in a university setting. This article describes the three-phase model for interdisciplinary learning and research developed through the project, providing a valuable case study for inquiry based art/science education.

Predicting Parkinson's Disease Progression With Smartphone Data, Pramod Anantharam, Krishnaprasad Thirunarayan, Vahid Taslimi, Amit P. Sheth

Kno.e.sis Publications

Most of the existing approaches for detecting diseases/risk score form observations (sensor and textual) ignore the presence of any prior knowledge of the disease. In this work, we start top-down by enumerating the symptoms of Parkinson's Disease (PD) and map the symptoms to its possible manifestations in sensor observations (bottom-up). We show such manifestations and further use these manifestations as features to build classifiers to differentiate between the PD patients and the control group.

What Kind Of #Conversation Is Twitter? Mining #Psycholinguistic Cues For Emergency Coordination, Hemant Purohit, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John M. Flach, Shreyansh Bhatt

Kno.e.sis Publications

The information overload created by social media messages in emergency situations challenges response organizations to find targeted content and users. We aim to select useful messages by detecting the presence of conversation as an indicator of coordinated citizen action. Using simple linguistic indicators associated with conversation analysis in social science, we model the presence of conversation in the communication landscape of Twitter in a large corpus of 1.5M tweets for various disaster and non-disaster events spanning different periods, lengths of time and varied social significance. Within Replies, Retweets and tweets that mention other Twitter users, we found that domain-independent, linguistic …

04. Botany, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

02. Animal Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

09. Environmental Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

07. Criminal Justice, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

11. Genetics, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

08. Engineering, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

13. Mathematics, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

14. Optometry, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

16. Physics, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

17. Psychology, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

19. Zoology, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

06. Computer Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

03. Biology, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

05. Chemistry, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

10. Forensic Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

12. Kinesiology, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.